Genome wide mapping of UBF binding-sites in mouse and human cell lines.
The upstream binding transcription factor (UBTF, also called UBF) is thought to function exclusively in RNA polymerase I (Pol I)-specific transcription of the ribosomal genes. We recently reported in Sanij et al. (2014) [1] that the two isoforms of UBF (UBF1/2) are enriched at Pol II-transcribed genes throughout the mouse and human genomes. By using chromatin immunoprecipitation coupled with deep sequencing (ChIP-seq) of UBF1/2, Pol I, Pol II, H3K9me3, H3K4me4, H3K9ac and H4 hyperacetylation, we reported a correlation of UBF1/2 binding with enrichments in Pol II and markers of active chromatin. In addition, we examined a functional role for UBF1/2 in mediating Pol II transcription by performing expression array analysis in control and UBF1/2 depleted NIH3T3 cells. Our data demonstrate that UBF1/2 bind highly active Pol II-transcribed genes and mediate their expression without recruiting Pol I. Furthermore, we reported ChIP-sequencing analysis of UBF1/2 in immortalized human epithelial cells and their isogenically matched transformed counterparts. Here we report the experimental design and the description of the ChIP-sequencing and microarray expression datasets uploaded to NCBI Sequence Research Archive (SRA) and Gene Expression Omnibus (GEO).
Division of Cancer Research, Peter MacCallum Cancer Centre, St. Andrews Place, East Melbourne, Victoria 3002, Australia ; Sir Peter MacCallum Department of Oncology, University of Melbourne, Parkville, Victoria 3010, Australia.
Jeannine
J
Diesch
Division of Cancer Research, Peter MacCallum Cancer Centre, St. Andrews Place, East Melbourne, Victoria 3002, Australia ; Sir Peter MacCallum Department of Oncology, University of Melbourne, Parkville, Victoria 3010, Australia ; Department of Biochemistry and Molecular Biology, Monash University, Clayton, Victoria 3800, Australia ; Department of Biochemistry and Molecular Biology, University of Melbourne, Parkville, Victoria 3010, Australia ; Division of Cancer Medicine, Peter MacCallum Cancer Centre, St. Andrews Place, East Melbourne, Victoria 3002, Australia ; School of Biomedical Sciences, University of Queensland, Brisbane, Queensland 4072, Australia.
Ross D
RD
Hannan
Division of Cancer Research, Peter MacCallum Cancer Centre, St. Andrews Place, East Melbourne, Victoria 3002, Australia ; Sir Peter MacCallum Department of Oncology, University of Melbourne, Parkville, Victoria 3010, Australia ; Department of Pathology, University of Melbourne, Parkville, Victoria 3010, Australia.
Elaine
E
Sanij
ChIP-seq; Histone modifications; RNA polymerase I; UBF