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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The research was supported by the Russian Science Foundation (grant #19–74-20075) and was performed using the equipment of the Resource Center “Molecular and Cell Technologies” (Saint Petersburg State University).
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AK conceived the study and supervised the project. AM performed 3D-FISH on chicken embryonic fibroblasts, image analysis, and 3D-measurements. TK, PS, and SR performed 2D-FISH on isolated lampbrush chromosomes. TK, AK, and SR performed bioinformatic analysis of the mapped genomic sequences. TK, AM, and AK drafted the manuscript. All authors have read and agreed to the final version of the manuscript.
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Kulikova, T., Maslova, A., Starshova, P. et al. Comparison of the somatic TADs and lampbrush chromomere-loop complexes in transcriptionally active prophase I oocytes. Chromosoma 131, 207–223 (2022). https://doi.org/10.1007/s00412-022-00780-5
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DOI: https://doi.org/10.1007/s00412-022-00780-5