Two independent transcription initiation codes overlap on vertebrate core promoters

Abstract

A core promoter is a stretch of DNA surrounding the transcription start site (TSS) that integrates regulatory inputs1 and recruits general transcription factors to initiate transcription2. The nature and causative relationship of DNA sequence and chromatin signals that govern the selection of most TSS by RNA polymerase II remain unresolved. Maternal to zygotic transition (MZT) represents the most dramatic change of the transcriptome repertoire in vertebrate life cycle3-6. Early embryonic development in zebrafish is characterized by a series of transcriptionally silent cell cycles regulated by inherited maternal gene products: zygotic genome activation commences at the 10th cell cycle, marking the midblastula transition (MBT)7. This transition provides a unique opportunity to study the rules of TSS selection and the hierarchy of events linking transcription initiation with key chromatin modifications. We analysed TSS usage during zebrafish early embryonic development at high resolution using cap analysis of gene expression (CAGE)8 and determined the positions of H3K4me3-marked promoter-associated nucleosomes9. We show that the transition from maternal to zygotic transcriptome is characterised by a switch between two fundamentally different modes of defining transcription initiation, which drive the dynamic change of TSS usage and promoter shape. A maternal-specific TSS selection, which requires an A/T-rich (W-box) motif, is replaced with a zygotic TSS selection grammar characterized by broader patterns of dinucleotide enrichments, precisely aligned with the first downstream (+1) nucleosome. The developmental dynamics of the H3K4me3-marked nucleosomes reveals their DNA sequence-associated positioning at promoters prior to zygotic transcription and subsequent transcription-independent adjustment to the final position downstream of zygotic TSS. The two TSS-defining grammars coexist often in physical overlap in core promoters of constitutively expressed genes to enable their expression in the two regulatory environments. The dissection of overlapping core promoter determinants represents a framework for future studies of promoter structure and function across different regulatory contexts.

Promoter architectures and developmental gene regulation

“…Remarkably, the position of the dominant TSS alone is highly predictive of the +1 nucleosome position and reveals the presence of a sequence pattern characteristic for nucleosome bound DNA downstream of the TSS in both zebrafish [26] and human [27], further corroborating the tight relationship between nucleosome positioning and TSS selection in broad promoters.…”

“…Even though most of the strong promoter motifs and their respective locations were estimated from relatively modest amounts of pre-genome data, CAGE has provided evidence that the distance between TSS and the motifs such as TATA box or DPE is much more constrained than thought previously [24,25] -indeed, promoters with single well defined TSS are usually characterised by a fixed spacing from a motif that defines them. In addition, even weaker motifs such as nucleosome positioning sequence and general GC composition have been shown to line up precisely with most commonly used TSS position in promoters with broader initiation pattern [26,27], revealing hitherto unknown global features of this type of promoter.…”

“…Developmental promoters likely evolved from one of the ancestral classes by acquiring ability to integrate a large number of regulatory inputs in a manner easily malleable by selection forces. On the other hand, it is still not known how widespread is the utilisation of different transcription initiation codes discovered between oocyte and somatic cells that overlap on thousands of, mostly ubiquitously active, vertebrate promoters [26]. …”

“…However, no clear rules or "codes" for TSS selection were evident from these analyses. By systematically analysing transcription initiation patterns and underlying sequence features in early development of zebrafish, a recent study revealed that the transcription initiation "code" in transcribing oocyte is different from that in somatic cells of the developing embryo, with different sequence elements that guide TSS selection at the promoter [26]. Most remarkably, the study showed that thousands of promoters that are active in both oocyte and somatic cells -including the "housekeeping" promoters -have both sets of promoter determinants, most often intertwined on the same physical stretch of DNA (Fig.…”

Core promoters across the genome

“…They have multiple, functionally distinct 1 and sometimes physically overlapping 2 architectures, which determine their responsiveness to long-range regulation and to developmental and differentiation regulatory programs (reviewed in ref. 3).…”