Identification of a functional network of human epigenetic silencing factors.
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.
Poleshko
Andrey
A
Institute for Cancer Research, Fox Chase Cancer Center, Philadelphia, Pennsylvania 19111, USA.
Einarson
Margret B
MB
Shalginskikh
Natalia
N
Zhang
Rugang
R
Adams
Peter D
PD
Skalka
Anna Marie
AM
Katz
Richard A
RA
D001374:Azacitidine / Q000494:pharmacology; D002469:Cell Separation; D056504:Chromatin Assembly Factor-1 / Q000378:metabolism; D002999:Clone Cells; D003587:Cytomegalovirus / Q000235:genetics; D000090205:DNA Methyltransferase 3A; D055785:Gene Knockdown Techniques; D020868:Gene Silencing / Q000187:drug effects; D017930:Genes, Reporter; D049452:Green Fluorescent Proteins / Q000378:metabolism; D006367:HeLa Cells; D057166:High-Throughput Screening Assays; D006657:Histones / Q000378:metabolism; D006801:Humans; D008957:Models, Genetic; D009687:Nuclear Proteins / Q000378:metabolism*; D011401:Promoter Regions, Genetic / Q000235:genetics; D011499:Protein Processing, Post-Translational / Q000187:drug effects; D034741:RNA, Small Interfering / Q000378:metabolism; D012097:Repressor Proteins / Q000378:metabolism; D015203:Reproducibility of Results; D016196:S Phase / Q000187:drug effects; D014157:Transcription Factors
C489780:CNOT8 protein, human; D056504:Chromatin Assembly Factor-1; C000717967:DNMT3A protein, human; D006657:Histones; D009687:Nuclear Proteins; D034741:RNA, Small Interfering; D012097:Repressor Proteins; D014157:Transcription Factors; D049452:Green Fluorescent Proteins; D000090205:DNA Methyltransferase 3A; D001374:Azacitidine