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De Grassi A, Lanave C, Saccone C. Genome duplication and gene-family evolution: the case of three OXPHOS gene families. Gene 2008; 421:1-6. [PMID: 18573316 DOI: 10.1016/j.gene.2008.05.011] [Citation(s) in RCA: 52] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2007] [Revised: 05/15/2008] [Accepted: 05/21/2008] [Indexed: 10/22/2022]
Abstract
DNA duplication is one of the main forces acting on the evolution of organisms because it creates the raw genetic material that natural selection can subsequently modify. Duplicated regions are mainly due to "errors" in different phases of meiosis, but DNA transposable elements and reverse transcription also contribute to amplify and move the genomic material to different genomic locations. As a result, redundancy affects genomes to variable degrees: from the single gene to the whole genome (WGD). Gene families are clusters of genes created by duplication and their size reflects the number of duplicated genes, called paralogs, in each species. The aim of this review is to describe the state of the art in the identification and analysis of gene families in eukaryotes, with specific attention to those generated by ancient large scale events in vertebrates (WGD or large segmental duplications). As a case study, we report our work on the evolution of gene families encoding subunits of the five OXPHOS (oxidative phosphorylation) complexes, fundamental and highly conserved in all respiring cells. Although OXPHOS gene families are smaller than the general trend in nuclear gene families, some exceptions are observed, such as three gene families with at least two paralogs in vertebrates. These gene families encode cytochrome c (Cyt c, the electron shuttle protein between complex III and IV), Lipid Binding Protein (LBP, the channel protein of complex V which transfers protons through the inner mitochondrial membrane) and the MLRQ subunit (MLRQ, a supernumerary subunit of the large complex I, with unknown function). We provide a two-step approach, based on structural genomic data, to demonstrate that these gene families should have arisen through WGD (or large segmental duplication) events at the origin of vertebrates and, only afterwards, underwent species-specific events of further gene duplications and loss. In summary, this review reflects the need to apply genome comparative approaches, deriving from both "classical" molecular phylogenetic analysis and "new" genome map analysis, to successfully define the complex evolutionary relations between gene family members which, in turn, are essential to obtain any other comparative phylogenetic or functional results.
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Affiliation(s)
- Anna De Grassi
- Istituto di Tecnologie Biomediche, Sede di Bari, CNR, Bari, Italy
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Long DD, Grosse I, Marx KA. Coding and non-coding DNA thermal stability differences in eukaryotes studied by melting simulation, base shuffling and DNA nearest neighbor frequency analysis. Biophys Chem 2004; 110:25-38. [PMID: 15223141 DOI: 10.1016/j.bpc.2004.01.001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2003] [Revised: 01/08/2004] [Accepted: 01/08/2004] [Indexed: 10/26/2022]
Abstract
The melting of the coding and non-coding classes of natural DNA sequences was investigated using a program, MELTSIM, which simulates DNA melting based upon an empirically parameterized nearest neighbor thermodynamic model. We calculated T(m) results of 8144 natural sequences from 28 eukaryotic organisms of varying F(GC) (mole fraction of G and C) and of 3775 coding and 3297 non-coding sequences derived from those natural sequences. These data demonstrated that the T(m) vs. F(GC) relationships in coding and non-coding DNAs are both linear but have a statistically significant difference (6.6%) in their slopes. These relationships are significantly different from the T(m) vs. F(GC) relationship embodied in the classical Marmur-Schildkraut-Doty (MSD) equation for the intact long natural sequences. By analyzing the simulation results from various base shufflings of the original DNAs and the average nearest neighbor frequencies of those natural sequences across the F(GC) range, we showed that these differences in the T(m) vs. F(GC) relationships are largely a direct result of systematic F(GC)-dependent biases in nearest neighbor frequencies for those two different DNA classes. Those differences in the T(m) vs. F(GC) relationships and biases in nearest neighbor frequencies also appear between the sequences from multicellular and unicellular organisms in the same coding or non-coding classes, albeit of smaller but significant magnitudes.
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Affiliation(s)
- Dang D Long
- Center for Intelligent Biomaterials, Department of Chemistry, University of Massachusetts Lowell, One University Ave., Lowell, MA 01854, USA
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3
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Fouquet C, DuBow MS. Effect of cis-located human satellite DNA on the electroporation efficiency of neo and HSV-1 tk containing plasmids. Mutat Res 1992; 284:321-8. [PMID: 1281283 DOI: 10.1016/0027-5107(92)90016-u] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Highly repetitive satellite DNAs comprise a significant portion of higher eukaryotic genomes and have been implicated in a variety of chromosome processes, such as centromere structure and function, that are related to their presence in heterochromatin. In addition, heterochromatin can induce metastable expression of adjacent genes. However, the role of highly repetitive satellite DNAs in these effects remains to be elucidated. In an effort to address this question, plasmids containing a human 1797-bp EcoRI satellite II DNA, plus the neo and the HSV-1 tk genes, were electroporated into a TK-/NEO- human cell line. The presence of the satellite DNA sequences within the electroporated plasmids was found to interfere with the generation of stable TK+, but not NEO+, transfectants depending on the location and/or orientation of the cloned satellite DNA.
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Affiliation(s)
- C Fouquet
- Department of Microbiology and Immunology, McGill University, Montreal, Que., Canada
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Barr FG, Emanuel BS. Application of a subtraction hybridization technique involving photoactivatable biotin and organic extraction to solution hybridization analysis of genomic DNA. Anal Biochem 1990; 186:369-73. [PMID: 2194401 DOI: 10.1016/0003-2697(90)90096-r] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
We have adapted a subtraction hybridization technique involving photoactivatable biotin, streptavidin binding, and organic extraction for solution hybridization analysis of mammalian genomic DNA. By combining maximal hybridization conditions of high salt, dextran sulfate, and formamide with successive hybridization steps and sequence enrichment by agarose gel electrophoresis, up to 97% of tracer DNA can be reproducibly driven to hybridize with photobiotinylated driver DNA. We demonstrate that the fractionation of hybridized from unhybridized sequences by this technique differs from hydroxyapatite chromatography with respect to the handling of nondenatured tracer, foldback sequences, and tracer-tracer hybrids. Strategies are presented to control the contribution of these species to the final subtracted product thereby making this technology a useful adjunct to solution hybridization approaches such as deletion cloning.
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Affiliation(s)
- F G Barr
- Division of Human Genetics and Molecular Biology, Children's Hospital of Philadelphia, Pennsylvania 19104
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Repetitive Deoxyribonucleic Acid (DNA) and Human Genome Variation—A Concise Review Relevant to Forensic Biology. J Forensic Sci 1988. [DOI: 10.1520/jfs12545j] [Citation(s) in RCA: 20] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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Sol K, Lapointe M, MacLeod M, Nadeau C, DuBow MS. A cloned fragment of HeLa DNA containing consensus sequences of satellite II and III DNA hybridizes with the Drosophila P-element and with the 1.8 kb family of human KpnI fragments. BIOCHIMICA ET BIOPHYSICA ACTA 1986; 868:128-35. [PMID: 3021224 DOI: 10.1016/0167-4781(86)90015-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
We have cloned a repetitive EcoRI fragment from the human genome which displays weak homologies with the Drosophila melanogaster transposable P-element. This cloned DNA appeared not to be a mobile element but, instead, a divergent member of human satellite II or III DNAs. We present here the first complete nucleotide sequence of a 1.797 kilobase pair (kb) satellite-like DNA. Moreover, this EcoRI satellite monomer contains a unique sequence of 49 basepairs (bp) that is devoid of the satellite consensus repeat 5'TTCCA3'. Southern hybridization analysis revealed that the cloned insert is closely related to a highly repetitive 1.8 kb KpnI family of tandemly organized satellite DNAs. Thus, the relationships among these satellite DNA families appear to be complex and may be a factor in their copy number, position and spatial organization.
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Verma RS, Rodriguez J, Dosik H. Chromatin of h regions of human chromosomes at high resolution. EXPERIENTIA 1984; 40:878-9. [PMID: 6468607 DOI: 10.1007/bf01952006] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
Segmentation of the secondary constriction region (h) of human chromosomes 1, 9 and 16 is demonstrated by a high resolution banding technique. Based on these staining properties, it is suggested that the composition of the h region in human chromosomes is heterochromatic as well as euchromatic.
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Moyzis RK, Bonnet J, Li DW, Ts'o PO. An alternative view of mammalian DNA sequence organization. II. Short repetitive sequences are organized into scrambled tandem clusters in Syrian hamster DNA. J Mol Biol 1981; 153:871-96. [PMID: 6283087 DOI: 10.1016/0022-2836(81)90457-5] [Citation(s) in RCA: 21] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
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Musti AM, Sobieski DA, Chen BB, Eden FC. Repeated deoxyribonucleic acid clusters in the chicken genome contain homologous sequence elements in scrambled order. Biochemistry 1981; 20:2889-99. [PMID: 6264949 DOI: 10.1021/bi00514a001] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
Part of the repeated deoxyribonucleic acid (DNA) in the chicken genome had a clustered organization. The following description of clustered repeated sequences is derived both from analysis of DNA segments cloned in lambda and from hybridization of individual cloned sequences to Southern blots of restricted total DNA. A cluster usually exceeds 20 kbp in length and consists principally, if not entirely, or repetitive DNA. Each cluster contains one cope of several different repeated sequences. The individual sequences occur several hundred times in the genome, but only once per cluster. Many of the clusters contain the same assortment of sequences but in scrambled order. In the genome, those repeated sequences that are elements of clusters occur mainly within the clustered context and are seldom, if ever, found as isolated elements flanked by nonrepeated DNA. These aspects of cluster organization suggest that the clustered sequences undergo limited rearrangement, maintaining the associations within clusters but allowing variability of sequence arrangement from cluster to cluster. The clusters that occupy the cloned DNA segments together represent at least 10% of the repetitive DNA of the chicken.
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Marx KA. Non-satellite repetitive human DNA families. Sequence properties and evidence for occurrence in chimpanzee DNA. BIOCHIMICA ET BIOPHYSICA ACTA 1980; 608:232-42. [PMID: 6156704 DOI: 10.1016/0005-2787(80)90169-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
Repetitive human DNA, fractionated on CsCl gradients following hydroxyapatite isolation, contains two complex DNA fractions, the 1.703 and 1.714 DNA families (Marx, K.A., Allen, J.R. and Hearst, J.E. (1976) Biochim. Biophys. Acta 425, 129-147). Biphasic Topt profiles, obtained in DNA excess hybridizations with cRNA tracers from each DNA family, have been shown to be the likely result of a fast kinetic component hybridizing at higher temperatures (67 degrees C peak) and this fast plus a slow kinetic component both hybridizing at lower temperatures (47 degrees C peak). Equilibrium CsCl gradient DNA-cRNA hybrid distributions support previous interpretations of the sequence composition of both DNA families. That is, the fast component is a relatively undiverged repetitive sequence of recent origin, while the slow component is a highly diverged, less thermally stabile, old primate sequence. This interpretation is further strengthened by cRNA tracer hybridization experiments in chimpanzee DNA excess where the fast component appears to be absent and the slow component present.
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12
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Rimpau J, Smith DB, Flavell RB. Sequence organisation in barley and oats chromosomes revealed by interspecies DNA/DNA hybridisation. Heredity (Edinb) 1980. [DOI: 10.1038/hdy.1980.12] [Citation(s) in RCA: 36] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
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Marx KA, Purdom IF, Jones KW. Primate repetitive DNAs: evidence for new satellite DNAs and similarities in non-satellite repetitive DNA sequence properties. Chromosoma 1979; 73:153-61. [PMID: 114378 DOI: 10.1007/bf00331568] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Repetitious DNA sequences have been isolated from a number of the primates in in both Suborders Anthropoidea and Prosimii by hydroxy-apatite chromatography at a Cot of 10. In addition to finding previously unreported possible AT-rich satellite DNAs in Orangutan, Gibbon, Rhesus and Slow Loris a clear similarity to human DNA was found in the nonsatellite repetitious DNA sequence properties of the primates in the Suborder Anthropoidea. This is based on the presence of the hydroxyapatitie isolated 1.703 and 1.714 g/cm3 DNA families in CsCl gradients in the analytical ultracentrifuge following renaturation and extensive DNA hyperpolymer network formation. Within the superfamily Hominoidea the amount of the 1.714 g/cm3 DNA family was greater than that of the 1.703 g/cm3 DNA family while the reverse situation was true within the Superfamily Cercopithecoidea. The orangutan 1.703 and 1.714 g/cm3 DNA families were shown to exhibit the same differential reassociation behavior demonstrated previously in human DNA (Marx et al., 1976a). These data are interpreted as preliminary evidence for a similar sequence organization in the Order Primates Suborder Anthropoidea.
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John B, Miklos GL. Functional aspects of satellite DNA and heterochromatin. INTERNATIONAL REVIEW OF CYTOLOGY 1979; 58:1-114. [PMID: 391760 DOI: 10.1016/s0074-7696(08)61473-4] [Citation(s) in RCA: 300] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
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Rinehart FP, Deininger PL, Schmid CW. A critical examination of possible fractionations of human DNA according to base composition. BIOCHIMICA ET BIOPHYSICA ACTA 1978; 520:21-37. [PMID: 81071 DOI: 10.1016/0005-2787(78)90004-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Human DNA has been fractionated according to base composition by sedimentation equilibrium in an HgCl2/Cs2SO4 density gradient, followed by sedimentation equilibrium in an actinomycin/cesium formate density gradient. The fractions of different base composition resulting from this procedure were subsequently analyzed by sedimentation equilibrium in CsCl, DNA renaturation kinetics, and electron microscopy. All fractions contain similar kinetic classes of repeated DNA sequences as judged by renaturation studies. Short (300 nucleotides) interspersed repeated sequences are found in all fractions with no noticeable enrichment for these sequences in any fraction. Repeated sequences from fractions of different base composition are partially able to cross-hybridize, demonstrating that nearly identical repeated sequences occur in molecules of different base composition. These findings are critically compared to reports of successful density gradient fractionations of different human DNA sequence classes.
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Rimpau J, Smith D, Flavell R. Sequence organisation analysis of the wheat and rye genomes by interspecies DNA/DNA hybridisation. J Mol Biol 1978; 123:327-59. [PMID: 691051 DOI: 10.1016/0022-2836(78)90083-9] [Citation(s) in RCA: 75] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
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18
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Houck CM, Rinehart FP, Schmid CW. Fractionation of renatured repetitive human DNA according to thermal stability, sequence length, and renaturation rate. BIOCHIMICA ET BIOPHYSICA ACTA 1978; 518:37-52. [PMID: 629979 DOI: 10.1016/0005-2787(78)90114-4] [Citation(s) in RCA: 19] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Renatured repetitive human DNA sequences have been fractionated according to three criteria: length, thermal stability, and rate of renaturation. Satellite sequences are found in the long repetitive sequence fractions and renatured satellite sequences are well base paired by the criterion of thermal stability. No satellites are observed in short repeated sequences. Short repeated sequences are interspersed with single copy sequences and are poorly base paired. This implies satellite components are relatively homogeneous in base sequence whereas short interspersed repeated sequences are inexact copies of each other. A method for isolating satellite DNAs based on their high thermal stabilities is discussed.
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Yamada M, Weissbach A. Abnormal sequence distribution in DNA synthesized by isolated nuclei from normal or mitomycin C-treated HeLa cells. Biochem Biophys Res Commun 1977; 77:642-9. [PMID: 901493 DOI: 10.1016/s0006-291x(77)80027-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
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20
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Gasaryan KG, Kuznetsova ED, Tarantul VZ, Sivak SA. Purification and characterization of two transcribed repetitive DNA fractions from the pigeon genome. Chromosoma 1977; 61:381-94. [PMID: 880844 DOI: 10.1007/bf00288621] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Two fractions of the repeats belonging to intermediate frequency repetitive DNA were isolated from the total pigeon nuclear DNA fragmented to about 450 nucleotides. One fraction was designated as "rare repeats" (repetition frequency about 35 per haploid genome) and another termed as "moderate repeats" (repetition frequency about 2500 per haploid genome). The rare repeats, which constitute about 7% of the total DNA, include at least 75% of the repetitive DNA sequences transcribed into the high molecular fraction (greater than 45S) of HnRNA in erythroid cells. These repeats have properties compatible with the characteristics of the class of low frequency interspersed DNA found in genomes of many other Metazoan species. The moderate repeats contribute only about 10-20% of the total repetitive DNA copies present in greater than 45S HnRNA and differ from the rare repeats in some other properties.--The possible role of the rare repeats in the genome is discussed.
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Guttmann T, Vítek A, Pivec L. High resolution thermal denaturation of mammalian DNAs. Nucleic Acids Res 1977; 4:285-97. [PMID: 840642 PMCID: PMC342432 DOI: 10.1093/nar/4.2.285] [Citation(s) in RCA: 20] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
High resolution melting profiles of different mammalian DNAs are presented. Melting curves of various mammalian DNAs were compared with respect to the degree of asymmetry, first moment, transition breath and Tmi of individual subtransitions. Quantitative comparison of the shape of all melting curves was made. Correlation between phylogenetical relations among mammals and shape of the melting profiles of their DNAs was demonstrated. The difference between multi-component heterogeneity of mammalian DNAs found by optical melting analysis and sedimentation in CsCl-netropsin density gradient is also discussed.
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Rinehart FP, Wilson VL, Schmid CW. Fractionation of the sequence organization of human DNA by preparative HgCl2/Cs2SO4 density gradients. BIOCHIMICA ET BIOPHYSICA ACTA 1977; 474:69-81. [PMID: 831812 DOI: 10.1016/0005-2787(77)90215-5] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Human DNA has been fractionated on preparative HgCl2/Cs2SO4 density gradients. Repetitious sequences are found in DNA components of all base compositions but the (G + C)-rich sequences are enriched for repetitive sequences in (A + T)-rich components are tandemly arranged; those in (G + C)-rich components tend to be interspersed with single copy sequences. It is concluded that the interspersed repetitious sequences have high (G + C) compositions.
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Marx KA, Allen JR, Hearst JE. Chromosomal localizations by in situ hybridization of the repetitious human DNA families and evidence of their satellite DNA equivalents. Chromosoma 1976; 59:23-42. [PMID: 1001164 DOI: 10.1007/bf00327707] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Four of the five major repetitious human DNA families have been mapped by the in situ hybridization technique at their TOPT values. Two of the lighter density DNA families have autoradiographic grain patterns over heterochromatic chromosomal regions that resemble those of known satellite DNAs. The two heaviest density DNA families have autoradiographic grain patterns of middle repetitious DNAs, with all chromosomes showing labelling. Some evidence suggests that one of these DNA families is concentrated in certain chromosomal regions. Both DNA families exhibit biphasic TOPT curves. The presence of two thermal stability classes of hybrids suggests sequence interspersion. By co-enrichment studies in Ag+-CS2SO4 gradients, evidence suggests the origin of the three lightest density renaturated human DNA families to be satellites I, II and III.
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