scholarly journals A Comprehensive Characterization of the Function of LincRNAs in Transcriptional Regulation Through Long-Range Chromatin Interactions

2016 ◽  
Vol 6 (1) ◽  
Author(s):  
Liuyang Cai ◽  
Huidan Chang ◽  
Yaping Fang ◽  
Guoliang Li
Keyword(s):  
Transcriptional Regulation ◽  
Long Range ◽  
Chromatin Interactions ◽  
Comprehensive Characterization

scholarly journals Large-scale multi-omics analysis suggests specific roles for intragenic cohesin in transcriptional regulation

2021 ◽  
Author(s):  
Jiankang Wang ◽  
Masashige Bando ◽  
Katsuhiko Shirahige ◽  
Ryuichiro Nakato
Keyword(s):  
Transcriptional Regulation ◽  
Rna Polymerase Ii ◽  
Binding Sites ◽  
Large Scale ◽  
Gene Activation ◽  
Cell Types ◽  
Chromatin Interaction ◽  
Context Specific ◽  
Comprehensive Characterization

Cohesin, an essential protein complex for chromosome segregation, regulates transcription through a variety of mechanisms. It is not a trivial task to genome-widely assign the diverse cohesin functions. Moreover, the context-specific roles of cohesin-mediated interactions, especially on intragenic regions, have not been thoroughly investigated. Here we performed a comprehensive characterization of cohesin binding sites in several human cell types. We integrated epigenomic, transcriptomic and chromatin interaction data with and without transcriptional stimulation, to explore context-specific functions of intragenic cohesin related to gene activation. We identified a new subset of cohesin binding sites, decreased intragenic cohesin sites (DICs), which have a different function from previously known ones. The intron-enriched DICs were negatively correlated with transcriptional regulation: a subgroup of DICs were related to enhancer markers and paused RNA polymerase II, whereas others contributed to chromatin architecture. We implemented machine learning and successfully isolated DICs with distinct genomic features. We observed DICs in various cell types, including cells from cohesinopathy patients. These results suggest a previously unidentified function of cohesin at intragenic regions for transcription regulation.

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