环状RNA：竞争性内源RNA新成员

环状RNA（circRNA）广泛存在于各种生物细胞中,具有结构稳定、丰度高和组织特异性表达等特征。最近的研究表明,一些circRNA作为竞争性内源NRNA（ceRNA）来发挥基因表达调控的作用。circRNA利用其microRNA（miRNA）应答元件结合miRNA,以阻断miRNA对其靶标表达的抑制作用,从而调控其他相关RNA的表达水平。circRNA在基因表达调控中重要作用的发现不仅丰富了人们对ceRNAiN控网络的认识,而且提示circRNA在药物开发和疾病诊治中具有良好的应用前景。     

DEBKS: A Tool to Detect Differentially Expressed Circular RNAs

Circular RNAs(circRNAs) are involved in various biological processes and disease pathogenesis. However, only a small number of functional circRNAs have been identified among hundreds of thousands of circ RNA species, partly because most current methods are based on circular junction counts and overlook the fact that a circ RNA is formed from the host gene by backsplicing(BS). To distinguish the expression difference originating from BS or the host gene, we present differentially expressed back-s...     

Independent evolution of functional MHC class II DRB genes in New World bat species

Genes of the major histocompatibility complex (MHC) play a pivotal role in the vertebrate immune system and are attractive markers for functional, fitness-related, genetic variation. Although bats (Chiroptera) represent the second largest mammalian order and are prone to various emerging infectious diseases, little is known about MHC evolution in bats. In the present study, we examined expressed MHC class II DRB sequences (exons 1 to 4) of New World bat species, Saccopteryx bilineata, Carollia perspicillata, Noctilio albiventris and Noctilio leporinus (only exon 2). We found a wide range of copy number variation of DRB loci with one locus detected in the genus Noctilio and up to ten functional loci observed in S. bilineata. Sequence variation between alleles of the same taxa was high with evidence for positive selection. We found statistical support for recombination or gene conversion events among sequences within the same but not between bat species. Phylogenetic relationships among DRB alleles provided strong evidence for independent evolution of the functional MHC class II DRB genes in the three investigated species, either by recent gene duplication, or homogenization of duplicated loci by frequent gene conversion events. Phylogenetic analysis of all available chiropteran DRB exon 2 sequences confirmed their monophyletic origin within families, but revealed a possible trans-species mode of evolution pattern in congeneric bat species, e.g. within the genera Noctilio and Myotis. This is the first study investigating phylogenetic relationships of MHC genes within bats and therefore contributes to a better understanding of MHC evolution in one of the most dominant mammalian order.     

A genomics approach to the detection of positive selection in cattle: adaptive evolution of the T-cell and natural killer cell-surface protein CD2

The detection of adaptive evolution at the molecular level is of interest not only as an insight into the process of evolution but also because of its functional implications for genes of interest. Here, we present the first genomics approach to detecting positive selection operating on the Bos taurus lineage, an important domestic species. This analysis led to the identification of the T-cell and natural killer (NK) cell receptor cluster of differentiation 2 (CD2) as having a strong signal of selection. Further detailed investigation of CD2 revealed that this gene was subject to positive selection during the evolution of a number of mammalian lineages. Moreover, we show that selection has operated primarily on the extracellular domain of CD2 and discuss the implications of this for an important regulator of the adaptive immune response.     

Episodic evolution of growth hormone in primates and emergence of the species specificity of human growth hormone receptor

Growth hormone (GH) evolution is very conservative among mammals, except for primates and ruminant artiodactyls. In fact, most known mammalian GH sequences differ from the inferred ancestral mammalian sequence by only a few amino acids. In contrast, the human GH sequence differs from the inferred ancestral sequence by 59 amino acids. However, it is not known when this rapid evolution of GH occurred during primate evolution or whether it was due to positive selection. Also, human growth hormone receptor (GHR) displays species specificity; i.e., it can interact only with human (or rhesus monkey) GH, not with nonprimate GHS: The species specificity of human GHR is largely due to the Leu-->Arg change at position 43, and it has been hypothesized that this change must have been preceded by the His-->Asp change at position 171 of GH. Is this hypothesis true? And when did these changes occur? To address the above issues, we sequenced GH and GHR genes in prosimians and simians. Our data supported the above hypothesis and revealed that the species specificity of human GHR actually emerged in the common ancestor of Old World primates, but the transitional phase still persists in New World monkeys. Our data showed that the rapid evolution of primate GH occurred during a relatively short period (in the common ancestor of higher primates) and that the rate of change was especially high at functionally important sites, suggesting positive selection. However, the nonsynonymous rate/synonymous rate ratio at these sites was <1, so relaxation of purifying selection might have played a role in the rapid evolution of the GH gene in simians, possibly as a result of multiple gene duplications. Similar to GH, GHR displayed an accelerated rate of evolution in primates. Our data revealed proportionally more amino acid replacements at the functionally important sites in both GH and GHR in simians but, surprisingly, showed few coincidental replacements of amino acids forming the same intermolecular contacts between the two proteins.     

circRNAs在植物中的研究进展

circular RNA(circRNA)是一类具有闭合环状结构的内源性非编码RNA,广泛存在于多种真核生物中,具有结构稳定、序列保守、表达特异性等特征。研究表明circRNAs可作为海绵(sponge)吸附microRNA(miRNA)并参与其表达调控过程,也可通过与蛋白互作调控基因表达等生物过程;发现circRNAs不仅参与植物激素信号转导等生理过程,而且还能在植物响应逆境胁迫中起到重要作用。该文主要对近年来国内外有关circRNAs的类型、形成机制、功能及其在植物生长发育过程中的研究进展进行了综述,并讨论了circRNAs的研究意义及存在的问题,为进一步研究circRNAs在植物中的作用机制及其基因调控网络提供参考。     

Evolutionary patterns of RNA-based duplication in non-mammalian chordates

The role of RNA-based duplication, or retroposition, in the evolution of new gene functions in mammals, plants, and Drosophila has been widely reported. However, little is known about RNA-based duplication in non-mammalian chordates. In this study, we screened ten non-mammalian chordate genomes for retrocopies and investigated their evolutionary patterns. We identified numerous retrocopies in these species. Examination of the age distribution of these retrocopies revealed no burst of young retrocopies in ancient chordate species. Upon comparing these non-mammalian chordate species to the mammalian species, we observed that a larger fraction of the non-mammalian retrocopies was under strong evolutionary constraints than mammalian retrocopies are, as evidenced by signals of purifying selection and expression profiles. For the Western clawed frog, Medaka, and Sea squirt, many retrogenes have evolved gonad and brain expression patterns, similar to what was observed in human. Testing of retrogene movement in the Medaka genome, where the nascent sex chrosomes have been well assembled, did not reveal any significant gene movement. Taken together, our analyses demonstrate that RNA-based duplication generates many functional genes and can make a significant contribution to the evolution of non-mammalian genomes.     

Genome-wide identification of circular RNAs in adult Schistosoma japonicum

Circular RNAs (circRNAs) are a class of novel, widespread, covalently closed RNAs that have played an essential role in animal gene regulation. To systematically explore circRNAs in the blood fluke Schistosoma japonicum, we performed RNA sequencing and bioinformatics analysis, and found that hundreds of circRNAs showed gender-associated expression. Among these identified circRNAs, more than 77.54% and 74.73% were putatively derived from the exon region of the genome and some circRNAs showed gender-associated expressions. The functional prediction of circRNAs (circ_003826 and circ_004690) showed potential binding sites and possibly acted as the sponge to regulate microRNAs (miRNAs) sja-miR-1, sja-miR-133 and sja-miR-3504. Altogether, these findings demonstrated that S. japonicum also contains circRNAs, which may have potential regulatory roles during schistosome development.     

Chromosome conformation capture uncovers potential genome-wide interactions between human conserved non-coding sequences

Comparative analyses of various mammalian genomes have identified numerous conserved non-coding (CNC) DNA elements that display striking conservation among species, suggesting that they have maintained specific functions throughout evolution. CNC function remains poorly understood, although recent studies have identified a role in gene regulation. We hypothesized that the identification of genomic loci that interact physically with CNCs would provide information on their functions. We have used circular chromosome conformation capture (4C) to characterize interactions of 10 CNCs from human chromosome 21 in K562 cells. The data provide evidence that CNCs are capable of interacting with loci that are enriched for CNCs. The number of trans interactions varies among CNCs; some show interactions with many loci, while others interact with few. Some of the tested CNCs are capable of driving the expression of a reporter gene in the mouse embryo, and associate with the oligodendrocyte genes OLIG1 and OLIG2. Our results underscore the power of chromosome conformation capture for the identification of targets of functional DNA elements and raise the possibility that CNCs exert their functions by physical association with defined genomic regions enriched in CNCs. These CNC-CNC interactions may in part explain their stringent conservation as a group of regulatory sequences.     

CIRCpedia v2: An Updated Database for Comprehensive Circular RNA Annotation and Expression Comparison

Circular RNAs (circRNAs) from back-splicing of exon(s) have been recently identified to be broadly expressed in eukaryotes, in tissue- and species-specific manners. Although functions of most circRNAs remain elusive, some circRNAs are shown to be functional in gene expression regulation and potentially relate to diseases. Due to their stability, circRNAs can also be used as biomarkers for diagnosis. Profiling circRNAs by integrating their expression among different samples thus provides molecular basis for further functional study of circRNAs and their potential application in clinic. Here, we report CIRCpedia v2, an updated database for comprehensive circRNA annotation from over 180 RNA-seq datasets across six different species. This atlas allows users to search, browse, and download circRNAs with expression features in various cell types/tissues, including disease samples. In addition, the updated database incorporates conservation analysis of circRNAs between humans and mice. Finally, the web interface also contains computational tools to compare circRNA expression among samples. CIRCpedia v2 is accessible at http://www.picb.ac.cn/rnomics/circpedia.     

Patterns of Historical Balancing Selection on the Salmonid Major Histocompatibility Complex Class II β Gene

Allelic variation in the major histocompatibility class (MHC) IIB gene of salmonids is analyzed for patterns indicative of natural selection acting at the molecular level. Sequence data for the second exon of this MHC gene were generated for 11 species in three salmonid genera: Oncorhynchus, Salmo, and Salvelinus. Phylogenetic analysis of nucleotide sequences revealed: (1) monophyletic grouping of alleles from each genus, (2) transspecies evolution of alleles within Salmo and Salvelinus, and (3) differential patterns of transspecies evolution within the genus Oncorhynchus. Within Oncorhynchus, five of seven species had alleles that were species-specific or nearly so, while the remaining two, O. mykiss and O. clarkii, retained ancestral polymorphisms. The different patterns in Oncorhynchus and the other two genera could be due to historical demographic effects or functional differences in MHC molecules in the three genera, but the two hypotheses could not be distinguished with the current dataset. An analysis of recombination/gene conversion identified numerous recombinant alleles, which is consistent with what has been found in other vertebrate taxa. However, these gene conversion events could not account for the species-specific allelic lineages observed in five of the Oncorhynchus species. Analyses of the relative rates of nonsynonymous and synonymous substitutions revealed the signature of selection on the class IIB gene in all 11 of the salmonid species for both the ABS and the non-ABS codons. Codon-based analyses of selection identified seven codons that have experienced selection in the majority of the species. More than half of these sites were mammalian ABS codons, but several were not, suggesting subtle functional differences in the mammalian and teleost fish MHC molecules.     

Conserved repressive regulation of connective tissue growth factor/hypertrophic chondrocyte-specific gene 24 (ctgf/hcs24) enabled by different elements and factors among vertebrate species

CTGF/Hcs24 is a multifunctional growth factor that potentiates the growth and differentiation of various cells. Our previous study revealed that the 3'-UTR of mammalian CTGF/Hcs24 mRNA contains a small segment that represses the gene expression in cis fashion. In this study, we isolated and characterized a chicken CTGF/Hcs24 cDNA clone. Chicken ctgf/hcs24 mRNA showed highly conserved homology in the ORF to that of mammalian species, whereas the homology in the 3'-UTR was relatively low. Northern blotting analysis revealed that chicken ctgf/hcs24 mRNA was expressed most strongly in cartilage, and also in brain, lung, heart, but faintly in liver. Thereafter we analyzed the functional potential of the 3'-UTR of ctgf/hcs24 cDNA to regulate its gene expression by reporter gene assay, and found that it repressed gene expression in cis fashion, specifically in avian cells, but not in mammalian cells. Conversely, the mammalian 3'-UTR showed less repressive activity in avian cells than in mammalian cells. Deletion analysis showed that a segment near the polyadenyl tail of the 3'-UTR of chicken ctgf/hcs24 played an important functional role, unlike in the mammalian species. Thus, we uncovered a novel mode of functional conservation of the ctgf/hcs24 3'-UTR among vertebrate species mediated by different factors.     

Evolution of MHC class I genes in the European badger (Meles meles)

The major histocompatibility complex (MHC) plays a central role in the adaptive immune system and provides a good model with which to understand the evolutionary processes underlying functional genes. Trans-species polymorphism and orthology are both commonly found in MHC genes; however, mammalian MHC class I genes tend to cluster by species. Concerted evolution has the potential to homogenize different loci, whereas birth-and-death evolution can lead to the loss of orthologs; both processes result in monophyletic groups within species. Studies investigating the evolution of MHC class I genes have been biased toward a few particular taxa and model species. We present the first study of MHC class I genes in a species from the superfamily Musteloidea. The European badger (Meles meles) exhibits moderate variation in MHC class I sequences when compared to other carnivores. We identified seven putatively functional sequences and nine pseudogenes from genomic (gDNA) and complementary (cDNA) DNA, signifying at least two functional class I loci. We found evidence for separate evolutionary histories of the α1 and α2/α3 domains. In the α1 domain, several sequences from different species were more closely related to each other than to sequences from the same species, resembling orthology or trans-species polymorphism. Balancing selection and probable recombination maintain genetic diversity in the α1 domain, evidenced by the detection of positive selection and a recombination event. By comparison, two recombination breakpoints indicate that the α2/α3 domains have most likely undergone concerted evolution, where recombination has homogenized the α2/α3 domains between genes, leading to species-specific clusters of sequences. Our findings highlight the importance of analyzing MHC domains separately.     

环状RNA在人类疾病中的作用及研究进展

环状RNA（circular RNA,circRNA）是一类广泛表达于真核细胞的环形RNA,多起源于蛋白编码基因。近年来发现circRNAs可通过如miRNA“海绵”等作用模式在基因的表达中发挥重要的调控作用,存在器官组织特异性的表达谱,并且越来越多的证据表明circRNAs可能是一种潜在的疾病标志物和治疗靶点。本文将对circRNAs近年在疾病中的研究进展进行综述,具体分为以下几个方面：（1）circRNAs的基本特征;（2）circRNAs的合成调控;（3）环状RNA介导基因表达的调控机制;（4）circRNAs在肿瘤性疾病中的作用;（5）circRNAs在感染免疫相关性疾病中的作用;（6）circRNAs在心血管疾病中的作用;（7）研究展望。     

Multifaceted mammalian transcriptome

Despite surprisingly a small number of protein-coding gene in mammalian genomes, a large variety of different RNAs is being produced. These RNAs are amazingly different in their number, size, cell localization, and mechanism of actions. Although new classes of short RNAs (sRNAs) are being continuously discovered, it is not yet obvious how many of the sRNAs are originated. Altogether, the research in the recent few years has identified an unexpectedly rich variety of mechanisms by which noncoding RNAs act, suggesting that we have identified probably only few of the many potential functional mechanism and more investigation will be needed to comprehensively understand the complex nature and biology of mammalian RNAome. Here, we focus on various aspects of the diversity of the biological role of these nonprotein-coding RNAs (ncRNAs), with emphasis on functional mechanisms recently elucidated.     

Jumping genes and AFLP maps: transforming lepidopteran color pattern genetics

The color patterns on the wings of lepidopterans are among the most striking patterns in nature and have inspired diverse biological hypotheses such as the ecological role of aposomatic coloration, the evolution of mimicry, the role of human activities in industrial melanism, and the developmental basis of phenotypic plasticity. Yet, the developmental mechanisms underlying color pattern development are not well understood for three reasons. First, few mutations that alter color patterns have been characterized at the molecular level, so there is little mechanistic understanding of how mutant phenotypes are produced. Second, although gene expression patterns resembling adult color patterns are suggestive, there are few data available showing that gene products have a functional role in color pattern formation. Finally, because with few exceptions (notably Bombyx), genetic maps for most species of Lepidoptera are rudimentary or nonexistent, it is very difficult to characterize spontaneous mutants or to determine whether mutations with similar phenotypes are because of lesions in the same gene or different genes. Discussed here are two strategies for overcoming these difficulties: germ-line transformation of lepidopteran species using transposon vectors and amplified frequency length polymorphism-based genetic mapping using variation between divergent strains within a species or between closely related and interfertile species. These advances, taken together, will create new opportunities for the characterization of existing genetic variants, the creation of new sequence-tagged mutants, and the testing of proposed functional genetic relationships between gene products, and will greatly facilitate our understanding of the evolution and development of lepidopteran color patterns.     

The interferon system of teleost fish

Interferons (IFNs) are secreted proteins, which induce vertebrate cells into an antiviral state. In mammals, three families of IFNs (type I IFN, type II IFN and IFN-lambda) can be distinguished on the basis of gene structure, protein structure and functional properties. Type I IFNs, which include IFN-alpha and IFN-beta, are encoded by intron lacking genes and have a major role in the first line of defense against viruses. The human IFN-lambdas have similar biological properties as type I IFNs, but are encoded by intron containing genes. Type II IFN is identical to IFN-gamma, which is produced by T helper 1 cells in response to mitogens and antigens and has a key role in adaptive cell mediated immunity. IFNs, which show structural and functional properties similar to mammalian type I IFNs, have recently been cloned from Atlantic salmon, channel catfish, pufferfish, and zebrafish. Teleost fish appear to have at least two type I IFN genes. Phylogenetic sequence analysis shows that the fish type I IFNs form a group separated from the avian type I IFNs and the mammalian IFN-alpha, -beta and -lambda groups. Interestingly, the fish IFNs possess the same exon/intron structure as the IFN-lambdas, but show most sequence similarity to IFN-alpha. Recently, IFN-gamma genes have also been cloned from several fish species and shown to have the same exon/intron structure as mammalian IFN-gamma genes. The antiviral effect of mammalian type I IFN is exerted through binding to the IFN-alpha/beta-receptor, which triggers signal transduction through the JAK-STAT signal transduction pathway resulting in expression of Mx and other antiviral proteins. Putative IFN receptor genes have been identified in pufferfish. Several interferon regulatory factors and members of the JAK-STAT pathway have also been identified in various fish species. Moreover, Mx and several other interferon stimulated genes have been cloned and studied in fish. Furthermore, antiviral activity of Mx protein from Atlantic salmon and Japanese flounder has recently been demonstrated.     

Nucleotide sequences and expression of cDNA clones for boar and bull transition protein 1 and its evolutionary conservation in mammals

During spermatogenesis, the nucleoproteins undergo several dramatic changes as the germinal cells differentiate to produce the mature sperm. With nuclear elongation and condensation, the histones are replaced by basic spermatidal transition proteins, which are themselves subsequently replaced by protamines. We have isolated cDNA clones for one of the transition proteins, namely for TP1, of bull and boar. It turned out that TP1 is a small, but very basic protein with 54 amino acids (21% arginine, 19% lysine) and is highly conserved during mammalian evolution at the nucleotide as well as at the amino-acid level. Gene expression is restricted to the mammalian testis, and the message first appears in round spermatids. Thus production of TP1 is an example of haploid gene expression in mammals. The size of the mRNA for TP1 was found to be identical in 11 different mammalian species at around 600 bp. Hybridization experiments were done with cDNAs from boar and bull, respectively. The positive results in all mammalian species give further evidence for the conservation of the TP1 gene during mammalian evolution and its functional importance in spermatid differentiation.     

Evidence for positive selection on the leptin gene in Cetacea and Pinnipedia

The leptin gene has received intensive attention and scientific investigation for its importance in energy homeostasis and reproductive regulation in mammals. Furthermore, study of the leptin gene is of crucial importance for public health, particularly for its role in obesity, as well as for other numerous physiological roles that it plays in mammals. In the present work, we report the identification of novel leptin genes in 4 species of Cetacea, and a comparison with 55 publicly available leptin sequences from mammalian genome assemblies and previous studies. Our study provides evidence for positive selection in the suborder Odontoceti (toothed whales) of the Cetacea and the family Phocidae (earless seals) of the Pinnipedia. We also detected positive selection in several leptin gene residues in these two lineages. To test whether leptin and its receptor evolved in a coordinated manner, we analyzed 24 leptin receptor gene (LPR) sequences from available mammalian genome assemblies and other published data. Unlike the case of leptin, our analyses did not find evidence of positive selection for LPR across the Cetacea and Pinnipedia lineages. In line with this, positively selected sites identified in the leptin genes of these two lineages were located outside of leptin receptor binding sites, which at least partially explains why co-evolution of leptin and its receptor was not observed in the present study. Our study provides interesting insights into current understanding of the evolution of mammalian leptin genes in response to selective pressures from life in an aquatic environment, and leads to a hypothesis that new tissue specificity or novel physiologic functions of leptin genes may have arisen in both odontocetes and phocids. Additional data from other species encompassing varying life histories and functional tests of the adaptive role of the amino acid changes identified in this study will help determine the factors that promote the adaptive evolution of the leptin genes in marine mammals.