Noncoding RNAs in Transcriptional Regulation and Chromatin Organization

Organizer: Alla Grishok, Columbia University

The goal of this group is to provide a forum for scientists engaged in research into the biology, biochemistry, and applications of RNAi silencing to discuss advances in this exciting new field and to promote interinstitutional and interdisciplinary dialogue.

Abstracts

Influence of RNA Silencing on Chromatin Insulator Nuclear Organization
Elissa Lei
NIDDK-NIH

Chromatin insulators promote higher order nuclear organization thereby establishing distinct transcriptional domains. Activity of the Drosophila melanogaster gypsy insulator is decreased when Argonaute genes are mutated, and insulator function is improved when the levels of the Rm62 helicase are reduced. Rm62 interacts physically with the DNA-binding insulator protein CP190 in an RNA-dependent manner. Finally, mutation of Rm62 results in dramatic nuclear reorganization of a compromised insulator. These results suggest a model in which RNAs processed by an RNA silencing pathway promote the ability of gypsy insulator complexes to form nuclear insulator bodies that serve as scaffolds for independent chromatin domains.

A Model for Initiation of Mosaic HOX Gene Expression Patterns by Non-Coding RNAs and Trithorax-Group Proteins in Early Embryos
Alexander Mazo
Thomas Jefferson University

Much of the genome is transcribed into long non-coding RNAs (ncRNAs) of unknown function. We propose that bxd and iab intergenic ncRNAs repress coding HOX genes Ultrabithorax and abdominal-A, respectively, in cis by transcriptional interference. The Trithorax complex TAC1 promotes transcriptional elongation of bxd ncRNAs. Based on these data, we suggest that bxd and iab ncRNAs regulated by the trithorax group of epigenetic regulators have an early transient role in repression of HOX genes at the BX-C. Later, we propose that repression by HOX proteins, and members of the Polycomb group take over from repression by ncRNAs.

Dicer-Related Helicases: Defining Conserved Complexes and New RNAi-Related Pathways
Darryl Conte
University of Massachusetts Medical Center

We have isolated novel alleles of drh-3 in forward genetic screens for RNAi deficient mutants. DRH-3 is essential for viability and functions in RNAi and chromosome segregation. These drh-3 alleles exhibit dominant silencing defects and hallmarks of mutator class mutants, including: temperature-sensitive lethality, high incidence of males, mobilization of transposable elements and desilencing of repetitive transgenes in the germline. We have identified a class of small RNAs that are dependent on DRH-3 but independent of Dicer. Small antisense RNAs corresponding to exon junctions implicate a role for RdRP in their biogenesis. Current work is aimed at not only identifying the RdRP and Argonaute proteins required for these small RNAs but also understanding the function of these small RNAs. Preliminary analyses indicate that these small RNAs are derived from a large fraction of the genome, suggesting that the entire genome may be subject to an RNAi-like process. We hypothesize that the DRH-3 dependent small RNAs may play a role in the formation or maintenance of heterochromatin. Finally, we have found that at least one human DRH homolog interacts with a Dicer complex in mammalian cells, suggesting that this complex is conserved through evolution. The human DRH homologs are involved in the antiviral interferon response, suggesting that these proteins may couple interferon signaling and RNAi in response to viral infection.

Heterochromatin Links to RNA in Mammals
Emily Bernstein
The Rockefeller University

An increasing body of evidence suggests that chromatin structure plays a fundamental role in modulating numerous cellular processes, including transcriptional regulation, chromosome segregation during mito