Identifying and functionally characterizing tissue-specific and ubiquitously expressed human lncRNAs
Chunjie Jiang,Yongsheng Li,Zheng Zhao,Jianping Lu,Hong Chen,Na Ding,Guangjuan Wang,Juan Xu,Xia Li +8 more
TL;DR: This work assembled and functionally characterized a consensus lncRNA transcriptome by curating hundreds of RNA-seq datasets across normal human tissues from 16 independent studies and found that UE lncRNAs are regulated at the transcriptional level and are associated with epigenetic modifications and post-transcriptional regulation.
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Abstract: Recent advances in transcriptome sequencing have made it possible to distinguish ubiquitously expressed long non-coding RNAs (UE lncRNAs) from tissue-specific lncRNAs (TS lncRNAs), thereby providing clues to their cellular functions. Here, we assembled and functionally characterized a consensus lncRNA transcriptome by curating hundreds of RNA-seq datasets across normal human tissues from 16 independent studies. In total, 1,184 UE and 2,583 TS lncRNAs were identified. These different lncRNA populations had several distinct features. Specifically, UE lncRNAs were associated with genomic compaction and highly conserved exons and promoter regions. We found that UE lncRNAs are regulated at the transcriptional level (with especially strong regulation of enhancers) and are associated with epigenetic modifications and post-transcriptional regulation. Based on these observations we propose a novel way to predict the functions of UE and TS lncRNAs through analysis of their genomic location and similarities in epigenetic modifications. Our characterization of UE and TS lncRNAs may provide a foundation for lncRNA genomics and the delineation of complex disease mechanisms.
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History, Discovery, and Classification of lncRNAs.
TL;DR: The many discoveries that led to the study of lncRNAs are discussed, from Friedrich Miescher's "nuclein" in 1869 to the elucidation of the human genome and transcriptome in the early 2000s, to focus on the biological relevance during lncRNA evolution and describe their basic features as genes and transcripts.
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TL;DR: The expanding knowledge of the metabolic behavior of tumor cells, whether from solid tumors or hematologic malignancies, may provide the basis for the development of tailor-made cancer therapies.
lncRNAKB, a knowledgebase of tissue-specific functional annotation and trait association of long noncoding RNA
Fayaz Seifuddin,Komudi Singh,Abhilash Suresh,Jennifer T Judy,Yun-Ching Chen,Vijender Chaitankar,Ilker Tunc,Xiangbo Ruan,Ping Li,Yi Chen,Haiming Cao,Richard S. Lee,Fernando S. Goes,Peter P. Zandi,M. Saleet Jafri,M. Saleet Jafri,Mehdi Pirooznia +16 more
TL;DR: Long non-coding RNA Knowledgebase (lncRNAKB) is an integrated resource for exploring lncRNA biology in the context of tissue-specificity and disease association and covers a comprehensive breadth and depth of lnc RNA annotation.
Long noncoding RNA MEG3 regulates rheumatoid arthritis by targeting NLRC5.
Yaru Liu,Yaru Liu,Lei Yang,Lei Yang,Qingqing Xu,Qingqing Xu,Xin‐Yi Lu,Xin‐Yi Lu,Taotao Ma,Taotao Ma,Cheng Huang,Cheng Huang,Jun Li,Jun Li +13 more
TL;DR: Results indicated that MEG3 regulates RA by targeting NLRC5 potentially, which may be responsible for the decreased level ofNLRC5 and inflammatory cytokine level.
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NCBI GEO: archive for functional genomics data sets—update
Tanya Barrett,Stephen E. Wilhite,Pierre Ledoux,Carlos Evangelista,Irene F. Kim,Maxim Tomashevsky,Kimberly A. Marshall,Katherine Phillippy,Patti M. Sherman,Michelle Holko,Andrey Yefanov,Hye Seung Lee,Naigong Zhang,Cynthia L. Robertson,Nadezhda Serova,Sean Davis,Alexandra Soboleva +16 more
TL;DR: The Gene Expression Omnibus is an international public repository for high-throughput microarray and next-generation sequence functional genomic data sets submitted by the research community and supports archiving of raw data, processed data and metadata which are indexed, cross-linked and searchable.
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