牛骨骼肌卫星细胞发育过程中的转录组和翻译组联合分析

doi:10.16431/j.cnki.1671-7236.2024.11.002

摘要/Abstract

摘要： 【目的】利用转录组测序(transcriptome sequencing，RNA-Seq)和全长翻译组测序(ribosome-nascent-chain-complex sequencing，RNC-Seq)分析比对转录和翻译两个不同水平上牛骨骼肌的生长发育过程，解析其发育特征和规律，并筛选出可能在转录组和翻译组共同参与牛肌肉生长发育过程的关键基因，为后续功能基因的筛选和利用提供目标靶点。【方法】采集4月龄牛胚胎的骨骼肌卫星细胞的增殖期(proliferative period，GM)和分化期第2天(the second day of differentiation，DM2)的样品进行RNA-Seq和RNC-Seq分析，对其差异表达基因进行生物信息学分析，从翻译调控的角度分析与骨骼肌发育相关的差异基因。【结果】 BSMSCs的DM2期相较于GM期差异基因筛选表明，转录组共筛选获得2 808个差异基因(上调基因1 749个，下调基因1 059个)，翻译组共筛选获得3 740个差异基因(上调基因1 769个，下调基因1 971个)，转录组和翻译组共有的差异表达基因725个，其中表达趋势相同的基因618个，表达趋势相反的基因107个。功能富集分析获得103个与骨骼肌发育相关的基因。进一步深入分析发现，转录水平的调控和翻译水平的调控具有相对独立性，且翻译调控对转录调控具有一定的回调作用，筛选获得了22个与牛肌肉的生长发育密切相关的标靶基因(CDK1、SERPINE1、THBS1、IGFBP3、CNB1、GADD45A、CYCS、CDK2、CCND1、CCNE2、ZMAT3、ACTB、ACTA1、TNNT1、MYH7、ACTG1、TUBA1C、TNNC1、KIF20A、TUBB4B、MYL3、TUBB3)及13个存在翻译回调现象的关键基因(GREM1、EGR1、SFRP4、NKD2、DKK3、IGFBP3、CTSK、ITGAV、CTSV、CDKN1A、SESN3、GADD45A、ZMAT3)。【结论】本研究筛选获得了22个可能与牛肌肉的生长发育密切相关的关键基因和13个存在翻译回调的关键基因，为进一步利用分子手段调节牛肌肉生长发育过程及进行新品种培育提供了重要的靶点。

关键词: 牛骨骼肌卫星细胞; 转录组测序; 全长翻译组测序; 生物信息学

Abstract: 【Objective】 The aim of this study was to analyze and compare the growth and development process of bovine skeletal muscle at two different levels of transcription and translation using transcriptome sequencing (RNA-Seq) and ribosome-nascent-chain-complex sequencing (RNC-Seq), analyze the developmental characteristics and patterns,and screen out key genes that might be involved in the growth and development process of bovine muscle in the transcriptome and translatome,in order to provide a target for the subsequent screening and utilization of functional genes. 【Method】 Samples of the proliferative period (GM) and the second day of differentiation (DM2) of skeletal muscle satellite cells from 4-month-old bovine embryos were collected for RNA-Seq and RNC-Seq analysis.The differentially expressed genes were analyzed using bioinformatics,and the differentially expressed genes related to skeletal muscle development were analyzed from the perspective of translational regulation. 【Result】 The differential gene screening of BSMSCs in DM2 phase compared to GM phase showed that a total of 2 808 differential genes (1 749 up-regulated genes and 1 059 down-regulated genes) were obtained from transcriptome screening,and 3 740 differential genes (1 769 up-regulated genes and 1 971 down-regulated genes) were obtained from translatome screening.There were 725 differentially expressed genes shared between transcriptome and translatome,including 618 genes with similar expression trends and 107 genes with opposite expression trends.The functional enrichment analysis results showed that 103 genes related to skeletal muscle development were obtained.Further in-depth analysis showed that the transcriptional and translational regulation were relatively independent and the translational regulation had a certain effect of retrogression on the transcriptional regulation,22 target genes closely related to the growth and development of bovine muscle (CDK1,SERPINE1,THBS1,IGFBP3,CNB1,GADD45A,CYCS,CDK2,CCND1,CCNE2,ZMAT3,ACTB,ACTA1,TNNT1,MYH7,ACTG1,TUBA1C,TNNC1,KIF20A,TUBB4B,MYL3 and TUBB3) and 13 key genes with translation retrogression (GREM1,EGR1,SFRP4,NKD2,DKK3,IGFBP3,CTSK,ITGAV,CTSV,CDKN1A,SESN3,GADD45A and ZMAT3) were obtained. 【Conclusion】 In this study,22 key genes that might be closely related to the growth and development of bovine muscles and 13 key genes with translation callbacks were screened,providing important targets for further regulating the process of bovine muscle growth and development through molecular means for new breed cultivation.

Key words: bovine skeletal muscle satellite cells; RNA-Seq; RNC-Seq; bioinformatics

中图分类号:

S813

马苏芳, 杨雯晴, 张冰冰, 郭若楠, 许赢心, 张林林, 郭益文, 胡德宝, 郭宏, 丁向彬, 李新. 牛骨骼肌卫星细胞发育过程中的转录组和翻译组联合分析[J]. 中国畜牧兽医, 2024, 51(11): 4665-4677.

MA Sufang, YANG Wenqing, ZHANG Bingbing, GUO Ruonan, XU Yingxin, ZHANG Linlin, GUO Yiwen, HU Debao, GUO Hong, DING Xiangbin, LI Xin. Joint Analysis of Transcriptome and Translatome During the Development of Bovine Skeletal Muscle Satellite Cells[J]. China Animal Husbandry and Veterinary Medicine, 2024, 51(11): 4665-4677.

参考文献

[1] WANG S S，JIN J J，XU Z Y，et al.Functions and regulatory mechanisms of lncRNAs in skeletal myogenesis,muscle disease and meat production[J].Cells，2019，8(9)：1107.
[2] MOHAMMADREZA M，BORDBAR F，JENSEN J，et al.Key genes regulating skeletal muscle development and growth in farm animals[J].Animals (Basel)，2021，11(3)：835.
[3] FRONTERA W R，OCHALA J.Skeletal muscle:A brief review of structure and function[J].Calcified Tissue International，2015，96(3)：183-195.
[4] TEDESCO F S，DELLAVALLE A，DIAZ-MANERA J，et al.Repairing skeletal muscle:Regenerative potential of skeletal muscle stem cells[J].Journal of Clinical Investigation，2010，120(1)：11-19.
[5] SCHMIDT M，SCHÜLER S C，HÜTTNER S S，et al.Adult stem cells at work:Regenerating skeletal muscle[J].Cellular and Molecular Life Sciences，2019，76(13)：2559-2570.
[6] LEPPER C，PARTRIDGE T A，FAN C M.An absolute requirement for Pax7-positive satellite cells in acute injury-induced skeletal muscle regeneration[J].Development，2011，138(17)：3639-3646.
[7] DUMONT N A，BENTZINGER C F，SINCESNES M C，et al.Satellite cells and skeletal muscle regeneration[J].Comprehensive Physiology，2015，5(3)：1027-1059.
[8] BRAUN T，GAUTEL M.Transcriptional mechanisms regulating skeletal muscle differentiation,growth and homeostasis[J].Nature Reviews Molecular Cell Biology，2011，12(6)：349.
[9] COHEN S，BRAULT J J，GYGI S P，et al.During muscle atrophy,thick,but not thin,filament components are degraded by MuRF1-dependent ubiquitylation[J].The Journal of Cell Biology，2009，185(6)：1083-1095.
[10] MORGAN J，PARTRIDGE T.Skeletal muscle in health and disease[J].Disease Models & Mechanisms，2020，13(2)：dmm042192.
[11] ALAMEDDINE H S，MORGAN J E.Matrix metalloproteinases and tissue inhibitor of metalloproteinases in inflammation and fibrosis of skeletal muscles[J].Journal of Neuromuscular Diseases，2016，3(4)：455-473.
[12] LAUMONIER T，MENETREY J.Muscle injuries and strategies for improving their repair[J].Journal of Experimental Orthopaedics，2016，3(1)：15.
[13] SAMBASIVAN R，TAJBAKHSH S.Adult skeletal muscle stem cells[J].Results and Problems in Cell Differentiation，2015，56：191-213.
[14] SOUSA-VICTOR P，GARCÍA-PRAT L，MUÑOZ-CÁNOVES P.Control of satellite cell function in muscle regeneration and its disruption in ageing[J].Nature Reviews Molecular Cell Biology，2022，23(3)：204-226.
[15] ZHANG M L，ZHAO K，XU X P，et al.A peptide encoded by circular form of LINC-PINT suppresses oncogenic transcriptional elongation in glioblastoma[J].Nature Communications，2018，9(1)：4475.
[16] 周清妍.利用转录组学和翻译组学关联分析中华鳖背甲脊发育的机理研究[D].合肥：安徽农业大学，2023.
ZHOU Q Y.Transcriptome and transcriptome correlation were used to analyze the development mechanism of the carapacial ridge of Pelodiscus sinensis[D].Hefei：Anhui Agricultural University，2023.(in Chinese)
[17] 胡海龙.陆川猪与杜洛克猪背最长肌组织的转录组与翻译组比较分析[D].南宁：广西大学，2021.
HU H L.Comparative analysis of translatome and transcriptome of the longest dorsal muscle tissue of Luchuan pigs and Duroc pigs[D].Nanning：Guangxi University，2021.(in Chinese)
[18] 王轶敏，代阳，刘新锋，等.牛骨骼肌卫星细胞的分离鉴定和诱导分化[J].中国畜牧兽医，2014，41(7)：142-147.
WANG Y M，DAI Y，LIU X F，et al.Isolation,identification and induced differentiation of bovine skeletal muscle satellite cells[J].China Animal Husbandry & Veterinary Medicine，2014，41(7)：142-147.(in Chinese)
[19] HU W Q，ZENG H T，SHI Y N，et al.Single-cell transcriptome and translatome dual-omics reveals potential mechanisms of human oocyte maturation[J].Nature Communications，2022，13(1)：5114.
[20] ZOU Z N，ZHANG C X，WANG Q Y，et al.Translatome and transcriptome co-profiling reveals a role of TPRXs in human zygotic genome activation[J].Science，2022，378(6615)：abo7923.
[21] 刘瑞莉，吴磊，袁玮，等.基于转录组筛选肉牛骨骼肌差异基因[J].华北农学报，2018，33 (S1)：64-72.
LIU R L，WU L，YUAN W，et al.Screening of skeletal muscle differential genes based on transcriptome[J]. Acta Agriculurae Boreali-Sinica，2018，33(S1)：64-72.(in Chinese)
[22] BAI X，ZHENG Z Q，LIU B，et al.Whole blood transcriptional profiling comparison between different milk yield of Chinese Holstein cows using RNA-Seq data[J].BMC Genomics，2016，17(Supp 7)：512.
[23] SHEET S，JANG S S，KIM J H，et al.A transcriptomic analysis of skeletal muscle tissues reveals promising candidate genes and pathways accountable or different daily weight gain in Hanwoo cattle[J].Scientific Reports，2024，14(1)：315.
[24] BILLEREY C，BOUSSAHA M，ESQUERRÉ D，et al.Identification of large intergenic non-coding RNAs in bovine muscle using next-generation transcriptomic sequencing[J].BMC Genomics，2014，15(1)：499.
[25] GORDON A M，HOMSHER E，REGNIER M.Regulation of contraction in striated muscle[J].Physiological Reviews，2000，80(2)：853-892.
[26] PERRY S V.Troponin T:Genetics,properties and function[J]. Journal of Muscle Research and Cell Motility，1998，19(6)：575-602.
[27] MALUMBRES M，BARBACID M.Cell cycle,CDKs and cancer:A changing paradigm[J].Nature Reviews Cancer，2009，9(3)：153-166.
[28] LIU S，YANG Y，JIANG S，et al.Corrigendum:miR-378a-5p regulates proliferation and migration in vascular smooth muscle cell by targeting CDK1[J].Frontiers in Genetics，2019，10：193.
[29] PALMER B M.Thick filament proteins and performance in human heart failure[J].Heart Failure Reviews，2005，10(7)：187-197.
[30] YOUSAF M，KHAN W A，SHAHZAD K，et al.Genetic association of beta-myosin heavy-chain gene (MYH7) with cardiac dysfunction[J].Genes，2022，13(9)：1554.
[31] HINNEBUSCH A G.Translational regulation of GCN4 and the general amino acid control of yeast[J].Annual Review of Microbiology，2005，59：407-450.
[32] LACKNER D H，SCHMIDT M W，WU S D，et al.Regulation of transcriptome,translation,and proteome in response to environmental stress in fission yeast[J].Gnome Biology，2012，13(4)：R25.
[33] LEI L，SHI J P，CHEN J，et al.Ribosome profiling reveals dynamic translational landscape in maize seedlings under drought stress[J].Plant Journal，2015，84(6)：1206-1218.