GSE136576
RNA-seq: Loss of a heterochromatin anchor rescues altered genome organization and EDMD muscle defects triggered by a laminopathy mutation
Point mutations in nuclear structural protein lamin A produce rare,  tissue-specific diseases called laminopathies. The introduction of a  human Emery Dreifuss Muscular Dystrophy (EDMD)-inducing mutation (lamin  A-Y45C) into C. elegans lamin (LMN-Y59C), recapitulates many EDMD  phenotypes, and correlates with hyper-sequestration of heterochromatic  arrays at the nuclear periphery. Using muscle-specific emerin Dam-ID, we  also document the misorganization of endogenous chromatin in the  LMN-Y59C mutant. We score increased perinuclear positioning along  chromosome arms, and enhanced release within chromosomal cores.  Coincidentally, Y59C worms have reduced locomotion and compromised  sarcomere integrity. By coupling the Y59C mutation with deletion of the  perinuclear chromodomain protein CEC-4, which tethers H3K9-methylated  chromatin, we rescue the EDMD-like physiology and ultrastructural  defects in sarcomeres. Deletion of cec-4 also rescued the Y59C-induced  changes in chromatin organization. The promoters of genes that change  position in the LMN-Y59C mutant, are enriched for E2F (EFL-1/-2) binding  sites, consistent with previous studies implicating the Rb-E2F  interaction with lamin A in muscle dysfunction. Gene expression changes  provoked by LMN-Y59C are also largely reversed by cec-4 deletion. In  summary, the ablation of a perinuclear H3K9me-anchor can counteract the  dominant muscle-specific defects provoked by a laminopathic mutation,  implicating peripheral chromatin organization in the control of muscle  integrity. Overall design: Total RNA-seq in synchronized L1 larval stage of Caenorhabditis elegans with the genotypes:  wild-type (samples: lmn_WT_a, lmn_WT_b) , cec-4 mutant (samples: cec4_a, cec4_b), mutant lamin (samples: lmn_Y59C_a, lmn_Y59C_b) and lamin mutant with cec-4 mutant (samples: lmn_Y59C_cec4_a, lmn_Y59C_cec4_b). 50 bp single-end sequencing was done on an Illumina HiSeq 2500.