Conservation of chromatin loops between mouse and human beta cells
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA806973 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR18028204_1.fastq.gz | Fastqsanger.gz | |||
| SRR18028204_2.fastq.gz | Fastqsanger.gz | |||
| SRR18028205_1.fastq.gz | Fastqsanger.gz | |||
| SRR18028205_2.fastq.gz | Fastqsanger.gz | |||
| SRR18028206_1.fastq.gz | Fastqsanger.gz |
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Project description:Studying the conservation and differences of regulation between human and mouse helps understand gene regulation on mouse models. Chromatin loop is an important gene regulatory mechanism to drive the 3D regulation between genes and their regulatory elements. Here, we performed eHi-C to profile genome wide contacts in mouse strains B6 and CAST islet beta cells, together with the loops identified in human islet alpha and beta cells from previous studies (GSE195523). The results show that the conserved chromation loop and open chromatin regions highlight the function of T2D risk loci and improve our understanding in islet biology.
2024-01-31 | GSE196729 | GEO
Project description:Using eHi-C to map chromatin loops in mouse beta cells
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Project description:The formation of R-loops is a natural consequence of the transcription process, caused by invasion of the DNA duplex by nascent transcripts. These structures have been considered rare transcriptional by-products with potential harmful effects on genome integrity, due to the fragility of the displaced DNA coding strand. However R-loops may also possess beneficial effects as their widespread formation has been detected over CpG island promoters in human genes. Furthermore we have previously shown that R-loops are particularly enriched over G-rich terminator elements. These facilitate RNA polymerase II (Pol II) pausing prior to efficient termination. Here we reveal an unanticipated link between R-loops and RNA interference (RNAi)-dependent H3K9me2 formation over pause site termination regions of mammalian protein coding genes. We show that R-loops induce antisense transcription over these pause elements which in turn lead to the generation of double-strand RNA (dsRNA) and recruitment of Dicer, Ago1, Ago2, and G9a histone lysine methyltransferase (HKMT). Consequently an H3K9me2 repressive mark is formed and Heterochromatin Protein 1γ (HP1γ) is recruited, that reinforces Pol II pausing prior to efficient transcriptional termination. We predict that R-loops promote a chromatin architecture that defines the termination region for a substantial subset of mammalian genes. PolIIS2ph ChIP-seq and input in untreated condition and treated with BIX and RNaseH1 overexpression in HeLa cells. The 4 samples have been multiplexed, pooled and sequenced on 3 lanes of Illumina HiSeq2000.
2014-09-29 | E-GEOD-59878 | biostudies-arrayexpress
Project description:R-loops are transcription by-products that may constitute a threat to genome integrity. In addition to specific enzymes to remove them, eukaryotes rely on a number of mRNP biogenesis factors such as the THO complex, to prevent co-transcriptional R-loop formation. We show in Saccharomyces cerevisiae that R-loops are tightly and specifically linked with histone H3-Ser10 phosphorylation (H3S10P), a mark of chromatin condensation. Importantly, ChIP-chip analyses reveal a clear H3S10P accumulation at the pericentromeric chromatin during the G1-phase of the cell cycle only in R loop-accumulating yeast strains but not in those non-accumulating R-loops, and a significantly higher accumulation during S-phase. Such a difference can also be detected in a number of genes along the genome. ChIP-chip studies were perfomed with antibodies against Histone H3 and the phosphorylated Histone H3 at Serine10 in the yeast S. cerevisiae.
2013-11-13 | E-GEOD-46627 | biostudies-arrayexpress
Project description:Physical interactions between distal regulatory elements in the genome play a key role in regulating gene expression, yet the extent to which these interactions vary between cell types and contribute to cell type-specific gene expression patterns remains unclear. To address this question we have mapped cohesin-bound chromatin loops in 24 diverse human cell types at high resolution using the chromatin interaction analysis by paired-end tag (ChIA-PET) sequencing approach. We combined a total of ~9.6 billion reads across all samples to generate a compendium of 124,830 loops, the most extensive resource currently available. We find that 39% of all chromatin loops vary across cell types, and such changes are effective at grouping cell types based on their tissue of origin, indicating commonalities in three-dimensional (3D) genome architecture amongst related cell types. In contrast, different cell types derived from the same individual show markedly different patterns of interactions indicating that the observed differences are mainly caused by epigenetic changes. Variation in chromatin loops correlates with changes in gene expression, especially for long-range contacts linking cell type-specific enhancers to promoters; moreover, genes contained within the same loop show coordinated co-expression changes in expression across cell types. We further find that loops specific to either blood or embryonic cell lines harbor distinct sets of genes relevant to cell type-specific function, and are enriched for lineage determining transcription factors, indicating a possible mechanism for the assembly of variable loops. Finally, we demonstrate that genetic variants identified in GWAS are enriched in variable loops in disease relevant cell types. Our results provide important insights in how changes in 3D chromatin organization potentially regulate cell type-specific functions.
2020-07-23 | GSE139099 | GEO
Project description:Physical interactions between distal regulatory elements in the genome play a key role in regulating gene expression, yet the extent to which these interactions vary between cell types and contribute to cell type-specific gene expression patterns remains unclear. To address this question we have mapped cohesin-bound chromatin loops in 24 diverse human cell types at high resolution using the chromatin interaction analysis by paired-end tag (ChIA-PET) sequencing approach. We combined a total of ~9.6 billion reads across all samples to generate a compendium of 124,830 loops, the most extensive resource currently available. We find that 39% of all chromatin loops vary across cell types, and such changes are effective at grouping cell types based on their tissue of origin, indicating commonalities in three-dimensional (3D) genome architecture amongst related cell types. In contrast, different cell types derived from the same individual show markedly different patterns of interactions indicating that the observed differences are mainly caused by epigenetic changes. Variation in chromatin loops correlates with changes in gene expression, especially for long-range contacts linking cell type-specific enhancers to promoters; moreover, genes contained within the same loop show coordinated co-expression changes in expression across cell types. We further find that loops specific to either blood or embryonic cell lines harbor distinct sets of genes relevant to cell type-specific function, and are enriched for lineage determining transcription factors, indicating a possible mechanism for the assembly of variable loops. Finally, we demonstrate that genetic variants identified in GWAS are enriched in variable loops in disease relevant cell types. Our results provide important insights in how changes in 3D chromatin organization potentially regulate cell type-specific functions.
2020-07-23 | GSE134743 | GEO
Project description:Physical interactions between distal regulatory elements in the genome play a key role in regulating gene expression, yet the extent to which these interactions vary between cell types and contribute to cell type-specific gene expression patterns remains unclear. To address this question we have mapped cohesin-bound chromatin loops in 24 diverse human cell types at high resolution using the chromatin interaction analysis by paired-end tag (ChIA-PET) sequencing approach. We combined a total of ~9.6 billion reads across all samples to generate a compendium of 124,830 loops, the most extensive resource currently available. We find that 39% of all chromatin loops vary across cell types, and such changes are effective at grouping cell types based on their tissue of origin, indicating commonalities in three-dimensional (3D) genome architecture amongst related cell types. In contrast, different cell types derived from the same individual show markedly different patterns of interactions indicating that the observed differences are mainly caused by epigenetic changes. Variation in chromatin loops correlates with changes in gene expression, especially for long-range contacts linking cell type-specific enhancers to promoters; moreover, genes contained within the same loop show coordinated co-expression changes in expression across cell types. We further find that loops specific to either blood or embryonic cell lines harbor distinct sets of genes relevant to cell type-specific function, and are enriched for lineage determining transcription factors, indicating a possible mechanism for the assembly of variable loops. Finally, we demonstrate that genetic variants identified in GWAS are enriched in variable loops in disease relevant cell types. Our results provide important insights in how changes in 3D chromatin organization potentially regulate cell type-specific functions.
2020-07-23 | GSE134744 | GEO
Project description:In most plants, centromeric DNA contains highly repetitive sequences, including tandem repeats and retrotransposons; however, the roles of these sequences in the structure and function of the centromere are unclear. Here, we found that retrotransposon-derived back-spliced RNA can bind to the centromere through R-loops and regulate the formation of centromeric chromatin loops. Multiple RNA sequences from centromeric retrotransposons (CRMs) were enriched in maize (Zea mays) centromeres and back spliced RNA from CRM1 were detected. We identified three types of circular CRM1 RNAs with the same back-splicing site based on the back-spliced sequences. These circular RNAs bound to the centromere through R-loops. Two R-loop sites inside a single circular RNA promoted the formation of chromatin loops in CRM1 regions. When RNAi was used to target the back-spliced site of the circular CRM1 RNAs, the levels of R-loops and chromatin loops formed by these circular RNAs decreased, while the levels of R-loops produced by linear RNAs with similar binding sites increased. Linear RNAs with only one R-loop site could not promote chromatin loop formation. Higher levels of R-loops and lower levels of chromatin loops in the CRM1 regions of RNAi plants led to a reduced localization of the centromeric H3 variant (CENH3). Our work reveals that centromeric chromatin organization by circular CRM1 RNAs via R-loops and chromatin loops. R-loops are integral components of centromeric chromatin. Proper centromere structure is essential for CENH3 localization. CRM1 elements may have helped to build a suitable chromatin environment during centromere evolution.
2020-01-01 | GSE137701 | GEO
Project description:Genome-wide chromatin interactions identify characteristic promoter-distal loops
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Project description:The formation of R-loops is a natural consequence of the transcription process, caused by invasion of the DNA duplex by nascent transcripts. These structures have been considered rare transcriptional by-products with potential harmful effects on genome integrity, due to the fragility of the displaced DNA coding strand. However R-loops may also possess beneficial effects as their widespread formation has been detected over CpG island promoters in human genes. Furthermore we have previously shown that R-loops are particularly enriched over G-rich terminator elements. These facilitate RNA polymerase II (Pol II) pausing prior to efficient termination. Here we reveal an unanticipated link between R-loops and RNA interference (RNAi)-dependent H3K9me2 formation over pause site termination regions of mammalian protein coding genes. We show that R-loops induce antisense transcription over these pause elements which in turn lead to the generation of double-strand RNA (dsRNA) and recruitment of Dicer, Ago1, Ago2, and G9a histone lysine methyltransferase (HKMT). Consequently an H3K9me2 repressive mark is formed and Heterochromatin Protein 1γ (HP1γ) is recruited, that reinforces Pol II pausing prior to efficient transcriptional termination. We predict that R-loops promote a chromatin architecture that defines the termination region for a substantial subset of mammalian genes.
2014-09-29 | GSE59878 | GEO