CpG islands and GC content dictate nucleosome depletion in a transcription-independent manner at mammalian promoters

Abstract

One clear hallmark of mammalian promoters is the presence of CpG islands (CGIs) at more than two-thirds of genes, whereas TATA boxes are only present at a minority of promoters. Using genome-wide approaches, we show that GC content and CGIs are major promoter elements in mammalian cells, able to govern open chromatin conformation and support paused transcription. First, we define three classes of promoters with distinct transcriptional directionality and pausing properties that correlate with their GC content. We further analyze the direct influence of GC content on nucleosome positioning and depletion and show that CpG content and CGI width correlate with nucleosome depletion both in vivo and in vitro. We also show that transcription is not essential for nucleosome exclusion but influences both a weak +1 and a well-positioned nucleosome at CGI borders. Altogether our data support the idea that CGIs have become an essential feature of promoter structure defining novel regulatory properties in mammals.[Supplemental material is available for this article.]How the transcriptional machinery accesses gene promoters is a central question for understanding gene regulation. Because eukaryotic genomes are highly compacted, most of the DNA is not easily accessible to transcription factors, to the notable exception of promoters that tend to be more open chromatin structures. In recent years, with the development of genome-wide approaches, several studies in various organisms have described that nucleosomes are at least partially dependent on the primary sequence for their positioning (Kaplan et al. 2009). In yeast and Drosophila, for example, AT-rich stretches at promoters exclude nucleosomes both in vivo and in vitro, although the correlation of both data sets has been discussed in the literature, as opposed to GC-rich regions, often found in gene bodies, which favor nucleosome occupancy (Kaplan et al. 2009(Kaplan et al. , 2010Zhang et al. 2009;Pugh 2010). In contrast, most mammalian promoters are enriched for GC-rich areas-also called CpG islands (CGIs)-whereas TATA boxes only appear in a minority of genes (Sandelin et al. 2007). CGIs are defined as large genomic areas of over-enriched CpG dinucleotides estimated to amount to between 20,000 and 30,000 in various mammalian genomes lacking counterparts in cold blooded organisms or other eukaryotes (Illingworth and Bird 2009;Sharif et al. 2010). Although recent works suggest a link between nucleosome depletion at promoters and the presence of CGIs, a direct correlation was never established (Li et al. 2011;Valouev et al. 2011). Furthermore, it remains to be determined whether nucleosome depletion is a cause or a consequence of promoter transcription because in vitro experimental approaches describe apparently contradictory results (Ramirez-Carrozzi et al. 2009;Valouev et al. 2011).In this study, we report that GC content and CGIs are major promoter elements in mammals able to govern open chromatin conformation and support paused transcription genome-wide. First, we define t...

Promoter architectures and developmental gene regulation

“…There is evidence for both transcription-independent DNA sequence-driven [48], and transcriptional activity-aided nucleosome organisation [43], suggesting that there might not be a single mechanism responsible for nucleosome positioning at all promoters, but might be dependent on the type of the promoter itself.…”

Genomes of Multicellular Organisms Have Evolved to Attract Nucleosomes to Promoter Regions

“…Since the earliest studies on baker's yeast, inquiries into nucleosome positioning have been extended to the genomes of many other organisms, such as Schizosaccharomyces pombe (21) and various other species of yeast (22), Caenorhabditis elegans (23,24), Plasmodium falciparum (25), flies (26), zebrafish (27), Arabidopsis thaliana (28), mice (29,30), and humans (30)(31)(32)(33)(34)(35). Most of these studies were conducted in vivo, and therefore do not allow for isolation of effects encoded into the genomic sequences.…”

Tandem repeat variation in human and great ape populations and its impact on gene expression divergence

“…We found that the association between TRs and the expression divergence holds for highly (P < 10 −117 in all organs) and lowly expressed genes (P < 10 −129 in all organs). Second, as CpG islands and promoter GC content have gene regulatory roles through epigenetic mechanisms (Fenouil et al 2012), we asked whether promoters with and without TRs differ in their CpG content. Although we found a small increase in GC in promoters with TRs (WRS, P = 0.02) (Supplemental Fig.…”