Next Generation Sequencing Facilitates Quantitative Analysis of chromatin interaction of lncRNA Gm4665 with regulatory region of target genes in male germ cells.

Purpose: The goals of this study are to examine the possibility that Gm4665 binds to regulatory region of target genes loci in male germ cells. Methods: we performed the Chromatin Isolation by RNA Purification (ChIRP) assay to examine the possibility that Gm4665 binds to regulatory region of target genes. Germ cell isolated from the testis of wild-type mouse were cross-linked, lysed and sonicated, and then incubated with probesets of Gm4665. Following hybridization of biotinylated probesets to Gm4665 transcript, Gm4665-bound chromatin was retrieved. The purified DNA fragments were sequenced using high throughput next generation sequencing (Illumina HiseqXten-PE150) Results: Analysis of the retrieved chromatin fragments by deep sequencing (ChIRP-seq) revealed Gm4665 occupancy sites were genome wide, specifically abundant enrich in intronic regions. Additionally, nearly 30% of chromatin fragments were enriched in the promoter regions of gene loci Overall design: Examination of chromatin interaction of lncRNA Gm4665 with regulatory region of target genes in male germ cells