Investigating the Role of TFIIIC Binding Sites in the Caenorhabditis elegans Genome

Abstract

Gene regulation is crucial to the development of multicellular organisms. How the genome is physically organized within the nucleus can a ect gene regulation, but the genomic el- ements and proteins that coordinate genome organization remain elusive. Transcription Factor IIIC (TFIIIC) is a component of the RNA Polymerase III (Pol III) transcriptional machinery that has been implicated in genome organization in several organisms. In this study, we investigate whether TFIIIC has a function in genome organization in the nema- tode Caenorhabditis elegans (C. elegans). Publicly available chromatin immunoprecipita- tion followed by high-throughput sequencing (ChIP-seq) data for two TFIIIC components in mixed-staged embryos and Pol III from mixed-staged embryos, third stage larvae (L3), and young adults of C. elegans were analyzed using a newly-de ned data processing pipeline that yields high-con dence classi cations of TFIIIC-bound sites based on Pol III co-occupancy. Analysis revealed two distinct classes of TFIIIC binding sites: TFIIIC binding sites that are occupied by Pol III (Pol III(+) sites; 748 sites) and those that lack Pol III binding (Pol III(􀀀) sites; 210 sites). The Pol III(􀀀) class constitutes approximately 20% of all TFIIIC binding sites in the genome, and the sites in this class appear to be unrelated to Pol III tran- scription. We identi ed a number of previously uncharacterized DNA sequence motifs that form a pattern characteristic of Pol III(􀀀) sites. We do not observe changes in nucleosome patterning or histone modi cations that characterize Pol III(􀀀) binding sites. A subclass of Pol III-lacking TFIIIC binding sites that were distinguished by being clustered in close proximity. Our ndings suggest that Pol III binding sites that gain Pol III occupancy in later developmental stages occur near Pol III(􀀀) TFIIIC binding sites. Overall, Pol III(􀀀) sites occur exclusively in the autosomes and are located near the pairing centers, genomic sites that initiate chromosome pairing during meiosis. Taken together, this study uncovered DNA sequence characteristics and chromosomal localization of Pol III(􀀀) TFIIIC binding sites and proposed their potential roles in nearby Pol III gene regulation and meiotic homolog pairing.