Anchoring Chromatin Loops to Cancer.
Sign Up to like & getrecommendations! Published in 2017 at "Developmental cell"
DOI: 10.1016/j.devcel.2017.07.013
Abstract: Although some genomic rearrangements are caused by replication or transcription, the etiology of others is unclear. Reporting in Cell, Canela et al. (2017) reveal that type II topoisomerase-mediated release of torsional strain at chromosomal loop anchors… read more here.
Keywords: loops cancer; chromatin loops; anchoring chromatin; etiology ... See more keywords
A supervised learning framework for chromatin loop detection in genome-wide contact maps
Sign Up to like & getrecommendations! Published in 2020 at "Nature Communications"
DOI: 10.1038/s41467-020-17239-9
Abstract: Accurately predicting chromatin loops from genome-wide interaction matrices such as Hi-C data is critical to deepening our understanding of proper gene regulation. Current approaches are mainly focused on searching for statistically enriched dots on a… read more here.
Keywords: genome wide; chromatin loops; framework; contact maps ... See more keywords
Transcription-dependent cohesin repositioning rewires chromatin loops in cellular senescence
Sign Up to like & getrecommendations! Published in 2020 at "Nature Communications"
DOI: 10.1038/s41467-020-19878-4
Abstract: Senescence is a state of stable proliferative arrest, generally accompanied by the senescence-associated secretory phenotype, which modulates tissue homeostasis. Enhancer-promoter interactions, facilitated by chromatin loops, play a key role in gene regulation but their relevance… read more here.
Keywords: chromatin loops; novo cohesin; cohesin; senescence ... See more keywords
Landscape of cohesin-mediated chromatin loops in the human genome
Sign Up to like & getrecommendations! Published in 2020 at "Nature"
DOI: 10.1038/s41586-020-2151-x
Abstract: Physical interactions between distal regulatory elements have a key role in regulating gene expression, but the extent to which these interactions vary between cell types and contribute to cell-type-specific gene expression remains unclear. Here, to… read more here.
Keywords: chromatin loops; cohesin mediated; gene expression; cell ... See more keywords
SnapHiC: a computational pipeline to identify chromatin loops from single-cell Hi-C data
Sign Up to like & getrecommendations! Published in 2021 at "Nature Methods"
DOI: 10.1038/s41592-021-01231-2
Abstract: Single-cell Hi-C (scHi-C) analysis has been increasingly used to map chromatin architecture in diverse tissue contexts, but computational tools to define chromatin loops at high resolution from scHi-C data are still lacking. Here, we describe… read more here.
Keywords: single cell; chromatin loops; pipeline; identify chromatin ... See more keywords
Be-1DCNN: a neural network model for chromatin loop prediction based on bagging ensemble learning.
Sign Up to like & getrecommendations! Published in 2023 at "Briefings in functional genomics"
DOI: 10.1093/bfgp/elad015
Abstract: The chromatin loops in the three-dimensional (3D) structure of chromosomes are essential for the regulation of gene expression. Despite the fact that high-throughput chromatin capture techniques can identify the 3D structure of chromosomes, chromatin loop… read more here.
Keywords: neural network; chromatin loop; chromatin loops; prediction ... See more keywords
CLNN-loop: a deep learning model to predict CTCF-mediated chromatin loops in the different cell lines and CTCF-binding sites (CBS) pair types
Sign Up to like & getrecommendations! Published in 2022 at "Bioinformatics"
DOI: 10.1093/bioinformatics/btac575
Abstract: MOTIVATION Three-dimensional (3D) genome organization is of vital importance in gene regulation and disease mechanisms. Previous studies have shown that CTCF-mediated chromatin loops are crucial to studying the 3D structure of cells. Although various experimental… read more here.
Keywords: loops different; clnn loop; different cell; cbs pair ... See more keywords
ChromLoops: a comprehensive database for specific protein-mediated chromatin loops in diverse organisms
Sign Up to like & getrecommendations! Published in 2022 at "Nucleic Acids Research"
DOI: 10.1093/nar/gkac893
Abstract: Abstract Chromatin loops (or chromatin interactions) are important elements of chromatin structures. Disruption of chromatin loops is associated with many diseases, such as cancer and polydactyly. A few methods, including ChIA-PET, HiChIP and PLAC-Seq, have… read more here.
Keywords: specific protein; protein mediated; mediated chromatin; chromatin loops ... See more keywords
SATB1 chromatin loops regulate Megakaryocyte/Erythroid Progenitor Expansion by facilitating HSP70 and GATA1 induction.
Sign Up to like & getrecommendations! Published in 2023 at "Stem cells"
DOI: 10.1093/stmcls/sxad025
Abstract: Diamond Blackfan Anemia (DBA) is an inherited bone marrow failure syndrome associated with severe anemia, congenital malformations and increased risk of developing cancer. The chromatin-binding SATB1 is downregulated in Megakaryocyte/Erythroid Progenitors (MEPs) in patients and… read more here.
Keywords: megakaryocyte erythroid; hsp70; gata1 induction; chromatin loops ... See more keywords
Rfx2 Stabilizes Foxj1 Binding at Chromatin Loops to Enable Multiciliated Cell Gene Expression
Sign Up to like & getrecommendations! Published in 2017 at "PLoS Genetics"
DOI: 10.1371/journal.pgen.1006538
Abstract: Cooperative transcription factor binding at cis-regulatory sites in the genome drives robust eukaryotic gene expression, and many such sites must be coordinated to produce coherent transcriptional programs. The transcriptional program leading to motile cilia formation… read more here.
Keywords: chromatin loops; transcription; rfx2; gene expression ... See more keywords