The Upstream Sequence Transcription Complex Dictates Nucleosome Positioning and Promoter Accessibility at piRNA Genes in the C. elegans germ line [ATAC-Seq]

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 piRNA precursor transcripts are expressed from >10,000 small, independently regulated genes clustered within two discrete domains of 1.5 and 3.5 MB on Chromosome IV. These large domains likely play a significant role in promoting germline-specific expression of piRNAs, but the underlying mechanisms are unclear. By examining the chromatin environment specifically in isolated germ nuclei, we demonstrate that piRNA clusters are located in closed chromatin, and confirm the enrichment for the inactive histone modification H3K27me3. The piRNA biogenesis factor USTC (Upstream Sequence Transcription Complex) plays two roles – it promotes a strong association of nucleosomes throughout the domain, and it organizes the local nucleosome environment to direct the exposure of individual piRNA genes. Overall, this work reveals new insight into how chromatin state coordinates transcriptional regulation over large genomic domains, which has implications for understanding global genome organization in the germ line. Assay for Transposase-Accessible Chromatin using sequencing (ATAC-seq) of isolated germline nuclei off wild-type and prde-1(mj207)V in C. elegans.

piRNA通路（piRNA pathway）是一类保守的生殖系特异性小RNA通路，负责维持基因组完整性并保障生殖能力的持续维持。在秀丽隐杆线虫（C. elegans）及其他线虫物种中，I型piRNA前体转录本由超过10000个小型独立调控基因转录产生，这些基因簇定位于四号染色体上两个分别为1.5 Mb和3.5 Mb的离散结构域内。这类大型结构域或在促进piRNA的生殖系特异性表达中发挥关键作用，但其潜在分子机制尚未阐明。本研究通过专门分析分离得到的生殖细胞核内的染色质环境，证实piRNA簇位于封闭染色质区域，并验证了非活性组蛋白修饰H3K27me3的富集现象。piRNA生成因子USTC（上游序列转录复合物，Upstream Sequence Transcription Complex）兼具双重功能：一方面可促进该结构域内核小体的紧密结合，另一方面可调控局部核小体环境以暴露单个piRNA基因。总体而言，本研究揭示了染色质状态如何协调大型基因组结构域的转录调控，这为理解生殖系中的全局基因组组织提供了新的研究视角。本数据集包含针对秀丽隐杆线虫野生型及prde-1(mj207)V突变体的分离生殖细胞核开展的转座酶可及性测序（Assay for Transposase-Accessible Chromatin using sequencing，ATAC-seq）分析数据。