LncRNA Mrhl orchestrates differentiation programs in mouse embryonic stem cells through chromatin mediated regulation

Earlier studies from our lab have characterized lncRNA Mrhl extensively in the context of male germ cell meiotic commitment and spermatogenesis, unraveling a negative feedback loop between Mrhl and a highly conserved context-dependant developmental pathway such as the WNT pathway. LncRNAs have been implicated for their functional roles in diverse developmental phenomena, cell fate specification events and differentiation of stem cells into various lineages. In purview of these, we aimed towards exploring lncRNA Mrhl and its functional relevance in mouse embryonic stem cells (mESCs) to understand its role in development and differentiation. Towards this end, we have addressed the targets of Mrhl in mouse embryonic stem cells. Our studies have revealed developmental processes, lineage specific transcription factors and lineage specific cell adhesion and receptor pathway genes to be majorly dysregulated upon Mrhl knockdown in mESCs with no perturbation in pluripotency status of the cells. This study has revealed context-dependant regulation of target genes by lncRNA Mrhl and implicated its role in regulating differentiation events in mESCs. Mouse ES cells were transiently transfected with either scrambled or sh-RNA against Mrhl and total RNA isolation was performed (DNase treated). Library preparation was done using TruSeq RNA sample prep kits (Illumina) as per the kit protocol. Control and shRNA samples were sequenced and analyzed in duplicates.