Higher organisms have evolved sophisticated mechanisms to regulate gene transcription by RNA polymerse II (Pol II) in response to a variety of developmental, environmental, and nutritional cues. Improper transcription regulation can lead to developmental defects and disease states. Our past studies of Drosophila melanogaster heat shock (HS) genes revealed that promoter-proximal pausing during early elongation was a rate-limiting and regulated step in transcription, but this stood in contrast to the canonical model of regulation at recruitment of the preinitiation complex (PIC). However, recent genome-wide studies in metazoans revealed a large fraction of gene regulation occurs after PIC formation during early elongation providing a paradigm shift. In this proposal, I focus our efforts on understanding the mechanisms underlying promoter-proximal pausing and regulated escape into productive elongation. Our overall approach is to examine Pol II pausing and regulated escape at very high resolution in vivo under normal conditions and after specifically disrupting promoters, transcription factors (TFs) or TF interactions.
In Aim 1, we employ a novel nuclear run-on method, called Precision GRO-seq (PRO-seq), to obtain high spatial (base pair) and temporal (minute) resolution data that quantitatively tracks Pol II pausing and its regulated escape into productive elongation in Drosophila during a time course of transcription activation. These genome-wide data will be used to refine existing, and generate new, hypotheses for the mechanisms that contribute to regulation.
In Aim 2, the roles of DNA sequences, specific TFs, and nucleosomes in regulation will be tested by applying disruption or inhibition strategies and evaluating changes in transcription and TF interactions at gene promoters in vivo using PRO-seq and other high resolution biochemical methods (e.g., ChIP-exo) and optical sectioning of live polytene nuclei. In addition to standard mutant and RNAi strategies, we will use well-defined drugs to specifically inhibit steps in initiation or pause escape, and also make use of a novel inhibitory RNA aptamer technology, expressing high affinity aptamers against key TFs to bind and inhibit their macromolecular interactions.
In Aim 3, we will again use PRO-seq and other genome-wide, high-resolution, methods to examine the effects of targeted perturbations by directing TALE- hybrids (engineered DNA binding domains fused to TFs or TF domains) to endogenous genes. Finally, because Aims 1-3 focus on the efficient and economical Drosophila systems, Aim 4 tests key hypotheses, which were developed and tested in Drosophila, in human tier1 ENCODE lines and mouse embryonic stem cells.

Public Health Relevance

The proper execution of gene regulatory programs is critical for human health and well-being;incorrect execution of these programs can lead to development defects and disease states, and infectious agents can usurp these regulatory mechanisms at the expense of the host. Therefore, a broad goal of this research is to understand basic gene regulatory mechanisms at the level of gene transcription into RNA during both normal and perturbed states. Such an understanding will provide critical information for making precise diagnoses, developing highly specific therapies, and obtaining optimal patient outcomes in the emergent field of medical genomics.

National Institute of Health (NIH)
National Institute of General Medical Sciences (NIGMS)
Research Project (R01)
Project #
Application #
Study Section
Molecular Genetics A Study Section (MGA)
Program Officer
Sledjeski, Darren D
Project Start
Project End
Budget Start
Budget End
Support Year
Fiscal Year
Total Cost
Indirect Cost
Cornell University
Schools of Arts and Sciences
United States
Zip Code
Booth, Gregory T; Parua, Pabitra K; Sansó, Miriam et al. (2018) Cdk9 regulates a promoter-proximal checkpoint to modulate RNA polymerase II elongation rate in fission yeast. Nat Commun 9:543
Tome, Jacob M; Tippens, Nathaniel D; Lis, John T (2018) Single-molecule nascent RNA sequencing identifies regulatory domain architecture at promoters and enhancers. Nat Genet 50:1533-1541
Chu, Tinyi; Rice, Edward J; Booth, Gregory T et al. (2018) Chromatin run-on and sequencing maps the transcriptional regulatory landscape of glioblastoma multiforme. Nat Genet 50:1553-1564
Vihervaara, Anniina; Duarte, Fabiana M; Lis, John T (2018) Molecular mechanisms driving transcriptional stress responses. Nat Rev Genet 19:385-397
Parua, Pabitra K; Booth, Gregory T; Sansó, Miriam et al. (2018) A Cdk9-PP1 switch regulates the elongation-termination transition of RNA polymerase II. Nature 558:460-464
Mahat, Dig B; Lis, John T (2017) Use of conditioned media is critical for studies of regulation in response to rapid heat shock. Cell Stress Chaperones 22:155-162
Boija, Ann; Mahat, Dig Bijay; Zare, Aman et al. (2017) CBP Regulates Recruitment and Release of Promoter-Proximal RNA Polymerase II. Mol Cell 68:491-503.e5
Vihervaara, Anniina; Mahat, Dig Bijay; Guertin, Michael J et al. (2017) Transcriptional response to stress is pre-wired by promoter and enhancer architecture. Nat Commun 8:255
Watters, Kyle E; Strobel, Eric J; Yu, Angela M et al. (2016) Cotranscriptional folding of a riboswitch at nucleotide resolution. Nat Struct Mol Biol 23:1124-1131
Booth, Gregory T; Wang, Isabel X; Cheung, Vivian G et al. (2016) Divergence of a conserved elongation factor and transcription regulation in budding and fission yeast. Genome Res 26:799-811

Showing the most recent 10 out of 132 publications