The Spatiotemporal Expression Patterns Of Transcripts And Its Correlation With Dynamic Chromatin Conformation During Tibetan Chicken Breast Muscle Development

The chromatin 3D structures of nucleus were elaborately constructed progressively with the adventure of Hi-C(Highthroughput Chromosome Conformation Capture)approach developed.They can regulate gene expression in a tissue-specific manner,but the role of chromatin in 3D space and its regulation in gene network during skeletal muscle development remains unknown.The development and composition of skeletal muscle is closely related to the productivity and quality of meat in poultry,above all,the myogenesis during embryonic days is a key stage that directly affects the performance and flavor of slaughter.In this study,a total of 58 samples of RNA-seq data-based analysis were made from the perspective of m RNAs,lnc RNAs and TUCPs,respectively.Firstly,we constructed the spatiotemporal expression patterns of 58 samples and the temporal expression profiles of 12 time points during development,we found that majority of transcripts in chicken skeletal muscle were spatiotemporally conserved,skeletal muscle expressed at a lower level than other tissues and decreased with development;and all the12 developmental stages could be divided into 4 sub-groups.The expression level of 3types of transcript was m RNAs > TUCPs > lnc RNAs;Pearson correlation coefficient between samples was m RNAs > TUCPs > lnc RNAs;indicating lnc RNAs had stronger spatiotemporal specificity than that of m RNAs and TUCPs.Furthermore,we identified 120 m RNAs,50 lnc RNAs and 32 TUCPs which were muscle-specific expressed during development,and found 24 lnc RNAs and 33 m RNAs which were involved in cis-regulatory networks.Finally,we identified 6 potential lnc RNAs which are involved in chicken skeletal muscle development,such as G12996,G10272,G2116,G166,G15490 and G2287.Subsequently,we selected 4 representative stages as objectives based on the phynotypes and physiological features to explore the genome topology,dissected its correlation with chromatin state and gene expression over time in chicken skeletal muscle according to the hierarchical nature of 3D chromatin organization: compartments(multimegabase scale),topologically associating domains(megabase scale)and chromatin loops(submegabase scale)at the resolution of 20 kb.Genome-wide contact matrix showed that,up to 69.02%contacts were intrachromosomal and most of them were short-range interactions within 20 kb.As for compartmentalization of chromosomes,we discovered that although overwhelming majority(79.33%)A/B compartments were unchangeable during the development of chicken skeletal muscle,the number of compartments that experienced A/B switch increased gradually with development.In addition,although the chromosome status change preceded gene expression,their trajectory was concordant during chicken skeletal muscle development.At the megabasescale,the average size of TAD was 776 kb,and up to 98.03% TAD boundaries were conserved during development,boundaries differed most during myogenesis,and they kept pretty steady after hatching till aging,the TAD structures would rearrange at Y8.Moreover,we obtained ～19,260 potential PEIs at each stage in chicken skeletal muscle,and nearly half PEIs were short range interactions(<20kb),among them,there were 23.39% stage-specific.At last,we explored the compartment and genes distributed in these stage-specific PEIs.Results showed that compartment A(autosomal chromatin)gradually increased with development,while compartment B(heterochromatin)decreased with age;Genes were downregulated with age in E12-,E18-and D36-specific PEIs,while genes of Y8-specific PEIs were initially upregulated and then downregulated.Functional enrichment analysis showed that genes in E12 mainly related to myogenesis;genes in E18 participated in all aspects biological functions of skeletal muscle;and muscle growth were enriched in D36;genes in Y8(aging)take part in biological functions similar with E12,which might be involved in the maintenance and repair of skeletal muscle.We identified muscle-associated differential interaction regionsl,such as Chr.12: 1220000-1260000(MUSTN1),Chr.17:7220000-7340000(ADAMTSL2,MYMK),Chr.12: 16840000-17160000(PDZRN3),Chr.4:20200000-20460000(FGB,FGA,FGG).To sum up,we identified 6 potential lnc RNAs and 4 chromatin differentially interaction regions which might relate to skeletal muscle development,these regulatory elements could be candidate factors for further study in exploration important economic traits in poultry.