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TranscriptomicsR-loops are marks for histone H3 Ser10 phosphorylation and chromatin compaction
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 ...
ORGANISM(S): Saccharomyces cerevisiae 
2013-11-13 | E-GEOD-46627 | biostudies-arrayexpress
GenomicsR-loops induce repressive chromatin marks over mammalian gene terminators
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 displace...
ORGANISM(S): Homo sapiens 
2014-09-29 | E-GEOD-59878 | biostudies-arrayexpress
TranscriptomicsCTCF binding polarity determines chromatin looping [4C]
CCCTC-binding factor (CTCF) is an architectural protein involved in the three-dimensional organization of chromatin. In this study, we systematically assayed the 3D genomic contact profiles of hundreds of CTCF binding sites in multiple tissues with high-resolution 4C-seq. We find both developmentall...
ORGANISM(S): Mus musculus 
2015-10-29 | E-GEOD-72539 | biostudies-arrayexpress
TranscriptomicsThe genomic landscape of cohesin-associated chromatin interactions
Cohesin is implicated in establishing tissue-specific DNA loops that target enhancers to promoters, and also localizes to sites bound by the insulator protein CTCF, which blocks enhancer-promoter communication. However, cohesin-associated interactions have not been characterized on a genome-wide sca...
ORGANISM(S): Mus musculus 
2013-05-22 | E-GEOD-42237 | biostudies-arrayexpress
GenomicsTCC in pluripotent and differentiated cells
Regulation of gene expression underlies the establishment and maintenance of cell identity. Chromatin structure and gene activity are linked. Recently CTCF anchored loops have been described as major features of chromatin organisation. However, the dynamics and role for these structures in differ...
ORGANISM(S): Mus musculus 
2018-11-08 | E-MTAB-4870 | biostudies-arrayexpress
TranscriptomicsCell type specificity of chromatin organization mediated by CTCF and cohesin
CTCF sites are abundant in the genomes of diverse species but their function is enigmatic. We used chromosome conformation capture to determine long-range interactions among CTCF/cohesin sites over 2 Mb on human chromosome 11 encompassing the β-globin locus and flanking olfactory receptor genes. Alt...
ORGANISM(S): Homo sapiens 
2011-01-13 | E-GEOD-26507 | biostudies-arrayexpress
TranscriptomicsGain of chromatin loops marks the exit from naïve pluripotency – in-situ Hi-C data
In-situ Hi-C data for mouse embryonic stem cells (ES cells, grown in the presence of FBS and LIF) and for NS cells.
ORGANISM(S): Mus musculus 
2018-11-08 | E-MTAB-6591 | biostudies-arrayexpress
ProteomicsNAT10-dependent N4-acetylcytidine (ac4C) reprograms R-loops and promotes cancer stem cell growth
R-loop remodeling dynamically regulates chromatin states and gene expression; however, its exploitation by cancer to sustain self-renewal and malignancy remains poorly understood. Here, we found that glioblastoma (GBM) stem cells (GSCs) display highly active R-loops compared to differentiated tumor ...
ORGANISM(S): Homo sapiens (Human) 
2026-04-10 | PXD077002 | Pride
Ac4c Cancer stem cell Nat10 Glioblastoma R-loop remodeling Glioblastoma stem cell 
UnknownTranscriptionally active chromatin loops contain both 'active' and 'inactive' histone modifications that exhibit exclusivity at the level of nucleosome clusters.
Not available
S-EPMC10962081 | biostudies-literature
UnknownCCIP: predicting CTCF-mediated chromatin loops with transitivity.
Not available
S-EPMC8665748 | biostudies-literature
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