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TAD border deletion at the Kit locus causes tissue-specific ectopic activation of a neighboring gene.
Kabirova, Evelyn; Ryzhkova, Anastasiya; Lukyanchikova, Varvara; Khabarova, Anna; Korablev, Alexey; Shnaider, Tatyana; Nuriddinov, Miroslav; Belokopytova, Polina; Smirnov, Alexander; Khotskin, Nikita V; Kontsevaya, Galina; Serova, Irina; Battulin, Nariman.
Afiliação
  • Kabirova E; Institute of Cytology and Genetics SB RAS, Novosibirsk, Russia.
  • Ryzhkova A; Institute of Cytology and Genetics SB RAS, Novosibirsk, Russia.
  • Lukyanchikova V; Institute of Cytology and Genetics SB RAS, Novosibirsk, Russia.
  • Khabarova A; Institute of Cytology and Genetics SB RAS, Novosibirsk, Russia.
  • Korablev A; Institute of Cytology and Genetics SB RAS, Novosibirsk, Russia.
  • Shnaider T; Institute of Cytology and Genetics SB RAS, Novosibirsk, Russia.
  • Nuriddinov M; Institute of Cytology and Genetics SB RAS, Novosibirsk, Russia.
  • Belokopytova P; Institute of Cytology and Genetics SB RAS, Novosibirsk, Russia.
  • Smirnov A; Novosibirsk State University, Novosibirsk, Russia.
  • Khotskin NV; Institute of Cytology and Genetics SB RAS, Novosibirsk, Russia.
  • Kontsevaya G; Institute of Cytology and Genetics SB RAS, Novosibirsk, Russia.
  • Serova I; Institute of Cytology and Genetics SB RAS, Novosibirsk, Russia.
  • Battulin N; Institute of Cytology and Genetics SB RAS, Novosibirsk, Russia.
Nat Commun ; 15(1): 4521, 2024 May 28.
Article em En | MEDLINE | ID: mdl-38806452
ABSTRACT
Topologically associated domains (TADs) restrict promoter-enhancer interactions, thereby maintaining the spatiotemporal pattern of gene activity. However, rearrangements of the TADs boundaries do not always lead to significant changes in the activity pattern. Here, we investigated the consequences of the TAD boundaries deletion on the expression of developmentally important genes encoding tyrosine kinase receptors Kit, Kdr, Pdgfra. We used genome editing in mice to delete the TADs boundaries at the Kit locus and characterized chromatin folding and gene expression in pure cultures of fibroblasts, mast cells, and melanocytes. We found that although Kit is highly active in both mast cells and melanocytes, deletion of the TAD boundary between the Kit and Kdr genes results in ectopic activation only in melanocytes. Thus, the epigenetic landscape, namely the mutual arrangement of enhancers and actively transcribing genes, is important for predicting the consequences of the TAD boundaries removal. We also found that mice without a TAD border between the Kit and Kdr genes have a phenotypic manifestation of the mutation - a lighter coloration. Thus, the data obtained shed light on the principles of interaction between the 3D chromatin organization and epigenetic marks in the regulation of gene activity.
Assuntos

Texto completo: 1 Coleções: 01-internacional Base de dados: MEDLINE Assunto principal: Cromatina / Proteínas Proto-Oncogênicas c-kit / Fibroblastos / Mastócitos / Melanócitos Limite: Animals Idioma: En Revista: Nat Commun Assunto da revista: BIOLOGIA / CIENCIA Ano de publicação: 2024 Tipo de documento: Article País de afiliação: Federação Russa

Texto completo: 1 Coleções: 01-internacional Base de dados: MEDLINE Assunto principal: Cromatina / Proteínas Proto-Oncogênicas c-kit / Fibroblastos / Mastócitos / Melanócitos Limite: Animals Idioma: En Revista: Nat Commun Assunto da revista: BIOLOGIA / CIENCIA Ano de publicação: 2024 Tipo de documento: Article País de afiliação: Federação Russa
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