Our lab is interested in understanding how gene expression is regulated across a eukaryotic genome, in normal cells and in disease. Nearly all cells respond to physiological or developmental cues by large-scale transcriptional reprogramming – altering the expression of hundreds to thousands of genes throughout the genome. Such sweeping changes in gene expression also underlie the development of diseases such as cancer, and they can also be caused by normal or abnormal genetic variation between individuals. We focus on gene expression at the level of transcription, regulated by transcription factors and chromatin structure (epigenetics), but are also interested in post-transcriptional regulation mediated by non-coding RNAs. We work in human cells and tumors, and also use yeast as a model system to address various questions regarding global gene regulation, using genomic and molecular experimental methods that rely heavily on deep sequencing, closely coupled with computational analyses. Broad research areas in the lab include 1) transcriptional regulatory networks in yeast, 2) role of chromatin structure and remodeling in transcriptional regulation, 3) regulatory networks during human cell proliferation, 4) regulation and function of miRNAs during proliferation, 5) relationship of transcription regulation with genetic variability among individuals. 6) Epigenetic profiling and non-coding somatic mutations in cancer.

Selected publications:

Shpak M, Hall A.W., Goldberg M.M., Derryberry D.Z., Ni Y., Iyer V.R. & Cowperthwaite M.C. An eQTL analysis of the human glioblastoma multiforme genome. Genomics. 103:252-63 (2014).

Park D., Morris A.R., Battenhouse A. & Iyer V.R. Simultaneous mapping of transcript ends at single-nucleotide resolution and identification of widespread promoter-associated non-coding RNA governed by TATA elements. Nucleic Acids Res. 42:3736-49 (2014).

Polioudakis D., Bhinge A.A., Killion P.J., Lee B.K., Abell N.S. & Iyer V.R. A Myc-microRNA network promotes exit from quiescence by suppressing the interferon response and cell-cycle arrest genes. Nucleic Acids Res 41: 2239-54 (2013).

Lee B.K., Bhinge A.A., Battenhouse A., McDaniell R.M., Liu Z., Song L., Ni Y., Birney E., Lieb J.D., Furey T.S., Crawford G.E. & Iyer V.R. Cell-type specific and combinatorial usage of diverse transcription factors revealed by genome-wide binding studies in multiple human cells. Genome Res 22: 9-24 (2012).

McDaniell R., Lee B.K., Song L., Liu Z., Boyle A.P., Erdos M.R., Scott L.J., Morken M.A., Kucera K.S., Battenhouse A., Keefe D., Collins F.S., Willard H.F., Lieb J.D., Furey T.S., Crawford G.E., Iyer V.R. & Birney E. Heritable individual-specific and allele-specific chromatin signatures in humans. Science 328: 235-9. (2010).