- Initial sequencing and analysis of the human genome
E S Lander
Whitehead Institute for Biomedical Research, Center for Genome Research, Cambridge, Massachusetts 02142, USA
Nature 409:860-921. 2001
..We also present an initial analysis of the data, describing some of the insights that can be gleaned from the sequence...
- Chromatin signature reveals over a thousand highly conserved large non-coding RNAs in mammals
Broad Institute of MIT and Harvard, 7 Cambridge Center, Cambridge, Massachusetts 02142, USA
Nature 458:223-7. 2009
..Together, these results define a unique collection of functional lincRNAs that are highly conserved and implicated in diverse biological processes...
- Selection of conserved blocks from multiple alignments for their use in phylogenetic analysis
European Molecular Biology Laboratory, Heidelberg, Germany
Mol Biol Evol 17:540-52. 2000
- Mauve: multiple alignment of conserved genomic sequence with rearrangements
Aaron C E Darling
Department of Computer Science, University of Wisconsin Madison, Madison, Wisconsin 53706, USA
Genome Res 14:1394-403. 2004
..We have evaluated the quality of Mauve alignments and drawn comparison to other methods through extensive simulations of genome evolution...
- Human MicroRNA targets
Computational Biology Center, Memorial Sloan Kettering Cancer Center, New York, New York, USA
PLoS Biol 2:e363. 2004
..microrna.org. Our analysis suggests that miRNA genes, which are about 1% of all human genes, regulate protein production for 10% or more of all human genes...
- Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project
Nature 447:799-816. 2007
..Together, these studies are defining a path for pursuit of a more comprehensive characterization of human genome function...
- MatInspector and beyond: promoter analysis based on transcription factor binding sites
Genomatix Software GmbH Landsberger Strasse 6, 80339 München, Germany
Bioinformatics 21:2933-42. 2005
..The next steps in promoter analysis can be tackled only with reliable predictions, e.g. finding phylogenetically conserved patterns or identifying higher order combinations of sites in promoters of co-regulated genes...
- Role for a bidentate ribonuclease in the initiation step of RNA interference
Cold Spring Harbor Laboratory, New York 11724, USA
Nature 409:363-6. 2001
..The enzyme has a distinctive structure, which includes a helicase domain and dual RNase III motifs. Dicer also contains a region of homology to the RDE1/QDE2/ARGONAUTE family that has been genetically linked to RNAi...
- Detection of nonneutral substitution rates on mammalian phylogenies
Katherine S Pollard
Gladstone Institutes, University of California, San Francisco, San Francisco, California 94158, USA
Genome Res 20:110-21. 2010
..We also describe new "Conservation" tracks in the UCSC Genome Browser that display both phyloP and phastCons scores for genome-wide alignments of 44 vertebrate species...
- A mammalian microRNA expression atlas based on small RNA library sequencing
Howard Hughes Medical Institute, Laboratory of RNA Molecular Biology, Box 186, The Rockefeller University, New York, NY 10021, USA
Cell 129:1401-14. 2007
..We also propose a subclassification scheme for miRNAs for assisting future experimental and computational functional analyses...
- ChIP-seq accurately predicts tissue-specific activity of enhancers
Genomics Division, MS 84 171, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
Nature 457:854-8. 2009
- Computational identification of plant microRNAs and their targets, including a stress-induced miRNA
Matthew W Jones-Rhoades
Whitehead Institute for Biomedical Research and Department of Biology, Massachusetts Institute of Technology, 9 Cambridge Center, Cambridge, MA 02142, USA
Mol Cell 14:787-99. 2004
..The expression of miR395, the sulfurylase-targeting miRNA, increases upon sulfate starvation, showing that miRNAs can be induced by environmental stress...
- Evolutionarily conserved elements in vertebrate, insect, worm, and yeast genomes
Center for Biomolecular Science and Engineering, University of California, Santa Cruz, Santa Cruz, California 95064, USA
Genome Res 15:1034-50. 2005
..Noncoding HCEs also show strong statistical evidence of an enrichment for RNA secondary structure...
- Conservation of the sequence and temporal expression of let-7 heterochronic regulatory RNA
A E Pasquinelli
Department of Molecular Biology, Massachusetts General Hospital, Harvard Medical School, Boston 02114, USA
Nature 408:86-9. 2000
..elegans and Drosophila, at 48 hours after fertilization in zebrafish, and in adult stages of annelids and molluscs. The let-7 regulatory RNA may control late temporal transitions during development across animal phylogeny...
- Initial sequencing and comparative analysis of the mouse genome
Robert H Waterston
Genome Sequencing Center, Washington University School of Medicine, Campus Box 8501, 4444 Forest Park Avenue, St Louis, Missouri 63108, USA
Nature 420:520-62. 2002
- Identification of novel genes coding for small expressed RNAs
Department of Cellular Biochemistry, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, , Germany
Science 294:853-8. 2001
..This suggests that sequence-specific, posttranscriptional regulatory mechanisms mediated by small RNAs are more general than previously appreciated...
- Distribution and intensity of constraint in mammalian genomic sequence
Gregory M Cooper
Department of Genetics, Stanford University, Stanford, California 94305, USA
Genome Res 15:901-13. 2005
..We anticipate that GERP and the types of analyses it facilitates will provide further insights and improved annotation for the human genome as mammalian genome sequence data become richer...
- The transcriptional landscape of the mammalian genome
Science 309:1559-63. 2005
..The data provide a comprehensive platform for the comparative analysis of mammalian transcriptional regulation in differentiation and development...
- An abundant class of tiny RNAs with probable regulatory roles in Caenorhabditis elegans
N C Lau
Whitehead Institute for Biomedical Research, and Department of Biology, Massachusetts Institute of Technology, 9 Cambridge Center, Cambridge, MA 02142, USA
Science 294:858-62. 2001
..The abundance of these tiny RNAs, their expression patterns, and their evolutionary conservation imply that, as a class, miRNAs have broad regulatory functions in animals...
- Sequencing of Aspergillus nidulans and comparative analysis with A. fumigatus and A. oryzae
James E Galagan
The Broad Institute of MIT and Harvard, 320 Charles Street, Cambridge, Massachusetts 02142, USA
Nature 438:1105-15. 2005
..These results enhance our understanding of these widely studied fungi as well as provide new insight into eukaryotic genome evolution and gene regulation...
- The genome of the Western clawed frog Xenopus tropicalis
Department of Energy Joint Genome Institute, Walnut Creek, CA 94598, USA
Science 328:633-6. 2010
..The genome exhibits substantial shared synteny with human and chicken over major parts of large chromosomes, broken by lineage-specific chromosome fusions and fissions, mainly in the mammalian lineage...
- Origin and evolution of spliceosomal introns
Igor B Rogozin
National Center for Biotechnology Information NLM NIH, 8600 Rockville Pike, Bldg, 38A, Bethesda, MD 20894, USA
Biol Direct 7:11. 2012
- Deep sequencing identifies novel and conserved microRNAs in peanuts (Arachis hypogaea L.)
Chuan Zhi Zhao
High Tech Research Center, Shandong Academy of Agricultural Sciences, Key Laboratory of Crop Genetic Improvement and Biotechnology, Huanghuaihai, Ministry of Agriculture, Jinan 250100, PR China
BMC Plant Biol 10:3. 2010
..Increasing investigations have been performed on important agricultural crops including soybean, conifers, and Phaselous vulgaris but no studies have been reported on discovering peanut miRNAs using a cloning strategy...
- Attributes of short linear motifs
Norman E Davey
Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
Mol Biosyst 8:268-81. 2012
..Finally, the most interesting conclusions are examined in regard to their functional consequences...
- Identification of grapevine microRNAs and their targets using high-throughput sequencing and degradome analysis
Istituto di Virologia Vegetale, Consiglio Nazionale delle Ricerche, Torino, Italy
Plant J 62:960-76. 2010
..Finally, 112 target mRNAs of known and 44 target mRNAs of new grapevine-specific miRNAs were identified by genomic-scale high-throughput sequencing of miRNA cleaved mRNAs...
- ChIP-Seq identification of weakly conserved heart enhancers
Matthew J Blow
Genomics Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
Nat Genet 42:806-10. 2010
..These results provide evidence for a large population of poorly conserved heart enhancers and suggest that the evolutionary conservation of embryonic enhancers can vary depending on tissue type...
- Comparative genomics of the neglected human malaria parasite Plasmodium vivax
Jane M Carlton
The Institute for Genomic Research J Craig Venter Institute, 9704 Medical Research Drive, Rockville, Maryland 20850, USA
Nature 455:757-63. 2008
..Completion of the P. vivax genome provides the scientific community with a valuable resource that can be used to advance investigation into this neglected species...
- Evolution, biogenesis, expression, and target predictions of a substantially expanded set of Drosophila microRNAs
J Graham Ruby
Whitehead Institute for Biomedical Research, Cambridge, Massachusetts 02142, USA
Genome Res 17:1850-64. 2007
- ConSurf: identification of functional regions in proteins by surface-mapping of phylogenetic information
The George S Wise Faculty of Life Sciences, Tel Aviv University, Ramat Aviv 69978, Israel
Bioinformatics 19:163-4. 2003
..We present a new web server, ConSurf, which automates these algorithmic tools. ConSurf may be used for high-throughput characterization of functional regions in proteins...
- Variation in homeodomain DNA binding revealed by high-resolution analysis of sequence preferences
Michael F Berger
Division of Genetics, Department of Medicine, Brigham and Women s Hospital and Harvard Medical School, Boston, MA 02115, USA
Cell 133:1266-76. 2008
..Our results provide an unprecedented level of resolution in the analysis of this simple domain structure and suggest that variation in sequence recognition may be a factor in its functional diversity and evolutionary success...
- CLANS: a Java application for visualizing protein families based on pairwise similarity
Max Planck Institut fuer Entwicklungsbiologie, Spemannstrasse 35, 72076 Tuebingen, Germany
Bioinformatics 20:3702-4. 2004
..AVAILABILITY: CLANS can be downloaded at http://protevo.eb.tuebingen.mpg.de/download...
- Conservation and divergence of plant microRNA genes
The Institute of Environmental and Human Health TIEHH, and Department of Environmental Toxicology, Texas Tech University, Lubbock, TX 79409 1163, USA
Plant J 46:243-59. 2006
..Regulation of gene expression by miRNAs appears to have existed at the earliest stages of plant evolution and has been tightly constrained (functionally) for more than 425 million years...
- An extensive class of small RNAs in Caenorhabditis elegans
R C Lee
Dartmouth Medical School, Department of Genetics, Hanover, NH 03755, USA
Science 294:862-4. 2001
..elegans larval development, and three of them have apparent homologs in mammals and/or insects. Small noncoding RNAs of the miRNA class appear to be numerous and diverse...
- Genome-wide analysis of NBS-LRR-encoding genes in Arabidopsis
Blake C Meyers
Department of Vegetable Crops, University of California, Davis, California 95616, USA
Plant Cell 15:809-34. 2003
..The observed diversity of these NBS-LRR proteins indicates the variety of recognition molecules available in an individual genotype to detect diverse biotic challenges...
- The Arabidopsis basic/helix-loop-helix transcription factor family
Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720, USA
Plant Cell 15:1749-70. 2003
..These data are consistent, in principle, with the operation of this combinatorial mechanism in Arabidopsis...
- MicroRNA targeting specificity in mammals: determinants beyond seed pairing
Howard Hughes Medical Institute, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
Mol Cell 27:91-105. 2007
..Because it predicts site efficacy without recourse to evolutionary conservation, the model also identifies effective nonconserved sites and siRNA off-targets...
- Genome sequence, comparative analysis and haplotype structure of the domestic dog
Broad Institute of Harvard and MIT, 320 Charles Street, Cambridge, Massachusetts 02141, USA
Nature 438:803-19. 2005
..The current SNP map now makes it possible for genome-wide association studies to identify genes responsible for diseases and traits, with important consequences for human and companion animal health...
- The amphioxus genome and the evolution of the chordate karyotype
Nicholas H Putnam
Department of Energy Joint Genome Institute, Walnut Creek, California 94598, USA
Nature 453:1064-71. 2008
..These genome-scale events shaped the vertebrate genome and provided additional genetic variation for exploitation during vertebrate evolution...
- High-throughput sequencing of Arabidopsis microRNAs: evidence for frequent birth and death of MIRNA genes
Center for Genome Research and Biocomputing, Department of Botany and Plant Pathology, Oregon State University, Corvallis, Oregon, United States of America
PLoS ONE 2:e219. 2007
..We suggest that MIRNA genes are undergoing relatively frequent birth and death, with only a subset being stabilized by integration into regulatory networks...
- Evolutionary conservation of sequence and secondary structures in CRISPR repeats
DOE Joint Genome Institute, Walnut Creek, CA 94598, USA
Genome Biol 8:R61. 2007
..It has been recently shown that CRISPR provides acquired resistance against viruses in prokaryotes...
- Evolutionary rate in the protein interaction network
Hunter B Fraser
Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720, USA
Science 296:750-2. 2002
..We confirm one predicted outcome of this process-namely, that interacting proteins evolve at similar rates...
- Natural selection on human microRNA binding sites inferred from SNP data
Center for Comparative Functional Genomics, Department of Biology, New York University, New York, New York 10003, USA
Nat Genet 38:1452-6. 2006
..selection in humans is stronger on computationally predicted conserved miRNA binding sites than on other conserved sequence motifs in 3' UTRs, thus providing independent support for the target prediction model and explicitly ..
- Segmental structure of the Brassica napus genome based on comparative analysis with Arabidopsis thaliana
Isobel A P Parkin
Department of Agronomy, University of Wisconsin, Madison, 53706, USA
Genetics 171:765-81. 2005
..The comparative map assists in exploiting the Arabidopsis genomic sequence for marker and candidate gene identification within the larger, intractable genomes of the Brassica polyploids...
- A genome-wide characterization of microRNA genes in maize
Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, United States of America
PLoS Genet 5:e1000716. 2009
..As maize is one of the principal models for plant growth and development, this study will serve as a foundation for future research into the functional roles of miRNA genes...
- Ultraconserved regions encoding ncRNAs are altered in human leukemias and carcinomas
George A Calin
Comprehensive Cancer Center, Ohio State University, Columbus, OH 43210, USA
Cancer Cell 12:215-29. 2007
..Our findings argue that ncRNAs and interaction between noncoding genes are involved in tumorigenesis to a greater extent than previously thought...
- Deep sequencing discovery of novel and conserved microRNAs in trifoliate orange (Citrus trifoliata)
College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China
BMC Genomics 11:431. 2010
..Deep sequencing technologies have facilitated identification of species-specific or lowly expressed as well as conserved or highly expressed miRNAs in plants...
- The deep evolution of metazoan microRNAs
Benjamin M Wheeler
Department of Computer Science, North Carolina State University, Raleigh, NC 27695, USA
Evol Dev 11:50-68. 2009
..We propose that miRNAs might be excellent phylogenetic markers, and suggest that the advent of morphological complexity might have its roots in miRNA innovation...
- Deep sequencing of tomato short RNAs identifies microRNAs targeting genes involved in fruit ripening
School of Computing, University of East Anglia, Norwich NR4 7TJ, United Kingdom
Genome Res 18:1602-9. 2008
..This study opens a new avenue in the field of fleshy fruit biology by raising the possibility that fruit development and ripening may be under miRNA regulation...
- Orthologs, paralogs, and evolutionary genomics
Eugene V Koonin
National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland 20894, USA
Annu Rev Genet 39:309-38. 2005
- Evidence that miRNAs are different from other RNAs
B H Zhang
The Institute of Environmental and Human Health TIEHH, and Department of Environmental Toxicology, Texas Tech University, Lubbock, Texas 79409 1163, USA
Cell Mol Life Sci 63:246-54. 2006
..001). The MFEI for miRNAs was 0.97, significantly higher than tRNAs (0.64), rRNAs (0.59), or mRNAs (0.65). Our findings should facilitate the prediction and identification of new miRNAs using computational and experimental strategies...
- In vivo enhancer analysis of human conserved non-coding sequences
Len A Pennacchio
US Department of Energy Joint Genome Institute, Walnut Creek, California 94598, USA
Nature 444:499-502. 2006
- Expansion and diversification of the Populus R2R3-MYB family of transcription factors
Department of Cell and Systems Biology and Centre for the Analysis of Genome Evolution and Function, University of Toronto, Toronto, Ontario, Canada M5S 3B2
Plant Physiol 149:981-93. 2009
- Structural basis for double-stranded RNA processing by Dicer
Ian J Macrae
Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720, USA
Science 311:195-8. 2006
..The 65 angstrom distance between the PAZ and RNase III domains matches the length spanned by 25 base pairs of RNA. Thus, Dicer itself is a molecular ruler that recognizes dsRNA and cleaves a specified distance from the helical end...
- Identification of novel and candidate miRNAs in rice by high throughput sequencing
Department of Biochemistry and Molecular Biology, Oklahoma State University, Stillwater, OK 74078, USA
BMC Plant Biol 8:25. 2008
..Deep sequencing of small RNA libraries is an effective approach to uncover rare and lineage- and/or species-specific microRNAs (miRNAs) in any organism...
- Functionality or transcriptional noise? Evidence for selection within long noncoding RNAs
MRC Functional Genetics Unit, Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford OX1 3QX, United Kingdom
Genome Res 17:556-65. 2007
..The proportion of conserved sequence (4.1%-5.5%) in these macroRNAs is comparable to the density of exons within protein-coding transcripts (5...
- Most Caenorhabditis elegans microRNAs are individually not essential for development or viability
Eric A Miska
Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
PLoS Genet 3:e215. 2007
..This study represents the first comprehensive genetic analysis of miRNA function in any organism and provides a unique, permanent resource for the systematic study of miRNAs...
- Discovering motifs in ranked lists of DNA sequences
Computer Science Department, Technion, Haifa, Israel
PLoS Comput Biol 3:e39. 2007
..DRIM is publicly available at http://bioinfo.cs.technion.ac.il/drim...
- MicroRNA gene evolution in Arabidopsis lyrata and Arabidopsis thaliana
Center for Genome Research and Biocomputing, Oregon State University, Corvallis, Oregon 97331, USA
Plant Cell 22:1074-89. 2010
..Additionally, target sites of younger miRNA were lost more frequently than for deeply conserved families. In summary, our systematic analyses emphasize the dynamic nature of the MIRNA complement of plant genomes...
- Proteomic analysis of a eukaryotic cilium
Gregory J Pazour
Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA 01605, USA
J Cell Biol 170:103-13. 2005
..The flagellum also contains many proteins that are conserved in humans but have not been previously characterized in any organism. The results indicate that flagella are far more complex than previously estimated...
- Extensive conservation of ancient microsynteny across metazoans due to cis-regulatory constraints
Department of Biology, Stanford University, Stanford, California 94305, USA
Genome Res 22:2356-67. 2012
- Rapid evolution of noncoding RNAs: lack of conservation does not mean lack of function
Ken C Pang
ARC Special Research Centre for Functional and Applied Genomics, Institute for Molecular Bioscience, University of Queensland, Brisbane QLD 4072, Australia
Trends Genet 22:1-5. 2006
..Our findings suggest that longer ncRNAs are under the influence of different evolutionary constraints and that the lack of conservation displayed by the thousands of candidate ncRNAs does not necessarily signify an absence of function...
- Disruption of an AP-2alpha binding site in an IRF6 enhancer is associated with cleft lip
Department of Pediatrics, University of Iowa, 2182 ML, S Grand Ave, Iowa City, Iowa 52242, USA
Nat Genet 40:1341-7. 2008
..Our findings place IRF6 and AP-2alpha in the same developmental pathway and identify a high-frequency variant in a regulatory element contributing substantially to a common, complex disorder...
- Evolution of pathogenicity and sexual reproduction in eight Candida genomes
UCD School of Biomolecular and Biomedical Science, Conway Institute, University College Dublin, Belfield, Dublin 4, Ireland
Nature 459:657-62. 2009
..Analysis of the CUG leucine-to-serine genetic-code change reveals that 99% of ancestral CUG codons were erased and new ones arose elsewhere. Lastly, we revise the Candida albicans gene catalogue, identifying many new genes...
- The birth and death of microRNA genes in Drosophila
Department of Ecology and Evolution, University of Chicago, 1101 East 57th Street, Chicago, Illinois 60637, USA
Nat Genet 40:351-5. 2008
..The estimated net gain of long-lived miRNA genes, which is not strongly affected by either the depth or the breadth (number of tissues) of sequencing, is 0.3 genes per Myr in Drosophila...
- GARD: a genetic algorithm for recombination detection
Sergei L Kosakovsky Pond
Department of Pathology, University of California San Diego, La Jolla, CA 92093, USA
Bioinformatics 22:3096-8. 2006
..The evolution of recombinant sequences can not be properly explained by a single phylogenetic tree, but several phylogenies may be used to correctly model the evolution of non-recombinant fragments...
- The role of nucleosome positioning in the evolution of gene regulation
Alexander M Tsankov
Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America
PLoS Biol 8:e1000414. 2010
..Our study sheds light on the molecular basis of chromatin organization, and on the role of chromatin organization in the evolution of gene regulation...
- Discovery of barley miRNAs through deep sequencing of short reads
Andreas W Schreiber
Australian Centre for Plant Functional Genomics, The University of Adelaide, South Australia 5064, Australia
BMC Genomics 12:129. 2011
..However, miRNAs from barley, one of the most important cereal crops, remain unknown...
- Protein sectors: evolutionary units of three-dimensional structure
Department of Pharmacology, University of Texas Southwestern Medical Center, Dallas, TX 75390 9050, USA
Cell 138:774-86. 2009
..We propose that sectors represent a structural organization of proteins that reflects their evolutionary histories...
- Comparative analysis of the small RNA transcriptomes of Pinus contorta and Oryza sativa
Ryan D Morin
Genome Sciences Centre, BC Cancer Agency, Vancouver V5Z 1L3, Canada
Genome Res 18:571-84. 2008
..Genomic mapping of all sequences to the O. sativa genome can be viewed at http://microrna.bcgsc.ca/cgi-bin/gbrowse/rice_build_3/...
- PISCES: a protein sequence culling server
Institute for Cancer Research, Fox Chase Cancer Center, 7701 Burholme Avenue, Philadelphia, PA 19111, USA
Bioinformatics 19:1589-91. 2003
..PDB sequences are updated weekly. PISCES can also cull non-PDB sequences provided by the user as a list of GenBank identifiers, a FASTA format file, or BLAST/PSI-BLAST output...
- Direct RNA motif definition and identification from multiple sequence alignments using secondary structure profiles
Centre d immunologie de Marseille Luminy, CNRS UMR 6102 INSERM U 136, Luminy Case 906, 13288 Marseille Cedex 09, France
J Mol Biol 313:1003-11. 2001
..Furthermore, since the translation of alignments into profiles is straightforward with ERPIN, iterative searches can easily be conducted to enrich collections of homologous RNAs...
- Genome duplication in the teleost fish Tetraodon nigroviridis reveals the early vertebrate proto-karyotype
UMR 8030 Genoscope, CNRS and Université d Evry, 2 rue Gaston Cremieux, 91057 Evry Cedex, France
Nature 431:946-57. 2004
- A gene-coexpression network for global discovery of conserved genetic modules
Joshua M Stuart
Stanford Medical Informatics, 251 Campus Drive, Medical School Office Building X 215, Stanford, CA 94305 5329, USA
Science 302:249-55. 2003
..By assembling these links into a gene-coexpression network, we found several components that were animal-specific as well as interrelationships between newly evolved and ancient modules...
- Confirming the phylogeny of mammals by use of large comparative sequence data sets
Arjun B Prasad
Genome Technology Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
Mol Biol Evol 25:1795-808. 2008
..g., in the case of Laurasiatheria), and demonstrate the valuable role that very large comparative sequence data sets can play in refining our understanding of the evolutionary relationships of vertebrates...
- Common functions for diverse small RNAs of land plants
Michael J Axtell
Department of Biology and Huck Institutes of the Life Sciences, Pensylvania State University, University Park, PA 16802, USA
Plant Cell 19:1750-69. 2007
..Diverse, lineage-specific, small RNAs can therefore perform common biological functions in plants...
- Sepsid even-skipped enhancers are functionally conserved in Drosophila despite lack of sequence conservation
Emily E Hare
Department of Molecular and Cell Biology, University of California Berkeley, Berkeley, California, United States of America
PLoS Genet 4:e1000106. 2008
..Together, these observations suggest that the local arrangement of binding sites relative to each other is more important than their overall arrangement into larger units of cis-regulatory function...
- Identification and characterization of maize microRNAs involved in the very early stage of seed germination
State Key Laboratory of Crop Biology, Shandong Agricultural University, Taian, Shandong 271018, PR China
BMC Genomics 12:154. 2011
..However, the number of miRNAs discovered in maize is relatively low and little is known about miRNAs involved in the very early stage during seed germination...
- Human developmental enhancers conserved between deuterostomes and protostomes
Shoa L Clarke
Department of Genetics, Stanford University, Stanford, California, United States of America
PLoS Genet 8:e1002852. 2012
- Deep sequencing of Brachypodium small RNAs at the global genome level identifies microRNAs involved in cold stress response
Key Laboratory of Photosynthesis and Environmental Molecular Physiology, Chinese Academy of Sciences, and National Centre for Plant Gene Research, Beijing 100093, PR China
BMC Genomics 10:449. 2009
..Brachypodium distachyon, with close evolutionary relationship to cool-season cereals, has recently emerged as a novel model plant. There are few reports of Brachypodium miRNAs...
- Methylation of a CTCF-dependent boundary controls imprinted expression of the Igf2 gene
A C Bell
Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892 0540, USA
Nature 405:482-5. 2000
..Our results reveal that DNA methylation can control gene expression by modulating enhancer access to the gene promoter through regulation of an enhancer boundary...
- A draft sequence of the rice genome (Oryza sativa L. ssp. japonica)
Stephen A Goff
Torrey Mesa Research Institute, Syngenta, 3115 Merryfield Row, San Diego, CA 92121, USA
Science 296:92-100. 2002
..Assignment of candidate rice orthologs to Arabidopsis genes is possible in many cases. The rice genome sequence provides a foundation for the improvement of cereals, our most important crops...
- MicroRNAs and their regulatory roles in animals and plants
The Institute of Environmental and Human Health, and Department of Environmental Toxicology, Texas Tech University, Lubbock, Texas 79409, USA
J Cell Physiol 210:279-89. 2007
..This review provides a general background and current advance on the discovery, history, biogenesis, genomics, mechanisms, and functions of miRNAs...
- Evolution of the Rab family of small GTP-binding proteins
J B Pereira-Leal
Cell and Molecular Biology Section, Division of Biomedical Sciences, Faculty of Medicine, Imperial College, London, SW7 2AZ, UK
J Mol Biol 313:889-901. 2001
..Rab functional groups can help the understanding of the functional evolution of the Rab family in particular and vesicular transport in general, and may be used to predict general functions for novel Rab sequences...
- Modulation of floral development by a gibberellin-regulated microRNA
Department of Cell and Developmental Biology, John Innes Centre, Norwich NR4 7UH, UK
Development 131:3357-65. 2004
..We propose that miR159 is a phytohormonally regulated homeostatic modulator of GAMYB activity, and hence of GAMYB-dependent developmental processes...
- Essential genes are more evolutionarily conserved than are nonessential genes in bacteria
I King Jordan
National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
Genome Res 12:962-8. 2002
..In contrast to the results obtained for eukaryotic genes, essential bacterial genes appear to be more conserved than are nonessential genes over both relatively short (microevolutionary) and longer (macroevolutionary) time scales...
- Forces shaping the fastest evolving regions in the human genome
Katherine S Pollard
Department of Biomolecular Engineering, University of California Santa Cruz, Santa Cruz, California, United States of America
PLoS Genet 2:e168. 2006
..A combination of evolutionary forces has contributed to accelerated evolution of the fastest evolving elements in the human genome...
- Molecular evolution of FOXP2, a gene involved in speech and language
Max Planck Institute for Evolutionary Anthropology, Inselstrasse 22, D 04103 Leipzig, Germany
Nature 418:869-72. 2002
..Here we show that human FOXP2 contains changes in amino-acid coding and a pattern of nucleotide polymorphism, which strongly suggest that this gene has been the target of selection during recent human evolution...
- daf-2, an insulin receptor-like gene that regulates longevity and diapause in Caenorhabditis elegans
K D Kimura
Department of Molecular Biology, Massachusetts General Hospital, Boston, MA 02114, USA
Science 277:942-6. 1997
..Life-span regulation by insulin-like metabolic control is analogous to mammalian longevity enhancement induced by caloric restriction, suggesting a general link between metabolism, diapause, and longevity...
- Long noncoding RNA genes: conservation of sequence and brain expression among diverse amniotes
Rebecca A Chodroff
Department of Physiology, Anatomy, and Genetics, Le Gros Clark Building South Parks Road, University of Oxford, Oxford OX1 3QX, UK
Genome Biol 11:R72. 2010
..This dearth of information is partially attributable to a lack of established non-protein-coding RNA (ncRNA) orthologs among birds and mammals within sequence and expression databases...
- The complete atomic structure of the large ribosomal subunit at 2.4 A resolution
Department of Molecular Biophysics and Biochemistry and Howard Hughes Medical Institute, New Haven, CT 06520 8114, USA
Science 289:905-20. 2000
..Most of the proteins stabilize the structure by interacting with several RNA domains, often using idiosyncratically folded extensions that reach into the subunit's interior...
- Analysis of the vertebrate insulator protein CTCF-binding sites in the human genome
Tae Hoon Kim
Ludwig Institute for Cancer Research, Department of Cellular and Molecular Medicine, University of California, San Diego School of Medicine, La Jolla, CA 92093 0653, USA
Cell 128:1231-45. 2007
..In addition, CTCF localization is largely invariant across different cell types. Our results provide a resource for investigating insulator function and possible other general and evolutionarily conserved activities of CTCF sites...
- Chromosomal rearrangement inferred from comparisons of 12 Drosophila genomes
Department of Molecular and Cellular Biology, Harvard University, Cambridge, Massachusetts 02138, USA
Genetics 179:1657-80. 2008
..On the other hand, an analysis of the disruption of syntenic blocks between species allowed the identification of fixed inversion breakpoints and estimates of breakpoint reuse and lineage-specific breakpoint event segregation...
- Predicting deleterious amino acid substitutions
P C Ng
Fred Hutchinson Cancer Research Center, Seattle, Washington 98109, USA
Genome Res 11:863-74. 2001
..may be used to identify plausible disease candidates among the SNPs that cause missense substitutions...
- Genome evolution in yeasts
Unité de Génétique Moléculaire des Levures, URA 2171 CNRS and UFR 927 Université Pierre et Marie Curie
Nature 430:35-44. 2004
- The Trichoplax genome and the nature of placozoans
Center for Integrative Genomics and Department of Molecular and Cell Biology, University of California, Berkeley, California 94720, USA
Nature 454:955-60. 2008
- Differential recognition of highly divergent downy mildew avirulence gene alleles by RPP1 resistance genes from two Arabidopsis lines
Anne P Rehmany
Warwick HRI, University of Warwick, Wellesbourne, Warwick CV35 9EF, United Kingdom
Plant Cell 17:1839-50. 2005
..The presence of the motif in additional secreted proteins from plant pathogenic oomycetes and its similarity to a host-targeting signal from malaria parasites suggest a conserved role in pathogenicity...
- InBase: the Intein Database
Francine B Perler
New England Biolabs Inc, 32 Tozer Road, Beverly, MA 01915, USA
Nucleic Acids Res 30:383-4. 2002
..It presents general information as well as detailed data for each intein, including tabulated comparisons and a comprehensive bibliography. An intein-specific BLAST server is now available to assist in identifying new inteins...
- A search for small noncoding RNAs in Staphylococcus aureus reveals a conserved sequence motif for regulation
Architecture et Reactivite de l ARN, Universite de Strasbourg, CNRS, IBMC, 15 rue Rene Descartes, F 67084 Strasbourg, France
Nucleic Acids Res 37:7239-57. 2009
..This study unexpectedly shows that most of the novel ncRNAs carry the conserved C-rich motif, suggesting that they are members of a class of ncRNAs that target mRNAs by a shared mechanism...
- Identification of conserved residues in the E2 envelope glycoprotein of the hepatitis C virus that are critical for CD81 binding
Ania M Owsianka
MRC Virology Unit, Institute of Virology, University of Glasgow, UK
J Virol 80:8695-704. 2006
..Specific amino acids conserved across all genotypes that were critical for CD81 binding were W420, Y527, W529, G530, and D535. These data significantly increase our understanding of the CD81 receptor-E2 binding process...
- MicroRNAs of Bombyx mori identified by Solexa sequencing
The Key Sericultural Laboratory of Agricultural Ministry, College of Biotechnology, Southwest University, Tiansheng Road, Beibei, Chongqing 400715, PR China
BMC Genomics 11:148. 2010