Chromatin-seq

Chromosomal DNA can be digested in vivo with exogenously-added nuclease enzymes such as micrococcal nuclease (MNase). MNase will digest protein-free regions of DNA in chromosomes whilst leaving intact those sequences associated with chromatin proteins such as nucleosomes. These nuclease-protected DNAs can then be purified and subjected to Illumina sequencing (so-called chromatin-seq/MNase-seq). By mapping the resulting sequence reads back to the original genome it is possible to infer the positions and structure of chromatin proteins with the aim of understanding gene regulation and chromosome structure.

Over the last year, the GRH has successfully generated high-quality chromatin-seq/MNase-seq datasets for a variety of non-mammalian model organisms. In addition to sequencing, we offer automated NeoPrep Nano library prep for nucleosome mapping samples, or manual libary preps for mapping both nucleosome and transcription factor complexes. Both workflows are custom GRH methods and benefit from the expertise of the Hub Academic Lead's laboratory. In addition to delivering high-quality chromatin-seq datasets the GRH can also advise on chromatin digestion methods, and offer bioinformatic analysis pipelines for subsequent data processing. We are currently trialling ATAC-seq protocols for the analysis of chromatin structure in higher eukaryotic systems such as human cells.