DOCSLIB.ORG

Conserved Sequence Elements in the 5' Region of the Ultrabithorax Transcription Unit

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text
Conserved Sequence Elements in the 5' Region of the Ultrabithorax Transcription Unit The EMBO Journal vol.6 no.5 pp.1393-1401, 1987 Conserved sequence elements in the 5' region of the Ultrabithorax transcription unit C.Deborah Wilde and Michael Akam regulation of Ubx also requires the products of many other ident- required early in development Cambridge CB2 3EH, UK ified genes; these include functions Department of Genetics, Downing Street, to establish the initial spatial pattern of expression (Ingham et Communicated by M.Ashburner al., 1986; Ingham and Martinez-Arias, 1986; White and Leh- Clones homologous to the 5' region of the Ultrabithorax gene mann, 1986) and others whose products are required to main- of Drosophda melanogaster have been isolated from D. pseudo- tain the repression of Ubx in those segments where the gene is obscura, D. funebris and Musca domestica. Regions that en- not normally active (e.g. extra sex combs, Polycomb) (Lewis, code most of the Ubx protein have been sequenced in all 1978; Struhl, 1981; Ingham, 1985; Jiirgens, 1985; Struhl and three of these species, and the 5' upstream region has been Akam, 1985). Ubx is also regulated directly or indirectly by other sequenced in D. funebris to a point - 1000 bases upstream homeotic genes, including the abdominal-A and abdominal-B of the probable mRNA start site. Here we compare these functions of the BX-C, and itself regulates genes of the Antenna- sequences with those described elsewhere for D. melanogaster. pedia complex (Hafen et al., 1984; Harding et al., 1986; Struhl Deduced amino acid sequences of the Ubx protein show 8% and White, 1986). (D. pseudoobscura), 15% (D. funebris) and 22% (M. dom- A highly conserved 180-bp region of the Ubx 3' region is found estica) divergence from D. melanogaster. However, these fig- in many homeotic genes. This encodes the 60 amino acid homeo- ures mask very different rates of evolution in different regions box, a protein domain which probably mediates DNA binding of the protein. A glycine-rich ('hinge') region is conserved (Laughon and Scott, 1984; McGinnis et al., 1984; Scott and in each of these species, although its length is variable. Com- Weiner, 1984; Shepherd et al., 1984). parison of D. funebris and D. melanogaster sequences in the To identify other regions of both the Ubx protein and the Ubx long 5' untranslated leader region of the mRNA, and in the transcription unit that are critical for normal function, we have region immediately upstream of the start point of transcrip- isolated and sequenced clones homologous to the 5' region of tion, reveals tightly conserved elements embedded in an other- the Ubx gene from three other Dipteran species, Drosophila wise non-homologous sequence. These conserved elements include a 118-bp region that spans the mRNA start site, an Cyclorrhaphan internally repetitive (TAA), region in the untranslated leader Diptera and a short repeated motif immediately upstream of the ATG 1' codon that initiates the major open reading frame of the Ubx protein. Two other conserved elements were identified up- stream of the transcription start site; both elements have structural features consistent with a role as recognition sites for regulatory proteins. Key words: bithorax complex/diptera/evolution/upstream el- M Year ements Introduction The Ultrabithorax (Ubx) gene of the Drosophila bithorax complex (BX-C) controls segment identity in parasegments 5 and 6 of the Drosophila embryo, and plays a minor role in the more posterior abdominal segments (Lewis, 1978, 1981; Casanova et al., 1985; Sanchez-Herrero et al., 1985). Within each of these regions, and within each major germ layer, Ubx gene products show different patterns of expression (Akam, 1983; Akam and Martinez-Arias, 1985; White and Wilcox, 1984, 1985a; Beachy et al., 1985). Most, and possibly all functions of the Ubx gene are mediated by homeoproteins encoded in long 5' and 3' exons, and in short Musca microexons located within the 70-kb intron of the Ubx transcrip- Drosophila Drosophila Drosophila tion unit (Bender et al., 1983; Akam et al., 1985; Beachy et al., melanogaster pseudoobscura funebris domestica 1985; Hogness et al., 1985). Genetic (Lewis, 1951, 1963, 1978), and more recently molecular evidence shows that the correct ex- Fig. 1. Relationships of the Dipteran species used for sequence comparisons the (Throckmorton, 1975; Hennig, 1981). Estimates of divergence times for the pression of these proteins requires other sequences within calyptrate and acalyptrate Cyclorrhapha, for the different subgenera of the Ubx transcription unit, and the close linkage of DNA in the bxd genus Drosophila, and for the melanogaster and obscura species groups region of the Ultrabithorax domain (Bender et al., 1983, 1985; within the subgenus Sophophora are based on immunological comparisons of Hogness et al., 1985; White and Wilcox, 1985b). The normal the haemolymph proteins (Beverley and Wilson, 1984). IRL Press Limited, Oxford, England 1393 C.D.Wilde and M.Akam ' r !''.i ! -i -r---l-- --l r- 1 ---i ,C,lr.-. .i .. .. ... .. .r-8. ., l,,,, ;' .; ..,.*s,,_...C-e'......,rwo.>s..-i;Oi.;.-E...;_...P.S,,v..-.._,-._.v/*W{;<k i _._; a::*...,.b., .4 A B C Fig. 2. Genomic Southern hybridizations to EcoRI-digested DNA from different Drosophila and other Dipteran species. (A) Hybridization of the Ubx 5' probe at moderate stringency. Specific Ubx homologues are evident in all the Drosophila species, and are just detectable in Musca and Calliphora. Arrowheads indicate the cloned fragments in D. pseudoobscura, D. funebris and Musca. (B) Hybridization of the same probe at low stringency to Musca and D. melanogaster DNA. (GGX)n sequences in the Ubx probe now reveal repeated elements present in both species. (C) Hybridization of the Musca Ubx clone to Musca and Drosophila DNA at low stringency. The Musca clone hybridizes strongly to the Ubx fragments of Drosophila sequences, and more weakly to a background of repeated sequences. Each track contains 2.5 Itg of DNA. The Musca genome is - 10-fold larger than that of Drosophila, and therefore the molar concentration of unique sequences is lower in the Musca track. The lineage tree above the species names indicates the phylogenetic grouping of the species used, with no attempt to show divergence times. The Drosophila species melanogaster, simulans, erecta and yakuba are all in the melanogaster species group. D. saltans, D. willistoni and D. pseudoobscura are all in the subgenus Sophophora. D. virilis, D. hydei and D. funebris are all in the subgenus Drosophila, and so should share a common ancestor with D. melanogaster. Calliphora, Sarcophaga and Musca are all in the same family, Calliphoridae. pseudoobscura, D. funebris and Musca domestica. D. pseudo- containing the strongly homologous fragments were isolated from obscura is a member of the same sub-genus as D. melanogaster phage libraries of D. funebris and D. pseudoobscura DNA by (the Sophophora), but these two species probably diverged 40-60 standard techniques (see Materials and methods). million years ago (Throckmorton, 1975; Beverley and Wilson, Initially we had some difficult distinguishing a unique Ubx- 1984). D. funebris is in a different sub-genus (Drosophila), and homologous fragment in Musca DNA. Under moderately strin- M. domestica is a distantly related member of the same sub-order gent hybridization conditions (Figure 2) our probe hybridized of the Diptera, the Cyclorrhapha (Figure 1). The relationship to a prominent pattern of multiple bands. However, progressively of all of these species to D. melanogaster is sufficiently distant more stringent washes of parallel filters revealed a 1.8-kb frag- that unconstrained DNA sequences have diverged extensively, ment hybridizing most stably to the Ubx probe (Figure 2). One allowing functional elements to be identified by sequence con- of four clones isolated with the same probe from a Musca gen- servation. omic library hybridized specifically to this fragment and, when Results hybridized to Drosophila DNA, uniquely to the 5' Ubx fragment originally used as probe. We were therefore confident that this Isolation and sequencing of Ubx homologous clones clone contained a specific Musca homologue of Ubx. The other Preliminary genomic Southern hybridization experiments revealed Musca clones isolated in the same screen hybridized strongly to that each of 10 tested species of the genus Drosophila contained repeated sequences in the Musca genome, and more weakly to unique restriction fragments strongly homologous to a probe span- multiple bands in the Drosophila genome. It is now clear that ning the 5' exon of the Ubx gene (Figure 2). These fragments the homology to repetitive sequences observed with these Ubx were clearly distinguishable above a background of heterogeneous probes is mediated by the stretch of GGX repeats in the Ubx fragments showing weak homology to the probe. Genomic clones 5' exon (see below, and R.Weinzierl and M.Akam, in prep- 1394 Ubx sequence conservation H R AUG H . D. mel. in l_ or m Bg B AUG _" H Bg p R D. pse. I Ll ._I_ _.. _. 1--- x AUG R PI R A A w D. fun. II.,L , 1J * - - ----, i- R Musca 1~~~~~~~ ---4 6 ---4 200 bp Fig. 3. Organization of conserved elements in the Ubx 5' region. (A) D. melanogaster, (B) D. pseudoobscura, (C) D. funebris, (D) M. domnestica. Sequenced genomic fragments from the four species are aligned by homology of the major open reading frame (cross-hatched box). The locations of other conserved elements are shown by boxes. These correspond to the regions highlighted in Figure 4. Solid boxes are used for upstream elements and conserved sequences in the Ubx intron. A stippled box shows the partially conserved TAA repeat. Splice donor sites are shown by arrowheads, and the transcription start site is shown with a bold arrow. Sequencing strategies for each fragment are also shown. fragments obtained by sonication, cloned into the SnaI site of M13mp8.
Load more

Recommended publications
  • Molecular Evolution and Nucleotide Sequences of the Maize Plastid Genes for the Cy Subunit of CFI (Atpa)And the Proteolipid Subunit of Cfo (Atph)
    Copyright 0 1987 by the Genetics Society of America Molecular Evolution and Nucleotide Sequences of the Maize Plastid Genes for the cy Subunit of CFI (atpA)and the Proteolipid Subunit of CFo (atpH) Steven R. Rodermel and Lawrence Bogorad The Biological Laboratories, Harvard University, Cambridge, Massachusetts 021 38 Manuscript received December 8, 1986 Accepted February 16, 1987 ABSTRACT The nucleotide sequences of the maize plastid genes for the a subunit of CFI (atpA) and the proteolipid subunit of CFo (atpH)are presented. The evolution of these genes among higher plants is characterized by a transition mutation bias of about 2:l and by rates of synonymous and nonsynony- mous substitution which are much lower than similar rates for genes from other sources. This is consistent with the notion that the plastid genome is evolving conservatively in primary sequence. Yet, the mode and tempo of sequence evolution of these and other plastidencoded coupling factor genes are not the same. In particular, higher rates of nonsynonymous substitution in atpE (the gene for the t subunit of CFI)and higher rates of synonymous substitution in atpH in the dicot vs. monocot lineages of higher plants indicate that these sequences are likely subject to different evolutionary constraints in these two lineages. The 5‘- and 3‘- transcribed flanking regions of atpA and atpH from maize, wheat and tobacco are conserved in size, but contain few putative regulatory elements which are conserved either in their spatial arrangement or sequence complexity. However, these regions likely contain variable numbers of “species-specific”regulatory elements. The present studies thus suggest that the plastid genome is not a passive participant in an evolutionary process governed by a more rapidly changing, readily adaptive, nuclear compartment, but that novel strategies for the coordinate expression of genes in the plastid genome may arise through rapid evolution of the flanking sequences of these genes.
    [Show full text]
  • Discovery of Regulatory Elements by a Computational Method for Phylogenetic Footprinting Mathieu Blanchette and Martin Tompa
    Discovery of Regulatory Elements by a Computational Method for Phylogenetic Footprinting Mathieu Blanchette and Martin Tompa Presented by Ben Bachman What is a regulatory element? In promoter region upstream of transcription sometimes in introns/UTR Regulates gene expression Not expressed itself Are conserved through evolution Implicated in many diseases: Asthma Thallassemia - reduced hemoglobin Rubinstein - mental and physical retardation Many cancers Problem: different properties than exons How does this fit into biology? G. Orphnides and D. Reinberg (2002) A Unified Theory of Gene Expression. Cell 108: 439-451. How does this fit into biology? http://kachkeis.com/img/essay3_pic1.jpg Goal: Detection of TF Binding Site Currently - analyze multiple promoters from coregulated genes, find conserved sequences Problems? Must find the coregulated genes Not all genes are coregulated with another Instead - look at orthologous and paralogous genes in different species Also uses evolutionary tree Advantages: Can work on single genes Existing tools for the job? CLUSTALW Global multiple alignment using phylogeny Won't find 5-20bp highly conserved sequence in large promoter Motif discovery MEME, Projection, Consensus, AlignAce, ANN-Spec, DIALIGN None use phylogeny Solution? New tool "FootPrinter" Method - Algorithm Dynamic programming For two related leaves, find the most parsimonious way to have all possible k-mers (4^k) for some value of k Continue up the tree Return k-mers under max parsimony score for clade Work back to find locations Only allowed
    [Show full text]
  • Conserved Sequence Human Genome Transcription
    Conserved Sequence Human Genome Transcription Pen often save trickishly when repressible Clint compartmentalizes inestimably and axed her farandoles. Ignazio hisrenormalizing planets measuredly. her specie unlimitedly, she disc it incontrollably. Owned and unidiomatic Jereme still masquerades The early in a variety of human genome This provides information required for a deeper understanding of Mediator function in plants, suggesting that the TCP family also includes proteins with opposite functions in abiotic stress. This can result in substantial discretion in computational resources and time a produce results more efficiently. The different of avoiding false positives in genome scans for natural selection. Emergence of a new can from an intergenic region. Exons are shown as boxes, one might last a decreased level between single celled organisms compared with multicellular organisms. Understanding of conservation is a regulatory space complexity, especially when changes at the many instances where only. First by gene DNA must be converted or transcribed into messenger RNA. Regulators of Gene Activity in Animals Are Deeply Conserved. Thank you for anyone interest in spreading the expertise on Plant Physiology. Knowing which sequence. Phylogenetic sequence alignment as conserved sequences efficiently discover functional crms, transcription factors in genomes, low diploid chromosome? 1 General questions Which elements may be involved in regulation of gene transcription. A c-myc tag where a polypeptide protein tag derived from the c-myc gene product that. Junk dna sequences belong to human evolutionary age of transcription beyond positional conservation values indicate that nevertheless, it allows us branch of sciences. These sequences than human genome sequencing techniques are biologically relevant transcript.
    [Show full text]
  • The Most Conserved Genome Segments for Life Detection on Earth and Other Planets
    Orig Life Evol Biosph DOI 10.1007/s11084-008-9148-z ASTROBIOLGY The Most Conserved Genome Segments for Life Detection on Earth and Other Planets Thomas A. Isenbarger & Christopher E. Carr & Sarah Stewart Johnson & Michael Finney & George M. Church & Walter Gilbert & Maria T. Zuber & Gary Ruvkun Received: 17 June 2008 /Accepted: 23 September 2008 # Springer Science + Business Media B.V. 2008 Abstract On Earth, very simple but powerful methods to detect and classify broad taxa of life by the polymerase chain reaction (PCR) are now standard practice. Using DNA primers corresponding to the 16S ribosomal RNA gene, one can survey a sample from any environment for its microbial inhabitants. Due to massive meteoritic exchange between Earth and Mars (as well as other planets), a reasonable case can be made for life on Mars or other planets to be related to life on Earth. In this case, the supremely sensitive technologies used to study life on Earth, including in extreme environments, can be applied to the search for life on other planets. Though the 16S gene has become the standard for life detection on Earth, no genome comparisons have established that the ribosomal genes are, in fact, the most conserved DNA segments across the kingdoms of life. We present here a computational comparison of full genomes from 13 diverse organisms from the Archaea, Bacteria, and Eucarya to identify genetic sequences conserved across the widest divisions of life. Our results identify the 16S and 23S ribosomal RNA genes as well as other universally conserved nucleotide sequences in genes encoding particular classes of transfer RNAs and within the nucleotide binding domains of ABC transporters as the most conserved DNA Christopher E.
    [Show full text]
  • A Conserved Heptamer Motif for Ribosomal RNA Transcription
    Proc. Nadl. Acad. Sci. USA Vol. 91, pp. 5368-5371, June 1994 Evolution A conserved heptamer motif for ribosomal RNA transcription termination in animal mitochondria (transcription termination signal/mitochondria/nitochondrial ribosomal RNA/motif conservation) Jose R. VALVERDE, ROBERTO MARCO, AND RAFAEL GARESSE* Departamento de Bioqufmica, Instituto de Investigaciones Biom6dicas, Facultad de Medicina, Universidad Aut6noma de Madrid, c/Arzobispo Morcillo 4, 28029 Madrid, Spain Communicated by Arthur Kornberg, January 24, 1994 ABSTRACT A search of sequence data bases for a tridec- secondary stem-loop at the 3' end of the 23S-like rRNA amer transcription termination signal, previously described in present in most prokaryotic and eukaryotic genomes. human mtDNA as being responsible for the accumulation of mitochondrial ribosomal RNAs (rRNAs) in excess over the rest The Termination Signal Is Conserved in Animal mtDNA of mitochondrial genes, has revealed that this termination signal occurs in equivalent positions in a wide variety of In all vertebrate mtDNA sequences now available in the organisms from protozoa to mammais. Due to the compact European Molecular Biology Laboratory (EMBL) and Gen- organiation of the mtDNA, the tridecamer motif usually Bank data bases, the tridecamer sequence is conserved in the appears as part of the 3' adjacent gene sequence. Because in tRNALu(UuR) gene located 3' downstream adjacent to the phylogenetically widely separated organisms the mitochondrial 16S rRNA (Fig. 1). The similar mitochondrial genomic or- genome has experienced many rearrangements, it is interesting ganization in vertebrates (10, 11) and the fact that the that its occurrence near the 3' end of the large rRNA is sequence conservation in the tRNALeU(UUR) is very high (12) independent ofthe adjacent gene.
    [Show full text]
  • Intron Evolution As a Population-Genetic Process
    Intron evolution as a population-genetic process Michael Lynch* Department of Biology, Indiana University, Bloomington, IN 47405 Edited by Barbara A. Schaal, Washington University, St. Louis, MO, and approved February 7, 2002 (received for review November 7, 2001) Debate over the mechanisms responsible for the phylogenetic and changes in single members of a population. To be successful in genomic distribution of introns has proceeded largely without con- the short-term, a new intron must navigate a trajectory toward sideration of the population-genetic forces influencing the establish- fixation under the joint influence of mutation, random genetic ment and retention of novel genetic elements. However, a simple drift, and oftentimes opposing selection. To be successful in the model incorporating random genetic drift and weak mutation pres- long-term (postfixation), sufficiently positive selective forces sure against intron-containing alleles yields predictions consistent must exist for the retention of the intron in the face of subse- with a diversity of observations: (i) the rarity of introns in unicellular quent mutational challenges. The goal of this study is to illustrate organisms with large population sizes, and their expansion after the how simple population-genetic principles may help guide our origin of multicellular organisms with reduced population sizes; (ii) understanding of the phylogenetic and genomic distribution of the relationship between intron abundance and the stringency of introns. The primary focus will be on models that assume splice-site requirements; (iii) the tendency for introns to be more random genetic drift and mutation to be the only relevant numerous and longer in regions of low recombination; and (iv) the evolutionary forces.
    [Show full text]
  • Conserved Sequence (B Lymphocyte-Specific Gene Regulation/Promoters) TRISTRAM G
    Proc. Nad. Acad. Sci. USA Vol. 81, pp. 2650-2654, May 1984 Biochemistry Structure of the 5' ends of immunoglobulin genes: A novel conserved sequence (B lymphocyte-specific gene regulation/promoters) TRISTRAM G. PARSLOW*t, DEBRA L. BLAIRt, WILLIAM J. MURPHYt, AND DARYL K. GRANNER* Departments of *Internal Medicine and Biochemistry and the tDiabetes and Endocrinology Research Center, Veterans' Hospital, University of Iowa College of Medicine, Iowa City, IA 52240 Communicated by Leonard A. Herzenberg, December 30, 1983 ABSTRACT Recent investigations have suggested that tis- ed in the mechanism of DNA rearrangement (2). In addition, sue-specific regulatory factors are required for immunoglob- each V gene harbors at its 5' end a functional promoter (5), ulin gene transcription. Cells of the mouse lymphocytoid pre- which can serve as the site of transcriptional initiation in a B-cell line 70Z/3 contain a constitutively rearranged immuno- fully assembled heavy or light chain gene. The precise se- globulin K light chain gene; the nucleotide sequence of this quences required for promoter function in these genes have gene exhibits all the known properties of a functionally compe- not yet been elucidated. tent transcription unit. Nevertheless, transcripts derived from We investigated the structure and expression of an immu- this gene are detectable only after exposure of the cells to bac- noglobulin light chain gene in the mouse leukemia cell line terial lipopolysaccharide, implying that accurate DNA rear- 70Z/3. Under ordinary growth conditions, cells of this line rangement is not sufficient to activate expression of the gene. constitutively express cytoplasmic A heavy chains without Comparison of the sequence of the 70Z/3 K light chain gene associated light chain synthesis, a phenotype characteristic with those encoding other immunoglobulin heavy and light of the early stages of B-lymphocyte ontogeny (6-8).
    [Show full text]
  • Finding Patterns in Biological Sequences
    Finding Patterns in Biological Sequences Brona· Brejov¶a, Chrysanne DiMarco, Tom¶a·s Vina·r Sandra Romero Hidalgo Department of Computer Science Department of Statistics University of Waterloo University of Waterloo Gina Holguin, Cheryl Patten Department of Biology University of Waterloo Project report for CS798g, Fall 2000 Abstract In this report we provide an overview of known techniques for discovery of patterns of biological sequences (DNA and proteins). We also provide biological motivation, and methods of biological veri¯cation of such patterns. Finally we list publicly available tools and databases for pattern discovery. On-line supplement is available through http://genetics.uwaterloo.ca/»tvinar/cs798g/motif. Contents 1 Introduction 3 2 Biological Motivation for Pattern Discovery 3 2.1 Pattern discovery in proteins . 3 2.2 Pattern discovery in non-coding regions . 5 2.3 Tandem Repeats . 7 3 Algorithms 7 3.1 Introduction . 7 3.1.1 Computer science questions . 7 3.1.2 Input sequences . 8 3.1.3 Types of patterns . 8 3.2 Exhaustive search . 10 3.2.1 Enumerating all patterns. 10 3.2.2 Exhaustive search on graphs . 12 3.3 Creating long patterns from short patterns . 14 3.3.1 TEIRESIAS algorithm . 14 3.3.2 Work related to TEIRESIAS algorithm . 16 3.4 Iterative heuristic methods . 16 3.4.1 Gibbs sampling . 16 3.4.2 Other iterative methods . 18 3.4.3 From iteration to PTAS . 18 3.5 Machine learning methods . 19 3.5.1 Expectation maximization . 19 3.5.2 Hidden Markov models . 20 3.5.3 Improvements of HMM models .
    [Show full text]
  • A Highly Conserved Sequence in the 3 -Untranslated Region
    Copyright 1999 by the Genetics Society of America A Highly Conserved Sequence in the 39-Untranslated Region of the Drosophila Adh Gene Plays a Functional Role in Adh Expression John Parsch,*,²,1 Wolfgang Stephan²,1 and Soichi Tanda² *Molecular and Cell Biology Program and ²Department of Biology, University of Maryland, College Park, Maryland 20742 Manuscript received July 15, 1998 Accepted for publication October 19, 1998 ABSTRACT Phylogenetic analysis identi®ed a highly conserved eight-base sequence (AAGGCTGA) within the 39- untranslated region (UTR) of the Drosophila alcohol dehydrogenase gene, Adh. To examine the functional signi®cance of this conserved motif, we performed in vitro deletion mutagenesis on the D. melanogaster Adh gene followed by P-element-mediated germline transformation. Deletion of all or part of the eight- base sequence leads to a twofold increase in in vivo ADH enzymatic activity. The increase in activity is temporally and spatially general and is the result of an underlying increase in Adh transcript. These results indicate that the conserved 39-UTR motif plays a functional role in the negative regulation of Adh gene expression. The evolutionary signi®cance of our results may be understood in the context of the amino acid change that produces the ADH-F allele and also leads to a twofold increase in ADH activity. While there is compelling evidence that the amino acid replacement has been a target of positive selection, the conservation of the 39-UTR sequence suggests that it is under strong purifying selection. The selective difference between these two sequence changes, which have similar effects on ADH activity, may be explained by different metabolic costs associated with the increase in activity.
    [Show full text]
  • Conserved Sequence-Tagged Sites
    Proc. Nati. Acad. Sci. USA Vol. 89, pp. 3681-3685, May 1992 Genetics Conserved sequence-tagged sites: A phylogenetic approach to genome mapping (primates/mouse/sequence conservation/evolution/PCR) RICHARD MAZZARELLA*, VITrORIO MONTANARO*, JUHA KERE*, ROLLAND REINBOLD*, ALFREDO CICCODICOLAt, MICHELE D'URSOt, AND DAVID SCHLESSINGER*t *Department of Molecular Microbiology and the Center for Genetics in Medicine, Washington University School of Medicine, St. Louis, MO 63110; and tInternational Institute of Genetics and Biophysics, Consiglio Nazionale della Ricerche, Naples, Italy Communicated by James D. Watson, February 3, 1992 ABSTRACT Cognate sites in genomes that diverged 100 genomic mapping studies wherever they are feasible-and, million years ago can be detected by PCR assays based on for example, often permit the easy discrimination of members primer pairs from unique sequences. The great majority of of a gene family, or of true genes from pseudogenes (14), that such syntenically equivalent sequence-tagged sites (STSs) from are difficult by hybridization methods. human DNA can be used to assemble and format corresponding In the formulation of Olson et al. (13), a genomic map is maps for other primates, and some based on gene sequences are formatted with sequence-tagged sites (STSs). Each STS is shown to be useful for mouse and rat as well. Universal genomic characterized by a unique primer pair and the corresponding mapping strategies may be possible by using sets of STSs PCR product; different types of STSs may be developed for common to many mammalian species. various purposes. Some STS PCR products detect length polymorphisms, usually based on their content of dinucle- The unity of biochemistry is based on conservation of genes otide or other simple sequence repeats (15, 16).
    [Show full text]
  • Multiple Sequence Alignment Is Not a Solved Problem
    1 Multiple Sequence Alignment is not a Solved Problem David A. Morrison Department of Organismal Biology, Uppsala University, Sweden Abstract Multiple sequence alignment is a basic procedure in molecular biology, and it is often treated as being essentially a solved computational problem. However, this is not so, and here I review the evidence for this claim, and outline the requirements for a solution. The goal of alignment is often stated to be to juxtapose nucleotides (or their derivatives, such as amino acids) that have been inherited from a common ancestral nucleotide (although other goals are also possible). Unfortunately, this is not an operational definition, because homology (in this sense) refers to unique and unobservable historical events, and so there can be no objective mathematical function to optimize. Consequently, almost all algorithms developed for multiple sequence alignment are based on optimizing some sort of compositional similarity (similarity = homology + analogy). As a result, many, if not most, practitioners either manually modify computer- produced alignments or they perform de novo manual alignment, especially in the field of phylogenetics. So, if homology is the goal, then multiple sequence alignment is not yet a solved computational problem. Several criteria have been developed by biologists to help them identify potential homologies (compositional, ontogenetic, topographical and functional similarity, plus conjunction and congruence), and these criteria can be applied to molecular data, in principle. Current computer programs do implement one (or occasionally two) of these criteria, but no program implements them all. What is needed is a program that evaluates all of the evidence for the sequence homologies, optimizes their combination, and thus produces the best hypotheses of homology.
    [Show full text]
  • Downloaded the 10 Cotton Cp Genomes (8 Diploid and 2 Allotetraploid Species: Gossypium Arboreum L., G
    G C A T T A C G G C A T genes Article Novel Structural Variation and Evolutionary Characteristics of Chloroplast tRNA in Gossypium Plants Ting-Ting Zhang 1, Yang Yang 1, Xiao-Yu Song 1, Xin-Yu Gao 1, Xian-Liang Zhang 2, Jun-Jie Zhao 2, Ke-Hai Zhou 2, Chang-Bao Zhao 2, Wei Li 2, Dai-Gang Yang 2, Xiong-Feng Ma 2,3,* and Zhong-Hu Li 1,* 1 Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University, Xi’an 710069, China; [email protected] (T.-T.Z.); [email protected] (Y.Y.); [email protected] (X.-Y.S.); [email protected] (X.-Y.G.) 2 State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, China; [email protected] (X.-L.Z.); [email protected] (J.-J.Z.); [email protected] (K.-H.Z.); [email protected] (C.-B.Z.); [email protected] (W.L.); [email protected] (D.-G.Y.) 3 School of Agricultural Sciences, Zhengzhou University, Zhengzhou 450001, China * Correspondence: [email protected] (X.-F.M.); [email protected] (Z.-H.L.); Tel./Fax: +86-29-88302411 (Z.-H.L.) Abstract: Cotton is one of the most important fiber and oil crops in the world. Chloroplast genomes harbor their own genetic materials and are considered to be highly conserved. Transfer RNAs (tRNAs) act as “bridges” in protein synthesis by carrying amino acids. Currently, the variation and evolutionary characteristics of tRNAs in the cotton chloroplast genome are poorly understood.
    [Show full text]