SynthesisPLoS computational biology2011
Podbat: a novel genomic tool reveals Swr1-independent H2A.Z incorporation at gene coding sequences through epigenetic meta-analysis.
Synthesis in PLoS computational biology, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 20 papers.
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Who cites it
20 citing papers in PubMed.
- Growth phase diets diminish histone acetyltransferase Gcn5 function and shorten lifespan of Drosophila males.EMBO reports · 2025Article
- Targeting Epigenetics to Cure HIV-1: Lessons From (and for) Cancer Treatment.Frontiers in cellular and infection microbiology · 2021Review
- Cdk9 and H2Bub1 signal to Clr6-CII/Rpd3S to suppress aberrant antisense transcription.Nucleic acids research · 2020Article
- The histone variant H2A.Z promotes splicing of weak introns.Genes & development · 2017Article
- The histone variant H2A.Z promotes efficient cotranscriptional splicing inGenes & development · 2017Article
- Pfh1 Is an Accessory Replicative Helicase that Interacts with the Replisome to Facilitate Fork Progression and Preserve Genome Integrity.PLoS genetics · 2016Article
- Regulating retrotransposon activity through the use of alternative transcription start sites.EMBO reports · 2016Article
- An interactive environment for agile analysis and visualization of ChIP-sequencing data.Nature structural & molecular biology · 2016Article
- The Paf1 complex factors Leo1 and Paf1 promote local histone turnover to modulate chromatin states in fission yeast.EMBO reports · 2015Article
- Histone Variant H2A.Z.2 Mediates Proliferation and Drug Sensitivity of Malignant Melanoma.Molecular cell · 2015Article
- A nucleosome turnover map reveals that the stability of histone H4 Lys20 methylation depends on histone recycling in transcribed chromatin.Genome research · 2015Article
- Panspecies small-molecule disruptors of heterochromatin-mediated transcriptional gene silencing.Molecular and cellular biology · 2015Article
- The essential Schizosaccharomyces pombe Pfh1 DNA helicase promotes fork movement past G-quadruplex motifs to prevent DNA damage.BMC biology · 2014Article
- ChIPseek, a web-based analysis tool for ChIP data.BMC genomics · 2014Article
- ACTIN-RELATED PROTEIN6 Regulates Female Meiosis by Modulating Meiotic Gene Expression in Arabidopsis.The Plant cell · 2014Article
- Centromeric histone H2B monoubiquitination promotes noncoding transcription and chromatin integrity.Nature structural & molecular biology · 2014Article
- The histone variant His2Av is required for adult stem cell maintenance in the Drosophila testis.PLoS genetics · 2013Article
- CHD1 remodelers regulate nucleosome spacing in vitro and align nucleosomal arrays over gene coding regions in S. pombe.The EMBO journal · 2012Article
- Factors that promote H3 chromatin integrity during transcription prevent promiscuous deposition of CENP-A(Cnp1) in fission yeast.PLoS genetics · 2012Article
- Deposition of histone variant H2A.Z within gene bodies regulates responsive genes.PLoS genetics · 2012Article
Corrections and comments
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Authors and funding
5 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Epigenetic regulation consists of a multitude of different modifications that determine active and inactive states of chromatin. Conditions such as cell differentiation or exposure to environmental stress require concerted changes in gene expression. To interpret epigenomics data, a spectrum of different interconnected datasets is needed, ranging from the genome sequence and positions of histones, together with their modifications and variants, to the transcriptional output of genomic regions. Here we present a tool, Podbat (Positioning database and analysis tool), that incorporates data from various sources and allows detailed dissection of the entire range of chromatin modifications simultaneously. Podbat can be used to analyze, visualize, store and share epigenomics data. Among other functions, Podbat allows data-driven determination of genome regions of differential protein occupancy or RNA expression using Hidden Markov Models. Comparisons between datasets are facilitated to enable the study of the comprehensive chromatin modification system simultaneously, irrespective of data-generating technique. Any organism with a sequenced genome can be accommodated. We exemplify the power of Podbat by reanalyzing all to-date published genome-wide data for the histone variant H2A.Z in fission yeast together with other histone marks and also phenotypic response data from several sources. This meta-analysis led to the unexpected finding of H2A.Z incorporation in the coding regions of genes encoding proteins involved in the regulation of meiosis and genotoxic stress responses. This incorporation was partly independent of the H2A.Z-incorporating remodeller Swr1. We verified an Swr1-independent role for H2A.Z following genotoxic stress in vivo. Podbat is open source software freely downloadable from www.podbat.org, distributed under the GNU LGPL license. User manuals, test data and instructions are available at the website, as well as a repository for third party-developed plug-in modules. Podbat requires Java version 1.6 or higher.
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Registered trials
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