Functional Interplay of Two Paralogs Encoding SWI/SNF Chromatin-Remodeling Accessory Subunits DuringCaenorhabditis elegansDevelopment

Abstract

SWI/SNF ATP-dependent chromatin-remodeling complexes have been related to several cellular processes such as transcription, regulation of chromosomal stability, and DNA repair. The Caenorhabditis elegans gene ham-3 (also known as swsn-2.1) and its paralog swsn-2.2 encode accessory subunits of SWI/SNF complexes. Using RNA interference (RNAi) assays and diverse alleles we investigated whether ham-3 and swsn-2.2 have different functions during C. elegans development since they encode proteins that are probably mutually exclusive in a given SWI/SNF complex. We found that ham-3 and swsn-2.2 display similar functions in vulva specification, germline development, and intestinal cell proliferation, but have distinct roles in embryonic development. Accordingly, we detected functional redundancy in some developmental processes and demonstrated by RNA sequencing of RNAi-treated L4 animals that ham-3 and swsn-2.2 regulate the expression of a common subset of genes but also have specific targets. Cell lineage analyses in the embryo revealed hyper-proliferation of intestinal cells in ham-3 null mutants whereas swsn-2.2 is required for proper cell divisions. Using a proteomic approach, we identified SWSN-2.2-interacting proteins needed for early cell divisions, such as SAO-1 and ATX-2, and also nuclear envelope proteins such as MEL-28. swsn-2.2 mutants phenocopy mel-28 loss-of-function, and we observed that SWSN-2.2 and MEL-28 colocalize in mitotic and meiotic chromosomes. Moreover, we demonstrated that SWSN-2.2 is required for correct chromosome segregation and nuclear reassembly after mitosis including recruitment of MEL-28 to the nuclear periphery.KEYWORDS SWI/SNF; Caenorhabditis elegans; chromatin; development; nuclear envelope C HROMATIN is a dynamic structure required not only for the packaging of large amounts of DNA in the limited space of eukaryotic nuclei, but also for the regulation of gene expression (Ho and Crabtree 2010;Narlikar et al. 2013). SWI/SNF complexes, which are conserved from yeast to mammals, modify the state of the chromatin in an ATPdependent manner and, therefore, the accessibility of distinct proteins to a given DNA region (Hargreaves and Crabtree 2011;Euskirchen et al. 2012). Such activity in the DNA regulates various cellular aspects like proliferation, differentiation, chromosomal stability, and DNA repair (Reisman et al. 2009;Lans et al. 2010;Euskirchen et al. 2011). SWI/SNF complexes are involved in gene-specific regulation since only a low percentage of gene expression (6% in budding yeast, 7.5% in Caenorhabditis elegans) is regulated by these complexes (Holstege et al. 1998;Riedel et al. 2013).A canonical SWI/SNF complex consists of a central ATPase subunit, two or three core components, and several (five to eight) accessory subunits (Hargreaves and Crabtree 2011). While all SWI/SNF complexes include core subunits that are in charge of remodeling nucleosomes (Phelan et al. 1999), the accessory proteins confer specificity to a given complex and their presence varies depending on the ...

Identification of Conserved MEL-28/ELYS Domains with Essential Roles in Nuclear Assembly and Chromosome Segregation

“…MEL-28 strongly accumulated on condensed oocyte chromosomes ( S1C Fig ; [ 9 , 18 ]). Moreover, we noted during our initial studies of mel-28 mutant or RNAi-treated embryos that formation and migration of the maternal pronucleus was often more severely affected than the paternal pronucleus [ 9 , 10 ].…”

Chromatin targeting of nuclear pore proteins induces chromatin decondensation

“…The data presented here provide functional and mechanistic evidence for the long-standing visual correlation between NPCs and open chromatin and validates the hypothesized relationship between them. Interestingly, previous genetic and proteomic experiments have reported interactions between the Caenorhabditis elegans homologue of Elys, MEL-28, and chromatin-remodeling complexes, including the SWI/SNF complex subunit SWSN-2.2 ( Fernandez et al, 2014 ; Ertl et al, 2016 ), suggesting an evolutionarily conserved role for Elys in regulating chromatin state. Furthermore, genetic and physical interactions between yeast NPC components and the chromatin-remodeling RSC complex have also been reported ( Titus et al, 2010 ; Van de Vosse et al, 2013 ).…”

Evolutionary plasticity in the innate immune function of Akirin

“…When we compared the list of 53 high confidence candidate AKIR-1 binding proteins with the 190 proteins identified as potential interactors of the nematode BAP60 homologue SWSN-2.2 (Ertl, Porta-de-la-Riva et al, 2016), we found only 3 common proteins, none of which have been characterized as being specific regulators of nlp-29p::gfp expression (i.e. found as Nipi genes (Zugasti et al, 2016); Table S2).…”

“…This suggests that in some contexts, but not during its regulation of AMP gene expression, AKIR-1 might interact with the SWI/SNF complex. This functional dichotomy was further reinforced by examining the genes differentially regulated following knockdown of swsn-2.2 and its paralogue ham-3 (Ertl et al, 2016). There were only a very small number (28/1468) of genes characterized as up-regulated by D. coniospora infection and among them, there were none encoding AMPs (JJE unpublished observations).…”

“…In all cases there are no significant differences between control and experimental values (paired two-sided student t test). (Ertl et al, 2016) and Table S1. The annotations come from Wormbase (WS257).…”