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。     

昆虫组蛋白修饰的研究进展

组蛋白修饰作为表观遗传修饰的一种主要形式,对基因表达和表型调控具有重要作用。组蛋白修饰的N端尾区可通过乙酰化、甲基化、磷酸化等修饰来改变染色质的状态以及调控基因的表达。与脊椎动物相比,昆虫种类繁多,且有变态发育、表型复杂等特征,可以成为探索动物社会行为、发育调控和毒理作用等表观遗传基础的模型。本文总结了昆虫组蛋白修饰的主要类型(乙酰化和甲基化修饰)及修饰酶的研究进展,对染色质免疫共沉淀测序技术(chromatin immunoprecipitation followed by sequencing,ChIP-seq)、染色质转座酶可及性测序技术(assay for transposase-accessible chromatin with high-throughput sequencing,ATAC-seq)、转录组测序技术(RNA-seq)、组蛋白修饰酶功能验证以及Western blot、免疫细胞化学(immunocytochemistry,ICC)、免疫组织化学(immunohistochemistry,IHC)、酶联免疫吸附测定(enzyme linked immunosor...     

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。     

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...     

Cross-protection interactions in insect pests: Implications for pest management in a changing climate

Agricultural insect pests display an exceptional ability to adapt quickly to natural and anthropogenic stressors. Emerging evidence suggests that frequent and varied sources of stress play an important role in driving protective physiological responses; therefore, intensively managed agroecosystems combined with climatic shifts might be an ideal crucible for stress adaptation. Cross-protection, where responses to one stressor offers protection against another type of stressor, has been well documented in many insect species, yet the molecular and epigenetic underpinnings that drive overlapping protective responses in insect pests remain unclear. In this perspective, we discuss cross-protection mechanisms and provide an argument for its potential role in increasing tolerance to a wide range of natural and anthropogenic stressors in agricultural insect pests. By drawing from existing literature on single and multiple stressor studies, we outline the processes that facilitate cross-protective interactions, including epigenetic modifications, which are understudied in insect stress responses. Finally, we discuss the implications of cross-protection for insect pest management, focusing on the consequences of cross-protection between insecticides and elevated temperatures associated with climate change. Given the multiple ways that insect pests are intensively managed in agroecosystems, we suggest that examining the role of multiple stressors can be important in understanding the wide adaptability of agricultural insect pests. © 2022 The Authors. Pest Management Science published by John Wiley & Sons Ltd on behalf of Society of Chemical Industry.     

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。     

牛印记基因的研究进展

基因组印记是一种表观调控机制,在哺乳动物的发育中具有重要作用。印记基因是仅一方亲本来源的同源基因表达,而来自另一亲本不表达的一种基因。近年来,印记基因被广泛研究。印记基因分为父系印记基因和母系印记基因,其表达具有组织特异性,而且在胚胎不同发育阶段的表达也具有一定差异,胚胎期的营养水平也影响印记基因的表达。DNA甲基化在调控印记基因的表达中起重要作用,影响细胞核移植过程细胞的表观重编程,并影响胎盘及内脏器官的正常发育;基因印记模式的改变也可以引起甲基化的改变进而导致基因印记的丢失等。本文综述了近年来关于牛的印记基因的研究进展情况,为印记基因的后续相关研究工作提供借鉴。     

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。