ABSTRACT
SUMMARY: In recent years, major initiatives such as the International Human Epigenome Consortium have generated thousands of high-quality genome-wide datasets for a large variety of assays and cell types. This data can be used as a reference to assess whether the signal from a user-provided dataset corresponds to its expected experiment, as well as to help reveal unexpected biological associations. We have developed the epiGenomic Efficient Correlator (epiGeEC) tool to enable genome-wide comparisons of very large numbers of datasets. A public Galaxy implementation of epiGeEC allows comparison of user datasets with thousands of public datasets in a few minutes. AVAILABILITY AND IMPLEMENTATION: The source code is available at https://bitbucket.org/labjacquespe/epigeec and the Galaxy implementation at http://epigeec.genap.ca. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.
Subject(s)
Epigenomics , Software , Animals , Computational Biology , Datasets as Topic , Genome , Humans , MiceABSTRACT
Termination of RNA polymerase II (RNAPII) transcription is a fundamental step of gene expression that is critical for determining the borders between genes. In budding yeast, termination at protein-coding genes is initiated by the cleavage/polyadenylation machinery, whereas termination of most noncoding RNA (ncRNA) genes occurs via the Nrd1-Nab3-Sen1 (NNS) pathway. Here, we find that NNS-like transcription termination is not conserved in fission yeast. Rather, genome-wide analyses show global recruitment of mRNA 3' end processing factors at the end of ncRNA genes, including snoRNAs and snRNAs, and that this recruitment coincides with high levels of Ser2 and Tyr1 phosphorylation on the RNAPII C-terminal domain. We also find that termination of mRNA and ncRNA transcription requires the conserved Ysh1/CPSF-73 and Dhp1/XRN2 nucleases, supporting widespread cleavage-dependent transcription termination in fission yeast. Our findings thus reveal that a common mode of transcription termination can produce functionally and structurally distinct types of polyadenylated and non-polyadenylated RNAs.
Subject(s)
RNA/genetics , Schizosaccharomyces/genetics , Transcription Termination, Genetic/physiology , DNA Helicases/genetics , DNA Helicases/metabolism , DNA Helicases/physiology , RNA Helicases/genetics , RNA Helicases/metabolism , RNA Helicases/physiology , RNA Polymerase II/metabolism , RNA Polymerase II/physiology , RNA-Binding Proteins/genetics , RNA-Binding Proteins/metabolism , RNA-Binding Proteins/physiology , Species SpecificityABSTRACT
In the analysis of experimental data corresponding to the signal enrichment of chromatin features such as histone modifications throughout the genome, it is often useful to represent the signal over known regions of interest, such as genes, using aggregate or individual profiles. In the present chapter, we describe and explain the best practices on how to generate such profiles as well as other usages of the versatile aggregate profiler (VAP) tool (Coulombe et al., Nucleic Acids Res 42:W485-W493, 2014), with a particular focus on the new functionalities introduced in version 1.1.0 of VAP.
