Epigenetic disruption of ribosomal RNA genes and nucleolar architecture in DNA methyltransferase 1 (Dnmt1) deficient cells.
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.
Espada
Jesús
J
Cancer Epigenetics Laboratory, Spanish National Cancer Centre (CNIO), Madrid, Spain.
Ballestar
Esteban
E
Santoro
Raffaella
R
Fraga
Mario F
MF
Villar-Garea
Ana
A
Németh
Attila
A
Lopez-Serra
Lidia
L
Ropero
Santiago
S
Aranda
Agustin
A
Orozco
Helena
H
Moreno
Vanessa
V
Juarranz
Angeles
A
Stockert
Juan Carlos
JC
Längst
Gernot
G
Grummt
Ingrid
I
Bickmore
Wendy
W
Esteller
Manel
M
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
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