1
|
Fu Y, Zhu Z, Meng G, Zhang R, Zhang Y. A CRISPR-Cas9 based shuffle system for endogenous histone H3 and H4 combinatorial mutagenesis. Sci Rep 2021; 11:3298. [PMID: 33558622 PMCID: PMC7870972 DOI: 10.1038/s41598-021-82774-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2020] [Accepted: 01/07/2021] [Indexed: 11/09/2022] Open
Abstract
Post-translational modifications of histone proteins greatly impact gene expression and cell fate decisions in eukaryotes. To study these, it is important to develop a convenient, multiplex, and efficient method to precisely introduce mutations to histones. Because eukaryotic cells usually contain multiple copies of histone genes, it is a challenge to mutate all histones at the same time by the traditional homologous recombination method. Here, we developed a CRISPR-Cas9 based shuffle system in Saccharomyces cerevisiae, to generate point mutations on both endogenous histone H3 and H4 genes in a rapid, seamless and multiplex fashion. Using this method, we generated yeast strains containing histone triple H3–K4R–K36R–K79R mutants and histone combinatorial H3–K56Q–H4–K59A double mutants with high efficiencies (70–80%). This CRISPR-Cas9 based mutagenesis system could be an invaluable tool to the epigenetics field.
Collapse
Affiliation(s)
- Yu Fu
- Laboratory of Feed Biotechnology, State Key Laboratory of Animal Nutrition, College of Animal Science and Technology, College of Veterinary Medicine, China Agricultural University, Haidian District, Beijing, 100193, China
| | - Zhenglin Zhu
- School of Life Sciences, Chongqing University, No. 55 Daxuecheng South Rd., Shapingba, Chongqing, 401331, China
| | - Geng Meng
- Laboratory of Feed Biotechnology, State Key Laboratory of Animal Nutrition, College of Animal Science and Technology, College of Veterinary Medicine, China Agricultural University, Haidian District, Beijing, 100193, China
| | - Rijun Zhang
- Laboratory of Feed Biotechnology, State Key Laboratory of Animal Nutrition, College of Animal Science and Technology, College of Veterinary Medicine, China Agricultural University, Haidian District, Beijing, 100193, China.
| | - Yueping Zhang
- Laboratory of Feed Biotechnology, State Key Laboratory of Animal Nutrition, College of Animal Science and Technology, College of Veterinary Medicine, China Agricultural University, Haidian District, Beijing, 100193, China.
| |
Collapse
|
2
|
Insights into the karyotype evolution and speciation of the beetle Euchroma gigantea (Coleoptera: Buprestidae). Chromosome Res 2018. [PMID: 29524007 DOI: 10.1007/s10577-018-9576-1] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
Abstract
Euchroma Dejean, 1833 (Buprestidae: Coleoptera) is a monotypic genus comprising the species Euchroma gigantea, with populations presenting a degree of karyotypic variation/polymorphism rarely found within a single taxonomic (specific) unit, as well as drastically incompatible meiotic configurations in populations from extremes of the species range. To better understand the complex karyotypic evolution of E. gigantea, the karyotypes of specimens from five populations in Brazil were investigated using molecular cytogenetics and phylogenetic approaches. Herein, we used FISH with histone genes as well as sequencing of the COI to determine differential distribution of markers and relationships among populations. The analyses revealed new karyotypes, with variability for chromosome number and morphology of multiple sex chromosome mechanisms, occurrence of B chromosome variants (punctiform and large ones), and high dispersion of histone genes in different karyotypes. These data indicate that chromosomal polymorphism in E. gigantea is greater than previously reported, and that the species can be a valuable model for cytogenetic studies. The COI phylogenetic and haplotype analyses highlighted the formation of three groups with chromosomally polymorphic individuals. Finally, we compared the different karyotypes and proposed a model for the chromosomal evolution of this species. The species E. gigantea includes at least three cytogenetically polymorphic lineages. Moreover, in each of these lineages, different chromosomal rearrangements have been fixed. Dispersion of repetitive sequences may have favored the high frequency of these rearrangements, which could be related to both adaptation of the species to different habitats and the speciation process.
Collapse
|
3
|
Mans BJ, de Klerk D, Pienaar R, de Castro MH, Latif AA. Next-generation sequencing as means to retrieve tick systematic markers, with the focus on Nuttalliella namaqua (Ixodoidea: Nuttalliellidae). Ticks Tick Borne Dis 2015; 6:450-62. [DOI: 10.1016/j.ttbdis.2015.03.013] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2014] [Revised: 03/06/2015] [Accepted: 03/08/2015] [Indexed: 10/23/2022]
|
4
|
Roehrdanz R, Heilmann L, Senechal P, Sears S, Evenson P. Histone and ribosomal RNA repetitive gene clusters of the boll weevil are linked in a tandem array. INSECT MOLECULAR BIOLOGY 2010; 19:463-471. [PMID: 20456508 DOI: 10.1111/j.1365-2583.2010.01006.x] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2023]
Abstract
Histones are the major protein component of chromatin structure. The histone family is made up of a quintet of proteins, four core histones (H2A, H2B, H3 & H4) and the linker histones (H1). Spacers are found between the coding regions. Among insects this quintet of genes is usually clustered and the clusters are tandemly repeated. Ribosomal DNA contains a cluster of the rRNA sequences 18S, 5.8S and 28S. The rRNA genes are separated by the spacers ITS1, ITS2 and IGS. This cluster is also tandemly repeated. We found that the ribosomal RNA repeat unit of at least two species of Anthonomine weevils, Anthonomus grandis and Anthonomus texanus (Coleoptera: Curculionidae), is interspersed with a block containing the histone gene quintet. The histone genes are situated between the rRNA 18S and 28S genes in what is known as the intergenic spacer region (IGS). The complete reiterated Anthonomus grandis histone-ribosomal sequence is 16,248 bp.
Collapse
Affiliation(s)
- R Roehrdanz
- Biosciences Research Laboratory, Red River Valley Agricultural Research Center, Agricultural Research Service, U.S. Department of Agriculture, Fargo, ND 58105, USA.
| | | | | | | | | |
Collapse
|
5
|
Martinez PA, de Araujo WC, Molina WF. Derived cytogenetic traits, multiple NORs and B chromosomes in the compact karyotype of Canthigaster figueiredoi (Tetraodontiformes). Mar Genomics 2010; 3:85-9. [DOI: 10.1016/j.margen.2010.07.001] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2010] [Revised: 07/21/2010] [Accepted: 07/22/2010] [Indexed: 10/19/2022]
|
6
|
Babenko VN, Makunin IV, Brusentsova IV, Belyaeva ES, Maksimov DA, Belyakin SN, Maroy P, Vasil'eva LA, Zhimulev IF. Paucity and preferential suppression of transgenes in late replication domains of the D. melanogaster genome. BMC Genomics 2010; 11:318. [PMID: 20492674 PMCID: PMC2887417 DOI: 10.1186/1471-2164-11-318] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2010] [Accepted: 05/21/2010] [Indexed: 01/17/2023] Open
Abstract
Background Eukaryotic genomes are organized in extended domains with distinct features intimately linking genome structure, replication pattern and chromatin state. Recently we identified a set of long late replicating euchromatic regions that are underreplicated in salivary gland polytene chromosomes of D. melanogaster. Results Here we demonstrate that these underreplicated regions (URs) have a low density of P-element and piggyBac insertions compared to the genome average or neighboring regions. In contrast, Minos-based transposons show no paucity in URs but have a strong bias to testis-specific genes. We estimated the suppression level in 2,852 stocks carrying a single P-element by analysis of eye color determined by the mini-white marker gene and demonstrate that the proportion of suppressed transgenes in URs is more than three times higher than in the flanking regions or the genomic average. The suppressed transgenes reside in intergenic, genic or promoter regions of the annotated genes. We speculate that the low insertion frequency of P-elements and piggyBacs in URs partially results from suppression of transgenes that potentially could prevent identification of transgenes due to complete suppression of the marker gene. In a similar manner, the proportion of suppressed transgenes is higher in loci replicating late or very late in Kc cells and these loci have a lower density of P-elements and piggyBac insertions. In transgenes with two marker genes suppression of mini-white gene in eye coincides with suppression of yellow gene in bristles. Conclusions Our results suggest that the late replication domains have a high inactivation potential apparently linked to the silenced or closed chromatin state in these regions, and that such inactivation potential is largely maintained in different tissues.
Collapse
Affiliation(s)
- Vladimir N Babenko
- Department of Molecular and Cellular Biology, Institute of Chemical Biology and Fundamental Medicine SB RAS, Novosibirsk, 630090, Russia
| | | | | | | | | | | | | | | | | |
Collapse
|
7
|
Vogel MJ, Guelen L, de Wit E, Hupkes DP, Lodén M, Talhout W, Feenstra M, Abbas B, Classen AK, van Steensel B. Human heterochromatin proteins form large domains containing KRAB-ZNF genes. Genome Res 2006; 16:1493-504. [PMID: 17038565 PMCID: PMC1665633 DOI: 10.1101/gr.5391806] [Citation(s) in RCA: 123] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Heterochromatin is important for gene regulation and chromosome structure, but the genes that are occupied by heterochromatin proteins in the mammalian genome are largely unknown. We have adapted the DamID method to systematically identify target genes of the heterochromatin proteins HP1 and SUV39H1 in human and mouse cells. Unexpectedly, we found that CBX1 (formerly HP1beta) and SUV39H1 bind to genes encoding KRAB domain containing zinc finger (KRAB-ZNF) transcriptional repressors. These genes constitute one of the largest gene families and are organized in clusters in the human genome. Preference of CBX1 for this gene family was observed in both human and mouse cells. High-resolution mapping on human chromosome 19 revealed that CBX1 coats large domains 0.1-4 Mb in size, which coincide with the position of KRAB-ZNF gene clusters. These domains show an intricate CBX1 binding pattern: While CBX1 is globally elevated throughout the domains, it is absent from the promoters and binds more strongly to the 3' ends of KRAB-ZNF genes. KRAB-ZNF domains contain large numbers of LINE elements, which may contribute to CBX1 recruitment. These results uncover a surprising link between heterochromatin and a large family of regulatory genes in mammals. We suggest a role for heterochromatin in the evolution of the KRAB-ZNF gene family.
Collapse
Affiliation(s)
- Maartje J. Vogel
- Division of Molecular Biology, Netherlands Cancer Institute, Amsterdam, the Netherlands
| | - Lars Guelen
- Division of Molecular Biology, Netherlands Cancer Institute, Amsterdam, the Netherlands
| | - Elzo de Wit
- Division of Molecular Biology, Netherlands Cancer Institute, Amsterdam, the Netherlands
| | - Daniel Peric Hupkes
- Division of Molecular Biology, Netherlands Cancer Institute, Amsterdam, the Netherlands
| | - Martin Lodén
- Division of Molecular Biology, Netherlands Cancer Institute, Amsterdam, the Netherlands
| | - Wendy Talhout
- Division of Molecular Biology, Netherlands Cancer Institute, Amsterdam, the Netherlands
| | - Marike Feenstra
- Division of Molecular Biology, Netherlands Cancer Institute, Amsterdam, the Netherlands
| | - Ben Abbas
- Division of Molecular Biology, Netherlands Cancer Institute, Amsterdam, the Netherlands
| | - Anne-Kathrin Classen
- Division of Molecular Biology, Netherlands Cancer Institute, Amsterdam, the Netherlands
| | - Bas van Steensel
- Division of Molecular Biology, Netherlands Cancer Institute, Amsterdam, the Netherlands
- Corresponding author.E-mail ; fax +31.20.669.1383
| |
Collapse
|
8
|
Roy V, Monti-Dedieu L, Chaminade N, Siljak-Yakovlev S, Aulard S, Lemeunier F, Montchamp-Moreau C. Evolution of the chromosomal location of rDNA genes in two Drosophila species subgroups: ananassae and melanogaster. Heredity (Edinb) 2005; 94:388-95. [PMID: 15726113 DOI: 10.1038/sj.hdy.6800612] [Citation(s) in RCA: 55] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022] Open
Abstract
The evolution of the chromosomal location of ribosomal RNA gene clusters and the organization of heterochromatin in the Drosophila melanogaster group were investigated using fluorescence in situ hybridization and DAPI staining to mitotic chromosomes. The investigation of 18 species (11 of which were being examined for the first time) belonging to the melanogaster and ananassae subgroups suggests that the ancestral configuration consists of one nucleolus organizer (NOR) on each sex chromosome. This pattern, which is conserved throughout the melanogaster subgroup, except in D. simulans and D. sechellia, was observed only in the ercepeae complex within the ananassae subgroup. Both sex-linked NORs must have been lost in the lineage leading to D. varians and in the ananassae and bipectinata complexes, whereas new sites, characterized by intra-species variation in hybridization signal size, appeared on the fourth chromosome related to heterochromatic rearrangements. Nucleolar material is thought to be required for sex chromosome pairing and disjunction in a variety of organisms including Drosophila. Thus, either remnant sequences, possibly intergenic spacer repeats, are still present in the sex chromosomes which have lost their NORs (as observed in D. simulans and D. sechellia), or an alternative mechanism has evolved.
Collapse
Affiliation(s)
- V Roy
- Laboratoire Populations, Génétique et Evolution, Centre National de la Recherche Scientifique, Gif-sur-Yvette Cedex, France
| | | | | | | | | | | | | |
Collapse
|
9
|
Eirín-López JM, Fernanda Ruiz M, González-Tizón AM, Martínez A, Sánchez L, Méndez J. Molecular evolutionary characterization of the mussel Mytilus histone multigene family: first record of a tandemly repeated unit of five histone genes containing an H1 subtype with "orphon" features. J Mol Evol 2004; 58:131-44. [PMID: 15042333 DOI: 10.1007/s00239-003-2531-5] [Citation(s) in RCA: 60] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2003] [Accepted: 07/21/2003] [Indexed: 11/30/2022]
Abstract
The present work represents the first characterization of a clustered histone repetitive unit containing an H1 gene in a bivalve mollusk. To complete the knowledge on the evolutionary history of the histone multigene family in invertebrates, we undertake its characterization in five mussel Mytilus species, as an extension of our previous work on the H1 gene family. We report the quintet H4-H2B-H2A-H3-H1 as the major organization unit in the genome of Mytilus galloprovincialis with two 5S rRNA genes with interspersed nontranscribed spacer segments linked to the unit, which is not justified by their cotranscription with histone genes. Surprisingly, 3' UTR regions of histone genes show two different mRNA termination signals, a stem-loop and a polyadenylation signal, both related to the evolution of histone gene expression patterns throughout the cell cycle. The clustered H1 histones characterized share essential features with "orphon" H1 genes, suggesting a common evolutionary origin for both histone subtypes which is supported by the reconstructed phylogeny for H1 genes. The characterization of histone genes in four additional Mytilus species revealed the presence of strong purifying selection acting among the members of the family. The chromosomal location of most of the core histone genes studied was identified by FISH close to telomeric regions in M. galloprovincialis. Further analysis on nucleotide variation would be necessary to assess if H1 proteins evolve according to the birth-and-death model of evolution and if the effect of the strong purifying selection maintaining protein homogeneity could account for the homologies detected between clustered and "orphon" variants.
Collapse
Affiliation(s)
- José M Eirín-López
- Departamento de Biología Celular y Molecular, Universidade da Coruña, Campus de A Zapateira s/n, E-15071-A Coruña, Spain
| | | | | | | | | | | |
Collapse
|
10
|
Chiche J, Brown SC, Leclerc JC, Siljak-Yakovlev S. Genome size, heterochromatin organisation, and ribosomal gene mapping in four species of Ribes. ACTA ACUST UNITED AC 2003. [DOI: 10.1139/b03-088] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Four wild Ribes species (Ribes alpinum L., Ribes petraeum Wulf., Ribes rubrum L., and Ribes uva- crispa L.; all 2n = 2x = 16) were surveyed for their chromosome and genome organisation. Their genome size was assessed using flow cytometry. Ribes alpinum had 5.3% more nuclear DNA than did the three other species, whose average was 2C = 1.91 pg with 40.4% GC. In addition, GC- and AT-rich heterochromatin and rDNA (18S5.8S26S and 5S) patterns were studied using fluorochrome banding and double-target fluorescence in situ hybridization (FISH), respectively. Only GC-rich heterochromatin was detected, co-localizing with 18S26S rDNA. Fluorochrome banding and FISH patterns revealed marked differences between species. Ribes alpinum and R. uva-crispa differed from R. rubrum and R. petraeum by the number of 18S26S sites and the localization of 5S rDNA. Ribes alpinum and R. uva-crispa were differentiated by the number of 5S sites. Ribes rubrum and R. petraeum also differed by the number of 5S sites and by the size of the GC-rich band on the satellite chromosome pair. These results should contribute to a better understanding of phylogenetic relationships among these species.Key words: Ribes, flow cytometry, fluorochrome banding, FISH, rDNA, NORs.
Collapse
|
11
|
Ranz JM, González J, Casals F, Ruiz A. Low occurrence of gene transposition events during the evolution of the genus Drosophila. Evolution 2003; 57:1325-35. [PMID: 12894940 DOI: 10.1111/j.0014-3820.2003.tb00340.x] [Citation(s) in RCA: 36] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The role played by gene transpositions during the evolution of eukaryotic genomes is still poorly understood and indeed has been analyzed in detail only in nematodes. In Drosophila, a limited number of transpositions have been detected by comparing the chromosomal location of genes between different species. The relative importance of gene transposition versus other types of chromosomal rearrangements, for example, inversions, has not yet been evaluated. Here, we use physical mapping to perform an extensive search for long-distance gene transpositions and assess their impact during the evolution of the Drosophila genome. We compare the relative order of 297 molecular markers that cover 60% of the euchromatic fraction of the genome between two related Drosophila species and conclude that the frequency of gene transpositions is very low, namely one order of magnitude lower than that of nematodes. In addition, gene transpositions seem to be events almost exclusively associated with genes of repetitive nature such as the Histone gene complex (HIS-C).
Collapse
Affiliation(s)
- José María Ranz
- Department de Genètica i de Microbiologia, Facultat de Ciències, Edifici C, Universitat Autònoma de Barcelona, 08193 Bellaterra, Barcelona, Spain.
| | | | | | | |
Collapse
|
12
|
Kelley RL, Kuroda MI. The Drosophila roX1 RNA gene can overcome silent chromatin by recruiting the male-specific lethal dosage compensation complex. Genetics 2003; 164:565-74. [PMID: 12807777 PMCID: PMC1462573 DOI: 10.1093/genetics/164.2.565] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The Drosophila MSL complex consists of at least six proteins and two noncoding roX RNAs that mediate dosage compensation. It acts to remodel the male's X chromatin by covalently modifying the amino terminal tails of histones. The roX1 and roX2 genes are thought to be nucleation sites for assembly and spreading of MSL complexes into surrounding chromatin where they roughly double the rates of transcription. We generated many transgenic stocks in which the roX1 gene was moved from its normal location on the X to new autosomal sites. Approximately 10% of such lines displayed unusual sexually dimorphic expression patterns of the transgene's mini-white eye-color marker. Males often displayed striking mosaic pigmentation patterns similar to those seen in position-effect variegation and yet most inserts were in euchromatic locations. In many of these stocks, female mini-white expression was very low or absent. The male-specific activation of mini-white depended upon the MSL complex. We propose that these transgenes are inserted in several different types of repressive chromatin environments that inhibit mini-white expression. Males are able to overcome this silencing through the action of the MSL complex spreading from the roX1 gene and remodeling the local chromatin to allow transcription. The potency with which an ectopic MSL complex overcomes silent chromatin suggests that its normal action on the X must be under strict regulation.
Collapse
MESH Headings
- Animals
- Animals, Genetically Modified
- Base Sequence
- Chromatin/metabolism
- Crosses, Genetic
- DNA/metabolism
- DNA Transposable Elements
- Dosage Compensation, Genetic
- Drosophila/genetics
- Drosophila Proteins/genetics
- Female
- Gene Expression Regulation
- Gene Silencing
- Genes, Insect
- Male
- Microscopy, Electron, Scanning
- Models, Biological
- Molecular Sequence Data
- Mosaicism
- Nuclear Proteins/metabolism
- Photoreceptor Cells, Invertebrate/pathology
- Photoreceptor Cells, Invertebrate/ultrastructure
- Pigmentation/genetics
- Sex Factors
- Transcription Factors/genetics
- Transcription, Genetic
- Transgenes
Collapse
Affiliation(s)
- Richard L Kelley
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, Texas 77030, USA.
| | | |
Collapse
|
13
|
Ranz JM, González J, Casals F, Ruiz A. LOW OCCURRENCE OF GENE TRANSPOSITION EVENTS DURING THE EVOLUTION OF THE GENUS DROSOPHILA. Evolution 2003. [DOI: 10.1554/02-468] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
|
14
|
González J, Ranz JM, Ruiz A. Chromosomal elements evolve at different rates in the Drosophila genome. Genetics 2002; 161:1137-54. [PMID: 12136017 PMCID: PMC1462194 DOI: 10.1093/genetics/161.3.1137] [Citation(s) in RCA: 49] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Recent results indicate that the rate of chromosomal rearrangement in the genus Drosophila is the highest found so far in any eukaryote. This conclusion is based chiefly on the comparative mapping analysis of a single chromosomal element (Muller's element E) in two species, D. melanogaster and D. repleta, representing the two farthest lineages within the genus (the Sophophora and Drosophila subgenera, respectively). We have extended the analysis to two other chromosomal elements (Muller's elements A and D) and tested for differences in rate of evolution among chromosomes. With this purpose, detailed physical maps of chromosomes X and 4 of D. repleta were constructed by in situ hybridization of 145 DNA probes (gene clones, cosmids, and P1 phages) and their gene arrangements compared with those of the homologous chromosomes X and 3L of D. melanogaster. Both chromosomal elements have been extensively reshuffled over their entire length. The number of paracentric inversions fixed has been estimated as 118 +/- 17 for element A and 56 +/- 8 for element D. Comparison with previous data for elements E and B shows that there are fourfold differences in evolution rate among chromosomal elements, with chromosome X exhibiting the highest rate of rearrangement. Combining all results, we estimated that 393 paracentric inversions have been fixed in the whole genome since the divergence between D. repleta and D. melanogaster. This amounts to an average rate of 0.053 disruptions/Mb/myr, corroborating the high rate of rearrangement in the genus Drosophila.
Collapse
Affiliation(s)
- Josefa González
- Departament de Genètica i de Microbiologia, Facultat de Ciències-Edifici C, Universitat Autònoma de Barcelona, 08193 Bellaterra (Barcelona), Spain
| | | | | |
Collapse
|
15
|
Matsuo Y. Evolutionary change of codon usage for the histone gene family in Drosophila melanogaster and Drosophila hydei. Mol Phylogenet Evol 2000; 15:283-91. [PMID: 10837157 DOI: 10.1006/mpev.1999.0749] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The nucleotide divergence in the protein-coding region for replication-dependent and replication-independent histone 3 and 4 genes of Drosophila melanogaster and Drosophila hydei occurred mostly at the synonymous site. Therefore, the pattern of codon usage was analyzed in the two species, considering the genomic codon bias, which is proposed for estimating the genomic composition pressure in the protein-coding regions. The results indicated that the codon usage in the histone gene family could be explained mostly by the genomic codon bias. However, biases for Ala and Arg were commonly observed for the histone 3 and histone 4 gene families, and biases for Ser, Leu, and Glu were observed in a gene-specific manner. This suggests that both genomic codon bias and gene- or codon-specific bias are responsible for the nucleotide differentiation in the protein-coding region of the histone genes.
Collapse
Affiliation(s)
- Y Matsuo
- Laboratory of Adaptive Evolution, Department of Mathematical and Natural Sciences, Faculty of Integrated Arts and Sciences, The University of Tokushima, Minamijosanjimacho 1-1, Tokushima, 770-8502, Japan
| |
Collapse
|
16
|
van Steensel B, Henikoff S. Identification of in vivo DNA targets of chromatin proteins using tethered dam methyltransferase. Nat Biotechnol 2000; 18:424-8. [PMID: 10748524 DOI: 10.1038/74487] [Citation(s) in RCA: 420] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
We have developed a novel technique, named DamID, for the identification of DNA loci that interact in vivo with specific nuclear proteins in eukaryotes. By tethering Escherichia coli DNA adenine methyltransferase (Dam) to a chromatin protein, Dam can be targeted in vivo to native binding sites of this protein, resulting in local DNA methylation. Sites of methylation can subsequently be mapped using methylation-specific restriction enzymes or antibodies. We demonstrate the successful application of DamID both in Drosophila cell cultures and in whole flies. When Dam is tethered to the DNA-binding domain of GAL4, targeted methylation is limited to a region of a few kilobases surrounding a GAL4 binding sequence. Using DamID, we identified a number of expected and unexpected target loci for Drosophila heterochromatin protein 1. DamID has potential for genome-wide mapping of in vivo targets of chromatin proteins in various eukaryotes.
Collapse
Affiliation(s)
- B van Steensel
- Fred Hutchinson Cancer Research Center and Howard Hughes Medical Institute, Seattle, WA 98109, USA.
| | | |
Collapse
|
17
|
Barzotti R, Pelliccia F, Bucciarelli E, Rocchi A. Organization, nucleotide sequence, and chromosomal mapping of a tandemly repeated unit containing the four core histone genes and a 5S rRNA gene in an isopod crustacean species. Genome 2000; 43:341-5. [PMID: 10791823 DOI: 10.1139/g99-142] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
A tandemly repeated unit of 6553 bp containing a copy of the four core histone genes H2B, H2A, H3, and H4, and also a 5S rRNA gene, was amplified by PCR from genomic DNA of the isopod crustacean Asellus aquaticus. The linkage between 5S rRNA genes and histone genes has been so far observed in only one other organism, the anostrac crustacean Artemia salina. The gene cluster was cloned and sequenced. The histone genes, in their 3' flanking region, have the interesting feature of possessing two different mRNA termination signals, the stem-loop structure and the AATAAA sequence. A part of the PCR product was used as a probe in FISH experiments to locate the gene cluster on an inter-individually variable number of chromosomes from 6 to 12 per diploid cell, always in a terminal position and never associated with the heterochromatic areas. Fluorescence in situ hybridization (FISH) was also performed on preparations of released chromatin and the reiteration level of the gene cluster was determined as approximately 200-300 copies per haploid genome.
Collapse
Affiliation(s)
- R Barzotti
- Dipartimento di Genetica e Biologia Molecolare, Università La Sapienza, Roma, Italia
| | | | | | | |
Collapse
|
18
|
Affiliation(s)
- I F Zhimulev
- Institute of Cytology and Genetics, Siberian Division of Russian Academy of Sciences, Novosibirsk, Russia
| |
Collapse
|
19
|
Fujiwara A, Abe S, Yamaha E, Yamazaki F, Yoshida MC. Chromosomal localization and heterochromatin association of ribosomal RNA gene loci and silver-stained nucleolar organizer regions in salmonid fishes. Chromosome Res 1998; 6:463-71. [PMID: 9865785 DOI: 10.1023/a:1009200428369] [Citation(s) in RCA: 113] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
Ribosomal RNA gene (rDNA) loci, including those of nucleolus-forming 18S, 5.8S and 28S (major) and non-nucleolus-forming 5S (minor) rDNA, were assigned using fluorescence in situ hybridization (FISH) to the embryonic chromosomes of rainbow trout (Oncorhynchus mykiss), masu salmon (O. masou), brook trout (Salvelinus fontinalis) and Japanese huchen (Hucho perryi). In these species, the minor rDNA loci were located basically on 2-4 chromosome pairs, whereas the major rDNA loci were found essentially on one chromosome pair, except for the brook trout. Its major rDNA loci were dispersed on about half of the chromosome complement, showing a considerable interindividual variation in the number and location. The major and minor rDNA loci were separated onto different chromosomes in the examined species, except for the rainbow trout, in which one chromosome pair had tandemly aligned minor and major rDNA loci. Chromosome regions containing both kinds of rDNA loci in each species were found to be stained with C-banding, showing an association of these loci with heterochromatin. Comparison of the assigned major rDNA loci and sequentially detected silver (Ag)-stained nucleolar organizer regions (AgNORs) in all the species revealed a considerable polymorphism in the number and size of AgNORs among or within those loci, suggesting a possible inter- or intralocus inactivation of the major rDNAs.
Collapse
Affiliation(s)
- A Fujiwara
- Laboratory of Cytogenetics, Graduate School of Environmental Earth Science, Hokkaido University, Sapporo, Japan
| | | | | | | | | |
Collapse
|
20
|
Zhimulev IF. Polytene chromosomes, heterochromatin, and position effect variegation. ADVANCES IN GENETICS 1997; 37:1-566. [PMID: 9352629 DOI: 10.1016/s0065-2660(08)60341-7] [Citation(s) in RCA: 41] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Affiliation(s)
- I F Zhimulev
- Institute of Cytology and Genetics, Siberian Division of the Russian Academy of Sciences, Novosibirsk, Russia
| |
Collapse
|
21
|
Ranz JM, Segarra C, Ruiz A. Chromosomal homology and molecular organization of Muller's elements D and E in the Drosophila repleta species group. Genetics 1997; 145:281-95. [PMID: 9071584 PMCID: PMC1207795 DOI: 10.1093/genetics/145.2.281] [Citation(s) in RCA: 40] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
Thirty-three DNA clones containing protein-coding genes have been used for in situ hybridization to the polytene chromosomes of two Drosophila repleta group species, D. repleta and D. buzzatii. Twenty-six clones gave positive results allowing the precise localization of 26 genes and the tentative identification of another nine. The results were fully consistent with the currently accepted chromosomal homologies and in no case was evidence for reciprocal translocations or pericentric inversions found. Most of the genes mapped to chromosomes 2 and 4 that are homologous, respectively, to chromosome arms 3R and 3L of D. melanogaster (Muller's elements E and D). The comparison of the molecular organization of-these two elements between D. melanogaster and D. repleta (two species that belong to different subgenera and diverged some 62 million years ago) showed an extensive reorganization via paracentric inversions. Using a maximum likelihood procedure, we estimated that 130 paracentric inversions have become fixed in element E after the divergence of the two lineages. Therefore, the evolution rate for element E is approximately one inversion per million years. This value is comparable to previous estimates of the rate of evolution of chromosome X and yields an estimate of 4.5 inversions per million years for the whole Drosophila genome.
Collapse
Affiliation(s)
- J M Ranz
- Departament de Genètica i de Microbiologia, Universitat Autònoma de Barcelona, Spain
| | | | | |
Collapse
|
22
|
Barzotti R, Pelliccia F, Rocchi A. Heterochromatin and ribosomal genes in Asellus aquaticus (Crust. Isop.). Chromosome Res 1996; 4:177-81. [PMID: 8793199 DOI: 10.1007/bf02254955] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
In the present investigation chromosomal preparations of Asellus aquaticus were sequentially stained with chromomycin A3 to reveal the heterochromatic areas, hybridized in situ with rDNA probes in order to map the ribosomal genes and finally silver stained to check the transcriptional activity of these genes. The results indicate the existence of a substantial correspondence of location and size among the heterochromatic regions and the regions over which the in situ hybridization signals spread. The ribosomal genes, quite independently of their location in the secondary constriction, can be silver stained and thus appear to be transcriptionally active. The ribosomal sequences also hybridize to the entire heterochromatic areas observed on the probable Y chromosome identified in some males of a natural population. These rRNA genes are only rarely transcriptionally active.
Collapse
Affiliation(s)
- R Barzotti
- Dipartimento di Genetica e Biologia Molecolare, Università La Sapienza, Rome, Italy
| | | | | |
Collapse
|
23
|
Pendás AM, Morán P, García-Vázquez E. Organization and chromosomal location of the major histone cluster in brown trout, Atlantic salmon and rainbow trout. Chromosoma 1994; 103:147-52. [PMID: 8055712 DOI: 10.1007/bf00352324] [Citation(s) in RCA: 39] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
The major histone cluster (hisDNA) was mapped by fluorescent in situ hybridization (FISH) to mitotic chromosomes of Atlantic salmon, brown trout, and rainbow trout. The data reveal that in the three species hisDNA is tandemly repeated in a single locus. Southern blots of genomic DNA indicate that these clusters are representative of the vast majority of the histone genes in these species. Similar reiteration values were found among the three species. Genetic variability in the hisDNA was found only in brown trout for an EcoRI site.
Collapse
Affiliation(s)
- A M Pendás
- Departamento de Biologia Funcional, Facultad de Medicina, Universidad de Oviedo, Spain
| | | | | |
Collapse
|
24
|
Pendás AM, Morán P, Garciía-Vázquez E. Multi-chromosomal location of ribosomal RNA genes and heterochromatin association in brown trout. Chromosome Res 1993; 1:63-7. [PMID: 8143090 DOI: 10.1007/bf00710608] [Citation(s) in RCA: 93] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
The ribosomal rRNA genes have been mapped by fluorescent in situ hybridization (FISH) to brown trout chromosomes. One major NOR chromosome pair and 8 novel minor NOR chromosome pairs have been found. Both major and minor NORs were closely related to polymorphic heterochromatin, as revealed by FISH and C-banding. These results are discussed with respect to NOR expression, the relationship between rDNA and heterochromatin, and evolutionary aspects.
Collapse
Affiliation(s)
- A M Pendás
- Departmento de Biologia Funcional, Area de Genetica, Facultad de Medicina, Universidad de Oviedo, Spain
| | | | | |
Collapse
|
25
|
Rogers SO, Bendich AJ. Variability and inheritance of histone genes H3 and H4 in Vicia faba. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 1992; 84:617-623. [PMID: 24201349 DOI: 10.1007/bf00224160] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/24/1991] [Accepted: 01/10/1992] [Indexed: 06/02/2023]
Abstract
We have compared copy numbers and blothybridization patterns of histone genes (H3 plus H4) between and within individuals of broad bean (Vicia faba). Copy number differences among individuals in the population of 200 individuals were as great as 27 fold, and as much as 3.2 fold among separate leaves of the same plant. Among F2 progeny from genetic crosses, up to a 5.4-fold range was seen (mean=3.5 fold), and among F1 progeny of self-pollinated plants, up to a 5.9-fold range was observed (mean=2.3 fold). Histone gene blot-hybridization patterns for EcoRI and HindIII were also variable among individuals and indicated that the genes are probably clustered in only a few chromosomal loci. The degree of variation in histone gene copy number per haploid genome (2-55 copies, or 27 fold) was similar to that found previously for ribosomal RNA genes (230-22000, or 95 fold) of V. faba. However, the two gene families change independently, since individuals with a high or low copy number for one gene can have either a high or low copy number for the other. The mechanisms(s) for rapid gene copy number change may be similar for these gene families.
Collapse
Affiliation(s)
- S O Rogers
- Department of Environmental and Forest Biology College of Envirnmental Science and Forestry, State University of New York, 13210, Syracuse, NY, USA
| | | |
Collapse
|
26
|
Croston GE, Lira LM, Kadonaga JT. A general method for purification of H1 histones that are active for repression of basal RNA polymerase II transcription. Protein Expr Purif 1991; 2:162-9. [PMID: 1821786 DOI: 10.1016/1046-5928(91)90066-r] [Citation(s) in RCA: 29] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
H1 histones were purified from extracts of salt-treated nuclei as a co-product of RNA polymerase II transcription factors from both Drosophila embryos and HeLa cells by a simple and general method. This procedure was also used to purify H1 as co-product of the core histones from calf thymus. The key steps in this purification exploit the solubility of H1 in 2.26 M ammonium sulfate and the chromatographic properties of the highly charged H1 molecules on a phenyl-Sepharose resin. H1 that is prepared by this procedure is active for in vitro repression of basal RNA polymerase II transcription. This method provides a new means of purifying H1 by a mild procedure that is likely to be generally useful for studies of transcription and chromatin structure.
Collapse
Affiliation(s)
- G E Croston
- Department of Biology, University of California, San Diego, La Jolla 92093
| | | | | |
Collapse
|
27
|
Strausbaugh LD, Bourke MT, Sommer MT, Coon ME, Berg CM. Probe mapping to facilitate transposon-based DNA sequencing. Proc Natl Acad Sci U S A 1990; 87:6213-7. [PMID: 2166950 PMCID: PMC54503 DOI: 10.1073/pnas.87.16.6213] [Citation(s) in RCA: 22] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
A promising strategy for DNA sequencing exploits transposons to provide mobile sites for the binding of sequencing primers. For such a strategy to be maximally efficient, the location and orientation of the transposon must be readily determined and the insertion sites should be randomly distributed. We demonstrate an efficient probe-based method for the localization and orientation of transposon-borne primer sites, which is adaptable to large-scale sequencing strategies. This approach requires no prior restriction enzyme mapping or knowledge of the cloned sequence and eliminates the inefficiency inherent in totally random sequencing methods. To test the efficiency of probe mapping, 49 insertions of the transposon gamma delta (Tn1000) in a cloned fragment of Drosophila melanogaster DNA were mapped and oriented. In addition, oligonucleotide primers specific for unique subterminal gamma delta segments were used to prime dideoxynucleotide double-stranded sequencing. These data provided an opportunity to rigorously examine gamma delta insertion sites. The insertions were quite randomly distributed, even though the target DNA fragment had both A + T-rich and G + C-rich regions; in G + C-rich DNA, the insertions were found in A + T-rich "valleys." These data demonstrate that gamma delta is an excellent choice for supplying mobile primer binding sites to cloned DNA and that transposon-based probe mapping permits the sequences of large cloned segments to be determined without any subcloning.
Collapse
Affiliation(s)
- L D Strausbaugh
- Department of Molecular and Cell Biology, University of Connecticut, Storrs 06269-3125
| | | | | | | | | |
Collapse
|