title: Human factors and pathways essential for mediating epigenetic gene silencing.
abstract: Cellular identity in both normal and disease processes is determined by programmed epigenetic activation or silencing of specific gene subsets. Here, we have used human cells harboring epigenetically silent GFP-reporter genes to perform a genome-wide siRNA knockdown screen for the identification of cellular factors that are required to maintain epigenetic gene silencing. This unbiased screen interrogated 21,121 genes, and we identified and validated a set of 128 protein factors. This set showed enrichment for functional categories, and protein-protein interactions. Among this set were known epigenetic silencing factors, factors with no previously identified role in epigenetic gene silencing, as well as unstudied factors. The set included non-nuclear factors, for example, components of the integrin-adhesome. A key finding was that the E1 and E2 enzymes of the small ubiquitin-like modifier (SUMO) pathway (SAE1, SAE2/UBA2, UBC9/UBE2I) are essential for maintenance of epigenetic silencing. This work provides the first genome-wide functional view of human factors that mediate epigenetic gene silencing. The screen output identifies novel epigenetic factors, networks, and mechanisms, and provides a set of candidate targets for epigenetic therapy and cellular reprogramming.
authors.affiliation: Fox Chase Cancer Center; Philadelphia, PA USA.
authors.forename: Andrey
authors.initials: A
authors.lastname: Poleshko
authors.affiliation: Center for Systems and Computational Biology; The Wistar Institute; Philadelphia, PA USA.
authors.forename: Andrew V
authors.initials: AV
authors.lastname: Kossenkov
authors.affiliation: Fox Chase Cancer Center; Philadelphia, PA USA.
authors.forename: Natalia
authors.initials: N
authors.lastname: Shalginskikh
authors.affiliation: Fox Chase Cancer Center; Philadelphia, PA USA.
authors.forename: Anna
authors.initials: A
authors.lastname: Pecherskaya
authors.affiliation: Fox Chase Cancer Center; Philadelphia, PA USA.
authors.forename: Margret B
authors.initials: MB
authors.lastname: Einarson
authors.affiliation: Fox Chase Cancer Center; Philadelphia, PA USA.
authors.forename: Anna
authors.initials: A
authors.lastname: Marie Skalka
authors.affiliation: Fox Chase Cancer Center; Philadelphia, PA USA.
authors.forename: Richard A
authors.initials: RA
authors.lastname: Katz
mesh_terms: D044127:Epigenesis, Genetic; D020868:Gene Silencing; D017930:Genes, Reporter; D049452:Green Fluorescent Proteins / Q000235:genetics / Q000378:metabolism; D006367:HeLa Cells; D006801:Humans; D011506:Proteins / Q000235:genetics / Q000378:metabolism*; D034741:RNA, Small Interfering / Q000235:genetics; D025842:SUMO-1 Protein / Q000235:genetics / Q000378:metabolism; D015398:Signal Transduction
chemical_list: D011506:Proteins; D034741:RNA, Small Interfering; D025842:SUMO-1 Protein; D049452:Green Fluorescent Proteins
keywords: SUMO pathway; epigenetic therapy; epigenetics; gene silencing; integrins; siRNA screen