Divergence of CpG island promoters: A consequence or cause of evolution?

Sharif, Jafar; Endo, Takaho A.; Toyoda, Tetsuro; Koseki, Haruhiko

doi:10.1111/j.1440-169x.2010.01193.x

Cited by 41 publications

(42 citation statements)

References 43 publications

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“…a different set of genes expressed) for the growth and differentiation of the placenta. In our previous work, we had observed a link between the evolution of placenta and genes that have CpG islands (CGIs) in their promoters [80].…”

Section: Do Iap Insertions Sensitize Host Genes To Environmental Cuesmentioning

confidence: 99%

Is there a role for endogenous retroviruses to mediate long-term adaptive phenotypic response upon environmental inputs?

Sharif

Shinkai

Koseki

2013

Phil. Trans. R. Soc. B

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Endogenous retroviruses (ERVs) are long terminal repeat-containing virus-like elements that have colonized approximately 10 per cent of the present day mammalian genomes. The intracisternal A particles (IAPs) are a class of ERVs that is currently highly active in the rodents. IAP elements can influence the transcription profile of nearby genes by providing functional promoter elements and modulating local epigenetic landscape through changes in DNA methylation and histone (H3K9) modifications. Despite the potential role for IAPs in gene regulation, the precise genomic locations where these elements are integrated are not well understood. To address this issue, we have identified more than 400 novel IAP insertion sites within/near annotated genes by searching the murine genome, which suggests that the impact of IAP elements on local and/or global gene regulation could be more profound than was previously expected. On the basis of our independent analyses and already published reports, here we argue that IAPs and ERV elements in general could have an evolutionary role for modulating phenotypic plasticity upon environmental inputs, and that this could be mediated through specific stages of embryonic development such as placentation during which the epigenetic constraints on IAP elements are partially relaxed.

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Section: Do Iap Insertions Sensitize Host Genes To Environmental Cuesmentioning

confidence: 99%

Is there a role for endogenous retroviruses to mediate long-term adaptive phenotypic response upon environmental inputs?

Sharif

Shinkai

Koseki

2013

Phil. Trans. R. Soc. B

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“…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).…”

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confidence: 99%

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

et al. 2012

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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...

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“…This bimodality is also observed in several other vertebrates including humans, chicken, frog and zebrafish [10]. However, the overall percentage of promoters that overlap a CpG island was later shown to be much lower in cold-blooded vertebrates (<20%) when compared to warm-blooded vertebrates (>40%) [11]. This suggested that very few promoters are unmethylated in cold-blooded vertebrates, or that the role of CpG-rich regions may differ between these two groups of organisms.…”

Section: Introductionmentioning

confidence: 73%

Improved Prediction of Non-methylated Islands in Vertebrates Highlights Different Characteristic Sequence Patterns

Huska

Vingron

2016

PLoS Comput Biol

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Non-methylated islands (NMIs) of DNA are genomic regions that are important for gene regulation and development. A recent study of genome-wide non-methylation data in vertebrates by Long et al. (eLife 2013;2:e00348) has shown that many experimentally identified non-methylated regions do not overlap with classically defined CpG islands which are computationally predicted using simple DNA sequence features. This is especially true in cold-blooded vertebrates such as Danio rerio (zebrafish). In order to investigate how predictive DNA sequence is of a region’s methylation status, we applied a supervised learning approach using a spectrum kernel support vector machine, to see if a more complex model and supervised learning can be used to improve non-methylated island prediction and to understand the sequence properties of these regions. We demonstrate that DNA sequence is highly predictive of methylation status, and that in contrast to existing CpG island prediction methods our method is able to provide more useful predictions of NMIs genome-wide in all vertebrate organisms that were studied. Our results also show that in cold-blooded vertebrates (Anolis carolinensis, Xenopus tropicalis and Danio rerio) where genome-wide classical CpG island predictions consist primarily of false positives, longer primarily AT-rich DNA sequence features are able to identify these regions much more accurately.

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Divergence of CpG island promoters: A consequence or cause of evolution?

Cited by 41 publications

References 43 publications

Is there a role for endogenous retroviruses to mediate long-term adaptive phenotypic response upon environmental inputs?

Is there a role for endogenous retroviruses to mediate long-term adaptive phenotypic response upon environmental inputs?

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

Improved Prediction of Non-methylated Islands in Vertebrates Highlights Different Characteristic Sequence Patterns

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