| Title |
Podbat: A Novel Genomic Tool Reveals Swr1-Independent H2A.Z Incorporation at Gene Coding Sequences through Epigenetic Meta-Analysis
|
|---|---|
| Published in |
PLoS Computational Biology, August 2011
|
| DOI | 10.1371/journal.pcbi.1002163 |
| Pubmed ID | |
| Authors |
Laia Sadeghi, Carolina Bonilla, Annelie Strålfors, Karl Ekwall, J. Peter Svensson |
| 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. |
X Demographics
The data shown below were collected from the profiles of 7 X users who shared this research output. Click here to find out more about how the information was compiled.
Geographical breakdown
| Country | Count | As % |
|---|---|---|
| United States | 1 | 14% |
| Colombia | 1 | 14% |
| Unknown | 5 | 71% |
Demographic breakdown
| Type | Count | As % |
|---|---|---|
| Members of the public | 2 | 29% |
| Scientists | 2 | 29% |
| Science communicators (journalists, bloggers, editors) | 2 | 29% |
| Unknown | 1 | 14% |
Mendeley readers
The data shown below were compiled from readership statistics for 79 Mendeley readers of this research output. Click here to see the associated Mendeley record.
Geographical breakdown
| Country | Count | As % |
|---|---|---|
| United States | 2 | 3% |
| Spain | 1 | 1% |
| Sweden | 1 | 1% |
| Unknown | 75 | 95% |
Demographic breakdown
| Readers by professional status | Count | As % |
|---|---|---|
| Researcher | 26 | 33% |
| Student > Ph. D. Student | 24 | 30% |
| Student > Master | 6 | 8% |
| Student > Bachelor | 4 | 5% |
| Student > Postgraduate | 3 | 4% |
| Other | 10 | 13% |
| Unknown | 6 | 8% |
| Readers by discipline | Count | As % |
|---|---|---|
| Agricultural and Biological Sciences | 48 | 61% |
| Biochemistry, Genetics and Molecular Biology | 17 | 22% |
| Medicine and Dentistry | 4 | 5% |
| Pharmacology, Toxicology and Pharmaceutical Science | 2 | 3% |
| Social Sciences | 1 | 1% |
| Other | 1 | 1% |
| Unknown | 6 | 8% |