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A Novel Approach to Identify Enhancer lincRNAs by Integrating Genome, Epigenome, and Regulatome

LincRNAs enriched with high H3K4me1 and low H3K4me3 signals often have the enhancer-like features which are named as enhancer-associated lincRNAs (elincRNAs). ElincRNAs are considered to be indispensable for target gene transcription, which play important roles in development, signaling events, and...

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Autores principales: Liu, Hui, Jiang, Tiantongfei, Wang, Shuyuan, Chen, Xiang, Jin, Xiaoyan, Wang, Qi, Li, Xinhui, Yin, Jiaqi, Shao, Tingting, Li, Yongsheng, Xu, Juan, Wu, Qiong
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Frontiers Media S.A. 2019
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6951418/
https://www.ncbi.nlm.nih.gov/pubmed/31956652
http://dx.doi.org/10.3389/fbioe.2019.00427
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author Liu, Hui
Jiang, Tiantongfei
Wang, Shuyuan
Chen, Xiang
Jin, Xiaoyan
Wang, Qi
Li, Xinhui
Yin, Jiaqi
Shao, Tingting
Li, Yongsheng
Xu, Juan
Wu, Qiong
author_facet Liu, Hui
Jiang, Tiantongfei
Wang, Shuyuan
Chen, Xiang
Jin, Xiaoyan
Wang, Qi
Li, Xinhui
Yin, Jiaqi
Shao, Tingting
Li, Yongsheng
Xu, Juan
Wu, Qiong
author_sort Liu, Hui
collection PubMed
description LincRNAs enriched with high H3K4me1 and low H3K4me3 signals often have the enhancer-like features which are named as enhancer-associated lincRNAs (elincRNAs). ElincRNAs are considered to be indispensable for target gene transcription, which play important roles in development, signaling events, and even diseases. In this study, we developed a regularized regression model to identify elincRNAs by integrating the genomic, epigenomic, and regulatory data. Application of the proposed method to mouse ESCs reveals that besides the basic well-known epigenetic features H3K4me1 and H3K4me3, more specific epigenetic features, such as high DNA methylation, high H3K122ac, and H3K36me3 were contributed to mark elincRNAs with the best accuracy and precision. Finally, 3729 elincRNAs were identified in mouse ESCs. Furthermore, the elincRNAs and canonical lincRNAs exhibit distinct genomic features, and elincRNAs have the higher CGI enrichment and lower sequence conservation. Through the analysis of transcription regulation, we found that elincRNAs were significantly regulated by NANOG, POU5F1, SOX2 and ESRRB, and were involved in the core transcriptional regulatory circuitry controlling ES cell state Function enrichment analysis further discovered that elincRNAs tended to regulate specific embryonic development biological processes. These results indicated that these two types of lincRNAs had both specific epigenetic and transcriptional regulation mechanism and display distinct functional characters. In conclusion, we presented a credible computational model to prioritize novel elincRNAs, and depicted the atlas of elincRNAs in mouse ESCs, which would help dissect the function roles of lncRNAs during the mammalian development and diseases.
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spelling pubmed-69514182020-01-17 A Novel Approach to Identify Enhancer lincRNAs by Integrating Genome, Epigenome, and Regulatome Liu, Hui Jiang, Tiantongfei Wang, Shuyuan Chen, Xiang Jin, Xiaoyan Wang, Qi Li, Xinhui Yin, Jiaqi Shao, Tingting Li, Yongsheng Xu, Juan Wu, Qiong Front Bioeng Biotechnol Bioengineering and Biotechnology LincRNAs enriched with high H3K4me1 and low H3K4me3 signals often have the enhancer-like features which are named as enhancer-associated lincRNAs (elincRNAs). ElincRNAs are considered to be indispensable for target gene transcription, which play important roles in development, signaling events, and even diseases. In this study, we developed a regularized regression model to identify elincRNAs by integrating the genomic, epigenomic, and regulatory data. Application of the proposed method to mouse ESCs reveals that besides the basic well-known epigenetic features H3K4me1 and H3K4me3, more specific epigenetic features, such as high DNA methylation, high H3K122ac, and H3K36me3 were contributed to mark elincRNAs with the best accuracy and precision. Finally, 3729 elincRNAs were identified in mouse ESCs. Furthermore, the elincRNAs and canonical lincRNAs exhibit distinct genomic features, and elincRNAs have the higher CGI enrichment and lower sequence conservation. Through the analysis of transcription regulation, we found that elincRNAs were significantly regulated by NANOG, POU5F1, SOX2 and ESRRB, and were involved in the core transcriptional regulatory circuitry controlling ES cell state Function enrichment analysis further discovered that elincRNAs tended to regulate specific embryonic development biological processes. These results indicated that these two types of lincRNAs had both specific epigenetic and transcriptional regulation mechanism and display distinct functional characters. In conclusion, we presented a credible computational model to prioritize novel elincRNAs, and depicted the atlas of elincRNAs in mouse ESCs, which would help dissect the function roles of lncRNAs during the mammalian development and diseases. Frontiers Media S.A. 2019-12-17 /pmc/articles/PMC6951418/ /pubmed/31956652 http://dx.doi.org/10.3389/fbioe.2019.00427 Text en Copyright © 2019 Liu, Jiang, Wang, Chen, Jin, Wang, Li, Yin, Shao, Li, Xu and Wu. http://creativecommons.org/licenses/by/4.0/ This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.
spellingShingle Bioengineering and Biotechnology
Liu, Hui
Jiang, Tiantongfei
Wang, Shuyuan
Chen, Xiang
Jin, Xiaoyan
Wang, Qi
Li, Xinhui
Yin, Jiaqi
Shao, Tingting
Li, Yongsheng
Xu, Juan
Wu, Qiong
A Novel Approach to Identify Enhancer lincRNAs by Integrating Genome, Epigenome, and Regulatome
title A Novel Approach to Identify Enhancer lincRNAs by Integrating Genome, Epigenome, and Regulatome
title_full A Novel Approach to Identify Enhancer lincRNAs by Integrating Genome, Epigenome, and Regulatome
title_fullStr A Novel Approach to Identify Enhancer lincRNAs by Integrating Genome, Epigenome, and Regulatome
title_full_unstemmed A Novel Approach to Identify Enhancer lincRNAs by Integrating Genome, Epigenome, and Regulatome
title_short A Novel Approach to Identify Enhancer lincRNAs by Integrating Genome, Epigenome, and Regulatome
title_sort novel approach to identify enhancer lincrnas by integrating genome, epigenome, and regulatome
topic Bioengineering and Biotechnology
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6951418/
https://www.ncbi.nlm.nih.gov/pubmed/31956652
http://dx.doi.org/10.3389/fbioe.2019.00427
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