Identification and characterisation of microRNAs and Piwi-interacting RNAs in cockerels’ spermatozoa by Solexa sequencing

1. There has been substantial research focused on the roles of microRNAs (miRNAs) and Piwi-interacting RNAs (piRNAs) derived from mammalian spermatozoa; however, comparatively little is known about the role of spermatozoa-derived miRNAs and piRNAs within breeding cockerels’ spermatozoa.

2. A small RNA library of cockerels’ spermatozoa was constructed using Illumina high-throughput sequencing technology. Unique sequences with lengths of 18–26 nucleotides were mapped to miRBase 21.0 and unique sequences with lengths of 25–37 nucleotides were mapped to a piRNA database. A total of 1311 miRNAs and 2448 potential piRNAs were identified. Based on stem-loop qRT-PCR, 8 miRNAs were validated.

3. Potential target genes of the abundant miRNAs were predicted, and further Kyoto Encyclopedia of Genes and Genomes database (KEGG) and Gene Ontology (GO) analyses were performed, which revealed that some candidate miRNAs were involved in the spermatogenesis process, spermatozoa epigenetic programming and further embryonic development.

5. GO and KEGG analyses based on mapping genes of expressed piRNAs were performed, which revealed that spermatozoal piRNAs could play important regulatory roles in embryonic development of offspring.

6. The search for endogenous spermatozoa miRNAs and piRNAs will contribute to a preliminary database for functional and molecular mechanistic studies in embryonic development and spermatozoa epigenetic programming.     

Genetic potential for residual feed intake and diet fed during early- to mid-gestation influences post-natal DNA methylation of imprinted genes in muscle and liver tissues in beef cattle

Discovery of epigenetic modifications associated with feed efficiency or other economically important traits would increase our understanding of the molecular mechanisms underlying these traits. In combination with known genetic markers, this would provide opportunity to improve genomic selection accuracy in cattle breeding programs. It would also allow cattle to be managed to improve favorable gene expression. The objective of this study was to identify variation in DNA methylation between beef cattle of differential pre-natal nutrition and divergent genetic potential for residual feed intake (RFI). Purebred Angus offspring with the genetic potential for either high (HRFI) or low (LRFI) RFI were prenatally exposed to either a restricted maternal diet of 0.5 kg/d average daily gain (ADG) or a moderate maternal diet of 0.7 kg/d ADG from 30 to 150 d of gestation. We performed DNA methylation analysis of differentially methylated regions (DMR) of imprinted genes (Insulin-like growth factor 2 (IGF2) DMR2, IGF2/H19 imprinting control region (ICR) and IGF2 receptor (IGF2R) DMR2) using post-natal samples of longissimus dorsi (LD) muscle taken from male and female calves at birth and weaning, and of LD muscle, semimembranosus (SM) muscle, and liver samples collected from steers at slaughter (17 months of age). Interestingly, for all three DMR investigated in liver, LRFI steers had higher levels of methylation than HRFI steers. In LD muscle, IGF2/H19 ICR methylation differences for heifers at birth were due to pre-natal diet, while for steers at birth they were mostly the result of genetic potential for RFI with LRFI steers again having higher levels of methylation than HRFI steers. While results from repeated measures analysis of DNA methylation in steers grouped by RFI revealed few differences, in steers grouped by diet, we found higher methylation levels of IGF2 DMR2 and IGF2R DMR2 in LD muscle of restricted diet steers at weaning and slaughter than at birth, as well as increased methylation in LD muscle of restricted diet steers compared with moderate diet steers at weaning and/or slaughter. Our results suggest that differential pre-natal nutrition, and divergent genetic potential for RFI, induces tissue- and sex-specific alterations in post-natal IGF2 and IGF2R methylation patterns and that these patterns can vary with age in Angus beef cattle.     

主要农作物 lncRNA 鉴定与分析研究进展

随着基因组和生物信息学技术的进步,特别是高通量测序技术的发展,人们发现了许多没有蛋白质编码潜力的转录单位。其中,长链非编码RNA(long non-coding RNAs,lncRNAs)是一种长度大于200 nt的非编码RNA,有着独特的二级结构且不编码蛋白质,lncRNAs可以在核内发挥作用,也可以在细胞质中发挥作用。大量的证据表明,lncRNAs几乎是每个细胞过程的调节器,其重要性引起了越来越多的人关注。lncRNAs主要与mRNA、DNA、蛋白质和miRNA相互作用,从而以多种方式在表观遗传、转录、转录后、翻译和翻译后水平调控基因表达。lncRNAs介导的调控在动物中已经被大量研究,而植物中的lncRNAs研究才刚刚起步,近期许多新的研究结果表明,lncRNAs在植物逆境胁迫、生长发育及系统进化的过程中起了非常重要的作用。概述了lncRNAs的来源、分类及lncRNAs在植物发育中的调控机制,列举了可用于植物lncRNAs分析的主要数据库资源,并就近年来玉米、水稻、小麦等主要农作物lncRNAs研究情况进行了梳理和总结,为今后深入挖掘植物lncRNAs的作用机制及其在农作物中的应用提供一定的参考。     

染色质开放性与动物胚胎发育关系的研究进展

染色质开放性是指核小体或转录因子等蛋白与真核生物染色质DNA结合后,对其他蛋白能否再结合的开放程度,这一特性能够反映转录活性.染色质结构是动态变化的,染色质开放性与动物生长发育、细胞分化等过程密切相关,基因组开放染色质高效精准定位可为解析基因表达调控机制提供重要线索.本文介绍染色质开放性检测方法、染色质开放性的影响因素...     

草食家畜母体营养对子代生命健康影响的研究进展

母体营养对胎儿基因表达的调节作用逐渐成为围产期生命营养科学研究的热点。妊娠期作为发育可塑性的关键窗口,甲基供体对胎儿发育的相关代谢基因起到修饰作用,表观遗传学可能涉及其中的分子机制。动物研究表明,母体营养供给不足或过剩都会限制胎儿的生长。结合国内外研究报道,探讨了草食家畜妊娠期母胎的营养需求、激素在稳态调节中发挥的作用以及妊娠期能量需求对妊娠健康的重要意义,概括了妊娠期草食动物营养在表观遗传学方面的研究进展,探讨了表观遗传相关技术在草食家畜育种中的应用,以期为制定草食动物妊娠期最佳营养策略、提高胚胎质量、培养高质量后代提供参考。     

巴西橡胶树表观遗传研究进展

表观遗传是指在不涉及基因组DNA序列改变的情况下,基因功能发生了可逆的、可遗传的改变。研究表明,表观遗传调控在植物的生长发育及逆境胁迫应答反应中起着重要的作用。目前,表观遗传学研究主要集中在DNA甲基化、小RNA调控、组蛋白修饰、染色质重塑及基因组印迹等。与模式植物相比,橡胶树表观遗传的研究相对滞后,主要涉及DNA甲基化及miRNAs研究这2个方面。本文就橡胶树DNA甲基化及miRNAs的相关研究进行了简要综述,并对表观遗传在橡胶树中的研究前景提出展望。     

入侵植物黄顶菊不同器官和不同发育阶段DNA表观遗传多样性变化特征

DNA甲基化是植物DNA普遍存在的一种表观遗传修饰方式,不仅在植物快速适应新环境中发挥重要的作用,还参与植物生长发育和器官分化特异性过程。本研究通过构建优化的甲基化敏感扩增多态性（MSAP）体系来分析入侵植物黄顶菊不同器官和同一器官不同发育阶段的组织甲基化变异特征。结果表明：器官特异性MSAP体系利用筛选的13对引物共扩增536条条带,其中引物EhHM7对表观遗传多样性贡献率最大,多态性百分比为92.45%;发育阶段特异性MSAP体系利用筛选的14对引物共扩增407条条带,其中EcHM1对表观遗传多样性贡献率最大,多态性百分比为80.56%。甲基化类型变异结果显示,黄顶菊不同器官（根、茎和叶）间以及同一器官不同发育阶段（老叶和嫩叶）的组织间均表现出显著的甲基化水平差异性,半甲基化、全甲基化和整体甲基化三种甲基化变异类型中茎组织的甲基化发生率最高,分别达到30.28%、19.37%和49.66%,老叶组织的全甲基化和整体甲基化率显著高于嫩叶组织,分别达到33.29%和52.77%。主成分分析结果显示,黄顶菊叶片个体分布较根、茎的个体分布更为密集,且嫩叶较老叶密集,表明根个体间和茎个体间均存在较大的差异,这种个体差异大于黄顶菊叶片的个体间差异,且老叶的个体差异大于嫩叶,这种个体间差异在样品采集时不可忽视。所以,在利用表观遗传学方法进行黄顶菊入侵性的研究中,必须要制定科学的采样方案,把植物器官和生长发育阶段特异性作为一个重要因素考虑在内。     

作物分子生态学研究与展望

从分子水平研究作物与环境的关系及其作用规律已成为当代作物栽培学研究的重要内容,也是现代分子生态学的热点问题之一。作者从作物生长发育相关基因的遗传生态特性入手,着重分析在作物生长发育过程中的遗传分子生态特性与环境分子生态效应,在此基础上,提出应根据各作物各生长发育阶段相关基因的遗传生态特性,制定科学的调控技术,以实现作物高产、优质、高效、环境友好、安全的生产目的。并进一步阐述了当前作物分子生态学亟待解决的几个理论问题及主攻方向。     

热应激影响动物生殖的表观遗传学机制研究进展

随着全球温室效应剧增,夏季高温作为一种热应激源对动物生殖产生越来越大的影响,对世界各国的畜牧生产带来严重损失,因此,亟需对热应激影响动物生殖的机制进行深入研究。同时,越来越多的报道指出,在动物生殖的诸多生理过程中,表观遗传机制起到广泛而又重要的作用。基于此,文章总结了近期国内外热应激影响动物生殖的表观机制的研究进展,以便为解决实际生产中的问题提供理论支持。     

瓜实蝇DNA甲基化的MSAP体系建立与优化

瓜实蝇[Bactrocera cucurbitae (Coquillett)]是中国重要的蔬菜害虫,但其DNA甲基化研究尚未见报道。甲基化敏感扩增多态性是研究DNA甲基化的重要技术之一。通过对酶切反应、连接、PCR扩增和引物筛选等条件优化,建立瓜实蝇MSAP反应体系,即：①20 μL酶切体系中加入10 U的限制性内切酶与600 ng基因组DNA,于37℃酶切反应过夜;②20 μL连接体系中加入T4 连接酶1 U,HpaⅡ-MspⅠ-adapter接头50 pmol,EcoR I-adapter接头5 pmol,并于16℃反应12 h;③连接产物稀释后进行PCR预扩增和选择性扩增,再经6%变性聚丙烯酰胺凝胶电泳和银染检测结果。通过该体系筛选出适用于瓜实蝇基因组DNA甲基化多态性研究的6对引物;瓜实蝇MSAP体系为瓜实蝇的表观遗传学研究提供了技术支持。