bwtool: a tool for bigWig files
Andy Pohl,Miguel Beato +1 more
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TLDR
Bwtool is a tool designed to read bigWig files rapidly and efficiently, providing functionality for extracting data and summarizing it in several ways, globally or at specific regions, as well as enabling the conversion of the positions of signal data from one genome assembly to another.Abstract:
BigWig files are a compressed, indexed, binary format for genomewide signal data for calculations (e.g. GC percent) or experiments (e.g. ChIP-seq/RNA-seq read depth). bwtool is a tool designed to read bigWig files rapidly and efficiently, providing functionality for extracting data and summarizing it in several ways, globally or at specific regions. Additionally, the tool enables the conversion of the positions of signal data from one genome assembly to another, also known as ‘lifting’. We believe bwtool can be useful for the analyst frequently working with bigWig data, which is becoming a standard format to represent functional signals along genomes. The article includes supplementary examples of running the software. Availability and implementation: TheCsourcecodeisfreelyavailable under the GNU public license v3 at http://cromatina.crg.eu/bwtool. Contact: andrew.pohl@crg.eu, andypohl@gmail.com Supplementary information: Supplementary data are available at Bioinformatics online.read more
Citations
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Primate-specific endogenous retrovirus-driven transcription defines naive-like stem cells
Jichang Wang,Gangcai Xie,Manvendra K. Singh,Avazeh T. Ghanbarian,Tamás Raskó,Attila Szvetnik,Huiqiang Cai,Daniel Besser,Alessandro Prigione,Nina V. Fuchs,Gerald G. Schumann,Wei Chen,Matthew C. Lorincz,Zoltán Ivics,Laurence D. Hurst,Zsuzsanna Izsvák +15 more
TL;DR: It is shown that a sub-population within cultures of human embryonic stem cells and induced pluripotent stem cells (hiPSCs) manifests key properties of naive state cells, and is defined as a hallmark of naive-like hESCs, and establishes novel primate-specific transcriptional circuitry regulating pluripotency.
Journal ArticleDOI
Cancer-Specific Retargeting of BAF Complexes by a Prion-like Domain.
Gaylor Boulay,Gabriel J. Sandoval,Nicolo Riggi,Sowmya Iyer,Rémi Buisson,Beverly Naigles,Mary E. Awad,Shruthi Rengarajan,Angela Volorio,Matthew J. McBride,Matthew J. McBride,Liliane C. Broye,Lee Zou,Ivan Stamenkovic,Cigall Kadoch,Cigall Kadoch,Miguel Rivera,Miguel Rivera +17 more
TL;DR: It is demonstrated that the physical properties of prion-like domains can retarget critical chromatin regulatory complexes to establish and maintain oncogenic gene expression programs in cancer.
Journal ArticleDOI
Developmental and genetic regulation of the human cortex transcriptome illuminate schizophrenia pathogenesis.
Andrew E. Jaffe,Richard E. Straub,Joo Heon Shin,Ran Tao,Yuan Gao,Leonardo Collado Torres,Tony Kam-Thong,Hualin S. Xi,Jie Quan,Qiang Chen,Carlo Colantuoni,William S Ulrich,Brady J. Maher,Amy Deep-Soboslay,Alan J. Cross,Nicholas J. Brandon,Jeffrey T. Leek,Thomas M. Hyde,Joel E. Kleinman,Daniel R. Weinberger +19 more
TL;DR: The authors surveyed gene expression across cortical development and in individuals with schizophrenia, finding 237 genes significantly differentially expressed between patients and controls, which replicated in an independent dataset, implicated synaptic processes, and were strongly regulated in early development.
Journal ArticleDOI
Chromatin environment, transcriptional regulation, and splicing distinguish lincRNAs and mRNAs.
Marta Melé,Kaia Mattioli,Kaia Mattioli,William Mallard,William Mallard,David M Shechner,David M Shechner,Chiara Gerhardinger,Chiara Gerhardinger,John L. Rinn,John L. Rinn,John L. Rinn +11 more
TL;DR: It is found that lincRNAs promoters are depleted of transcription factor (TF) binding sites, yet enriched for some specific factors such as GATA and FOS relative to mRNA promoters, and H3K9me3-a histone modification typically associated with transcriptional repression-is more enriched at the promoters of active lincRNA loci than at those of active mRNAs.
Journal ArticleDOI
Smarca4 ATPase mutations disrupt direct eviction of PRC1 from chromatin
Benjamin Z. Stanton,Courtney Hodges,Joseph P Calarco,Simon M. G. Braun,Wai Lim Ku,Cigall Kadoch,Keji Zhao,Gerald R. Crabtree,Gerald R. Crabtree +8 more
TL;DR: It is found that recurrent disease-associated mutations in BAF subunits induce genome-wide increases in PRC deposition and activity, establishing a new mechanism for the widespread BAF–PRC opposition underlying development and disease.
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