2. 中国农业大学动物科技学院, 北京 100193
2. College of Animal Science and Technology, China Agricultural University, Beijing 100193, China
表观遗传学和传统遗传学作为两个相对的概念，共同揭秘基因表达水平的变化，并遗传给下一代，其两者最大的区别在于DNA序列是否发生改变[1]。表观遗传学中DNA序列没有变化，其主要包括DNA甲基化、RNA修饰、组蛋白修饰、染色体重塑和非编码RNA五种方式。
在人类和小鼠前期的研究表明，印迹基因对哺乳动物的生长、代谢和生理有重大影响，即来自父母遗传的两个等位基因中的一个表达被减弱或完全沉默。在畜禽的研究中也发现受这种表观遗传调控的基因与一些表型性状相关，其中，影响最大的是肌肉品质和脂肪沉积[7]。而脂肪沉积作为畜禽肉质评价的重要因素之一，在畜牧业遗传育种中的重要性不言而喻[8]，表观遗传修饰可能通过激活或者是沉默脂肪沉积过程中的关键基因来调控这一过程。研究畜禽中脂肪沉积机制具有重要的经济价值。因此，本文重点对DNA甲基化、RNA修饰、组蛋白修饰、染色体重塑和非编码RNA调控在畜禽脂肪沉积中的研究进展进行综述。
1 表观遗传调控分子机制及作用 1.1 DNA甲基化修饰DNA甲基化是目前研究的最深入，也是最早发现的表观遗传修饰之一[11]。在DNA甲基转移酶催化作用下，S-腺苷甲硫氨酸作为甲基供体，将S-腺苷甲硫氨酸的甲基转移到胞嘧啶的第五位碳原子上，从而形成5-甲基胞嘧啶产生DNA甲基化，通常在转录水平调控基因表达[12]。其甲基化的程度与表达水平呈负相关[13]，在维持动物细胞的正常功能[14]、基因表达调控[15]、基因印迹[16]、胚胎发育[17]和肿瘤形成[18]等方面发挥着极其重要的作用。研究发现DNA甲基化使某些基因的表达功能关闭，去甲基化则诱导基因的重新活化和表达[19]。早在1984年就有学者研究发现DNA甲基化在脂肪形成过程中发挥着重要作用[20]。近年来，在猪[21]、鸡[22]和牛[23]等畜禽上也有脂肪沉积相关的报道，发现DNA甲基化调控脂肪沉积相关基因的表达，从而参与脂肪细胞分化和脂肪组织的生长发育过程。
1.2 RNA甲基化修饰RNA在不同的细胞中发挥重要的作用，如携带遗传信息、调节生化反应以及在亚细胞器中提供结构支架等[24]。除4种碱基外，还有一百多种经过化学修饰的核苷酸来帮助RNA在转录后水平对基因表达起调节作用，其中RNA甲基化修饰约占RNA修饰的60%，主要包括N6-腺苷酸甲基化(m6A)和N1-腺苷酸甲基化(m1A)等[25]。而m6A修饰是高等生物mRNA中最为普遍的修饰，是腺苷核苷酸第6位上的N发生甲基化修饰，在真核生物中也是最保守的化学修饰之一[26]。其主要是从以下两种途径来发挥功能：通过对甲基化转录本结构调控来诱导或者阻止蛋白与RNA相互作用；或者是识别m6A结合蛋白诱发后续的反应(图 1)。已被证实的m6A结合蛋白主要有YTHDF1、YTHDF2、YTHDF3、YTHDC1和YTHDC2[27]，在哺乳动物中m6A修饰在转录后水平调控RNA的剪切、翻译、稳定性、运输，并且发现可以决定干细胞的命运[28]。在畜禽中，m6A修饰主要是通过甲基转移酶FTO、去甲基酶复合体和m6A结合蛋白IGFBP1及其重要成脂基因的m6A修饰在脂肪沉积过程中发挥作用[29-30]。
1.3 组蛋白修饰
组蛋白修饰也是目前表观遗传修饰中研究得比较热门的机制之一，主要是通过组蛋白的N端发生修饰来影响基因表达的改变[32]，包括组蛋白磷酸化、乙酰化、甲基化和泛素化等。尤其是乙酰化和甲基化修饰，为调控蛋白提供其在组蛋白上的附着位点来改变染色质的结构和活性。组蛋白甲基化修饰位点不同而起着转录抑制或者转录激活的作用[33]。此外，组蛋白甲基化作为最稳定的组蛋白修饰方式，通过调控脂肪细胞分化过程中转录因子及脂肪组织特异性基因表达，从而影响脂肪组织的形成机制[34]。组蛋白乙酰化是一种可逆的动态过程，其稳态的维持主要是靠多种组蛋白乙酰基转移酶和去乙酰基酶共同作用的结果，乙酰化被发现与转录激活有关，而去乙酰化则与转录抑制有关。目前在人和小鼠上开展的研究较多，主要是对代谢疾病的表观遗传机制研究[35]。在畜禽脂肪沉积上关于组蛋白修饰的研究较少，仅仅在猪[36]和鸡[37]的脂肪沉积上有相关研究，利用脂肪沉积差异的品种进行RNA-seq和ChIP-seq联合分析，在全基因组范围内鉴定乙酰化修饰位点及预测差异峰值的转录因子结合位点，鉴定出与脂肪沉积相关的组蛋白修饰位点。
1.4 染色体重塑染色质作为真核生物遗传物质的载体，其结构高度致密，使得机体能更有效地储存遗传物质，同时也为生命活动的正常进行设置了屏障[38]。研究表明，在调节小鼠胚胎干细胞增殖和分化中染色体重塑发挥着重要作用[39]。目前，染色体重塑上的研究主要是对脂肪分化过程中标志性转录因子PPAR-γ和C/EBPα的研究[40]。对3T3-L1细胞进行诱导分化后，PPAR-γ基因座发生染色质重塑，呈开放状态[41]。在3T3-L1细胞分化的早期，C/EBPs蛋白与PPARγ2启动子结合，随后聚合酶Ⅱ及基础转录因子组装于PPARγ2启动子区，最后SWI/SNF染色质重塑复合物和转录因子TFIIH才组装于PPARγ2启动子上，促进转录起始复合物的形成[42]。迄今为止，染色体重塑在畜禽上还没有对脂肪沉积过程相关的研究。
1.5 非编码RNA非编码RNA作为一种重要的转录后基因表达调控因子，在真核生物中普遍存在，占总RNA的98%，参与调控多种生理代谢过程，研究的较多是miRNA、lncRNA和circRNA。miRNA长度为20~24 nt，可导致翻译抑制、组蛋白修饰和启动子位点的DNA甲基化，通过与靶基因的mRNA不完全互补配对来促进或者抑制靶基因mRNA的表达[43]。miRNA在畜禽的生长发育、疾病、免疫应答和肉质调控等过程起着重要作用[44]。在过去的十年中，miRNA已被证明是肌肉和脂肪组织代谢稳态的关键调节因子[45]。在脂肪形成过程中，miRNA还可以促进或抑制脂肪细胞分化和调节脂肪组织发育[46-47]。lncRNA，长度大于200 nt，广泛分布于细胞质或细胞核中，具有表达特异性，在转录和转录后水平影响基因表达[48]，其作为miRNA的海绵，通过降低miRNA的表达活性来促进靶基因的表达，这是目前lncRNA研究的最为详细的作用机制。此外，lncRNA还可以与特定的蛋白质结合来改变其定位和表达活性，以及诱导染色质重塑和组蛋白修饰[49]。circRNA主要是作为一种竞争性内源RNA(ceRNA)，以反向剪接的方式形成没有3′和5′的共价闭合的非编码RNA，在维持机体正常生长发育、调节机体平衡方面发挥重要作用[50]。circRNA作用机制与lncRNA类似，可作为miRNA海绵来影响基因的调控与表达，通过结合miRNA，使得miRNA不能靶向结合mRNA，进一步影响mRNA的正常翻译过程。与miRNA调控网络相比，ceRNA调控网络更加精细复杂，涉及到的RNA分子也更多，可以帮助解释一些生物学现象。目前，在畜禽脂肪沉积上ncRNA的研究主要是通过高通量测序的方法找到差异表达及高表达的ncRNA，qPCR来验证结果的准确性；利用生物信息学的方法来预测ncRNA的靶基因，双荧光素酶报告系统进行miRNA和mRNA/lncRNA/circRNA互作结果的验证；通过转染ncRNA过表达或者干扰载体来验证其功能。
2 表观遗传调控在畜禽脂肪沉积机制中的研究进展 2.1 DNA甲基化调控畜禽脂肪沉积DNA甲基化，作为维持基因沉默的关键表观遗传学因素，通过影响脂肪沉积过程中特异性基因、转录因子和转录辅助因子的表达来调控畜禽脂肪沉积过程。有学者对东北大学培育的肉鸡腹部脂肪组织CEBPA启动子区域357 bp的CpG位点甲基化进行研究，发现第2、3、7周龄的低脂型肉鸡的甲基化水平显著高于高脂型的肉鸡，表明CEBPA在脂肪组织中被甲基化，并可能调控肉鸡早期脂肪发育[22]。在瘦肉型和脂肪型猪的启动子区域也发现DNA甲基化存在差异，许多受差异甲基化启动子调控的基因与脂质代谢、嗅觉和感觉活动以及ATP酶活性等过程相关[21]。Zhang等[21]对长白猪(瘦肉型猪)和荣昌猪(脂肪型猪)脂肪酸代谢进行全基因组DNA甲基化的比较，发现长白猪背部脂肪的DNA甲基化水平高于荣昌猪，发现的483个差异甲基化区域位于启动子区域，主要影响嗅觉和脂质代谢，在长白猪中与ATP酶活性相关的基因启动子的甲基化明显更强。Li等[51]在不同背膘型猪全基因组DNA甲基化中也发现薄背膘型猪部分基因启动子区的甲基化水平显著高于厚背膘型。对韩国牛背最长肌的肌肉和肌内脂肪进行甲基化分析发现，PPARG1和FABP4基因的mRNA水平与相应基因CpG位点调控区域的DNA甲基化水平呈负相关[52]。SIRT6是一种ADP -核糖转移酶和NAD+-依赖的乙酰基和长链脂肪酸酰基脱酰基酶，已被证明是胰岛素分泌、糖代谢、脂代谢和癌症的调节剂[53]。Hong等[23]发现SIRT6在牛脂肪组织中表达水平高，CEBPB、CMYB和E2F1是SIRT6启动子活性的转录抑制因子，去甲基化显著增强了NRF1和E2F1与SIRT6核心启动子的结合，阐明了牛脂肪细胞中SIRT6表达的甲基化和转录调控的潜在机制。这些结果表明，位于启动子区的DNA甲基化与基因表达呈负相关，高甲基化会抑制脂肪分化过程中特异性基因的转录，而低甲基化则会促进特异性基因的转录。
2.2 m6A修饰调控畜禽脂肪沉积在脂肪分化过程中，m6A主要是通过去甲基化酶、甲基转移酶复合体、m6A结合蛋白以及脂肪沉积特异性基因来发挥作用。其中FTO作为去甲基化酶和脂肪特异性表达的基因参与脂肪分化过程，FTO表达与m6A水平呈负相关，促进脂肪形成[54]。2017年，Tao等[55]首次对野猪、荣昌猪和长白猪构建脂肪组织的m6A修饰图谱，发现m6A峰主要富集在终止密码子、编码区和3′UTR，与人和小鼠的分布方式类似。在猪前体脂肪细胞中，去甲基化酶FTO和YTHDF2均可以直接靶向Atg5和Atg7转录本，并以m6A修饰的方式介导它们的表达和脂肪细胞的自噬过程，以此来影响脂肪组织的形成[56]。在断奶仔猪的日粮中支链氨基酸(BCAA)添加过量或者不足均会使猪腹侧和背侧脂肪组织沉积减少，并且过量的BCAA会导致脂肪组织中m6A修饰的总体丰度下降，ACACA和FASN的m6A修饰减少[57]。2021年，Cheng等[58]首次构建低脂型和高脂型肉鸡的脂肪组织的甲基化图谱，发现m6A修饰在脂肪组织中存在差异，并且在高脂型肉鸡中，多个脂肪形成的重要基因(ACSL1和FASN)的甲基化程度与mRNA表达水平更高，表明m6A修饰可能通过调控mRNA的稳定性影响鸡肉脂肪沉积。鸡的肝组织中发现FTO基因通过介导肝组织mRNA去甲基化从而诱导脂肪沉积，表明FTO可以通过介导mRNA修饰加工，在脂肪沉积的过程中发挥重要作用。
2.3 组蛋白修饰调控畜禽脂肪沉积关于组蛋白修饰对脂肪形成重要基因表达作用的研究，大多数都是在细胞系和小鼠模型上进行的。在畜禽的脂肪组织中，对组蛋白修饰的研究还处于起步阶段，仅在猪和鸡上有相关的研究。在波兰大白猪、杜洛克猪和皮耶特兰猪的脂肪组织样本中研究其关键基因与组蛋白修饰之间的关系，发现在6个基因中，BSCL2、COPA、SCD和FABP4的转录水平与组蛋白修饰相关[36]。比较健康和脂肪肝出血综合征鸡的全基因组H3K27ac图谱和肝组织转录组，鉴定出1 321个H3K27ac差异区，443个差异表达基因，其中涉及脂质和能量代谢的主要是PCK1、APOA1、ANGPTL4和FABP1，结果进一步证实H3K27乙酰化失调和PPAR信号通路参与了肝组织中脂肪的过度积累和脂质代谢紊乱的发生[37]。在其他畜禽中还没有相关的研究，研究人员发现组蛋白修饰在畜禽脂肪沉积过程中扮演重要角色，但目前为止相关的研究还是比较少，而且组蛋白修饰的其他方式如磷酸化和泛素化等在畜禽脂肪沉积上还没有涉及，其详细的调控作用还需要进一步的研究。
2.4 ncRNA调控畜禽脂肪沉积ncRNA作为一类不编码蛋白质的RNA分子，主要是通过调控脂肪沉积特异性基因的表达，对脂肪沉积及脂肪细胞的分化发挥重要作用。在畜禽上，大量关于ncRNA调控脂肪沉积的研究，主要集中在miRNA、lncRNA和circRNA上。
2.4.1 miRNA调控畜禽脂肪沉积 研究人员通过RNA-seq技术在畜禽中不断挖掘影响脂肪沉积的重要miRNAs。Wang等[59]在不同的腹部脂肪含量的肉鸡系的腹部脂肪组织中发现了33个差异表达的miRNAs，其中最丰富的是let-7家族。Abdalla等[60]在家禽中发现了一些miRNAs(miR-3od、miR-26a、let7c、letzj、letrf、letzb和letza)多次在腹部脂肪组织中受到高度调控，这表明它们在脂肪沉积过程中重要的作用。在成年肉牛中，miRNAs在不同脂肪组织中表达有差异。在牛脂肪组织和乳腺中共鉴定出154个差异miRNAs，其中54个是脂肪组织特异的miRNAs[61]。此外，miRNA通过调控与脂肪沉积相关的靶基因来调控这一过程。在延边牛肌内脂肪中发现miR-22-3p通过WFIKKN2基因控制脂肪分化[62]。Bta-miR-376a可靶向KLF15负调控秦川牛脂肪细胞的增殖和分化[63]。MiR-106a通过靶向p21和BAMBI促进猪前体脂肪细胞的增殖和分化[64]。从1月龄羔羊骨骼肌组织中分离基质血管细胞，诱导其分化为成熟脂肪细胞，转染miR-340-5p过表达和干扰质粒，发现miR-340-5p抑制脂肪细胞分化特异基因的表达和脂滴的形成[65]。对湖羊和藏羊尾部脂肪进行miRNA测序，筛选出155个差异表达的miRNAs，其中17个被报道与脂质代谢有关。双荧光素酶验证发现miR-379-5p与HOXC9具有靶向关系[66]。在绵羊前体脂肪细胞中，oar-miR-432抑制脂肪分化，靶向正调控BMP2的表达[67]。此外，一些重要的miRNAs已被证实参与畜禽脂肪沉积调控(表 1)。
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表 1 参与畜禽脂肪分化调控的miRNAs Table 1 miRNAs involved in regulation of adipose differentiation in livestock and poultry |
2.4.2 lncRNA调控畜禽脂肪沉积 lncRNA是一类长度超过200 bp的ncRNA，其通过DNA、RNA和转录因子参与畜禽脂肪分化过程。2017年，Zhang等[86]在鸡腹部脂肪中鉴定出1 336个差异的lncRNAs和1 759个mRNAs，通过生物信息学分析发现其中有9个lncRNAs与mRNA有靶向关系，lncRNAs可能顺式作用于相邻的蛋白编码基因，从而控制腹部前脂肪细胞的分化。Li等[87]在牛前体脂肪细胞和脂肪细胞中发现16个lncRNAs在脂肪细胞分化过程中存在差异表达。在这些lncRNAs中，lncRNA-ADNCR在前体脂肪细胞中的表达明显高于分化的脂肪细胞，并通过靶向miR-204抑制成脂分化。利用RNA-seq技术对莱芜猪和大白猪肌内脂肪进行分析，发现XLOC_046142、XLOC_004398和XLOC_015408可能分别以MAPKAPK2、NR1D2和AKR1C4为靶点，在猪肌内脂肪生成和脂质积累中发挥重要调控作用[88]。Yi等[89]发现, lncIMF2基因的下调抑制了猪肌内脂肪细胞的增殖，lncIMF2基因的敲除抑制成脂分化标记基因PPAR-γ和ATGL的表达。对兰州大尾羊、小尾寒羊和藏羊的尾部脂肪进行lncRNA测序，发现其中4个差异表达的lncRNA(TCONS_00372767、TCONS_00171926、TCONS_00054953和TCONS_00373007)可能在尾部脂肪沉积过程中作为核心lncRNA发挥关键作用[90]。lncRNABADLNCR1作为牛脂肪细胞分化过程中的调节因子，可以负调控GLRX5的表达来抑制脂肪细胞的分化[91]。此外，还有lncRNA通过与miRNA的互作，减少miRNA和mRNA的结合来影响脂肪分化过程。Gga-miR-19b-3p通过下调ACSL1基因表达成为ACSL1的直接靶点。过表达gga-miR-19b-3p可以促进前体脂肪细胞的增殖及其随后的分化，敲除lncAD可顺式抑制其上游基因TXNRD1的表达，从而减少肌内前体脂肪细胞成脂分化，促进细胞增殖[92]。lncPRDM16抑制前体脂肪细胞增殖和调节lncPRDM16和PRDM16启动子活性[93]。这些结果表明，lncRNA可能顺式作用于邻近蛋白编码基因，影响腹部前体脂肪细胞的分化。lncRNA在脂肪沉积过程中的研究还有很多(表 2)。
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表 2 参与畜禽脂肪分化调控的lncRNAs Table 2 lncRNAs involved in regulation of adipose differentiation in livestock and poultry |
2.4.3 circRNA调控畜禽脂肪沉积 circRNA由于其环状结构，具有更强的稳定性和保守性。随着对circRNA研究的深入，大量的研究结果表明circRNA在机体脂肪沉积过程中发挥重要作用，在畜禽脂肪沉积上也有相关研究。Jin等[104]在固始鸡的腹部脂肪中发现gga_circ_0002520通过miR-215-5p可靶向NCOA3在腹部脂肪组织发育和脂肪沉积过程中发挥关键作用。Zhang等[105]首次在牦牛脂肪细胞分化过程中发现circRNA的表达模式，揭示了6种与脂肪形成相关的circRNA (novel_circ_ 0009127、novel_circ_0000628、novel_circ_0011513、novel_circ_0010775、novel_circ_0006981和novel_circ_0001494)。Feng等[106]在水牛中发现circMARK3通过上调成脂的标志基因PPARG、C/EBPa和FABP4的表达水平，促进水牛脂肪细胞和3T3-L1细胞成脂分化。circLCLAT1、circFNDC3AL、circlec19a和circARMH1可能通过PPAR和脂肪酸代谢相关通路调控miRNAs来影响脂肪形成[107]。最近的研究表明，circINSR通过减轻miR-15/16对靶基因的抑制来抑制牛前体脂肪细胞的脂肪形成[108-109]。还有其他一些circRNA在脂肪沉积中发挥重要作用(表 3)。综合前期的研究结果表明，circRNAs和lncRNAs以miRNAs为基，结合miRNA响应元件，形成影响基因表达的信号通路或轴。与miRNA调控网络相比，导致circRNA或lncRNA水平升高的ceRNA机制更加复杂，涉及的RNA分子也更多，这种新的基因表达调控模式有望成为新的研究热点。
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表 3 参与畜禽脂肪分化调控的circRNAs Table 3 circRNAs involved in regulation of adipose differentiation in livestock and poultry |
表观遗传学一方面解决了一些DNA序列无法解释的问题，另一方面对遗传与环境之间的关系提供了更好的理解，但这其中还有很多的未知需要去探索。以往对脂肪沉积的研究集中在小鼠上，重点关注其在脂肪细胞分化过程中的影响。在畜禽上，脂肪的沉积直接影响畜产品的品质，关乎养殖户的经济效应，同时对人类的健康也有间接影响，但脂肪沉积的研究还仅仅是找到一些重要的单基因的表观修饰，在全基因组范围内的表观修饰还是很少，详细的脂肪沉积机制更是没有找到。可以借鉴小鼠上的研究思路，找到适合畜禽的表观遗传机制调控的方法，深入研究畜禽脂肪沉积的表观遗传调控机制，提高畜牧业经济，还可以将表观遗传信息纳入基因组评价来提高育种值的预测精度，加速畜禽优秀品种的培育。同时，了解脂肪沉积如何受遗传因素和饲料管理及营养等方面的影响，是后续应该关注的重点；结合新的三代测序、三维基因组和空间转录组等新技术也可以拓宽脂肪沉积的研究思路。
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(编辑 郭云雁)