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noncoding sequences Near Duplicated Genes Evolve Rapidly

GENOME BIOLOGY AND EVOLUTION 2010年第0期2卷 518-533页

作者： Kostka, Dennis Hahn, Matthew W. Pollard, Katherine S. Univ Calif San Francisco Gladstone Inst Gladstone Inst Cardiovasc Dis San Francisco CA 94143 USA Indiana Univ Dept Biol Bloomington IN 47405 USA Indiana Univ Sch Informat & Comp Bloomington IN 47405 USA Univ Calif San Francisco Inst Human Genet San Francisco CA 94143 USA Univ Calif San Francisco Div Biostat San Francisco CA 94143 USA

Gene expression divergence and chromosomal rearrangements have been put forward as major contributors to phenotypic differences between closely related species. It has also been established that duplicated genes show enhanced rates of positive selection in their amino acid sequences. If functional divergence is largely due to changes in gene expression, it follows that regulatory sequences in duplicated loci should also evolve rapidly. To investigate this hypothesis, we performed likelihood ratio tests (LRTs) on all noncoding loci within 5 kb of every transcript in the human genome and identified sequences with increased substitution rates in the human lineage since divergence from Old World Monkeys. The fraction of rapidly evolving loci is significantly higher nearby genes that duplicated in the common ancestor of humans and chimps compared with nonduplicated genes. We also conducted a genome-wide scan for nucleotide substitutions predicted to affect transcription factor binding. Rates of binding site divergence are elevated in noncoding sequences of duplicated loci with accelerated substitution rates. Many of the genes associated with these fast-evolving genomic elements belong to functional categories identified in previous studies of positive selection on amino acid sequences. In addition, we find enrichment for accelerated evolution nearby genes involved in establishment and maintenance of pregnancy, processes that differ significantly between humans and monkeys. Our findings support the hypothesis that adaptive evolution of the regulation of duplicated genes has played a significant role in human evolution.

关键词： accelerated substitution noncoding sequence gene duplication

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Selective constraint on noncoding regions of hominid genomes

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PLOS COMPUTATIONAL BIOLOGY 2005年第7期1卷 593-598页

作者： Bush, Eliot C. Lahn, Bruce T. Univ Chicago Howard Hughes Med Inst Dept Human Genet Chicago IL 60637 USA

An important challenge for human evolutionary biology is to understand the genetic basis of human-chimpanzee differences. One influential idea holds that such differences depend, to a large extent, on adaptive changes in gene expression. An important step in assessing this hypothesis involves gaining a better understanding of selective constraint on noncoding regions of hominid genomes. In noncoding sequence, functional elements are frequently small and can be separated by large nonfunctional regions. For this reason, constraint in hominid genomes is likely to be patchy. Here we use conservation in more distantly related mammals and amniotes as a way of identifying small sequence windows that are likely to be functional. We find that putatively functional noncoding elements defined in this manner are subject to significant selective constraint in hominids.

关键词： .PLoS identifying functional elements windows account distantly selective constraint human–chimpanzee Regions of Hominid noncoding sequence mammals and amniotes small sequence constraint in hominids

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Evolution of the dystrophin muscular promoter and 5′ flanking region in primates

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JOURNAL OF MOLECULAR EVOLUTION 1998年第2期46卷 168-179页

作者： Fracasso, C Patarnello, T Univ Padua Dept Biol I-35121 Padua Italy

About 1.6 kb of the noncoding region upstream of the muscular dystrophin gene was sequenced in human and other primates. The alignment showed the existence of many stretches of conserved sequences among the compared species distributed all along the investigated fragment, including the 5' end. In correspondence to these conserved boxes, we identified several new putative cis-acting elements that have similarity to known control regions of other muscle-specific genes. In some cases, however, the conserved sequences did not correspond to any known transcription factor binding sites. The rate of evolution estimated site by site all along the investigated region revealed a nonhomogeneous distribution of the substitution rate, several sequences exhibited a very slow rate of evolution suggesting that evolutionary forces of different nature may be at work. On the basis of the sequence alignment, we reconstructed the phylogenetic relationships within the hominoid lineage. In addition, we estimated the relative rate of evolution between hominoid and Old World monkeys, confirming the existence of an evolutionary slowdown in the hominoid lineage.

关键词： muscular dystrophin promoter noncoding sequence evolution primates transcription factors phylogenetic footprints

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RNA expression in a cartilaginous fish cell line reveals ancient 3′ noncoding regions highly conserved in vertebrates

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PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA 2007年第4期104卷 1224-1229页

作者： Forest, David Nishikawa, Ryuhei Kobayashi, Hiroshi Parton, Angela Bayne, Christopher J. Barnes, David W. Mt Desert Isl Biol Lab Salsbury Cove ME 04672 USA

We have established a cartilaginous fish cell line [Squalus acanthias embryo cell line (SAE)], a mesenchymal stem cell line derived from the embryo of an elasmobranch, the spiny dogfish shark S. acanthias. Elasmobranchs (sharks and rays) first appeared > 400 million years ago, and existing species provide useful models for comparative vertebrate cell biology, physiology, and genomics. Comparative vertebrate genomics among evolutionarily distant organisms can provide sequence conservation information that facilitates identification of critical coding and noncoding regions. Although these genomic analyses are informative, experimental verification of functions of genomic sequences depends heavily on cell culture approaches. Using ESTs defining mRNAs derived from the SAE cell line, we identified lengthy and highly conserved gene-specific nucleotide sequences in the noncoding 3' UTRs of eight genes involved in the regulation of cell growth and proliferation. Conserved noncoding 3' mRNA regions detected by using the shark nucleotide sequences as a starting point were found in a range of other vertebrate orders, including bony fish, birds, amphibians, and mammals. Nucleotide identity of shark and human in these regions was remarkably well conserved. Our results indicate that highly conserved gene sequences dating from the appearance of jawed vertebrates and representing potential cis-regulatory elements can be identified through the use of cartilaginous fish as a baseline. Because the expression of genes in the SAE cell line was prerequisite for their identification, this cartilaginous fish culture system also provides a physiologically valid tool to test functional hypotheses on the role of these ancient conserved sequences in comparative cell biology.

关键词： noncoding sequence sequence conservation Squalus acanthias

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Phylogeny of South African Gnaphalieae (Asteraceae) based on two noncoding chloroplast sequences

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AMERICAN JOURNAL OF BOTANY 2000年第2期87卷 259-272页

作者： Bayer, RJ Puttock, CF Kelchner, SA CSIRO Ctr Plant Biodivers Res Australian Natl Herbarium Canberra ACT Australia Australian Natl Univ Div Bot & Zool Canberra ACT Australia

The Gnaphalieae are a group of sunflowers that have their greatest diversity in South America, Southern Africa, and Australia. The objective of this study was to reconstruct a phylogeny of the South African Gnaphalieae using sequence data from two noncoding chloroplast DNA sequences, the trnL intron and trnL/trnF intergenic spacer. Included in this investigation are the genera of the Gnaphalieae from the African basal groups, members of the subtribes Cassiniinae, Gnaphaliinae, and Relhaniinae, and African representatives from the large Old World genus Helichrysum. Results indicate that two Gnaphaloid genera, Printzia and Callilepis, should be excluded from the Gnaphalieae. In most trees the Relhaniinae s.s. (sensu stricto) and some of the basal taxa comprise a clade that is sister to the remainder of the tribe Gnaphalieae. The Relhaniinae, which are restricted to Africa, are not a monophyletic group as presently circumscribed, nor are the South African members of Helichrysum, the Cassiniinae and Gnaphaliinae. There is general agreement between our molecular analysis and that of morphology, particularly in the terminal branches of the trees.

关键词： asteraceae Cape Flora chloroplast DNA Gnaphalieae noncoding sequence phylogeny Relhaniinae South Africa

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GENERATION OF HIGH SPECIFICITY OF EFFECT THROUGH LOW-SPECIFICITY BINDING OF PROTEINS TO DNA

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FEBS LETTERS 1988年第2期231卷 291-298页

作者： ZUCKERKANDL, E VILLET, R USDA ARS BELTSVILLE AGR RES CTRBELTSVILLE AGR RES CTR WNPABLDG 055BELTSVILLEMD 20705

It is proposed that proteins can bind with relatively low-affinity and specificity to multiple sites, defined as sequence motifs, on polynucleotide chains, and that such binding can collectively be turned into high-affinity, high-specificity binding through cooperative effects, especially when the sequence motifs recur periodically. The selection of individual nucleotides has in general been thought to be the condition of the existence and conservation of function in most of the noncoding sequences. This condition seems unnecessary. Calculations are presented as a step in the direction of giving credibility to a model of stable gene repression.

关键词： Gene regulation noncoding sequence sequence motif, Cooperative binding Distributive specificity c -Value paradox Genetic load Determination

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Deep intronic NIPBL de novo mutations and differential diagnoses revealed by whole genome and RNA sequencing in Cornelia de Lange syndrome patients

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HUMAN MUTATION 2022年第12期43卷 1882-1897页

作者： Coursimault, Juliette Cassinari, Kevin Lecoquierre, Francois Quenez, Olivier Coutant, Sophie Derambure, Celine Vezain, Myriam Drouot, Nathalie Vera, Gabriella Schaefer, Elise Philippe, Anais Doray, Berenice Lambert, Laetitia Ghoumid, Jamal Smol, Thomas Rama, Melanie Legendre, Marine Lacombe, Didier Fergelot, Patricia Olaso, Robert Boland, Anne Deleuze, Jean-Francois Goldenberg, Alice Saugier-Veber, Pascale Nicolas, Gael Normandie Univ UNIROUEN Inserm U1245 F-76000 Rouen France CHU Rouen Dept Genet F-76000 Rouen France Reference Ctr Dev Disorders FHU G4 Genom F-76000 Rouen France Hop Univ Strasbourg Inst Genet Med Alsace IGMA Serv Genet Med Strasbourg France Ctr Hosp Univ Felix Guyon Serv Genet Med Bellepierre St Denis France CHRU Nancy Serv Genet Clin F-54000 Nancy France UMR INSERM U 1256 N GERE F-54000 Nancy France Univ Lille CHU Lille ULR7364 RADEME Clin Genet Guy Fontaine F-59000 Lille France Univ Lille FHU G4 Genom F-59000 Lille France Univ Lille CHU Lille ULR7364 RADEME Inst Genet Med F-59000 Lille France CHU Lille Inst Genet Med Lille France CHU Bordeaux Serv Genet Med Bordeaux France Univ Bordeaux INSERM U1211 Bordeaux France CHU Bordeaux Genet Med Bordeaux France Univ Paris Saclay CEA Ctr Natl Rech Genom Humaine CNRGH F-91057 Evry France

Cornelia de Lange syndrome (CdLS;MIM# 122470) is a rare developmental disorder. Pathogenic variants in 5 genes explain approximately 50% cases, leaving the other 50% unsolved. We performed whole genome sequencing (WGS) +/- RNA sequencing (RNA-seq) in 5 unsolved trios fulfilling the following criteria: (i) clinical diagnosis of classic CdLS, (ii) negative gene panel sequencing from blood and saliva-isolated DNA, (iii) unaffected parents' DNA samples available and (iv) proband's blood-isolated RNA available. A pathogenic de novo mutation (DNM) was observed in a CdLS differential diagnosis gene in 3/5 patients, namely POU3F3, SPEN, and TAF1. In the other two, we identified two distinct deep intronic DNM in NIPBL predicted to create a novel splice site. RT-PCRs and RNA-Seq showed aberrant transcripts leading to the creation of a novel frameshift exon. Our findings suggest the relevance of WGS in unsolved suspected CdLS cases and that deep intronic variants may account for a proportion of them.

关键词： clustered mutations Cornelia de Lange syndrome kataegis neurodevelopmental disorder NIPBL noncoding sequence whole genome sequencing

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A series of ENU-induced single-base substitutions in a long-range cis-element altering Sonic hedgehog expression in the developing mouse limb bud

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GENOMICS 2007年第2期89卷 207-214页

作者： Masuya, Hiroshi Sezutsu, Hideki Sakuraba, Yoshiyuki Sagai, Tomoko Hosoya, Masaki Kaneda, Hideki Miura, Ikuo Kobayashi, Kimio Sumiyama, Kenta Shimizu, Aya Nagano, Junko Yokoyama, Haruka Kaneko, Satoko Sakurai, Noriko Okagaki, Yuka Noda, Tetsuo Wakana, Shigeharu Gondo, Yoichi Shiroishi, Toshihiko RIKEN Mouse Funct Genom Res Grp GSC Tsukuba Ibaraki 3050074 Japan RIKEN Populat & Quantitat Genom Team GSC Tsurumi Ku Yokohama Kanagawa 2300045 Japan Natl Inst Genet Mammalian Genet Lab Mishima Shizuoka 4118540 Japan Natl Inst Genet Div Populat Genet Mishima Shizuoka 4118540 Japan

Mammal-fish-conserved-sequence 1 (MFCS1) is a highly conserved sequence that acts as a limb-specific cis-acting regulator of Sonic hedgehog (Shh) expression, residing 1 Mb away from the Shh coding sequence in mouse. Using gene-driven screening of an ENU-mutagenized mouse archive, we obtained mice with three new point mutations in MFCS 1: M101116, M10111 7, and M101192. Phenotype analysis revealed that M101116 mice exhibit preaxial polydactyly and ectopic Shh expression at the anterior margin of the limb buds like a previously identified mutant, M100081. In contrast, M10111 7 and M101192 show no marked abnon-nalities in limb morphology. Furthermore, transgenic analysis revealed that the M101116 and MI00081 sequences drive ectopic reporter gene expression at the anterior margin of the limb bud, in addition to the normal posterior expression. Such ectopic expression was not observed in the embryos carrying a reporter transgeDe driven by M101117. These results suggest that M101116 and M100081 affect the negative regulatory activity of MFCSI, which suppresses anterior Shh expression in developing limb buds. Thus, this study shows that gene-driven screening for ENU-induced mutations is an effective approach for exploring the function of conserved, noncoding sequences and potential cis-regulatory elements. (c) 2006 Elsevier Inc. All rights reserved.

关键词： cis-regulatory element MFCS1 sonic hedgehog noncoding sequence ENU mutagenesis single nucleotide polymorphism limb development axis formation

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Computational prediction of transcription-factor binding site locations

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Genome Biology 2004年第1期5卷 1-11页

作者： Bulyk, Martha L. Division of Genetics Department of Medicine Brigham and Women's Hospital Boston MA 02115 77 Avenue Louis Pasteur United States

Identifying genomic locations of transcription-factor binding sites, particularly in higher eukaryotic genomes, has been an enormous challenge. Various experimental and computational approaches have been used to detec... 详细信息

关键词： Functional Element noncoding sequence Position Weight Matrix Phylogenetic Footprinting Transcriptional Enhancer

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Chimp genome released

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Genome Biology 2003年第1期4卷 1-3页

作者： Russo, Eugene

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