Conservation of RET regulatory function from human to zebrafish without sequence similarity

Evolutionary sequence conservation is an accepted criterion to identify noncoding regulatory sequences. We have used a transposon-based transgenic assay in zebrafish to evaluate noncoding sequences at the zebrafish ret locus, conserved among teleosts, and at the human RET locus, conserved among mammals. Most teleost sequences directed ret-specific reporter gene expression, with many displaying overlapping regulatory control. The majority of human RET noncoding sequences also directed ret-specific expression in zebrafish. Thus, vast amounts of functional sequence information may exist that would not be detected by sequence similarity approaches.     

Accelerated evolution of conserved noncoding sequences in humans

Changes in gene regulation likely influenced the profound phenotypic divergence of humans from other mammals, but the extent of adaptive substitution in human regulatory sequences remains unknown. We identified 992 conserved noncoding sequences (CNSs) with a significant excess of human-specific substitutions. These accelerated elements were disproportionately found near genes involved in neuronal cell adhesion. To assess the uniqueness of human noncoding evolution, we examined CNSs accelerated in chimpanzee and mouse. Although we observed a similar enrichment near neuronal adhesion genes in chimpanzee, the accelerated CNSs themselves exhibited almost no overlap with those in human, suggesting independent evolution toward different neuronal phenotypes in each species. CNSs accelerated in mouse showed no bias toward neuronal cell adhesion. Our results indicate that widespread cis-regulatory changes in human evolution may have contributed to uniquely human features of brain development and function.     

Evolutionarily assembled cis-regulatory module at a human ciliopathy locus

Neighboring genes are often coordinately expressed within cis-regulatory modules, but evidence that nonparalogous genes share functions in mammals is lacking. Here, we report that mutation of either TMEM138 or TMEM216 causes a phenotypically indistinguishable human ciliopathy, Joubert syndrome. Despite a lack of sequence homology, the genes are aligned in a head-to-tail configuration and joined by chromosomal rearrangement at the amphibian-to-reptile evolutionary transition. Expression of the two genes is mediated by a conserved regulatory element in the noncoding intergenic region. Coordinated expression is important for their interdependent cellular role in vesicular transport to primary cilia. Hence, during vertebrate evolution of genes involved in ciliogenesis, nonparalogous genes were arranged to a functional gene cluster with shared regulatory elements.     

Evolutionary discrimination of mammalian conserved non-genic sequences (CNGs)

Analysis of the human and mouse genomes identified an abundance of conserved non-genic sequences (CNGs). The significance and evolutionary depth of their conservation remain unanswered. We have quantified levels and patterns of conservation of 191 CNGs of human chromosome 21 in 14 mammalian species. We found that CNGs are significantly more conserved than protein-coding genes and noncoding RNAS (ncRNAs) within the mammalian class from primates to monotremes to marsupials. The pattern of substitutions in CNGs differed from that seen in protein-coding and ncRNA genes and resembled that of protein-binding regions. About 0.3% to 1% of the human genome corresponds to a previously unknown class of extremely constrained CNGs shared among mammals.     

Ancient noncoding elements conserved in the human genome

Cartilaginous fishes represent the living group of jawed vertebrates that diverged from the common ancestor of human and teleost fish lineages about 530 million years ago. We generated approximately 1.4x genome sequence coverage for a cartilaginous fish, the elephant shark (Callorhinchus milii), and compared this genome with the human genome to identify conserved noncoding elements (CNEs). The elephant shark sequence revealed twice as many CNEs as were identified by whole-genome comparisons between teleost fishes and human. The ancient vertebrate-specific CNEs in the elephant shark and human genomes are likely to play key regulatory roles in vertebrate gene expression.     

Human genome ultraconserved elements are ultraselected

Ultraconserved elements in the human genome are defined as stretches of at least 200 base pairs of DNA that match identically with corresponding regions in the mouse and rat genomes. Most ultraconserved elements are noncoding and have been evolutionarily conserved since mammal and bird ancestors diverged over 300 million years ago. The reason for this extreme conservation remains a mystery. It has been speculated that they are mutational cold spots or regions where every site is under weak but still detectable negative selection. However, analysis of the derived allele frequency spectrum shows that these regions are in fact under negative selection that is much stronger than that in protein coding genes.     

延边黄牛转铁蛋白受体2基因克隆与序列分析

【目的】克隆延边黄牛转铁蛋白受体2（transferrin receptor 2,TFR2）基因,并分析该基因在不同组织器官中的表达分布。【方法】通过提取肝脏组织总RNA,采用RT-PCR及RACE方法克隆延边黄牛TfR2基因,采用生物信息学软件进行序列分析,用半定量PCR（SqRT-PCR）方法分析TfR2基因在不同组织器官中的表达分布规律。【结果】①成功克隆出了延边黄牛TfR2基因完整ORF区及3′UTR区（GenBank登录号：GU553087）,该基因全长2 901 bp,ORF区2 412 bp,编码803个氨基酸;②延边黄牛TfR2基因核苷酸序列与其它物种的同源性在80%以上,不同物种间TfR2基因氨基酸序列,尤其是影响其功能的关键氨基酸位点高度保守;③各物种TfR2蛋白功能结构域同样高度保守;④牛TfR2基因主要在肝脏中表达,其它组织,如脾脏、心脏、肾脏和肠道（十二指肠）中也存在少量表达。【结论】不同物种间TfR2基因具有高度同源性,功能结构域及组织分布规律具有高度保守性。     

Human-specific gain of function in a developmental enhancer

Changes in gene regulation are thought to have contributed to the evolution of human development. However, in vivo evidence for uniquely human developmental regulatory function has remained elusive. In transgenic mice, a conserved noncoding sequence (HACNS1) that evolved extremely rapidly in humans acted as an enhancer of gene expression that has gained a strong limb expression domain relative to the orthologous elements from chimpanzee and rhesus macaque. This gain of function was consistent across two developmental stages in the mouse and included the presumptive anterior wrist and proximal thumb. In vivo analyses with synthetic enhancers, in which human-specific substitutions were introduced into the chimpanzee enhancer sequence or reverted in the human enhancer to the ancestral state, indicated that 13 substitutions clustered in an 81-base pair module otherwise highly constrained among terrestrial vertebrates were sufficient to confer the human-specific limb expression domain.     

CNS and hypoderm regulatory elements of the Drosophila melanogaster dopa decarboxylase gene

Expression of the dopa decarboxylase gene (Ddc) is regulated in a tissue- and developmental stage-specific manner throughout the life cycle of the fruit fly, Drosophila melanogaster. Essential Ddc regulatory elements lie within 208 base pairs upstream from the RNA start point. Functional elements within this 5' flanking region were mapped by deletion analysis, which assayed expression in vivo after germline integration via P element vectors. One of the elements is essential for expression in both the larval and adult central nervous system, and at least two other elements are necessary for quantitatively normal expression in the hypoderm. Within each of the intervals that have regulatory effects are found sequence elements conserved between the Ddc genes of two distantly related species of flies. On the basis of this correlation, regulatory functions for these sequence elements can be postulated.     

哺乳动物BMP4基因A型启动子的比较分析

以鸭嘴兽BMP4基因组序列为模型,采用比较基因组学方法分析哺乳动物BMP4基因A型启动子的结构特点。该研究分离出一段长112bp的进化上高度保守的核心启动子序列以及多个转录因子结合位点和CpG岛结构,并且在BMP4核心启动子区域发现了2种具有重要生物学功能的回文结构,为进一步研究该型启动子的转录调控功能提供了理论基础。同时以鸭嘴兽基因组为参照模型,也为今后研究其他哺乳动物进化上保留下来的基因提供更多新信息。     

The Xist RNA gene evolved in eutherians by pseudogenization of a protein-coding gene

The Xist noncoding RNA is the key initiator of the process of X chromosome inactivation in eutherian mammals, but its precise function and origin remain unknown. Although Xist is well conserved among eutherians, until now, no homolog has been identified in other mammals. We show here that Xist evolved, at least partly, from a protein-coding gene and that the loss of protein-coding function of the proto-Xist coincides with the four flanking protein genes becoming pseudogenes. This event occurred after the divergence between eutherians and marsupials, which suggests that mechanisms of dosage compensation have evolved independently in both lineages.     

The Release 5.1 annotation of Drosophila melanogaster heterochromatin

The repetitive DNA that constitutes most of the heterochromatic regions of metazoan genomes has hindered the comprehensive analysis of gene content and other functions. We have generated a detailed computational and manual annotation of 24 megabases of heterochromatic sequence in the Release 5 Drosophila melanogaster genome sequence. The heterochromatin contains a minimum of 230 to 254 protein-coding genes, which are conserved in other Drosophilids and more diverged species, as well as 32 pseudogenes and 13 noncoding RNAs. Improved methods revealed that more than 77% of this heterochromatin sequence, including introns and intergenic regions, is composed of fragmented and nested transposable elements and other repeated DNAs. Drosophila heterochromatin contains "islands" of highly conserved genes embedded in these "oceans" of complex repeats, which may require special expression and splicing mechanisms.     

胃泌素和胆囊收缩素及其受体氨基酸序列信息学比较分析

【目的】胃泌素(GAS)和胆囊收缩素(CCK)具有较多相似性,但两种激素与其受体(CCK-A和CCK-B)亲和力不同,研究利用生物信息学的方法,比对羊GAS和CCK及其受体氨基酸序列与其它动物序列的不同,为不同动物这两种多肽及其受体蛋白抗原设计和活性多肽筛选等提供参考。【方法】通过UniProt数据库检索各种动物GAS和CCK及其受体氨基酸序列进行比对,并进行全氨基酸序列进化树分析。【结果】除了鸡和鱼,其他动物GAS的C-端7个氨基酸完全相同;除了豚鼠外,CCK的C-端10个氨基酸序列完全相同;羊与牛的GAS-34及CCK-33氨基酸序列完全相同。羊与牛,大鼠与小鼠、狗与猫的CCK-A和CCK-B均分别在同一个分支上;从GAS和CCK及受体全氨基酸序列(包括信号肽和原肽)来看,禽类和鱼类序列同哺乳动物差距均较大;绵羊CCK-A与CCK-B氨基酸序列相似性仅为45.094%。【结论】GAS和CCK的C-端氨基酸序列在不同动物之间均具有高度的保守性,而N-端为变化区域。