玻璃化冷冻牛GV卵母细胞全基因组甲基化模式初探

旨在研究玻璃化冷冻对牛GV期卵母细胞全基因组甲基化的影响。本研究收集新鲜、玻璃化冷冻的牛GV卵母细胞,采用单细胞全基因组甲基化测序(ScWGBS)技术对新鲜、玻璃化法冷冻牛GV卵母细胞的全基因组甲基化水平进行检测,旨在揭示两者DNA甲基化模式的差异。结果表明,玻璃化冷冻不会对牛GV卵母细胞的全基因甲基化水平造成显著影响。基于基因本体(GO)和信号通路(KEGG)对140个差异甲基化区域(DMRs)进行分析,发现DMRs主要参与细胞发育、细胞骨架组织等功能,主要富集在PI3K-Akt信号通路、GnRH信号通路等,并筛选出与卵母细胞成熟(TSC2)、细胞骨架(NUDC)、细胞活力(MAFK)等相关的基因。上述结果,可为提高GV卵母细胞玻璃化冷冻效率奠定信息基础和研究方向。     

新鲜、玻璃化冷冻牛卵母细胞体外受精囊胚全基因组甲基化模式初探

旨在初步分析新鲜及玻璃化冷冻牛卵母细胞体外受精囊胚全基因组甲基化模式。本研究采用单细胞全基因组甲基化测序技术(scWGMS)检测新鲜、玻璃化冷冻牛卵母细胞体外受精囊胚全基因组甲基化水平和差异甲基化区域(DMR),探讨两者之间DNA甲基化水平上的差异。结果表明,新鲜卵母细胞体外受精囊胚的整体甲基化水平显著高于玻璃化冷冻卵母细胞体外受精囊胚的整体甲基化水平(P<0.05)。采用基因本体分析(GO)和相关信号通路(KEGG)对143个DMRs分析,发现生物学过程主要显著富集在新陈代谢、生长发育、细胞定位、细胞刺激反应等,通路主要富集在生长发育、核酸结合及组蛋白乙酰化上,并筛选出几个与之相关的候选基因(FARP2、PI4KA、FAM3D、NCOR2、ZNF827等)。本研究初步发现,玻璃化冷冻牛卵母细胞体外受精囊胚的全基因组甲基化水平显著降低,且DMR区域主要集中在ATP结合、生长发育及组蛋白乙酰化,为提高玻璃化冷冻卵母细胞体外受精囊胚质量提供信息参考。     

滩羊和湖羊背最长肌全基因组甲基化差异分析

本研究旨在通过不同品种绵羊背最长肌的全基因组甲基化差异分析,鉴定差异甲基化区域（DMR）和差异甲基化基因（DMG）,为解析绵羊骨骼肌发育差异奠定基础。采用全基因组重亚硫酸盐测序（WGBS）技术开展了周岁龄滩羊、湖羊和滩湖F2代背最长肌全基因组DNA的甲基化水平检测和差异甲基化区域分析,探讨品种间DNA甲基化水平的差异。结果显示,全基因组范围内滩羊、湖羊和滩湖F2代胞嘧啶（C）甲基化（mC）率分别为3.55%、3.18%和3.56%,3个群体的甲基化水平基本一致。对滩羊和湖羊的甲基化水平进行比较,在不同序列环境下共检测到97 731个DMRs和10 784个DMGs。在CG、CHH、CHG序列环境下3个群体甲基化水平无显著差异。对DMGs通过基因本体（GO）和相关信号通路（KEGG）分析,共检测到419个GO条目和20个信号通路,显著富集在细胞过程、细胞组分、结合、长期抑制等相关条目中。筛选出5个与肌肉调控有关的候选基因ACTA2、ROCK1、CALD1、MYH3、MYH10。本研究绘制了滩羊、湖羊和滩湖F2代全基因组甲基化图谱,为表观遗传调控肌肉发育研究和肉质候选基因的筛选提供理论参考。     

产蛋前期和产蛋高峰期鸡全基因组甲基化差异及其对肝脏转录组影响的研究

旨在通过对产蛋前期和产蛋高峰期鸡肝全基因组甲基化差异进行分析,解析基因组甲基化对不同发育阶段肝中基因表达差异的影响。本研究采用全基因组重亚硫酸盐测序（WGBS）技术对产蛋前期（20周龄）和产蛋高峰期（30周龄,各3只DNA混池）卢氏绿壳蛋鸡肝全基因组的甲基化水平进行检测,并与已有的肝mRNA转录组数据进行整合分析,探讨基因组甲基化对不同生理阶段基因表达差异的影响。结果表明,全基因组范围约有4%的胞嘧啶（C）发生了甲基化（mC）;两个生理阶段的总体甲基化水平基本一致。共检测到670个差异甲基化区域（DMRs）和356个差异甲基化基因（DMGs）。基因本体（GO）和相关信号通路（KEGG）分析发现,超甲基化DMGs显著富集在发育的正向调控、细胞形态改变的调控、VEGF信号通路、肌动蛋白细胞骨架的调控、粘着斑及间隙连接等相关过程,低甲基化DMGs显著富集在胚胎消化道形态的发生、间充质细胞增殖的正向调控、淀粉和蔗糖代谢及Wnt信号通路等相关过程。基因不同功能区域甲基化水平与基因表达水平有关,启动子（promoter）及基因体（gene body）区域甲基化水平与基因表达水平呈显著负相关,其他区域（内含子、3'UTR）的甲基化水平与基因的表达水平无明显关系。其中,与肝脂质代谢相关的候选基因RASD1、HAO1、UBE2O、MSRB3受甲基化调控。本研究绘制了不同生理时期卢氏绿壳蛋鸡全基因组甲基化图谱,结合mRNA转录组数据阐述了DNA甲基化在基因表达方面的调控作用,并鉴定出了不同生理时期受甲基化调控的基因,为深入研究表观遗传调控在不同生理时期蛋鸡肝代谢中的作用机制提供参考。     

鸡繁殖性能近交衰退相关CpG岛差异甲基化基因的筛选

鸡繁殖性能近交衰退是地方鸡遗传资源活体保种过程中面临的重要问题之一,本研究旨在探讨全基因组CpG岛（CpG island,CGI）区DNA甲基化在鸡繁殖性能近交衰退中的作用。分别从狼山鸡高近交组和低近交组中各选取健康母鸡3只,即试验分2个组,每组3个重复,然后采用全基因组重亚硫酸盐测序（WGBS）技术,检测分析两组个体性腺轴组织（包括卵巢和下丘脑）全基因组DNA甲基化差异,筛选差异甲基化区域（DMRs）,并对CpG岛区差异甲基化基因进行功能注释和富集分析。结果表明,狼山鸡高近交组和低近交组比较,其卵巢和下丘脑基因组整体甲基化水平均不存在显著差异（P>0.05）;高、低近交组间差异甲基化区域检测发现,下丘脑和卵巢中分别检测到5 948和4 593个差异甲基化区域,其中1 798和995个差异甲基化区域位于基因组CpG岛区,分别注释到1 020和552个基因;下丘脑中,这些CpG岛区差异甲基化基因显著富集在信号转导、神经系统发育、生殖系统发育和卵母细胞成熟调控等繁殖相关的GO条目,以及转化生长因子β信号通路、乙型肝炎、脂肪酸代谢、胰岛素信号通路等19条KEGG信号通路（P<0.05）;卵巢中,CpG岛区差异甲基化基因显著富集于12条信号通路（P<0.05）,包括慢性骨髓白血病、流感A、精氨酸和脯氨酸代谢、粘着连接等,一些与卵子发育和性激素分泌相关的信号通路也被富集到,如黄体酮介导的卵母细胞成熟、卵母细胞减数分裂、GnRH信号通路、雌激素信号通路等,其中包含CDC27、ADCY8、AKT3等10个差异甲基化基因。因此,本研究在狼山鸡高、低近交组间检测到了大量差异甲基化区域,并发现大量差异甲基化基因与繁殖性状相关,推测这些基因CpG岛区DNA甲基化可能在狼山鸡繁殖性能近交衰退调控中发挥重要作用,研究结果为进一步深入探索鸡繁殖性能近交衰退调控机制奠定了基础,为物种资源保护和家禽育种工作提供了理论参考依据。     

玻璃化冻存对蒙古驴卵母细胞甲基化及GFM1、MRPL15基因表达水平的影响

旨在探讨玻璃化冷冻对驴卵母细胞发育的影响。采集新鲜驴卵巢组织,将收集的卵母细胞分别按以下3种方式进行处理:直接冷冻(T1组)、冷冻复苏+成熟处理20h(T2组)、冷冻复苏+成熟处理40h(T3组);同时,取新鲜的GV期卵母细胞,分别设置相应的对照处理方式:新鲜细胞不进行成熟处理(C1组)、成熟处理20h(C2组),成熟处理40h(C3组)。各处理组细胞经转录组测序后,采用Trimmomatic(v0.36)软件对原始数据进行过滤,并对后续数据进行分析。过滤后将原始数据与参考基因库比对,进行注释分析和甲基化位点识别,比较各处理组之间的甲基化水平。结果显示,T1、T2组甲基化水平分别大于C1、C2组,T3组甲基化水平小于C3组;各冷冻处理组卵母细胞的CpGs甲基化水平为T1组>T2组>T3组。共选择出总体差异基因1269个,玻璃化冷冻处理细胞与未冷冻处理细胞之间具有差异的基因确定为677个。GFM1与MRPL15基因甲基化差异最为显著,基因通路富集到线粒体延伸途径中,这是导致玻璃化冷冻后驴卵母细胞成熟率较低的因素。研究结果为确定卵母细胞冷冻最佳条件奠定了试验基础。     

基于全基因组差异甲基化分析鉴别影响苏姜猪体重的候选基因

本研究旨在分析不同体重苏姜猪的全基因组DNA甲基化差异，以期筛选出影响苏姜猪体重的差异甲基化基因（differentially methylated genes，DMGs）。利用全基因组重亚硫酸盐测序（whole genome bisulfite sequencing，WGBS）技术分析了3头180日龄高体重和3头180日龄低体重苏姜猪的全基因组DNA的甲基化程度、差异甲基化区域（differentially methylated regions，DMRs）和DMGs，对DMGs进行GO和KEGG分析，鉴别影响苏姜猪体重的候选基因。结果显示，苏姜猪全基因组范围内胞嘧啶（C）的平均甲基化率为4.1%，胞嘧啶（C）甲基化平均98.41%发生在CG序列上，CG序列环境下外显子、内含子和3'UTR的甲基化水平高于启动子和5'UTR。本研究共检测出1 657个DMRs和575个DMGs，8号染色体上DMRs分布最多，88.89%的DMRs的长度在500 bp以内，62.78%的DMRs分布在远端基因间区，98个DMGs显著富集于TOR信号的负调控、碳水化合物衍生物分解代谢过程、脂肪细胞因子信号通路、FoxO信号通路等53个GO条目和29个信号通路，鉴别到5个与苏姜猪体重相关的候选基因：瘦素受体（leptin receptor，LEPR）基因、肿瘤坏死因子受体相关因子6（tumor necrosis factor receptor associated factor 6，TRAF6）基因、生肌因子6（myogenic factor 6，MYF6）基因、钙依赖性分泌激活因子2（calcium dependent secretion activator 2，CADPS2）基因和表皮生长因子（epidermal growth factor，EGF）基因。本研究利用WGBS绘制了高、低体重组苏姜猪的全基因组DNA甲基化图谱，为深入研究苏姜猪体重差异的分子机制奠定了基础。     

采用dCas9-SunTag-DNMT3A技术调控玻璃化冷冻牛卵母细胞IVF囊胚中IGF2R基因甲基化水平

旨在探究dCas9-SunTag-DNMT3A编辑系统对玻璃化冷冻牛卵母细胞IVF囊胚中IGF2R基因甲基化水平及胚胎发育能力的影响,为冷冻卵母细胞/胚胎特定位点DNA甲基化的精确调控奠定基础。本研究将经过体外成熟的牛卵母细胞进行玻璃化冷冻,随后进行体外受精,将受精所得到的原核胚进行dCas9-SunTag-DNMT3A编辑系统的注射,统计并计算卵母细胞的发育情况;通过亚硫酸盐测序的方式检测IGF2R基因启动子的甲基化水平,并利用荧光定量PCR检测IGF2R及相关基因的表达水平。与冷冻组相比,注射不同浓度的dCas9-SunTag-DNMT3A编辑系统后,只有40 ng·μL^-1组显著地提高了玻璃化冷冻卵母细胞IVF后的发育能力(P＜0.05),20和60 ng·μL^-1组间差异不显著(P＞0.05),但40 ng·μL^-1组发育效果仍然显著低于新鲜对照组(P＜0.05);对检测冷冻组、新鲜组、40 ng·μL^-1组IGF2R基因启动子甲基化水平分析发现,40 ng·μL^-1组水平与新鲜组相似,显著高于冷冻组(P＜0.05);荧光定量试验结果显示,40 ng·μL^-1组IGF2R基因mRNA表达水平相较于冷冻组显著降低(P＜0.05),与新鲜组相似。注射40 ng·μL^-1的dCas9-SunTag-DNMT3A甲基化编辑系统能够通过有效升高IGF2R基因启动子甲基化水平(P＜0.05)及显著降低其mRNA表达水平(P＜0.05),来正向调节玻璃化冷冻卵母细胞IVF胚胎的发育情况,提高胚胎发育能力,使得其卵裂率和囊胚率都得到显著提高(P＜0.05),同时促进胚胎发育相关基因的表达。     

玻璃化冷冻对哺乳动物MⅡ期卵母细胞表观遗传学的影响

玻璃化冷冻作为一种操作简单、成功率高的细胞保存方式具有诸多优点，广泛应用于农业、医学、生物等领域。但相较于新鲜卵母细胞，玻璃化冷冻后的卵母细胞仍存在许多问题，如玻璃化冷冻后的卵母细胞妊娠率和产活仔率低于新鲜的卵母细胞、基因表达异常等。表观遗传学是研究基因在核苷酸序列不发生改变的情况下基因表达的可遗传变化的一门学科。表观遗传修饰在不改变DNA序列的情况下使基因和环境之间产生相互作用。在体外胚胎生产过程中，外界环境因素会对表观遗传修饰造成影响。作者从表观遗传学方面综述了玻璃化冷冻对哺乳动物MⅡ期卵母细胞DNA和全基因组甲基化、组蛋白甲基化和乙酰化、磷酸化及泛素化、基因印迹、microRNA的影响，以及玻璃化冷冻MⅡ卵母细胞后表观遗传修饰的改变对转录过程中基因的表达影响，为揭示并调控玻璃化冷冻卵母细胞后表观遗传修饰事件、进一步提高玻璃化冷冻后卵母细胞的质量提供参考。     

玻璃化冷冻对牦牛未成熟卵母细胞发育能力及COC转录组的影响

旨在探讨玻璃化冷冻-解冻对牦牛未成熟卵母细胞发育能力及卵丘-卵母细胞复合体（COCs）转录组的影响，为完善牦牛COCs冷冻保存技术提供理论依据。本研究将未经成熟培养的牦牛COCs进行玻璃化冷冻-解冻后分为2组，A组：COCs体外成熟（IVM）后用普通牛精子进行体外受精（IVF），获得的受精卵在G-1胚胎培养液中培养72 h后转入G-2培养液培养96 h；B组：IVF后，受精卵在G-1培养液培养120 h后转入G-2培养液培养48 h；以未进行冷冻处理的新鲜COCs作为对照组（C组）：IVF后，受精卵在G-1培养液培养72 h后转入G-2培养液培养96 h。对牦牛新鲜COCs（n=3）和玻璃化冷冻-解冻的COCs（n=3）进行扩增、建库和转录组测序（RNA-seq）分析。结果发现，B组的卵裂率、囊胚率显著高于A组（P<0.05），但A组和B组的卵裂率、囊胚率均显著低于C组（P<0.05）。以|log₂（fold change）|≥ 2，Q<0.05为阈值，牦牛冻融COCs相对于新鲜COCs共筛选出851个差异表达基因（DEGs），其中上调846个，下调5个。GO分析表明，DEGs主要富集于生物过程、细胞组分和分子功能3大类；KEGG注释结果表明，DEGs富集到258条通路，其中16条通路显著富集（P<0.05）。研究表明，IVF后在G-1培养液中培养120 h可以提高牦牛玻璃化冷冻卵母细胞的后续发育能力；玻璃化冷冻影响牦牛COCs转录组，从而降低卵母细胞的发育潜力。该发现为完善牦牛COCs玻璃化冷冻技术提供了一定的理论基础。     

Effect of vitrification at different meiotic stages on epigenetic characteristics of bovine oocytes and subsequently developing embryos

Vitrification by the Cryotop method is frequently used for bovine oocyte cryopreservation. Nevertheless, vitrified oocytes still have reduced developmental competency compared with fresh counterparts. The objective of this study was to compare the effect of vitrification either at the germinal vesicle (GV) stage or at the metaphase II (MII) stage on epigenetic characteristics of bovine oocytes and subsequently developing embryos. Our results demonstrated that vitrification of oocytes at each meiotic stage significantly reduced blastocyst development after in vitro fertilization (IVF). However, vitrification at the GV stage resulted in higher blastocyst development than did vitrification at the MII stage. Irrespective of the meiotic stage, oocyte vitrification did not affect 5-methylcytosine (5mC) immunostaining intensity in oocyte DNA. However, at both stages, it caused a similar reduction of 5mC levels in DNA of subsequently developing blastocysts. Oocyte vitrification had no effect on the intensity of H3K9me3 and acH3K9 immunostaining in oocytes and subsequent blastocysts. The results suggest that irrespective of meiotic stage, oocyte vitrification alters global methylation in resultant embryos although such alteration in the oocytes was not detected. Oocyte vitrification might not influence histone acetylation and methylation in oocytes and resultant embryos. Vitrification at the immature stage was more advantageous for blastocyst development than at the mature stage.     

Cryopreservation of Immature Bovine Oocytes to Reconstruct Artificial Gametes by Germinal Vesicle Transplantation

Joining immature gamete cryopreservation and germinal vesicle transplantation (GVT) technique could greatly improve assisted reproductive technologies in animal breeding and human medicine. The present work was aimed to assess the most suitable cryopreservation protocol between slow freezing and vitrification for immature denuded bovine oocytes, able to preserve both nuclear and cytoplasmic competence after thawing. In addition, the outcome of germinal vesicle transfer procedure and gamete reconstruction was tested on the most effective cryopreservation system. Oocytes, isolated from slaughterhouse ovaries, were stored after cumulus cells removal either by slow freezing or by vitrification in open pulled straws. After thawing, oocytes were matured for 24 h in co-culture with an equal number of just isolated intact cumulus enclosed oocytes, and fixed in order to evaluate the stage of meiotic progression and cytoskeleton organization. Our results showed that after warming, vitrified oocytes reached metaphase II (MII) in a percentage significantly higher than oocytes cryopreserved by slow freezing (76.2% and 36.5% respectively, p < 0.05). Moreover, vitrification process preserved the organization of cytoskeleton elements in a higher proportion of oocytes than slow freezing procedure. Therefore vitrification has been identified as the elective method for denuded immature oocytes banking and it has been applied in the second part of the study. Our results showed that 38.3% of oocytes reconstructed from vitrified gametes reached the MII of meiotic division, with efficiency not different from oocytes reconstructed with fresh gametes. We conclude that vitrification represents a suitable method of GV stage denuded oocyte banking since both nuclear and cytoplasmic components derived from cryopreserved immature oocytes can be utilized for GVT.     

Vitrification of fully grown and growing porcine oocytes using germinal vesicle transfer

The survival rate of vitrified germinal vesicle (GV) stage porcine oocytes is very low, and it is not known if the vitrification damages the nucleus, cytoplasm or both. We have evaluated the eventual GV or cytoplasmic damage in fully grown (FG) and growing vitrified oocytes. Fifty-five percent of nonvitrified FG cumulus-denuded oocytes reached the metaphase II (MII) stage in culture. When growing oocytes from preantral (PA) and early antral (EA) follicles were matured in vitro, almost all oocytes were arrested at the GV stage (GV stage: PA 88.9 and EA 79.5%, respectively). When fresh GVs from FG, PA and EA oocytes were transferred into fresh enucleated FG oocytes and matured in vitro, some of them reached the MII stage (MII stage: FG/FG 57.5%, PA/FG 9.3% and EA/FG 35.3%, respectively). The maturation rate of vitrified FG oocytes was only 6.1% but increased dramatically when vitrified GVs from FG, PA and EA oocytes were transferred into fresh enucleated FG oocytes (MII stage: VitFG/FG 43.9%, VitPA/FG 7.1% and VitEA/FG 26.3%, respectively). These results were not significantly different from those for the nonvitrified groups (MII stage: FG/FG 57.5%, PA/FG 9.3% and EA/FG 35.3%, respectively). We activated the reconstructed oocytes that received fresh or vitrified GVs (FG/FG, EA/FG, VitFG/FG and VitEA/FG) and examined their embryonic development. Cleaved embryos (nonvitrified groups 13.0-61.8%, vitrified groups 33.3-40.0%) and blastocysts (nonvitrified groups 0.0-18.2%, vitrified groups 0.0-2.9%) were obtained after activation. These results demonstrate that vitrified porcine GVs maintain maturational and developmental competence and that vitrification predominantly damages the cytoplasm.     

猪卵母细胞在GV期与MⅡ期的冷冻保存效果比较研究

为比较猪卵母细胞在GV期与MⅡ期的冷冻保存效果,试验在这两个成熟阶段对其进行玻璃化冷冻,GV期卵母细胞解冻后培养至成熟,MⅡ期卵母细胞解冻后恢复2 h,然后采用免疫荧光标记、Western blotting和链霉蛋白酶溶解方法分别检测它们的皮质颗粒分布、CD9蛋白表达水平和透明带消化时间上的差异。结果表明,GV期卵母细胞在解冻后2 h的存活率显著低于MⅡ期卵母细胞（P<0.05）,但极体排出率与对照卵母细胞无明显差异（P>0.05）;在冷冻MⅡ期卵母细胞中,皮质颗粒的皮质区分布比例和CD9的蛋白表达水平显著下降（P<0.05）,但冷冻GV期卵母细胞经体外成熟后则无明显变化（P>0.05）;冷冻GV期与MⅡ期卵母细胞均不会影响透明带的消化时间（P>0.05）。由此可见,猪卵母细胞在GV期的冷冻存活率虽然较MⅡ期低,但其体外成熟后极体排出率、皮质颗粒分布和CD9蛋白表达水平均未受到冷冻的影响。     

Comparative Effects of Porcine Oocytes Vitrified at the GV and MⅡ Stages

This study was designed to compare the efficiency of porcine oocytes vitrified at the GV and MⅡ stages. The vitrified GV oocytes were matured in vitro and then evaluated their cortical granule distribution with immunofluorescence, CD9 protein level with Western blotting and zona pellucida dissolution time with pronse digestion method, as compared to vitrified MⅡ oocytes.The results showed that the survival percentages of oocytes vitrified at the GV stage were significantly lower than those vitrified at the MⅡ stage after 2 h of warming (P<0.05);However, there was no difference in maturation rate between vitrified and fresh oocytes (P>0.05). The oocytes vitrified at MⅡ stage resulted in significantly decreased normal cortical granule distribution and CD9 protein level (P<0.05), but no such results were found in vitrified GV oocytes after maturation (P>0.05). In addition, vitrification did not affect the dissolution time of zona pellucida in GV and MⅡ oocytes (P>0.05). The data demonstrated that despite of lower survival rate compared with MⅡ oocytes, vitrified porcine GV oocytes after maturation showed normal polar body extrusion, cortical granule distribution and CD9 protein level.