Literature DB >> 23382218

Divergent transcription of long noncoding RNA/mRNA gene pairs in embryonic stem cells.

Alla A Sigova1, Alan C Mullen, Benoit Molinie, Sumeet Gupta, David A Orlando, Matthew G Guenther, Albert E Almada, Charles Lin, Phillip A Sharp, Cosmas C Giallourakis, Richard A Young.   

Abstract

Many long noncoding RNA (lncRNA) species have been identified in mammalian cells, but the genomic origin and regulation of these molecules in individual cell types is poorly understood. We have generated catalogs of lncRNA species expressed in human and murine embryonic stem cells and mapped their genomic origin. A surprisingly large fraction of these transcripts (>60%) originate from divergent transcription at promoters of active protein-coding genes. The divergently transcribed lncRNA/mRNA gene pairs exhibit coordinated changes in transcription when embryonic stem cells are differentiated into endoderm. Our results reveal that transcription of most lncRNA genes is coordinated with transcription of protein-coding genes.

Entities:  

Mesh：

Substances：

Year:  2013        PMID： 23382218      PMCID： PMC3581948          DOI： 10.1073/pnas.1221904110

Source DB:  PubMed          Journal:  Proc Natl Acad Sci U S A        ISSN： 0027-8424            Impact factor:   11.205


  49 in total

1.  Complete sequencing and characterization of 21,243 full-length human cDNAs.

Authors:  Toshio Ota; Yutaka Suzuki; Tetsuo Nishikawa; Tetsuji Otsuki; Tomoyasu Sugiyama; Ryotaro Irie; Ai Wakamatsu; Koji Hayashi; Hiroyuki Sato; Keiichi Nagai; Kouichi Kimura; Hiroshi Makita; Mitsuo Sekine; Masaya Obayashi; Tatsunari Nishi; Toshikazu Shibahara; Toshihiro Tanaka; Shizuko Ishii; Jun-ichi Yamamoto; Kaoru Saito; Yuri Kawai; Yuko Isono; Yoshitaka Nakamura; Kenji Nagahari; Katsuhiko Murakami; Tomohiro Yasuda; Takao Iwayanagi; Masako Wagatsuma; Akiko Shiratori; Hiroaki Sudo; Takehiko Hosoiri; Yoshiko Kaku; Hiroyo Kodaira; Hiroshi Kondo; Masanori Sugawara; Makiko Takahashi; Katsuhiro Kanda; Takahide Yokoi; Takako Furuya; Emiko Kikkawa; Yuhi Omura; Kumi Abe; Kumiko Kamihara; Naoko Katsuta; Kazuomi Sato; Machiko Tanikawa; Makoto Yamazaki; Ken Ninomiya; Tadashi Ishibashi; Hiromichi Yamashita; Katsuji Murakawa; Kiyoshi Fujimori; Hiroyuki Tanai; Manabu Kimata; Motoji Watanabe; Susumu Hiraoka; Yoshiyuki Chiba; Shinichi Ishida; Yukio Ono; Sumiyo Takiguchi; Susumu Watanabe; Makoto Yosida; Tomoko Hotuta; Junko Kusano; Keiichi Kanehori; Asako Takahashi-Fujii; Hiroto Hara; Tomo-o Tanase; Yoshiko Nomura; Sakae Togiya; Fukuyo Komai; Reiko Hara; Kazuha Takeuchi; Miho Arita; Nobuyuki Imose; Kaoru Musashino; Hisatsugu Yuuki; Atsushi Oshima; Naokazu Sasaki; Satoshi Aotsuka; Yoko Yoshikawa; Hiroshi Matsunawa; Tatsuo Ichihara; Namiko Shiohata; Sanae Sano; Shogo Moriya; Hiroko Momiyama; Noriko Satoh; Sachiko Takami; Yuko Terashima; Osamu Suzuki; Satoshi Nakagawa; Akihiro Senoh; Hiroshi Mizoguchi; Yoshihiro Goto; Fumio Shimizu; Hirokazu Wakebe; Haretsugu Hishigaki; Takeshi Watanabe; Akio Sugiyama; Makoto Takemoto; Bunsei Kawakami; Masaaki Yamazaki; Koji Watanabe; Ayako Kumagai; Shoko Itakura; Yasuhito Fukuzumi; Yoshifumi Fujimori; Megumi Komiyama; Hiroyuki Tashiro; Akira Tanigami; Tsutomu Fujiwara; Toshihide Ono; Katsue Yamada; Yuka Fujii; Kouichi Ozaki; Maasa Hirao; Yoshihiro Ohmori; Ayako Kawabata; Takeshi Hikiji; Naoko Kobatake; Hiromi Inagaki; Yasuko Ikema; Sachiko Okamoto; Rie Okitani; Takuma Kawakami; Saori Noguchi; Tomoko Itoh; Keiko Shigeta; Tadashi Senba; Kyoka Matsumura; Yoshie Nakajima; Takae Mizuno; Misato Morinaga; Masahide Sasaki; Takushi Togashi; Masaaki Oyama; Hiroko Hata; Manabu Watanabe; Takami Komatsu; Junko Mizushima-Sugano; Tadashi Satoh; Yuko Shirai; Yukiko Takahashi; Kiyomi Nakagawa; Koji Okumura; Takahiro Nagase; Nobuo Nomura; Hisashi Kikuchi; Yasuhiko Masuho; Riu Yamashita; Kenta Nakai; Tetsushi Yada; Yusuke Nakamura; Osamu Ohara; Takao Isogai; Sumio Sugano
Journal:  Nat Genet       Date:  2003-12-21       Impact factor: 38.330

2.  Core transcriptional regulatory circuitry in human embryonic stem cells.

Authors:  Laurie A Boyer; Tong Ihn Lee; Megan F Cole; Sarah E Johnstone; Stuart S Levine; Jacob P Zucker; Matthew G Guenther; Roshan M Kumar; Heather L Murray; Richard G Jenner; David K Gifford; Douglas A Melton; Rudolf Jaenisch; Richard A Young
Journal:  Cell       Date:  2005-09-23       Impact factor: 41.582

3.  The Evf-2 noncoding RNA is transcribed from the Dlx-5/6 ultraconserved region and functions as a Dlx-2 transcriptional coactivator.

Authors:  Jianchi Feng; Chunming Bi; Brian S Clark; Rina Mady; Palak Shah; Jhumku D Kohtz
Journal:  Genes Dev       Date:  2006-05-16       Impact factor: 11.361

4.  RNA maps reveal new RNA classes and a possible function for pervasive transcription.

Authors:  Philipp Kapranov; Jill Cheng; Sujit Dike; David A Nix; Radharani Duttagupta; Aarron T Willingham; Peter F Stadler; Jana Hertel; Jörg Hackermüller; Ivo L Hofacker; Ian Bell; Evelyn Cheung; Jorg Drenkow; Erica Dumais; Sandeep Patel; Gregg Helt; Madhavan Ganesh; Srinka Ghosh; Antonio Piccolboni; Victor Sementchenko; Hari Tammana; Thomas R Gingeras
Journal:  Science       Date:  2007-05-17       Impact factor: 47.728

5.  A chromatin landmark and transcription initiation at most promoters in human cells.

Authors:  Matthew G Guenther; Stuart S Levine; Laurie A Boyer; Rudolf Jaenisch; Richard A Young
Journal:  Cell       Date:  2007-07-13       Impact factor: 41.582

6.  The noncoding RNA taurine upregulated gene 1 is required for differentiation of the murine retina.

Authors:  T L Young; T Matsuda; C L Cepko
Journal:  Curr Biol       Date:  2005-03-29       Impact factor: 10.834

7.  Epigenetic silencing of tumour suppressor gene p15 by its antisense RNA.

Authors:  Wenqiang Yu; David Gius; Patrick Onyango; Kristi Muldoon-Jacobs; Judith Karp; Andrew P Feinberg; Hengmi Cui
Journal:  Nature       Date:  2008-01-10       Impact factor: 49.962

8.  The transcriptional landscape of the mammalian genome.

Authors:  P Carninci; T Kasukawa; S Katayama; J Gough; M C Frith; N Maeda; R Oyama; T Ravasi; B Lenhard; C Wells; R Kodzius; K Shimokawa; V B Bajic; S E Brenner; S Batalov; A R R Forrest; M Zavolan; M J Davis; L G Wilming; V Aidinis; J E Allen; A Ambesi-Impiombato; R Apweiler; R N Aturaliya; T L Bailey; M Bansal; L Baxter; K W Beisel; T Bersano; H Bono; A M Chalk; K P Chiu; V Choudhary; A Christoffels; D R Clutterbuck; M L Crowe; E Dalla; B P Dalrymple; B de Bono; G Della Gatta; D di Bernardo; T Down; P Engstrom; M Fagiolini; G Faulkner; C F Fletcher; T Fukushima; M Furuno; S Futaki; M Gariboldi; P Georgii-Hemming; T R Gingeras; T Gojobori; R E Green; S Gustincich; M Harbers; Y Hayashi; T K Hensch; N Hirokawa; D Hill; L Huminiecki; M Iacono; K Ikeo; A Iwama; T Ishikawa; M Jakt; A Kanapin; M Katoh; Y Kawasawa; J Kelso; H Kitamura; H Kitano; G Kollias; S P T Krishnan; A Kruger; S K Kummerfeld; I V Kurochkin; L F Lareau; D Lazarevic; L Lipovich; J Liu; S Liuni; S McWilliam; M Madan Babu; M Madera; L Marchionni; H Matsuda; S Matsuzawa; H Miki; F Mignone; S Miyake; K Morris; S Mottagui-Tabar; N Mulder; N Nakano; H Nakauchi; P Ng; R Nilsson; S Nishiguchi; S Nishikawa; F Nori; O Ohara; Y Okazaki; V Orlando; K C Pang; W J Pavan; G Pavesi; G Pesole; N Petrovsky; S Piazza; J Reed; J F Reid; B Z Ring; M Ringwald; B Rost; Y Ruan; S L Salzberg; A Sandelin; C Schneider; C Schönbach; K Sekiguchi; C A M Semple; S Seno; L Sessa; Y Sheng; Y Shibata; H Shimada; K Shimada; D Silva; B Sinclair; S Sperling; E Stupka; K Sugiura; R Sultana; Y Takenaka; K Taki; K Tammoja; S L Tan; S Tang; M S Taylor; J Tegner; S A Teichmann; H R Ueda; E van Nimwegen; R Verardo; C L Wei; K Yagi; H Yamanishi; E Zabarovsky; S Zhu; A Zimmer; W Hide; C Bult; S M Grimmond; R D Teasdale; E T Liu; V Brusic; J Quackenbush; C Wahlestedt; J S Mattick; D A Hume; C Kai; D Sasaki; Y Tomaru; S Fukuda; M Kanamori-Katayama; M Suzuki; J Aoki; T Arakawa; J Iida; K Imamura; M Itoh; T Kato; H Kawaji; N Kawagashira; T Kawashima; M Kojima; S Kondo; H Konno; K Nakano; N Ninomiya; T Nishio; M Okada; C Plessy; K Shibata; T Shiraki; S Suzuki; M Tagami; K Waki; A Watahiki; Y Okamura-Oho; H Suzuki; J Kawai; Y Hayashizaki
Journal:  Science       Date:  2005-09-02       Impact factor: 47.728

9.  Anatomic demarcation by positional variation in fibroblast gene expression programs.

Authors:  John L Rinn; Chanda Bondre; Hayes B Gladstone; Patrick O Brown; Howard Y Chang
Journal:  PLoS Genet       Date:  2006-07       Impact factor: 5.917

10.  CPC: assess the protein-coding potential of transcripts using sequence features and support vector machine.

Authors:  Lei Kong; Yong Zhang; Zhi-Qiang Ye; Xiao-Qiao Liu; Shu-Qi Zhao; Liping Wei; Ge Gao
Journal:  Nucleic Acids Res       Date:  2007-07       Impact factor: 16.971
View more
  230 in total

1.  Relationships between PROMPT and gene expression.

Authors:  Marta Lloret-Llinares; Christophe K Mapendano; Lasse H Martlev; Søren Lykke-Andersen; Torben Heick Jensen
Journal:  RNA Biol       Date:  2016       Impact factor: 4.652

Review 2.  Long non-coding RNAs in corticogenesis: deciphering the non-coding code of the brain.

Authors:  Julieta Aprea; Federico Calegari
Journal:  EMBO J       Date:  2015-10-29       Impact factor: 11.598

Review 3.  Unique features of long non-coding RNA biogenesis and function.

Authors:  Jeffrey J Quinn; Howard Y Chang
Journal:  Nat Rev Genet       Date:  2016-01       Impact factor: 53.242

4.  Using both strands: The fundamental nature of antisense transcription.

Authors:  Struan C Murray; Jane Mellor
Journal:  Bioarchitecture       Date:  2016

5.  RNA polymerase II promoter-proximal pausing in mammalian long non-coding genes.

Authors:  Heeyoun Bunch; Brian P Lawney; Adam Burkholder; Duanduan Ma; Xiaofeng Zheng; Shmulik Motola; David C Fargo; Stuart S Levine; Yaoyu E Wang; Guang Hu
Journal:  Genomics       Date:  2016-07-16       Impact factor: 5.736

6.  The long noncoding RNA Wisper controls cardiac fibrosis and remodeling.

Authors:  Rudi Micheletti; Isabelle Plaisance; Brian J Abraham; Alexandre Sarre; Ching-Chia Ting; Michael Alexanian; Daniel Maric; Damien Maison; Mohamed Nemir; Richard A Young; Blanche Schroen; Arantxa González; Samir Ounzain; Thierry Pedrazzini
Journal:  Sci Transl Med       Date:  2017-06-21       Impact factor: 17.956

Review 7.  MYC and transcription elongation.

Authors:  Peter B Rahl; Richard A Young
Journal:  Cold Spring Harb Perspect Med       Date:  2014-01-01       Impact factor: 6.915

Review 8.  RNA polymerase II transcription elongation control.

Authors:  Jiannan Guo; David H Price
Journal:  Chem Rev       Date:  2013-08-06       Impact factor: 60.622

9.  Deep transcriptome profiling of mammalian stem cells supports a regulatory role for retrotransposons in pluripotency maintenance.

Authors:  Alexandre Fort; Kosuke Hashimoto; Daisuke Yamada; Md Salimullah; Chaman A Keya; Alka Saxena; Alessandro Bonetti; Irina Voineagu; Nicolas Bertin; Anton Kratz; Yukihiko Noro; Chee-Hong Wong; Michiel de Hoon; Robin Andersson; Albin Sandelin; Harukazu Suzuki; Chia-Lin Wei; Haruhiko Koseki; Yuki Hasegawa; Alistair R R Forrest; Piero Carninci
Journal:  Nat Genet       Date:  2014-04-28       Impact factor: 38.330

Review 10.  Long noncoding RNAs in innate and adaptive immunity.

Authors:  Katherine A Fitzgerald; Daniel R Caffrey
Journal:  Curr Opin Immunol       Date:  2013-12-22       Impact factor: 7.486
View more

北京卡尤迪生物科技股份有限公司 © 2022-2023.