Why do you think your paper is highly cited?

This paper represents a shift in the way we think about regulation of gene transcription. Our finding that the majority of human genes experience transcriptional initiation runs contrary to previously held views that Pol II recruitment is the rate-limiting or principle regulatory step in gene transcription. This paper suggests that regulation of transcriptional elongation is much more important to establishing cell-specific gene expression programs than previously realized.

 Does it describe a new discovery, methodology, or synthesis of knowledge?

We have discovered that most protein-coding genes, including most genes thought to be transcriptionally inactive, experience transcriptional initiation. Previous studies of a few genes, including the Drosophila heat shock genes, have demonstrated that Polymerase II molecules could be transcriptionally engaged at genes that were not producing full-length mRNA.

These "paused" or "poised" polymerase molecules could produce a complete mRNA transcript once an elongation block had been removed. This behavior was thought to be a little-utilized exception rather than the general transcriptional rule. We now show that this polymerase pausing, or a highly similar mechanism, is utilized across the vast majority of human genes.

 Would you summarize the significance of your paper in layman's terms?

The proper control of gene transcription (which genes are turned on and which genes are turned off at any given time) is critical to cell function and development. Previously, it was thought that when a gene needed to be turned on, an RNA Polymerase II molecule was recruited at that time to the gene in order to produce a full-length gene transcript (the mark of an active gene).

We now show that most human genes have already begun the act of gene transcription, even if they are indeed silent (turned off). This "polymerase poising" indicates that many silent genes are already partially turned on, but are waiting for further instructions that tell it to be "fully turned on." Determining what these "further instructions" are, and which proteins carry them out, will be of great importance in deciphering how humans and other organisms develop properly.

 How did you become involved in this research, and were there any problems along the way?

We discovered the basis for this paper while mapping the gene regulatory circuitry in embryonic stem cells and relating this information to chromatin regulatory events (initially H3K4me3 modification). The initial discovery was surprising and had to be verified in multiple ways using various techniques.

 Where do you see your research leading in the future?

The finding that transcriptional initiation occurs at most genes suggests that regulation of transcriptional elongation is a central event in determining cell-specific gene regulatory programs. As such, regulation of development via transcriptional elongation control (by polymerase pausing factors, elongation factors, kinases etc.) is likely to become a rich area of exploration. Identifying these factors and how they act in a gene-specific manner will be important in understanding human development (including stem-cell biology and regenerative medicine) and disease (such as cancer).

Matthew Guenther, Ph.D.
Whitehead Institute for Biomedical Research
Cambridge, MA, USA
Web

Keywords: gene transcription, transcriptional initiation, transcriptional elongation, Polymerase II recruitment, Polymerase II molecules, cell-specific gene expression programs, protein-coding genes, Drosophila heat shock genes, polymerase pausing, polymerase poising, complete mRNA transcript, embryonic stem cells, chromatin regulatory events, H3K4me3 modification.