SUMOylation of the Chromodomain Factor MRG-1 in C. Elegans Affects Chromatin-Regulatory Dynamics

Abstract

Epigenetic mechanisms control chromatin accessibility and gene expression to ensure proper cell fate specification. Histone proteins are integral chromatin components, and their modification promotes gene expression regulation. Specific proteins recognize modified histones such as the chromodomain protein MRG-1. MRG-1 is the Caenorhabditis elegans ortholog of mammalian MRG15, which is involved in DNA repair. MRG-1 binds methylated histone H3 and is important for germline maturation and safeguarding. To elucidate interacting proteins that modulate MRG-1 activity, we performed in-depth protein–protein interaction analysis using immunoprecipitations coupled with mass spectrometry. We detected strong association with the Small ubiquitin-like modifier SUMO, and found that MRG-1 is post-translationally modified by SUMO. SUMOylation affects chromatin-binding dynamics of MRG-1, suggesting an epigenetic regulation pathway, which may be conserved.

SIN3 acts in distinct complexes to regulate the germline transcriptional program inC. elegans

“…The above experiments, together with previous data using CFP-1 or MRG-1 as bait in IP-MS experiments (Beurton et al, 2019; Baytek et al, 2022), confirm the presence of SIN-3 in a smaller complex related to yeast and mammalian Rpd3/SIN3S (Carrozza et al, 2005b; Jelinic et al, 2011) containing ATHP-1/PHF12, MRG-1/MRG15, CFP-1 and HDA-1 as the only HDAC. In addition we identify a second complex that we will refer to as SIN3L and that contains SUDS-3, HDA-3, HDA-1, ARID-1/ARID4, NAP-1 and the transcription factor C01G6.5 (Figure 2B).…”

“…Although SIN3L subunits alone may not be required for fertility, the observation that athp-1; hda-3 and athp-1; suds-3 double mutants are fully sterile suggests at least partial redundancy of the two complexes, or additional functions for the encoded subunits independent of SIN-3. Interestingly, while mammalian HDAC1 and HDAC2 are mostly considered to be functionally redundant, we found that both HDA-3 and HDA-1 are present in the SIN3L complex identified in this study, while SIN3S components only copurify with HDA-1 (Baytek et al, 2022;Beurton et al, 2019).…”

“…Interestingly, while mammalian HDAC1 and HDAC2 are mostly considered to be functionally redundant, we found that both HDA-3 and HDA-1 are present in the SIN3L complex identified in this study, while SIN3S components only copurify with HDA-1(Baytek et al, 2022; Beurton et al, 2019). While HDA-1 has been found in at least two additional complexes, NuRD and MEC (Passannante et al, 2010; Kim et al, 2021), an HDA-3 containing complex has not been described to date.…”

“…Like SIN-3, SIN3S component MRG-1 is required for silencing of the X chromosome and fertility (Takasaki et al, 2007), and both SIN-3 and MRG-1 are required for piRNA silencing in the germline (Kim et al, 2021). These shared phenotypes are consistent with common functions as part of the same complex, although MRG-1 most likely has additional functions alone or in the context of additional complexes (Baytek et al, 2022;Hajduskova et al, 2018;Bleuyard et al, 2017;Iwamori et al, 2016;Iwamori et al, 2016;Smith et al, 2013). Although SIN3L subunits alone may not be required for fertility, the observation that athp-1; hda-3 and athp-1; suds-3 double mutants are fully sterile suggests at least partial redundancy of the two complexes, or additional functions for the encoded subunits independent of SIN-3.…”

“…MES-4 instead deposits the activating mark H3K36me3 on germline expressed autosomal genes and antagonizes H3K27me3, leading to its concentration on the X (Gaydos et al, 2014; Bender et al, 2006). MRG-1, a component of several chromatin complexes in addition to SIN3S (Chen et al, 2010; Huang et al, 2017; Smith et al, 2013; Yochum and Ayer, 2002; Baytek et al, 2022), also contributes to silencing of the X in the C. elegans germline (Takasaki et al, 2007). Comparison of our list of sin-3(syb2172 ) upregulated genes on the X with a list of MES-3 and MRG-1 targets on the X (Cockrum and Strome, 2022) revealed commonly upregulated genes in the three mutants (37), as well as a larger set genes uniquely in common between mes-3 and mrg-1, as previously described ( Figure 4B) (Cockrum and Strome, 2022).…”