A capped Tudor domain within a core subunit of the Sin3L/Rpd3L histone deacetylase complex binds to nucleic acid G-quadruplexes

Abstract

Chromatin-modifying complexes containing histone deacetylase (HDAC) activities play critical roles in the regulation of gene transcription in eukaryotes. These complexes are thought to lack intrinsic DNA-binding activity, but according to a well-established paradigm, they are recruited via protein–protein interactions by gene-specific transcription factors and posttranslational histone modifications to their sites of action on the genome. The mammalian Sin3L/Rpd3L complex, comprising more than a dozen different polypeptides, is an ancient HDAC complex found in diverse eukaryotes. The subunits of this complex harbor conserved domains and motifs of unknown structure and function. Here, we show that Sds3, a constitutively-associated subunit critical for the proper functioning of the Sin3L/Rpd3L complex, harbors a type of Tudor domain that we designate the capped Tudor domain. Unlike canonical Tudor domains that bind modified histones, the Sds3 capped Tudor domain binds to nucleic acids that can form higher-order structures such as G-quadruplexes and shares similarities with the knotted Tudor domain of the Esa1 histone acetyltransferase that was previously shown to bind single-stranded RNA. Our findings expand the range of macromolecules capable of recruiting the Sin3L/Rpd3L complex and draw attention to potentially new biological roles for this HDAC complex.

Cryo-EM structure of the Saccharomyces cerevisiae Rpd3L histone deacetylase complex

“…A maltose-binding protein (MBP)-tagged human BRMS1 (residues 51–179) construct in the pMCSG23 vector was co-expressed with a His 6 -tagged mouse SDS3 (residues 43–234) construct in the pMCSG7 vector in E. coli at 16 °C and was combined with His 6 -tagged human ARID4A R2 domain (residues 1164–1230) construct in the pMCSG7 vector that was separately expressed in E. coli at the same temperature 39 . The proteins were purified using Ni 2+ -NTA affinity chromatography as described previously 40 . The purified proteins were then concentrated and subjected to size-exclusion chromatography (SEC) using a Superdex 75 GL column (GE Healthcare) and a running buffer comprising 25 mM MOPS (pH 7.5), 150 mM NaCl, and 1 mM TCEP.…”

Distinct regions within SAP25 recruit O-linked glycosylation, DNA demethylation, and ubiquitin ligase and hydrolase activities to the Sin3/HDAC complex

“…It also plays a significant role in breast cancer metastasis (4), activating autophagy (5), contributing to pulmonary arterial hypertension (6), and influencing triple-negative breast cancer (7). In addition to the SIN3A/B paralogues, several proteins bind with the Sin/HDAC complexes including RBBP4/RBBP7 and HDAC1/2, which are shared with other transcriptional repressor complexes, and the Sin3-associated proteins SAP30/SAP30L, SUDS3, BRMS1/BRMS1L, ING1/2, ARID4A/B, SAP18, FAM60A, and SAP25 (8)(9)(10)(11). While SIN3/HDACSin3/HDAC complexes mainly regulate gene transcription (12), several by deacetylating histone tails and altering the chromatin environment , components of the Sin3/HDAC complex interact with proteins carrying various enzymatic activities (11,13,14).…”