Dissecting the control of transcription elongation

The National Institute of General Medical Sciences awarded President and Fellows of Harvard College $165,279 on August 1, 2026, under the Biomedical Research and Research Training program (CFDA 93.859) to support research dissecting the control of transcription elongation by RNA polymerase II and coordinated messenger RNA processing in gene expression regulation.

The research investigates how promoter-proximal pausing and release of RNA polymerase II (RNAPII) control metazoan gene expression, with focus on the pause-inducing factors NELF and DSIF, the kinase P-TEFB that triggers pause release, and the integrator complex that drives promoter-proximal termination through endonuclease-mediated cleavage and phosphatase-dependent phosphorylation removal. The work also examines obstacles to elongation across gene bodies, particularly in long genes with expansive first introns, and the interplay between transcription and RNA splicing factors required for full-length messenger RNA synthesis and prevention of aberrant transcripts that trigger immune responses or deleterious protein translation.

Harvard Medical School, operating through President and Fellows of Harvard College's Office of Research Administration, is the recipient. The award funds research performed in Boston, Massachusetts, with a period of performance from August 1, 2026, through May 31, 2031. The assistance type is a Project Grant.

Abstract

Precise control of gene expression in response to external signals is essential for organismal development, growth, and homeostasis. Accordingly, gene activity is regulated at multiple steps, with tight control over transcription elongation by RNA polymerase II (rnapii) and the coordinated processing of messenger RNA (mrna). A critical step in metazoan gene control involves the promoter-proximal pausing of rnapii and its release into gene bodies. Association of the pause-inducing factors nelf and dsif with the early elongation complex stabilize rnapii while awaiting the signal for pause release. Pause release is triggered by the kinase p-tefb, which phosphorylates rnapii and dsif to dissociate nelf and promote productive elongation. However, paused rnapii can experience an alternate fate: IT can be targeted by the integrator complex (INT), a multi-subunit termination machine. INT drives promoter-proximal termination, with rnapii releasing a short, unstable RNA. Importantly, we found that INT facilitates termination using two distinct catalytic activities: endonuclease-mediated cleavage of the nascent RNA and phosphatase-dependent removal of stimulatory phosphorylation. In this way, INT prevents spurious transcription and can potently attenuate the expression of select mrnas. Indeed, the loss of INT causes rapid upregulation of a repertoire of stress- and signal responsive genes. Notably, rnapii faces further obstacles to elongation across gene bodies. We and others have shown that long genes, especially those with expansive first introns, pose challenges for the transcription machinery, and that a precise interplay between transcription and RNA splicing factors is required for full-length mrna synthesis. Premature termination within introns produces aberrant transcripts whose export to the cytoplasm can trigger anti-viral immune responses or lead to the translation of deleterious proteins. As such, defects in rnapii elongation and RNA processing have emerged as key contributors to disease, including inflammatory and neurological disorders and cancer. Over the next five years, my lab will systematically dissect the CIS-acting sequences and trans-acting proteins that determine the fate of the elongating rnapii and nascent RNA, leveraging synergistic cell-free and cell-based systems. We will define the molecular mechanisms and interfaces that control productive elongation and address central questions about how INT activity is regulated. Given the established role of INT in attenuating stress-responsive genes during normal cell growth, we will determine how stress signaling can activate these genes, and how INT deficiency perturbs stress responses. We will build on our finding that association of the U1 small nuclear RNP (snrnp) with rnapii at 5' splice sites is a primary determinant of rnapii processivity, to investigate the mechanisms underlying this activity. Our studies will provide insights into the crosstalk between transcription and RNA processing machines, to illuminate how cells ensure the formation of mature mrna species, while rapidly terminating spurious transcription.