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Results for “gene expression evolution”

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At least 127 records · Page 7Linked to original sources
PubMed1997

The human hepatocyte nuclear factor 3/fork head gene FKHL13: genomic structure and pattern of expression.

We describe the isolation and characterization of the cDNA for FKHL13, the human homologue of the mouse hepatocyte nuclear factor 3/fork head homologue 4 (HFH-4) gene, a member of the HNF-3/fork head (also called winged helix) gene family. Members of this gene family contain a conserved DNA binding region of approx. 110 amino acids and are thought to play an important role in cell-specific differentiation. Previous analysis of the mouse and rat HFH-4 cDNAs revealed a distinct pattern of expression for this gene, suggesting that the gene plays an important role in the differentiation of lung and oviduct/ampulla epithelial cells and testicular spermatids. Analysis of the human FKHL13 gene confirmed this pattern of expression. We also found expression in adult human brain cortex, which we were able to confirm for the mouse. The expression pattern of FKHL13/HFH-4, confined to cilia/flagella-producing cells, leads us to believe that the gene plays an important role in the regulation of axonemal structural proteins. We show that the human gene for FKHL13 lies on chromosome 17 (comparison with the chromosomal location of the mouse gene strongly suggests 17q22-q25) and that the gene, which is approx. 6 kb, contains a single intron disrupting the fork head DNA binding domain. Such a disruption of a functional unit provides strong evidence for the theory of intron insertion during gene evolution. The expression of the gene is probably controlled by the CpG island, which is located in the promoter region of the gene. We also demonstrate that the FKHL13 gene is highly conserved among a wide variety of species, including birds.

Adult↗
PubMed2003

AmphiNk2-tin, an amphioxus homeobox gene expressed in myocardial progenitors: insights into evolution of the vertebrate heart.

We isolated a full-length cDNA clone of amphioxus AmphiNk2-tin, an NK2 gene similar in sequence to vertebrate NK2 cardiac genes, suggesting a potentially similar function to Drosophila tinman and to vertebrate NK2 cardiac genes during heart development. During the neurula stage of amphioxus, AmphiNk2-tin is expressed first within the foregut endoderm, then transiently in muscle precursor cells in the somites, and finally in some mesoderm cells of the visceral peritoneum arranged in an approximately midventral row running beneath the midgut and hindgut. The peritoneal cells that express AmphiNk2-tin are evidently precursors of the myocardium of the heart, which subsequently becomes morphologically detectable ventral to the gut. The amphioxus heart is a rostrocaudally extended tube consisting entirely of myocardial cells (at both the larval and adult stages); there are no chambers, valves, endocardium, epicardium, or other differentiated features of vertebrate hearts. Phylogenetic analysis of the AmphiNk2-tin sequence documents its close relationship to vertebrate NK2 class cardiac genes, and ancillary evidence suggests a relationship with the Drosophila NK2 gene tinman. Apparently, an amphioxus-like heart, and the developmental program directing its development, was the foundation upon which the vertebrate heart evolved by progressive modular innovations at the genetic and morphological levels of organization.

Amino Acid Sequence↗
PubMed1996

The rat amelogenin gene--some aspects of evolution and expression.

This study presents data to support the hypothesis that a major portion of the coding sequence of the amelogenin gene may have arisen by tandem duplication of internal sequences which as a consequence has introduced several additional potential RNA splice acceptor sites into the sequence. This duplication of splice sites has led to an increase in the heterogeneity of amelogenin forms found in developing enamel. By screening a rat enamel organ cDNA library for alternatively spliced products, it appears that as much as 20% of the amelogenin mRNA molecules may be alternatively spliced forms.

Alternative Splicing↗
PubMed1981

Dispersed 5S RNA genes in N. crassa: structure, expression and evolution.

The 5S RNA genes (5S genes) in N. crassa are not tandemly arranged or tightly clustered as in other eucaryotes that have been examined. 55 RNA or cloned 5S DNA hybridizes to at least 30 different restriction fragments of Neurospora DNA. Of 34 5S DNA clones examined, each contains a single 5S gene. Saturation hybridization analyses indicate that there are about 100 copies of 5S genes in the genome of this organism. We have partially or completely sequenced the 5S region of 15 clones. Both identical and highly divergent 5S coding regions were found. Nine are of one type (alpha). The other six include four different types (beta, beta', gamma and delta) which differ from each other and from the alpha genes to various degrees. Eleven of 15 genes have distinct flanking regions. Analysis of Neurospora 5S RNA showed that it consists of one principal species which matches the alpha-type gene sequence. Additional 5S species corresponding to the less abundant 5S gene types were also detected. The pattern of nucleotide substitutions between the predicted Neurospora 5S RNAs and between these and S. cerevisiae 5S RNA suggests that a particular 5S RNA secondary structure occurs in vivo and is conserved.

Base Sequence↗
PubMed2002

Organization, expression and evolution of a disease resistance gene cluster in soybean.

PCR amplification was previously used to identify a cluster of resistance gene analogues (RGAs) on soybean linkage group J. Resistance to powdery mildew (Rmd-c), Phytophthora stem and root rot (Rps2), and an ineffective nodulation gene (Rj2) map within this cluster. BAC fingerprinting and RGA-specific primers were used to develop a contig of BAC clones spanning this region in cultivar "Williams 82" [rps2, Rmd (adult onset), rj2]. Two cDNAs with homology to the TIR/NBD/LRR family of R-genes have also been mapped to opposite ends of a BAC in the contig Gm_Isb001_091F11 (BAC 91F11). Sequence analyses of BAC 91F11 identified 16 different resistance-like gene (RLG) sequences with homology to the TIR/NBD/LRR family of disease resistance genes. Four of these RLGs represent two potentially novel classes of disease resistance genes: TIR/NBD domains fused inframe to a putative defense-related protein (NtPRp27-like) and TIR domains fused inframe to soybean calmodulin Ca(2+)-binding domains. RT-PCR analyses using gene-specific primers allowed us to monitor the expression of individual genes in different tissues and developmental stages. Three genes appeared to be constitutively expressed, while three were differentially expressed. Analyses of the R-genes within this BAC suggest that R-gene evolution in soybean is a complex and dynamic process.

Amino Acid Sequence↗
PubMed2003

Selective instability: maternal effort and the evolution of gene activation and deactivation rates.

We previously used simulations of gene expression to demonstrate that rapid activation and deactivation rates stabilized outcomes in stochastic systems. We hypothesized that transient single allele inactivation of an autosomal gene during gametogenesis or very early embryogenesis could have a selective advantage if it permits the functional sampling of each allele and precludes committing maternal effort to an embryo with a deleterious mutation. To test this hypothesis, we simulated the evolution of gene expression activation and deactivation rates and imposed two different selective pressures on the populations: (a). late selection against individuals that cannot maintain a threshold level of gene product that occurs after the investment of maternal effort (i.e., after birth); or (b). early selection: in addition to late selection, maintenance of the gene product above a threshold level was necessary for early development prior to commitment of maternal effort. We found that the opportunity to save reproductive effort from early selection caused the evolution of higher deactivation rates and lower activation rates than in the late selection condition. Thus, we predict that in the special case where early selection can save maternal investment in non-viable offspring, gene expression activation rates and deactivation rates might be selected to permit sampling of the product from each allele.

Evolution, Molecular↗
PubMed2005

Rates of protein evolution are positively correlated with developmental timing of expression during mouse spermatogenesis.

Male reproductive genes often evolve very rapidly, and sexual selection is thought to be a primary force driving this divergence. We investigated the molecular evolution of 987 genes expressed at different times during mouse spermatogenesis to determine if the rate of evolution and the intensity of positive selection vary across stages of male gamete development. Using mouse-rat orthologs, we found that rates of protein evolution were positively correlated with the developmental timing of expression. Genes expressed early in spermatogenesis had rates of divergence similar to the genome median, while genes expressed after the onset of meiosis were found to evolve much more quickly. Rates of protein evolution were fastest for genes expressed during the dramatic morphogenesis of round spermatids into spermatozoa. Late-expressed genes were also more likely to be specific to the male germline. To test for evidence of positive selection, we analyzed the ratio of nonsynonymous to synonymous changes using a maximum likelihood framework in comparisons among mouse, rat, and human. Many genes showed evidence of positive selection, and most of these genes were expressed late in spermatogenesis and were testis specific. Overall, these data suggest that the intensity of positive selection associated with the evolution of male gametes varies considerably across development and acts primarily on phenotypes that develop late in spermatogenesis.

Animals↗
PubMed2005

Compensatory cis-trans evolution and the dysregulation of gene expression in interspecific hybrids of Drosophila.

Hybrids between species are often characterized by novel gene-expression patterns. A recent study on allele-specific gene expression in hybrids between species of Drosophila revealed cases in which cis- and trans-regulatory elements within species had coevolved in such a way that changes in cis-regulatory elements are compensated by changes in trans-regulatory elements. We hypothesized that such coevolution should often lead to gene misexpression in the hybrid. To test this hypothesis, we estimated allele-specific expression and overall expression levels for 31 genes in D. melanogaster, D. simulans, and their F1 hybrid. We found that 13 genes with cis-trans compensatory evolution are in fact misexpressed in the hybrid. These represent candidate genes whose dysregulation might be the consequence of coevolution of cis- and trans-regulatory elements within species. Using a mathematical model for the regulation of gene expression, we explored the conditions under which cis-trans compensatory evolution can lead to misexpression in interspecific hybrids.

Alleles↗
PubMed2000

Rice PHYC gene: structure, expression, map position and evolution.

Although sequences representing members of the phytochrome (phy) family of photoreceptors have been reported in numerous species across the phylogenetic spectrum, relatively few phytochrome genes (PHY) have been fully characterized. Using rice, we have cloned and characterized the first PHYC gene from a monocot. Comparison of genomic and cDNA PHYC sequences shows that the rice PHYC gene contains three introns in the protein-coding region typical of most angiosperm PHY genes, in contrast to Arabidopsis PHYC, which lacks the third intron. Mapping of the transcription start site and 5'-untranslated region of the rice PHYC transcript indicates that it contains an unusually long, intronless, 5'-untranslated leader sequence of 715 bp. PHYC mRNA levels are relatively low compared to PHYA and PHYB mRNAs in rice seedlings, and are similar in dark- and light-treated seedlings, suggesting relatively low constitutive expression. Genomic mapping shows that the PHYA, PHYB, and PHYC genes are all located on chromosome 3 of rice, in synteny with these genes in linkage group C (sometimes referred to as linkage group A) of sorghum. Phylogenetic analysis indicates that rice phyC is closely related to sorghum phyC, but relatively strongly divergent from Arabidopsis phyC, the only full-length dicot phyC sequence available.

Amino Acid Sequence↗
PubMed2005

The transcriptional consequences of mutation and natural selection in Caenorhabditis elegans.

The evolutionary importance of gene-expression divergence is unclear: some studies suggest that it is an important mechanism for evolution by natural selection, whereas others claim that most between-species regulatory changes are neutral or nearly neutral. We examined global transcriptional divergence patterns in a set of Caenorhabditis elegans mutation-accumulation lines and natural isolate lines to provide insights into the evolutionary importance of transcriptional variation and to discriminate between the forces of mutation and natural selection in shaping the evolution of gene expression. We detected the effects of selection on transcriptional divergence patterns and characterized them with respect to coexpressed gene sets, chromosomal clustering of expression changes and functional gene categories. We directly compared observed transcriptional variation patterns in the mutation-accumulation and natural isolate lines to a neutral model of transcriptome evolution to show that strong stabilizing selection dominates the evolution of transcriptional change for thousands of C. elegans expressed sequences.

Animals↗
PubMed2026

Evolution and Expression Divergence of Legume PAL Genes Suggest Associations with Drought Response and Root Nodule Development.

Comparative genomic analyses provide insight into the mechanisms underlying gene-family evolution and crop adaptation. Here, we used the legume phenylalanine ammonia-lyase (PAL) gene family as a model and integrated pan-genomic, phylogenetic, molecular evolutionary, duplication-mode, and transcriptomic analyses, while developing GFtool for gene family identification. Across 45 genomes, we identified 302 PAL genes and classified them into five Groups. Groups 1-3 represented ancient lineages shared with outgroups, whereas Groups 4 and 5 were legume-specific. Molecular-clock analyses placed the divergence of Group 2 near the Paleocene-Eocene transition, while Groups 4 and 5 diversified from the middle Eocene to the early Oligocene. WGD/segmental duplication broadly contributed to PAL copy-number expansion, whereas tandem duplication was enriched in Group 5 of Papilionoideae. Group 2 genes showed drought-induced expression, whereas Group 5 genes were associated with early root nodule development. GFtool provides a scalable framework for gene-family studies.

Fabaceae↗
PubMed2002

Nucleotide sequence of phospholipase A(2) gene expressed in snake pancreas reveals the molecular evolution of toxic phospholipase A(2) genes.

We have cloned two phospholipase A(2) (PLA(2)) DNA complementary to RNA that contained nucleotide sequences encoding pancreas loop by the reverse transcription-polymerase chain reaction cloning procedure using messenger RNA isolated from Laticauda semifasciata pancreas. Additionally, a gene clone encoding PLA(2) with the pancreatic loop sequence was isolated from a L. semifasciata genomic library. Subsequent sequence analysis revealed that PLA(2) clones encoding group IB" PLA(2). Comparative analysis of group IA and IB" PLA(2) genes revealed that the exon-intron organization is conserved in the genes of both groups. The invaded sequences in the second intron were very similar to those of the L. semifasciata group IA gene. This observation suggested that the integration of the invaded sequences occurred before the divergence of groups IA and IB" during the evolution of PLA(2) gene. The comparative analysis revealed that the arising of group IA PLA(2) occurred by the deletion and substitution of nucleotide sequences in exon III region during the process of accelerated evolution.

Amino Acid Sequence↗
PubMed2006

Enhanced adaptive evolution of sperm-expressed genes on the mammalian X chromosome.

Genes on the mammalian X chromosome may be under unique evolutionary pressure due to their hemizygous expression in males. Since any recessive deleterious mutation would immediately be expressed in males and, therefore, efficiently removed from the population, selective constraint could be more pronounced in X-linked genes. Conversely, if a recessive mutation were beneficial, its immediate exposure to selection would be advantageous, and would facilitate adaptive evolution. We tested for positive selection in a total of 86 genes using a maximum likelihood approach, including 40 sperm-expressed and 46 non-sperm, tissue-specific genes. We find evidence to suggest that X-linkage enhances the effects of positive selection in sperm-expressed genes in terms of the number of codons affected, and report a general trend for positively selected genes to reside on the X chromosome rather than on the autosomes. Our data suggest that hemizygous expression in males makes the X chromosome a preferred location for positively selected sperm genes that do not require postmeiotic transcription.

Adaptation, Physiological↗
PubMed2000

The prepro vasoactive intestinal contractor (VIC)/endothelin-2 gene (EDN2): structure, evolution, production, and embryonic expression.

Murine vasoactive intestinal contractor (VIC) and its human analog endothelin-2 (ET2) are potent vasoactive hormones composed of 21 amino acids. To study the structural characteristics of the VIC/ET2 gene (HGMW-approved symbol EDN2), we isolated the full length of the mouse VIC gene. Sequence analysis indicates that a biologically active mature VIC peptide is produced from a 175-residue precursor protein; preproVIC (PPVIC). Several remarkable similarities of the PPVIC gene to the human preproendothelin-1 gene strongly suggest that the two genes have arisen from a common progenitor by gene duplication. Transfection of ACHN adenocarcinoma cells with the cDNA resulted in the production of VIC peptide. VIC production was increased by the deletion of the 3'-untranslated region, which contains an AU-rich mRNA destabilizing sequence. Increased PPVIC gene expression during the late embryonic stage suggests an important function in development. This study provides the basis for disruption and regulation analysis of the gene, which may lead to a better understanding of VIC/ET2's physiological significance.

Amino Acid Sequence↗
PubMed2004

A neutral model of transcriptome evolution.

Microarray technologies allow the identification of large numbers of expression differences within and between species. Although environmental and physiological stimuli are clearly responsible for changes in the expression levels of many genes, it is not known whether the majority of changes of gene expression fixed during evolution between species and between various tissues within a species are caused by Darwinian selection or by stochastic processes. We find the following: (1) expression differences between species accumulate approximately linearly with time; (2) gene expression variation among individuals within a species correlates positively with expression divergence between species; (3) rates of expression divergence between species do not differ significantly between intact genes and expressed pseudogenes; (4) expression differences between brain regions within a species have accumulated approximately linearly with time since these regions emerged during evolution. These results suggest that the majority of expression differences observed between species are selectively neutral or nearly neutral and likely to be of little or no functional significance. Therefore, the identification of gene expression differences between species fixed by selection should be based on null hypotheses assuming functional neutrality. Furthermore, it may be possible to apply a molecular clock based on expression differences to infer the evolutionary history of tissues.

Animals↗