mRNA sequencing of DVE-1 knockdown in C. elegans

Telomeres comprise repetitive DNA sequences bound by specialized proteins at the end of linear chromosomes. Although some proteins have been identified and characterized in the nematode Caenorhabditis elegans, additional remain to be discovered, validated, and characterized. In our previous quantitative proteomics screen for telomere-binding proteins of C. elegans, we identified several candidates. One of these candidates was the homeobox protein DVE-1, a homolog of mammalian SATB proteins and transcription factor that plays a central role in the mitochondrial unfolded protein response. In this study, we validate DVE-1 as a telomere-binding protein in C. elegans. We show in vitro binding of DVE-1 to telomeric sequences and in vivo co-localization with the known telomere binding protein POT-1. Further, these results are supported by findings of DVE-1 ChIPseq analysis and RNA interference experiments followed by transcriptome and proteome analysis. Finally, we identified all core members of the nucleosome remodeling and deacetylase (NuRD) complex by DVE-1 immunoprecipitation and subsequent mass spectrometry experiments and bring them in the context of telomere organization.