Department of Molecular Biology
Simches Research Center
Boston, MA 02114
About Mridula Ray
Epigenetic mechanisms underlie the regulation of gene expression patterns. The goal of my research is to isolate and identify chromatin-related non-coding RNAs (ncRNAs) that functionally impact the epigenetic state in a cell. While increasing evidence indicates that the mammalian genome codes for a large number of long ncRNAs, validation of ncRNA identity and function are technically challenging with respect to distinguishing RNAs that bind chromatin modifying machinery from artifacts. Recent studies have shown that a class of long ncRNAs may play a role in the activity or recruitment of the epigenetic factors the Polycomb group (PcG) proteins to genomic sites. To further test this idea and enrich for bonafide ncRNA-PcG interactions on the DNA, chromatin (the substrate of the PcG proteins) was isolated away from the cytoplasm and soluble fraction of the nucleus in crosslinked HeLa cells. PcG components Bmi1 and a stable FLAG-Bmi1 were then specifically immunoprecipitated from the chromatin extract. Bmi1-associated ncRNAs were biochemically isolated and further studied with the aim of validating and understanding the roles of individual ncRNAs in PcG biology. We have identified strong candidates that are specifically enriched at known ncRNA sites and are expressed from loci with distinct chromatin signatures. These candidates are currently being compared with immunoprecipitations against replicate Bmi1 samples, additional PcG components and other chromatin protein controls (CTCF, H3K27me3, H3K4me3). This technology offers an advantage over current RNA immunoprecipitation techniques by enriching the input for ncRNA-chromatin interactions, cross-validating results and employing stringent wash conditions and controls. Application of this technology to a variety of chromatin proteins yields distinct spectra of candidate ncRNA-chromatin interactions.Publications
- Boyer LA, Plath K, Zeitlinger J, Brambrink T, Medeiros LA, Lee TI, Levine SS, Wernig M, Tajonar A, Ray MK, Bell GW, Otte AP, Vidal M, Gifford DK, Young RA, Jaenisch R. Polycomb complexes repress developmental regulators in murine embryonic stem cells. Nature 2006 May 18; 441(7091):349-53.