UC San Diego

Chromatin organization and accessibility is an important layer for regulating gene expression. We wanted to learn how chromatin changes by exploring either data of cells going through mitosis or cells responding to an acute removal of a key regulator, BRD4.

Nucleosome Depleted Regions (NDRs) are active genomic locations for transcription machinery or other regulatory factors to bind. In mitosis, cells lose higher-order chromatin structure and have drastic reduction in transcription level. We are interested in revealing chromatin structure changes at enhancers during mitosis in terms of NDR patterns of histone marks, especially for enhancers relating to TSSs that were shown to have distinctive NDR patterns previously. We found disappearance of NDRs at all enhancers because of entry of a nucleosome, which has methylated but deacetylated histones. By analyzing data for H3K9ac following the inhibition of HDACs, we confirmed the key involvement of HDACs in maintaining mitotic NDR pattern at enhancers, by observing acetylated histones at enhancer centers with decreasing signal in surrounding regions.

To explore immediate chromatin structure changes after BRD4 removal, we used an inducible degradation system utilizing dTAG molecules to link target proteins to cells’ ubiquitin proteasome machinery. We analyzed ATAC-seq following the dTAG treatment, to identify changes in open chromatin. We found that after 48-hour of degrading BRD4, new chromatin opening/closing sites appear: interestingly, some exposed sites are involved in cell death regulation and increasing cancer incidence. Thus, BRD4 might contribute to maintenance of chromatin structure by keeping regular opening sites exposed for interactions while silencing others.