PMID- 32467328
OWN - NLM
STAT- MEDLINE
DCOM- 20210621
LR  - 20230829
IS  - 1477-9137 (Electronic)
IS  - 0021-9533 (Linking)
VI  - 133
IP  - 12
DP  - 2020 Jun 24
TI  - Investigating cell cycle-dependent gene expression in the context of nuclear 
      architecture at single-allele resolution.
LID - jcs246330 [pii]
LID - 10.1242/jcs.246330 [doi]
AB  - Nuclear architecture is the organization of the genome within a cell nucleus with 
      respect to different nuclear landmarks such as the nuclear lamina, nuclear matrix 
      or nucleoli. Recently, nuclear architecture has emerged as a major regulator of 
      gene expression in mammalian cells. However, studies connecting nuclear 
      architecture with gene expression are largely population-averaged and do not 
      report on the heterogeneity in genome organization or gene expression within a 
      population. In this report we present a method for combining 3D DNA fluorescence 
      in situ hybridization (FISH) with single-molecule RNA FISH (smFISH) and 
      immunofluorescence to study nuclear architecture-dependent gene regulation on a 
      cell-by-cell basis. We further combine our method with imaging-based cell cycle 
      staging to correlate nuclear architecture with gene expression across the cell 
      cycle. We present this in the context of the cyclin-A2 (CCNA2) gene, which has 
      known cell cycle-dependent expression. We show that, across the cell cycle, the 
      expression of a CCNA2 gene copy is stochastic and depends neither on its 
      sub-nuclear position - which usually lies close to nuclear lamina - nor on the 
      expression from other copies of the gene.This article has an associated First 
      Person interview with the first author of the paper.
CI  - (c) 2020. Published by The Company of Biologists Ltd.
FAU - Dhuppar, Shivnarayan
AU  - Dhuppar S
AUID- ORCID: 0000-0001-8772-1721
AD  - TIFR Centre for Interdisciplinary Sciences, Tata Institute of Fundamental 
      Research Hyderabad, 36/P, Gopanpally, Serlingampally Mandal, Hyderabad 500046, 
      Telangana, India shuppar@gmail.com aprotim@tifrh.res.in.
FAU - Mazumder, Aprotim
AU  - Mazumder A
AUID- ORCID: 0000-0002-3443-3010
AD  - TIFR Centre for Interdisciplinary Sciences, Tata Institute of Fundamental 
      Research Hyderabad, 36/P, Gopanpally, Serlingampally Mandal, Hyderabad 500046, 
      Telangana, India shuppar@gmail.com aprotim@tifrh.res.in.
LA  - eng
PT  - Journal Article
PT  - Research Support, Non-U.S. Gov't
DEP - 20200624
PL  - England
TA  - J Cell Sci
JT  - Journal of cell science
JID - 0052457
SB  - IM
MH  - Alleles
MH  - Animals
MH  - Cell Cycle/genetics
MH  - *Cell Nucleus/genetics
MH  - Gene Expression
MH  - In Situ Hybridization, Fluorescence
OTO - NOTNLM
OT  - 3D nuclear architecture
OT  - Cell cycle
OT  - Central dogma
OT  - Cyclin-A2
OT  - DNA fluorescence in situ hybridization
OT  - Immunofluorescence
OT  - Nuclear lamina
OT  - Single-molecule RNA fluorescence in situ hybridization
COIS- Competing interestsThe authors declare no competing or financial interests.
EDAT- 2020/05/30 06:00
MHDA- 2021/06/22 06:00
CRDT- 2020/05/30 06:00
PHST- 2020/03/13 00:00 [received]
PHST- 2020/05/10 00:00 [accepted]
PHST- 2020/05/30 06:00 [pubmed]
PHST- 2021/06/22 06:00 [medline]
PHST- 2020/05/30 06:00 [entrez]
AID - jcs.246330 [pii]
AID - 10.1242/jcs.246330 [doi]
PST - epublish
SO  - J Cell Sci. 2020 Jun 24;133(12):jcs246330. doi: 10.1242/jcs.246330.