Literature DB >> 25349914

Analytical tools and current challenges in the modern era of neuroepigenomics.

Ian Maze1, Li Shen2, Bin Zhang3, Benjamin A Garcia4, Ningyi Shao2, Amanda Mitchell5, HaoSheng Sun2, Schahram Akbarian5, C David Allis6, Eric J Nestler2.   

Abstract

Over the past decade, rapid advances in epigenomics research have extensively characterized critical roles for chromatin regulatory events during normal periods of eukaryotic cell development and plasticity, as well as part of aberrant processes implicated in human disease. Application of such approaches to studies of the CNS, however, is more recent. Here we provide a comprehensive overview of available tools for analyzing neuroepigenomics data, as well as a discussion of pending challenges specific to the field of neuroscience. Integration of numerous unbiased genome-wide and proteomic approaches will be necessary to fully understand the neuroepigenome and the extraordinarily complex nature of the human brain. This will be critical to the development of future diagnostic and therapeutic strategies aimed at alleviating the vast array of heterogeneous and genetically distinct disorders of the CNS.

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Year:  2014        PMID: 25349914      PMCID: PMC4262187          DOI: 10.1038/nn.3816

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


  141 in total

1.  Open mass spectrometry search algorithm.

Authors:  Lewis Y Geer; Sanford P Markey; Jeffrey A Kowalak; Lukas Wagner; Ming Xu; Dawn M Maynard; Xiaoyu Yang; Wenyao Shi; Stephen H Bryant
Journal:  J Proteome Res       Date:  2004 Sep-Oct       Impact factor: 4.466

2.  An integrative genomics approach to infer causal associations between gene expression and disease.

Authors:  Eric E Schadt; John Lamb; Xia Yang; Jun Zhu; Steve Edwards; Debraj Guhathakurta; Solveig K Sieberts; Stephanie Monks; Marc Reitman; Chunsheng Zhang; Pek Yee Lum; Amy Leonardson; Rolf Thieringer; Joseph M Metzger; Liming Yang; John Castle; Haoyuan Zhu; Shera F Kash; Thomas A Drake; Alan Sachs; Aldons J Lusis
Journal:  Nat Genet       Date:  2005-06-19       Impact factor: 38.330

3.  Alzheimer's disease: From big data to mechanism.

Authors:  Vivek Swarup; Daniel H Geschwind
Journal:  Nature       Date:  2013-07-24       Impact factor: 49.962

4.  Identification of 67 histone marks and histone lysine crotonylation as a new type of histone modification.

Authors:  Minjia Tan; Hao Luo; Sangkyu Lee; Fulai Jin; Jeong Soo Yang; Emilie Montellier; Thierry Buchou; Zhongyi Cheng; Sophie Rousseaux; Nisha Rajagopal; Zhike Lu; Zhen Ye; Qin Zhu; Joanna Wysocka; Yang Ye; Saadi Khochbin; Bing Ren; Yingming Zhao
Journal:  Cell       Date:  2011-09-16       Impact factor: 41.582

5.  Substance-specific and shared transcription and epigenetic changes in the human hippocampus chronically exposed to cocaine and alcohol.

Authors:  Zhifeng Zhou; Qiaoping Yuan; Deborah C Mash; David Goldman
Journal:  Proc Natl Acad Sci U S A       Date:  2011-04-04       Impact factor: 11.205

6.  Purification of proteins associated with specific genomic Loci.

Authors:  Jérôme Déjardin; Robert E Kingston
Journal:  Cell       Date:  2009-01-09       Impact factor: 41.582

7.  Proteomic and genomic characterization of chromatin complexes at a boundary.

Authors:  Alan J Tackett; David J Dilworth; Megan J Davey; Michael O'Donnell; John D Aitchison; Michael P Rout; Brian T Chait
Journal:  J Cell Biol       Date:  2005-04-11       Impact factor: 10.539

Review 8.  Identification and interrogation of combinatorial histone modifications.

Authors:  Kelly R Karch; Jamie E Denizio; Ben E Black; Benjamin A Garcia
Journal:  Front Genet       Date:  2013-12-20       Impact factor: 4.599

9.  Genome-wide association analysis identifies 13 new risk loci for schizophrenia.

Authors:  Stephan Ripke; Colm O'Dushlaine; Kimberly Chambert; Jennifer L Moran; Anna K Kähler; Susanne Akterin; Sarah E Bergen; Ann L Collins; James J Crowley; Menachem Fromer; Yunjung Kim; Sang Hong Lee; Patrik K E Magnusson; Nick Sanchez; Eli A Stahl; Stephanie Williams; Naomi R Wray; Kai Xia; Francesco Bettella; Anders D Borglum; Brendan K Bulik-Sullivan; Paul Cormican; Nick Craddock; Christiaan de Leeuw; Naser Durmishi; Michael Gill; Vera Golimbet; Marian L Hamshere; Peter Holmans; David M Hougaard; Kenneth S Kendler; Kuang Lin; Derek W Morris; Ole Mors; Preben B Mortensen; Benjamin M Neale; Francis A O'Neill; Michael J Owen; Milica Pejovic Milovancevic; Danielle Posthuma; John Powell; Alexander L Richards; Brien P Riley; Douglas Ruderfer; Dan Rujescu; Engilbert Sigurdsson; Teimuraz Silagadze; August B Smit; Hreinn Stefansson; Stacy Steinberg; Jaana Suvisaari; Sarah Tosato; Matthijs Verhage; James T Walters; Douglas F Levinson; Pablo V Gejman; Kenneth S Kendler; Claudine Laurent; Bryan J Mowry; Michael C O'Donovan; Michael J Owen; Ann E Pulver; Brien P Riley; Sibylle G Schwab; Dieter B Wildenauer; Frank Dudbridge; Peter Holmans; Jianxin Shi; Margot Albus; Madeline Alexander; Dominique Campion; David Cohen; Dimitris Dikeos; Jubao Duan; Peter Eichhammer; Stephanie Godard; Mark Hansen; F Bernard Lerer; Kung-Yee Liang; Wolfgang Maier; Jacques Mallet; Deborah A Nertney; Gerald Nestadt; Nadine Norton; Francis A O'Neill; George N Papadimitriou; Robert Ribble; Alan R Sanders; Jeremy M Silverman; Dermot Walsh; Nigel M Williams; Brandon Wormley; Maria J Arranz; Steven Bakker; Stephan Bender; Elvira Bramon; David Collier; Benedicto Crespo-Facorro; Jeremy Hall; Conrad Iyegbe; Assen Jablensky; Rene S Kahn; Luba Kalaydjieva; Stephen Lawrie; Cathryn M Lewis; Kuang Lin; Don H Linszen; Ignacio Mata; Andrew McIntosh; Robin M Murray; Roel A Ophoff; John Powell; Dan Rujescu; Jim Van Os; Muriel Walshe; Matthias Weisbrod; Durk Wiersma; Peter Donnelly; Ines Barroso; Jenefer M Blackwell; Elvira Bramon; Matthew A Brown; Juan P Casas; Aiden P Corvin; Panos Deloukas; Audrey Duncanson; Janusz Jankowski; Hugh S Markus; Christopher G Mathew; Colin N A Palmer; Robert Plomin; Anna Rautanen; Stephen J Sawcer; Richard C Trembath; Ananth C Viswanathan; Nicholas W Wood; Chris C A Spencer; Gavin Band; Céline Bellenguez; Colin Freeman; Garrett Hellenthal; Eleni Giannoulatou; Matti Pirinen; Richard D Pearson; Amy Strange; Zhan Su; Damjan Vukcevic; Peter Donnelly; Cordelia Langford; Sarah E Hunt; Sarah Edkins; Rhian Gwilliam; Hannah Blackburn; Suzannah J Bumpstead; Serge Dronov; Matthew Gillman; Emma Gray; Naomi Hammond; Alagurevathi Jayakumar; Owen T McCann; Jennifer Liddle; Simon C Potter; Radhi Ravindrarajah; Michelle Ricketts; Avazeh Tashakkori-Ghanbaria; Matthew J Waller; Paul Weston; Sara Widaa; Pamela Whittaker; Ines Barroso; Panos Deloukas; Christopher G Mathew; Jenefer M Blackwell; Matthew A Brown; Aiden P Corvin; Mark I McCarthy; Chris C A Spencer; Elvira Bramon; Aiden P Corvin; Michael C O'Donovan; Kari Stefansson; Edward Scolnick; Shaun Purcell; Steven A McCarroll; Pamela Sklar; Christina M Hultman; Patrick F Sullivan
Journal:  Nat Genet       Date:  2013-08-25       Impact factor: 38.330

10.  Comparison of software packages for detecting differential expression in RNA-seq studies.

Authors:  Fatemeh Seyednasrollah; Asta Laiho; Laura L Elo
Journal:  Brief Bioinform       Date:  2013-12-02       Impact factor: 11.622

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  42 in total

Review 1.  The Molecular Basis of Drug Addiction: Linking Epigenetic to Synaptic and Circuit Mechanisms.

Authors:  Eric J Nestler; Christian Lüscher
Journal:  Neuron       Date:  2019-04-03       Impact factor: 17.173

Review 2.  Role of the Brain's Reward Circuitry in Depression: Transcriptional Mechanisms.

Authors:  Eric J Nestler
Journal:  Int Rev Neurobiol       Date:  2015-08-21       Impact factor: 3.230

Review 3.  An epigenetic view of developmental diseases: new targets, new therapies.

Authors:  Pei Xie; Li-Qun Zang; Xue-Kun Li; Qiang Shu
Journal:  World J Pediatr       Date:  2016-06-29       Impact factor: 2.764

4.  Differential peak calling of ChIP-seq signals with replicates with THOR.

Authors:  Manuel Allhoff; Kristin Seré; Juliana F Pires; Martin Zenke; Ivan G Costa
Journal:  Nucleic Acids Res       Date:  2016-08-02       Impact factor: 16.971

Review 5.  Decoding neural transcriptomes and epigenomes via high-throughput sequencing.

Authors:  Jaehoon Shin; Guo-li Ming; Hongjun Song
Journal:  Nat Neurosci       Date:  2014-10-28       Impact factor: 24.884

Review 6.  Neuroepigenetic Editing.

Authors:  Peter J Hamilton; Carissa J Lim; Eric J Nestler; Elizabeth A Heller
Journal:  Methods Mol Biol       Date:  2018

Review 7.  Epigenetic Etiology of Intellectual Disability.

Authors:  Shigeki Iwase; Nathalie G Bérubé; Zhaolan Zhou; Nael Nadif Kasri; Elena Battaglioli; Marilyn Scandaglia; Angel Barco
Journal:  J Neurosci       Date:  2017-11-08       Impact factor: 6.167

Review 8.  Peripheral biomarkers of major depression and antidepressant treatment response: Current knowledge and future outlooks.

Authors:  Bharathi S Gadad; Manish K Jha; Andrew Czysz; Jennifer L Furman; Taryn L Mayes; Michael P Emslie; Madhukar H Trivedi
Journal:  J Affect Disord       Date:  2017-07-05       Impact factor: 4.839

Review 9.  Epigenetic mechanisms underlying nervous system diseases.

Authors:  Irfan A Qureshi; Mark F Mehler
Journal:  Handb Clin Neurol       Date:  2018

Review 10.  RDoC and translational perspectives on the genetics of trauma-related psychiatric disorders.

Authors:  Janitza L Montalvo-Ortiz; Joel Gelernter; James Hudziak; Joan Kaufman
Journal:  Am J Med Genet B Neuropsychiatr Genet       Date:  2015-11-22       Impact factor: 3.568

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