GENCODE: The reference human genome annotation for The ENCODE Project
Jennifer Harrow,Adam Frankish,José M. González,Electra Tapanari,Mark Diekhans,Felix Kokocinski,Bronwen Aken,Daniel Barrell,Amonida Zadissa,Stephen M. J. Searle,If H. A. Barnes,Alexandra Bignell,Veronika Boychenko,Toby Hunt,M. Kay,Gaurab Mukherjee,Jeena Rajan,Gloria Despacio-Reyes,Gary Saunders,Charles A. Steward,Rachel A. Harte,Michael F. Lin,Cédric Howald,Andrea Tanzer,Thomas Derrien,Jacqueline Chrast,Nathalie Walters,Suganthi Balasubramanian,Baikang Pei,Michael L. Tress,Jose Manuel Rodriguez,Iakes Ezkurdia,Jeltje Van Baren,Michael R. Brent,David Haussler,Manolis Kellis,Alfonso Valencia,Alexandre Reymond,Mark Gerstein,Roderic Guigó,Tim Hubbard +40 more
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TLDR
This work has examined the completeness of the transcript annotation and found that 35% of transcriptional start sites are supported by CAGE clusters and 62% of protein-coding genes have annotated polyA sites, and over one-third of GENCODE protein-Coding genes aresupported by peptide hits derived from mass spectrometry spectra submitted to Peptide Atlas.Abstract:
The GENCODE Consortium aims to identify all gene features in the human genome using a combination of computational analysis, manual annotation, and experimental validation. Since the first public release of this annotation data set, few new protein-coding loci have been added, yet the number of alternative splicing transcripts annotated has steadily increased. The GENCODE 7 release contains 20,687 protein-coding and 9640 long noncoding RNA loci and has 33,977 coding transcripts not represented in UCSC genes and RefSeq. It also has the most comprehensive annotation of long noncoding RNA (lncRNA) loci publicly available with the predominant transcript form consisting of two exons. We have examined the completeness of the transcript annotation and found that 35% of transcriptional start sites are supported by CAGE clusters and 62% of protein-coding genes have annotated polyA sites. Over one-third of GENCODE protein-coding genes are supported by peptide hits derived from mass spectrometry spectra submitted to Peptide Atlas. New models derived from the Illumina Body Map 2.0 RNA-seq data identify 3689 new loci not currently in GENCODE, of which 3127 consist of two exon models indicating that they are possibly unannotated long noncoding loci. GENCODE 7 is publicly available from gencodegenes.org and via the Ensembl and UCSC Genome Browsers.read more
Citations
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The long non-coding RNA NEAT1 is responsive to neuronal activity and is associated with hyperexcitability states.
Guy Barry,Guy Barry,James Briggs,Do Won Hwang,Sam P Nayler,Patrick R.J. Fortuna,Nicky Jonkhout,Fabien Dachet,Jesper L.V. Maag,Jesper L.V. Maag,Pieter Mestdagh,Erin M. Singh,Lotta Avesson,Dominik C. Kaczorowski,Ezgi Ozturk,Nigel C. Jones,Irina Vetter,Luis Arriola-Martinez,Jianfei Hu,Glória Regina Franco,Glória Regina Franco,Victoria M. Warn,Andrew Gong,Marcel E. Dinger,Marcel E. Dinger,Frank Rigo,Leonard Lipovich,Margaret J. Morris,Terence J. O'Brien,Dong Soo Lee,Jeffrey A. Loeb,Seth Blackshaw,John S. Mattick,John S. Mattick,Ernst J. Wolvetang +34 more
TL;DR: A role for NEAT1 in modulating human neuronal activity is indicated and a novel mechanistic link between an activity-dependent long non-coding RNA and epilepsy is suggested.
Journal ArticleDOI
Mitigation of off-target toxicity in CRISPR-Cas9 screens for essential non-coding elements
Josh Tycko,Michael Wainberg,Georgi K. Marinov,Oana Ursu,Gaelen T. Hess,Braeden K. Ego,Aradhana,Amy Li,Alisa Truong,Alexandro E. Trevino,Kaitlyn Spees,David Yao,Irene M. Kaplow,Peyton Greenside,David W. Morgens,Douglas H. Phanstiel,Douglas H. Phanstiel,Michael Snyder,Lacramioara Bintu,William J. Greenleaf,Anshul Kundaje,Michael C. Bassik +21 more
TL;DR: The authors find Cas9 nuclease, CRISPRi/a each have distinct off-target effects, and that these can be accurately identified and removed using the GuideScan sgRNA specificity score.
Journal ArticleDOI
Transposable elements modulate human RNA abundance and splicing via specific RNA-protein interactions
David R. Kelley,David R. Kelley,David G. Hendrickson,David G. Hendrickson,Danielle Tenen,Danielle Tenen,John L. Rinn,John L. Rinn,John L. Rinn +8 more
TL;DR: A meta-analysis of 75 CLIP-Seq experiments suggests a widespread role for TEs in shaping RNA-protein regulatory networks in the human genome.
Journal ArticleDOI
miRGate: a curated database of human, mouse and rat miRNA-mRNA targets
TL;DR: The miRGate database as discussed by the authors is a database containing novel computational predicted miRNA-mRNA pairs that are calculated using well-established algorithms, such as sequence matching, thermodynamics and conservation, among other approaches.
Journal ArticleDOI
Human Blood CD1c+ Dendritic Cells Encompass CD5high and CD5low Subsets That Differ Significantly in Phenotype, Gene Expression, and Functions.
Xiangyun Yin,Haisheng Yu,Xiaoyang Jin,Jingyun Li,Hao Guo,Quanxing Shi,Zhao Yin,Yong Xu,Xuefei Wang,Rong Liu,Shouli Wang,Liguo Zhang +11 more
TL;DR: The present study showed that human blood CD1c+ cDCs (cDC2s) can be further separated into two subpopulations according to their CD5 expression status, and proposed that these two subsets of human cDC 2s could potentially play contrasting roles in immunity or tolerance.
References
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