Description:

The Simpson Querrey Institute for Epigenetics presents:

Kevin Struhl, PhD

David Wesley Gaiser Professor
Department of Biological Chemistry and Molecular Pharmacology
Harvard Medical School

"Non-Canonical Enhancer Functions and Links between Chromatin, Transcriptional Elongation, Polyadenylation, and mRNA Stability"

Abstract:

Enhancers contain multiple binding sites for activator proteins that stimulate transcription by RNA polymerase II in response to environmental and developmental signals. By virtue of their unique ability to generate nucleosome-depleted regions in a highly regulated manner, enhancers are the key regulators of other DNA-based processes. Enhancers regulate cell-type-specific transcription of tRNA genes by RNA polymerase III. They are also responsible for binding of the ORC complex to DNA replication origins, thereby regulating origin utilization, replication timing, and replication-dependent chromosome breaks. Additionally, enhancers regulate V(D)J recombination by increasing access of the RAG recombinase to target sites and by generating non-coding enhancer RNAs and localized regions of tri-methylated histone H3-K4 recognized by the RAG2 PHD domain. Thus, enhancers represent the first step in decoding the genome, and hence they regulate biological processes that, unlike Pol II transcription, do not have dedicated regulatory proteins.

The Pol II elongation rate influences poly(A) site selection, with slow and fast Pol II derivatives causing upstream and downstream shifts, respectively, in poly(A) site utilization. These shifts in poly(A) profiles occur continuously from one isoform to the next, even when isoforms are separated by a single nucleotide. This indicates that the cleavage/polyadenylation and Pol II elongation complexes are physically, coupled, strongly suggesting that polyadenylation occurs rapidly upon emergence of the nascent RNA from the Pol II elongation complex. Depletion of either of the histone chaperones FACT or Spt6 decrease the Pol II elongation rate and cause upstream-shifted poly(A) site profiles. In contrast, depletion of histone H3 or H4 causes a downstream shift of poly(A) sites, indicating that nucleosomes inhibit the Pol II elongation rate in vivo. Thus, chromatin-based control of the Pol II elongation rate is a potential mechanism, distinct from direct effects on the cleavage/polyadenylation machinery, to regulate alternative polyadenylation in response to genetic or environmental changes.

In yeast, near-identical 3’ mRNA isoforms can possess dramatically different structures throughout the 3’UTR, often due to trans-acting factors. Sequences responsible for isoformspecific structures, differential association with the poly(A)-binding protein, and mRNA stability are evolutionarily conserved, indicating biological function. A compensatory mechanism between polyadenylation and mRNA turnover regulates steady-state mRNA levels. During polyadenylation in the nucleus, mRNA isoforms may be marked in a manner (perhaps poly(A) tail length) that persists upon translocation to the cytoplasm to affect mRNA degradation.