GENOMICS

8,411-414

(1990)

BRIEF REPORT Mapping of the Gene for CNBP, a Finger Protein, to Human Chromosome 3ql3.3-q24 A. J. LUSIS,* T. 6. RAJAVASHISTH,*,’

C. HEINZMANN,*

I. KLlSAK,t

T. MOHANDAS,*

AND

R. s. %wwst

*Departments of Medicine and Microbiology and Molecular Biology Institute, University of California, Los Angeles, California 90024; t Department of Medicine, University of California, Los Angeles, California 90024; and *Division of Medical Genetics, Harbor-UCLA Medical Center, Torrance, California 90509 Received

November

28, 1989;

Cholesterol homeostasis is maintained in part by negative feedback regulation of the genes for proteins involved in cholesterol synthesis and the cellular uptake of cholesterol (Brown and Goldstein, 1986; Clarke et aZ., 1987). The apparent coordinate regulation of several such genes, including 3-hydroxy-3-methylglutaryl coenzyme A (HMG-CoA) reductase, HMG-CoA synthase, farnesyl pyrophosphate synthetase, and the low-density lipoprotein receptor, suggested that these genes may be regulated by a common trans-acting factor that is able to “sense” the levels of cellular sterols (Brown and Goldstein, 1986; Mehrabian et al., 1986; Ashby and Edwards, 1989). This notion received strong support from the identification of a sterol regulatory element (SREl) containing a conserved octamer core sequence in the promoters for each of these genes (Osborne et al., 1988; Dawson et al., 1988; discussed in Rajavashisth et aZ., 1989). Although several positive transcription factors that interact with the promoters for these genes have been characterized, it has proved difficult to identify the SREl core binding protein by techniques such as gel retardation and DNase I footprinting (Gil et aZ.,1988; Dawson et aZ., 1988). Recently, we attempted to identify the core binding protein by directly screening a human hepatoma cDNA expression library with a synthetic oligonucleotide corresponding to the HMG-CoA reductase SREl sequence (Rajavashisth et al., 1989). One of the clones identified in the search exhibited the expected sequence specificity. The cDNA encoded a 19-kDa protein containing seven highly conserved zinc finger repeats with remarkable sequence similarity to the finger domains of the family of retroviral nucleic acid binding proteins (NBPs). We designated the protein “cellular NBP” or CNBP. In common with the viral NBPs, CNBP appears to have a strong preference for single-stranded DNA. Although 1 Present ical Center,

address: Department of Pediatrics, Torrance, CA 90509.

Harbor-UCLA

revised

May

11, 1990

certain observations are consistent with the possibility that CNBP functions in the regulation of sterol-responsive genes, the evidence for this is circumstantial (Rajavashisth et al., 1989). As part of an effort to elucidate the function of CNBP through genetic analysis, and also to clarify its relationship to other finger proteins, we report here the chromosomal mapping of the human CNBP gene. The chromosomal localization of the CNBP gene was examined by Southern blot analysis of DNA from a panel of 17 mouse-human somatic cell hybrids. Under the stringent conditions used for hybridization and washing, the CNBP cDNA (1.5 kb in length) hybridized to a small number of bands in digests of mouse or human genomic DNA (Fig. lA), suggesting that the gene is present as a single-copy sequence. Restriction of DNA isolated from the hybrid cells with EcoRI yielded a mouse band of 13.5 kb and two human bands of 6.7 and 4.5 kb (Fig. 1B). The two human bands cosegregated among all hybrids, and correlation of the human bands with the human chromosome content of the clones showed that the CNBP gene resides on chromosome 3 (Table 1). Thus, there was complete concordance among all the hybrid cell clones examined for the cosegregation of CNBP and chromosome 3, and all other clones showed at least three discordancies. The regional localization of the gene was performed using in situ hybridization to metaphase chromosomes. The full-length human cDNA was labeled with 3H-labeled deoxynucleotides and hybridized to metaphase chromosomes as previously described (Heinzmann et al., 1989). Slides were exposed for about 1 week and all silver grains touching chromosomes were scored. The only significant accumulation of grains occurred over chromosome 3, consistent with the somatic cell hybrid studies. Peak accumulation, corresponding to about 14% of the total grains scored, occurred over the region 3q13.3-q24, indicating that the CNBP gene resides within this segment (Fig. 2).

Med-

411

OSSS-7543/90 $3.00 Copyright 0 1990 by Academic Press, Inc. All rights of reproduction in any form reserved.

412

BRIEF

-II

MH

REPORT

MH

-13.5Kb -6.7Kb

5.6Kb4.9Kb-

-4.5Kb

FIG. 1. Southern blot analysis of CNBP gene in mouse-human somatic cell hybrids. (A) Genomic DNA isolated from mice (M) or (H) was digested with either HindI or EcoRI, electrophoresed through 1% agarose gels, transferred to nylon membranes, and probed 32P-labeled full-length human CNBP cDNA insert as previously described, except that blots were washed at 65’C in 15 n&f NaCI, sodium citrate, pH 8.0, containing 0.1% SDS (11). The sizes of the hybridizing fragments are indicated in kilobases. (B) A panel of cell hybrid clones was constructed as previously described (14) and individual clones were examined by Southern hybridization [see the presence of the human 6.7- and 4.5-kb CNBP bands. GM0347A is the mouse parental cell line and IMR91 is the human parental

A large number of finger proteins have now been identified (discussed in Rajavashisth et al., 1989), and a number of these have been mapped in humans. These include genes for members of the steroid hormone re-

ceptor family (Evans, 1988) mapping to human chromosomes 4, 5, 6, 11, 16, and 17 (discussed in Francke and Foellmer, 1989), the putative testis-determining factor on the Y chromosome (Page et al., 1987), and

TABLE Segregation

of CNBP

Gene with

Human

1

Chromosome Human

Hybrid clone 84-2 84-3 84-4 84-5 84-7 84-13 84-20 84-21 84-25 84-26 84-27 84-30 84-34 84-35 84-37 84-38 83-39 % Discordancy

CNBP”

1

2

3

+ + + +

++-+++++--+ ++++-+++-+++++-+++-f--+++-+++ -++-++-+----++-+++--+

+ + + + + + +

+ + -

(+) + -

47

4

5

6

-

1 --+ ++ -+ -+ ++ + +-

+ + + + + (+) + + + (+) -

+-+ +++ ++ ++ ++ + + -+

57

0

41

41

+

67

7

+

+ +

41

8

9

humans with a 1.4 mA4 somatic (A)] for cell line.

10

11

3 in Mouse-Human

12

13

+ -

+++++ +++-+++

+ + + + + + (+) + +

-++ - - (+) (+) -++ -+ + (+) + -++ --+ - + (+) -++ + -+ - - + + - + ---

38

65

88

Cell Hybrids

chromosomesb

+

47

Somatic

57

14

(+) + -+-++--

15

-

17

18

19

20

21

+

+ +--+--+---

-+-

+

-

+ -

+ + + + + + + - + -

+ + + + + + + + + + + +

+ + + + + + - (+) + + + -

25

35

35

29

+ + + f -

+

16

++-+ +++

29

59

+

44

53

+

22

+

-

-

59

53

x

Y

+

+ -

(+) -

(+I + -

57

57

o + indicates CNBP sequences in the hybrid clone determined by the presence of the human band; - indicates absence of the gene. b + indicates presence of the human chromosome in greater than 30% of metaphases analyzed; (+) indicates presence of the chromosome in lo-30% of metaphases analyzed, - indicates absence of the human chromosome. Cells containing chromosomes in lO-30% of metaphases were ignored in calculations of % discordancy.

BRIEF

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REPORT

111 13

14

15

16

17

18

19

20

21 22

x

Y

3

CHROMOSOMES

FIG. 2. Localization of the CNBP gene by in situ hybridization. (A) In situ hybridization to normal lymphocyte chromosomes was by Cannizzaro and Emanuel (4)]. A full-length human CNBP cDNA probe (17) was performed essentially as described [Ref. (lo), as modified labeled to a specific activity of about 3 X 10’ cpm/pg and hybridized to the chromosomes. The slides were coated with a photographic emulsion, exposed for about 1 week and developed, and grains touching chromosomes were scored. In the experiment shown, a total of 119 cells were scored for grains. Of these, 70% contained grains and about 14% of all grains were on the long arm of chromosome 3. In a separate experiment (not shown), similar results were obtained with about 30% of all grains residing on the long arm of chromosome 3. (B) A schematic representation of human chromosome 3 showing the distribution of grains along the bands.

three Kruppel-related finger proteins on chromosomes 5,12, and 17 (discussed in Ashworth et al., 1989). Thus, there is no evidence for the clustering of finger protein genes and the CNBP gene is not located near any other finger proteins that have been mapped in humans. The structural motif of the CNBP finger repeats is very similar to that of repeats of certain finger proteins of plants and insects as well as certain vertebrate retroviruses, but it is unique among mammalian zinc finger proteins studied so far (Rajavashisth et al., 1989). Thus, CNBP is probably only distantly related to the latter. To date, no other genes functionally or structurally related to CNBP have been mapped to 3q13.3-q24, nor have any human disorders involving cholesterol me-

tabolism been assigned to this segment (Human Mapping 10, 1989).

Gene

ACKNOWLEDGMENTS This work was supported by NIH Grants HL30568 and HL42488. C.H., R.S.S., and A.J.L. were also supportedby NIH Grant HL28481. A.J.L. is an Established Investigator of the American Heart Association, with funds contributed in part by the Greater Los Angeles Affiliate.

REFERENCES 1.

ASHBY, M. N., AND EDWARDS, P. A. (1989). Identification and regulation of a rat liver cDNA encoding famesyl pyrophosphate synthetase. J. Biol. Chem. 264: 635-640.

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2. ASHWORTH, A., WILLIAMS, B. P., BUCHBERG, A. M., GOODFELLOW, P. N., SOLOMON, E., POTTER, J., AND WILSON, K. R. (1989). Chromosomal localization of zinc finger protein genes in man and mouse. Genomics 4: 323-327. 3. BROWN, M. S., AND GOLDSTEIN, J. L. (1986). A receptor mediated pathway for cholesterol homeostasis. Science 232: 3447. 4. CANNIZZARO,L. A., AND EMANUEL, B. S. (1984). An improved method for G-banding chromosomes after in situ hybridization. Cytogenet.

Cell Genet.

38:

308-309.

5. CLARKE, C. F., EDWARDS, P. A., AND FOGELMAN, A. M. (1987). Cellular regulation of cholesterol metabolism. In “Plasma Lipoproteins” (A. M. Gotto, Jr., Ed.), pp. 261-276, Elsevier, Amsterdam. 6. DAWSON, P. A., HOFMANN, S. L., VAN DER WESTHUYZEN, D. R., SUDHOF, J. C., BROWN, M. C., AND GOLDSTEIN, J. L. (1988). Sterol-dependent repression of a low density lipoprotein receptor promoter mediated by 16-base pair sequence adjacent to binding site for transcription factor Spl. J. Biol. Chem. 263: 3372-3379.

7. EVANS, R. (1988). The steroid and thyroid hormone receptor superfamily. Science 240: 889-895. 8. GIL, G., OSBORNE, T. F., GOLDSTEIN, J. L., AND BROWN, M. S. (1988). Purification of a protein doublet that binds six TGGcontaining sequences in the promoter for hamster 3-hydroxy3-methylglutaryl coenzyme A reductase. J. Biol. Chem. 263: 19,009-19,019. 9. FRANCKE, U., AND FOELLMER, B. E. (1989). The glucocorticoid receptor gene is in 5q-q23. Genomics 4: 610-612. 10. HARPER, M. E., AND SAUNDERS, G. F. (1981). Localization of single copy DNA sequences on G-banded human chromosomes by in situ hybridization. Chromosoma 63: 431-439.

11. HEINZMANN, C., CLARKE, C. F., KLISAK, I., MOHANDAS, J., SPARKES, R. S., EDWARDS, P. A., AND LUSIS, A. J. (1989). Dispersed family of human genes with sequence similarity to farnesyl pyrophosphate synthetase. Genomics 6: 493-500. 12. Human Gene Mapping 10 (1989). New Haven Conference: Tenth International Workship on Human Gene Mapping. Cytogenet.

Cell Genet.

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13. MEHRABIAN, M., CALLAWAY, K. A., CLARKE, C. F., TANAKA, R. D., GREENSPAN,M., LUSIS, A. J., SPARKES,R. S., MOHANDAS, T., EDMOND, J., FOGELMAN, A. M., AND EDWARDS, P. A. (1986). Regulation of rat liver 3-hydroxy-3-methylgluaryl coenzyme A synthase and the chromosomal localization of the human gene. J. Biol. Chem. 261: 16,249-16,255. 14. MOHANDAS, T., HEINZMANN, C., SPARKES, R. S., WASMUTH, J. EDWARDS, P., AND LUSIS, A. J. (1986). Assignment of human 3-hydroxy-3-methylglutaryl coenzyme A reductase gene to q13q23 region of chromosome 5. Somatic Cell. Mol. Genet. 12: 8994.

15. OSBORNE, T. F., GIL, G., GOLDSTEIN, J. L., AND BROWN, M. S. (1988). Operator constitutive mutation of 3-hydroxy-3-methylglutaryl coenzyme A reductase promoter abolishes protein binding to sterol regulatory element. J. Biol. Chem. 263: 33803367. 16. PAGE, D. C., MOSHER, R., SIMPSON, E. M., FISCHER, F. M. C., MARDON, G., POLLACK, J., MCGILLIURAY, B., DELA CHAPELLE, A., AND BROWN, L. G. (1987). The sex-determining region of the human Y chromosome encodes a finger protein. Cell 61: 1091-1104. 17. RAJAVASHISTH, T. B., TAYLOR, A. K., ANDALIBI, A., SVENSON, K. L., AND LUSIS, A. J. (1989). Identification of a zinc finger protein that binds to the sterol regulatory element. Science 246: 640-643.

Mapping of the gene for CNBP, a finger protein, to human chromosome 3q13.3-q24.

GENOMICS 8,411-414 (1990) BRIEF REPORT Mapping of the Gene for CNBP, a Finger Protein, to Human Chromosome 3ql3.3-q24 A. J. LUSIS,* T. 6. RAJAVASHI...
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