iyer lab


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. Our lab is interested in understanding how gene expression is regulated across a eukaryotic genome. We focus on gene expression at the level of transcription, but are also interested in post-transcriptional regulation mediated by miRNAs.

We work in human cells and also use yeast as a model system to address various questions regarding global gene regulation. We use genomic and molecular experimental methods coupled with computational analyses. The genomic methods involve extensive use of DNA microarrays and next-generation sequencing (Illumina, SOLiD). Some major lines of research in the lab are as follows.

Transcriptional regulatory networks in yeast

Transcription factors bind and regulate the expression of hundreds of target genes throughout the yeast genome to form extended transcriptional regulatory networks. We are interested in reconstructing these global networks and determining how they change when cells respond to perturbations. We have used a genetic approach to reconstruct a genome-wide, functional transcriptional regulatory network including more than 260 transcription factors and their target genes. We are combining expression profiling using microarrays (to look at mRNA expression levels) and ChIP-chip (to look at transcription factor-promoter interactions), and constructing regulatory networks mediated by several transcription factors during the response of yeast cells to stress.

Role of chromatin in gene regulation

Chromatin structure - the positioning of nucleosomes and the modifications of histones - strongly affects gene expression. We are using next-generation sequencing to examine dynamic nucleosome remodeling across the genome. We are using antibodies specific for histone modifications to look at how genome-wide changes in these histone marks correlate with changes in transcription. We have successfully used these approaches in yeast, and are beginning to employ them in human cells.

Regulatory networks in human cell proliferation

Using a simple model for the transition of quiescent human cells into proliferation, we have identified dozens of transcription factors that are potentially involved in mediating this transition, as well as signaling pathways that are active. We are identifying regulatory networks mediated by key transcriptional regulators such as Myc, E2F, SRF and others during proliferation, using a combination of ChIP-chip, ChIP-seq, and expression profiling after modulating the transcriptional regulator.

Regulation and function of miRNAs during proliferation

The changing expression profiles of miRNAs in our cell culture model suggest that in addition to transcription factors, miRNAs could also play a role in mediating the transition of quiescent cells to proliferation. We are using microarrays to profile the expression of miRNAs, and thereby identify potentially relevant miRNAs. We are identifying downstream targets of miRNAs using a cDNA expression profiling approach. Our overall goal is to reconstruct networks involving the regulation of miRNAs and transcription factors by one another, and understand how they work in concert to regulate downstream target genes.

The ENCODE Project

Our lab is part of the ENCODE Consortium, whose goal is to identify all the functional elements in the human genome. With our ENCODE project collaborators, we are examining the relationship of binding of specific transcription factors such as the insulator binding protein CTCF and RNA pol II with open chromatin regions throughout the genome, in a variety of cell types. The use of ChIP-seq for this project also allows us to look at transcription factor binding and gene regulation in conjunction with normal human genetic variation.

research overview