Literature DB >> 25921091

De Novo Reconstruction of Adipose Tissue Transcriptomes Reveals Long Non-coding RNA Regulators of Brown Adipocyte Development.

Juan R Alvarez-Dominguez1,2, Zhiqiang Bai3, Dan Xu3, Bingbing Yuan1, Kinyui Alice Lo4, Myeong Jin Yoon3, Yen Ching Lim3, Marko Knoll1, Nikolai Slavov2, Shuai Chen5, Chen Peng6, Harvey F Lodish1,2, Lei Sun3,4.   

Abstract

Brown adipose tissue (BAT) protects against obesity by promoting energy expenditure via uncoupled respiration. To uncover BAT-specific long non-coding RNAs (lncRNAs), we used RNA-seq to reconstruct de novo transcriptomes of mouse brown, inguinal white, and epididymal white fat and identified ∼1,500 lncRNAs, including 127 BAT-restricted loci induced during differentiation and often targeted by key regulators PPARγ, C/EBPα, and C/EBPβ. One of them, lnc-BATE1, is required for establishment and maintenance of BAT identity and thermogenic capacity. lnc-BATE1 inhibition impairs concurrent activation of brown fat and repression of white fat genes and is partially rescued by exogenous lnc-BATE1 with mutated siRNA-targeting sites, demonstrating a function in trans. We show that lnc-BATE1 binds heterogeneous nuclear ribonucleoprotein U and that both are required for brown adipogenesis. Our work provides an annotated catalog for the study of fat depot-selective lncRNAs and establishes lnc-BATE1 as a regulator of BAT development and physiology.
Copyright © 2015 Elsevier Inc. All rights reserved.

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Year:  2015        PMID: 25921091      PMCID: PMC4429916          DOI: 10.1016/j.cmet.2015.04.003

Source DB:  PubMed          Journal:  Cell Metab        ISSN: 1550-4131            Impact factor:   27.287


  50 in total

1.  Transcriptional control of brown fat determination by PRDM16.

Authors:  Patrick Seale; Shingo Kajimura; Wenli Yang; Sherry Chin; Lindsay M Rohas; Marc Uldry; Geneviève Tavernier; Dominique Langin; Bruce M Spiegelman
Journal:  Cell Metab       Date:  2007-07       Impact factor: 27.287

2.  Integrative annotation of human large intergenic noncoding RNAs reveals global properties and specific subclasses.

Authors:  Moran N Cabili; Cole Trapnell; Loyal Goff; Magdalena Koziol; Barbara Tazon-Vega; Aviv Regev; John L Rinn
Journal:  Genes Dev       Date:  2011-09-02       Impact factor: 11.361

Review 3.  Long noncoding RNAs during normal and malignant hematopoiesis.

Authors:  Juan R Alvarez-Dominguez; Wenqian Hu; Austin A Gromatzky; Harvey F Lodish
Journal:  Int J Hematol       Date:  2014-03-09       Impact factor: 2.490

4.  Taking control over intracellular fatty acid levels is essential for the analysis of thermogenic function in cultured primary brown and brite/beige adipocytes.

Authors:  Yongguo Li; Tobias Fromme; Sabine Schweizer; Theresa Schöttl; Martin Klingenspor
Journal:  EMBO Rep       Date:  2014-08-18       Impact factor: 8.807

5.  Gene set enrichment analysis: a knowledge-based approach for interpreting genome-wide expression profiles.

Authors:  Aravind Subramanian; Pablo Tamayo; Vamsi K Mootha; Sayan Mukherjee; Benjamin L Ebert; Michael A Gillette; Amanda Paulovich; Scott L Pomeroy; Todd R Golub; Eric S Lander; Jill P Mesirov
Journal:  Proc Natl Acad Sci U S A       Date:  2005-09-30       Impact factor: 11.205

6.  Long noncoding RNAs regulate adipogenesis.

Authors:  Lei Sun; Loyal A Goff; Cole Trapnell; Ryan Alexander; Kinyui Alice Lo; Ezgi Hacisuleyman; Martin Sauvageau; Barbara Tazon-Vega; David R Kelley; David G Hendrickson; Bingbing Yuan; Manolis Kellis; Harvey F Lodish; John L Rinn
Journal:  Proc Natl Acad Sci U S A       Date:  2013-02-11       Impact factor: 11.205

7.  A long noncoding RNA transcriptional regulatory circuit drives thermogenic adipocyte differentiation.

Authors:  Xu-Yun Zhao; Siming Li; Guo-Xiao Wang; Qi Yu; Jiandie D Lin
Journal:  Mol Cell       Date:  2014-07-04       Impact factor: 17.970

8.  A PGC1-α-dependent myokine that drives brown-fat-like development of white fat and thermogenesis.

Authors:  Pontus Boström; Jun Wu; Mark P Jedrychowski; Anisha Korde; Li Ye; James C Lo; Kyle A Rasbach; Elisabeth Almer Boström; Jang Hyun Choi; Jonathan Z Long; Shingo Kajimura; Maria Cristina Zingaretti; Birgitte F Vind; Hua Tu; Saverio Cinti; Kurt Højlund; Steven P Gygi; Bruce M Spiegelman
Journal:  Nature       Date:  2012-01-11       Impact factor: 49.962

9.  Essential role for miR-196a in brown adipogenesis of white fat progenitor cells.

Authors:  Masaki Mori; Hironori Nakagami; Gerardo Rodriguez-Araujo; Keisuke Nimura; Yasufumi Kaneda
Journal:  PLoS Biol       Date:  2012-04-24       Impact factor: 8.029

10.  An encyclopedia of mouse DNA elements (Mouse ENCODE).

Authors:  John A Stamatoyannopoulos; Michael Snyder; Ross Hardison; Bing Ren; Thomas Gingeras; David M Gilbert; Mark Groudine; Michael Bender; Rajinder Kaul; Theresa Canfield; Erica Giste; Audra Johnson; Mia Zhang; Gayathri Balasundaram; Rachel Byron; Vaughan Roach; Peter J Sabo; Richard Sandstrom; A Sandra Stehling; Robert E Thurman; Sherman M Weissman; Philip Cayting; Manoj Hariharan; Jin Lian; Yong Cheng; Stephen G Landt; Zhihai Ma; Barbara J Wold; Job Dekker; Gregory E Crawford; Cheryl A Keller; Weisheng Wu; Christopher Morrissey; Swathi A Kumar; Tejaswini Mishra; Deepti Jain; Marta Byrska-Bishop; Daniel Blankenberg; Bryan R Lajoie; Gaurav Jain; Amartya Sanyal; Kaun-Bei Chen; Olgert Denas; James Taylor; Gerd A Blobel; Mitchell J Weiss; Max Pimkin; Wulan Deng; Georgi K Marinov; Brian A Williams; Katherine I Fisher-Aylor; Gilberto Desalvo; Anthony Kiralusha; Diane Trout; Henry Amrhein; Ali Mortazavi; Lee Edsall; David McCleary; Samantha Kuan; Yin Shen; Feng Yue; Zhen Ye; Carrie A Davis; Chris Zaleski; Sonali Jha; Chenghai Xue; Alex Dobin; Wei Lin; Meagan Fastuca; Huaien Wang; Roderic Guigo; Sarah Djebali; Julien Lagarde; Tyrone Ryba; Takayo Sasaki; Venkat S Malladi; Melissa S Cline; Vanessa M Kirkup; Katrina Learned; Kate R Rosenbloom; W James Kent; Elise A Feingold; Peter J Good; Michael Pazin; Rebecca F Lowdon; Leslie B Adams
Journal:  Genome Biol       Date:  2012-08-13       Impact factor: 13.583

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  83 in total

1.  A Long Non-coding RNA, lncLGR, Regulates Hepatic Glucokinase Expression and Glycogen Storage during Fasting.

Authors:  Xiangbo Ruan; Ping Li; Andrew Cangelosi; Ling Yang; Haiming Cao
Journal:  Cell Rep       Date:  2016-02-18       Impact factor: 9.423

Review 2.  Long noncoding RNAs and the regulation of innate immunity and host-virus interactions.

Authors:  Megha Basavappa; Sara Cherry; Jorge Henao-Mejia
Journal:  J Leukoc Biol       Date:  2019-02-28       Impact factor: 4.962

3.  De novo RNA sequence assembly during in vivo inflammatory stress reveals hundreds of unannotated lincRNAs in human blood CD14+ monocytes and in adipose tissue.

Authors:  Chenyi Xue; Xuan Zhang; Hanrui Zhang; Jane F Ferguson; Ying Wang; Christine C Hinkle; Mingyao Li; Muredach P Reilly
Journal:  Physiol Genomics       Date:  2017-04-07       Impact factor: 3.107

Review 4.  Melanocortin neurons: Multiple routes to regulation of metabolism.

Authors:  Wen-Jie Shen; Ting Yao; Xingxing Kong; Kevin W Williams; Tiemin Liu
Journal:  Biochim Biophys Acta Mol Basis Dis       Date:  2017-05-09       Impact factor: 5.187

5.  Omics, big data and machine learning as tools to propel understanding of biological mechanisms and to discover novel diagnostics and therapeutics.

Authors:  Nikolaos Perakakis; Alireza Yazdani; George E Karniadakis; Christos Mantzoros
Journal:  Metabolism       Date:  2018-08-08       Impact factor: 8.694

6.  Genome-wide interrogation reveals hundreds of long intergenic noncoding RNAs that associate with cardiometabolic traits.

Authors:  Rachel L Ballantyne; Xuan Zhang; Sara Nuñez; Chenyi Xue; Wei Zhao; Eric Reed; Danish Salaheen; Andrea S Foulkes; Mingyao Li; Muredach P Reilly
Journal:  Hum Mol Genet       Date:  2016-06-10       Impact factor: 6.150

Review 7.  The development and controversy of competitive endogenous RNA hypothesis in non-coding genes.

Authors:  Weimin Lin; Hongcheng Liu; Yonghang Tang; Yuchen Wei; Wei Wei; Lifan Zhang; Jie Chen
Journal:  Mol Cell Biochem       Date:  2020-09-25       Impact factor: 3.396

Review 8.  Long Noncoding RNA and Cancer: A New Paradigm.

Authors:  Arunoday Bhan; Milad Soleimani; Subhrangsu S Mandal
Journal:  Cancer Res       Date:  2017-07-12       Impact factor: 12.701

9.  Therapeutic discovery for marrow failure with MDS predisposition using pluripotent stem cells.

Authors:  Melisa Ruiz-Gutierrez; Özge Vargel Bölükbaşı; Gabriela Alexe; Adriana G Kotini; Kaitlyn Ballotti; Cailin E Joyce; David W Russell; Kimberly Stegmaier; Kasiani Myers; Carl D Novina; Eirini P Papapetrou; Akiko Shimamura
Journal:  JCI Insight       Date:  2019-04-30

Review 10.  Development, activation, and therapeutic potential of thermogenic adipocytes.

Authors:  Margo P Emont; Dong-Il Kim; Jun Wu
Journal:  Biochim Biophys Acta Mol Cell Biol Lipids       Date:  2018-05-22       Impact factor: 4.698

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