Genome wide nucleosome landscape shapes 3D chromatin organization
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Genome wide nucleosome landscape shapes 3D chromatin organization. / Fouziya, Shah; Krietenstein, Nils; Mir, Ulfat Syed; Mieczkowski, Jakub; Khan, Masood A.; Baba, Aemon; Dar, Mohmmad Abaas; Altaf, Mohammad; Wani, Ajazul H.
In: Science Advances, Vol. 10, No. 23, eadn2955, 2024.Research output: Contribution to journal › Journal article › Research › peer-review
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TY - JOUR
T1 - Genome wide nucleosome landscape shapes 3D chromatin organization
AU - Fouziya, Shah
AU - Krietenstein, Nils
AU - Mir, Ulfat Syed
AU - Mieczkowski, Jakub
AU - Khan, Masood A.
AU - Baba, Aemon
AU - Dar, Mohmmad Abaas
AU - Altaf, Mohammad
AU - Wani, Ajazul H.
N1 - Publisher Copyright: Copyright © 2024 The Authors, some rights reserved
PY - 2024
Y1 - 2024
N2 - The hierarchical chromatin organization begins with formation of nucleosomes, which fold into chromatin domains punctuated by boundaries and ultimately chromosomes. In a hierarchal organization, lower levels shape higher levels. However, the dependence of higher-order 3D chromatin organization on the nucleosome-level organization has not been studied in cells. We investigated the relationship between nucleosome-level organization and higher-order chromatin organization by perturbing nucleosomes across the genome by deleting Imitation SWItch (ISWI) and Chromodomain Helicase DNA-binding (CHD1) chromatin remodeling factors in budding yeast. We find that changes in nucleosome-level properties are accompanied by changes in 3D chromatin organization. Short-range chromatin contacts up to a few kilo–base pairs decrease, chromatin domains weaken, and boundary strength decreases. Boundary strength scales with accessibility and moderately with width of nucleosome-depleted region. Change in nucleosome positioning seems to alter the stiffness of chromatin, which can affect formation of chromatin contacts. Our results suggest a biomechanical “bottom-up” mechanism by which nucleosome distribution across genome shapes 3D chromatin organization.
AB - The hierarchical chromatin organization begins with formation of nucleosomes, which fold into chromatin domains punctuated by boundaries and ultimately chromosomes. In a hierarchal organization, lower levels shape higher levels. However, the dependence of higher-order 3D chromatin organization on the nucleosome-level organization has not been studied in cells. We investigated the relationship between nucleosome-level organization and higher-order chromatin organization by perturbing nucleosomes across the genome by deleting Imitation SWItch (ISWI) and Chromodomain Helicase DNA-binding (CHD1) chromatin remodeling factors in budding yeast. We find that changes in nucleosome-level properties are accompanied by changes in 3D chromatin organization. Short-range chromatin contacts up to a few kilo–base pairs decrease, chromatin domains weaken, and boundary strength decreases. Boundary strength scales with accessibility and moderately with width of nucleosome-depleted region. Change in nucleosome positioning seems to alter the stiffness of chromatin, which can affect formation of chromatin contacts. Our results suggest a biomechanical “bottom-up” mechanism by which nucleosome distribution across genome shapes 3D chromatin organization.
U2 - 10.1126/sciadv.adn2955
DO - 10.1126/sciadv.adn2955
M3 - Journal article
C2 - 38848364
AN - SCOPUS:85195533992
VL - 10
JO - Science advances
JF - Science advances
SN - 2375-2548
IS - 23
M1 - eadn2955
ER -
ID: 395391459