title: Analysis of paired end Pol II ChIP-seq and short capped RNA-seq in MCF-7 cells.
abstract: While a role of promoter-proximal RNA Polymerase II (Pol II) pausing in regulation of eukaryotic gene expression is implied, the mechanisms and dynamics of this process are poorly understood. We performed genome-wide analysis of short capped RNAs (scRNAs) and Pol II chromatin immunoprecipitation sequencing (ChIP-seq) in human breast cancer MCF-7 cells to better understand Pol II pausing (Samarakkody, A., Abbas, A., Scheidegger, A., Warns, J., Nnoli, O., Jokinen, B., Zarns, K., Kubat, B., Dhasarathy, A. and Nechaev, S. (2015) RNA polymerase II pausing can be retained or acquired during activation of genes involved in the epithelial to mesenchymal transition.Nucleic Acids Res43, 3938-3949). The data are available at the NCBI Gene Expression Omnibus under accession number GSE67041. For both ChIP and scRNA samples, we used paired end sequencing on the Illumina MiSeq instrument. For ChIP-seq, the use of paired end sequencing allowed us to avoid ambiguities in center-read definition. For scRNA seq, this allowed us to identify both the 5'-end and the 3'-end in the same run that represent, respectively, the transcription start sites and the locations of Pol II pausing. The sharpening of Pol II ChIP-seqmetagene profiles when aligned against 5'-ends of scRNAs indicates that these RNAs can be used to define the start sites for the majority of mRNA transcription events.
authors.affiliation: Department of Basic Sciences, University of North Dakota School of Medicine, Grand Forks, ND 58202, USA.
authors.forename: Adam
authors.initials: A
authors.lastname: Scheidegger
authors.affiliation: Center for Integrative Bioinformatics, National Institute of Environmental Health Sciences, Research Triangle Park, NC 27709, USA.
authors.forename: Adam
authors.initials: A
authors.lastname: Burkholder
authors.affiliation: Department of Basic Sciences, University of North Dakota School of Medicine, Grand Forks, ND 58202, USA.
authors.forename: Ata
authors.initials: A
authors.lastname: Abbas
authors.affiliation: Department of Computer Sciences, University of North Dakota, Grand Forks, ND 58202, USA.
authors.forename: Kris
authors.initials: K
authors.lastname: Zarns
authors.affiliation: Department of Basic Sciences, University of North Dakota School of Medicine, Grand Forks, ND 58202, USA.
authors.forename: Ann
authors.initials: A
authors.lastname: Samarakkody
authors.affiliation: Department of Basic Sciences, University of North Dakota School of Medicine, Grand Forks, ND 58202, USA.
authors.forename: Sergei
authors.initials: S
authors.lastname: Nechaev
keywords: Paired end ChIP-sequencing; Pol II pausing; Short capped RNA