title: Epigenetic disruption of ribosomal RNA genes and nucleolar architecture in DNA methyltransferase 1 (Dnmt1) deficient cells.
abstract: The nucleolus is the site of ribosome synthesis in the nucleus, whose integrity is essential. Epigenetic mechanisms are thought to regulate the activity of the ribosomal RNA (rRNA) gene copies, which are part of the nucleolus. Here we show that human cells lacking DNA methyltransferase 1 (Dnmt1), but not Dnmt33b, have a loss of DNA methylation and an increase in the acetylation level of lysine 16 histone H4 at the rRNA genes. Interestingly, we observed that SirT1, a NAD+-dependent histone deacetylase with a preference for lysine 16 H4, interacts with Dnmt1; and SirT1 recruitment to the rRNA genes is abrogated in Dnmt1 knockout cells. The DNA methylation and chromatin changes at ribosomal DNA observed are associated with a structurally disorganized nucleolus, which is fragmented into small nuclear masses. Prominent nucleolar proteins, such as Fibrillarin and Ki-67, and the rRNA genes are scattered throughout the nucleus in Dnmt1 deficient cells. These findings suggest a role for Dnmt1 as an epigenetic caretaker for the maintenance of nucleolar structure.
authors.affiliation: Cancer Epigenetics Laboratory, Spanish National Cancer Centre (CNIO), Madrid, Spain.
authors.forename: Jesús
authors.initials: J
authors.lastname: Espada
authors.forename: Esteban
authors.initials: E
authors.lastname: Ballestar
authors.forename: Raffaella
authors.initials: R
authors.lastname: Santoro
authors.forename: Mario F
authors.initials: MF
authors.lastname: Fraga
authors.forename: Ana
authors.initials: A
authors.lastname: Villar-Garea
authors.forename: Attila
authors.initials: A
authors.lastname: Németh
authors.forename: Lidia
authors.initials: L
authors.lastname: Lopez-Serra
authors.forename: Santiago
authors.initials: S
authors.lastname: Ropero
authors.forename: Agustin
authors.initials: A
authors.lastname: Aranda
authors.forename: Helena
authors.initials: H
authors.lastname: Orozco
authors.forename: Vanessa
authors.initials: V
authors.lastname: Moreno
authors.forename: Angeles
authors.initials: A
authors.lastname: Juarranz
authors.forename: Juan Carlos
authors.initials: JC
authors.lastname: Stockert
authors.forename: Gernot
authors.initials: G
authors.lastname: Längst
authors.forename: Ingrid
authors.initials: I
authors.lastname: Grummt
authors.forename: Wendy
authors.initials: W
authors.lastname: Bickmore
authors.forename: Manel
authors.initials: M
authors.lastname: Esteller
mesh_terms: D045744:Cell Line, Tumor; D002466:Cell Nucleolus / Q000235:genetics / Q000648:ultrastructure*; D000076123:DNA (Cytosine-5-)-Methyltransferase 1; D004248:DNA (Cytosine-5-)-Methyltransferases / Q000235:genetics / Q000502:physiology*; D019175:DNA Methylation; D004275:DNA, Ribosomal / Q000378:metabolism*; D044127:Epigenesis, Genetic; D017353:Gene Deletion; D020459:Genes, rRNA; D006657:Histones / Q000378:metabolism; D006801:Humans; D056564:Sirtuin 1; D037761:Sirtuins / Q000378:metabolism; D014158:Transcription, Genetic
chemical_list: D004275:DNA, Ribosomal; D006657:Histones; D000076123:DNA (Cytosine-5-)-Methyltransferase 1; D004248:DNA (Cytosine-5-)-Methyltransferases; C000619380:DNMT1 protein, human; C447939:SIRT1 protein, human; D056564:Sirtuin 1; D037761:Sirtuins