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
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Specification of CNS macrophage subsets occurs postnatally in defined niches
Takahiro Masuda,Lukas Amann,Giovanni Monaco,Roman Sankowski,Ori Staszewski,Martin Krueger,Francesca Del Gaudio,Liqun He,Neil Paterson,Elisa Nent,Francisco Fernández-Klett,Ayato Yamasaki,Maximilian Frosch,Maximilian Fliegauf,Lance Fredrick Pahutan Bosch,Hatice Ulupinar,Nora Hagemeyer,Dietmar Schreiner,Cayce E. Dorrier,Makoto Tsuda,Claudia Grothe,Anne Joutel,Richard Daneman,Christer Betsholtz,Urban Lendahl,Klaus-Peter Knobeloch,Tim Lämmermann,Josef Priller,Katrin Kierdorf,Marco Prinz +29 more
TL;DR: Together, the data reveal a precisely timed process in distinct anatomical niches for the establishment of macrophage subsets in the CNS, and show that microglia and meningeal macrophages originate from a common prenatal precursor, but that perivascular Macrophages are derived postnatally from meningeals.
Journal ArticleDOI
Combining RT-PCR-seq and RNA-seq to catalog all genic elements encoded in the human genome.
Cédric Howald,Andrea Tanzer,Jacqueline Chrast,Felix Kokocinski,Thomas Derrien,Nathalie Walters,José M. González,Adam Frankish,Bronwen Aken,Thibaut Hourlier,Jan-Hinnerk Vogel,Simon D. M. White,Stephen M. J. Searle,Jennifer Harrow,Tim Hubbard,Roderic Guigó,Alexandre Reymond +16 more
TL;DR: This work demonstrates that the cataloging of all of the genic elements encoded in the human genome will necessitate a coordinated effort between unbiased and targeted approaches, like RNA-seq and RT-PCR-seq.
Journal ArticleDOI
Targeting IRF3 as a YAP agonist therapy against gastric cancer
Shi Jiao,Jingmin Guan,Min Chen,Wenjia Wang,Chuanchuan Li,Yugong Wang,Yunfeng Cheng,Zhaocai Zhou,Zhaocai Zhou +8 more
TL;DR: This study identifies IRF3 as a positive regulator for YAP, highlighting a new therapeutic target against YAP-driven cancers.
Journal ArticleDOI
Epigenomic map of human liver reveals principles of zonated morphogenic and metabolic control
Mario Brosch,Kathrin Kattler,A Herrmann,Witigo von Schönfels,Karl Nordström,Daniel Seehofer,Georg Damm,Thomas Becker,Sebastian Zeissig,S Nehring,Fabian Reichel,V Moser,RV Thangapandi,Felix Stickel,Gustavo B. Baretton,Christoph Röcken,Michael H. Muders,Madlen Matz-Soja,Michael Krawczak,Gilles Gasparoni,Hella Hartmann,Andreas Dahl,Clemens Schafmayer,Jörn Walter,Jochen Hampe +24 more
TL;DR: A spatially resolved epigenomic and transcriptomic map of human liver is provided and porto-central gradients in metabolic and morphogen networks and transcription factor binding sites are shown as a basis to better understand liver regeneration and function.
Journal ArticleDOI
Specification of CNS macrophage subsets occurs postnatally in defined niches
Takahiro Masuda,Lukas Amann,Giovanni Monaco,Roman Sankowski,Ori Staszewski,Martin Krueger,Francesca Del Gaudio,Liqun He,Neil Paterson,Elisa Nent,Francisco Fernández-Klett,Ayato Yamasaki,Maximilian Frosch,Maximilian Fliegauf,Lance Fredrick Pahutan Bosch,Hatice Ulupinar,Nora Hagemeyer,Dietmar Schreiner,Cayce E. Dorrier,Makoto Tsuda,Claudia Grothe,Anne Joutel,Richard Daneman,Christer Betsholtz,Urban Lendahl,Klaus-Peter Knobeloch,Tim Lämmermann,Josef Priller,Katrin Kierdorf,Marco Prinz +29 more
References
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