Using Open Chromatin Enrichment and Network Hi-C (OCEAN-C) to Identify Open Chromatin Interactions.
Sign Up to like & getrecommendations! Published in 2021 at "Methods in molecular biology"
DOI: 10.1007/978-1-0716-1597-3_12
Abstract: The open chromatin enrichment and network Hi-C (OCEAN-C) was developed not only for identifying large-scale chromatin structures, including topologically associated domains (TADs) and A/B compartments, but also for globally mapping hubs of open chromatin interactions (HOCIs)… read more here.
Keywords: chromatin interactions; chromatin; network ocean; open chromatin ... See more keywords
Global analysis of histone modifications and long-range chromatin interactions revealed the differential cistrome changes and novel transcriptional players in human dilated cardiomyopathy.
Sign Up to like & getrecommendations! Published in 2020 at "Journal of molecular and cellular cardiology"
DOI: 10.1016/j.yjmcc.2020.06.001
Abstract: BACKGROUND Acetylation and methylation of histones alter the chromatin structure and accessibility that affect transcriptional regulators binding to enhancers and promoters. The binding of transcriptional regulators enables the interaction between enhancers and promoters, thus affecting… read more here.
Keywords: chromatin interactions; analysis; histone modifications; heart failure ... See more keywords
Histone H3 lysine 4 monomethylation modulates long-range chromatin interactions at enhancers
Sign Up to like & getrecommendations! Published in 2018 at "Cell Research"
DOI: 10.1038/cr.2018.1
Abstract: Long-range chromatin interactions between enhancers and promoters are essential for transcription of many developmentally controlled genes in mammals and other metazoans. Currently, the exact mechanisms that connect distal enhancers to their specific target promoters remain… read more here.
Keywords: chromatin interactions; range chromatin; interactions enhancers; chromatin ... See more keywords
Functional genomics: Identifying global RNA–chromatin interactions by GRID-seq
Sign Up to like & getrecommendations! Published in 2017 at "Nature Reviews Genetics"
DOI: 10.1038/nrg.2017.81
Abstract: A number of techniques can detect interactions between RNA molecules and chromatin, but these techniques only capture chromatin interactions of individual RNAs. Now, Li et al. describe a new method that maps global RNA interactions… read more here.
Keywords: chromatin interactions; rna; cell; global rna ... See more keywords
Stress-induced RNA–chromatin interactions promote endothelial dysfunction
Sign Up to like & getrecommendations! Published in 2020 at "Nature Communications"
DOI: 10.1038/s41467-020-18957-w
Abstract: Chromatin-associated RNA (caRNA) has been proposed as a type of epigenomic modifier. Here, we test whether environmental stress can induce cellular dysfunction through modulating RNA-chromatin interactions. We induce endothelial cell (EC) dysfunction with high glucose… read more here.
Keywords: chromatin interactions; induced rna; dysfunction; stress ... See more keywords
PHC1 maintains pluripotency by organizing genome-wide chromatin interactions of the Nanog locus
Sign Up to like & getrecommendations! Published in 2021 at "Nature Communications"
DOI: 10.1038/s41467-021-22871-0
Abstract: Polycomb group (PcG) proteins maintain cell identity by repressing gene expression during development. Surprisingly, emerging studies have recently reported that a number of PcG proteins directly activate gene expression during cell fate determination process. However,… read more here.
Keywords: chromatin interactions; genome wide; nanog locus; pluripotency ... See more keywords
Cross-species chromatin interactions drive transcriptional rewiring in Epstein–Barr virus–positive gastric adenocarcinoma
Sign Up to like & getrecommendations! Published in 2020 at "Nature Genetics"
DOI: 10.1038/s41588-020-0665-7
Abstract: Epstein–Barr virus (EBV) is associated with several human malignancies including 8–10% of gastric cancers (GCs). Genome-wide analysis of 3D chromatin topologies across GC lines, primary tissue and normal gastric samples revealed chromatin domains specific to… read more here.
Keywords: chromatin interactions; epstein barr; cross species; ebv positive ... See more keywords
FIND: difFerential chromatin INteractions Detection using a spatial Poisson process.
Sign Up to like & getrecommendations! Published in 2018 at "Genome research"
DOI: 10.1101/gr.212241.116
Abstract: Polymer-based simulations and experimental studies indicate the existence of a spatial dependency between the adjacent DNA fibers involved in the formation of chromatin loops. However, the existing strategies for detecting differential chromatin interactions assume that… read more here.
Keywords: chromatin interactions; chromatin; spatial poisson; differential chromatin ... See more keywords
MAPS: Model-based analysis of long-range chromatin interactions from PLAC-seq and HiChIP experiments
Sign Up to like & getrecommendations! Published in 2019 at "PLoS Computational Biology"
DOI: 10.1371/journal.pcbi.1006982
Abstract: Hi-C and chromatin immunoprecipitation (ChIP) have been combined to identify long-range chromatin interactions genome-wide at reduced cost and enhanced resolution, but extracting information from the resulting datasets has been challenging. Here we describe a computational… read more here.
Keywords: chromatin interactions; chromatin; seq hichip; plac seq ... See more keywords
HiCuT: An efficient and low input method to identify protein-directed chromatin interactions
Sign Up to like & getrecommendations! Published in 2022 at "PLoS Genetics"
DOI: 10.1371/journal.pgen.1010121
Abstract: 3D genome organization regulates gene expression, and disruption of these long-range (>20kB) DNA-protein interactions results in pathogenic phenotypes. Chromosome conformation methods in conjunction with chromatin immunoprecipitation were used to decipher protein-directed chromatin interactions. However, these… read more here.
Keywords: directed chromatin; chromatin interactions; protein directed; method ... See more keywords