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Krasikova A, Kulikova T, Rodriguez Ramos JS, Maslova A. Assignment of the somatic A/B compartments to chromatin domains in giant transcriptionally active lampbrush chromosomes. Epigenetics Chromatin 2023; 16:24. [PMID: 37322523 DOI: 10.1186/s13072-023-00499-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2023] [Accepted: 06/04/2023] [Indexed: 06/17/2023] Open
Abstract
BACKGROUND The three-dimensional configuration of the eukaryotic genome is an emerging area of research. Chromosome conformation capture outlined genome segregation into large scale A and B compartments corresponding mainly to transcriptionally active and repressive chromatin. It remains unknown how the compartmentalization of the genome changes in growing oocytes of animals with hypertranscriptional type of oogenesis. Such oocytes are characterized by highly elongated chromosomes, called lampbrush chromosomes, which acquire a typical chromomere-loop appearance, representing one of the classical model systems for exploring the structural and functional organization of chromatin domains. RESULTS Here, we compared the distribution of A/B compartments in chicken somatic cells with chromatin domains in lampbrush chromosomes. We found that in lampbrush chromosomes, the extended chromatin domains, restricted by compartment boundaries in somatic cells, disintegrate into individual chromomeres. Next, we performed FISH-mapping of the genomic loci, which belong to A or B chromatin compartments as well as to A/B compartment transition regions in embryonic fibroblasts on isolated lampbrush chromosomes. We found, that in chicken lampbrush chromosomes, clusters of dense compact chromomeres bearing short lateral loops and enriched with repressive epigenetic modifications generally correspond to constitutive B compartments in somatic cells. A compartments align with lampbrush chromosome segments with smaller, less compact chromomeres, longer lateral loops, and a higher transcriptional status. Clusters of small loose chromomeres with relatively long lateral loops show no obvious correspondence with either A or B compartment identity. Some genes belonging to facultative B (sub-) compartments can be tissue-specifically transcribed during oogenesis, forming distinct lateral loops. CONCLUSIONS Here, we established a correspondence between the A/B compartments in somatic interphase nucleus and chromatin segments in giant lampbrush chromosomes from diplotene stage oocytes. The chromomere-loop structure of the genomic regions corresponding to interphase A and B compartments reveals the difference in how they are organized at the level of chromatin domains. The results obtained also suggest that gene-poor regions tend to be packed into chromomeres.
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Affiliation(s)
- Alla Krasikova
- Saint-Petersburg State University, Saint-Petersburg, Russia.
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Kulikova T, Maslova A, Starshova P, Rodriguez Ramos JS, Krasikova A. Comparison of the somatic TADs and lampbrush chromomere-loop complexes in transcriptionally active prophase I oocytes. Chromosoma 2022. [PMID: 36031655 DOI: 10.1007/s00412-022-00780-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2021] [Revised: 07/26/2022] [Accepted: 08/01/2022] [Indexed: 11/03/2022]
Abstract
In diplotene oocyte nuclei of all vertebrate species, except mammals, chromosomes lack interchromosomal contacts and chromatin is linearly compartmentalized into distinct chromomere-loop complexes forming lampbrush chromosomes. However, the mechanisms underlying the formation of chromomere-loop complexes remain unexplored. Here we aimed to compare somatic topologically associating domains (TADs), recently identified in chicken embryonic fibroblasts, with chromomere-loop complexes in lampbrush meiotic chromosomes. By measuring 3D-distances and colocalization between linear equidistantly located genomic loci, positioned within one TAD or separated by a TAD border, we confirmed the presence of predicted TADs in chicken embryonic fibroblast nuclei. Using three-colored FISH with BAC probes, we mapped equidistant genomic regions included in several sequential somatic TADs on isolated chicken lampbrush chromosomes. Eight genomic regions, each comprising two or three somatic TADs, were mapped to non-overlapping neighboring lampbrush chromatin domains - lateral loops, chromomeres, or chromomere-loop complexes. Genomic loci from the neighboring somatic TADs could localize in one lampbrush chromomere-loop complex, while genomic loci belonging to the same somatic TAD could be localized in neighboring lampbrush chromomere-loop domains. In addition, FISH-mapping of BAC probes to the nascent transcripts on the lateral loops indicates transcription of at least 17 protein-coding genes and 2 non-coding RNA genes during the lampbrush stage of chicken oogenesis, including genes involved in oocyte maturation and early embryo development.
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Keinath MC, Davidian A, Timoshevskiy V, Timoshevskaya N, Gall JG. Characterization of axolotl lampbrush chromosomes by fluorescence in situ hybridization and immunostaining. Exp Cell Res 2021; 401:112523. [PMID: 33675804 PMCID: PMC8123938 DOI: 10.1016/j.yexcr.2021.112523] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2020] [Revised: 02/08/2021] [Accepted: 02/15/2021] [Indexed: 10/25/2022]
Abstract
The lampbrush chromosomes (LBCs) in oocytes of the Mexican axolotl (Ambystoma mexicanum) were identified some time ago by their relative lengths and predicted centromeres, but they have never been associated completely with the mitotic karyotype, linkage maps or genome assembly. We identified 9 of the axolotl LBCs using RNAseq to identify actively transcribed genes and 13 BAC (bacterial artificial clone) probes containing pieces of active genes. Using read coverage analysis to find candidate centromere sequences, we developed a centromere probe that localizes to all 14 centromeres. Measurements of relative LBC arm lengths and polymerase III localization patterns enabled us to identify all LBCs. This study presents a relatively simple and reliable way to identify each axolotl LBC cytologically and to anchor chromosome-length sequences (from the axolotl genome assembly) to the physical LBCs by immunostaining and fluorescence in situ hybridization. Our data will facilitate a more detailed transcription analysis of individual LBC loops.
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Affiliation(s)
| | - Asya Davidian
- Carnegie Institution for Science, Baltimore, MD, USA; Saint Petersburg State University, Saint Petersburg, Russia
| | | | | | - Joseph G Gall
- Carnegie Institution for Science, Baltimore, MD, USA.
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Kulikova T, Surkova A, Zlotina A, Krasikova A. Mapping epigenetic modifications on chicken lampbrush chromosomes. Mol Cytogenet 2020; 13:32. [PMID: 32774459 PMCID: PMC7397634 DOI: 10.1186/s13039-020-00496-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2020] [Accepted: 06/16/2020] [Indexed: 11/10/2022] Open
Abstract
Background The epigenetic regulation of genome is crucial for implementation of the genetic program of ontogenesis through establishing and maintaining differential gene expression. Thus mapping of various epigenetic modifications to the genome is relevant for studying the regulation of gene expression. Giant transcriptionally active lampbrush chromosomes are an established tool for high resolution physical mapping of the genome and its epigenetic modifications. This study is aimed at characterizing the epigenetic status of compact chromatin domains (chromomeres) of chicken lampbrush macrochromosomes. Results Distribution of three epigenetic modifications – 5-methylcytosine, histone H3 trimethylated at lysine 9 and hyperacetylated histone H4 – along the axes of chicken lampbrush chromosomes 1–4, Z and W was analyzed in details. Enrichment of chromatin domains with the investigated epigenetic modifications was indicated on the cytological chromomere-loop maps for corresponding chicken lampbrush chromosomes. Heterogeneity in the distribution of 5-methylcytosine and histone H3 trimethylated at lysine 9 along the chromosome axes was revealed. Conclusions On examples of certain chromomeres of chicken lampbrush chromosomes 1, 3, 4 and W we demonstrated that a combination of immunofluorescent staining and fluorescence in situ hybridization allows to relate the epigenetic status and a DNA sequence context of individual chromomeres.
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Affiliation(s)
| | - Anna Surkova
- Saint Petersburg State University, Saint-Petersburg, Russia
| | - Anna Zlotina
- Saint Petersburg State University, Saint-Petersburg, Russia
| | - Alla Krasikova
- Saint Petersburg State University, Saint-Petersburg, Russia
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Abstract
When in the lampbrush configuration, chromosomes display thousands of visible DNA loops that are transcribed at exceptionally high rates by RNA polymerase II (pol II). These transcription loops provide unique opportunities to investigate not only the detailed architecture of pol II transcription sites but also the structural dynamics of chromosome looping, which is receiving fresh attention as the organizational principle underpinning the higher-order structure of all chromosome states. The approach described here allows for extended imaging of individual transcription loops and transcription units under conditions in which loop RNA synthesis continues. In intact nuclei from lampbrush-stage Xenopus oocytes isolated under mineral oil, highly specific targeting of fluorescent fusions of the RNA-binding protein CELF1 to nascent transcripts allowed functional transcription loops to be observed and their longevity assessed over time. Some individual loops remained extended and essentially static structures over time courses of up to an hour. However, others were less stable and shrank markedly over periods of 30-60 min in a manner that suggested that loop extension requires continued dense coverage with nascent transcripts. In stable loops and loop-derived structures, the molecular dynamics of the visible nascent RNP component were addressed using photokinetic approaches. The results suggested that CELF1 exchanges freely between the accumulated nascent RNP and the surrounding nucleoplasm, and that it exits RNP with similar kinetics to its entrance. Overall, it appears that on transcription loops, nascent transcripts contribute to a dynamic self-organizing structure that exemplifies a phase-separated nuclear compartment.
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Affiliation(s)
- Garry T Morgan
- School of Life Sciences, University of Nottingham, Queens Medical Centre, Nottingham, NG7 2UH, UK.
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Komissarov AS, Galkina SA, Koshel EI, Kulak MM, Dyomin AG, O'Brien SJ, Gaginskaya ER, Saifitdinova AF. New high copy tandem repeat in the content of the chicken W chromosome. Chromosoma 2017; 127:73-83. [PMID: 28951974 DOI: 10.1007/s00412-017-0646-5] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2017] [Revised: 09/13/2017] [Accepted: 09/18/2017] [Indexed: 11/26/2022]
Abstract
The content of repetitive DNA in avian genomes is considerably less than in other investigated vertebrates. The first descriptions of tandem repeats were based on the results of routine biochemical and molecular biological experiments. Both satellite DNA and interspersed repetitive elements were annotated using library-based approach and de novo repeat identification in assembled genome. The development of deep-sequencing methods provides datasets of high quality without preassembly allowing one to annotate repetitive elements from unassembled part of genomes. In this work, we search the chicken assembly and annotate high copy number tandem repeats from unassembled short raw reads. Tandem repeat (GGAAA)n has been identified and found to be the second after telomeric repeat (TTAGGG)n most abundant in the chicken genome. Furthermore, (GGAAA)n repeat forms expanded arrays on the both arms of the chicken W chromosome. Our results highlight the complexity of repetitive sequences and update data about organization of sex W chromosome in chicken.
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Affiliation(s)
- Aleksey S Komissarov
- Theodosius Dobzhansky Center for Genome Bioinformatics, Saint Petersburg State University, Sredniy av. 41, 199034, Saint Petersburg, Russia
| | - Svetlana A Galkina
- Department of Genetics and Biotechnology, Saint Petersburg State University, Universitetskaya emb. 7/9, 199034, Saint Petersburg, Russia
- Saint Petersburg Association of Scientists and Scholars, Universitetskaya emb. 5, Saint Petersburg, 199034, Russia
| | - Elena I Koshel
- Department of Cytology and Histology, Saint Petersburg State University, Universitetskaya emb. 7/9, 199034, Saint Petersburg, Russia
| | - Maria M Kulak
- Department of Cytology and Histology, Saint Petersburg State University, Universitetskaya emb. 7/9, 199034, Saint Petersburg, Russia
| | - Aleksander G Dyomin
- Saint Petersburg Association of Scientists and Scholars, Universitetskaya emb. 5, Saint Petersburg, 199034, Russia
- Chromas Research Resource Center, Saint Petersburg State University, Oranienbaumskoye sh. 2, 198504, Saint Petersburg, Russia
| | - Stephen J O'Brien
- Theodosius Dobzhansky Center for Genome Bioinformatics, Saint Petersburg State University, Sredniy av. 41, 199034, Saint Petersburg, Russia
- Oceanographic Center, Nova Southeastern University, Fort Lauderdale, Florida, 33004, USA
| | - Elena R Gaginskaya
- Department of Cytology and Histology, Saint Petersburg State University, Universitetskaya emb. 7/9, 199034, Saint Petersburg, Russia
| | - Alsu F Saifitdinova
- Chromas Research Resource Center, Saint Petersburg State University, Oranienbaumskoye sh. 2, 198504, Saint Petersburg, Russia.
- International Centre of Reproductive Medicine, Komendantskiy av. 53-1, Saint Petersburg, 197350, Russia.
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Galkina S, Fillon V, Saifitdinova A, Daks A, Kulak M, Dyomin A, Koshel E, Gaginskaya ER. Chicken Microchromosomes in the Lampbrush Phase: A Cytogenetic Description. Cytogenet Genome Res 2017; 152:46-54. [PMID: 28564645 DOI: 10.1159/000475563] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/01/2017] [Indexed: 11/19/2022] Open
Abstract
Lampbrush chromosomes are giant, transcriptionally active, meiotic chromosomes found in oocytes of all vertebrates with the exception of mammals. Lampbrush chromosomes offer a convenient tool for cytogenetic mapping and, in particular, have been instrumental in mapping genes and linkage groups on chicken (GGA) chromosomes. Whereas cytogenetic maps of macrochromosome GGA1-10 and microchromosome GGA11-16 lampbrush bivalents have been established, identification and description of smaller microchromosome bivalents are still missing. In this work, we used specific FISH probes for the identification of 12 chicken lampbrush chromosomes formed by GGA17-28. Our observations on chromomere and lateral loop arrangement and chiasma position allowed us to construct the respective cytogenetic maps for these microchromosomes. For the 10 smallest chicken microchromosomes, GGA29-38, no individual molecular tags are available, yet they can be collectively marked using the PO41 repeat. The reported results contribute to building of working cytogenetic maps of the chicken karyotype.
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Affiliation(s)
- Svetlana Galkina
- Biological Faculty, Saint Petersburg State University, Saint Petersburg, Russia
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Tworzydlo W, Marek M, Kisiel E, Bilinski SM. Meiosis, Balbiani body and early asymmetry of Thermobia oocyte. Protoplasma 2017; 254:649-655. [PMID: 27180195 PMCID: PMC5309285 DOI: 10.1007/s00709-016-0978-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/15/2016] [Accepted: 04/28/2016] [Indexed: 06/05/2023]
Abstract
The meiotic division guarantees maintenance of a genetic diversity; it consists of several stages, with prophase I being the longest and the most complex. We decided to follow the course of initial stages of meiotic division in ovaries of Thermobia domestica using modified techniques of squash preparations, semithin sections, and electron microscopy. We show that germaria contain numerous germline cells that can be classified into three categories: cystoblasts, meiotic oocytes, and growing previtellogenic oocytes. The cystoblasts are located most apically. The meiotic oocytes occupy the middle part of the germarium, and the previtellogenic oocytes can be found in the most basal part, near the vitellarium. Analyses of the semithin sections and squash preparations show that post leptotene meiotic chromosomes gather in one region of the nucleoplasm where they form the so-called bouquet. The telomeres of the bouquet chromosomes are attached to a relatively small area (segment) of the nuclear envelope. Next to this envelope segment, the nucleolar organizers are also located. We show that in concert to sequential changes inside the oocyte nuclei, rearrangement of organelles within the ooplasm (oocyte cytoplasm) takes place. This leads to the formation of the Balbiani body and consequent asymmetry of the ooplasm. These early nuclear and cytoplasmic asymmetries, however, are transient. During diplotene, the chromosome bouquet disappears, while the Balbiani body gradually disperses throughout the ooplasm. Finally, our observations indicate the presence of lampbrush chromosomes in the nuclei of previtellogenic oocytes. In the close vicinity to lampbrush chromosomes, characteristic spherical nuclear bodies are present.
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Affiliation(s)
- Waclaw Tworzydlo
- Department of Developmental Biology and Morphology of Invertebrates, Institute of Zoology, Jagiellonian University, Krakow, Poland.
| | - Magdalena Marek
- Department of Developmental Biology and Morphology of Invertebrates, Institute of Zoology, Jagiellonian University, Krakow, Poland
| | - Elzbieta Kisiel
- Department of Developmental Biology and Morphology of Invertebrates, Institute of Zoology, Jagiellonian University, Krakow, Poland
| | - Szczepan M Bilinski
- Department of Developmental Biology and Morphology of Invertebrates, Institute of Zoology, Jagiellonian University, Krakow, Poland
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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