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

Standard

Comparison of the somatic TADs and lampbrush chromomere-loop complexes in transcriptionally active prophase I oocytes. / Kulikova, Tatiana ; Maslova, Antonina ; Starshova, Polina ; Rodriguez Ramos, Juan Sebastian ; Krasikova, Alla.

In: Chromosoma, Vol. 131, No. 4, 12.2022, p. 207-223.

Research output: Contribution to journal › Article › peer-review

BibTeX

@article{35186158e3374c839f7d945631b53595,

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

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.",

keywords = "Chicken genome, Chromatin domain, Chromomere, Chromomere-loop complex, FISH-mapping, Gene expression, Lampbrush chromosomes, Meiotic chromosomes, Nascent transcripts, Oocyte nucleus, Oogenesis, Topologically associating domain, Transcription, Transcription loops",

author = "Tatiana Kulikova and Antonina Maslova and Polina Starshova and {Rodriguez Ramos}, {Juan Sebastian} and Alla Krasikova",

note = "Publisher Copyright: {\textcopyright} 2022, The Author(s), under exclusive licence to Springer-Verlag GmbH Germany, part of Springer Nature.",

year = "2022",

month = dec,

doi = "10.1007/s00412-022-00780-5",

language = "English",

volume = "131",

pages = "207--223",

journal = "Chromosoma",

issn = "0009-5915",

publisher = "Springer Nature",

number = "4",

}

RIS

TY - JOUR

T1 - Comparison of the somatic TADs and lampbrush chromomere-loop complexes in transcriptionally active prophase I oocytes

AU - Kulikova, Tatiana

AU - Maslova, Antonina

AU - Starshova, Polina

AU - Rodriguez Ramos, Juan Sebastian

AU - Krasikova, Alla

PY - 2022/12

Y1 - 2022/12

N2 - 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.

AB - 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.

KW - Chicken genome

KW - Chromatin domain

KW - Chromomere

KW - Chromomere-loop complex

KW - FISH-mapping

KW - Gene expression

KW - Lampbrush chromosomes

KW - Meiotic chromosomes

KW - Nascent transcripts

KW - Oocyte nucleus

KW - Oogenesis

KW - Topologically associating domain

KW - Transcription

KW - Transcription loops

UR - http://www.scopus.com/inward/record.url?scp=85137019610&partnerID=8YFLogxK

UR - https://www.mendeley.com/catalogue/9c77c779-306b-382b-b69f-d02e530184b3/

U2 - 10.1007/s00412-022-00780-5

DO - 10.1007/s00412-022-00780-5

M3 - Article

C2 - 36031655

AN - SCOPUS:85137019610

VL - 131

SP - 207

EP - 223

JO - Chromosoma

JF - Chromosoma

SN - 0009-5915

IS - 4

ER -

ID: 99845645