SUMMARY
A defined amount of transcript is produced from the transcription start site (TSS) of each gene, suggesting that the binding frequency of RNA polymerase varies among genes. However, what structural feature of the genome controls this frequency remains elusive. We established a method to fractionate chromatin according to its degree of compaction. Histone H3 was evenly detected in open and compact chromatin, but histone H1 was enriched in compact chromatin. Similarly, HP1α and MBD2b were more abundant in compact chromatin, but the levels of tri-methylated H3 (lysine 9) and 5-methyl cytosine subtly increased. Via a genome-wide analysis, nearly the entire genome was found to exist in compact chromatin with no variations between repeat and non-repeat sequences; however, active TSSs were rarely found in compact chromatin. Based on a correlation between weak compaction and RNA polymerase binding at TSSs, it appears that the local state of chromatin compaction establishes transcription levels.
