BEND3 represses rDNA transcription by stabilizing a NoRC component via USP21 deubiquitinase

Abstract

Ribosome biogenesis dictates the translational capacity of cells. Several mechanisms establish and maintain transcriptional output from eukaryotic ribosomal DNA (rDNA) loci. rDNA silencing is one such mechanism that ensures the inactivity and hence the maintenance of a silenced state of a subset of rRNA gene copies. Whereas oncogenic agents stimulate rRNA gene transcription, tumor suppressors decrease rRNA gene transcription. We demonstrate in mammalian cells that BANP, E5R, and Nac1 (BEN) domain 3 (BEND3), a quadruple BEN domain-containing protein, localizes in nucleoli and binds to ribosomal RNA gene promoters to help repress rRNA genes. Loss of BEND3 increases histone H3K4 trimethylation and, correspondingly, decreases rDNA promoter DNA methylation, consistent with a role for BEND3 in rDNA silencing. BEND3 associates with the nucleolar-remodeling complex (NoRC), and SUMOylated BEND3 stabilizes NoRC component TTF-1-interacting protein 5 via association with ubiquitin specific protease 21 (USP21) debiquitinase. Our results provide mechanistic insights into how the novel rDNA transcription repressor BEND3 acts together with NoRC to actively coordinate the establishment of rDNA silencing.

BEND3 mediates transcriptional repression and heterochromatin organization

“…In our recent work, we show that SUMOylation of BEND3 is important for the stability of NoRC. 8 We find that Tip5 undergoes ubiquitin-mediated degradation in the presence of a BEND3 sumo double mutant (BEND3-SDM) but not in the presence of the wild type protein (BEND3-WT). Tip5 is deubiquitinated in the presence of BEND3-WT, thereby stabilizing and preventing its degradation.…”

“…27 BEN domain has been shown to posses sequence specific DNA binding activity 28,29 and, indeed, we have also shown that BEND3 can directly bind to DNA as well. 8 Apart from BEND3, the only other BEN domain-containing protein in mammals studied so far is BEND6 which is a BEN-solo domain protein involved in Notch signaling. 29 We have shown that BEND3, a quadruple BEN domain-containing protein, plays an important role in rDNA silencing.…”

“…1A). 8 Note the bright BEND3 foci (green) represent the BEND3 localizing to the rDNA (Fig. 1A) A recent study identified BEND3 to be associated with telomeres and showed that BEND3 colocalizes with telomeric repeat binding factor 2 (TRF2), a marker for telomeres.…”

“…In our recent work, we have shown that BEND3 is a novel interactor of the NoRC. 8 The role of NoRC in rDNA silencing is well documented. 9,10,22 Overexpression of BEND3 phenocopies most of the Tip5 gain-of-function phenotypes observed with regard to epigenetic changes at the rDNA locus.…”

The S-phase-induced lncRNA SUNO1 promotes cell proliferation by controlling YAP1/Hippo signaling pathway

“…Similarly, 5 µg of IgG was used to pull 50 µg of cross-linked and sheared chromatin as a control. Pol II ChIP was performed as reported earlier ( Khan et al, 2015 ). Briefly, cells were fixed using freshly prepared 1% Formaldehyde solution for ten minutes at room temperature followed by quenching with 0.125 M Glycine solution.…”