Long noncoding RNA CCDC144NL-AS1 knockdown induces naïve-like state conversion of human pluripotent stem cells

Human naïve pluripotency state cells can be derived from direct isolation of inner cell mass or primed-to-naïve resetting of human embryonic stem cells (hESCs) through different combinations of transcription factors, small molecular inhibitors and growth factors. Long noncoding RNAs (lncRNAs) have been identified to be crucial in diverse biological processes, including pluripotency regulatory circuit of mouse pluripotent stem cells (PSCs), but few are involved in human PSCs' regulation of pluripotency and naïve pluripotency derivation. This study initially planned to discover more lncRNAs possibly playing significant roles in the regulation of human PSCs' pluripotency, but accidently identified a lncRNA whose knockdown in human PSCs induced naïve-like pluripotency conversion. The results indicated that knockdown of CCDC144NL-AS1 induces naïve-like state conversion of human PSCs in the absence of additional transcription factors or small molecular inhibitors. CCDC144NL-AS1-KD human PSCs reveal naïve-like pluripotency features, such as elevated expression of naïve pluripotency associated genes, increased developmental capacity, analogous transcriptional profiles to human naïve PSCs, and global reduction of repressive chromatin modification marks. Furthermore, CCDC144NL-AS1-KD human PSCs display inhibition of MAPK (ERK), accumulation of active ß-catenin, and upregulation of some LIF/STAT3 target genes, and all of these are concordant with previous reported traits of human naïve PSCs. Overall design: The transcriptional profiles of CCDC144NL-AS1-KD-H9, NC-H9, CCDC144NL-AS1-KD-H14, NC-H14, CCDC144NL-AS1-KD-HDF-iPS, NC-HDF-iPS cells were generated by deep sequencing, the epigenetic landscape of CCDC144NL-AS1-KD-H9 cells and NC-H9 cells were analysed by chromatin immunoprecipitation followed by deep sequencing (ChIP-Seq) of H3k4me3 and H3K27me3, using the Illumina platform.