Identifying LncRNAs Associated With Skeletal Muscle Growth And Development Based On Integrative Analysis Of RNA-seq Data In Pigs

Long non-coding RNAs?lncRNAs?are a class of RNA that have transcript length greater than 200 bp and are considered to have less protein-coding potential.They exert biological functions through various mechanisms involved in chromatin modification,X-chromosome silencing and genomic imprinting,transcriptional activation,nuclear transport and other important regulatory processes,involving in epigenetic regulation of transcriptional regulation and post-transcriptional regulation.With the implementation of ENCODE project and related studies on lncRNA of model organism such as human and mouse.The study of non-coding RNA in pigs has been gradually started.But the research progress is relatively backward.On the other hand,the growth and development of skeletal muscle is a complex process.There are significant difference in meat yield traits between Chinese local obese-type pigs and foreign lean-type pigs,which provides a good experiment material for the study of the molecular mechanism skeletal muscle growth and development.This study integrates transcriptome data downloading from the SRA database of NCBI and High-throughput sequencing data from our laboratory,including 12 tissues invloving in skeletal muscle,fat et al.,651 biological samples,19 Bioprojects,a total of 1.3 TB data.Due to differences of data sequencing methods in the database,we only focus on lincRNAs?long intergenic non-coding RNA?.And all samples are subjected to lincRNA system identification,characteristic analysis of lincRNA,tissue specificity analysis and mining lincRNA related to skeletal muscle growth and development.The results of the study are as follows:?1?A set of rigorous filtration procedures for identification linc RNAs was established,including eight filtration steps,which starting with transcripts length of less than 200 bp.We totally identified 12,564 candidate lincRNAs.?2?The characteristics of lincRNA and protein-coding genes are as follows: 1,196,822 and 908 chromosomes are relatively abundant on 1,6and 13 chromosomes,respectively.However,the numbers of lincRNAs on other chromosomes are evenly distributed.These results suggest that lincRNAs have a certain degree of chromosomal bias.The average length of lincRNA was 1380 bp and linc RNA with a length of 201-1000 bp accounted for 57%.The length of 1000 2000 bp accounted for 19%.The transcript of the protein-coding gene is 2800 bp.The average exon distribution of lincRNA was 3.2.Meanwhile,the average exon of protein-coding genes was 8.7.Compared to previous studies,we found 211 homologous sequences to NONCODE and1,538 homologous to ALDB database.?3?LincRNAs showed the most specific expression in the ovary?537,accounting for 32.14% of all specifically expressed lincRNAs?,and the number of lincRNAs specifically expressed were 179,136,128,124,123,114,90,74,58,56 and 52 in the kidney,lung,uterus,spleen,blood,liver,ear tissue,heart,muscle,brain,and adipose tissue,respectively.Among the linc RNAs that are specifically expressed in these tissues,we also have found candidate lincRNAs,related to their biological function.And expression pattern of lincRNA is more tissue-specific than protein-coding genes.?4?Twenty seven developmental time points of skeletal muscle samples were divided into four stages: early embryonic stage?E33-E65?,fetal stage?E70-E105?,neonatal stage?D0-D60?and mature stage?D80-D180?.Differential expression results of lincRNA betweendevelopmental stages showed that the number of lincRNAs expressed distinctly from fetal to neonatal periods?409 lincRNAs?.The functional enrichment analysis showed that lincRNAs were associated with embryonic development,myocyte metabolism and the binding of growth factor receptors during skeletal muscle development,including 179 lincRNAs such as linc_TCONS₀0326005,linc_TCONS₀0326798,linc_TCONS₀0323540 and et al.In summary,we firstly integrated RNA-seq of existing databases in pigs,identified and analyzed linc RNA characteristics,specific expressed lincRNA related to tissues function and lincRNAs involved in the growth and development of skeletal muscles.This study provides candidate biomarkers for pig breeding.