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 ...
Retinitis pigmentosa (RP) is a rare genetic disease that causes gradual blindness through retinal degeneration. Intriguingly, seven of the 24 genes identified as responsible for the autosomal-dominant form (adRP) are ubiquitous spliceosome components whose impairment causes disease only in the retina. The fact that these proteins are essential in all organisms hampers genetic, genomic, and physiological studies, but we addressed these difficulties by using RNAi in Caenorhabditis elegans. Our study of worm phenotypes produced by RNAi of splicing-related adRP (s-adRP) genes functionally distinguishes between components of U4 and U5 snRNP complexes, because knockdown of U5 proteins produces a stronger phenotype. RNA-seq analyses of worms where s-adRP genes were partially inactivated by RNAi, revealed mild intron retention in developing animals but not in adults, suggesting a positive correlation between intron retention and transcriptional activity. Interestingly, RNAi of s-adRP genes produces an increase in the expression of atl-1 (homolog of human ATR), which is normally activated in response to replicative stress and certain DNA-damaging agents. The up-regulation of atl-1 correlates with the ectopic expression of the pro-apoptotic gene egl-1 and apoptosis in hypodermal cells, which produce the cuticle, but not in other cell types. Our model in C. elegans resembles s-adRP in two aspects: The phenotype caused by global knockdown of s-adRP genes is cell type-specific and associated with high transcriptional activity. Finally, along with a reduced production of mature transcripts, we propose a model in which the retina-specific cell death in s-adRP patients can be induced through genomic instability.
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