Model-based Analysis of ChIP-Seq (MACS)
Yong Zhang,Tao Liu,Clifford A. Meyer,Jérôme Eeckhoute,David S. Johnson,Bradley E. Bernstein,Bradley E. Bernstein,Chad Nusbaum,Richard M. Myers,Myles Brown,Wei Li,X. Shirley Liu +11 more
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TLDR
This work presents Model-based Analysis of ChIP-Seq data, MACS, which analyzes data generated by short read sequencers such as Solexa's Genome Analyzer, and uses a dynamic Poisson distribution to effectively capture local biases in the genome, allowing for more robust predictions.Abstract:
We present Model-based Analysis of ChIP-Seq data, MACS, which analyzes data generated by short read sequencers such as Solexa's Genome Analyzer. MACS empirically models the shift size of ChIP-Seq tags, and uses it to improve the spatial resolution of predicted binding sites. MACS also uses a dynamic Poisson distribution to effectively capture local biases in the genome, allowing for more robust predictions. MACS compares favorably to existing ChIP-Seq peak-finding algorithms, and is freely available.read more
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Journal ArticleDOI
m 6 A modulates neuronal functions and sex determination in Drosophila
Tina Lence,Junaid Akhtar,Marc Bayer,Katharina Schmid,Laura Spindler,Cheuk Hei Ho,Nastasja Kreim,Miguel A. Andrade-Navarro,Burkhard Poeck,Mark Helm,Jean-Yves Roignant +10 more
TL;DR: This work carries out a comprehensive molecular and physiological characterization of the individual components of the methyl transferase complex, as well as of the YTH domain-containing nuclear reader protein in Drosophila melanogaster, and identifies the member of the split ends protein family, Spenito, as a novel bona fide subunit of themethyltransferase complex.
Journal ArticleDOI
Obesity and Bariatric Surgery Drive Epigenetic Variation of Spermatozoa in Humans.
Ida Donkin,Soetkin Versteyhe,Lars R. Ingerslev,Kui Qian,Mie Mechta,Loa Nordkap,Brynjulf Mortensen,Brynjulf Mortensen,Emil V. R. Appel,Niels Jørgensen,Viggo B. Kristiansen,Torben Hansen,Christopher T. Workman,Christopher T. Workman,Juleen R. Zierath,Juleen R. Zierath,Romain Barrès +16 more
TL;DR: Evidence is provided that the epigenome of human spermatozoa dynamically changes under environmental pressure and offers insight into how obesity may propagate metabolic dysfunction to the next generation.
Journal ArticleDOI
Highly expressed loci are vulnerable to misleading ChIP localization of multiple unrelated proteins
Leonid Teytelman,Deborah M. Thurtle,Jasper Rine,Alexander van Oudenaarden,Alexander van Oudenaarden +4 more
TL;DR: An artifact in ChIP is discovered that leads to reproducible but biologically meaningless enrichment of proteins at highly expressed genes, caused by high levels of polymerase II and polymerase III transcription, which calls into question reports of unexpected localization of transcription factors, repressors, and cytosolic proteins to highly expression genes.
Journal ArticleDOI
Atypical Teratoid/Rhabdoid Tumors Are Comprised of Three Epigenetic Subgroups with Distinct Enhancer Landscapes
Pascal Johann,Pascal Johann,Serap Erkek,Marc Zapatka,Kornelius Kerl,Ivo Buchhalter,Volker Hovestadt,David T.W. Jones,Dominik Sturm,Dominik Sturm,Carl Hermann,Maia Segura Wang,Andrey Korshunov,Andrey Korshunov,Marina Rhyzova,Susanne Gröbner,Sebastian Brabetz,Lukas Chavez,Susanne Bens,Stefan Gröschel,Fabian Kratochwil,Andrea Wittmann,Laura Sieber,Christina Geörg,Stefan Wolf,Katja Beck,Florian Oyen,David Capper,David Capper,Peter van Sluis,Richard Volckmann,Jan Koster,Rogier Versteeg,Andreas von Deimling,Andreas von Deimling,Till Milde,Till Milde,Olaf Witt,Olaf Witt,Andreas E. Kulozik,Martin Ebinger,Tarek Shalaby,Michael A. Grotzer,David Sumerauer,Josef Zamecnik,Jaume Mora,Nada Jabado,Michael D. Taylor,Annie Huang,Eleonora Aronica,Anna Marta Maria Bertoni,Bernhard Radlwimmer,Torsten Pietsch,Ulrich Schüller,Reinhard Schneppenheim,Paul A. Northcott,Jan O. Korbel,Reiner Siebert,Michael C. Frühwald,Michael C. Frühwald,Peter Lichter,Roland Eils,Amar Gajjar,Martin Hasselblatt,Stefan M. Pfister,Stefan M. Pfister,Marcel Kool +66 more
TL;DR: Three distinct molecular subgroups of ATRTs, associated with differences in demographics, tumor location, and type of SMARCB1 alterations, were identified, leading to the identification of subgroup-specific regulatory networks and potential therapeutic targets.
Journal ArticleDOI
Target analysis by integration of transcriptome and ChIP-seq data with BETA
Su Wang,Hanfei Sun,Jian Ma,Chongzhi Zang,Chenfei Wang,Juan Wang,Qianzi Tang,Clifford A. Meyer,Yong Zhang,X. Shirley Liu +9 more
TL;DR: BETA is a software package that integrates ChIP-seq of TFs or chromatin regulators with differential gene expression data to infer direct target genes and identifies the motif of the factor and its collaborators, which might modulate the factor's activating or repressive function.
References
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