Literature DB >> 25765321

RNA-binding proteins in neurodegeneration: Seq and you shall receive.

Julia K Nussbacher1, Ranjan Batra1, Clotilde Lagier-Tourenne2, Gene W Yeo3.   

Abstract

As critical players in gene regulation, RNA binding proteins (RBPs) are taking center stage in our understanding of cellular function and disease. In our era of bench-top sequencers and unprecedented computational power, biological questions can be addressed in a systematic, genome-wide manner. Development of high-throughput sequencing (Seq) methodologies provides unparalleled potential to discover new mechanisms of disease-associated perturbations of RNA homeostasis. Complementary to candidate single-gene studies, these innovative technologies may elicit the discovery of unexpected mechanisms, and enable us to determine the widespread influence of the multifunctional RBPs on their targets. Given that the disruption of RNA processing is increasingly implicated in neurological diseases, these approaches will continue to provide insights into the roles of RBPs in disease pathogenesis.
Copyright © 2015 Elsevier Ltd. All rights reserved.

Entities:  

Keywords:  RNA binding protein; high-throughput sequencing; neurodegeneration; polyadenylation; splicing

Mesh:

Substances:

Year:  2015        PMID: 25765321      PMCID: PMC4403644          DOI: 10.1016/j.tins.2015.02.003

Source DB:  PubMed          Journal:  Trends Neurosci        ISSN: 0166-2236            Impact factor:   13.837


  123 in total

1.  An mRNA surveillance mechanism that eliminates transcripts lacking termination codons.

Authors:  Pamela A Frischmeyer; Ambro van Hoof; Kathryn O'Donnell; Anthony L Guerrerio; Roy Parker; Harry C Dietz
Journal:  Science       Date:  2002-03-22       Impact factor: 47.728

2.  Physical isolation of nascent RNA chains transcribed by RNA polymerase II: evidence for cotranscriptional splicing.

Authors:  J Wuarin; U Schibler
Journal:  Mol Cell Biol       Date:  1994-11       Impact factor: 4.272

3.  Increased RNA editing in EAAT2 pre-mRNA from amyotrophic lateral sclerosis patients: involvement of a cryptic polyadenylation site.

Authors:  Rachel Flomen; Andrew Makoff
Journal:  Neurosci Lett       Date:  2011-05-05       Impact factor: 3.046

4.  RNA targets of TDP-43 identified by UV-CLIP are deregulated in ALS.

Authors:  Shangxi Xiao; Teresa Sanelli; Samar Dib; David Sheps; Joseph Findlater; Juan Bilbao; Julia Keith; Lorne Zinman; Ekaterina Rogaeva; Janice Robertson
Journal:  Mol Cell Neurosci       Date:  2011-03-21       Impact factor: 4.314

5.  Transcriptome-wide regulation of pre-mRNA splicing and mRNA localization by muscleblind proteins.

Authors:  Eric T Wang; Neal A L Cody; Sonali Jog; Michela Biancolella; Thomas T Wang; Daniel J Treacy; Shujun Luo; Gary P Schroth; David E Housman; Sita Reddy; Eric Lécuyer; Christopher B Burge
Journal:  Cell       Date:  2012-08-17       Impact factor: 41.582

6.  Splicing factor SFRS1 recognizes a functionally diverse landscape of RNA transcripts.

Authors:  Jeremy R Sanford; Xin Wang; Matthew Mort; Natalia Vanduyn; David N Cooper; Sean D Mooney; Howard J Edenberg; Yunlong Liu
Journal:  Genome Res       Date:  2008-12-30       Impact factor: 9.043

7.  LIN28 binds messenger RNAs at GGAGA motifs and regulates splicing factor abundance.

Authors:  Melissa L Wilbert; Stephanie C Huelga; Katannya Kapeli; Thomas J Stark; Tiffany Y Liang; Stella X Chen; Bernice Y Yan; Jason L Nathanson; Kasey R Hutt; Michael T Lovci; Hilal Kazan; Anthony Q Vu; Katlin B Massirer; Quaid Morris; Shawn Hoon; Gene W Yeo
Journal:  Mol Cell       Date:  2012-09-06       Impact factor: 17.970

8.  Genome-wide analysis in vivo of translation with nucleotide resolution using ribosome profiling.

Authors:  Nicholas T Ingolia; Sina Ghaemmaghami; John R S Newman; Jonathan S Weissman
Journal:  Science       Date:  2009-02-12       Impact factor: 47.728

Review 9.  Repeat-associated non-ATG (RAN) translation in neurological disease.

Authors:  John D Cleary; Laura P W Ranum
Journal:  Hum Mol Genet       Date:  2013-08-04       Impact factor: 6.150

10.  Topology of the human and mouse m6A RNA methylomes revealed by m6A-seq.

Authors:  Dan Dominissini; Sharon Moshitch-Moshkovitz; Schraga Schwartz; Mali Salmon-Divon; Lior Ungar; Sivan Osenberg; Karen Cesarkas; Jasmine Jacob-Hirsch; Ninette Amariglio; Martin Kupiec; Rotem Sorek; Gideon Rechavi
Journal:  Nature       Date:  2012-04-29       Impact factor: 49.962

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  48 in total

Review 1.  Phenotypic Suppression of ALS/FTD-Associated Neurodegeneration Highlights Mechanisms of Dysfunction.

Authors:  Mathieu Bartoletti; Daryl A Bosco; Sandrine Da Cruz; Clotilde Lagier-Tourenne; Nicole Liachko; Sebastian Markmiller; Kristin M Webster; Kristi A Wharton
Journal:  J Neurosci       Date:  2019-10-16       Impact factor: 6.167

2.  Protein-RNA Networks Regulated by Normal and ALS-Associated Mutant HNRNPA2B1 in the Nervous System.

Authors:  Fernando J Martinez; Gabriel A Pratt; Eric L Van Nostrand; Ranjan Batra; Stephanie C Huelga; Katannya Kapeli; Peter Freese; Seung J Chun; Karen Ling; Chelsea Gelboin-Burkhart; Layla Fijany; Harrison C Wang; Julia K Nussbacher; Sara M Broski; Hong Joo Kim; Rea Lardelli; Balaji Sundararaman; John P Donohue; Ashkan Javaherian; Jens Lykke-Andersen; Steven Finkbeiner; C Frank Bennett; Manuel Ares; Christopher B Burge; J Paul Taylor; Frank Rigo; Gene W Yeo
Journal:  Neuron       Date:  2016-10-20       Impact factor: 17.173

3.  Imaging mRNA and protein interactions within neurons.

Authors:  Carolina Eliscovich; Shailesh M Shenoy; Robert H Singer
Journal:  Proc Natl Acad Sci U S A       Date:  2017-02-21       Impact factor: 11.205

4.  Capture and Identification of RNA-binding Proteins by Using Click Chemistry-assisted RNA-interactome Capture (CARIC) Strategy.

Authors:  Rongbing Huang; Mengting Han; Liying Meng; Xing Chen
Journal:  J Vis Exp       Date:  2018-10-19       Impact factor: 1.355

5.  The minor spliceosome could be the major key for FUS/TLS mutants in ALS.

Authors:  Emanuele Buratti
Journal:  EMBO J       Date:  2016-06-10       Impact factor: 11.598

6.  TDP-43 and Tau Oligomers in Alzheimer's Disease, Amyotrophic Lateral Sclerosis, and Frontotemporal Dementia.

Authors:  Mauro Montalbano; Salome McAllen; Filippa Lo Cascio; Urmi Sengupta; Stephanie Garcia; Nemil Bhatt; Anna Ellsworth; Eric A Heidelman; Omar D Johnson; Samantha Doskocil; Rakez Kayed
Journal:  Neurobiol Dis       Date:  2020-10-14       Impact factor: 5.996

7.  CRISPR/Cas9-mediated integration enables TAG-eCLIP of endogenously tagged RNA binding proteins.

Authors:  Eric L Van Nostrand; Chelsea Gelboin-Burkhart; Ruth Wang; Gabriel A Pratt; Steven M Blue; Gene W Yeo
Journal:  Methods       Date:  2016-12-18       Impact factor: 3.608

8.  TDP-43 functions within a network of hnRNP proteins to inhibit the production of a truncated human SORT1 receptor.

Authors:  Fatemeh Mohagheghi; Mercedes Prudencio; Cristiana Stuani; Casey Cook; Karen Jansen-West; Dennis W Dickson; Leonard Petrucelli; Emanuele Buratti
Journal:  Hum Mol Genet       Date:  2015-11-27       Impact factor: 6.150

Review 9.  The neurogenetics of alternative splicing.

Authors:  Celine K Vuong; Douglas L Black; Sika Zheng
Journal:  Nat Rev Neurosci       Date:  2016-05       Impact factor: 34.870

10.  Resources for the Comprehensive Discovery of Functional RNA Elements.

Authors:  Balaji Sundararaman; Lijun Zhan; Steven M Blue; Rebecca Stanton; Keri Elkins; Sara Olson; Xintao Wei; Eric L Van Nostrand; Gabriel A Pratt; Stephanie C Huelga; Brendan M Smalec; Xiaofeng Wang; Eurie L Hong; Jean M Davidson; Eric Lécuyer; Brenton R Graveley; Gene W Yeo
Journal:  Mol Cell       Date:  2016-03-17       Impact factor: 17.970

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