Literature DB >> 26167905

Coexpression networks identify brain region-specific enhancer RNAs in the human brain.

Pu Yao1, Peijie Lin1, Akira Gokoolparsadh1, Amelia Assareh1, Mike W C Thang2, Irina Voineagu1.   

Abstract

Despite major progress in identifying enhancer regions on a genome-wide scale, the majority of available data are limited to model organisms and human transformed cell lines. We have identified a robust set of enhancer RNAs (eRNAs) expressed in the human brain and constructed networks assessing eRNA-gene coexpression interactions across human fetal brain and multiple adult brain regions. Our data identify brain region-specific eRNAs and show that enhancer regions expressing eRNAs are enriched for genetic variants associated with autism spectrum disorders.

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Year:  2015        PMID： 26167905     DOI： 10.1038/nn.4063

Source DB:  PubMed          Journal:  Nat Neurosci        ISSN： 1097-6256            Impact factor:   24.884


  58 in total

Review 1.  Characterization of enhancer function from genome-wide analyses.

Authors:  Glenn A Maston; Stephen G Landt; Michael Snyder; Michael R Green
Journal:  Annu Rev Genomics Hum Genet       Date:  2012-06-11       Impact factor: 8.929

2.  Neurodevelopmental and neuropsychiatric disorders represent an interconnected molecular system.

Authors:  A S Cristino; S M Williams; Z Hawi; J-Y An; M A Bellgrove; C E Schwartz; L da F Costa; C Claudianos
Journal:  Mol Psychiatry       Date:  2013-02-26       Impact factor: 15.992

3.  Large-scale identification of coregulated enhancer networks in the adult human brain.

Authors:  Marit W Vermunt; Peter Reinink; Jeroen Korving; Ewart de Bruijn; Paul M Creyghton; Onur Basak; Geert Geeven; Pim W Toonen; Nico Lansu; Charles Meunier; Sebastiaan van Heesch; Hans Clevers; Wouter de Laat; Edwin Cuppen; Menno P Creyghton
Journal:  Cell Rep       Date:  2014-10-16       Impact factor: 9.423

4.  SoxC transcription factors are required for neuronal differentiation in adult hippocampal neurogenesis.

Authors:  Lifang Mu; Lucia Berti; Giacomo Masserdotti; Marcela Covic; Theologos M Michaelidis; Kathrin Doberauer; Katharina Merz; Frederick Rehfeld; Anja Haslinger; Michael Wegner; Elisabeth Sock; Veronique Lefebvre; Sebastien Couillard-Despres; Ludwig Aigner; Benedikt Berninger; D Chichung Lie
Journal:  J Neurosci       Date:  2012-02-29       Impact factor: 6.167

5.  Analysis of nascent RNA identifies a unified architecture of initiation regions at mammalian promoters and enhancers.

Authors:  Leighton J Core; André L Martins; Charles G Danko; Colin T Waters; Adam Siepel; John T Lis
Journal:  Nat Genet       Date:  2014-11-10       Impact factor: 38.330

6.  A promoter-level mammalian expression atlas.

Authors:  Alistair R R Forrest; Hideya Kawaji; Michael Rehli; J Kenneth Baillie; Michiel J L de Hoon; Vanja Haberle; Timo Lassmann; Ivan V Kulakovskiy; Marina Lizio; Masayoshi Itoh; Robin Andersson; Christopher J Mungall; Terrence F Meehan; Sebastian Schmeier; Nicolas Bertin; Mette Jørgensen; Emmanuel Dimont; Erik Arner; Christian Schmidl; Ulf Schaefer; Yulia A Medvedeva; Charles Plessy; Morana Vitezic; Jessica Severin; Colin A Semple; Yuri Ishizu; Robert S Young; Margherita Francescatto; Intikhab Alam; Davide Albanese; Gabriel M Altschuler; Takahiro Arakawa; John A C Archer; Peter Arner; Magda Babina; Sarah Rennie; Piotr J Balwierz; Anthony G Beckhouse; Swati Pradhan-Bhatt; Judith A Blake; Antje Blumenthal; Beatrice Bodega; Alessandro Bonetti; James Briggs; Frank Brombacher; A Maxwell Burroughs; Andrea Califano; Carlo V Cannistraci; Daniel Carbajo; Yun Chen; Marco Chierici; Yari Ciani; Hans C Clevers; Emiliano Dalla; Carrie A Davis; Michael Detmar; Alexander D Diehl; Taeko Dohi; Finn Drabløs; Albert S B Edge; Matthias Edinger; Karl Ekwall; Mitsuhiro Endoh; Hideki Enomoto; Michela Fagiolini; Lynsey Fairbairn; Hai Fang; Mary C Farach-Carson; Geoffrey J Faulkner; Alexander V Favorov; Malcolm E Fisher; Martin C Frith; Rie Fujita; Shiro Fukuda; Cesare Furlanello; Masaaki Furino; Jun-ichi Furusawa; Teunis B Geijtenbeek; Andrew P Gibson; Thomas Gingeras; Daniel Goldowitz; Julian Gough; Sven Guhl; Reto Guler; Stefano Gustincich; Thomas J Ha; Masahide Hamaguchi; Mitsuko Hara; Matthias Harbers; Jayson Harshbarger; Akira Hasegawa; Yuki Hasegawa; Takehiro Hashimoto; Meenhard Herlyn; Kelly J Hitchens; Shannan J Ho Sui; Oliver M Hofmann; Ilka Hoof; Furni Hori; Lukasz Huminiecki; Kei Iida; Tomokatsu Ikawa; Boris R Jankovic; Hui Jia; Anagha Joshi; Giuseppe Jurman; Bogumil Kaczkowski; Chieko Kai; Kaoru Kaida; Ai Kaiho; Kazuhiro Kajiyama; Mutsumi Kanamori-Katayama; Artem S Kasianov; Takeya Kasukawa; Shintaro Katayama; Sachi Kato; Shuji Kawaguchi; Hiroshi Kawamoto; Yuki I Kawamura; Tsugumi Kawashima; Judith S Kempfle; Tony J Kenna; Juha Kere; Levon M Khachigian; Toshio Kitamura; S Peter Klinken; Alan J Knox; Miki Kojima; Soichi Kojima; Naoto Kondo; Haruhiko Koseki; Shigeo Koyasu; Sarah Krampitz; Atsutaka Kubosaki; Andrew T Kwon; Jeroen F J Laros; Weonju Lee; Andreas Lennartsson; Kang Li; Berit Lilje; Leonard Lipovich; Alan Mackay-Sim; Ri-ichiroh Manabe; Jessica C Mar; Benoit Marchand; Anthony Mathelier; Niklas Mejhert; Alison Meynert; Yosuke Mizuno; David A de Lima Morais; Hiromasa Morikawa; Mitsuru Morimoto; Kazuyo Moro; Efthymios Motakis; Hozumi Motohashi; Christine L Mummery; Mitsuyoshi Murata; Sayaka Nagao-Sato; Yutaka Nakachi; Fumio Nakahara; Toshiyuki Nakamura; Yukio Nakamura; Kenichi Nakazato; Erik van Nimwegen; Noriko Ninomiya; Hiromi Nishiyori; Shohei Noma; Shohei Noma; Tadasuke Noazaki; Soichi Ogishima; Naganari Ohkura; Hiroko Ohimiya; Hiroshi Ohno; Mitsuhiro Ohshima; Mariko Okada-Hatakeyama; Yasushi Okazaki; Valerio Orlando; Dmitry A Ovchinnikov; Arnab Pain; Robert Passier; Margaret Patrikakis; Helena Persson; Silvano Piazza; James G D Prendergast; Owen J L Rackham; Jordan A Ramilowski; Mamoon Rashid; Timothy Ravasi; Patrizia Rizzu; Marco Roncador; Sugata Roy; Morten B Rye; Eri Saijyo; Antti Sajantila; Akiko Saka; Shimon Sakaguchi; Mizuho Sakai; Hiroki Sato; Suzana Savvi; Alka Saxena; Claudio Schneider; Erik A Schultes; Gundula G Schulze-Tanzil; Anita Schwegmann; Thierry Sengstag; Guojun Sheng; Hisashi Shimoji; Yishai Shimoni; Jay W Shin; Christophe Simon; Daisuke Sugiyama; Takaai Sugiyama; Masanori Suzuki; Naoko Suzuki; Rolf K Swoboda; Peter A C 't Hoen; Michihira Tagami; Naoko Takahashi; Jun Takai; Hiroshi Tanaka; Hideki Tatsukawa; Zuotian Tatum; Mark Thompson; Hiroo Toyodo; Tetsuro Toyoda; Elvind Valen; Marc van de Wetering; Linda M van den Berg; Roberto Verado; Dipti Vijayan; Ilya E Vorontsov; Wyeth W Wasserman; Shoko Watanabe; Christine A Wells; Louise N Winteringham; Ernst Wolvetang; Emily J Wood; Yoko Yamaguchi; Masayuki Yamamoto; Misako Yoneda; Yohei Yonekura; Shigehiro Yoshida; Susan E Zabierowski; Peter G Zhang; Xiaobei Zhao; Silvia Zucchelli; Kim M Summers; Harukazu Suzuki; Carsten O Daub; Jun Kawai; Peter Heutink; Winston Hide; Tom C Freeman; Boris Lenhard; Vladimir B Bajic; Martin S Taylor; Vsevolod J Makeev; Albin Sandelin; David A Hume; Piero Carninci; Yoshihide Hayashizaki
Journal:  Nature       Date:  2014-03-27       Impact factor: 49.962

7.  Spatio-temporal transcriptome of the human brain.

Authors:  Hyo Jung Kang; Yuka Imamura Kawasawa; Feng Cheng; Ying Zhu; Xuming Xu; Mingfeng Li; André M M Sousa; Mihovil Pletikos; Kyle A Meyer; Goran Sedmak; Tobias Guennel; Yurae Shin; Matthew B Johnson; Zeljka Krsnik; Simone Mayer; Sofia Fertuzinhos; Sheila Umlauf; Steven N Lisgo; Alexander Vortmeyer; Daniel R Weinberger; Shrikant Mane; Thomas M Hyde; Anita Huttner; Mark Reimers; Joel E Kleinman; Nenad Sestan
Journal:  Nature       Date:  2011-10-26       Impact factor: 49.962

8.  Tissue-specific RNA expression marks distant-acting developmental enhancers.

Authors:  Han Wu; Alex S Nord; Jennifer A Akiyama; Malak Shoukry; Veena Afzal; Edward M Rubin; Len A Pennacchio; Axel Visel
Journal:  PLoS Genet       Date:  2014-09-04       Impact factor: 5.917

9.  Exome sequencing in sporadic autism spectrum disorders identifies severe de novo mutations.

Authors:  Brian J O'Roak; Pelagia Deriziotis; Choli Lee; Laura Vives; Jerrod J Schwartz; Santhosh Girirajan; Emre Karakoc; Alexandra P Mackenzie; Sarah B Ng; Carl Baker; Mark J Rieder; Deborah A Nickerson; Raphael Bernier; Simon E Fisher; Jay Shendure; Evan E Eichler
Journal:  Nat Genet       Date:  2011-05-15       Impact factor: 38.330

10.  Integrative analysis of 111 reference human epigenomes.

Authors:  Anshul Kundaje; Wouter Meuleman; Jason Ernst; Misha Bilenky; Angela Yen; Alireza Heravi-Moussavi; Pouya Kheradpour; Zhizhuo Zhang; Jianrong Wang; Michael J Ziller; Viren Amin; John W Whitaker; Matthew D Schultz; Lucas D Ward; Abhishek Sarkar; Gerald Quon; Richard S Sandstrom; Matthew L Eaton; Yi-Chieh Wu; Andreas R Pfenning; Xinchen Wang; Melina Claussnitzer; Yaping Liu; Cristian Coarfa; R Alan Harris; Noam Shoresh; Charles B Epstein; Elizabeta Gjoneska; Danny Leung; Wei Xie; R David Hawkins; Ryan Lister; Chibo Hong; Philippe Gascard; Andrew J Mungall; Richard Moore; Eric Chuah; Angela Tam; Theresa K Canfield; R Scott Hansen; Rajinder Kaul; Peter J Sabo; Mukul S Bansal; Annaick Carles; Jesse R Dixon; Kai-How Farh; Soheil Feizi; Rosa Karlic; Ah-Ram Kim; Ashwinikumar Kulkarni; Daofeng Li; Rebecca Lowdon; GiNell Elliott; Tim R Mercer; Shane J Neph; Vitor Onuchic; Paz Polak; Nisha Rajagopal; Pradipta Ray; Richard C Sallari; Kyle T Siebenthall; Nicholas A Sinnott-Armstrong; Michael Stevens; Robert E Thurman; Jie Wu; Bo Zhang; Xin Zhou; Arthur E Beaudet; Laurie A Boyer; Philip L De Jager; Peggy J Farnham; Susan J Fisher; David Haussler; Steven J M Jones; Wei Li; Marco A Marra; Michael T McManus; Shamil Sunyaev; James A Thomson; Thea D Tlsty; Li-Huei Tsai; Wei Wang; Robert A Waterland; Michael Q Zhang; Lisa H Chadwick; Bradley E Bernstein; Joseph F Costello; Joseph R Ecker; Martin Hirst; Alexander Meissner; Aleksandar Milosavljevic; Bing Ren; John A Stamatoyannopoulos; Ting Wang; Manolis Kellis
Journal:  Nature       Date:  2015-02-19       Impact factor: 69.504
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  39 in total

Review 1.  Searching for convergent pathways in autism spectrum disorders: insights from human brain transcriptome studies.

Authors:  Akira Gokoolparsadh; Gavin J Sutton; Alexiy Charamko; Nicole F Oldham Green; Christopher J Pardy; Irina Voineagu
Journal:  Cell Mol Life Sci       Date:  2016-07-12       Impact factor: 9.261

Review 2.  Enhancers as non-coding RNA transcription units: recent insights and future perspectives.

Authors:  Wenbo Li; Dimple Notani; Michael G Rosenfeld
Journal:  Nat Rev Genet       Date:  2016-03-07       Impact factor: 53.242

3.  Shared molecular neuropathology across major psychiatric disorders parallels polygenic overlap.

Authors:  Michael J Gandal; Jillian R Haney; Neelroop N Parikshak; Virpi Leppa; Gokul Ramaswami; Chris Hartl; Andrew J Schork; Vivek Appadurai; Alfonso Buil; Thomas M Werge; Chunyu Liu; Kevin P White; Steve Horvath; Daniel H Geschwind
Journal:  Science       Date:  2018-02-09       Impact factor: 47.728

Review 4.  Spatial genome organization and cognition.

Authors:  Prashanth Rajarajan; Sergio Espeso Gil; Kristen J Brennand; Schahram Akbarian
Journal:  Nat Rev Neurosci       Date:  2016-10-06       Impact factor: 34.870

5.  Aging Shapes the Population-Mean and -Dispersion of Gene Expression in Human Brains.

Authors:  Candice L Brinkmeyer-Langford; Jinting Guan; Guoli Ji; James J Cai
Journal:  Front Aging Neurosci       Date:  2016-08-03       Impact factor: 5.750

Review 6.  Exploring the secrets of brain transcriptional regulation: developing methodologies, recent significant findings, and perspectives.

Authors:  Zhe Ding; Luyun Sun; Cen Yang; Aihua Liu; Fukai Bao
Journal:  Brain Struct Funct       Date:  2021-02-05       Impact factor: 3.270

7.  Adolescent Alcohol Exposure Epigenetically Suppresses Amygdala Arc Enhancer RNA Expression to Confer Adult Anxiety Susceptibility.

Authors:  Evan J Kyzar; Huaibo Zhang; Subhash C Pandey
Journal:  Biol Psychiatry       Date:  2019-01-14       Impact factor: 13.382

8.  Chromosome conformation elucidates regulatory relationships in developing human brain.

Authors:  Hyejung Won; Luis de la Torre-Ubieta; Jason L Stein; Neelroop N Parikshak; Jerry Huang; Carli K Opland; Michael J Gandal; Gavin J Sutton; Farhad Hormozdiari; Daning Lu; Changhoon Lee; Eleazar Eskin; Irina Voineagu; Jason Ernst; Daniel H Geschwind
Journal:  Nature       Date:  2016-10-19       Impact factor: 49.962

9.  Modulation of Brain Pathology by Enhancer RNAs in Cerebral Ischemia.

Authors:  Sunil Bhattarai; Aparna Akella; Atish Gandhi; Ashutosh Dharap
Journal:  Mol Neurobiol       Date:  2020-11-17       Impact factor: 5.590

10.  Sex-based eRNA expression and function in ischemic stroke.

Authors:  Diandra Ruiz; Sunil Bhattarai; Ashutosh Dharap
Journal:  Neurochem Int       Date:  2021-08-03       Impact factor: 3.921
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