Abstract
Epigenetic silencing is mediated by families of factors that place, remove, read, and transmit repressive histone and DNA methylation marks on chromatin. How the roles for these functionally diverse factors are specified and integrated is the subject of intense study. To address these questions, HeLa cells harboring epigenetically silent green fluorescent protein reporter genes were interrogated with a small interference RNA library targeting 200 predicted epigenetic regulators, including potential activators, silencers, chromatin remodelers, and ancillary factors. Using this approach, individual, or combinatorial requirements for specific epigenetic silencing factors could be detected by measuring green fluorescent protein reactivation after small interference RNA-based factor knockdown. In our analyses, we identified a specific subset of 15 epigenetic factors that are candidates for participation in a functional epigenetic silencing network in human cells. These factors include histone deacetylase 1, de novo DNA methyltransferase 3A, components of the polycomb PRC1 complex (RING1 and HPH2), and the histone lysine methyltransferases KMT1E and KMT5C. Roles were also detected for two TRIM protein family members, the cohesin component Rad21, and the histone chaperone CHAF1A (CAF-1 p150). Remarkably, combinatorial knockdown of factors was not required for reactivation, indicating little functional redundancy. Consistent with this interpretation, knockdown of either KMT1E or CHAF1A resulted in a loss of multiple histone-repressive marks and concomitant gain of activation marks on the promoter during reactivation. These results reveal how functionally diverse factors may cooperate to maintain gene silencing during normal development or in disease. Furthermore, the findings suggest an avenue for discovery of new targets for epigenetic therapies.
Highlights
422 JOURNAL OF BIOLOGICAL CHEMISTRY that drive development and maintain cellular identity
The prominent epigenetic regulatory marks on eukaryotic chromatin are histone modifications and DNA cytosine methylation (5meCpG), which are placed by enzyme complexes containing members of the histone modifying and DNA methyltransferase (DNMT)4 families, respectively
Upon removal of the HDAC inhibitors (HDACi), expression of GFP became re-silenced and remained silenced during long term cell passage. Using this GFP-silent cell population, we found that siRNA-mediated knockdown of several factors among a candidate set promoted GFP reactivation (e.g. HDAC1) [23]
Summary
Both HDAC- and DNMT-based epigenetic silencing can sometimes be reversed by chemical inhibitors (9 –15). Silencing of viral genomes by epigenetic mechanisms can contribute to pathogenesis by promoting a latent viral state [17] In both cases, reversal of epigenetic silencing by inhibitors (e.g. HDACi) may provide therapeutic benefits (9 –15). A variety of combinatorial, temporal, dynamic, and context-dependent histone modifications have been described (2–5, 7, 18 –21) In view of these vast complexities, we have implemented a functional assay to identify silencing factor repertoires. This strategy has uncovered an epigenetic network in human cells and provides a general method for the identification of factors that may serve as targets for epigenetic therapies
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