PMID- 37013988
OWN - NLM
STAT- MEDLINE
DCOM- 20230626
LR  - 20231116
IS  - 1362-4962 (Electronic)
IS  - 0305-1048 (Print)
IS  - 0305-1048 (Linking)
VI  - 51
IP  - 11
DP  - 2023 Jun 23
TI  - Probabilistic establishment of speckle-associated inter-chromosomal interactions.
PG  - 5377-5395
LID - 10.1093/nar/gkad211 [doi]
AB  - Inter-chromosomal interactions play a crucial role in genome organization, yet 
      the organizational principles remain elusive. Here, we introduce a novel 
      computational method to systematically characterize inter-chromosomal 
      interactions using in situ Hi-C results from various cell types. Our method 
      successfully identifies two apparently hub-like inter-chromosomal contacts 
      associated with nuclear speckles and nucleoli, respectively. Interestingly, we 
      discover that nuclear speckle-associated inter-chromosomal interactions are 
      highly cell-type invariant with a marked enrichment of cell-type common 
      super-enhancers (CSEs). Validation using DNA Oligopaint fluorescence in situ 
      hybridization (FISH) shows a strong but probabilistic interaction behavior 
      between nuclear speckles and CSE-harboring genomic regions. Strikingly, we find 
      that the likelihood of speckle-CSE associations can accurately predict two 
      experimentally measured inter-chromosomal contacts from Hi-C and Oligopaint DNA 
      FISH. Our probabilistic establishment model well describes the hub-like structure 
      observed at the population level as a cumulative effect of summing individual 
      stochastic chromatin-speckle interactions. Lastly, we observe that CSEs are 
      highly co-occupied by MAZ binding and MAZ depletion leads to significant 
      disorganization of speckle-associated inter-chromosomal contacts. Taken together, 
      our results propose a simple organizational principle of inter-chromosomal 
      interactions mediated by MAZ-occupied CSEs.
CI  - (c) The Author(s) 2023. Published by Oxford University Press on behalf of Nucleic 
      Acids Research.
FAU - Joo, Jaegeon
AU  - Joo J
AD  - Department of Biological Sciences, Korea Advanced Institute of Science and 
      Technology (KAIST), Daejeon 34141, Republic of Korea.
FAU - Cho, Sunghyun
AU  - Cho S
AD  - Department of Mechanical Engineering, Seoul National University, Seoul 08826, 
      Republic of Korea.
FAU - Hong, Sukbum
AU  - Hong S
AD  - Department of Mechanical Engineering, Seoul National University, Seoul 08826, 
      Republic of Korea.
FAU - Min, Sunwoo
AU  - Min S
AD  - Department of Biological Sciences, Korea Advanced Institute of Science and 
      Technology (KAIST), Daejeon 34141, Republic of Korea.
FAU - Kim, Kyukwang
AU  - Kim K
AD  - Department of Biological Sciences, Korea Advanced Institute of Science and 
      Technology (KAIST), Daejeon 34141, Republic of Korea.
FAU - Kumar, Rajeev
AU  - Kumar R
AD  - Department of Chemistry and Chemistry Institute for Functional Materials, Pusan 
      National University, Busan 46241, Republic of Korea.
FAU - Choi, Jeong-Mo
AU  - Choi JM
AUID- ORCID: 0000-0003-2656-4851
AD  - Department of Chemistry and Chemistry Institute for Functional Materials, Pusan 
      National University, Busan 46241, Republic of Korea.
FAU - Shin, Yongdae
AU  - Shin Y
AUID- ORCID: 0000-0003-3441-1986
AD  - Department of Mechanical Engineering, Seoul National University, Seoul 08826, 
      Republic of Korea.
AD  - Interdisciplinary Program in Bioengineering, Seoul National University, 
      Seoul 08826, Republic of Korea.
FAU - Jung, Inkyung
AU  - Jung I
AUID- ORCID: 0000-0002-5885-2754
AD  - Department of Biological Sciences, Korea Advanced Institute of Science and 
      Technology (KAIST), Daejeon 34141, Republic of Korea.
LA  - eng
PT  - Journal Article
PT  - Research Support, Non-U.S. Gov't
PL  - England
TA  - Nucleic Acids Res
JT  - Nucleic acids research
JID - 0411011
RN  - 0 (Chromatin)
RN  - 9007-49-2 (DNA)
SB  - IM
MH  - Humans
MH  - In Situ Hybridization, Fluorescence
MH  - *Chromosomes
MH  - *Chromatin/genetics/metabolism
MH  - Cell Nucleus/metabolism
MH  - DNA/genetics/metabolism
PMC - PMC10287923
EDAT- 2023/04/05 06:00
MHDA- 2023/06/26 06:42
PMCR- 2023/04/04
CRDT- 2023/04/04 07:22
PHST- 2023/03/25 00:00 [accepted]
PHST- 2023/03/08 00:00 [revised]
PHST- 2022/06/19 00:00 [received]
PHST- 2023/06/26 06:42 [medline]
PHST- 2023/04/05 06:00 [pubmed]
PHST- 2023/04/04 07:22 [entrez]
PHST- 2023/04/04 00:00 [pmc-release]
AID - 7103213 [pii]
AID - gkad211 [pii]
AID - 10.1093/nar/gkad211 [doi]
PST - ppublish
SO  - Nucleic Acids Res. 2023 Jun 23;51(11):5377-5395. doi: 10.1093/nar/gkad211.