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Koo DH, Zhao H, Jiang J. Chromatin-associated transcripts of tandemly repetitive DNA sequences revealed by RNA-FISH. Chromosome Res 2016; 24:467-480. [PMID: 27590598 DOI: 10.1007/s10577-016-9537-5] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2016] [Revised: 08/18/2016] [Accepted: 08/24/2016] [Indexed: 02/05/2023]
Abstract
Tandemly repetitive DNA sequences, also named satellite repeats, are major DNA components of heterochromatin and are often organized as long arrays in the pericentromeric, centromeric, and subtelomeric regions of eukaryotic chromosomes. An increasing amount of evidence indicates that transcripts derived from some satellite repeats play important roles in various biological functions. We used a RNA-fluorescence in situ hybridization (RNA-FISH) technique to investigate the transcription of the four well-characterized satellite repeats of maize (Zea mays), including the 180-bp knob repeat, the telomeric (TTTAGGG)n repeat, the 156-bp centromeric repeat CentC, and a 350-bp subtelomeric repeat. Although few transcripts derived from these four repeats were found in the expressed sequence tag and RNA-seq databases, RNA-FISH consistently detected the transcripts from three of the four repeats on interphase nuclei, suggesting that the transcripts from the three repeats are largely integrated into chromatin. The transcripts from the knob and telomeric repeats were mapped to the related DNA loci. In contrast, the transcripts from the CentC repeats were mainly localized to the nucleolus, although nucleoplasmic CentC transcripts were also detectable. The nucleolus and nuclear RNAs appeared to be important for the nuclear localization for at least one centromeric protein, Mis12. We demonstrate that RNA-FISH is a powerful tool to assess the level of transcription as well as to physically map the nuclear locations of the transcripts derived from satellite repeats.
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Affiliation(s)
- Dal-Hoe Koo
- Department of Horticulture, University of Wisconsin-Madison, Madison, WI, 53706, USA.,Department of Plant Pathology, Kansas State University, Manhattan, KS, 66506, USA
| | - Hainan Zhao
- Department of Horticulture, University of Wisconsin-Madison, Madison, WI, 53706, USA
| | - Jiming Jiang
- Department of Horticulture, University of Wisconsin-Madison, Madison, WI, 53706, USA.
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Tomás D, Brazão J, Viegas W, Silva M. Differential Effects of High-Temperature Stress on Nuclear Topology and Transcription of Repetitive Noncoding and Coding Rye Sequences. Cytogenet Genome Res 2012; 139:119-27. [DOI: 10.1159/000343754] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/16/2012] [Indexed: 12/25/2022] Open
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Gong X, Hong D, Chen S, Shen L, Li P, Yan C. Isolation and characterization of five rice telomere-associated sequences. ACTA ACUST UNITED AC 2011; 41:372-80. [PMID: 18726253 DOI: 10.1007/bf02882736] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/1997] [Indexed: 10/22/2022]
Abstract
Acoording to the telomere-repeated sequences of rice, two primers: (TTTAGGG11)(3) and (CCC-TAA.A)(3)CCC were used to amplify rice telomere-assciated sequences (TASs). Fox PCR template preparation. total DNA was digested with restrictive endonuclease and then ligated. Using the ligates or total DNA sa template, eight fragments were obtained with the single primer by the PCR reaction. To confirm that the sequences are derived from telomeric DNA, we conducted Bal31 digestion analysis. Of the eight fragments, seven were susceptible to Bal31 treatment, suggesting that they were TASs. These DNA fragments were further demonstrated u, be rice sub-telomeric sequences by RFLP mapping Five sequences have been mapped to the distal ends on rice chromme 5,6,7 and 9, and two other sequences have been mapped at interstitial sites, suggesting that (TTTAGGG)(n). also exist in the middle of rice chromosomes-All eight fragments were sequenced and characterized.
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Affiliation(s)
- X Gong
- Institute of Genetics, Chinese Academy of Sciences, 100101, Beijing, China
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Zhang D, Yang Q, Ding Y, Cao X, Xue Y, Cheng Z. Cytological characterization of the tandem repetitive sequences and their methylation status in the Antirrhinum majus genome. Genomics 2008; 92:107-14. [PMID: 18559290 DOI: 10.1016/j.ygeno.2008.04.008] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2008] [Revised: 04/17/2008] [Accepted: 04/19/2008] [Indexed: 12/21/2022]
Abstract
Tandem repetitive sequences are DNA motifs common in the genomes of eukaryotic species and are often embedded in heterochromatic regions. In most eukaryotes, ribosomal genes, as well as centromeres and telomeres or subtelomeres, are associated with abundant tandem arrays of repetitive sequences and typically represent the final barriers to completion of whole-genome sequencing. The nature of these repeats makes it difficult to estimate their actual sizes. In this study, combining the two cytological techniques DNA fiber-FISH and pachytene chromosome FISH allowed us to characterize the tandem repeats distributed genome wide in Antirrhinum majus and identify four types of tandem repeats, 45S rDNA, 5S rDNA, CentA1, and CentA2, representing the major tandem repetitive components, which were estimated to have a total length of 18.50 Mb and account for 3.59% of the A. majus genome. FISH examination revealed that all the tandem repeats correspond to heterochromatic knobs along the pachytene chromosomes. Moreover, the methylation status of the tandem repeats was investigated in both somatic cells and pollen mother cells from anther tissues using an antibody against 5-methylcytosine combined with sequential FISH analyses. Our results showed that these repeats were hypomethylated in anther tissues, especially in the pollen mother cells at pachytene stage.
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Affiliation(s)
- Dongfen Zhang
- State Key Laboratory of Plant Genomics and Center for Plant Gene Research, Beijing 100101, China
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Hsing YI, Chern CG, Fan MJ, Lu PC, Chen KT, Lo SF, Sun PK, Ho SL, Lee KW, Wang YC, Huang WL, Ko SS, Chen S, Chen JL, Chung CI, Lin YC, Hour AL, Wang YW, Chang YC, Tsai MW, Lin YS, Chen YC, Yen HM, Li CP, Wey CK, Tseng CS, Lai MH, Huang SC, Chen LJ, Yu SM. A rice gene activation/knockout mutant resource for high throughput functional genomics. PLANT MOLECULAR BIOLOGY 2007; 63:351-64. [PMID: 17120135 DOI: 10.1007/s11103-006-9093-z] [Citation(s) in RCA: 130] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/24/2006] [Accepted: 09/12/2006] [Indexed: 05/12/2023]
Abstract
Using transfer DNA (T-DNA) with functions of gene trap and gene knockout and activation tagging, a mutant population containing 55,000 lines was generated. Approximately 81% of this population carries 1-2 T-DNA copies per line, and the retrotransposon Tos17 was mostly inactive in this population during tissue culture. A total of 11,992 flanking sequence tags (FSTs) have been obtained and assigned to the rice genome. T-DNA was preferentially ( approximately 80%) integrated into genic regions. A total of 19,000 FSTs pooled from this and another T-DNA tagged population were analyzed and compared with 18,000 FSTs from a Tos17 tagged population. There was difference in preference for integrations into genic, coding, and flanking regions, as well as repetitive sequences and centromeric regions, between T-DNA and Tos17; however, T-DNA integration was more evenly distributed in the rice genome than Tos17. Our T-DNA contains an enhancer octamer next to the left border, expression of genes within genetics distances of 12.5 kb was enhanced. For example, the normal height of a severe dwarf mutant, with its gibberellin 2-oxidase (GA2ox) gene being activated by T-DNA, was restored upon GA treatment, indicating GA2ox was one of the key enzymes regulating the endogenous level of GA. Our T-DNA also contains a promoterless GUS gene next to the right border. GUS activity screening facilitated identification of genes responsive to various stresses and those regulated temporally and spatially in large scale with high frequency. Our mutant population offers a highly valuable resource for high throughput rice functional analyses using both forward and reverse genetic approaches.
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Affiliation(s)
- Yue-Ie Hsing
- Institute of Plant and Microbial Biology, Academia Sinica, Nankang, Taipei 115, Taiwan, ROC
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Contento A, Heslop-Harrison JS, Schwarzacher T. Diversity of a major repetitive DNA sequence in diploid and polyploid Triticeae. Cytogenet Genome Res 2005; 109:34-42. [PMID: 15753556 DOI: 10.1159/000082379] [Citation(s) in RCA: 64] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2004] [Indexed: 11/19/2022] Open
Abstract
About 90 members of a major tandemly repeated DNA sequence family originally described in rye as pSc119.2 have been isolated from 11 diploid and polyploid Triticeae species using primers from along the length of the sequence for PCR amplification. Alignment and similarity analysis showed that the 120-bp repeat unit family is diverse with single nucleotide changes and few insertions and deletions occurring throughout the sequence, with no characteristic genome or species-specific variants having developed during evolution of the extant genomes. Fluorescent in situ hybridization showed that each of the large blocks of the repeat at chromosomal sites harboured many variants of the 120-bp repeat. There were substantial copy number differences between genomes, with abundant sub-terminal sites in rye, interstitial sites in the B genome of wheat, and relatively few sites in the A and D genome. We conclude that sequence homogenization events have not been operative in this repeat and that the common ancestor of the Triticeae tribe had multiple sequences of the 120-bp repeat with a range of variation not unlike that seen within and between species today. This diversity has been maintained when sites are moved within the genome and in all species since their divergence within the Triticeae.
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Affiliation(s)
- A Contento
- Department of Biology, University of Leicester, Leicester, UK
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Cheng Z, Presting GG, Buell CR, Wing RA, Jiang J. High-resolution pachytene chromosome mapping of bacterial artificial chromosomes anchored by genetic markers reveals the centromere location and the distribution of genetic recombination along chromosome 10 of rice. Genetics 2001; 157:1749-57. [PMID: 11290728 PMCID: PMC1461616 DOI: 10.1093/genetics/157.4.1749] [Citation(s) in RCA: 120] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023] Open
Abstract
Large-scale physical mapping has been a major challenge for plant geneticists due to the lack of techniques that are widely affordable and can be applied to different species. Here we present a physical map of rice chromosome 10 developed by fluorescence in situ hybridization (FISH) mapping of bacterial artificial chromosome (BAC) clones on meiotic pachytene chromosomes. This physical map is fully integrated with a genetic linkage map of rice chromosome 10 because each BAC clone is anchored by a genetically mapped restriction fragment length polymorphism marker. The pachytene chromosome-based FISH mapping shows a superior resolving power compared to the somatic metaphase chromosome-based methods. The telomere-centromere orientation of DNA clones separated by 40 kb can be resolved on early pachytene chromosomes. Genetic recombination is generally evenly distributed along rice chromosome 10. However, the highly heterochromatic short arm shows a lower recombination frequency than the largely euchromatic long arm. Suppression of recombination was found in the centromeric region, but the affected region is far smaller than those reported in wheat and barley. Our FISH mapping effort also revealed the precise genetic position of the centromere on chromosome 10.
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Affiliation(s)
- Z Cheng
- Department of Horticulture, University of Wisconsin, Madison, Wisconsin 53706, USA
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Yuan Q, Liang F, Hsiao J, Zismann V, Benito MI, Quackenbush J, Wing R, Buell R. Anchoring of rice BAC clones to the rice genetic map in silico. Nucleic Acids Res 2000; 28:3636-41. [PMID: 10982886 PMCID: PMC110739 DOI: 10.1093/nar/28.18.3636] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
A wealth of molecular resources have been developed for rice genomics, including dense genetic maps, expressed sequence tags (ESTs), yeast artificial chromosome maps, bacterial artificial chromosome (BAC) libraries and BAC end sequence databases. Integration of genetic and physical maps involves labor-intensive empirical experiments. To accelerate the integration of the bacterial clone resources with the genetic map for the International Rice Genome Sequencing Project, we cleaned and filtered the available EST and BAC end sequences for repetitive sequences and then searched all available rice genetic markers with our filtered databases. We identified 418 genetic markers that aligned with at least one BAC end sequence with >95% sequence identity, providing a set of large insert clones with an average separation of 1 Mb that can serve as nucleation points for the sequencing phase of the International Rice Genome Sequencing Project.
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Affiliation(s)
- Q Yuan
- The Institute for Genomic Research, 9712 Medical Center Drive, Rockville, MD 20850, USA
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Horáková M, Fajkus J. TAS49--a dispersed repetitive sequence isolated from subtelomeric regions of Nicotiana tomentosiformis chromosomes. Genome 2000; 43:273-84. [PMID: 10791815 DOI: 10.1139/g99-126] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
We have isolated and characterized a new repetitive sequence, TAS49, from terminal restriction fragments of Nicotiana tomentosiformis genomic DNA by means of a modified vectorette approach. The TAS49 was found directly attached to telomeres of N. tabacum and one of its ancestors, N. tomentosiformis, and also at inner chromosome locations. No association with telomeres was detected neither in N. otophora nor in the second tobacco ancestor, N. sylvestris. PCR and Southern hybridization reveal similarities in the arrangement of TAS49 on the chromosomes of 9 species of the genus Nicotiana, implying its occurrence as a subunit of a conserved complex DNA repeat. TAS49 belongs to the family of dispersed repetitive sequences without features of transposons. The copy number of TAS49 varies widely in the genomes of 8 species analyzed being lowest in N. sylvestris, with 3300 copies per diploid genome. In N. tomentosiformis, TAS49 forms about 0.56% of the diploid genome, corresponding to 17400 copies. TAS49 units are about 460 bp long and show about 90% of mutual homology, but no significant homology to DNA sequences deposited in GenBank and EMBL. Although genomic clones of TAS49 contain an open reading frame encoding a proline-rich protein similar to plant extensins, no mRNA transcript was detected. TAS49 is extensively methylated at CpG and CpNpG sites and its chromatin forms nucleosomes phased with a 170 +/- 8 bp periodicity.
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Affiliation(s)
- M Horáková
- Masaryk University, Department of Analysis of Biologically Important Molecular Complexes, Brno, Czech Republic
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Grebenstein B, Grebenstein O, Sauer W, Hemleben V. Distribution and complex organization of satellite DNA sequences in Aveneae species. Genome 1996; 39:1045-50. [PMID: 8983180 DOI: 10.1139/g96-131] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
Distribution, organization, and molecular analysis of four unrelated satellite DNA components in Aveneae species are described. Highly repeated DNA elements were cloned from Helictotrichon convolutum (CON1 and CON2) and Helictotrichon compressum (COM1 and COM2). The lengths of the repeat monomers are 365 bp (CON1), 562 bp (CON2), 346 bp (COM1), and 476 bp (COM2). Similar repeats were detected by dot blots, Southern blots, and by DNA sequencing in other species of the genus Helictotrichon, in Aveneae species, and in species of the tribes Andropogoneae and Oryzeae. All four satellite DNAs are differently distributed in the taxonomic groups mentioned above. Remarkably, the longer elements are built up in a complex pattern of either shorter subrepeats arranged in tandem (COM2) or by duplications inserted into an original 369-bp element (CON2). Shorter representatives, 190 bp, similar to CON1 elements occur in Holcus species. In Koeleria species, COM1-related repeats are only 180 bp in length. No similarity was found among the sequences CON2, COM1, and COM2 or with sequences of other repetitive DNA elements of the grasses, but CON1 shows sequence similarity to an A genome specific repetitive DNA of Oryza (rice).
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Affiliation(s)
- B Grebenstein
- Lehrstuhl für Spezielle Botanik, Universität Tübingen, Deutschland
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Nickerson JA, Blencowe BJ, Penman S. The architectural organization of nuclear metabolism. INTERNATIONAL REVIEW OF CYTOLOGY 1996; 162A:67-123. [PMID: 8575888 DOI: 10.1016/s0074-7696(08)61229-2] [Citation(s) in RCA: 66] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
Nucleic acid metabolism is structurally organized in the nucleus. DNA replication and transcription have been localized to particular nuclear domains. Additional domains have been identified by their morphology or by their composition; for example, by their high concentration of factors involved in RNA splicing. The domain organization of the nucleus is maintained by the nuclear matrix, a nonchromatin nuclear scaffolding that holds most nuclear RNA and organizes chromatin into loops. The nuclear matrix is built on a network of highly branched core filaments that have an average diameter of 10 nm. Many of the intermediates and the regulatory and catalytic factors of nucleic acid metabolism are retained in nuclear matrix preparations, suggesting that nucleic acid synthesis and processing are structure-bound processes in cells. Tissue-specific and malignancy-induced variations in nuclear structure and metabolism may result from altered matrix architecture and composition.
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Affiliation(s)
- J A Nickerson
- Department of Biology, Massachusetts Institute of Technology, Cambridge 02139, USA
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Abstract
Yeast chromosome ends are similar in structure and function to chromosome ends in most, if not all, eukaryotic organisms. There is a G-rich terminal repeat at the ends which is maintained by telomerase. In addition to the classical functions of protecting the end from degradation and end-to-end fusions, and completing replication, yeast telomeres have several interesting properties including: non-nucleosomal chromatin structure; transcriptional position effect variegation for genes with adjacent telomeres; nuclear peripheral localization; apparent physical clustering; non-random recombinational interactions. A number of genes have been identified that are involved in modifying one or more of these properties. These include genes involved in general DNA metabolism, chromatin structure and telomere maintenance. Adjacent to the terminal repeat is a mosaic of middle repetitive elements that exhibit a great deal of polymorphism both between individual strains and among different chromosome ends. Much of the sequence redundancy in the yeast genome is found in the sub-telomeric regions (within the last 25 kb of each end). The sub-telomeric regions are generally low in gene density, low in transcription, low in recombination, and they are late replicating. The only element which appears to be shared by all chromosome ends is part of the previously defined X element containing an ARS consensus. Most of the 'core' X elements also contain an Abf1p binding site and a URS1-like element, which may have consequences for the chromatin structure, nuclear architecture and transcription of native telomeres. Possible functions of sub-telomeric repeats include: fillers for increasing chromosome size to some minimum threshold level necessary for chromosome stability; barrier against transcriptional silencing; a suitable region for adaptive amplification of genes; secondary mechanism of telomere maintenance via recombination when telomerase activity is absent.
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Affiliation(s)
- E J Louis
- Yeast Genetics, Institute of Molecular Medicine, John Radcliffe Hospital, Oxford, UK.
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