Chromatin structure-dependent histone incorporation revealed by a genome-wide deposition assay

Abstract

In eukaryotes, histone variant distribution within the genome is the key epigenetic feature. To understand how each histone variant is targeted to the genome, we developed a new method, the RhIP (Reconstituted histone complex Incorporation into chromatin of Permeabilized cell) assay, in which epitope-tagged histone complexes are introduced into permeabilized cells and incorporated into their chromatin. Using this method, we found that H3.1 and H3.3 were incorporated into chromatin in replication-dependent and -independent manners, respectively. We further found that the incorporation of histones H2A and H2A.Z mainly occurred at less condensed chromatin (open), suggesting that condensed chromatin (closed) is a barrier for histone incorporation. To overcome this barrier, H2A, but not H2A.Z, uses a replication-coupled deposition mechanism. Our study revealed that the combination of chromatin structure and DNA replication dictates the differential histone deposition to maintain the epigenetic chromatin states.

Comparison of the Amyloid Plaque Proteome in Down Syndrome, Early-Onset Alzheimer’s Disease and Late-Onset Alzheimer’s Disease

“…Moreover, proteins linked to chromatin structure were consistently altered in non-plaque tissue in all groups studied, most prominently in LOAD and EOAD. Our observations align with previous research suggesting structural changes in chromatin accessibility and consequent altered gene expression in AD (115)(116)(117)(118). Studies using murine models of DS and trisomy 21 iPSCs have elucidated reduced global transcription activity and changes resembling those observed in senescent cells such as 'chromosomal introversion', disruption of the nuclear lamina, and altered chromatin accessibility (119,120).…”

Expansion microscopy of neutrophil nuclear structure and extracellular traps

“…Although chromatin and histone H1 or NPM1 are located together in the nucleus, their distribution is not identical ( Figs. 3 , A and B , 7 , S11 , and S12 ), which is in line with previously published literature ( 46 , 47 ). These differences were suitably imaged by expansion microscopy, where conventional microscopy with nonexpanded cells failed to show differences.…”

Expansion microscopy of nuclear structure and dynamics in neutrophils

“…Expansion microscopy significantly lowered the Pearson’s coefficient, as shown by Mann-Whitney U tests in Figure 4. Although chromatin and histone H1 or NPM1 are located together in the nucleus, their distribution is not identical (Figures 3A, 3B, and 7), which is in line with previously published literature 46,47 . These differences were suitably imaged by expansion microscopy, where conventional microscopy with non-expanded cells failed to show differences.…”