1. EZH2 RIP-seq Identifies Tissue-specific Long Non-coding RNAs
- Author
-
Wang, Yan, Xie, Yinping, Li, Lili, He, Yuan, Zheng, Di, Yu, Pengcheng, Yu, Ling, Tang, Lixu, Wang, Yibin, and Wang, Zhihua
- Subjects
Biological Sciences ,Bioinformatics and Computational Biology ,Genetics ,Human Genome ,Biotechnology ,Animals ,Base Sequence ,Enhancer of Zeste Homolog 2 Protein ,Gene Expression Profiling ,Gene Expression Regulation ,Humans ,Liver ,Male ,Mice ,Inbred C57BL ,Nucleic Acid Conformation ,Organ Specificity ,Protein Binding ,RNA Isoforms ,RNA ,Long Noncoding ,Epigenetics ,Long non-coding RNA ,Tissue specificity ,PRC2 ,EZH2 ,Histone methylation ,Tissue specificity. ,Medical and Health Sciences ,Biological sciences ,Biomedical and clinical sciences ,Health sciences - Abstract
BackgroundPolycomb Repressive Complex 2 (PRC2) catalyzes histone methylation at H3 Lys27, and plays crucial roles during development and diseases in numerous systems. Its catalytic subunit EZH2 represents a key nuclear target for long non-coding RNAs (lncRNAs) that emerging to be a novel class of epigenetic regulator and participate in diverse cellular processes. LncRNAs are characterized by high tissue-specificity; however, little is known about the tissue profile of the EZH2- interacting lncRNAs.ObjectiveHere we performed a global screening for EZH2-binding lncRNAs in tissues including brain, lung, heart, liver, kidney, intestine, spleen, testis, muscle and blood by combining RNA immuno- precipitation and RNA sequencing. We identified 1328 EZH2-binding lncRNAs, among which 470 were shared in at least two tissues while 858 were only detected in single tissue. An RNA motif with specific secondary structure was identified in a number of lncRNAs, albeit not in all EZH2-binding lncRNAs. The EZH2-binding lncRNAs fell into four categories including intergenic lncRNA, antisense lncRNA, intron-related lncRNA and promoter-related lncRNA, suggesting diverse regulations of both cis and trans-mechanisms. A promoter-related lncRNA Hnf1aos1 bound to EZH2 specifically in the liver, a feature same as its paired coding gene Hnf1a, further confirming the validity of our study. In addition to the well known EZH2-binding lncRNAs like Kcnq1ot1, Gas5, Meg3, Hotair and Malat1, majority of the lncRNAs were firstly reported to be associated with EZH2.ConclusionOur findings provide a profiling view of the EZH2-interacting lncRNAs across different tissues, and suggest critical roles of lncRNAs during cell differentiation and maturation.
- Published
- 2018