FISH in Lampbrush Chromosomes

Zlotina, Anna; Krasikova, Alla

doi:10.1007/978-3-662-52959-1_45

Cited by 7 publications

(10 citation statements)

References 28 publications

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“…Fluorescence in situ hybridization (FISH) was performed on selected lampbrush chromosome preparations after immunostaining according to a DNA/(DNA + RNA) hybridization protocol [ 7 ]. Hybridization mixture contained 20 ng/μl DNA probe, 50% formamide, 10% dextran sulfate, 2 × SSC (0.3 M NaCl, 30 mM Na 3 C 6 H 5 O 7 ), 1 μg/μl salmon sperm DNA and deionized water for PCR generated DNA probes; for oligonucleotide probe formamide concentration was decreased to 42%.…”

Section: Methodsmentioning

confidence: 99%

“…Being highly decondensed and enriched with morphological markers, lampbrush chromosomes represent a promising tool for high-resolution physical gene mapping [ 6 ]. Individual genes or tandem repeat families can be mapped precisely to certain lampbrush chromomeres or lateral loops by fluorescence in situ hybridization (FISH) according to DNA/DNA and/or DNA/RNA hybridization protocols [ 7 ]. Moreover, lampbrush chromosomes allow to investigate the pattern of various epigenetic modifications in both completely decondensed (lateral loops) and condensed (chromomeres) chromatin domains.…”

Section: Introductionmentioning

confidence: 99%

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Mapping epigenetic modifications on chicken lampbrush chromosomes

et al. 2020

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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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Section: Methodsmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Mapping epigenetic modifications on chicken lampbrush chromosomes

et al. 2020

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“…2D-FISH procedures were applied to lampbrush chromosome preparations according to DNA/DNA+RNA protocol preserving RNA (Solovei et al . 1994; Zlotina and Krasikova 2017). In particular, RNAase treatment was omitted.…”

Section: Methodsmentioning

confidence: 99%

Comparison of the somatic TADs and lampbrush chromomere-loop complexes in transcriptionally active prophase I oocytes

Kulikova

Maslova

Starshova

et al. 2021

Preprint

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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 juxtapose 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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“…To obtain pictures of native chromomeres, freshly prepared lampbrush chromosomes were stained with 1 μg/ml DAPI in antifade solution described above and imaged with Leica DM4000 fluorescent microscope before FISH. 2D-FISH procedures were applied to lampbrush chromosome preparations according to DNA/DNA+RNA protocol preserving RNA (Solovei et al 1994;Zlotina and Krasikova 2017). In particular, RNAase treatment was omitted.…”

Section: D Fishmentioning

confidence: 99%

Comparison of the somatic TADs and lampbrush chromomere-loop complexes in transcriptionally active prophase I oocytes

et al. 2022

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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 juxtapose 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 domainslateral 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 chromomereloop 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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FISH in Lampbrush Chromosomes

Cited by 7 publications

References 28 publications

Mapping epigenetic modifications on chicken lampbrush chromosomes

Mapping epigenetic modifications on chicken lampbrush chromosomes

Comparison of the somatic TADs and lampbrush chromomere-loop complexes in transcriptionally active prophase I oocytes

Comparison of the somatic TADs and lampbrush chromomere-loop complexes in transcriptionally active prophase I oocytes

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