PMID- 30591009
OWN - NLM
STAT- MEDLINE
DCOM- 20190204
LR  - 20200225
IS  - 1471-2105 (Electronic)
IS  - 1471-2105 (Linking)
VI  - 19
IP  - Suppl 17
DP  - 2018 Dec 28
TI  - Reconstructing high-resolution chromosome three-dimensional structures by Hi-C 
      complex networks.
PG  - 496
LID - 10.1186/s12859-018-2464-z [doi]
LID - 496
AB  - BACKGROUND: Hi-C data have been widely used to reconstruct chromosomal 
      three-dimensional (3D) structures. One of the key limitations of Hi-C is the 
      unclear relationship between spatial distance and the number of Hi-C contacts. 
      Many methods used a fixed parameter when converting the number of Hi-C contacts 
      to wish distances. However, a single parameter cannot properly explain the 
      relationship between wish distances and genomic distances or the  locations of 
      topologically associating domains (TADs). RESULTS: We have addressed one of the 
      key issues of using Hi-C data, that is, the unclear relationship between spatial 
      distances and the number of Hi-C contacts, which is crucial to understand 
      significant biological functions, such as the enhancer-promoter interactions. 
      Specifically, we developed a new method to infer this converting parameter and 
      pairwise Euclidean distances based on the topology of the Hi-C complex network 
      (HiCNet). The inferred distances were modeled by clustering coefficient and 
      multiple other types of constraints. We found that our inferred distances between 
      bead-pairs within the same TAD were apparently smaller than those distances 
      between bead-pairs from different TADs. Our inferred distances had a higher 
      correlation with fluorescence in situ hybridization (FISH) data, fitted the 
      localization patterns of Xist transcripts on DNA, and better matched 156 pairs of 
      protein-enabled long-range chromatin interactions detected by ChIA-PET. Using the 
      inferred distances and another round of optimization, we further reconstructed 
      40 kb high-resolution 3D chromosomal structures of mouse male ES cells. The 
      high-resolution structures successfully illustrate TADs and DNA loops (peaks in 
      Hi-C contact heatmaps) that usually indicate enhancer-promoter interactions. 
      CONCLUSIONS: We developed a novel method to infer the wish distances between DNA 
      bead-pairs from Hi-C contacts. High-resolution 3D structures of chromosomes were 
      built based on the newly-inferred wish distances. This whole process has been 
      implemented as a tool named HiCNet, which is publicly available at 
      http://dna.cs.miami.edu/HiCNet/ .
FAU - Liu, Tong
AU  - Liu T
AD  - Department of Computer Science, University of Miami, 1365 Memorial Drive, Coral 
      Gables, FL, 33124, USA.
FAU - Wang, Zheng
AU  - Wang Z
AD  - Department of Computer Science, University of Miami, 1365 Memorial Drive, Coral 
      Gables, FL, 33124, USA. zheng.wang@miami.edu.
LA  - eng
GR  - R15 GM120650/GM/NIGMS NIH HHS/United States
PT  - Journal Article
DEP - 20181228
PL  - England
TA  - BMC Bioinformatics
JT  - BMC bioinformatics
JID - 100965194
RN  - 0 (RNA, Antisense)
RN  - 0 (RNA, Long Noncoding)
RN  - 0 (XIST non-coding RNA)
SB  - IM
MH  - Animals
MH  - Chromatin Immunoprecipitation
MH  - Chromosomes, Mammalian/*chemistry/*genetics
MH  - Cluster Analysis
MH  - In Situ Hybridization, Fluorescence
MH  - Mice
MH  - Mouse Embryonic Stem Cells/metabolism
MH  - RNA, Antisense/metabolism
MH  - RNA, Long Noncoding/metabolism
PMC - PMC6309071
OTO - NOTNLM
OT  - Chromosomal three-dimensional structure
OT  - Converting parameter
OT  - Hi-C complex network
OT  - Small-world network
OT  - Topologically associating domain
OT  - Wish distance
COIS- AUTHORS' INFORMATION: Not applicable. ETHICS APPROVAL AND CONSENT TO PARTICIPATE: 
      Not applicable. CONSENT FOR PUBLICATION: Not applicable. COMPETING INTERESTS: The 
      authors declare that they have no competing interests. PUBLISHER'S NOTE: Springer 
      Nature remains neutral with regard to jurisdictional claims in published maps and 
      institutional affiliations.
EDAT- 2018/12/29 06:00
MHDA- 2019/02/05 06:00
PMCR- 2018/12/28
CRDT- 2018/12/29 06:00
PHST- 2018/12/29 06:00 [entrez]
PHST- 2018/12/29 06:00 [pubmed]
PHST- 2019/02/05 06:00 [medline]
PHST- 2018/12/28 00:00 [pmc-release]
AID - 10.1186/s12859-018-2464-z [pii]
AID - 2464 [pii]
AID - 10.1186/s12859-018-2464-z [doi]
PST - epublish
SO  - BMC Bioinformatics. 2018 Dec 28;19(Suppl 17):496. doi: 10.1186/s12859-018-2464-z.