A Nucleosome Destabilizing Factor that Facilitates Transcription in Chromatin

Our understanding of transcription by RNA polymerase II (Pol II) is limited by our knowledge of the factors that mediate this critically important process. Here we describe the identification of NDF, a nucleosome destabilizing factor that facilitates Pol II transcription in chromatin. NDF has a PWWP motif, interacts with nucleosomes near the dyad, destabilizes nucleosomes in an ATP-independent manner, and facilitates transcription by Pol II through nucleosomes in a purified and defined transcription system as well as in cell nuclei. Upon transcriptional induction, NDF is recruited to the transcribed regions of thousands of genes and co-localizes with a subset of H3K36me3-enriched regions. Notably, the recruitment of NDF to gene bodies is accompanied by an increase in the transcript levels of many of the NDF-enriched genes. In addition, the global loss of NDF results in a decrease in the RNA levels of many genes. In humans, NDF is present at high levels in all tested tissue types, is essential in stem cells, and is frequently overexpressed in breast cancer. These findings indicate that NDF is a nucleosome destabilizing factor that is recruited to gene bodies during transcriptional activation and facilitates Pol II transcription through nucleosomes. Overall design: ChIP-seq analysis of NDF and H3K36me3 in HeLa S3 (WT) and NDF CRISPR-knockout (KO) cells; ChIP-seq of NDF and H3K36me3 in mouse primary bone marrow-derived macrophages (BMDM) treated with Kdo2-Lipid A (KLA) for 0 h or 6 h; RNA-seq of HeLa WT and KO cells; RNA-seq of mouse BMDMs treated with KLA for 0h or 6 h; GRO-seq analysis of WT and NDF KO cells. Please note that the 'diffNDF7regions_F8_6hKLA_vs_notx.*' files (available on Series records) are generated from both BMDM_ChIP_NDF7_0hKLA and BMDM_ChIP_NDF7_6hKLA samples.