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

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 which correlate with their GC content. We further analyze the direct influence of GC content on nucleosome positioning and depletion, and show that CGIs 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. Nucleosome density and positioning were studied by high-throughput sequencing of DNA previously treated with Mnase. In parallel, chIPseq for PolII and H3K27ac were performed in mouse and human with different conditions to assess a potential effect of transcription on nucleosomes properties. To investigate transcription at promoters, we analyzed together with genome-wide Pol II accumulation by ChIP-Seq, paused bidirectional transcripts associated with transcription start sites (TSS RNAs).

ORGANISM(S): Mus musculus

SUBMITTER: Romain Fenouil

PROVIDER: E-GEOD-38560 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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

Project description: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 which correlate with their GC content. We further analyze the direct influence of GC content on nucleosome positioning and depletion, and show that CGIs 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. Nucleosome density and positioning were studied by high-throughput sequencing of DNA previously treated with Mnase. In parallel, chIPseq for PolII and H3K27ac were performed in mouse and human with different conditions to assess a potential effect of transcription on nucleosomes properties.

2012-06-12 | E-GEOD-38561 | biostudies-arrayexpress

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

Project description:This SuperSeries is composed of the following subset Series: GSE38560: CpG islands and GC content dictate nucleosome depletion in a transcription independent manner at mammalian promoters (RNA-seq) GSE38561: CpG islands and GC content dictate nucleosome depletion in a transcription independent manner at mammalian promoters (ChIP-seq) GSE38562: CpG islands and GC content dictate nucleosome depletion in a transcription independent manner at mammalian promoters (genomic SEQ) GSE38563: CpG islands and GC content dictate nucleosome depletion in a transcription independent manner at mammalian promoters (MNase-seq) GSE38564: CpG islands and GC content dictate nucleosome depletion in a transcription independent manner at mammalian promoters (5) Refer to individual Series

2012-06-11 | E-GEOD-38577 | biostudies-arrayexpress

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

2012-06-12 | E-GEOD-38563 | biostudies-arrayexpress

Transcriptional landscape of Rag2 -/- thymocytes [ShortRNA-Seq]

Project description:We performed ChIP-Seq for hallmark TFs (Ets1, Runx1), histone modification marks (H3K4me1, H3K4me2, H3K4me3, H3K27me3, H3K36me3), total RNA Pol II, short RNA-Seq as well as nucleosome mapping mainly in murine Rag2 -/- thymocytes. We also performed ChIP-Seq for E47 as well as nucleosome mapping, gene expression microarray analysis in CD4+ CD8+ DP thymocytes. Overall, we find a key role for the transcription factor Ets1, contributing towards alpha beta T cell lineage commitment via differential transactivation of stage-specific genes orchestrated by dynamic, co-association -mediated chromatin remodeling, as well as transcription dependent generation of a specialized chromatin structure at the TCR beta locus. Genome-wide analysis via ChIP-Seq for Ets1, Runx1, total RNA Pol II binding, H3K4me1, H3K4me2, H3K4me3, H3K27me3, H3K36me3, short RNA-Seq, Mnase-Seq in murine Rag2 -/- thymocytes, ChIP-Seq for E47, Mnase-Seq and gene expression microarray analysis in DP thymocytes This Series represents ShortRNA-Seq data.

2014-04-01 | E-GEOD-56358 | biostudies-arrayexpress

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

Project description: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 which correlate with their GC content. We further analyze the direct influence of GC content on nucleosome positioning and depletion, and show that CGIs 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. Nucleosome density and positioning were studied by high-throughput sequencing of DNA previously treated with Mnase. In parallel, ChIP-seq for PolII and H3K27ac were performed in mouse and human with different conditions to assess a potential effect of transcription on nucleosomes properties. To exclude a possible MNase digestion bias or sequencing artefact within CGIs, we performed additional controls such as nucleosome mapping using an alternative method based on DNA digestion by a chemical agent (phenanthroline) in human Raji B-cells.

2012-06-12 | E-GEOD-38564 | biostudies-arrayexpress

CpG islands and GC content dictate nucleosome depletion in a transcription independent manner at mammalian promoters (genomic SEQ)

2012-06-11 | E-GEOD-38562 | biostudies-arrayexpress

Transcriptional landscape of Rag2 -/- thymocytes

Project description:This SuperSeries is composed of the SubSeries listed below. Refer to individual Series

2014-04-01 | E-GEOD-56395 | biostudies-arrayexpress

Long-range bidirectional transcription is a general feature of developmental gene promoters in mammals (ChIP-Seq 1)

Project description:Recent studies have revealed a myriad of non-coding transcripts in different organisms. For instances, the presence of short bidirectional transcripts is a hallmark of active promoters in mammals, while upstream non-coding transcripts can be detected at most expressed genes in conditions where the RNA degradation machinery is inhibited. Here, we used RNA-seq with very high sequencing depth to characterize strand specific transcripts from primary mouse tissues. We found that a substantial fraction of gene promoters sustain expression of long non-coding antisense transcripts. These transcripts have an average size of 6 kb, have features of mature transcripts, but remain associated with the chromatin. We named this new class of non-coding RNAs Long Upstream Antisense Transcripts (LUAT). Strikingly, the LUAT and coding gene pairs are usually co-regulated, with the associated genes often/generally coding for transcriptional regulators functioning during development and cell differentiation. Indeed, these bidirectional promoters share several characteristic of developmental gene promoters, including large CpG islands and high degree of conservation, and display symetrical GC skews. Finally, we found that bidirectional promoters have enlarged platforms of Pol II initiation, associated with an intensified rate of early transcriptional elongation. We concluded that promoters of developmental regulators are characterized by a specialized mechanism of Pol II transcription, whereby Pol II poising is directly coupled to relaxed bidirectional transcription. H3K79me2 ChIP in CD4+,CD8+ double positive thymocytes from C57BL/6 mice was studied, using Illumina sequencer

2014-01-01 | E-GEOD-44577 | biostudies-arrayexpress

Tyrosine phosphorylation of RNA Polymerase II CTD is associated with antisense promoter transcription and active enhancers in mammalian cells

Project description:In mammals, the carboxy-terminal domain (CTD) of RNA polymerase (Pol) II consists of 52 conserved heptapeptide repeats containing the consensus sequence Tyr1-Ser2-Pro3-Thr4-Ser5-Pro6-Ser7. Post-translational modifications of the CTD coordinate the transcription cycle and various steps of mRNA maturation. Here we describe Tyr1 phosphorylation (Tyr1P) as a hallmark of initiating Pol II in mammalian cells, in contrast to what was described in yeast. Tyr1P is predominantly found in antisense orientation at promoters but is also specifically enriched at active enhancers. Mutation of Tyr1 to phenylalanine (Y1F) prevents the formation of the hyper-phosphorylated Pol IIO form, induces degradation of Pol II to the Pol IIB form and results in a lethal phenotype. Our results suggest that Tyr1P has evolved specialized and essential functions in higher eukaryotes associated with antisense promoter and enhancer transcription, and Pol II stability. This study was performed in a human Raji cell line. It contains ChIP-seq data for H3K36me3 (two replicates), H3K4me1 (two replicates), H3K4me3 (two replicates), Pol II (three replicates), Ser2P (two replicates), Ser5P (two replicates), Ser7P (two replicates), Tyr1P 3D12 (two replicates) and Tyr1P 8G5 (one replicate). MNase-experiment for nucleosomes was performed in paired-end sequencing on one replicate, 4 replicates for the input genomic DNA was used and one replicate was generated for the short strand specific RNA experiment.

2014-06-01 | E-GEOD-52914 | biostudies-arrayexpress

Epigenetic conservation at gene regulatory elements revealed by non-methylated DNA profiling in seven vertebrates

Project description:Two-thirds of gene promoters in mammals are associated with regions of non-methylated DNA, called CpG islands (CGIs), which counteract the repressive effects of DNA methylation. In lower vertebrates, computational CGI predictions often reside away from gene promoters, suggesting a major divergence in gene promoter architecture across vertebrates. By experimentally identifying non-methylated DNA in the genomes of seven diverse vertebrates, we instead reveal that non-methylated islands (NMIs) of DNA are a central feature of vertebrate gene promoters. Furthermore, NMIs are present at orthologous genes across vast evolutionary distances, revealing a surprising level of conservation in this epigenetic feature. By profiling NMIs in different tissues and developmental stages we uncover a unifying set of features that are central to the function of NMIs in vertebrates. Together these findings demonstrate an ancient logic for NMI usage at gene promoters and reveal an unprecedented level of epigenetic conservation across vertebrate evolution. Bio-CAP was used to identify non-methylated regions of the genome in seven diverse vertebrates (human, mouse, platypus, chicken, lizard, frog and zebrafish) across a number of tissues.

2013-01-22 | E-GEOD-43512 | biostudies-arrayexpress

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