PMID- 34050337
OWN - NLM
STAT- MEDLINE
DCOM- 20210720
LR  - 20220419
IS  - 1750-2799 (Electronic)
IS  - 1750-2799 (Linking)
VI  - 16
IP  - 7
DP  - 2021 Jul
TI  - Hi-CO: 3D genome structure analysis with nucleosome resolution.
PG  - 3439-3469
LID - 10.1038/s41596-021-00543-z [doi]
AB  - The nucleosome is the basic organizational unit of the genome. The folding 
      structure of nucleosomes is closely related to genome functions, and has been 
      reported to be in dynamic interplay with binding of various nuclear proteins to 
      genomic loci. Here, we describe our high-throughput chromosome conformation 
      capture with nucleosome orientation (Hi-CO) technology to derive 3D nucleosome 
      positions with their orientations at every genomic locus in the nucleus. This 
      technology consists of an experimental procedure for nucleosome proximity 
      analysis and a computational procedure for 3D modeling. The experimental 
      procedure is based on an improved method of high-throughput chromosome 
      conformation capture (Hi-C) analysis. Whereas conventional Hi-C allows spatial 
      proximity analysis among genomic loci with 1-10 kbp resolution, our Hi-CO allows 
      proximity analysis among DNA entry or exit points at every nucleosome locus. This 
      analysis is realized by carrying out ligations among the entry/exit points in 
      every nucleosome in a micrococcal-nuclease-fragmented genome, and by quantifying 
      frequencies of ligation products with next-generation sequencing. Our protocol 
      has enabled this analysis by cleanly excluding unwanted non-ligation products 
      that are abundant owing to the frequent genome fragmentation by micrococcal 
      nuclease. The computational procedure is based on simulated annealing-molecular 
      dynamics, which allows determination of optimized 3D positions and orientations 
      of every nucleosome that satisfies the proximity ligation data sufficiently well. 
      Typically, examination of the Saccharomyces cerevisiae genome with 130 million 
      sequencing reads facilitates analysis of a total of 66,360 nucleosome loci with 
      6.8 nm resolution. The technique requires 2-3 weeks for sequencing library 
      preparation and 2 weeks for simulation.
FAU - Ohno, Masae
AU  - Ohno M
AUID- ORCID: 0000-0002-0860-6790
AD  - Laboratory for Cell Systems Control, RIKEN Center for Biosystems Dynamics 
      Research, Osaka, Japan.
AD  - Institute for Integrated Cell-Material Sciences (iCeMS), Kyoto University, Kyoto, 
      Japan.
FAU - Ando, Tadashi
AU  - Ando T
AD  - Laboratory for Biomolecular Function Simulation, Quantitative Biology Center, 
      RIKEN, Kobe, Japan.
AD  - Department of Applied Electronics, Faculty of Advanced Engineering, Tokyo 
      University of Science, Tokyo, Japan.
FAU - Priest, David G
AU  - Priest DG
AD  - Laboratory for Cell Systems Control, RIKEN Center for Biosystems Dynamics 
      Research, Osaka, Japan.
AD  - Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and 
      Biotechnology Institute, University of Melbourne, Melbourne, VIC, Australia.
FAU - Taniguchi, Yuichi
AU  - Taniguchi Y
AUID- ORCID: 0000-0001-5677-8901
AD  - Laboratory for Cell Systems Control, RIKEN Center for Biosystems Dynamics 
      Research, Osaka, Japan. ytaniguchi@icems.kyoto-u.ac.jp.
AD  - Institute for Integrated Cell-Material Sciences (iCeMS), Kyoto University, Kyoto, 
      Japan. ytaniguchi@icems.kyoto-u.ac.jp.
AD  - Graduate School of Biostudies, Kyoto University, Kyoto, Japan. 
      ytaniguchi@icems.kyoto-u.ac.jp.
LA  - eng
GR  - JPMJPR15F7/MEXT | JST | Precursory Research for Embryonic Science and Technology 
      (PRESTO)/
GR  - 20H00460/MEXT | Japan Society for the Promotion of Science (JSPS)/
GR  - 26650055/MEXT | Japan Society for the Promotion of Science (JSPS)/
GR  - 19H05545/MEXT | Japan Society for the Promotion of Science (JSPS)/
GR  - 20K20458/MEXT | Japan Society for the Promotion of Science (JSPS)/
GR  - 23115005/MEXT | Japan Society for the Promotion of Science (JSPS)/
PT  - Journal Article
PT  - Research Support, Non-U.S. Gov't
DEP - 20210528
PL  - England
TA  - Nat Protoc
JT  - Nature protocols
JID - 101284307
RN  - 0 (Nucleosomes)
SB  - IM
MH  - Base Sequence
MH  - *Genome, Fungal
MH  - High-Throughput Nucleotide Sequencing/*methods
MH  - Molecular Dynamics Simulation
MH  - Nucleosomes/*genetics
MH  - Saccharomyces cerevisiae/*genetics
EDAT- 2021/05/30 06:00
MHDA- 2021/07/21 06:00
CRDT- 2021/05/29 06:14
PHST- 2020/03/27 00:00 [received]
PHST- 2021/03/23 00:00 [accepted]
PHST- 2021/05/30 06:00 [pubmed]
PHST- 2021/07/21 06:00 [medline]
PHST- 2021/05/29 06:14 [entrez]
AID - 10.1038/s41596-021-00543-z [pii]
AID - 10.1038/s41596-021-00543-z [doi]
PST - ppublish
SO  - Nat Protoc. 2021 Jul;16(7):3439-3469. doi: 10.1038/s41596-021-00543-z. Epub 2021 
      May 28.