Enhancer LncRNAs Influence Chromatin Interactions in Different Ways.
Yue Hou,Rong Xin Zhang,Xiao Sun +2 more
TLDR
It was found that elncRNAs were highly enriched surrounding chromatin loop anchors and the G-quadruplexes on enhancers were highly related to the expression of elnc RNAs, and elncRNA expression levels were positively correlated with the interaction frequency of enhancer–promoter pairs.Abstract:
More than 98% of the human genome does not encode proteins, and the vast majority of the noncoding regions have not been well studied. Some of these regions contain enhancers and functional non-coding RNAs. Previous research suggested that enhancer transcripts could be potent independent indicators of enhancer activity, and some enhancer lncRNAs (elncRNAs) have been proven to play critical roles in gene regulation. Here, we identified enhancer–promoter interactions from high-throughput chromosome conformation capture (Hi-C) data. We found that elncRNAs were highly enriched surrounding chromatin loop anchors. Additionally, the interaction frequency of elncRNA-associated enhancer–promoter pairs was significantly higher than the interaction frequency of other enhancer–promoter pairs, suggesting that elncRNAs may reinforce the interactions between enhancers and promoters. We also found that elncRNA expression levels were positively correlated with the interaction frequency of enhancer–promoter pairs. The promoters interacting with elncRNA-associated enhancers were rich in RNA polymerase II and YY1 transcription factor binding sites. We clustered enhancer–promoter pairs into different groups to reflect the different ways in which elncRNAs could influence enhancer–promoter pairs. Interestingly, G-quadruplexes were found to potentially mediate some enhancer–promoter interaction pairs, and the interaction frequency of these pairs was significantly higher than that of other enhancer–promoter pairs. We also found that the G-quadruplexes on enhancers were highly related to the expression of elncRNAs. G-quadruplexes located in the promoters of elncRNAs led to high expression of elncRNAs, whereas G-quadruplexes located in the gene bodies of elncRNAs generally resulted in low expression of elncRNAs.read more
Citations
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YY1 Is a Structural Regulator of Enhancer-Promoter Loops
Alla A. Sigova,Nancy M. Hannett,Daniel S. Day,Brian J. Abraham,Malkiel A. Cohen,Behnam Nabet,Dennis L. Buckley,Yang Eric Guo,Denes Hnisz,James E. Bradner,Nathanael S. Gray,Abraham S. Weintraub,Charles H. Li,Alicia Zamudio Montes de Oca,Rudolf Jaenisch,Richard A. Young +15 more
TL;DR: In this paper, the ubiquitously expressed transcription factor Yin Yang 1 (YY1) contributes to enhancer-promoter structural interactions in a manner analogous to DNA interactions mediated by CTCF.
Cohesin Loss Eliminates All Loop Domains
Suhas S.P. Rao,Su-Chen Huang,Brian Glenn St Hilaire,Jesse M. Engreitz,Elizabeth M. Perez,Kyong-Rim Kieffer-Kwon,Adrian L. Sanborn,Sarah E. Johnstone,Gavin D. Bascom,Ivan D. Bochkov,Xingfan Huang,Muhammad S. Shamim,Jaeweon Shin,Douglass Turner,Ziyi Ye,Arina D. Omer,James T. Robinson,Tamar Schlick,Bradley E. Bernstein,Rafael Casellas,Erez Lieberman Aiden,Eric S. Lander +21 more
TL;DR: All loop domains are eliminated, but neither compartment domains nor histone marks are affected, and many megabase-sized loops recovered in under an hour, consistent with a model where loop extrusion is rapid.
Journal ArticleDOI
BET inhibition disrupts transcription but retains enhancer-promoter contact
Nicholas T. Crump,Erica Ballabio,Laura Godfrey,Ross Thorne,Emmanouela Repapi,Jon Kerry,Marta Tapia,Marta Tapia,Peng Hua,Christoffer Lagerholm,Panagis Filippakopoulos,James O.J. Davies,Thomas A. Milne +12 more
TL;DR: It is shown that pharmacological targeting of cells with inhibitors of BET (Bromodomain and Extra-Terminal domain) proteins can have a strong impact on transcription but very little impact on enhancers-promoter interactions, suggesting that activation of transcription and maintenance of enhancer- Promoter interactions are separable events.
Journal ArticleDOI
LncRNA SNHG11 facilitates tumor metastasis by interacting with and stabilizing HIF-1α.
Linguo Xu,Lin Huan,Tianan Guo,Yangjun Wu,Yanfang Liu,Qifeng Wang,Shenglin Huang,Ye Xu,Linhui Liang,Xianghuo He +9 more
TL;DR: A SNHG11/ HIF-1α axis that plays a pivotal role in tumor invasion and metastasis is identified that is associated with poor prognosis in CRC patients and upregulated by promotor hypomethylation.
Journal ArticleDOI
Long Non-Coding RNA HOTAIR in Breast Cancer Therapy
Monica Cantile,Maurizio Di Bonito,Margherita Cerrone,Francesca Collina,Michelino De Laurentiis,Gerardo Botti +5 more
TL;DR: The role of HOTAIR in cancer progression and drug resistance, in particular in BC, is summarized, and the main approaches for silencing it are illustrated.
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