Effects Of CG Methylation Erasure On The Composition And Expression Of Long Non-coding RNA(lncRNA) In Oryza Sativa L.

Related studies about the biogenesis and function of lnc RNA have demonstrated its regulation in expression of coding genes,which supports that lnc RNA is no longer a"dark matter"in the genome.Artificially regulating the lnc RNA expression has been applied in improving the crop cultivars and also affecting the disease-related signal transduction,which eventually interferes the occurrence,development and cure of certain diseases.As an important epigenetic modification in regulating the expression of various genomic elements,it is still under-explored about whether and how DNA methylation（mainly refers to 5-^mC）regulates the expression of genomic lnc RNA and affects the adjacent protein coding genes（abbreviated as PCgenes）.In a previous study,a methytransferase rice mutant(Os MET1-2^-/-)was constructed by inserting Tos17transposon into the exon of MET1-2 gene under the tissue culture condition,which disrupted its original intact ORF and resulted in the null mutation of Met1-2 enzyme.Compared to its wild-type control(Os MET1-2^+/+),genome-wide bisulfite sequencing had demonstrated the erasure of ^mCG in the null mutant.In this study,based upon foregoing wild type and mutant rice,the profile of lnc RNA in respective material were characterized by our own established bioinformatic pipeline,which involved the prediction,classification and comparison after inputting the strand-specific transcriptome sequencing data.It turns out that our characterized lnc RNA in both materials were authentic in terms of its intrinsic characteristics such as the number of exons,the length of the transcript,the expression level,and etc.Those lnc RNAs were also categorized into two main group,which includes the linc RNA（long intergenic noncoding RNA）and the lnc NAT（long noncoding natural antisense transcript）.All those results supports the authenticity of our characterized lnc RNA.We found that the dramatic erasure of methylation in the null mutation resulted in significant variation in the composition and expression of those lnc RNAs.Specifically,the common lnc RNAs shared by both wild type and null mutant displayed differential expression;within the null mutant,the elimination of CG DNA methylation also induced the expression of novel lnc RNA.Tracing the origin of those novel expressed lnc RNAs revealed that the newly formed lnc RNAs mainly intersected with the transposon-inserted sequences in terms of their position,which indicates that the transposon may play an important role in the formation of those lnc RNA.In order to uncover the possible function of those conserved whereas differentially expressed linc RNA and lnc NAT,we also analyzed the differential expression and function GO terms of those PCgenes corresponding to respective linc RNA and lnc NAT.Although it is still unclear about the underpinning mechanisms and the impacting extent,the expression variation of both linc RNA and lnc NAT were determined to affect the expression of their PCgenes.Our study made an initial novel trial to explore the relationship between CG DNA methylation and lnc RNA expression and their contribution in regulating PCgenes of respective lnc RNA.Related research results offers more experimental and theoretical references for understanding the expression regulation of lnc RNAs and their adjacent PCgenes.