HITS-CLIP and Integrative Modeling Define the Rbfox Splicing-Regulatory Network Linked to Brain Development and Autism
Sebastien M. Weyn-Vanhentenryck,Aldo Mele,Qinghong Yan,Shuying Sun,Shuying Sun,Natalie G. Farny,Zuo Zhang,Zuo Zhang,Chenghai Xue,Margaret Herre,Pamela A. Silver,Michael Q. Zhang,Michael Q. Zhang,Adrian R. Krainer,Robert B. Darnell,Chaolin Zhang +15 more
Reads0
Chats0
TLDR
Al Alteration of Rb fox targets in some autistic brains is correlated with downregulation of all three Rbfox proteins, supporting the potential clinical relevance of the splicing-regulatory network.About:
This article is published in Cell Reports.The article was published on 2014-03-27 and is currently open access. It has received 338 citations till now. The article focuses on the topics: HITS-CLIP.read more
Citations
More filters
Journal ArticleDOI
Synaptic, transcriptional and chromatin genes disrupted in autism
Silvia De Rubeis,Xin-Xin He,Arthur P. Goldberg,Christopher S. Poultney,Kaitlin E. Samocha,A. Ercument Cicek,Yan Kou,Li Liu,Menachem Fromer,Menachem Fromer,R. Susan Walker,Tarjinder Singh,Lambertus Klei,Jack A. Kosmicki,Shih-Chen Fu,Branko Aleksic,Monica Biscaldi,Patrick Bolton,Jessica M. Brownfeld,Jinlu Cai,Nicholas G. Campbell,Angel Carracedo,Angel Carracedo,Maria H. Chahrour,Andreas G. Chiocchetti,Hilary Coon,Emily L. Crawford,Lucy Crooks,Sarah Curran,Geraldine Dawson,Eftichia Duketis,Bridget A. Fernandez,Louise Gallagher,Evan T. Geller,Stephen J. Guter,R. Sean Hill,R. Sean Hill,Iuliana Ionita-Laza,Patricia Jiménez González,Helena Kilpinen,Sabine M. Klauck,Alexander Kolevzon,Irene Lee,Jing Lei,Terho Lehtimäki,Chiao-Feng Lin,Avi Ma'ayan,Christian R. Marshall,Alison L. McInnes,Benjamin M. Neale,Michael John Owen,Norio Ozaki,Mara Parellada,Jeremy R. Parr,Shaun Purcell,Kaija Puura,Deepthi Rajagopalan,Karola Rehnström,Abraham Reichenberg,Aniko Sabo,Michael Sachse,Stephen Sanders,Chad M. Schafer,Martin Schulte-Rüther,David Skuse,David Skuse,Christine Stevens,Peter Szatmari,Kristiina Tammimies,Otto Valladares,Annette Voran,Li-San Wang,Lauren A. Weiss,A. Jeremy Willsey,Timothy W. Yu,Timothy W. Yu,Ryan K. C. Yuen,Edwin H. Cook,Christine M. Freitag,Michael Gill,Christina M. Hultman,Thomas Lehner,Aarno Palotie,Aarno Palotie,Aarno Palotie,Gerard D. Schellenberg,Pamela Sklar,Matthew W. State,James S. Sutcliffe,Christopher A. Walsh,Christopher A. Walsh,Stephen W. Scherer,Michael E. Zwick,Jeffrey C. Barrett,David J. Cutler,Kathryn Roeder,Bernie Devlin,Mark J. Daly,Mark J. Daly,Joseph D. Buxbaum +99 more
TL;DR: Using exome sequencing, it is shown that analysis of rare coding variation in 3,871 autism cases and 9,937 ancestry-matched or parental controls implicates 22 autosomal genes at a false discovery rate of < 0.05, plus a set of 107 genes strongly enriched for those likely to affect risk (FDR < 0.30).
Journal ArticleDOI
m 6 A RNA methylation promotes XIST -mediated transcriptional repression
Deepak P. Patil,Chun-Kan Chen,Brian F. Pickering,Amy Y. M. Chow,Constanza Jackson,Mitchell Guttman,Samie R. Jaffrey +6 more
TL;DR: The long non-coding RNA X-inactive specific transcript (XIST) mediates the transcriptional silencing of genes on the X chromosome and is highly methylated with at least 78 N6-methyladenosine (m6A) residues, revealing a pathway of m6A formation and recognition required for XIST-mediated transcriptional repression.
Journal ArticleDOI
Single-nucleotide-resolution mapping of m6A and m6Am throughout the transcriptome
Bastian Linder,Anya V. Grozhik,Anthony O. Olarerin-George,Cem Meydan,Christopher E. Mason,Samie R. Jaffrey +5 more
TL;DR: m6A individual-nucleotide-resolution cross-linking and immunoprecipitation (miCLIP) is developed and used to demonstrate that antibodies to m6A can induce specific mutational signatures at m 6A residues after ultraviolet light–induced antibody-RNA cross- linking and reverse transcription.
Journal ArticleDOI
Robust transcriptome-wide discovery of RNA-binding protein binding sites with enhanced CLIP (eCLIP)
Eric L. Van Nostrand,Gabriel A. Pratt,Alexander A. Shishkin,Chelsea Gelboin-Burkhart,Mark Y. Fang,Balaji Sundararaman,Steven M. Blue,Thai B. Nguyen,Christine Surka,Keri Elkins,Rebecca Stanton,Frank Rigo,Mitchell Guttman,Gene W. Yeo +13 more
TL;DR: An enhanced CLIP (eCLIP) protocol is developed that decreases requisite amplification by ∼1,000-fold, decreasing discarded PCR duplicate reads by ∼60% while maintaining single-nucleotide binding resolution, and improves specificity in the discovery of authentic binding sites.
Journal ArticleDOI
Mechanisms and Regulation of Alternative Pre-mRNA Splicing
Yeon J. Lee,Donald C. Rio +1 more
TL;DR: These studies provide mechanistic insights into how spliceosome assembly, dynamics, and catalysis occur; how alternative splicing is regulated and evolves; and how splicing can be disrupted by cis- and trans-acting mutations leading to disease states.
References
More filters
Journal ArticleDOI
Controlling the false discovery rate: a practical and powerful approach to multiple testing
Yoav Benjamini,Yosef Hochberg +1 more
TL;DR: In this paper, a different approach to problems of multiple significance testing is presented, which calls for controlling the expected proportion of falsely rejected hypotheses -the false discovery rate, which is equivalent to the FWER when all hypotheses are true but is smaller otherwise.
Journal ArticleDOI
DAVID: Database for Annotation, Visualization, and Integrated Discovery
Glynn Dennis,Brad T. Sherman,Douglas A. Hosack,Jun Jun Yang,Wei Gao,H. Clifford Lane,Richard A. Lempicki +6 more
TL;DR: DAMID is a web-accessible program that integrates functional genomic annotations with intuitive graphical summaries that assists in the interpretation of genome-scale datasets by facilitating the transition from data collection to biological meaning.
Proceedings Article
Fitting a mixture model by expectation maximization to discover motifs in biopolymers.
Timothy L. Bailey,Charles Elkan +1 more
TL;DR: The algorithm described in this paper discovers one or more motifs in a collection of DNA or protein sequences by using the technique of expectation maximization to fit a two-component finite mixture model to the set of sequences.
Journal ArticleDOI
Alternative Isoform Regulation in Human Tissue Transcriptomes
Eric T. Wang,Rickard Sandberg,Rickard Sandberg,Shujun Luo,Irina Khrebtukova,Lu Zhang,Christine Mayr,Stephen F. Kingsmore,Gary P. Schroth,Christopher B. Burge +9 more
TL;DR: An in-depth analysis of 15 diverse human tissue and cell line transcriptomes on the basis of deep sequencing of complementary DNA fragments yielding a digital inventory of gene and mRNA isoform expression suggested common involvement of specific factors in tissue-level regulation of both splicing and polyadenylation.
Journal ArticleDOI
Genome-Wide Analysis in Vivo of Translation with Nucleotide Resolution Using Ribosome Profiling
TL;DR: A ribosomesome-profiling strategy based on the deep sequencing of ribosome-protected mRNA fragments is presented and enables genome-wide investigation of translation with subcodon resolution and is used to monitor translation in budding yeast under both rich and starvation conditions.