RESEARCH HIGHLIGHTS Nature Reviews Genetics | AOP, published online 4 March 2014; doi:10.1038/nrg3697
GENE EXPRESSION
a code conferring such universal activity might not exist
Genome-wide analyses have revealed a great diversity of transcription initiation complexes that can bind to promoters transcribed by RNA polymerase II (Pol II) and, correspondingly, variation in core promoter features, but the implications of these findings were unknown. By mapping the genome-wide activity of Pol II promoters during precisely defined embryonic developmental stages in the zebrafish, Haberle et al. now show that two different determinants for transcription initiation lie, and often overlap, within the same core promoter sequence of genes and that they represent an additional regulatory level during vertebrate development. Embryogenesis is characterized by the transition from early transcription-arrested phases under the control of the maternal (oocyte) transcriptome, through the midblastula stage in which zygotic (that is, the embryo’s own) transcription switches on and maternal RNA is degraded, until organogenesis is under full control of the zygotic transcriptome. Using cap analysis of gene expression (CAGE) technology, the researchers mapped transcription start sites (TSSs) during 12 developmental stages, from the unfertilized oocyte up to 33 hours after fertilization. By creating a ‘snapshot’ of the 5ʹ ends of the mRNA population in a sample, CAGE can produce a genome-wide map of transcription initiation events at single base-pair resolution to assess the dynamics of individual TSS usage. “When we looked at the singlenucleotide level distribution of transcription initiation signals at individual promoters across the
different stages, we saw something remarkable,” recounts Boris Lenhard (Imperial College London), who led the study together with Ferenc Müller and Piero Carninci. “At practically all transcribed promoters, the exact preferences for nucleotide positions at which transcription starts were markedly different.” This finding suggested that maternal and zygotic stages have different transcription initiation ‘codes’. The investigators then characterized the main properties of these codes. They analysed high-resolution chromatin immunoprecipitation followed by sequencing (ChIP–seq) data of nucleosomes carrying histone H3 lysine 4 trimethylation (H3K4me3) — a promoter-specific histone modification associated with active transcription — and its relation to the TSS preference at various developmental stages, which enabled them to directly assign sequence features to both TSS choice and nucleosome positioning. This showed that zygotic transcription initiation is precisely lined up with the position of the first downstream nucleosome and its underlying positioning sequence, whereas maternal TSS did not seem to be related to a nucleosome positioning sequence signal. Dinucleotide density maps at shifting promoters centred according to either the maternal or the zygotic dominant TSS showed that maternal TSS selection is predicted by a ~30‑bp upstream AT-rich motif known as W-box — a degenerate equivalent of the TATA box. Unlike the canonical TATA box, more than one W-box can exist per promoter,
NATURE REVIEWS | GENETICS
Tom Wilson/NPG
Transcription initiation codes — the tip of the iceberg?
with transcription starting at fixed spacing downstream of each motif. By contrast, no such motif was found to initiate zygotic transcription. To experimentally verify the functional relevance of this sequence determinant, Lenhard and colleagues used reporter transgene experiments to mutate the W-box; using single-locus CAGE — a novel TSS analysis tool developed for single-gene analysis — they could demonstrate that these TATA-like sequences are required for correct TSS determination in the oocyte but not in the embryo. The distinctive features of TATAdependent and TATA-less initiation were known but thought to be characteristic of separate classes of promoters. “We show that thousands of genes must have elements that enable both the maternal (that is, TATA-like motif-dependent) and the zygotic (that is, nucleosome positioning signal-related) transcription initiation,” says Lenhard. “This is surprising because it was thought that, in particular, housekeeping genes had the kind of promoter code that enables expression in all cell types; our results indicate that a code conferring such universal activity might not exist and that at least two codes must be present to ensure ubiquitous expression.” Somewhere in the germ line the zygotic code needs to switch again to the maternal code that generates the oocyte transcriptome of the next generation. It will be interesting to see at which stage this switch happens, what transcription factors cause it, and/or what other epigenetic and chromatin changes accompany this switch. Moreover, the question remains whether this study represents the tip of the iceberg: are more than two overlapping codes embedded in promoters?
Linda Koch
ORIGINAL RESEARCH PAPER Haberle, V. et al. Two independent transcription initiation codes overlap on vertebrate core promoters. Nature http://dx.doi.org/10.1038/nature12974 (2014)
VOLUME 15 | APRIL 2014 © 2014 Macmillan Publishers Limited. All rights reserved
GENE EXPRESSION
a code conferring such universal activity might not exist
Genome-wide analyses have revealed a great diversity of transcription initiation complexes that can bind to promoters transcribed by RNA polymerase II (Pol II) and, correspondingly, variation in core promoter features, but the implications of these findings were unknown. By mapping the genome-wide activity of Pol II promoters during precisely defined embryonic developmental stages in the zebrafish, Haberle et al. now show that two different determinants for transcription initiation lie, and often overlap, within the same core promoter sequence of genes and that they represent an additional regulatory level during vertebrate development. Embryogenesis is characterized by the transition from early transcription-arrested phases under the control of the maternal (oocyte) transcriptome, through the midblastula stage in which zygotic (that is, the embryo’s own) transcription switches on and maternal RNA is degraded, until organogenesis is under full control of the zygotic transcriptome. Using cap analysis of gene expression (CAGE) technology, the researchers mapped transcription start sites (TSSs) during 12 developmental stages, from the unfertilized oocyte up to 33 hours after fertilization. By creating a ‘snapshot’ of the 5ʹ ends of the mRNA population in a sample, CAGE can produce a genome-wide map of transcription initiation events at single base-pair resolution to assess the dynamics of individual TSS usage. “When we looked at the singlenucleotide level distribution of transcription initiation signals at individual promoters across the
different stages, we saw something remarkable,” recounts Boris Lenhard (Imperial College London), who led the study together with Ferenc Müller and Piero Carninci. “At practically all transcribed promoters, the exact preferences for nucleotide positions at which transcription starts were markedly different.” This finding suggested that maternal and zygotic stages have different transcription initiation ‘codes’. The investigators then characterized the main properties of these codes. They analysed high-resolution chromatin immunoprecipitation followed by sequencing (ChIP–seq) data of nucleosomes carrying histone H3 lysine 4 trimethylation (H3K4me3) — a promoter-specific histone modification associated with active transcription — and its relation to the TSS preference at various developmental stages, which enabled them to directly assign sequence features to both TSS choice and nucleosome positioning. This showed that zygotic transcription initiation is precisely lined up with the position of the first downstream nucleosome and its underlying positioning sequence, whereas maternal TSS did not seem to be related to a nucleosome positioning sequence signal. Dinucleotide density maps at shifting promoters centred according to either the maternal or the zygotic dominant TSS showed that maternal TSS selection is predicted by a ~30‑bp upstream AT-rich motif known as W-box — a degenerate equivalent of the TATA box. Unlike the canonical TATA box, more than one W-box can exist per promoter,
NATURE REVIEWS | GENETICS
Tom Wilson/NPG
Transcription initiation codes — the tip of the iceberg?
with transcription starting at fixed spacing downstream of each motif. By contrast, no such motif was found to initiate zygotic transcription. To experimentally verify the functional relevance of this sequence determinant, Lenhard and colleagues used reporter transgene experiments to mutate the W-box; using single-locus CAGE — a novel TSS analysis tool developed for single-gene analysis — they could demonstrate that these TATA-like sequences are required for correct TSS determination in the oocyte but not in the embryo. The distinctive features of TATAdependent and TATA-less initiation were known but thought to be characteristic of separate classes of promoters. “We show that thousands of genes must have elements that enable both the maternal (that is, TATA-like motif-dependent) and the zygotic (that is, nucleosome positioning signal-related) transcription initiation,” says Lenhard. “This is surprising because it was thought that, in particular, housekeeping genes had the kind of promoter code that enables expression in all cell types; our results indicate that a code conferring such universal activity might not exist and that at least two codes must be present to ensure ubiquitous expression.” Somewhere in the germ line the zygotic code needs to switch again to the maternal code that generates the oocyte transcriptome of the next generation. It will be interesting to see at which stage this switch happens, what transcription factors cause it, and/or what other epigenetic and chromatin changes accompany this switch. Moreover, the question remains whether this study represents the tip of the iceberg: are more than two overlapping codes embedded in promoters?
Linda Koch
ORIGINAL RESEARCH PAPER Haberle, V. et al. Two independent transcription initiation codes overlap on vertebrate core promoters. Nature http://dx.doi.org/10.1038/nature12974 (2014)
VOLUME 15 | APRIL 2014 © 2014 Macmillan Publishers Limited. All rights reserved
