conserved regions in bioinformatics

MOTIF-EM has been used to extract conserved domains occurring in large macromolecular assembly maps, including as those of viruses P22 and epsilon 15, Ribosome 70S, GroEL, that remain structurally conserved in different functional states. BMC Bioinformatics 2006, 7: 201. 13, 6472 (2003). Genome Res. The 16S rRNA gene has been a mainstay of sequence-based bacterial analysis for decades. Bulyk, M. L., Gentalen, E., Lockhart, D. J. In fact, these two mitochondrial genes share similar structures and functions in organisms ranging from bacteria to humans, despite the fact that the sequences exhibit numerous inter- and intraspecific nucleotide variations. 12, 493502 (2002). official website and that any information you provide is encrypted Shultzaberger, R. K. & Schneider, T. D. Using sequence logos and information analysis of Lrp DNA binding sites to investigate discrepancies between natural selection and SELEX. Bioinformatics 19 (Suppl. Proc. PASS2: an automated database of protein alignments organised as structural superfamilies. Wallance, D. C. Mitochondrial diseases in man and mouse. & Syuiti, A. Science 295, 16691678 (2002). In contrast to traditional differential gene expression microarrays that require a specific capture sequence for each gene, diagnostic arrays mandate capture sequences that can detect a range of related sequences. Two best neural networks using structure, Structural mapping of SCR predictions for ( a ) d1u9da_ from the Tautomerase/MIF, MeSH Article PubMed Central PubMed Google Scholar . Gabriela Loots , Ivan Ovcharenko, ECRbase: database of evolutionary conserved regions, promoters, and transcription factor binding sites in vertebrate genomes, Bioinformatics, Volume 23, Issue 1, January 2007, Pages 122124, https://doi.org/10.1093/bioinformatics/btl546. Nucleic Acids Res. 13, 10291241 (2003). A greedy algorithm is applied to obtain the maximum number of possible positions following each start site, stopping when the next position is None or when the next position causes the exception count to exceed the number of allowed exceptions (Nex) to the maximum entropy. Bookshelf Biol. El-Metwally S, Hamza T, Zakaria M, Helmy M. PLoS Comput Biol. Then, efficient high-throughput data stream clustering is used to group highly similar segments into so called quasi-alignments. Motivation: Evolutionary conservation of DNA sequences provides a tool for the identification of functional elements in genomes. PipTools: a computational toolkit to annotate and analyze pairwise comparisons of genomic sequences. Attardi, G. & Schatz, G. Biogenesis of mitochondria. Schwartz, S. et al. The results with the highest identities (the first BLAST hits) in the mitochondrial 12S rRNA gene were located in the mitochondrial genomes of the expected species. Liu, R., McEachin, R. C. & States, D. J. Computationally identifying novel NF- B-regulated immune genes in the human genome. Genomics 78, 7382 (2001). Evol. Huang, Ivan K., Jimin Pei, and Nick V. Grishin. Bull 91, 619627 (1993). Mol. Parmacek, M. S. et al. Therefore, it is necessary to perform species identification with both the 12S and the 16S rRNA mitochondrial genes. Nonetheless, when we attempted to design conserved primers to obtain the full mtDNA genomic sequences of mouse and Plecoglossus altivelis (fish), we found that some mtDNA regions in the mitochondrial genomes of these two species were highly similar to those in human mtDNA, particularly in the mitochondrial 12S and 16S rRNA genes. OPTIONS Search against database: Expect Value threshold: Apply low-complexity filter In recent years, multiple DNA-based approaches have been developed for species identification, including DNA hybridization, restriction enzyme digestion, random PCR amplification, species-specific PCR primer use and DNA sequencing3,4,5,6,7,8,9,10,11,12. -, Smith TF, Waterman MS. Other researchers have used species-specific mitochondrial 12S rRNA and/or 16S rRNA gene primers to identify species of shrimp, fish, poultry, fruit flies and snakes (from venom), among others.27,28,29,30,31,32,33,34,35,36,37,38,39,40. Schmid, C. D., Praz, V., Delorenzi, M., Perier, R. & Bucher, P. The Eukaryotic Promoter Database EPD: the impact of in silico primer extension. Therefore, this fly was most closely related to Muscidae fly and was not Pogonota barbata, Norellia striolata, or blowfly (Table 3 and S2). Br Poult Sci 48, 1626 (2007). Mitochondrial DNA 19, 394400 (2008). Giles, R. E., Blanc, H., Cann, H. M. & Wallance, D. C. Maternal inheritance of human mitochondrial DNA. Results . CAS J. Mol. Genome Res. BMC Bioinformatics. These primers were more specific and accurate for the mitochondrial 12S rRNA gene than were previously reported primers. 2), II16II25 (2003). 31, 36663668 (2003). Journal of Molecular Biology. Contact: The samples are respectively labeled as 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20 and 21. 2007 Apr 1;23(7):802-8. doi: 10.1093/bioinformatics/btm017. & Wunsch, C. D. A general method applicable to the search for similarities in the amino acid sequence of two proteins. MATCH: a tool for searching transcription factor binding sites in DNA sequences. Bioinformatics. 13, 579588 (2003). The locations of the universal primers are indicated by the non-continuous lines. Aerts, S., Van Loo, P., Thijs, G., Moreau, Y. Detecting conserved regulatory elements with the model genome of the Japanese puffer fish, Fugu rubripes. Similar to other mitochondrial genes, in animal mtDNA, these two mitochondrial genes have numerous nucleotide substitutions. doi: 10.1371/journal.pcbi.1003345. (in the press). CAS Google Scholar. (Serial analysis of gene expression). and JavaScript. For example, the underlined nucleotide sequences in the previously reported 12S rRNA gene primers L1091 (5-AAAAAGCTTCAAACTGGGATTAGATACCCCACTAT-3) and H1478 (5-TGACTGCAGAGGGTGACGGGCGGTGTGT-3)39,41 are not highly conserved from lower-level animals (fish and amphibians) to humans, as shown in Figure 5. Promoter prediction software can succeed for the 50% of genes with CpG islands or for genes with abundant transcript data. Correspondence to Motivation: The structures of homologous proteins are generally better conserved than their sequences. L.Y. Conserved features annotated Phylogenetic organization Literature references (evidence for biological/evolutionary annotations) What is a domain family hierarchy? Sci. Finding functional features in Saccharomyces genomes by phylogenetic footprinting. government site. Bagheri-Fam, S., Ferraz, C., Demaille, J., Scherer, G. & Pfeifer, D. Comparative genomics of the SOX9 region in human and Fugu rubripes: conservation of short regulatory sequence elements within large intergenic regions. Evol. Lenhard, B. A set of laboratory procedures for the identification of representative sets of ligands for a protein. Kel-Margoulis, O. V., Ivanova, T. G., Wingender, E. & Kel, A. E. Automatic annotation of genomic regulatory sequences by searching for composite clusters. Mol. The sample correction that is added when assessing the probability to correct for small sample sizes (that is, few binding sites). Barr, N. B. et al. HMMs are valuable because they enable a search or alignment algorithm to be built on firm probabilistic bases. A few highly conserved regions were identified in the mitochondrial 12S rRNA and 16S rRNA genes, including those from fish and amphibians to mammals including human beings. Bioinformatics 18, 12721273 (2002). USA (2003). BMC Bioinformatics. Bioinformatics 17, 9981010 (2001). Neither the 12S rRNA nor the 16S rRNA PCR amplicons shared 100% identity with the respective top BLAST hits for 5 of the 21 tissues and DNA samples. The PileUp results from the GenBank data of the mitochondrial 12S rRNA and 16S rRNA genes from 11 animal species. 27 December 2022, Receive 12 print issues and online access, Prices may be subject to local taxes which are calculated during checkout. In contrast to the human genome, the variation in the number of ECRs and the genome coverage is relatively small for vertebrates occupying distant and distinct niches in the evolutionary tree. Nature 409, 860921 (2001). Cell. For other species, either the 12S or the 16S rRNA PCR amplicon shared 100% identity with the mitochondrial genome (cow, rabbit, chicken, alligator, cat and dog for 12S and frog, rat and eel for 16S). A. Our method has many potential applications such as finding characteristic signature sequences for families of organisms and studying conserved and variable regions in, for example, 16S rRNA. 2004;32:17921797. Nine highly conserved regions with a minimum length of 9-mers were identified, which could serve as potential immune targets against rhinoviruses. Cosegregation of C-insertion at position 961 with the A1555G mutation of the mitochondrial 12S rRNA gene in a large Chinese family with maternally inherited hearing loss. Gerasimova, T. I. Next Generation Sequencing techniques are producing enormous amounts of biological sequence data and analysis becomes a major computational problem. Fickett, J. W. Coordinate positioning of MEF2 and myogenin binding sites. Article Shannon, M. F. & Rao, S. Transcription: of chips and ChIPs. 2013;9(12):e1003345. Mol. & Wasserman, W. W. TFBS: computational framework for transcription factor binding site analysis. Int J Legal Med 121, 4237 (2007). To amplify the highly variable mitochondrial 12S and 16S rRNA gene sequences from various animal species, universal oligodeoxynucleotide primers were synthesized (shown in Table 2). The detection of local similarities between two sequences. The locations of the sequences in mitochondrial genomes, including the 12S and 16S rRNA genes and identities with similar mitochondrial gene sequences were listed and the maternal origins, classes and subclasses of the DNA samples were determined from sequence BLAST hits (Table 3). Frazer, K. A., Elnitski, L., Church, D. M., Dubchak, I. Search for other works by this author on: Computation Directorates, Lawrence Livermore National Laboratory, 7000 East Avenue, Livermore, CA, 94550, USA, Regulatory roles of conserved intergenic domains in vertebrate Dlx bigene clusters, The UCSC Genome Browser Database: update 2006, The dog genome: survey sequencing and comparative analysis, Identification of a coordinate regulator of interleukins 4, 13, and 5 by cross-species sequence comparisons, TRANSFAC and its module TRANSCompel: transcriptional gene regulation in eukaryotes, Scanning human gene deserts for long-range enhancers, Mulan: multiple-sequence local alignment and visualization for studying function and evolution, Interpreting mammalian evolution using fugu genome comparisons, An apolipoprotein influencing triglycerides in humans and mice revealed by comparative sequencing, Close sequence comparisons are sufficient to identify human cis-regulatory elements, NCBI Reference Sequence (RefSeq): a curated non-redundant sequence database of genomes, transcripts and proteins, Identification of co-regulated genes through Bayesian clustering of predicted regulatory binding sites, Genome-wide associations of gene expression variation in humans, The general transcription machinery and general cofactors, Initial sequencing and comparative analysis of the mouse genome, Highly conserved non-coding sequences are associated with vertebrate development, The Author 2006. The fly, an invertebrate species and other tissues/cells, including double-blind samples and 9 known DNA samples, were amplified with these universal primers (Figure 2). Our method can also been used to build atomic models for some maps. Typical animal mtDNA has a high mutation rate and an exceptional organizational economy, with rare non-coding segments. Comparative analysis of regulatory patterns in bacterial genomes. In recent years, evolutionary conservation has guided the discovery of novel genes (Pennacchio et al., 2001) and regulatory elements (Woolfe et al., 2005). We designed two pairs of primers to target sequences in the 12S rRNA and 16S rRNA genes and thus amplify homologous mitochondrial genomic sequences from a wide variety of animal species. Down, T. A. Cliften, P. et al. We designated these universal primers as M13U12S-F and M13U12S-R for 12S rRNA and M13U16S-F and M13U16S-R for 16S rRNA. Brief Bioinform. Accessibility Toucan: deciphering the cis-regulatory logic of coregulated genes. Nature Genet. Genome-wide identification of Calcineurin B-Like (CBL) gene family of plants reveals novel conserved motifs and evolutionary aspects in calcium signaling events. 32, D35D40 (2004). The PCR amplicon sequences labeled M13 forward (18bp) and M13 reverse (18bp) were obtained with the M13 forward or M13 reverse primers, respectively (the sequence alignments from 9 species of tissues are shown in Figure 3) and then analyzed via BLAST searches at the NCBI website (see Methods). Also, automatically pre-computed lists of the most conserved, coreECRs (Ovcharenko et al., 2004) are made available and can be used as candidate regulatory elements in highly conserved loci. To obtain Biol. All BioEdit scores have been divided by ln(2) to normalize the entropy scales. Open Access (HMM). This phenomenon is demonstrated by the prevalence of structurally conserved regions (SCRs) even in highly divergent protein families. Ureta-Vidal, A., Ettwiller, L. & Birney, E. Comparative genomics: genome-wide analysis in metazoan eukaryotes. Bioinformatics. Google Scholar. Nature Reviews Genetics Surveys the genetic consequences of changes in binding sites. The GPRIME package: computer programs for identifying the best regions of aligned genes to target in nucleic acid hybridization-based diagnostic tests, and their use with plant viruses, Realities and enigmas of human viral influenza: pathogenesis, epidemiology and control, Mapping of genomic segments of influenza B virus strains by an oligonucleotide microarray method, Primer design for specific diagnosis by PCR of highly variable RNA viruses: typing of foot-and-mouth disease virus, Comparison of the directigen flu A+B test, the QuickVue influenza test, and clinical case definition to viral culture and reverse transcription-PCR for rapid diagnosis of influenza virus infection, New chips for molecular biology and diagnostics. and transmitted securely. Nucleic Acids Research. To test whether these sequences are universally conserved, primers were designed to target the conserved regions of these two genes and were used to amplify DNA from 21 animal tissues, including two of unknown origin. & Zhang, M. Q. Computational identification of promoters and first exons in the human genome. The advent of next-generation sequencing methods allows the investigation of rare variants otherwise hidden deep in large populations, but requires attention to population diversity and primer localization in relatively conserved regions, in addition to recognized constraints typically considered in primer design. Genet. The GenBank Accession numbers, full mitochondrial genome lengths and locations and lengths of the 12S and 16S rRNA genes for these mtDNA are shown in Table 1. Google Scholar. Sequence and organization of the human mitochondrial genome. 1, 357371 (2000). One exception concerned the eel species identification. Source code, documentation, and a precompiled DOS executable are available for download at Author Webpage. Currently, it includes data generated from 10 vertebrates: human, rhesus monkey, dog, opossum, rat, mouse, chicken, frog, fugu and zebrafish. Mol. Li, R. et al. Species identification through mitochondrial rRNA genetic analysis. For Permissions, please email: https://doi.org/10.1093/bioinformatics/bti719, Receive exclusive offers and updates from Oxford Academic, DIRECTOR, CENTER FOR SLEEP & CIRCADIAN RHYTHMS, Academic Pulmonary Sleep Medicine Physician Opportunity in Scenic Central Pennsylvania. A sequence family database built on ECOD structural domains. Gelfand, M. S., Novichkov, P. S., Novichkova, E. S. & Mironov, A. Would you like email updates of new search results? M indicates the 100-bp DNA ladder. Whole-genome shotgun assembly and analysis of the genome of Fugu rubripes. Scientific Reports Internet Explorer). The 3 ends of the 12S rRNA and 16S rRNA mitochondrial gene sequences were found to be conserved, in agreement with other studies20. The recovered oligonucleotides are sequenced and analysed to reveal the binding specificity of the protein. We have created a database of evolutionary conserved regions (ECRs) in vertebrate genomes, entitled ECRbase, which is constructed from a collection of whole-genome alignments produced by the ECR Browser. 2006 Jul 1;34(Web Server issue):W394-9. (Systematic evolution of ligands by exponential amplification). Nature 420, 563573 (2002). Felsenfeld, G. Quantitative approaches to problems of eukaryotic gene expression. & Hardison, R. C. Cross-species sequence comparisons: a review of methods and available resources. Characterisation of peacock (Pavo cristatus) mitochondrial 12S rRNA sequence and its use in differentiation from closely related poultry species. In addition, genetic variation in these elements may be responsible for individual variability of gene expression, which can therefore define susceptibility to disease (Stranger et al., 2005). While transcription is known to depend on promoter functiona paradigm that has long been established (Thomas and Chiang, 2006)increasing lines of evidence highlight the importance of highly conserved cis-acting regulatory elements that are positioned at great distances from the genes they regulate (Ghanem et al., 2003; Nobrega et al., 2003). Levitsky, V. G., Podkolodnaya, O. PubMed 60, 16471658 (2003). Accessibility Quasi-alignment-based algorithms can detect highly similar regions and conserved areas across multiple sequences. ECRbase currently includes human, rhesus macaque, dog, opossum, rat, mouse, chicken, frog, zebrafish and fugu genomes. The database is created on a platform that allows for constant growth to accommodate the dynamic nature of genome research where newly emerging genomes and improved releases of current genomes are constantly made available to the public (see Supplementary material for technical details on implemented data extraction and analysis methods). Defining SCRs requires the comparison of two or more homologous structures and is affected by their availability and divergence, and our ability to deduce structurally equivalent positions among them. Genome Res. Start sites must have an entropy score lower than Hmax. Designed to work with a large number of closely related, highly variable sequences, ConFind provides robust handling of alignments containing partial sequences and ambiguous characters. Nucleic Acids Res. Wang, B. et al. Shiraki, T. et al. European Bioinformatics Institute servers: ClustalW2 general purpose multiple sequence alignment . Alignment of Next-Generation Sequencing Reads. Pirger, Z., Rcz, B. Provided by the Springer Nature SharedIt content-sharing initiative, Nature Reviews Genetics (Nat Rev Genet) Sequence analysis of mitochondrial 12S rRNA gene can identify meat species. Genomic DNA, including mtDNA, was extracted from the following tissues: cultured fly, human and mouse cells; eel, shrimp, fish, pig, cow, chicken and rabbit tissues of commercial origin; 2 double-blinded tissues; and 9 DNA samples (alligator, cat, deer, dog, donkey, duck, equine, pigeon and turkey) that were purchased from ZYAGEN. 2011 Jun 30;12:271. doi: 10.1186/1471-2105-12-271. The PCR conditions were identical to those of previous reports21,22. The mitochondrial 12S rRNA and/or 16S rRNA genes have been used as molecular markers to identify mammals, birds, shrimp and other species using species-specific primers that amplify the 12S rRNA or 16S rRNA gene regions from mtDNA23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39. Birstein, V. J. Symp. Nucleic Acids Res. USA 99, 81678172 (2002). & Rubin, E. M. rVista for comparative sequence-based discovery of functional transcription factor binding sites. The forward primers were selected from the middle regions of the 12S and 16S rRNA genes (yellow in Figure 1a and green in Figure 1b, respectively). Annu. Nat Rev Genet 5, 276287 (2004). Nucleic Acids Res. Gharrett, A. J., Gray, A. K. & Heifetz, J. Genome Res. The algorithm is computationally demanding, restricting its direct application to sequences of modest length. The https:// ensures that you are connecting to the Nucleic Acids Res. Disclaimer. Proc. 16, 437441 (1996). It is freely accessible at Author Webpage. Nature Rev. In the absence of multiple homologous structures, it is necessary to predict SCRs of a protein using information from only a set of homologous sequences and (if available) a single structure. ISSN 1471-0064 (online) CAS Published by Oxford University Press. West, A. G., Gaszner, M. & Felsenfeld, G. Insulators: many functions, many mechanisms. The reported short PCR products (approximately 100bp) from the mitochondrial 12S rRNA gene40 might hinder species identification because multiple similar sequences exist in closely related species, as well as homologous nuclear sequences. This maternal inheritance greatly simplifies the interpretation of species identification results. Centre for Molecular Medicine and Therapeutics and British Columbia Women's and Children's Hospitals, 3018-950 West 28th Avenue, Vancouver, V5Z 4H4, British Columbia, Canada, Department of Medical Genetics, University of British Columbia, Vancouver, V5Z 4H4, British Columbia, Canada, Center for Genomics and Bioinformatics, Karolinska Institutet, Berzelius vg 35, Stockholm, SE-171 77, Sweden, You can also search for this author in
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