Genomic localization and functions of MBD-2 with and without NuRD in DNA methylation-free C. elegans [RNA-Seq]

While mammalian MBD2 is a well-established 5-Methylcytosine reader and component of the essential Nucleosome Remodeling and Deacetylase (NuRD) complex, the function and binding pattern of C. elegans MBD2 (Cel-MBD-2) in its 5mC-free genome remained uncharacterized. In our study, Cel-mbd-2 null mutation resulted in a wide range of severe morphological defects and sterility. Coiled-coild domain deletion of Cel-mbd-2 phenocopied the null mutant and led to similar transcriptomic changes. We have also confirmed that Cel-MBD-2 is a key transcriptional modulator that can regulate genes in both directions. The MBD-2 binding patterns in the gene promoter or gene body are linked with the gene regulatory directions and display distinct correlations with histone modifications within and outside the context of NuRD complex. Overall design: RNA-seq of N2 wildtype and mbd-2 null mutant synchronized young adult worms. The mutant is maintained as a heterozygous stock balanced with hT2 balancer, we performed RNA-seq for both homozygous null mutants sired by heterozygous null mutant (P0) and homozygous null mutants sired by homozygous null mutant (F1) adult worms. RNA-seq of gfp::3xflag::mbd-2 (control) and gfp::3xflag::mbd-2?CC (coiled-coil domain deletion) mutant synchronized young adult worms. The mutant is maintained as a heterozygous stock balanced with hT2 balancer, we performed RNA-seq for both homozygous coiled-coil domain deletion mutants sired by heterozygous coiled-coil domain deletion mutant (P0) and homozygous coiled-coil domain deletion mutants sired by homozygous coiled-coil domain deletion mutant (F1) adult worms.