Epitranscriptomic or RNA epigenetic modifications take place at the post-transcriptional level in transcribed RNAs without altering any RNA nucleotides/nucleosides. Until now, over 150 different types of RNA modifications have been identified in a range of different classes of RNAs, in various organisms ranging from yeast to mammals. However, recent advancement in high throughput sequencing technology can able to map only a few of these modifications transcriptome-wide in a precise manner that enables to understand the molecular and biological functions of the RNA modifications. To date, METTL3 (an m6A- methyltransferase) and its associated factor (ZC3H13) have been shown to play an important role in embryonic stem cells (ESCs). However, roles of other RNA modifications including, 5-methylcytosine (m5C) is currently unexplored in ESCs. In this study, we focused on m5C RNA modification that is catalysed by m5C methyltransferases (m5C writers) – TRDMT1 and NSUN1-7. These m5C writers mostly methylate tRNAs, rRNAs, mitochondrial RNAs. Only NSUN2 (the best-studied m5C methyltransferase) has been found to methylate a small number of mRNAs. To investigate the detailed functions of m5C in ESCs, we generated the Nsun2 KO in mouse ESCs (mESCs) using CRISPR-Cas9 that display self-renewal defects. Subsequent molecular analyses using RNA-seq (transcriptomic), m5c BS RNA-seq (epitranscriptomic) and PRO-seq (detects nascent transcripts) reveal “multidimensional” functions of NSUN2 through “transcriptional” and/or “post-transcriptional” regulation of maternal Meg3, Rian, Mirg long non-coding RNAs (from the Dlk1-Dio3 imprinted locus), c-Myc, Dicer-1, and Ccnd-1,2 that ultimately control self-renewal of the mESCs. Thus, our findings uncover the novel function of NSUN2, which orchestrates multidimensional gene regulatory functions to control self-renewal for the maintenance of mESC state.