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Maclary ET, Holt C, Concepcion GT, Sović I, Vickrey AI, Yandell M, Kronenberg Z, Shapiro MD. Assembly and annotation of 2 high-quality columbid reference genomes from sequencing of a Columba livia × Columba guinea F1 hybrid. G3 (BETHESDA, MD.) 2024; 14:jkad280. [PMID: 38066578 PMCID: PMC10849363 DOI: 10.1093/g3journal/jkad280] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/12/2023] [Revised: 11/28/2023] [Accepted: 12/01/2023] [Indexed: 12/19/2023]
Abstract
Pigeons and doves (family Columbidae) are one of the most diverse extant avian lineages, and many species have served as key models for evolutionary genomics, developmental biology, physiology, and behavioral studies. Building genomic resources for columbids is essential to further many of these studies. Here, we present high-quality genome assemblies and annotations for 2 columbid species, Columba livia and Columba guinea. We simultaneously assembled C. livia and C. guinea genomes from long-read sequencing of a single F1 hybrid individual. The new C. livia genome assembly (Cliv_3) shows improved completeness and contiguity relative to Cliv_2.1, with an annotation incorporating long-read IsoSeq data for more accurate gene models. Intensive selective breeding of C. livia has given rise to hundreds of breeds with diverse morphological and behavioral characteristics, and Cliv_3 offers improved tools for mapping the genomic architecture of interesting traits. The C. guinea genome assembly is the first for this species and is a new resource for avian comparative genomics. Together, these assemblies and annotations provide improved resources for functional studies of columbids and avian comparative genomics in general.
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Affiliation(s)
- Emily T Maclary
- School of Biological Sciences, University of Utah, Salt Lake City, UT 84112, USA
| | - Carson Holt
- Department of Human Genetics, University of Utah, Salt Lake City, UT 84112, USA
| | | | - Ivan Sović
- Pacific Biosciences, Menlo Park, CA 94025, USA
- Digital BioLogic d.o.o, Ivanić-Grad 10310, Croatia
| | - Anna I Vickrey
- School of Biological Sciences, University of Utah, Salt Lake City, UT 84112, USA
| | - Mark Yandell
- Department of Human Genetics, University of Utah, Salt Lake City, UT 84112, USA
| | | | - Michael D Shapiro
- School of Biological Sciences, University of Utah, Salt Lake City, UT 84112, USA
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2
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Maclary ET, Holt C, Concepcion GT, Sović I, Vickrey AI, Yandell M, Kronenberg Z, Shapiro MD. Assembly and annotation of two high-quality columbid reference genomes from sequencing of a Columba livia x Columba guinea F 1 hybrid. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.10.11.561892. [PMID: 37873124 PMCID: PMC10592783 DOI: 10.1101/2023.10.11.561892] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/25/2023]
Abstract
Pigeons and doves (family Columbidae) are one of the most diverse extant avian lineages, and many species have served as key models for evolutionary genomics, developmental biology, physiology, and behavioral studies. Building genomic resources for colubids is essential to further many of these studies. Here, we present high-quality genome assemblies and annotations for two columbid species, Columba livia and C. guinea. We simultaneously assembled C. livia and C. guinea genomes from long-read sequencing of a single F1 hybrid individual. The new C. livia genome assembly (Cliv_3) shows improved completeness and contiguity relative to Cliv_2.1, with an annotation incorporating long-read IsoSeq data for more accurate gene models. Intensive selective breeding of C. livia has given rise to hundreds of breeds with diverse morphological and behavioral characteristics, and Cliv_3 offers improved tools for mapping the genomic architecture of interesting traits. The C. guinea genome assembly is the first for this species and is a new resource for avian comparative genomics. Together, these assemblies and annotations provide improved resources for functional studies of columbids and avian comparative genomics in general.
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Affiliation(s)
- Emily T. Maclary
- School of Biological Sciences, University of Utah, Salt Lake City, UT, USA
| | - Carson Holt
- Department of Human Genetics, University of Utah, Salt Lake City, UT, USA
| | | | - Ivan Sović
- Pacific Biosciences, Menlo Park, CA, USA
- Digital BioLogic d.o.o, Ivanić-Grad, Croatia
| | - Anna I. Vickrey
- School of Biological Sciences, University of Utah, Salt Lake City, UT, USA
| | - Mark Yandell
- Department of Human Genetics, University of Utah, Salt Lake City, UT, USA
| | | | - Michael D. Shapiro
- School of Biological Sciences, University of Utah, Salt Lake City, UT, USA
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3
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Ponomartsev N, Zilov D, Gushcha E, Travina A, Sergeev A, Enukashvily N. Overexpression of Pericentromeric HSAT2 DNA Increases Expression of EMT Markers in Human Epithelial Cancer Cell Lines. Int J Mol Sci 2023; 24:ijms24086918. [PMID: 37108080 PMCID: PMC10138405 DOI: 10.3390/ijms24086918] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2023] [Revised: 04/02/2023] [Accepted: 04/04/2023] [Indexed: 04/29/2023] Open
Abstract
Pericentromeric tandemly repeated DNA of human satellites 1, 2, and 3 (HS1, HS2, and HS3) is actively transcribed in some cells. However, the functionality of the transcription remains obscure. Studies in this area have been hampered by the absence of a gapless genome assembly. The aim of our study was to map a transcript that we have previously described as HS2/HS3 on chromosomes using a newly published gapless genome assembly T2T-CHM13, and create a plasmid overexpressing the transcript to assess the influence of HS2/HS3 transcription on cancer cells. We report here that the sequence of the transcript is tandemly repeated on nine chromosomes (1, 2, 7, 9, 10, 16, 17, 22, and Y). A detailed analysis of its genomic localization and annotation in the T2T-CHM13 assembly revealed that the sequence belonged to HSAT2 (HS2) but not to the HS3 family of tandemly repeated DNA. The transcript was found on both strands of HSAT2 arrays. The overexpression of the HSAT2 transcript increased the transcription of the genes encoding the proteins involved in the epithelial-to-mesenchymal transition, EMT (SNAI1, ZEB1, and SNAI2), and the genes that mark cancer-associated fibroblasts (VIM, COL1A1, COL11A1, and ACTA2) in cancer cell lines A549 and HeLa. Co-transfection of the overexpression plasmid and antisense nucleotides eliminated the transcription of EMT genes observed after HSAT2 overexpression. Antisense oligonucleotides also decreased transcription of the EMT genes induced by tumor growth factor beta 1 (TGFβ1). Thus, our study suggests HSAT2 lncRNA transcribed from the pericentromeric tandemly repeated DNA is involved in EMT regulation in cancer cells.
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Affiliation(s)
- Nikita Ponomartsev
- Institute of Cytology, Russian Academy of Sciences, St. Petersburg 194064, Russia
| | - Danil Zilov
- Institute of Cytology, Russian Academy of Sciences, St. Petersburg 194064, Russia
- Applied Genomics Laboratory, SCAMT Institute, ITMO University, Saint Petersburg 191002, Russia
| | - Ekaterina Gushcha
- Institute of Cytology, Russian Academy of Sciences, St. Petersburg 194064, Russia
| | - Alexandra Travina
- Institute of Cytology, Russian Academy of Sciences, St. Petersburg 194064, Russia
| | - Alexander Sergeev
- Institute of Cytology, Russian Academy of Sciences, St. Petersburg 194064, Russia
| | - Natella Enukashvily
- Institute of Cytology, Russian Academy of Sciences, St. Petersburg 194064, Russia
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4
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Kulak M, Komissarov A, Fillon V, Tsukanova K, Saifitdinova A, Galkina S. Genome organization of major tandem repeats and their specificity for heterochromatin of macro- and microchromosomes in Japanese quail. Genome 2022; 65:391-403. [PMID: 35776982 DOI: 10.1139/gen-2022-0012] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Tandemly repeated DNAs form heterochromatic regions of chromosomes, including the vital centromeric chromatin. Despite the progress in new genomic technologies tandem repeats remain poorly deciphered and need targeted analysis in the species of interest. The Japanese quail is one of the highest-producing poultry species as well as a model organism. Its genome differs by a noticeable accumulation of heterochromatin, which led to an increase by 1/7 compared to the chicken genome size. Prominent heterochromatin blocks occupy the short arms of acrocentric macrochromosomes and of microchromosomes. We have applied de novo repeat finder approach to unassembled raw reads of the Japanese quail genome. We identified the 20 most common tandem repeats with the abundance >1 Mb, which represent about 4.8% of the genome. We found that tandem repeat CjapSAT primarily contribute to the centromeric regions of the macrochromosomes CJA1-8. Cjap31B together with previously characterized BglII make up centromere regions of microchromosomes and W chromosome. Other repeats populate heterochromatin of microchromosomal short arms in unequal proportions, as revealed by FISH. The Cjap84A, Cjap408A and CjapSAT repeat sequences show similarities with retrotransposon motifs. This suggests that retroelements may have played a crucial role in the distribution of repeats throughout the Japanese quail genome.
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Affiliation(s)
- Maria Kulak
- Saint Petersburg State University, Saint Petersburg, Russian Federation;
| | | | - Valerie Fillon
- INRA Toulouse-Occitanie, Castanet Tolosan, Occitanie, France;
| | - Kseniya Tsukanova
- Saint Petersburg State University, Saint Petersburg, Russian Federation;
| | - Alsu Saifitdinova
- Herzen State Pedagogical University of Russia, 104720, Saint Petersburg, Russian Federation;
| | - Svetlana Galkina
- Saint Petersburg State University, Saint Petersburg, Russian Federation;
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5
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Takki O, Komissarov A, Kulak M, Galkina S. Identification of Centromere-Specific Repeats in the Zebra Finch Genome. Cytogenet Genome Res 2022; 162:55-63. [DOI: 10.1159/000521716] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2021] [Accepted: 12/25/2021] [Indexed: 11/19/2022] Open
Abstract
Tandem repetitive sequences represent a significant part of many genomes but remain poorly characterized due to various methodological difficulties. Here, we describe the tandem repeat composition in the genome of zebra finch, <i>Taeniopygia guttata</i>, a species that has long served as an animal model, primarily in neurobiology and comparative genomics. Using available genome sequencing raw read datasets, we bioinformatically reconstructed consensus sequences of several tandem repeats and proved that the most abundant ones, <i>Tgut191A</i> and <i>Tgut716A</i>, are centromere-associated in chromosomes. Each centromeric region can have a different number of copies of each repeat, with <i>Tgut716A</i> enrichment in almost all microchromosomes and sex chromosomes. Sequences similar to <i>Tgut191A</i> and <i>Tgut716A</i> found in other Estrildidae and Viduidae species can be considered as candidate centromeric sequences, but this requires further cytogenetic verification.
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Saifitdinova AF, Galkina SA, Gaginskaya ER. The Evolution of Concepts about the Biological Role of Lampbrush Chromosomes. RUSS J GENET+ 2021. [DOI: 10.1134/s1022795421050100] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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7
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Dobrynin MA, Korchagina NM, Prjibelski AD, Shafranskaya D, Ostromyshenskii DI, Shunkina K, Stepanova I, Kotova AV, Podgornaya OI, Enukashvily NI. Human pericentromeric tandemly repeated DNA is transcribed at the end of oocyte maturation and is associated with membraneless mitochondria-associated structures. Sci Rep 2020; 10:19634. [PMID: 33184340 PMCID: PMC7665179 DOI: 10.1038/s41598-020-76628-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2020] [Accepted: 10/29/2020] [Indexed: 01/25/2023] Open
Abstract
Most of the human genome is non-coding. However, some of the non-coding part is transcriptionally active. In humans, the tandemly repeated (TR) pericentromeric non-coding DNA-human satellites 2 and 3 (HS2, HS3)-are transcribed in somatic cells. These transcripts are also found in pre- and post-implantation embryos. The aim of this study was to analyze HS2/HS3 transcription and cellular localization of transcripts in human maturating oocytes. The maternal HS2/HS3 TR transcripts transcribed from both strands were accumulated in the ooplasm in GV-MI oocytes as shown by DNA-RNA FISH (fluorescence in-situ hybridization). The transcripts' content was higher in GV oocytes than in somatic cumulus cells according to real-time PCR. Using bioinformatics analysis, we demonstrated the presence of polyadenylated HS2 and HS3 RNAs in datasets of GV and MII oocyte transcriptomes. The transcripts shared a high degree of homology with HS2, HS3 transcripts previously observed in cancer cells. The HS2/HS3 transcripts were revealed by a combination of FISH and immunocytochemical staining within membraneless RNP structures that contained DEAD-box helicases DDX5 and DDX4. The RNP structures were closely associated with mitochondria, and are therefore similar to membraneless bodies described previously only in oogonia. These membraneless structures may be a site for spatial sequestration of RNAs and proteins in both maturating oocytes and cancer cells.
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Affiliation(s)
- M A Dobrynin
- Institute of Cytology RAS, Saint Petersburg, Russia
| | - N M Korchagina
- Ava-Peter - Scandinavia Assisted Reproductive Technology Clinic, Saint Petersburg, Russia
- Faculty of Biology, St. Petersburg State University, Saint Petersburg, Russia
| | - A D Prjibelski
- Center for Algorithmic Biotechnology, St. Petersburg State University, Saint Petersburg, Russia
| | - D Shafranskaya
- Center for Algorithmic Biotechnology, St. Petersburg State University, Saint Petersburg, Russia
| | | | - K Shunkina
- Ava-Peter - Scandinavia Assisted Reproductive Technology Clinic, Saint Petersburg, Russia
| | - I Stepanova
- Institute of Cytology RAS, Saint Petersburg, Russia
| | - A V Kotova
- Institute of Cytology RAS, Saint Petersburg, Russia
- North-Western State Medical University Named After I.I. Mechnikov, Saint Petersburg, Russia
| | - O I Podgornaya
- Institute of Cytology RAS, Saint Petersburg, Russia
- Faculty of Biology, St. Petersburg State University, Saint Petersburg, Russia
| | - N I Enukashvily
- Institute of Cytology RAS, Saint Petersburg, Russia.
- North-Western State Medical University Named After I.I. Mechnikov, Saint Petersburg, Russia.
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8
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Zlotina A, Maslova A, Pavlova O, Kosyakova N, Al-Rikabi A, Liehr T, Krasikova A. New Insights Into Chromomere Organization Provided by Lampbrush Chromosome Microdissection and High-Throughput Sequencing. Front Genet 2020; 11:57. [PMID: 32127797 PMCID: PMC7038795 DOI: 10.3389/fgene.2020.00057] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2019] [Accepted: 01/17/2020] [Indexed: 11/13/2022] Open
Abstract
Giant lampbrush chromosomes (LBCs) typical for growing oocytes of various animal species are characterized by a specific chromomere-loop appearance and massive transcription. Chromomeres represent universal units of chromatin packaging at LBC stage. While quite good progress has been made in investigation of LBCs structure and function, chromomere organization still remains poorly understood. To extend our knowledge on chromomere organization, we applied microdissection to chicken LBCs. In particular, 31 and 5 individual chromomeres were dissected one by one along the macrochromosome 4 and one microchromosome, respectively. The data on genomic context of individual chromomeres was obtained by high-throughput sequencing of the corresponding chromomere DNA. Alignment of adjacent chromomeres to chicken genome assembly provided information on chromomeres size and genomic boarders, indicating that prominent marker chromomeres are about 4–5 Mb in size, while common chromomeres of 1.5–3.5 Mb. Analysis of genomic features showed that the majority of chromomere-loop complexes combine gene-dense and gene-poor regions, while massive loopless DAPI-positive chromomeres lack genes and are remarkably enriched with different repetitive elements. Finally, dissected LBC chromomeres were compared with chromatin domains (topologically associated domains [TADs] and A/B-compartments), earlier identified by Hi-C technique in interphase nucleus of chicken embryonic fibroblasts. Generally, the results obtained suggest that chromomeres of LBCs do not correspond unambiguously to any type of well-established spatial domains of interphase nucleus in chicken somatic cells.
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Affiliation(s)
- Anna Zlotina
- Saint Petersburg State University, Saint Petersburg, Russia
| | | | - Olga Pavlova
- Saint Petersburg State University, Saint Petersburg, Russia
| | - Nadezda Kosyakova
- Institute of Human Genetics, Jena University Hospital, Jena, Germany
| | - Ahmed Al-Rikabi
- Institute of Human Genetics, Jena University Hospital, Jena, Germany
| | - Thomas Liehr
- Institute of Human Genetics, Jena University Hospital, Jena, Germany
| | - Alla Krasikova
- Saint Petersburg State University, Saint Petersburg, Russia
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9
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Krasikova A, Kulikova T. Identification of Genomic Loci Responsible for the Formation of Nuclear Domains Using Lampbrush Chromosomes. Noncoding RNA 2019; 6:ncrna6010001. [PMID: 31881720 PMCID: PMC7151628 DOI: 10.3390/ncrna6010001] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2019] [Revised: 12/19/2019] [Accepted: 12/22/2019] [Indexed: 12/12/2022] Open
Abstract
In the cell nuclei, various types of nuclear domains assemble as a result of transcriptional activity at specific chromosomal loci. Giant transcriptionally active lampbrush chromosomes, which form in oocyte nuclei of amphibians and birds enable the mapping of genomic sequences with high resolution and the visualization of individual transcription units. This makes avian and amphibian oocyte nuclei an advantageous model for studying locus-specific nuclear domains. We developed two strategies for identification and comprehensive analysis of the genomic loci involved in nuclear domain formation on lampbrush chromosomes. The first approach was based on the sequential FISH-mapping of BAC clones containing genomic DNA fragments with a known chromosomal position close to the locus of a nuclear domain. The second approach involved mechanical microdissection of the chromosomal region adjacent to the nuclear domain followed by the generation of FISH-probes and DNA sequencing. Furthermore, deciphering the DNA sequences from the dissected material by high throughput sequencing technologies and their mapping to the reference genome helps to identify the genomic region responsible for the formation of the nuclear domain. For those nuclear domains structured by nascent transcripts, identification of genomic loci of their formation is a crucial step in the identification of scaffold RNAs.
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10
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Affiliation(s)
- Joseph G Gall
- Department of Embryology, Carnegie Institution for Science, Baltimore, MD, 21218, USA.
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11
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Bogolyubov DS. Karyosphere (Karyosome): A Peculiar Structure of the Oocyte Nucleus. INTERNATIONAL REVIEW OF CELL AND MOLECULAR BIOLOGY 2018; 337:1-48. [PMID: 29551157 DOI: 10.1016/bs.ircmb.2017.12.001] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
The karyosphere, aka the karyosome, is a meiosis-specific structure that represents a "knot" of condensed chromosomes joined together in a limited volume of the oocyte nucleus. The karyosphere is an evolutionarily conserved but morphologically rather "multifaceted" structure. It forms at the diplotene stage of meiotic prophase in many animals, from hydra and Drosophila to human. Karyosphere formation is generally linked with transcriptional silencing of the genome. It is believed that karyosphere/karyosome is a prerequisite for proper completion of meiotic divisions and further development. Here, a brief review on the karyosphere features in some invertebrates and vertebrates is provided. Special emphasis is made on terminology, since current discrepancies in this field may lead to confusions. In particular, it is proposed to distinguish the karyosphere with a capsule and the karyosome (a karyosphere devoid of a capsule). The "inverted" karyospheres are also considered, in which the chromosomes situate externally to an extrachromosomal structure (e.g., in human oocytes).
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Affiliation(s)
- Dmitry S Bogolyubov
- Institute of Cytology of the Russian Academy of Science, St. Petersburg, Russia.
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12
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Krasikova AV, Kulikova TV. Distribution of heterochromatin markers in lampbrush chromosomes in birds. RUSS J GENET+ 2017. [DOI: 10.1134/s1022795417090071] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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13
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Garrido-Ramos MA. Satellite DNA: An Evolving Topic. Genes (Basel) 2017; 8:genes8090230. [PMID: 28926993 PMCID: PMC5615363 DOI: 10.3390/genes8090230] [Citation(s) in RCA: 227] [Impact Index Per Article: 32.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2017] [Revised: 09/12/2017] [Accepted: 09/13/2017] [Indexed: 12/22/2022] Open
Abstract
Satellite DNA represents one of the most fascinating parts of the repetitive fraction of the eukaryotic genome. Since the discovery of highly repetitive tandem DNA in the 1960s, a lot of literature has extensively covered various topics related to the structure, organization, function, and evolution of such sequences. Today, with the advent of genomic tools, the study of satellite DNA has regained a great interest. Thus, Next-Generation Sequencing (NGS), together with high-throughput in silico analysis of the information contained in NGS reads, has revolutionized the analysis of the repetitive fraction of the eukaryotic genomes. The whole of the historical and current approaches to the topic gives us a broad view of the function and evolution of satellite DNA and its role in chromosomal evolution. Currently, we have extensive information on the molecular, chromosomal, biological, and population factors that affect the evolutionary fate of satellite DNA, knowledge that gives rise to a series of hypotheses that get on well with each other about the origin, spreading, and evolution of satellite DNA. In this paper, I review these hypotheses from a methodological, conceptual, and historical perspective and frame them in the context of chromosomal organization and evolution.
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Affiliation(s)
- Manuel A Garrido-Ramos
- Departamento de Genética, Facultad de Ciencias, Universidad de Granada, 18071 Granada, Spain.
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14
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Trofimova I, Krasikova A. Transcription of highly repetitive tandemly organized DNA in amphibians and birds: A historical overview and modern concepts. RNA Biol 2016; 13:1246-1257. [PMID: 27763817 PMCID: PMC5207375 DOI: 10.1080/15476286.2016.1240142] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2016] [Revised: 09/13/2016] [Accepted: 09/20/2016] [Indexed: 10/20/2022] Open
Abstract
Tandemly organized highly repetitive DNA sequences are crucial structural and functional elements of eukaryotic genomes. Despite extensive evidence, satellite DNA remains an enigmatic part of the eukaryotic genome, with biological role and significance of tandem repeat transcripts remaining rather obscure. Data on tandem repeats transcription in amphibian and avian model organisms is fragmentary despite their genomes being thoroughly characterized. Review systematically covers historical and modern data on transcription of amphibian and avian satellite DNA in somatic cells and during meiosis when chromosomes acquire special lampbrush form. We highlight how transcription of tandemly repetitive DNA sequences is organized in interphase nucleus and on lampbrush chromosomes. We offer LTR-activation hypotheses of widespread satellite DNA transcription initiation during oogenesis. Recent explanations are provided for the significance of high-yield production of non-coding RNA derived from tandemly organized highly repetitive DNA. In many cases the data on the transcription of satellite DNA can be extrapolated from lampbrush chromosomes to interphase chromosomes. Lampbrush chromosomes with applied novel technical approaches such as superresolution imaging, chromosome microdissection followed by high-throughput sequencing, dynamic observation in life-like conditions provide amazing opportunities for investigation mechanisms of the satellite DNA transcription.
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Affiliation(s)
| | - Alla Krasikova
- Saint-Petersburg State University, Saint-Petersburg, Russia
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15
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Kulikova T, Khodyuchenko T, Petrov Y, Krasikova A. Low-voltage scanning electron microscopy study of lampbrush chromosomes and nuclear bodies in avian and amphibian oocytes. Sci Rep 2016; 6:36878. [PMID: 27857188 PMCID: PMC5114574 DOI: 10.1038/srep36878] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2016] [Accepted: 10/24/2016] [Indexed: 12/01/2022] Open
Abstract
Nucleus is a highly compartmentalized part of the cell where the key processes of genome functionality are realized through the formation of non-membranous nuclear domains. Physically nuclear domains appear as liquid droplets with different viscosity stably maintained throughout the interphase or during the long diplotene stage of meiosis. Since nuclear body surface represents boundary between two liquid phases, the ultrastructural surface topography of nuclear domains is of an outstanding interest. The aim of this study was to examine ultrathin surface topography of the amphibian and avian oocyte nuclear structures such as lampbrush chromosomes, nucleoli, histone-locus bodies, Cajal body-like bodies, and the interchromatin granule clusters via low-voltage scanning electron microscopy. Our results demonstrate that nuclear bodies with similar molecular composition may differ dramatically in the surface topography and vice versa, nuclear bodies that do not share common molecular components may possess similar topographical characteristics. We also have analyzed surface distribution of particular nuclear antigens (double stranded DNA, coilin and splicing snRNA) using indirect immunogold labeling with subsequent secondary electron detection of gold nanoparticles. We suggest that ultrastructural surface morphology reflects functional status of a nuclear body.
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Affiliation(s)
| | | | - Yuri Petrov
- Saint-Petersburg State University, Saint-Petersburg, Russia
| | - Alla Krasikova
- Saint-Petersburg State University, Saint-Petersburg, Russia
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16
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Koshel E, Galkina S, Saifitdinova A, Dyomin A, Deryusheva S, Gaginskaya E. Ribosomal RNA gene functioning in avian oogenesis. Cell Tissue Res 2016; 366:533-542. [PMID: 27339801 DOI: 10.1007/s00441-016-2444-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2016] [Accepted: 05/18/2016] [Indexed: 12/18/2022]
Abstract
Despite long-term exploration into ribosomal RNA gene functioning during the oogenesis of various organisms, many intriguing problems remain unsolved. In this review, we describe nucleolus organizer region (NOR) activity in avian oocytes. Whereas oocytes from an adult avian ovary never reveal the formation of the nucleolus in the germinal vesicle (GV), an ovary from juvenile birds possesses both nucleolus-containing and non-nucleolus-containing oocytes. The evolutionary diversity of oocyte NOR functioning and the potential non-rRNA-related functions of the nucleolus in oocytes are also discussed.
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Affiliation(s)
- Elena Koshel
- Department of Cytology and Histology, Saint-Petersburg State University, Saint-Petersburg, 199034, Russia
| | - Svetlana Galkina
- Department of Cytology and Histology, Saint-Petersburg State University, Saint-Petersburg, 199034, Russia
| | - Alsu Saifitdinova
- Department of Cytology and Histology, Saint-Petersburg State University, Saint-Petersburg, 199034, Russia
| | - Alexandr Dyomin
- Department of Cytology and Histology, Saint-Petersburg State University, Saint-Petersburg, 199034, Russia
| | - Svetlana Deryusheva
- Department of Cytology and Histology, Saint-Petersburg State University, Saint-Petersburg, 199034, Russia.,Department of Embryology, Carnegie Institution for Science, Baltimore, MD 21218, USA
| | - Elena Gaginskaya
- Department of Cytology and Histology, Saint-Petersburg State University, Saint-Petersburg, 199034, Russia.
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17
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Kulikova T, Chervyakova D, Zlotina A, Krasikova A, Gaginskaya E. Giant poly(A)-rich RNP aggregates form at terminal regions of avian lampbrush chromosomes. Chromosoma 2015; 125:709-24. [DOI: 10.1007/s00412-015-0563-4] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2015] [Revised: 11/12/2015] [Accepted: 11/24/2015] [Indexed: 01/30/2023]
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Ishishita S, Tsuruta Y, Uno Y, Nakamura A, Nishida C, Griffin DK, Tsudzuki M, Ono T, Matsuda Y. Chromosome size-correlated and chromosome size-uncorrelated homogenization of centromeric repetitive sequences in New World quails. Chromosome Res 2014; 22:15-34. [PMID: 24532185 DOI: 10.1007/s10577-014-9402-3] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Many families of centromeric repetitive DNA sequences isolated from Struthioniformes, Galliformes, Falconiformes, and Passeriformes are localized primarily to microchromosomes. However, it is unclear whether chromosome size-correlated homogenization is a common characteristic of centromeric repetitive sequences in Aves. New World and Old World quails have the typical avian karyotype comprising chromosomes of two distinct sizes, and C-positive heterochromatin is distributed in centromeric regions of most autosomes and the whole W chromosome. We isolated six types of centromeric repetitive sequences from three New World quail species (Colinus virginianus, CVI; Callipepla californica, CCA; and Callipepla squamata, CSQ; Odontophoridae) and one Old World quail species (Alectoris chukar, ACH; Phasianidae), and characterized the sequences by nucleotide sequencing, chromosome in situ hybridization, and filter hybridization. The 385-bp CVI-MspI, 591-bp CCA-BamHI, 582-bp CSQ-BamHI, and 366-bp ACH-Sau3AI fragments exhibited tandem arrays of the monomer unit, and the 224-bp CVI-HaeIII and 135-bp CCA-HaeIII fragments were composed of minisatellite-like and microsatellite-like repeats, respectively. ACH-Sau3AI was a homolog of the chicken nuclear membrane repeat sequence, whose homologs are common in Phasianidae. CVI-MspI, CCA-BamHI, and CSQ-BamHI showed high homology and were specific to the Odontophoridae. CVI-MspI was localized to microchromosomes, whereas CVI-HaeIII, CCA-BamHI, and CSQ-BamHI were mapped to almost all chromosomes. CCA-HaeIII was localized to five pairs of macrochromosomes and most microchromosomes. ACH-Sau3AI was distributed in three pairs of macrochromosomes and all microchromosomes. Centromeric repetitive sequences may be homogenized in chromosome size-correlated and -uncorrelated manners in New World quails, although there may be a mechanism that causes homogenization of centromeric repetitive sequences primarily between microchromosomes, which is commonly observed in phasianid birds.
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Affiliation(s)
- Satoshi Ishishita
- Laboratory of Animal Genetics, Department of Applied Molecular Biosciences, Graduate School of Bioagricultural Sciences, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Aichi, 464-8601, Japan
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19
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Camacho JPM, Ruiz-Ruano FJ, Martín-Blázquez R, López-León MD, Cabrero J, Lorite P, Cabral-de-Mello DC, Bakkali M. A step to the gigantic genome of the desert locust: chromosome sizes and repeated DNAs. Chromosoma 2014; 124:263-75. [PMID: 25472934 DOI: 10.1007/s00412-014-0499-0] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2014] [Revised: 11/24/2014] [Accepted: 11/25/2014] [Indexed: 10/24/2022]
Abstract
The desert locust (Schistocerca gregaria) has been used as material for numerous cytogenetic studies. Its genome size is estimated to be 8.55 Gb of DNA comprised in 11 autosomes and the X chromosome. Its X0/XX sex chromosome determinism therefore results in females having 24 chromosomes whereas males have 23. Surprisingly, little is known about the DNA content of this locust's huge chromosomes. Here, we use the Feulgen Image Analysis Densitometry and C-banding techniques to respectively estimate the DNA quantity and heterochromatin content of each chromosome. We also identify three satellite DNAs using both restriction endonucleases and next-generation sequencing. We then use fluorescent in situ hybridization to determine the chromosomal location of these satellite DNAs as well as that of six tandem repeat DNA gene families. The combination of the results obtained in this work allows distinguishing between the different chromosomes not only by size, but also by the kind of repetitive DNAs that they contain. The recent publication of the draft genome of the migratory locust (Locusta migratoria), the largest animal genome hitherto sequenced, invites for sequencing even larger genomes. S. gregaria is a pest that causes high economic losses. It is thus among the primary candidates for genome sequencing. But this species genome is about 50 % larger than that of L. migratoria, and although next-generation sequencing currently allows sequencing large genomes, sequencing it would mean a greater challenge. The chromosome sizes and markers provided here should not only help planning the sequencing project and guide the assembly but would also facilitate assigning assembled linkage groups to actual chromosomes.
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Affiliation(s)
- J P M Camacho
- Departamento de Genética, Facultad de Ciencias, Universidad de Granada, Fuentenueva S/N, 18071, Granada, Spain
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Abstract
Lampbrush chromosomes (LBCs) are transcriptionally active chromosomes found in the germinal vesicle (GV) of large oocytes of many vertebrate and invertebrate animals and also in the giant single-celled alga Acetabularia. These cells are all in prophase of the first meiotic division. Nevertheless, many meiotic cells do not develop LBCs, arguing that LBCs are not an essential feature of meiosis. LBCs probably represent the most active transcriptional state that can be attained by cells that must give rise to diploid progeny. Polyploidy permits cells to reach higher rates of transcription per nucleus but precludes a return to diploidy. In this sense, LBCs represent a relatively inefficient transcriptional compromise employed by large meiotic cells. These considerations help to explain why transcriptionally active GVs develop LBCs, but they do not explain why LBCs have never been seen in somatic cells, diploid or otherwise. If LBCs are truly limited to germ cells, then some of their unusual features may reflect reprogramming of the genome. If this is the case, LBCs provide unique opportunities to study reprogramming at the level of the individual transcription unit.
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Krasikova A, Fukagawa T, Zlotina A. High-resolution mapping and transcriptional activity analysis of chicken centromere sequences on giant lampbrush chromosomes. Chromosome Res 2013; 20:995-1008. [PMID: 23143648 DOI: 10.1007/s10577-012-9321-0] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Exploration into morphofunctional organisation of centromere DNA sequences is important for understanding the mechanisms of kinetochore specification and assembly. In-depth epigenetic analysis of DNA fragments associated with centromeric nucleosome proteins has demonstrated unique features of centromere organisation in chicken karyotype: there are both mature centromeres, which comprise chromosome-specific homogeneous arrays of tandem repeats, and recently evolved primitive centromeres, which consist of non-tandemly organised DNA sequences. In this work, we describe the arrangement and transcriptional activity of chicken centromere repeats for Cen1, Cen2, Cen3, Cen4, Cen7, Cen8, and Cen11 and non-repetitive centromere sequences of chromosomes 5, 27, and Z using highly elongated lampbrush chromosomes, which are characteristic of the diplotene stage of oogenesis. The degree of chromatin packaging and fine spatial organisations of tandemly repetitive and non-tandemly repetitive centromeric sequences significantly differ at the lampbrush stage. Using DNA/RNA FISH, we have demonstrated that during the lampbrush stage, DNA sequences are transcribed within the centromere regions of chromosomes that lack centromere-specific tandem repeats. In contrast, chromosome-specific centromeric repeats Cen1, Cen2, Cen3, Cen4, Cen7, Cen8, and Cen11 do not demonstrate any transcriptional activity during the lampbrush stage. In addition, we found that CNM repeat cluster localises adjacent to non-repetitive centromeric sequences in chicken microchromosome 27 indicating that centromere region in this chromosome is repeat-rich. Cross-species FISH allowed localisation of the sequences homologous to centromeric DNA of chicken chromosomes 5 and 27 in centromere regions of quail orthologous chromosomes.
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Affiliation(s)
- Alla Krasikova
- Saint-Petersburg State University, Oranienbaumskoie sch. 2, Stary Peterhof, Saint-Petersburg, 198504, Russia.
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Dedukh D, Mazepa G, Shabanov D, Rosanov J, Litvinchuk S, Borkin L, Saifitdinova A, Krasikova A. Cytological maps of lampbrush chromosomes of European water frogs (Pelophylax esculentus complex) from the Eastern Ukraine. BMC Genet 2013; 14:26. [PMID: 23590698 PMCID: PMC3648425 DOI: 10.1186/1471-2156-14-26] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2013] [Accepted: 04/04/2013] [Indexed: 11/10/2022] Open
Abstract
Background Hybridogenesis (hemiclonal inheritance) is a kind of clonal reproduction in which hybrids between parental species are reproduced by crossing with one of the parental species. European water frogs (Pelophylax esculentus complex) represent an appropriate model for studying interspecies hybridization, processes of hemiclonal inheritance and polyploidization. P. esculentus complex consists of two parental species, P. ridibundus (the lake frog) and P. lessonae (the pool frog), and their hybridogenetic hybrid – P. esculentus (the edible frog). Parental and hybrid frogs can reproduce syntopically and form hemiclonal population systems. For studying mechanisms underlying the maintenance of water frog population systems it is required to characterize the karyotypes transmitted in gametes of parental and different hybrid animals of both sexes. Results In order to obtain an instrument for characterization of oocyte karyotypes in hybrid female frogs, we constructed cytological maps of lampbrush chromosomes from oocytes of both parental species originating in Eastern Ukraine. We further identified certain molecular components of chromosomal marker structures and mapped coilin-rich spheres and granules, chromosome associated nucleoli and special loops accumulating splicing factors. We recorded the dissimilarities between P. ridibundus and P. lessonae lampbrush chromosomes in the length of orthologous chromosomes, number and location of marker structures and interstitial (TTAGGG)n-repeat sites as well as activity of nucleolus organizer. Satellite repeat RrS1 was mapped in centromere regions of lampbrush chromosomes of the both species. Additionally, we discovered transcripts of RrS1 repeat in oocytes of P. ridibundus and P. lessonae. Moreover, G-rich transcripts of telomere repeat were revealed in association with terminal regions of P. ridibundus and P. lessonae lampbrush chromosomes. Conclusions The constructed cytological maps of lampbrush chromosomes of P. ridibundus and P. lessonae provide basis to define the type of genome transmitted within individual oocytes of P. esculentus females with different ploidy and from various population systems.
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Affiliation(s)
- Dmitry Dedukh
- Saint-Petersburg State University, Saint-Petersburg, Russia
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23
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Centromere positions in chicken and Japanese quail chromosomes: de novo centromere formation versus pericentric inversions. Chromosome Res 2012; 20:1017-32. [DOI: 10.1007/s10577-012-9319-7] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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Non-canonical Cajal bodies form in the nucleus of late stage avian oocytes lacking functional nucleolus. Histochem Cell Biol 2012; 138:57-73. [PMID: 22382586 DOI: 10.1007/s00418-012-0938-z] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/12/2012] [Indexed: 10/28/2022]
Abstract
In the somatic cell nucleus, there are several universal domains such as nucleolus, SC35-domains, Cajal bodies (CBs) and histone locus bodies (HLBs). Among them, CBs were described more than 100 years ago; however, we still do not have a final understanding of their nature and biological significance. The giant nucleus of avian and amphibian growing oocytes represents an advantageous model for analysis of functions and biogenesis of various nuclear domains. Nevertheless, in large-sized avian oocytes that contain transcriptionally active lampbrush chromosomes, CB-like organelles have not been identified yet. Here we demonstrate that in the pigeon (Columba livia) oocyte nucleus, characterized by absence of any functional nucleoli, extrachromosomal spherical bodies contain TMG-capped spliceosomal snRNAs, core proteins of Sm snRNPs and the protein coilin typical for CBs, but not splicing factor SC35 nor the histone pre-mRNA 3'-end processing factor symplekin. The results establish that coilin-rich nuclear organelles in pigeon late-stage oocyte are not the equivalents of HLBs but belong to a group of CBs. At the same time, they do not contain the snoRNP/scaRNP protein fibrillarin involved in 2'-O-methylation of snoRNAs and snRNAs. Thus, the nucleus of late-stage pigeon oocytes houses CB-like organelles that have an unusual molecular composition and are implicated in the snRNP biogenesis pathway. These data demonstrate that snRNP-rich non-canonical CBs can form in the absence of nucleolus. We argue that pigeon oocytes represent a new promising model to investigate CB modular organization, functions and formation mechanism.
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Deryusheva S, Krasikova A, Kulikova T, Gaginskaya E. Tandem 41-bp repeats in chicken and Japanese quail genomes: FISH mapping and transcription analysis on lampbrush chromosomes. Chromosoma 2007; 116:519-30. [PMID: 17619894 DOI: 10.1007/s00412-007-0117-5] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2007] [Revised: 06/09/2007] [Accepted: 06/10/2007] [Indexed: 10/23/2022]
Abstract
The chromosomal distribution of 41-bp repeats, known as CNM and PO41 repeats in the chicken genome and BglII repeats in the Japanese quail, was analyzed precisely using giant lampbrush chromosomes (LBC) from chicken, Japanese quail, and turkey growing oocytes. The PO41 repeat is conserved in all galliform species, whereas the other repeats are species specific. In chicken and quail, the centromere and subtelomere regions share homologous satellite sequences. RNA polymerase II transcribes the 41-bp repeats in both centromere and subtelomere regions. Ongoing transcription of these repeats was demonstrated by incorporation of BrUTP injected into oocytes at the lampbrush stage. RNA complementary to both strands of CNM and PO41 repeats is present on chicken LBC loops, whereas strand-specific G-rich transcripts are characteristic of BglII repeats in the Japanese quail. The RNA from 41-bp repeats does not undergo cotranscriptional U snRNP-dependent splicing. At the same time, the ribonucleoprotein matrix of transcription units with C-rich RNA of CNM and PO41 repeats was enriched with hnRNP protein K. Potential promoters for satellite transcription are discussed.
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Affiliation(s)
- Svetlana Deryusheva
- Biological Research Institute, Saint-Petersburg State University, Oranienbaumskoie sch. 2, Stary Peterhof, Saint-Petersburg 198504, Russia
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26
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Krasikova A, Deryusheva S, Galkina S, Kurganova A, Evteev A, Gaginskaya E. On the positions of centromeres in chicken lampbrush chromosomes. Chromosome Res 2006; 14:777-89. [PMID: 17115332 DOI: 10.1007/s10577-006-1085-y] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2006] [Revised: 07/24/2006] [Accepted: 07/24/2006] [Indexed: 10/23/2022]
Abstract
Using immunostaining with antibodies against cohesin subunits, we show here that cohesin-enriched structures analogous to the so-called centromere protein bodies (PB) are the characteristic of galliform lampbrush chromosomes. Their centromeric location was verified by FISH with certain DNA probes. PB-like structures were used as markers for centromere localization in chicken lampbrush chromosomes. The gap predicted to be centromeric in current chicken chromosome 3 sequence assembly was found to correspond to the non-centromeric cluster of CNM repeat on the q-arm of chromosome 3; the centromere is proposed to be placed at another position. The majority of chicken microchromosomes were found to be acrocentric, in contrast to Japanese quail microchromosomes which are biarmed. Centromere cohesin-enriched structures on chicken and quail lampbrush microchromosomes co-localize with pericentromeric CNM and BglII- repeats respectively. FISH to the nascent transcripts on chicken lampbrush chromosomes revealed numerous non-centromeric CNM clusters in addition to pericentromeric arrays. Complementary CNM transcripts from both C- and G-rich DNA strands were revealed during the lampbrush stage.
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Affiliation(s)
- Alla Krasikova
- Biological Research Institute, Saint-Petersburg State University, Oranienbaumskoie sch. 2, Stary Peterhof, Saint-Petersburg, 198504, Russia
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27
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Galkina S, Deryusheva S, Fillon V, Vignal A, Crooijmans R, Groenen M, Rodionov A, Gaginskaya E. FISH on avian lampbrush chromosomes produces higher resolution gene mapping. Genetica 2006; 128:241-51. [PMID: 17028954 DOI: 10.1007/s10709-005-5776-7] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2005] [Accepted: 12/07/2005] [Indexed: 10/24/2022]
Abstract
Giant lampbrush chromosomes, which are characteristic of the diplotene stage of prophase I during avian oogenesis, represent a very promising system for precise physical gene mapping. We applied 35 chicken BAC and 4 PAC clones to both mitotic metaphase chromosomes and meiotic lampbrush chromosomes of chicken (Gallus gallus domesticus) and Japanese quail (Coturnix coturnix japonica). Fluorescence in situ hybridization (FISH) mapping on lampbrush chromosomes allowed us to distinguish closely located probes and revealed gene order more precisely. Our data extended the data earlier obtained using FISH to chicken and quail metaphase chromosomes 1-6 and Z. Extremely low levels of inter- and intra-chromosomal rearrangements in the chicken and Japanese quail were demonstrated again. Moreover, we did not confirm the presence of a pericentric inversion in Japanese quail chromosome 4 as compared to chicken chromosome 4. Twelve BAC clones specific for chicken chromosome 4p and 4q showed the same order in quail as in chicken when FISH was performed on lampbrush chromosomes. The centromeres of chicken and quail chromosomes 4 seem to have formed independently after centric fusion of ancestral chromosome 4 and a microchromosome.
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Affiliation(s)
- Svetlana Galkina
- Biological Research Institute, Saint-Petersburg State University, Oranienbaumskoie shosse 2, Stary Peterhof, 198504, Saint-Petersburg, Russia
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Krasikova A, Barbero JL, Gaginskaya E. Cohesion proteins are present in centromere protein bodies associated with avian lampbrush chromosomes. Chromosome Res 2005; 13:675-85. [PMID: 16235117 DOI: 10.1007/s10577-005-1005-6] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2005] [Accepted: 08/22/2005] [Indexed: 10/25/2022]
Abstract
Proteins of sister chromatid cohesion are important for maintenance of meiotic chromosome structure and retention of homologous chromosomes in bivalents during diplotene. Localization of the cohesion proteins within nuclei of growing oocytes merits special attention, particularly in avian oocytes, in which diplotene chromosomes assume the form of lampbrush chromosomes (LBCs). We performed indirect immunostaining using antibodies against cohesins SMC1alpha, SMC1beta, SMC3, Rad21, and the SA/STAG family on chaffinch, pigeon and duck LBCs spreads, and frozen ovary sections. On LBCs spreads, antibodies to the majority of cohesins showed punctate staining on chromosome axes. LBC lateral loops, where sister chromatids are separated, did not show cohesin components. The spherical entities attached to the LBCs centromeres in avian germinal vesicles, the so-called protein bodies (PBs), were enriched in SMC1alpha, SMC3, Rad21, STAG1 and STAG2. The synaptonemal complex component SYCP3, which also participates in cohesion, was detected in the axes of avian lampbrush bivalents and, to a greater degree, in the PBs. In vitellogenic oocytes, cohesion proteins persist in the PBs associated with condensing bivalents when they concentrate into the karyosphere. These results indicate that cohesion proteins accumulate in centromere PBs in avian oocytes and are involved into structural maintenance of lampbrush chromosome axes.
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Affiliation(s)
- Alla Krasikova
- Biological Research Institute, Saint-Petersburg State University, Oranienbaumskoie sch. 2, Stary Peterhof, Saint-Petersburg 198504, Russia
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Kuznetsova IS, Prusov AN, Enukashvily NI, Podgornaya OI. New types of mouse centromeric satellite DNAs. Chromosome Res 2005; 13:9-25. [PMID: 15791408 DOI: 10.1007/s10577-005-2346-x] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2004] [Revised: 10/15/2004] [Accepted: 10/15/2004] [Indexed: 11/28/2022]
Abstract
Genomic databases do not contain complete sequences of the centromeric regions. We created a pUC19-based library of DNA fragments from isolated chromocentres of interphase nuclei. In this library we have found major satellite (MaSat) and two new satellite sequences - MS3 and MS4. The computer analysis of MS3 and MS4 sequences by alignment, fragment curved state and search for MAR motifs in comparison with the mouse major and minor satellite (MiSat) DNA has shown them to be new satellite fragments. Southern blot of MS3 and MS4 with total DNA digested by restriction enzymes shows the ladder characteristic of satellite DNA. 2.2% of the total DNA consists of MS3, the monomer of which is 150 bp long. The MS4 monomer is 300 bp long and accounts for 1.6% of the total DNA. On metaphase chromosomes MS3 and MS4 are located at the centromeric region. FISH analysis of L929 nuclei during the cell cycle showed relative positions of MaSat, MiSat, MS3, and MS4. All mapped satDNA fragments except MaSat belong to the outer layer of the chromocentres in the G0/G1 phase. MS3 is likely to be involved in the centromere formation. The mouse genome contains at least four satDNA types: AT-rich (MaSat and MiSat), and CG-rich (MS3 and MS4).
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Affiliation(s)
- Inna S Kuznetsova
- Institute of Cytology, Russian Academy of Sciences, St. Petersburg 194064, Russia
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Lee HR, Zhang W, Langdon T, Jin W, Yan H, Cheng Z, Jiang J. Chromatin immunoprecipitation cloning reveals rapid evolutionary patterns of centromeric DNA in Oryza species. Proc Natl Acad Sci U S A 2005; 102:11793-8. [PMID: 16040802 PMCID: PMC1187982 DOI: 10.1073/pnas.0503863102] [Citation(s) in RCA: 132] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023] Open
Abstract
The functional centromeres of rice (Oryza sativa, AA genome) chromosomes contain two key DNA components: the CRR centromeric retrotransposons and a 155-bp satellite repeat, CentO. However, several wild Oryza species lack the CentO repeat. We developed a chromatin immunoprecipitation-based technique to clone DNA fragments derived from chromatin containing the centromeric histone H3 variant CenH3. Chromatin immunoprecipitation cloning was carried out in the CentO-less species Oryza rhizomatis (CC genome) and Oryza brachyantha (FF genome). Three previously uncharacterized genome-specific satellite repeats, CentO-C1, CentO-C2, and CentO-F, were discovered in the centromeres of these two species. An 80-bp DNA region was found to be conserved in CentO-C1, CentO, and centromeric satellite repeats from maize and pearl millet, species which diverged from rice many millions of years ago. In contrast, the CentO-F repeat shows no sequence similarity to other centromeric repeats but has almost completely replaced other centromeric sequences in O. brachyantha, including the CRR-related sequences that normally constitute a significant fraction of the centromeric DNA in grass species.
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Affiliation(s)
- Hye-Ran Lee
- Department of Horticulture, University of Wisconsin-Madison, Madison, WI 53706, USA
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31
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Rouleux-Bonnin F, Bigot S, Bigot Y. Structural and transcriptional features of Bombus terrestris satellite DNA and their potential involvement in the differentiation process. Genome 2005; 47:877-88. [PMID: 15499402 DOI: 10.1139/g04-053] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
A unique satellite DNA family was characterized in the genome of the bumble bee, Bombus terrestris. Sequence analysis revealed that it contains two wide palindromes of about 160 and 190 bp, respectively, that span 75% of the repeated unit. One feature of this satellite DNA is that it accounts for different amounts of genomic DNA in males and females. The DNA curvature and bendability were determined by migration on PAGE and by computer analysis. It has been correlated with the presence of dA/dT stretches repeated in phase with the helix turn and with the presence of the deformable dinucleotide CA-TG embedded in some of these A-T-rich regions. Transcription of the satellite DNA was also analyzed by Northern blot hybridization and RT-PCR. Multimeric transcripts spanning several satellite DNA units were found in RNA samples from males, workers, and queens. These transcripts resulted from a specific transcription occurring on one DNA strand in the embryos or on both DNA strands in imagoes. The involvement of DNA curvature in the organization of the satellite DNA and the function of the satellite transcripts is discussed.
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Affiliation(s)
- Florence Rouleux-Bonnin
- Laboratoire d'Etude des Parasites Génétiques (LEPG), UFR des Sciences et Techniques, Université François Rabelais, Parc Grandmont, 37200 Tours, France.
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Krasikova A, Kulikova T, Saifitdinova A, Derjusheva S, Gaginskaya E. Centromeric protein bodies on avian lampbrush chromosomes contain a protein detectable with an antibody against DNA topoisomerase II. Chromosoma 2004; 113:316-23. [PMID: 15616868 DOI: 10.1007/s00412-004-0321-5] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2004] [Revised: 10/01/2004] [Accepted: 10/06/2004] [Indexed: 10/26/2022]
Abstract
In the oocyte nuclei (germinal vesicle or GV) of a variety of avian species, prominent spherical entities termed protein bodies (PBs) arise at the centromeric regions of the lampbrush chromosomes (LBCs). In spite of the obvious protein nature of PBs, nothing is known about their composition. We show that an antibody against DNA topoisomerase II (topo II), the DNA unwinding enzyme, recognizes PBs from chaffinch and pigeon oocytes. In later chaffinch oocytes, the PBs fuse to form a karyosphere, which is also labeled by the anti-topo II antibody. Furthermore, we show that proteins characteristic of Cajal bodies and B-snurposomes are not found in PBs, despite morphological similarities among these structures. Using immunoelectron microscopy and immunofluorescent laser scanning microscopy we demonstrated that topo II localizes predominantly in the dense material of PBs. Two antigens of approximately 170 kDa (which corresponds to topo II) and approximately 100 kDa were revealed with the antibody against topo II on immunoblots of avian GV proteins. We propose that the smaller protein results from oocyte specific topo II cleavage, since it was not detected in nuclei from testis cells. This represents the first report of a defined protein in the centromeric PBs on avian LBCs.
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Affiliation(s)
- Alla Krasikova
- Biological Research Institute, Saint-Petersburg State University, Saint Petersburg, 198504, Russia
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33
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Saifitdinova A, Derjusheva S, Krasikova A, Gaginskaya E. Lampbrush chromosomes of the chaffinch (Fringilla coelebs L.). Chromosome Res 2003; 11:99-113. [PMID: 12733637 DOI: 10.1023/a:1022859713777] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
The seven macrochromosomes of the chaffinch (Fringilla coelebs L.) are described in their lampbrush form. The relative lengths of bivalents, the positions and arrangements of chromosomal regions with lateral loops of similar length and appearance, as well as the positions of protein bodies and loops of peculiar morphology have been defined and mapped, so that each of the seven lampbrush macrobivalents may be identified in oocytes from every individual of the species. This morphological analysis has been supplemented by determining the positions of certain loci and objects that are specifically and consistently labelled after immunostaining or fluorescence in-situ hybridization with defined molecular probes.
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Affiliation(s)
- Alsu Saifitdinova
- Biological Research Institute, Saint-Petersburg State University, Oranienbaumskoie sch. 2, Stary Peterhof, Saint-Petersburg, 198504, Russia
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Podgornaya OI, Voronin AP, Enukashvily NI, Matveev IV, Lobov IB. Structure-specific DNA-binding proteins as the foundation for three-dimensional chromatin organization. INTERNATIONAL REVIEW OF CYTOLOGY 2003; 224:227-96. [PMID: 12722952 DOI: 10.1016/s0074-7696(05)24006-8] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
Any functions of tandem repetitive sequences need proteins that specifically bind to them. Telomere-binding TRF2/MTBP attaches telomeres to the nuclear envelope in interphase due to its rod-domain-like motif. Interphase nuclei organized as a number of sponge-like ruffly round chromosome territories that could be rotated from outside. SAF-A/hnRNP-U and p68-helicase are proteins suitable to do that. Their location in the interchromosome territory space, ATPase domains, and the ability to be bound by satellite DNAs (satDNA) make them part of the wires used to help chromosome territory rotates. In case of active transcription p68-helicase can be involved in the formation of local "gene expression matrices" and due to its satDNA-binding specificity cause the rearrangement of the local chromosome territory. The marks of chromatin rearrangement, which have to be heritable, could be provided by SAF-A/hnRNP-U. During telophase unfolding the proper chromatin arrangement is restored according to these marks. The structural specificity of both proteins to the satDNAs provides a regulative but relatively stable mode of binding. The structural specificity of protein binding could help to find the "magic" centromeric sequence. With future investigations of proteins with the structural specificity of binding during early embryogenesis, when heterochromatin formation goes on, the molecular mechanisms of the "gene gating" hypothesis (Blobel, 1985) will be confirmed.
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Affiliation(s)
- O I Podgornaya
- Institute of Cytology, Russian Academy of Sciences, St. Petersburg 194064, Russia
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Itoh Y, Mizuno S. Molecular and cytological characterization of SspI-family repetitive sequence on the chicken W chromosome. Chromosome Res 2003; 10:499-511. [PMID: 12489831 DOI: 10.1023/a:1020944414750] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
A genomic clone, pWS44, isolated from the chicken W chromosome-specific genomic library contained a partial (226-bp) sequence of a novel SspI-family repetitive sequence. A genomic clone, pWPRS09, containing a 508-bp SspI fragment (a repeating unit of the family) was subsequently obtained and sequenced. This 0.5-kb unit is tandemly repeated about 11,300 times. FISH to mitotic and lampbrush W chromosomes indicates that the SspI-family is located on the chromomere 6 between heterochromatic and distal non-heterochromatic regions on the short arm. The SspI-family sequence was proved to be a good positional marker in FISH mapping of active genes in the non-heterochromatic region on the lampbrush W chromosome. The presence of SspI-family repetitive sequence is limited to the genus Gallus (chickens and jungle fowls). The 0.5-kb repeating unit contains a 120-bp stretch of polypurine/polypyrimidine sequence (GGAGA repeats), shows no DNA curvature, and rapid electrophoretic mobility in 4% polyacrylamide gel at 4 degrees C. The SspI-family forms a relatively diffused chromatin structure in nuclei. These features are distinctly different from those of XhoI- and EcoRI-family sequences on the W chromosome. The total amount of non-repetitive DNA in the chicken W chromosome is estimated to be about 10 Mb.
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Affiliation(s)
- Yuichiro Itoh
- Laboratory of Molecular Biology, Department of Molecular and Cell Biology, Graduate School of Agricultural Science, Tohoku University, 1-1 Tsutsumidori-Amamiyamachi, Aoba-ku, Sendai 981-8555, Japan
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Yamada K, Nishida-Umehara C, Matsuda Y. Characterization and chromosomal distribution of novel satellite DNA sequences of the lesser rhea (Pterocnemia pennata) and the greater rhea (Rhea americana). Chromosome Res 2003; 10:513-23. [PMID: 12489832 DOI: 10.1023/a:1020996431588] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
Two different types of novel satellite DNA (stDNA) sequences were cloned from the lesser rhea (Ptercnemia pennata) and the greater rhea (Rhea americana) after digestion of genomic DNAs with a restriction endonuclease Pvu II, and characterized by filter hybridization and in-situ hybridization to metaphase chromosomes. These nucleotide sequences consisted of GC-rich 288-bp and 332-bp repeated elements in P. pennata and 288-bp and 336-bp repeated elements in R. americana, all of which were organized in tandem arrays in the genome. The 288-bp and 332-bp elements of P. pennata displayed strong sequence similarity with the 288-bp and 336-bp elements of R. americana, respectively. The 332-bp and 336-bp elements were located on almost all the microchromosomes in both the species. The other type of repeated elements, the 288-bp element, was located on four and nine pairs of microchromosomes in P. pennata and R. americana, respectively. All the stDNA sequences were not crosshybridized to genomic DNAs of another three ratite species, ostrich (Struthio camelus), cassowary (Casuarius casuarius) and emu (Dromaius novaehollandiae), suggesting that these stDNA sequences are conserved in the same family but fairly divergent among the different families of Struthioniformes.
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Affiliation(s)
- Kazuhiko Yamada
- Laboratory of Cytogenetics, Division of Bioscience, Graduate School of Environmental Earth Science, Hokkaido University, North 10, West 8, Kita-ku, Sapporo 060-0810, Japan
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Morgan GT. Lampbrush chromosomes and associated bodies: new insights into principles of nuclear structure and function. Chromosome Res 2002; 10:177-200. [PMID: 12067208 DOI: 10.1023/a:1015227020652] [Citation(s) in RCA: 78] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
The lampbrush chromosomes and assorted nuclear bodies of amphibian and avian oocytes provide uniquely advantageous and amenable experimental material for cell biologists to study the structure and function of the eukaryotic nucleus, and in particular to address the processes of nuclear gene expression. Recent findings discussed here include the molecular analysis of the actively elongating RNA polymerase complexes associated with lampbrush chromosome loops and of the association between loop nascent transcripts and RNA processing components. In addition, several types of chromosome structure that do not outwardly resemble simple extended loops and that may house novel nuclear functions have recently been studied in detail. Among these a type of chromosomal body that can also exist free in the oocyte nucleus, the Cajal body, has been shown to possess a range of characteristics that suggest it is involved in the assembly of macromolecular complexes required for gene expression. Homologous structures have also been described in somatic nuclei. Fundamental aspects of the looped organization exhibited by lampbrush as well as other chromosomes have also been addressed, most notably by the application of a technique for de-novo chromosome assembly.
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Affiliation(s)
- Garry T Morgan
- Institute of Genetics, University of Nottingham, Queens Medical Centre, UK.
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Lorite P, Renault S, Rouleux-Bonnin F, Bigot S, Periquet G, Palomeque T. Genomic organization and transcription of satellite DNA in the ant Aphaenogaster subterranea (Hymenoptera, Formicidae). Genome 2002; 45:609-16. [PMID: 12175063 DOI: 10.1139/g02-022] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
A satellite DNA family (APSU) was isolated and characterized in the ant Aphaenogaster subterranea. This satellite DNA is organized in tandem repeats of 162 bp and is relatively AT rich (51.9%). Sequence analysis showed a high level of homogeneity between monomers. Loss of satellite DNA has been detected in queens in relation to workers, because the amount of satellite DNA in queens is about 25% of the amount found in workers. Restriction analysis of the total DNA with methylation-sensitive enzymes suggests that this DNA is not methylated. Analysis of the electrophoretic mobility of satellite DNA on non-denaturing polyacrylamide showed that this satellite DNA is only very lightly curved. Their possible transcription was analyzed using reverse transcription and polymerase chain reaction (RT-PCR). The satellite DNA is transcribed on the two DNA strands at the same level in worker and queen pupae, as well as in worker adults.
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Affiliation(s)
- P Lorite
- Departamento de Biología Experimental, Universidad de Jaén, Spain
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Saifitdinova AF, Derjusheva SE, Malykh AG, Zhurov VG, Andreeva TF, Gaginskaya ER. Centromeric tandem repeat from the chaffinch genome: Isolation and molecular characterization. Genome 2001. [DOI: 10.1139/g00-098] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
A new family of avian centromeric satellites is described. The highly repeated sequence, designated FCP (Fringilla coelebs PstI element), was cloned from the 500-bp PstI digest fraction of the chaffinch (Fringilla coelebs L.) genomic DNA, sequenced, and characterized. The FCP repeat was found to have 505506 bp length of monomer, 57% content of GC, to compose about 0.9% of the chaffinch genome, and to be highly methylated. Results of Southern-blot hybridization of cloned FCP element onto genomic DNA digested with different restriction enzymes, and sequencing directly from total genomic DNA using FCP-specific primers and ThermoFidelase enzyme (Fidelity Systems Inc.) were in agreement with a tandem arrangement of this repeat in the chaffinch genome. Five positions of single-nucleotide polymorphism (SNP) were found in the FCP monomers using direct genomic sequencing. Fluorescence in situ hybridization (FISH) with FCP probe and primed in situ labelling (PRINS) with FCP specific primers showed that the FCP elements occupy pericentric regions of all chaffinch chromosomes. On chromosome spreads, the fluorescent signals were also observed in the intercentromeric connectives between nonhomologous chromosomes. The results suggest that the centromeric FCP repeat is responsible for chromosome ordering during mitosis in chaffinch.Key words: satellite DNA, centromeric heterochromatin, Fringilla coelebs.
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Saffery R, Earle E, Irvine DV, Kalitsis P, Choo KH. Conservation of centromere protein in vertebrates. Chromosome Res 1999; 7:261-5. [PMID: 10461871 DOI: 10.1023/a:1009222729850] [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: 11/12/2022]
Abstract
The chicken genome comprises 78 chromosomes which include several macrochromosomes and many microchromosomes. Very little information is currently available concerning chicken centromere structure and function and it is unclear if the two types of chromosomes share a common centromere mechanism or whether this mechanism resembles those in other species. Immunofluorescence studies using antibodies to mammalian constitutive centromere proteins CENP-A, CENP-B, and CENP-C and the passenger proteins CENP-E, and CENP-F revealed the presence of each of these proteins at the centromeres of both macro- and microchromsomes. CENP-A, CENP-B, and CENP-E levels showed variability between metaphase centromeres while CENP-C and CENP-F levels were relatively constant. These results suggest a common centromere mechanism for both types of chromosomes as well as indicating a high degree of conservation of individual proteins between widely divergent vertebrate classes and an overall conservation of centromere function throughout vertebrate evolution.
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Affiliation(s)
- R Saffery
- The Murdoch Institute, Royal Children's Hospital, Parkville, Australia.
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Renault S, Rouleux-Bonnin F, Periquet G, Bigot Y. Satellite DNA transcription in Diadromus pulchellus (Hymenoptera). INSECT BIOCHEMISTRY AND MOLECULAR BIOLOGY 1999; 29:103-111. [PMID: 10196733 DOI: 10.1016/s0965-1748(98)00113-1] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
Previous studies have shown that the satellite DNAs in Hymenoptera account for 1-25% of the genome. They mainly correspond to a single family, or to several subfamilies having the same evolutionary origin. We have now showed that the satellite DNAs in the genomes of the hymenopterans Diadromus pulchellus, Diadromus collaris, Eupelmus vuilletti and Eupelmus orientalis are transcribed in both males and females. Satellite DNA transcripts could only be extracted with NP40/Urea, indicating that they are strongly associated with proteins. The satellite DNA in D. pulchellus was transcribed on the two DNA strands. The satellite DNA transcripts were single-stranded and not polyadenylated in vivo. The transcripts were found in embryos, larvae and imagos stages. The transcripts detected included one major transcript (1.9 kb) and several discrete smaller transcripts. The in vivo synthesis of these satellite DNA transcripts was explored by identifying their putative initiation sites.
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Affiliation(s)
- S Renault
- Institut de Recherche sur la Biologie de l'Insecte, UPRESA CNRS 6035, Faculté des Sciences, Université F. Rabelais, Tours, France.
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