TY - JOUR
T1 - Differential contributions of nuclear lamina association and genome compartmentalization to gene regulation
AU - Das, Priyojit
AU - San Martin, Rebeca
AU - McCord, Rachel Patton
N1 - Publisher Copyright:
© 2023 The Author(s). Published by Informa UK Limited, trading as Taylor & Francis Group.
PY - 2023
Y1 - 2023
N2 - Chromatin regions that interact with the nuclear lamina are often heterochromatic, repressed in gene expression, and in the spatial B compartment. However, exceptions to this trend allow us to examine the relative impact of lamin association and spatial compartment on gene regulation. Here, we compared lamin association, gene expression, Hi-C, and histone mark datasets from cell lines representing different states of differentiation across different cell-type lineages. With these data, we compare, for example, gene expression differences when a B compartment region is associated with the nuclear lamina in one cell type but not in another. In general, we observed an additive rather than redundant effect of lamin association and compartment status. But, whether compartment status or lamin association had a dominant influence on gene expression varied by cell type. Finally, we identified how compartment and lamin association influence the likelihood of gene induction or repression in response to physicochemical treatment.
AB - Chromatin regions that interact with the nuclear lamina are often heterochromatic, repressed in gene expression, and in the spatial B compartment. However, exceptions to this trend allow us to examine the relative impact of lamin association and spatial compartment on gene regulation. Here, we compared lamin association, gene expression, Hi-C, and histone mark datasets from cell lines representing different states of differentiation across different cell-type lineages. With these data, we compare, for example, gene expression differences when a B compartment region is associated with the nuclear lamina in one cell type but not in another. In general, we observed an additive rather than redundant effect of lamin association and compartment status. But, whether compartment status or lamin association had a dominant influence on gene expression varied by cell type. Finally, we identified how compartment and lamin association influence the likelihood of gene induction or repression in response to physicochemical treatment.
KW - Gene regulation
KW - Hi-C
KW - Nuclear lamina
KW - Nucleus architecture
KW - cell differentiation
UR - http://www.scopus.com/inward/record.url?scp=85151802481&partnerID=8YFLogxK
UR - http://www.scopus.com/inward/citedby.url?scp=85151802481&partnerID=8YFLogxK
U2 - 10.1080/19491034.2023.2197693
DO - 10.1080/19491034.2023.2197693
M3 - Article
C2 - 37017584
AN - SCOPUS:85151802481
SN - 1949-1034
VL - 14
JO - Nucleus
JF - Nucleus
IS - 1
M1 - 2197693
ER -