"The Upstream Sequence Transcription Complex Dictates Nucleosome Positi" by Nancy Sanchez

The Upstream Sequence Transcription Complex Dictates Nucleosome Positioning and Promoter Accessibility at piRNA Genes in the C. elegans Germ Line

Date of Award

Spring 2024

Document Type

Dissertation

Degree Name

Doctor of Philosophy (PhD)

Department

Genetics

First Advisor

Reinke, Valerie

Abstract

The piRNA pathway is a conserved germline-specific small RNA pathway that ensures genomic integrity and continued fertility. In C. elegans and other nematodes, Type-I piRNAs are expressed from >10,000 independently transcribed genes clustered within two discrete domains of 1.5 and 3.5 MB on Chromosome IV. Clustering of piRNA genes contributes to their germline-specific expression, but the underlying mechanisms are unclear, in part because previous genomic studies in C. elegans were performed in whole animals and lacked germline-specific resolution. piRNA expression is promoted by the Upstream Sequence Transcription Complex (USTC) which binds strongly across the piRNA gene cluster and forms distinct subnuclear foci in the germ line. In this dissertation, I observed that the TATA box protein 1 (TBP-1) forms USTC-dependent foci that bind to the piRNA gene cluster. I also analyzed isolated germ nuclei to demonstrate that the piRNA genomic domains are located in a heterochromatin-like environment. USTC promotes strong association of nucleosomes throughout piRNA clusters, yet organizes the local nucleosome environment to direct the exposure of individual piRNA genes to RNA Polymerase II transcription machinery. Localization of USTC to the piRNA domains depends upon the ATPase chromatin remodeler ISW-1, which maintains high nucleosome density across piRNA clusters. Overall, this work provides insight into how chromatin states coordinate transcriptional regulation over large genomic domains, with implications for global genome organization.

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