MCB Accepts, published online ahead of print on 6 January 2014 Mol. Cell. Biol. doi:10.1128/MCB.01195-13 Copyright © 2014, American Society for Microbiology. All Rights Reserved.

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Zac1 regulates cell cycle arrest in neuronal

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progenitors via Tcf4

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running title: Zac1 regulates Tcf4 expression

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Udo Schmidt-Edelkraut1, Guillaume Daniel1#, Anke Hoffmann and Dietmar

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Spengler*

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Max Planck Institute of Psychiatry, Molecular Neuroendocrinology, Kraepelinstr. 2-10,

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80804 Munich, Germany

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#

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Switzerland

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these authors contributed equally to this work

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*

corresponding author

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Dietmar Spengler, Molecular Neuroendocrinology, Max Planck Institute of Psychiatry,

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Kraepelinstr. 2-10, 80804 Munich, Germany, Phone: ++49 89 30622559, Fax: ++49 89

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30622605, Email: [email protected]

present address: École polytechnique fédérale de Lausanne, LMNR, CH-1015 Lausanne,

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word count (Materials and Methods) : 853

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word count (Introduction, Results, and Discussion) : 3124

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ABSTRACT

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Imprinted genes play a critical role in brain development and mental health although the

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underlying molecular and cellular mechanisms remain incompletely understood. The family

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of basic Helix-Loop-Helix (bHLH) proteins directs the proliferation, differentiation and

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specification of distinct neuronal progenitor populations. Here, we identified the bHLH factor

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Tcf4 as a direct target gene of Zac1/Plagl1, a maternally imprinted transcriptional regulator,

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during early neurogenesis. Zac1 and Tcf4 expression concomitantly increased during neuronal

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progenitor differentiation; moreover, Zac1 interacts with two cis-regulatory elements in the

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Tcf4 gene locus and these elements together confer synergistic activation of the Tcf4 gene.

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Tcf4 upregulation enhances the expression of the cyclin-dependent kinase inhibitor p57Kip2, a

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paternally imprinted Tcf4 target gene, and increases the number of cells in G1 phase. Overall,

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we show that Zac1 controls cell cycle arrest function in neuronal progenitors through

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induction of p57Kip2 via Tcf4 and provide evidence for a co-operation between imprinted

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genes and a bHLH factor in early neurodevelopment.

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INTRODUCTION

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Multiple factors and signaling pathways control in a concerted manner cell fate decisions and

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differentiation during brain development. Among these, the family of basic Helix-Loop-Helix

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(bHLH) proteins coordinates proliferation, specification, differentiation and migration of

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progenitors during neurogenesis (1, 2). These proteins are characterized by the presence of a

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basic helix-loop-helix domain that allows them upon homo- or heterodimerization to bind to

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specific DNA sequences (CANNTG), known as E-box (3). The bHLH family comprises two

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major classes, the so called specification factors (i.e. Neurogenin, Math, Mash and NeuroD),

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whose expression is spatiotemporally controlled, and their ubiquitously expressed

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dimerization partners, the E-proteins (4, 5). Proneural factors are expressed at low levels in

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proliferating undifferentiated progenitors while with the onset of neurogenesis the expression

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of specification factors and E-protein family members (the two splice variants of E2A: E12

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and E47, HEB and TCF4 (alias E2-2, SEF2 or ITF2) increases and inhibits progenitor

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proliferation and astrogliogenesis through the induction of target genes that are required for

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terminal neuronal differentiation (6, 7).

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The maternally imprinted Zac1 gene (zinc finger protein regulating apoptosis and cell cycle

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arrest) is transiently expressed in proliferating stem/progenitor cells of the telencephalic and

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cerebellar ventricular zones (8–10), the external granular cell layer (11), and the retina (12,

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13), the function of which is, however, poorly understood. Imprinted genes encompass a

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subset of mammalian genes that are subject to developmentally determined, parent-of-origin

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dependent, epigenetic modifications resulting in monoallelic expression. On the other hand,

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loss of imprinting, i.e. biallelic expression, frequently manifests with severe metabolic and

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neurodevelopmental syndromes across prenatal and postnatal life (14).

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3

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Zac1 encodes a zinc finger protein conferring transcriptional activation and repression

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following monomer or dimer binding to GC-rich palindromic and repeat DNA elements (15–

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17). Direct Zac1 target genes identified so far include the G-protein coupled receptor Pac1

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(pituitary adenylate activating receptor 1) (18–20), the nuclear receptor Pparγ1 (peroxisome

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proliferator activated receptor) (21), the cyclin-dependent kinase inhibitor p21Waf1/Cip1 (22)

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and the exchange factor Rasgrf1 (RAS protein-specific guanine nucleotide-releasing factor 1)

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(23) all of which share a role in the regulation of apoptosis, cell cycle arrest and

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differentiation across different tissues and stages of development.

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Moreover, we recently found that Zac1 expression prevents precocious astroglial

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differentiation by restraining Jak/Stat3 signaling in embryonic and adult neural stem cells

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(NSC) through transcriptional induction of Socs3 (24). Here, we further show that Tcf4 is a

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lineage-specific target gene of Zac1 in the control of neuronal progenitor cell cycle arrest

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function consistent with a role of Zac1 in both lineage decisions.

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MATERIALS AND METHODS

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Cell culture and transfection experiments. The mouse C17.2 NSC line was cultured in

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Dulbecco’s modified Eagle’s medium (DMEM) supplemented with 10% fetal calf serum

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(both Life Technologies GmbH, Darmstadt, Germany). Tetracycline (Tc) regulated Zac1

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expression in C17.2 cells was established and proliferation measured as described (21, 23).

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The mouse embryonic stem cell line 46C was grown and neuronal differentiation performed

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as reported (25). In addition, cells were differentiated by treatment with all-trans retinoic acid

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(RA; 0.1 μM) or embryoid body (EB) formation as reported elsewhere (26). The mouse

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embryonic NS-5 and adult O4ANS NSC lines were grown as reported (24). Primary cells

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from whole fetal brain (embryonic day 15; E15) of CD1 mice were dissected as described

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previously (24) and grown as suspension in DMEM/F12 and Neurobasal medium (1:1)

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supplemented with N2 (1% v/v), B27 (2% v/v) (all Life Technologies GmbH), EGF 4

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(epidermal growth factor), and FGF (fibroblast growth factor) (both 10 ng/ml; PeproTech,

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Hamburg, Germany). Neurospheres were dissociated with Accutase (Millipore, Schwalbach,

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Germany) and grown as monolayers on poly-D-lysine hydrobromide (Sigma, Munich,

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Germany) coated plates in the presence of EGF and FGF. Neuronal differentiation was

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initiated with FGF (10 ng/ml) on matrigel coated dishes (0.4 μl/ml; BD Bioscience,

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Heidelberg, Germany). For astroglial differentiation, cells were kept with 1% FCS. All media

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contained penicillin/streptomycin (Life Technologies GmbH).

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Transient and stable transfections were performed using Turbofect transfection reagent

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(Fermentas, St. Leon-Roth, Germany) according to manufacturers’ instructions using 1−5 x

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105 cells/cm² as described (24). To knock-down Zac1, p57Kip2 or Tcf4 expression the

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following shRNA vectors (Mission shRNA, Sigma) were used: pLKO.1-Pur-Zac1.pool (clone

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NM_009538), pLKO.1-Neo-p57Kip2 (clone NM_009876.2-1060s1c1), pLKO.1-Neo-Tcf4

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(clone NM_013685.1-571s1c1) and pLKO.1-Pur-Non-Target shRNA (SHC016), which

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served as a control. The region of Tcf4 targeted by shRNA is shown in Figure S1 of the

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supplemental material.

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Transfection of primary NSCs (E15) in knock-down experiments was performed with 1 μg of

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the appropriate expression vectors (24). For quantitative analysis, images of 50 GFP positive

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cells per transfection corresponding to a total number of 2,000-4,000 cells were scored for

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Ki67 immunoreactivity by an independent investigator. Nucleofection of primary NSCs (E15)

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was performed with Amaxa Basic Neuron SCN Nucleofector Kit and the Nucleofector

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technology (Lonza, Tokyo, Japan) according to manufacturers’ instructions. Luciferase

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reporter activities were normalized on β-galactosidase activity of a cotransfected expression

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vector (27). Amounts of transfected plasmids are indicated in the corresponding figure

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legends.

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Plasmids. Fragments of the Tcf4 promoter, intron and regulatory element (RE) were

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amplified by polymerase chain reaction (PCR), sequence verified and cloned in the pGL3

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basic vector (Promega, Mannheim, Germany). Details on the generation of the constructs are

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available on request. Zac1 expression constructs are described elsewhere (17). The

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pCDEF3.Flag-Tcf4 expression vector was described previously (28).

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Chromatin immunoprecipitation (ChIP), RNA extraction and PCR experiments. ChIP

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assays were performed as described (29) with rabbit polyclonal Zac1 (21, 25) or rabbit

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polyclonal Tcf4 (aa 32-154) (Pineda, Berlin, Germany) antisera. The specificity of the Tcf4

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antibody was verified by immunoblotting (see Fig. S1 in the supplemental material). Brain

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punches enclosing the neocortical VZ/SVZ were obtained by micro-dissection under

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histological control, whereby tissues from five (E15) or three (E18) animals were pooled for

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each experiment. Data are diagrammed as percent of input normalized to control sera (IgG or

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preimmune-serum). RNA extraction and PCR experiments were done as described (25).

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Primers for PCR and ChIP experiments are listed in Table S1 of the supplemental material.

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The housekeeping genes Gapdh (glycerinaldehyde-3-phosphat-dehydrogenase), Atp5j (ATP

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synthase-coupling factor 6) or β-actin served for normalization.

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Immunoblotting, immunocytochemistry and immunohistochemistry. Whole cell extracts

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(30 to 100 µg) were fractionated by SDS-PAGE gel electrophoresis and tested with the

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following antibodies: mouse monoclonal Tcf4 [clone Ri-3B9, aa 1-183, see Fig. S1 in the

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supplemental material (30)], actin (sc-8432, Santa Cruz), Flag (F3165, Sigma), or Zac1

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(rabbit polyclonal) (21, 25). For immunocytochemistry, cells were grown on poly-D-lysine

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hydrobromide coated coverslips, fixed with 4% formaldehyde, permeabilized with 0.1%

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saponin (Sigma) in phosphate buffered saline (PBS), blocked with donkey normal serum

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(Sigma) and subjected to indirect immunofluorescence with antibodies to Tcf4 (clone Ri6

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3B9), Gfap (Z0334, Dako, Hamburg, Germany), Tuj1 (ab7751, Abcam), Nestin (ab6142,

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Abcam), p57Kip2 (sc-8298, Santa Cruz) and Zac1 (guinea pig polyclonal) (23, 24). Nuclei

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were stained with 2-(4-Amidinophenyl)-6-indolecarbamidine-dihydrochloride (DAPI).

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Immunohistochemistry was performed on 4% paraformaldehyde-fixed, cryopreserved brain

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sections (30 μm) from CD1 mice with antibodies to Nestin, Dcx (sc-8066, Santa Cruz),

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p57Kip2, Tcf4 (clone Ri-3B9) and Zac1 (guinea pig polyclonal). Nuclei were stained with

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DAPI.

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Microscopic analysis was done with fluorescence microscope (BX61, Olympus, Hamburg,

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Germany) and CCD camera (E-620 SRL, Olympus) or confocal microscope (FluoView 1000,

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Olympus). All images were captured using identical laser power and gain settings.

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Fluorescence-Activated Cell Sorting Analysis

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Cells (2 x 106) were stained with propidium iodide and analyzed on a Beckman Coulter Epics

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XL using Expo32 ADC analysis as described previously (24).

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Software and statistical analysis. Computational analysis of the Tcf4 and p57Kip2 gene was

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done with Genomatix MatInspector™. Results represent the means and standard deviations

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from at least four independent experiments. Numerical data were analyzed by unpaired

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Student’s t test and ANOVA with post-hoc Tukey test. The threshold for significance was set

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at * P < 0.05 and ** P < 0.01.

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RESULTS

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Zac1 transactivates Tcf4. To identify Zac1 target genes in neural progenitors, we generated

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a panel of inducible Zac1 clones in the C17.2 cerebellar neural stem cell line using a Tet-off

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system. Comparative, genome-wide expression analysis for two representative Zac1 clones

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(21) showed enhanced expression of Tcf4 (1.7-fold, data not shown) after Zac1 induction. 7

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Quantitative RT-PCR (qRT-PCR) corroborated a transient increase in Zac1 expression

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peaking at 9 h and declining at 24 h after tetracycline removal. At the same time, a similar

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pattern of regulation was detected for Tcf4 (Fig. 1A). Moreover, transient transfection of a

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Zac1 expression vector into parental C17.2 cells caused a robust increase in both Tcf4 gene

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expression and protein levels of the b-isoform (hereafter referred to as Tcf4), while the a-

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isoform was unaffected (Fig. 1B and C, see Fig. S1 in the supplemental material and data not

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shown). Together, these findings raised the possibility that Zac1 up-regulates Tcf4.

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Zac1’s function as transactivator (15, 16) or coactivator (25, 31) was assessed by transfection

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of C17.2 cells with constructs either defective in DNA binding or in transactivation due to a

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mutation in zinc finger seven (ZF7mt) or to absence of the central transactivation domain

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(ΔLPR) (17). RNA (qRT-PCR) and immunoblot analysis evidenced that Tcf4 was barely

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induced by either ZF7mt or ΔLPR when compared to wild type Zac1 (Fig. 1D and E)

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although these constructs were expressed at similar levels (Fig. 1E). Because Zac1’s

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coactivator function is maintained in the absence of the central transactivation domain (25),

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we conclude that Zac1’s transactivation and DNA binding domains are required for Tcf4

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regulation pointing to a role as transcription factor.

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Computational analysis of the Tcf4 locus revealed multiple potential GC-rich palindromic

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and repeat Zac1 binding sites (17) at both the promoter and first intron as schematically

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depicted in Figure 1F. In contrast, no corresponding sites could be identified at the Tcf4-a

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promoter (data not shown). Chromatin immunoprecipitation (ChIP) experiments using a Zac1

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antiserum showed that Zac1 occupies exclusively the Tcf4 proximal promoter and the center

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of the first intron (Fig. 1G).

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In sum, these findings suggest that Zac1 directly regulates Tcf4 following binding at the

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proximal promoter and/or the first intron in mouse C17.2 stem cells.

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Zac1 and Tcf4 are upregulated during neuronal differentiation of mouse embryonic

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stem cells. Mouse embryonic stem cells (ESC) were used as a model for early neuronal

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differentiation (25). Upon withdrawal of Leukemia inhibitory factor (Lif), cell clusters

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flattened and spread to give rise to single cells that acquired progressively neuronal

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morphology within 6 days (Fig. 2A). At the same time, expression of the pluripotency marker

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Oct4 and the late neuronal differentiation marker Tuj1 rapidly decreased and increased,

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respectively (Fig. 2B and C). Moreover, both Zac1 and Tcf4 mRNA and protein expression

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steadily rose with progressive neuronal differentiation (Fig. 2D and E).

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We further studied co-induction of Zac1 and Tcf4 under embryoid body formation or retinoid

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acid treatment, simulating early embryo formation (32) and posterior brain development (33),

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respectively. Both protocols promoted efficient neuronal differentiation (loss of Oct4

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expression, upregulation of the progenitor marker Nestin and the neuronal markers N-

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cadherin and Tuj1) and upregulation of Zac1 and Tcf4 (see Fig. S2 in the supplemental

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material). Together, these results indicate that co-induction of Zac1 and Tcf4 is common to

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different models of neuronal stem cell differentiation.

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Zac1 binding transactivates Tcf4. ChIP experiments revealed barely detectable Zac1

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binding at the Tcf4 locus under Lif conditions, whereas differentiation caused a marked

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increase at the proximal promoter, particularly at the core region (-485 and -89 bp), and at the

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center of the first intron (+1933 bp) (Fig. 3A). The contribution of the different binding sites

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to transactivation was studied by cloning various fragments encoding either the proximal

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promoter or the first intron separately, or jointly (including the intervening exon) in front of a

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luciferase reporter gene (Fig. 3B). Each fragment showed strong transcriptional activity when

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compared to the parent vector with a strong decrease (50 to 100 fold) in the reverse (3´ to 5´)

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orientation (Fig. 3C). Increasing doses of Zac1 transactivated the separate promoter and intron

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constructs about 2.5-fold and 1.5-fold, respectively, and resulted in a 5.5-fold transactivation 9

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in case of their joint presence. None of these reporter plasmids responded to the DNA binding

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defective construct ZF7mt (Fig. 3D).

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The intron was additionally cloned downstream of the thymidine kinase (TK) promoter

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(devoid of Zac1 binding sites) and showed robust basal promoter activity when compared to

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the parent vector (data not shown). However, Zac1 was ineffective to confer transactivation to

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this chimeric reporter (Fig. 3E) and similar results were obtained when the intron was cloned

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downstream of the SV40 promoter (data not shown). Moreover, insertion of the intron in the

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reverse orientation adjacent to the promoter region prevented transactivation when compared

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to the parent composite Tcf4 reporter construct (Fig. 3E).

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In sum, these experiments suggest that Zac1 transactivates Tcf4 in a synergistic manner

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through binding to the promoter and intron. Excluding a role as autonomous enhancer, the

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intron operates solely in conjunction with the homologous promoter to confer Zac1

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transactivation in an orientation-dependent manner.

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Zac1-dependent regulation of Tcf4 is lineage-specific. Neural stem cell lines derived from

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mouse embryonic (NS-5) and adult (O4ANS) brain (24) served to investigate Zac1-dependent

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induction of Tcf4 across different developmental stages. Although Zac1 expression was up-

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regulated under either neuronal or astroglial differentiation, Tcf4 increased solely in the

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neuronal lineage (Fig. 4A and data not shown). Consistent with this finding, enhanced Zac1

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occupancy at the Tcf4 promoter and first intron occurred exclusively under neuronal

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differentiation as evidenced by ChIP experiments (Fig. 4B).

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Epigenetic mechanisms, comprising DNA methylation and chromatin modifications among

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others, are recognized for their role in directing NSC specification. To elucidate if lineage-

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specific Zac1 binding and Tcf4 regulation is controlled at the level of DNA methylation, the

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two CpG islands overlapping the 5’ end of Tcf4 (see Fig. S3 in the supplemental material)

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were analyzed by MeDIP. We detected minor DNA methylation at these two regions that did 10

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not change following neuronal or astroglial differentiation (see Fig. S3 in the supplemental

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material).

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Therefore, we additionally performed sequential ChIP experiments with antisera against

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active (pan-acetyl histone 3, acH3) or repressive (dimethyl lysine 9 of histone 3, H3K9me2)

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histone marks followed by immunoprecipitation with Zac1 antiserum. An increase in acH3

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concomitant to a decrease in H3K9me2 was measured at the Tcf4 5’ end regulatory region

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under neuronal differentiation whereas the opposite pattern emerged upon astroglial

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differentiation (Fig. 4C and D). Moreover, Zac1 preferentially associated with chromatin

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containing the active histone mark at the Tcf4 gene (Fig. 4E and F).

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Taken together, changes in DNA methylation are unlikely to contribute directly to lineage-

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specific Tcf4 regulation by Zac1. Neuronal differentiation induces however a more open

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chromatin configuration at the Tcf4 5’ end regulatory region and associated with Zac1

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binding.

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Zac1 regulates Tcf4 in primary NSCs. Long-term cultivation of stem cells can compromise

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aspects of cellular identity and differentiation potential (24). Therefore, Zac1-dependent Tcf4

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induction was studied in primary cells of embryonic mice brain from day 15 (E15).

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Neurosphere-derived cells show the capacity for self-renewal, Nestin immunoreactivity and

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the ability to differentiate into neurons, astrocytes and oligodendrocytes (34). After 2 days of

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monolayer culture, the cell population consisted mainly of Nestin positive radial glial-like

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cells, which co-expressed Zac1 and Tcf4 (Fig. 5A). Cells were subsequently maintained under

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different conditions to enhance neuronal versus astroglial differentiation (Fig. 5B). Across 6

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days of differentiation, Zac1 was up-regulated under either condition with concomitant

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increases in Tcf4 occurring solely in neurons (Fig. 5C and D).

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In agreement with the results from above, Zac1 transactivated the composite Tcf4 reporter

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construct in primary NSCs under neuronal, but barely under astroglial differentiation or 11

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undifferentiated conditions (Fig. 5E). Moreover, Zac1 occupancy at the Tcf4 promoter and

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first intron increased exclusively during neuronal differentiation as evidenced by ChIP

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experiments (Fig. 5F) despite similar amounts of Zac1 protein expression under either

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condition (Fig. 5D). These findings corroborate that Zac1 binding to the Tcf4 locus is

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confined to the neuronal lineage.

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Zac1 and Tcf4 colocalize in the neocortical ventricular zone. Neurogenesis generally

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precedes astrogliogenesis in the developing mammalian brain, with the same progenitor

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domains switching developmental programs from neuron to oligodendrocyte or astrocyte

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production. Progenitors produce predominantly neuronal lineages in the ventricular and

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subventricular zone (VZ/SVZ) from early (E9) to late (E17) embryonic stages in mice. To

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investigate Zac1 and Tcf4 expression in the neocortical ventricular zone, we co-stained

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coronal sections of E11 (early neurogenesis) and E15 (mid-neurogenesis) mice brains using

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Zac1 and Tcf4 antisera. We detected colocalization of the two proteins in progenitor cells of

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the VZ/SVZ hinting to a shared function between the two transcription factors (Fig. 6A and

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B). As expected, Tcf4 positive cells colocalized with the progenitor marker Nestin and the

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neuroblast marker Doublecortin (Dcx) in agreement with the findings from above (see Fig. S4

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in the supplemental material).

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Zac1 binding to the Tcf4 gene locus during neurogenesis at E15 was studied by ChIP

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experiments with brain punches of the VZ/SVZ; thereby punches from subsequent

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astrogliogenesis at E18 served as a negative control. Zac1 efficiently occupied the Tcf4 locus

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at the time of neurogenesis but barely during astrogliogenesis. (Fig. 6C). Moreover,

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transfection of dissociated cells encompassing the neocortical VZ/SVZ (E15) with increasing

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amounts of Zac1 caused a robust increase in the activity of the composite Tcf4 reporter

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construct (Fig. 6D).

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In sum, Zac1 and Tcf4 colocalize in the VZ/SVZ during neurogenesis. At the same time, Zac1

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occupies the Tcf4 regulatory regions and confers transactivation to a Tcf4 reporter construct.

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Zac1, Tcf4 and p57Kip2 are co-regulated during brain development. The biological

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function of Tcf4 regulation by Zac1 was addressed by the study of Tcf4-dependent target

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genes during neurogenesis. The paternally imprinted cyclin-dependent kinase inhibitor p57Kip2

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is an interesting candidate in this respect. Firstly, it is co-regulated with Zac1 in the context of

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an imprinted gene network (35). Secondly, p57Kip2 plays an important role in differentiation

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and migration of radial glia and progenitor cells during early and mid-neurogenesis (36).

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Thirdly, Zac1, Tcf4 and p57Kip2 share a cell cycle arrest function (30, 37). In this respect, E-

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proteins induce cell cycle arrest via p57Kip2 in the human neuroectodermal cell line SK-N-SH

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(38).

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Several potential E-box motifs were predicted in the distal p57Kip2 promoter region by

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computational analysis (see Fig. S5 in the supplemental material). Following transfection of

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C17.2 cells with a Zac1 or Tcf4 expression vector, we measured a 2-fold and 1.6-fold

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induction of p57Kip2, respectively, as evidenced by qRT-PCR (Fig. 7A).

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The role of endogenous Zac1 for Tcf4 and p57Kip2 expression was further studied by knock-

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down experiments. Transfection of shRNA-Zac1, but not of scrambled shRNA, depleted Zac1

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mRNA levels by 40 % and resulted in a reduced expression of Tcf4, and p57Kip2 (Fig. 7B and

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C). Of note, knock-down of Tcf4 decreased the expression of p57Kip2 without altering the

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expression of Zac1 (Fig. 7D and E).

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Having shown that Zac1 regulates p57Kip2 via Tcf4 in C17.2 stem cells, we asked whether this

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applies also to early (E11) and mid (E15) neurogenesis. Zac1 and Tcf4 were widely expressed

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in neuronal progenitor cell populations of the caudal brain regions, the pallium and

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prethalamic eminence at E11 and showed hereby a broad co-expression (see Fig. S6 in the 13

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supplemental material) in accord with previous studies (5, 8, 9). On the other hand, p57Kip2

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expression was more restricted and localized particularly to the subpallium and peduncular

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hypothalamus in which triple positive moderately p57Kip2 expressing cells were visualized

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(see Fig. S6 in the supplemental material).

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In view of the limited amount of tissue available from this region for functional studies, we

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focused on neuronal progenitors from the neocortical zone (E15), which co-express Zac1 and

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Tcf4 (Fig. 6B). Immunohistochemistry also evidenced p57Kip2 co-expression in Tcf4 positive

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cells (Fig. 7F).

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Consistent with this finding, in vivo ChIP experiments revealed Tcf4 binding to the p57Kip2

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gene at the predicted E-boxes in the distal promoter. A region devoid of E-box motifs served

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as a negative control in this experiments (Fig. 7G and Fig. S5 in the supplemental material).

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Zac1 regulates cell cycle arrest in NSCs. Recombinant pools of O4ANS cells that contained

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either Flag-tagged Zac1 or Zac1 shRNA expression vectors showed a doubling or reduction

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by 80% of Zac1 mRNA levels with corresponding changes in protein expression (24). Here,

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we detected concordant changes in Tcf4 and p57Kip2 mRNA levels in proliferating and

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differentiating O4ANS cells consistent with the role of Tcf4 as lineage-specific Zac1 target

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gene (Fig. 8A). In contrast, expression of the isoform Tcf4-a did not change under either

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condition and served as a negative control in these experiments.

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Zac1 overexpression increased the number of cells in G1-phase concomitant to a decrease in

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G2/M-phase during early time points (Fig. 8B). On the other hand, Zac1 knock-down

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diminished the number of cells in G1-phase and led to concomitant increases in S- and G2/M-

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phase.

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Zac1’s role in antiproliferation was additionally investigated by cotransfection experiments in

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primary NSCs (E15). Following 1 day of neuronal differentiation, Zac1 transfection reduced

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the number of Ki67 positive cells consistent with a role in antiproliferation (Fig. 8C and D). 14

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In contrast, cotransfection of a Tcf4 shRNA expression vector restored Ki67

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immunoreactivity in Zac1 positive cells similar to the one detected in p57Kip2 shRNA

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transfected cells.

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Together, these findings are consistent with the hypothesis that Tcf4 and p57Kip2 are

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downstream to Zac1 antiproliferation in NSCs.

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DISCUSSION

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The present study uncovers a co-operation between imprinted genes and the bHLH factor

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Tcf4 in cell cycle regulation. Zac1 is induced in differentiating neural progenitors and confers

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in a lineage-specific manner transactivation of Tcf4. Subsequently, Tcf4 drives upregulation

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of the cyclin-dependent kinase inhibitor p57Kip2, a critical mediator of G1 arrest function

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during neurodevelopment.

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Expression profiling in C17.2 NSCs identified Tcf4 as potential Zac1 target gene. Given

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Zac1’s expression pattern in the developing nervous system (8, 9), we focused on Zac1-

364

dependent Tcf4 regulation in ESCs and NSCs. Although Zac1 is expressed in both glia and

365

neurons, upregulation of Tcf4 was restricted to neuronal differentiation under in vitro and in

366

vivo conditions. Thereby, Zac1 coordinately occupied the proximal promoter and first intron

367

of Tcf4 and these two elements together conferred synergistic transactivation of the Tcf4 gene.

368

The first intron did not fulfill, however, a role as an autonomous Zac1 enhancer.

369 370

Tcf4 is known to control proliferation, migration and differentiation of distinct neuronal

371

progenitors, pointing to the importance of this factor for brain development (39).

372

Mechanistically, increased Tcf4 expression might counteract the association of its natural

373

inhibitors, the Id proteins, with the proneural factors (40), or the lineage-specific repressor

374

function of Hes proteins (41, 42). 15

375

Alternatively, we suggest that Zac1 transactivation of Tcf4 contributes to enhanced p57Kip2

376

expression in differentiating neuronal precursors as evidenced by overexpression and knock-

377

down experiments in C17.2 and primary NSCs. Cyclin-dependent kinase inhibitors are key

378

effectors of cell cycle arrest during differentiation. In support of this view, we detected

379

colocalization between Zac1, Tcf4 and p57Kip2 during early and late neurogenesis and showed

380

that in the neocortical ventricular zone Tcf4 directly binds to E-box motifs present in the

381

p57Kip2 promoter.

382

The p57Kip2 gene regulates cell cycle dynamics of radial glia and progenitor cells, controls

383

precursor pool size, neuronal differentiation, cortical size and laminar patterning (36, 43, 44).

384

Because cell cycle exit of precursor cells correlates with their laminar destination, neuronal

385

fate is coupled to the cell cycle machinery. Hence, we propose that Zac1 might finetune the

386

timing and fate of neuronal differentiation by enhancing p57Kip2 expression via Tcf4.

387 388

In support of our present findings, Zac1 and p57Kip2 have been hypothesized to be connected

389

in the context of an imprinting gene network (IGN) that regulates early mouse development

390

(35). The mechanisms underlying such connectivity remained, however, incompletely

391

understood. In this regard, we recently showed that Zac1 directly represses the paternally

392

imprinted gene Rasgrf1 leading to an inhibition of glucose-stimulated insulin secretion in

393

pancreatic β-cells (23). Here we show that imprinted genes can be also connected via

394

regulatory networks that involve proneural factors such as Tcf4. On the other hand, the

395

proneural genes Neurogenin 2 and Archaete scute homolog 1 have been found to regulate the

396

imprinted Dlk1-Gtl2 locus in the developing telencephalon (45). Overall, we propose that

397

such reciprocal interactions between imprinted and proneural genes can critically contribute to

398

progenitor cell fate decisions and early neural development.

399

16

400

ACKNOWLEDGEMENT

401

The help of A. Patchev and A. Varga in animal experiments is appreciated. The NSC lines

402

and the Tcf4 antibody were generously provided by A. Smith (Cambridge University, UK)

403

and A. Herbst (University of Munich, Germany), respectively. The pCDEF3.Flag-Tcf4-b

404

expression vector was kindly gifted by S. Itoh (University of Tsukuba, Japan). This work was

405

supported by the Deutsche Forschungsgemeinschaft (SP 386/5-1 to D.S.) The authors declare

406

no competing financial interests.

407

17

408 409 410 411 412 413 414 415 416 417 418 419 420 421 422 423 424 425 426 427 428 429 430 431 432 433 434 435 436 437 438 439 440 441 442 443 444 445 446 447 448 449 450 451 452 453 454 455

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39. Sobrado VR, Moreno-Bueno G, Cubillo E, Holt LJ, Nieto MA, Portillo F, Cano A. 2009. The class I bHLH factors E2-2A and E2-2B regulate EMT. J. Cell. Sci. 122:1014– 1024. 40. Jung S, Park R, Kim S, Jeon Y, Ham D, Jung M, Kim S, Lee Y, Park C, Suh-Kim H. 2010. Id proteins facilitate self-renewal and proliferation of neural stem cells. Stem Cells Dev. 19:831–841. 41. Nakamura Y, Sakakibara Si, Miyata T, Ogawa M, Shimazaki T, Weiss S, Kageyama R, Okano H. 2000. The bHLH gene hes1 as a repressor of the neuronal commitment of CNS stem cells. J. Neurosci. 20:283–293. 42. Holmberg J, Hansson E, Malewicz M, Sandberg M, Perlmann T, Lendahl U, Muhr J. 2008. SoxB1 transcription factors and Notch signaling use distinct mechanisms to regulate proneural gene function and neural progenitor differentiation. Development 135:1843–1851. 43. Mairet-Coello G, Tury A, van Buskirk E, Robinson K, Genestine M, DiCicco-Bloom E. 2012. p57(KIP2) regulates radial glia and intermediate precursor cell cycle dynamics and lower layer neurogenesis in developing cerebral cortex. Development 139:475–487. 44. Tury A, Mairet-Coello G, DiCicco-Bloom E. 2012. The multiple roles of the cyclindependent kinase inhibitory protein p57(KIP2) in cerebral cortical neurogenesis. Dev Neurobiol 72:821–842. 45. Seibt J, Armant O, Le Digarcher A, Castro D, Ramesh V, Journot L, Guillemot F, Vanderhaeghen P, Bouschet T. 2012. Expression at the imprinted dlk1-gtl2 locus is regulated by proneural genes in the developing telencephalon. PLoS ONE 7:e48675. doi:10.1371/journal.pone.0048675.

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FIGURE LEGENDS

589

Zac1 transactivates Tcf4. (A) C17.2 neural stem cells harbouring Tet-off regulated Zac1

590

expression were grown in the presence or absence of tetracycline (Tc). Zac1 and Tcf4

591

expression following Tc removal for the indicated periods were measured by qRT-PCR. (B)

592

Parental C17.2 cells were transfected with the indicated amount of Zac1 vector and

593

expression of Tcf4-a and Tcf4-b isoforms was detected by qRT-PCR analysis. (C)

594

Immunoblot analysis (30 μg whole cell extract, WCE) of Zac1, Tcf4-b and β-actin expression

595

following Zac1 transfection (100 ng). (D) Expression of Tcf4 in C17.2 cells was measured by

596

qRT-PCR following transfection of the indicated Zac1 constructs (100 ng each). (E) Protein

597

levels of Tcf4 and the different Zac1 constructs (100 ng each) were assessed by immunoblot

598

analysis (30 μg WCE). The asterisk indicates the ΔLPR specific signal. (F) Schematic

599

representation of the Tcf4 promoter and first intron. The 2 first alternative exons I and exon II

600

are represented by grey boxes and Roman numbers. Putative Zac1 binding sites are depicted

601

as black squares and triangles. Underlined regions and numbers indicate the genomic fractions

602

amplified in ChIP experiments with respect to the transcriptional start site (+1). (G) ChIP

603

assays revealed Zac1 occupancy at the Tcf4 proximal promoter and first intron, but not at the

604

promoter of the isoform a (Tcf4-a). Representative results from three (C and E) or means ±

605

SD from four (B and G) or six (A and D) independent experiments are shown. * P < 0.05 and

606

** P < 0.01.

Figure 1

607 608

Figure 2

609

Zac1 and Tcf4 are upregulated during neuronal differentiation of mouse embryonic

610

stem cells. (A) Bright-light microscopy of 46C ESCs during neuronal differentiation

611

following leukemia inhibitory factor (Lif) withdrawal for the indicated number of days. Scale

612

bar, 100 μm. (B) Expression of the pluripotency marker Oct4 and (C) neuronal marker Tuj1 22

613

following Lif withdrawal for the indicated number of days was measured by qRT-PCR. (D)

614

Time course analysis of Zac1 and Tcf4 mRNA expression upon Lif withdrawal as detected by

615

qRT-PCR. (E) Immunoblot analysis (100 μg WCE) of ESCs grown for the indicated number

616

of days in the absence of Lif revealed co-regulation of Zac1 and Tcf4. Representative results

617

from three (A and E) or means ± SD from four (B and C) or six (D) independent experiments

618

are shown.

619 620

Figure 3

621

Coordinated Zac1 binding regulates Tcf4 expression. (A) ChIP assays in 46C ESCs with a

622

Zac1 antibody were conducted in the presence (+) or absence (-) of Lif for the indicated

623

number of days. In the presence of Lif, Zac1 binding is barely detectable at the Tcf4 locus,

624

whereas upon Lif withdrawal a strong association between Zac1 and the Tcf4 proximal

625

promoter (-89) and first intron (+1933) was detected. (B) Schematic representation of the Tcf4

626

5’ end and the various Tcf4 promoter fragments used in reporter assays. (C) Reporter assays

627

(note the logarithmic ordinate) with the different Tcf4 promoter fragments (500 ng each) in

628

46C ESCs grown for 3 days in the absence of Lif. Reverse orientation of Tcf4 promoter

629

constructs strongly reduced luciferase activity. Luciferase activity of the parent vector was set

630

to 1. (D) Promoter reporter assays in 46C ESCs. Cells were grown for 3 days in the absence

631

of Lif and subsequently cotransfected with the indicated Tcf4 promoter constructs (500 ng

632

each) and increasing amounts of Zac1 and ZF7mt (10 and 25 ng each) or the empty vector,

633

which was set to 1. Synergistic Zac1 transactivation depended on the joint promoter and

634

intronic regions. (E) Activity of the first Tcf4 intron was measured by reporter assays in 46C

635

cells. Cells were grown for 3 days in the absence of Lif and subsequently cotransfected with

636

the indicated Tcf4 constructs (500 ng each) and Zac1 (25 ng) or the empty vector, which was

637

set to 1. The Tcf4 first intron does not behave as an autonomous Zac1 enhancer when fused to

638

the thymidine kinase (TK) promoter and prevented transactivation when inserted in the 23

639

reverse orientation adjacent to the Tcf4 promoter region. The arrow illustrates the orientation

640

of the intron. Means ± SD from four (A and C) or five (D and E) independent experiments are

641

shown. * P < 0.05 and ** P < 0.01.

642 643

Figure 4

644

Zac1 associates with active chromatin at the Tcf4 locus during neuronal differentiation.

645

(A) Neuronal and astroglial differentiation of O4ANS cells.

646

expression was measured by qRT-PCR across 1 week of differentiation. Note the separate

647

ordinate for Zac1 and Tcf4 regulation. (B-D) ChIP assays in O4ANS cells following 4 days of

648

neuronal or astroglial differentiation using antibodies against Zac1 (B), acH3 (C), and

649

H3K9me2 (D). (E and F) Sequential ChIP analysis following neuronal or astroglial

650

differentiation for 4 days. During neuronal differentiation, Zac1 associated with chromatin

651

containing active marks (acH3/Zac1) at the Tcf4 locus, whereas association with repressive

652

chromatin marks (H3K9me2/Zac1) decreased. Means ± SD from four (C to F) or six (A and

653

B) independent experiments are shown. * P < 0.05 and ** P < 0.01.

Zac1 and Tcf4 mRNA

654 655

Figure 5

656

Zac1 regulates Tcf4 expression during neuronal differentiation of primary NSCs. (A)

657

Immunocytochemistry of NSCs maintained under growth conditions (NSC) or following

658

neuronal or astroglial differentiation for 6 days. Cells were subjected to indirect

659

immunofluorescence with antibodies against Nestin (green), Tuj1 (green), Gfap (green), Zac1

660

(red) or Tcf4 (c, g, k: red and d, h, l: green). Nuclei were stained with DAPI (blue). Scale bar

661

50 μm. (B) Quantitative analysis of the NSC specific marker Nestin, and the neuronal and

662

astroglial markers Tuj1 and Gfap, respectively. Cells were kept under growth conditions or in

663

the appropriate differentiation medium for 6 days. Unknown cellular phenotypes are indicated

664

as non-defined (n/d). Mean of five analyzed images of the type shown in (A). (C) Time 24

665

course analysis of Zac1 and Tcf4 mRNA expression during neuronal and astroglial

666

differentiation as measured by qRT-PCR. (D) Immunoblot analysis (100 μg WCE) of Zac1

667

and Tcf4 expression during neuronal or astroglial differentiation. (E) Promoter reporter assays

668

in undifferentiated NSCs or following neuronal or astroglial differentiation for 6 days. Cells

669

were cotransfected with the composite Tcf4 promoter construct (500 ng) and the indicated

670

amounts of Zac1 or the empty vector, which was set to 1. Highest induction occurred

671

following neuronal differentiation. (F) ChIP analysis following neuronal or astroglial

672

differentiation for 6 days evidenced Zac1 occupancy at the Tcf4 promoter and first intron

673

solely during the former. Representative results from three (A and D) or means ± SD from

674

four (F) or five (C and E) independent experiments are shown. * P < 0.05 and ** P < 0.01.

675 676

Figure 6

677

Zac1 and Tcf4 colocalize in the neocortical ventricular zone. (A and B) Immunohisto-

678

chemistry of mouse brain sections. Upper panel, sections from E11 (A) and E15 (B) were

679

stained with antibodies for Zac1 (red) and Tcf4 (green). Representative images of the

680

subventricular and ventricular zones are shown. Nuclei were stained with DAPI (blue). Scale

681

bar 100 μm. Lower panels show regions with higher magnification corroborating

682

colocalization of Zac1 and Tcf4. Scale bar 40 μm. (C) ChIP analysis of Zac1 occupancy at the

683

Tcf4 promoter in the neocortical VZ/SVZ during neurogenesis (E15) or astrogliogenesis

684

(E18). (D) Induction of the composite Tcf4 promoter construct (500 ng) following

685

cotransfection of increasing amounts of Zac1 or the empty vector, which was set to 1, in cells

686

dissected from the neocortical VZ/SVZ at E15. Representative results from three (A and B) or

687

means ± SD from five (C and D) independent experiments are shown. * P < 0.05 and ** P