PMID- 28186153
OWN - NLM
STAT- MEDLINE
DCOM- 20181105
LR  - 20211204
IS  - 2045-2322 (Electronic)
IS  - 2045-2322 (Linking)
VI  - 7
DP  - 2017 Feb 10
TI  - Superresolution imaging of nanoscale chromosome contacts.
PG  - 42422
LID - 10.1038/srep42422 [doi]
LID - 42422
AB  - Co-expression of a specific group of genes requires physical associations among 
      these genes, which form functional chromosomal contacts. While DNA fluorescence 
      in situ hybridization (FISH) pinpoints the localization of genes within the 3D 
      nuclear architecture, direct evidence of physical chromosomal contacts is still 
      lacking. Here, we report a method for the direct visualization of 
      transcription-dependent chromosomal contacts formed in two distinct mechanical 
      states of cells. We prepared open chromatin spreads from isolated nuclei, 
      ensuring 2D rendering of chromosome organization. Superresolution imaging of 
      these chromatin spreads resolved the nanoscale organization of genome contacts. 
      We optimized our imaging method using chromatin spreads from serum+/- cells. We 
      then showed direct visualization of functional gene clusters targeted by YAP 
      (Yes-associated protein) and SRF (Serum response factor) transcription factors. 
      In addition, we showed the association of NF-kappaB bound gene clusters induced by 
      TNF-alpha addition. Furthermore, EpiTect ChIP qPCR results showed that these 
      nanoscale clusters were enriched with corresponding transcription factors. Taken 
      together, our method provides a robust platform to directly visualize and study 
      specific genome-wide chromosomal contacts.
FAU - Wang, Yejun
AU  - Wang Y
AD  - Mechanobiology Institute and Department of Biological Sciences, National 
      University of Singapore 117411, Singapore.
FAU - Ratna, Prasuna
AU  - Ratna P
AD  - Mechanobiology Institute and Department of Biological Sciences, National 
      University of Singapore 117411, Singapore.
AD  - FIRC Institute for Molecular Oncology (IFOM), Milan 20139, Italy.
FAU - Shivashankar, G V
AU  - Shivashankar GV
AD  - Mechanobiology Institute and Department of Biological Sciences, National 
      University of Singapore 117411, Singapore.
AD  - FIRC Institute for Molecular Oncology (IFOM), Milan 20139, Italy.
LA  - eng
PT  - Journal Article
PT  - Research Support, Non-U.S. Gov't
DEP - 20170210
PL  - England
TA  - Sci Rep
JT  - Scientific reports
JID - 101563288
RN  - 0 (Adaptor Proteins, Signal Transducing)
RN  - 0 (Cell Cycle Proteins)
RN  - 0 (Chromatin)
RN  - 0 (NF-kappa B)
RN  - 0 (Phosphoproteins)
RN  - 0 (Serum Response Factor)
RN  - 0 (Transcription Factors)
RN  - 0 (YAP-Signaling Proteins)
RN  - 0 (Yap1 protein, mouse)
SB  - IM
MH  - Adaptor Proteins, Signal Transducing
MH  - Animals
MH  - Cell Cycle Proteins
MH  - Cell Line
MH  - Cell Nucleus
MH  - Chromatin/genetics/metabolism
MH  - Chromatin Immunoprecipitation
MH  - Chromosomes/*genetics/*metabolism
MH  - High-Throughput Nucleotide Sequencing
MH  - Humans
MH  - *In Situ Hybridization, Fluorescence/methods
MH  - Mice
MH  - NF-kappa B/metabolism
MH  - Phosphoproteins
MH  - Protein Binding
MH  - Serum Response Factor/metabolism
MH  - Transcription Factors/metabolism
MH  - YAP-Signaling Proteins
PMC - PMC5301241
COIS- The authors declare no competing financial interests.
EDAT- 2017/02/12 06:00
MHDA- 2018/11/06 06:00
PMCR- 2017/02/10
CRDT- 2017/02/11 06:00
PHST- 2016/08/23 00:00 [received]
PHST- 2017/01/09 00:00 [accepted]
PHST- 2017/02/11 06:00 [entrez]
PHST- 2017/02/12 06:00 [pubmed]
PHST- 2018/11/06 06:00 [medline]
PHST- 2017/02/10 00:00 [pmc-release]
AID - srep42422 [pii]
AID - 10.1038/srep42422 [doi]
PST - epublish
SO  - Sci Rep. 2017 Feb 10;7:42422. doi: 10.1038/srep42422.