Talk abstracts
Talk on Saturday 08:45-09:00am submitted by Rajendra K c
Data-driven maps of RNA polymerase III transcription and macromolecular interactions identifies new gene targets and regulatory mechanisms
Rajendra KC (Center of Biophysics and Quantitative Biology, University of Illinois Urbana-Champaign, Urbana, IL 61801, USA), Ruiying Cheng (Cell Developmental Biology, University of Illinois Urbana-Champaign, Urbana, IL 61801, USA), Sihang Zhou (Cell Developmental Biology, University of Illinois Urbana-Champaign, Urbana, IL 61801, USA), Simon Lizarazo (Department of Molecular and Integrative Physiology, University of Illinois Urbana-Champaign, Urbana, IL 61801, USA), Duncan Smith (Department of Biology, New York University, New York, NY), Kevin Van Bortle (Cell Developmental Biology, University of Illinois Urbana-Champaign, Urbana, IL 61801, USA)
Abstract:
RNA polymerase III (Pol III) is responsible for transcribing a diverse array of small non-coding RNAs (ncRNAs), including tRNA, 5S rRNA, 7SL, BC200, and others. Pol III also exhibits dynamic activity across various tissues and cancer cells. Despite its crucial role, our understanding of the full spectrum of Pol III transcription and the mechanisms underlying its context-specific activities remains limited, highlighting the need for a comprehensive study of Pol III transcription and its macromolecular interactions. Recent findings have revealed Pol III's involvement in miRNA transcription and its co-transcription with Pol II of certain ncRNAs (e.g., RPPH1, U6, 7SK), adding complexity to the Pol III transcriptome. This underscores the necessity for a meta-study integrating Pol III activity with other RNA polymerases, a challenge compounded by limited genomics data. To address this, we developed a unified framework for quantifying polymerase occupancy using ChIP-seq data across various tissues and conditions. By intersecting this occupancy map with a comprehensive multi-class promoter set—including protein-coding genes (PCGs), non-coding genes, and repetitive elements— we identified widespread Pol III occupancy across thousands of PCGs. Our innovative quantification of Pol III termination using the T4score revealed the production of small nascent RNA transcripts at these PCGs, ending with a run of four thymidines. Additionally, we discovered hundreds of unannotated genomic regions exhibiting high Pol III activity and sensitivity to SSB knockdown, many of which may represent potential new Pol III target genes. In parallel, limited proteomics data have constrained efforts to elucidate Pol III's macromolecular interaction partners. To overcome this, we constructed an extensive protein-protein interaction (PPI) network from the BIOGRID database, modeled as an electrical circuit network. By applying effective conductance as a measure of protein proximity, we identified several new Pol III interaction partners, uncovering additional potential regulatory roles for Pol III.
Keywords: metamap, RNA, polymerase