固始鸡1日龄和36周龄下丘脑高丰度差异性MiRNA的鉴定及功能预测分析

为鉴定鸡下丘脑发育相关特异性表达miRNA,基于固始鸡1日龄和36周龄下丘脑小RNA的Solexa测序数据,共鉴定到266种2个发育阶段共表达的miRNA,其中157种miRNA的表达水平被显著下调,22种被显著上调.聚类分析显示,鸡下丘脑高丰度差异性miRNA主要集中于let-7、mir-181、mir-30、mir-99、mir-1和mir-17等基因家族.另外,预测了10种高丰度差异性miRNA的靶基因,并进行了相应的GO分析和KEGG通路分析.结果显示,预测靶基因在发育过程、代谢过程、细胞过程和生物学过程调节等4个生物学过程以及细胞周期、粘着斑、TGF-beta信号通路和MAPK信号通路等通路中显著富集.研究结果为进一步揭示miRNA调控鸡下丘脑发育的分子机制提供了有益线索.     

miRNA-9基因家族进化分析及其靶基因预测

microRNAs(miRNA)是真核生物中一类长度约为21～25个核苷酸的非编码小分子RNA,在转录后水平调控基因的表达。该文在miRBase中搜索后生动物的mir-9基因序列。47个物种中共搜索到120条mir-9基因序列,说明mir-9基因家族广泛存在于不同物种中。基因定位显示86%的mir-9基因存在于基因间隔区(IGR),多序列比对发现miR-9基因家族成熟序列的第2位到第8位碱基以及第14位到第18位碱基为保守碱基。进化分析表明mir-9b和mir-9c可能是此基因家族最早出现的基因形式,即祖先基因。这些祖先基因经过串联重复、大片段重复、个别碱基的缺失及突变等方式形成了脊椎动物中miR-9-1至miR-9-7数个基因。分别采用四个miRNA靶基因预测软件对mmu-miR-9的靶基因进行预测,发现miR-9与神经系统发育、心肌系统疾病和跨膜运输系统等密切相关。该研究为今后进一步研究miRNA调控的神经系统发生和神经细胞生长与分化的机制奠定了基础。     

鸡mir-17-92基因簇的结构、功能及其调控

mir-17-92基因簇(mir-17-92 cluster)是脊椎动物的一个保守miRNA基因簇,在哺乳动物细胞增殖、分化、凋亡及发育等多种生物学过程中起重要的调控作用.同时,mir- 17-92基因簇又是一个癌基因,在多种肿瘤中表达.尽管对mir-17-92基因簇的研究非常广泛,但其作用机制还不完全清楚.鸡mir- 17-92基因簇的结构组成特点、功能及其作用机制尚未见研究报道.该文根据同一miRNA基因簇的miRNAs在功能上相关的特点,以鸡mir- 17-92基因簇序列为研究对象,采用生物信息学研究方法和手段,开展了鸡mir- 17-92基因簇的基因组结构、miRNAs序列组成、靶生物学过程和信号通路以及miRNAs结合位点分布特点等分析研究.结果发现,鸡mir- 17-92基因簇调控MAPK、Wnt和TGF-β等多个重要细胞信号通路;miRNA结合位点分布分析显示,该miRNA基因簇多个成员共同作用于同一个靶基因,提示该基因簇的miRNAs成员以组合和协同的方式调控靶基因.该研究为深入了解mir-17-92基因簇如何调控癌症和发育中的关键细胞过程奠定了基础.     

miR-34基因家族的分子进化

根据miRNA基因在进化中高度保守的特点,利用生物信息学方法在目前已测序的动物物种中搜寻参与哺乳动物早期发育调控的mir-34基因的同源序列,在33个不同的动物物种中获得了miR-34基因的54条同源序列,其中18条为新发现的序列。表明miR-34是高度保守的,广泛存在于后生动物中。目前发现的mir-34基因80%位于基因间隔区,少数位于蛋白编码基因的内含子区和3′UTR上。不同动物中,mir-34基因成熟序列的同源性为68%,前体序列为38.89%。在无脊椎动物中只有一个mir-34,而在几乎所有的脊椎动物中都有mir-34a,mir-34b,mir-34c,形成miR-34基因家族。系统进化分析表明,脊椎动物中miR-34基因家族是通过基因的串联和局部重复形成的,这个过程中伴随着个别碱基的变异。     

植物microRNA的保守性及其分布的分析

MicroRNA(miRNA)是真核生物中具有重要调控作用的小分子非编码RNA。本文对miRNA官网miRBase数据库Release 22.1中隶属于植物界的绿藻门、苔藓植物门、蕨类植物门、裸子植物门、被子植物门共计82个物种的miRNA进行了统计分析。miRBase共收录植物miRNA 前体8 615个,成熟miRNA 10 414条,隶属于2 892个miRNA家族。绿藻门miRNA与其他4个门miRNA无同源性;对其他4个门植物miRNA的保守性进行研究,发现存在于2个植物门的miRNA家族有26个,属于中度保守miRNA家族;14个miRNA家族存在于3个及3个以上植物门中,属于高度保守miRNA家族,其中7个miRNA家族系苔藓、蕨类、裸子和被子植物共有,是植物中最保守的miRNA。分析表明,超过30个miRNA家族的植物有35种。进一步对40个中度或者高度保守miRNA在35种植物中的分布进行研究,发现miRNA家族及其成员在物种间的分布存在较大的差异。这些分布上的差异一方面反映不同植物中miRNA的研究深度不同,另一方面也反映出miRNA在植物进化过程中的适应性调整。研究不同植物中miRNA家族的分布,可在miRNA水平为植物早期进化同源性的研究提供分子依据。     

植物microRNA的保守性及其分布的分析

MicroRNA(miRNA)是真核生物中具有重要调控作用的小分子非编码RNA。本文对miRNA官网miRBase数据库Release 22.1中隶属于植物界的绿藻门、苔藓植物门、蕨类植物门、裸子植物门、被子植物门共计82个物种的miRNA进行了统计分析。miRBase共收录植物miRNA 前体8 615个,成熟miRNA 10 414条,隶属于2 892个miRNA家族。绿藻门miRNA与其他4个门miRNA无同源性;对其他4个门植物miRNA的保守性进行研究,发现存在于2个植物门的miRNA家族有26个,属于中度保守miRNA家族;14个miRNA家族存在于3个及3个以上植物门中,属于高度保守miRNA家族,其中7个miRNA家族系苔藓、蕨类、裸子和被子植物共有,是植物中最保守的miRNA。分析表明,超过30个miRNA家族的植物有35种。进一步对40个中度或者高度保守miRNA在35种植物中的分布进行研究,发现miRNA家族及其成员在物种间的分布存在较大的差异。这些分布上的差异一方面反映不同植物中miRNA的研究深度不同,另一方面也反映出miRNA在植物进化过程中的适应性调整。研究不同植物中miRNA家族的分布,可在miRNA水平为植物早期进化同源性的研究提供分子依据。     

miR-34基因家族的分子进化

根据miRNA基因在进化中高度保守的特点，利用生物信息学方法在目前已测序的动物物种中搜寻参与哺乳动物早期发育调控的mir-34基因的同源序列，在33个不同的动物物种中获得了miR-34基因的54条同源序列，其中18条为新发现的序列。表明miR-34是高度保守的，广泛存在于后生动物中。目前发现的mir-34基因80％位于基因间隔区，少数位于蛋白编码基因的内含子区和3′UTR上。不同动物中，mir-34基因成熟序列的同源性为68%，前体序列为38.89%。在无脊椎动物中只有一个mir-34，而在几乎所有的脊椎动物中都有mir-34a，mir-34b，mir-34c, 形成miR-34基因家族。系统进化分析表明,脊椎动物中miR-34基因家族是通过基因的串联和局部重复形成的，这个过程中伴随着个别碱基的变异。     

日本七鳃鳗物种特异性microRNAs及其前体的识别与验证

MicroRNAs(miRNAs)对参与多种生物代谢过程的基因在转录及转录后水平进行负调控。近年来,随着深度测序及芯片技术的应用,有关miRNA的发现和功能分析在植物和动物中得到广泛研究。文章利用第二代测序技术对日本七鳃鳗(Lampetra japonica)白细胞的小RNA进行了高通量测序,共得到5 207 787条小RNA序列,其中4 739 346条序列可以拼接为10 989种mi RNA变体。基于序列相似性分析,发现这10 989个变体序列与306个已知的保守mi RNA家族成员序列相匹配;其中,6个保守miRNA家族成员呈极高丰度表达,表明mi RNA在物种间具有保守性。70个未注释序列被预测为新的miRNA。通过miRNA微阵列技术鉴定与验证了34个新预测的mi RNA在免疫处理的日本七鳃鳗白细胞中表达,其中16个mi RNA前体的最低折叠自由能系数大于0.85,说明日本七鳃鳗存在特异性miRNA。这些物种特异性miRNAs的存在可能在日本七鳃鳗的白细胞生长、发育和对疾病的反应中发挥重要的调控作用。     

基于小RNA测序的风轮菜microRNA及其靶基因分析

本研究以风轮菜(Clinopodium chinense(Benth.)O.Kuntze)为材料,采用BGISEQ-500测序平台对风轮菜根、茎和叶的小RNA进行转录组测序,并对其黄酮类物质合成途径中参与调控的microRNA(miRNA)及其靶基因进行了分析.结果显示,鉴定出的保守miRNA有86个,属于26个家族,...     

砀山酥梨TCP基因家族全基因组鉴定与分析

TCP蛋白是植物特有的转录因子家族之一,在植物生长和发育等多个过程起到重要作用。本研究利用生物信息学方法对砀山酥梨TCP基因家族成员、染色体定位、进化分析、亚组分类、保守域结构和保守元件进行了相关分析。结果显示,梨TCP基因家族含有34个成员;进化分析表明,根据进化树拓扑结构将其分为两类:ClassⅠ和ClassⅡ,其中ClassⅡ可被分为CYC/TB1和CIN两个小组。结构域分析表明,梨TCP基因家族TCP结构域高度保守;保守元件分析表明,梨TCP基因家族包含5个保守元件:元件1是TCP保守域;元件2为R结构域,元件3、4和5为功能尚未鉴定的结构域,所有梨TCP蛋白都含有元件1,ClassⅡ组中CYC/TB1小组包含特异元件2。以上结果将为今后揭示梨TCP基因的功能提供重要的理论基础。     

A subset of skin-expressed microRNAs with possible roles in goat and sheep hair growth based on expression profiling of mammalian microRNAs

The microRNAs (miRNAs) are an extensive class of small noncoding RNAs (18-25 nucleotides) with probable roles in the regulation of gene expression. Due to the fact that miRNAs are conserved in closely related eukaryotes and some are also conserved across a larger evolutionary distance, their potential functions in mammalian development are under active study. In order to identify mammalian miRNAs that might function in hair growth, we characterized the expression of 159 miRNAs in adult body side skin and ear skin from goat and sheep using microarray analysis. Of these, 19 miRNAs were specifically expressed or greatly enriched in body side skin in goats and sheep. This suggests hair growth-specific functions for miRNAs. Of the coexpressed 105 miRNAs, the degree of correlation within species is higher than interspecies. Nine of the expressed miRNAs were detected exclusively in the goat body side skin area where more cashmere was grown than coat hair; mmu-miR-720 and mmu-miR-199b were expressed primarily in goat skin. The identification of 105 of skin-expressed miRNAs whose expression behavior is conserved in goats and sheep differentiating hair follicles implicates these miRNAs have functions in mammalian hair follicles growth and development. We demonstrate that miRNAs previously associated with hair follicles in the mouse are also expressed in the adult skin of goats and sheep. In addition, 69 more conserved miRNAs cross-species were discerned in the study. Of them, the let-7, mir-17, mir-30, mir-15, and mir-8 gene families were expressed in high frequency. These results reveal critical roles of them in skin and hair follicle development and function.     

Evolution of coding and non-coding genes in HOX clusters of a marsupial

ABSTRACT: BACKGROUND: The HOX gene clusters are thought to be highly conserved amongst mammals and othervertebrates, but the long non-coding RNAs have only been studied in detail in human andmouse. The sequencing of the kangaroo genome provides an opportunity to use comparativeanalyses to compare the HOX clusters of a mammal with a distinct body plan to those ofother mammals. RESULTS: Here we report a comparative analysis of HOX gene clusters between an Australian marsupialof the kangaroo family and the eutherians. There was a strikingly high level of conservationof HOX gene sequence and structure and non-protein coding genes including the microRNAsmiRNA-196a, miRNA-196b, miRNA-10a and miRNA-10b and the long non-coding RNAsHOTAIR, HOTAIRM1 and HOXA11AS that play critical roles in regulating gene expressionand controlling development. By microRNA deep sequencing and comparative genomicanalyses, two conserved microRNAs (miR-10a and miR-10b) were identified and one newcandidate microRNA with typical hairpin precursor structure that is expressed in bothfibroblasts and testes was found. The prediction of microRNA target analysis showed thatseveral known microRNA targets, such as mir-10, mir-414 and mir-464, were found in thetammar HOX clusters. In addition, several novel and putative miRNAs were identified thatoriginated from elsewhere in the tammar genome and that target the tammar HOXB andHOXD clusters. CONCLUSIONS: This study confirms that the emergence of known long non-coding RNAs in the HOXclusters clearly predate the marsupial-eutherian divergence 160 Ma ago. It also identified anew potentially functional microRNA as well as conserved miRNAs. These non-codingRNAs may participate in the regulation of HOX genes to influence the body plan of thismarsupial.     

Identification and profiling of microRNAs from skeletal muscle of the common carp

The common carp is one of the most important cultivated species in the world of freshwater aquaculture. The cultivation of this species is particularly productive due to its high skeletal muscle mass; however, the molecular mechanisms of skeletal muscle development in the common carp remain unknown. It has been shown that a class of non-coding ～22 nucleotide RNAs called microRNAs (miRNAs) play important roles in vertebrate development. They regulate gene expression through sequence-specific interactions with the 3' untranslated regions (UTRs) of target mRNAs and thereby cause translational repression or mRNA destabilization. Intriguingly, the role of miRNAs in the skeletal muscle development of the common carp remains unknown. In this study, a small-RNA cDNA library was constructed from the skeletal muscle of the common carp, and Solexa sequencing technology was used to perform high throughput sequencing of the library. Subsequent bioinformatics analysis identified 188 conserved miRNAs and 7 novel miRNAs in the carp skeletal muscle. The miRNA expression profiling showed that, miR-1, miR-133a-3p, and miR-206 were specifically expressed in muscle-containing organs, and that miR-1, miR-21, miR-26a, miR-27a, miR-133a-3p, miR-206, miR-214 and miR-222 were differentially expressed in the process of skeletal muscle development of the common carp. This study provides a first identification and profiling of miRNAs related to the muscle biology of the common carp. Their identification could provide clues leading towards a better understanding of the molecular mechanisms of carp skeletal muscle development.