Study Of Binding Profiles Of Key Transcriptional Factors In LncRNA Region During Mouse Somatic Cell Reprogramming

Induced pluripotent stem cells(iPSCs)find potential application in regenerative medicine,disease modeling and drug discovery.Nevertheless,the inefficiency of reprogramming restricts the application of iPSC.Key transcriptional factors(TFs)in somatic cell reprogramming including Oct4,Sox2,Klf4,cMyc(OSKM)play a pioneering regulatory role in somatic cell identity transformation.Previous studies on the OSKM-targeted regulation of somatic cell genome reprogramming mainly focused on protein-coding gene promoter region and screened out some substitutable key genes.Recently,an increasing number of evidence indicate that long non-coding RNAs(lncRNAs)play an equal important regulatory role in somatic cell reprogramming,yet the dynamics of key TFs-targeted regulation of this region have not been systematically analyzed and studied.Here,at first we mapped chromosomal distribution patterns of six TFs including Oct4,Sox2,Klf4,cMyc,Nanog and Esrrb at key timepoints of mouse somatic cell reprogramming,showing that pluripotent TFs regulation was mainly distribute in autosome 9,10,13 and 17,and they tended to bind to lincRNA with promoter containing endogenous retrovirus K(ERVK).Further,combining with ATAC-seq data,we found that OSKM successively co-bind to genome-wide target sites during somatic cell reprogramming,and OSKM occupancy was consistent with opening of chromatin.Next,combining with TF-binding motif analysis,we found that binding of somatic cell specific TFs on lncRNA promoter and enhancer regions declined during reprogramming,but that of pluripotency TFs gradually increased;OSKM binding on promoter cooperated with histone modifications H3K4me3,H3K27me3,H3K79me2 and histone variant H3.3 to regulate the transcription of lncRNA;In addition,we explored the relationship between preference of OSKM binding on promoter and lncRNA characteristics,including lncRNA type,transposable element(TE)content,transcript length,first exon length,first intron length,and distance to pluripotency genes.It was found that OSKM preferentially bind to lncRNAs of types those overlapped with protein coding sequences,such as sense overlapping and antisense,and lncRNAs containing ERVK in promoter,longer transcript,longer first intron,and within 10-20 kb range of pluripotency genes.Further,based on correlation analysis of iPSC pluripotency protein-coding(PC)genes and lncRNA,we found 210 iPSC pluripotency network related lncRNAs,constructed a PC-lncRNA genes co-expression network,and obtained several key lncRNAs probably play vital roles in the network.Among them,Platr family,Panct2,D230017M19 Rik and 4930461G14 Rik have been reported,which to some extent confirms the reliability of our results.Meanwhile,we also excavated a series of new lncRNAs,such as Tnfsf13 os,Gm44699,Gm26917,Gm31793,Gm16302,Gm48604,etc.Together,we depicted binding profiles of key TFs in lncRNA region during mouse somatic cell reprogramming,studied the coordinated regulation of lncRNA transcription by key TFs and epigenetic modifications,and built an iPSC pluripotency related PC-lncRNA genes co-expresssion network.Our findings may be significant in elucidating molecular mechanisms of the regulation of lncRNAs by key TFs,and may provide some theoretic help for further identification of reprogramming non-coding RNA markers.