TY - JOUR

T1 - TAD border deletion at the Kit locus causes tissue-specific ectopic activation of a neighboring gene

AU - Kabirova, Evelyn

AU - Ryzhkova, Anastasiya

AU - Lukyanchikova, Varvara

AU - Khabarova, Anna

AU - Korablev, Alexey

AU - Shnaider, Tatyana

AU - Nuriddinov, Miroslav

AU - Belokopytova, Polina

AU - Smirnov, Alexander

AU - Khotskin, Nikita V

AU - Kontsevaya, Galina

AU - Serova, Irina

AU - Battulin, Nariman

N1 - This work was supported with the budget project of Institute of Cytology and Genetics SB RAS (state project FWNR-2022-0019). Experiment with M. castaneus hybrids was supported by Russian Science Foundation grant #22-14-00247. Hi-C experiments sequencing was performed using equipment of the Novosibirsk State University, supported by the Ministry of Education and Science of Russian Federation, grant #FSUS-2024- 0018. Illumina data analysis was supported by the strategic academic leadership program “Priority 2030” in Novosibirsk State University. Cell culturing was performed at the Collective Center of ICG SB RAS “Collection of Pluripotent Human and Mammalian Cell Cultures for Biological and Biomedical Research”, project number FWNR-2022-0019. © 2024. The Author(s).

PY - 2024/12

Y1 - 2024/12

N2 - 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.

AB - 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.

KW - Animals

KW - Proto-Oncogene Proteins c-kit/genetics

KW - Mice

KW - Mast Cells/metabolism

KW - Melanocytes/metabolism

KW - Fibroblasts/metabolism

KW - Chromatin/metabolism

KW - Vascular Endothelial Growth Factor Receptor-2/genetics

KW - Promoter Regions, Genetic/genetics

KW - Enhancer Elements, Genetic/genetics

KW - Receptor, Platelet-Derived Growth Factor alpha/genetics

KW - Epigenesis, Genetic

KW - Genetic Loci

KW - Mice, Inbred C57BL

KW - Organ Specificity/genetics

KW - Gene Editing

KW - Ectopic Gene Expression

KW - Male

UR - https://www.scopus.com/record/display.uri?eid=2-s2.0-85194896456&origin=inward&txGid=3f90f380a1a6ee0e1ff2f6f01680a0a6

U2 - 10.1038/s41467-024-48523-7

DO - 10.1038/s41467-024-48523-7

M3 - Article

C2 - 38806452

VL - 15

JO - Nature Communications

JF - Nature Communications

SN - 2041-1723

IS - 1

M1 - 4521

ER -