NucPosDB: a database of nucleosome positioning in vivo and nucleosomics of cell-free DNA

• DOI: 10.1007/s00412-021-00766-9
• Publication Date: 2022-01-21T07:02:52Z
• Authors: Mariya Shtumpf; Kristan V. Piroeva; Shivam P. Agrawal; Divya R. Jacob; Vladimir B. Teif
• Keywords: 570; 0303 health sciences; 03 medical and health sciences; 610; Humans; Original Article; DNA; Chromatin Assembly and Disassembly; Cell-Free Nucleic Acids; Chromatin; Nucleosomes; 3. Good health

Abstract Nucleosome positioning is involved in many gene regulatory processes happening the cell, and it may change as cells differentiate or respond to changing microenvironment a healthy diseased organism. One important implication of nucleosome clinical epigenetics its use “nucleosomics” analysis cell-free DNA (cfDNA) for purpose patient diagnostics liquid biopsies. The rationale this that apoptotic nucleases digest chromatin dying mostly cut between nucleosomes. Thus, short pieces body fluids reflect positions nucleosomes origin. Here, we report systematic nucleosomics database — NucPosDB curating published datasets vivo well sequenced situ Users can select subsets by number criteria then obtain raw processed data. also reports originally determined regions with stable occupancy across several individuals given condition. An additional section provides catalogue computational tools cfDNA experiments theoretical algorithms prediction preferences from sequence. We provide an overview field, describe structure context, demonstrate data variability using examples different medical conditions. useful both fundamental regulation training models based on cfDNA. currently curates ~ 400 publications cell lines > 10,000 patients volunteers. For open-access key MNase-seq human cells, allows downloading mapped addition occupancy. available at https://generegulation.org/nucposdb/ .