Transcription factories revealed by integrative analysis of Hi-C and ChIP-Seq databases
Hyeongrin Jeon1, Tae-Young Roh2
1
Department of Life Sciences, 2Department of Integrative Biosciences and Biotechnology,
Pohang University of Science and Technology (POSTECH), Pohang, Korea
The transcription factory model has been believed to serve as an active domain tethered with multiple
RNA polymerase II and specialized in the transcription of a similar active gene cluster. Previous
experiments imply that it is involved in the regulation of transcription initiation and elongation as
well as the mobilization of genes in the nucleus. We examined the co-regulation of genes in
transcription factories of human embryonic stem cells using publicly available Hi-C data mapping
genome-wide chromatin interactions and ChIP-Seq data measuring occupancy of RNA polymerase
II and histone modifications. By the combination of Hi-C and ChIP-Seq analyses, we could define
active transcription factory networks which include 326 sub-networks. Among these networks, a
distinct transcription factory including histone gene cluster-1 (HIST1) shows significantly high level
of co-expression of genes. Besides, sub-network genes located in the same transcription factory have
more functional similarities each other than randomly selected genes. The mutual ranks of gene pairs
in a transcription factory are relatively lower, implying that the genes in the same transcription factory
have a higher chance to be co-expressed. Taken together, our integrative genome-wide analysis should
provide an implication for the active and unified transcriptional co-regulation by transcription factory
in the three dimensional nucleus space.