Abstract
Genome topologically associating domains (TADs) are mega base pair (Mbp) sized genomic regions that may be the structural and functional units of the genome. To better understand their structural properties and the relationship between structural properties and genetic and epigenetic features, we designed and benchmarked two measures to capture the three-dimensional structural signature of TADs. We modified the original definition of radius of gyration so that it could measure the spatial compactness of TADs weighted by one or more genetic or epigenetic feature(s). Another structural measure we have benchmarked is folding degree. We found correlations between structural measures and genetic and epigenetic features. We obtained similar correlations if considering the spatial compactness of the DNA segments containing transcription start sites, RNA polymerase II, and H3K4me3 peaks. Moreover, we designed a new objective function for reconstructing chromosome 3D structures using multidimensional scaling and compared it with two existent objective functions. The three objective functions have been implemented as web-based and standalone tools. The web server and source code are available at http://dna.cs.miami.edu/3DChrom/.
| Original language | English (US) |
|---|---|
| Title of host publication | Proceedings - 2018 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2018 |
| Editors | Harald Schmidt, David Griol, Haiying Wang, Jan Baumbach, Huiru Zheng, Zoraida Callejas, Xiaohua Hu, Julie Dickerson, Le Zhang |
| Publisher | Institute of Electrical and Electronics Engineers Inc. |
| Pages | 21-28 |
| Number of pages | 8 |
| ISBN (Electronic) | 9781538654880 |
| DOIs | |
| State | Published - Jan 21 2019 |
| Event | 2018 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2018 - Madrid, Spain Duration: Dec 3 2018 → Dec 6 2018 |
Publication series
| Name | Proceedings - 2018 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2018 |
|---|
Conference
| Conference | 2018 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2018 |
|---|---|
| Country | Spain |
| City | Madrid |
| Period | 12/3/18 → 12/6/18 |
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Keywords
- 3D genome
- Hi-C
- Structural Properties.
- Topologically Associating Domains
ASJC Scopus subject areas
- Biomedical Engineering
- Health Informatics
Cite this
Measuring the three-dimensional structural properties of topologically associating domains. / Liu, Tong; Wang, Zheng.
Proceedings - 2018 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2018. ed. / Harald Schmidt; David Griol; Haiying Wang; Jan Baumbach; Huiru Zheng; Zoraida Callejas; Xiaohua Hu; Julie Dickerson; Le Zhang. Institute of Electrical and Electronics Engineers Inc., 2019. p. 21-28 8621459 (Proceedings - 2018 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2018).Research output: Chapter in Book/Report/Conference proceeding › Conference contribution
}
TY - GEN
T1 - Measuring the three-dimensional structural properties of topologically associating domains
AU - Liu, Tong
AU - Wang, Zheng
PY - 2019/1/21
Y1 - 2019/1/21
N2 - Genome topologically associating domains (TADs) are mega base pair (Mbp) sized genomic regions that may be the structural and functional units of the genome. To better understand their structural properties and the relationship between structural properties and genetic and epigenetic features, we designed and benchmarked two measures to capture the three-dimensional structural signature of TADs. We modified the original definition of radius of gyration so that it could measure the spatial compactness of TADs weighted by one or more genetic or epigenetic feature(s). Another structural measure we have benchmarked is folding degree. We found correlations between structural measures and genetic and epigenetic features. We obtained similar correlations if considering the spatial compactness of the DNA segments containing transcription start sites, RNA polymerase II, and H3K4me3 peaks. Moreover, we designed a new objective function for reconstructing chromosome 3D structures using multidimensional scaling and compared it with two existent objective functions. The three objective functions have been implemented as web-based and standalone tools. The web server and source code are available at http://dna.cs.miami.edu/3DChrom/.
AB - Genome topologically associating domains (TADs) are mega base pair (Mbp) sized genomic regions that may be the structural and functional units of the genome. To better understand their structural properties and the relationship between structural properties and genetic and epigenetic features, we designed and benchmarked two measures to capture the three-dimensional structural signature of TADs. We modified the original definition of radius of gyration so that it could measure the spatial compactness of TADs weighted by one or more genetic or epigenetic feature(s). Another structural measure we have benchmarked is folding degree. We found correlations between structural measures and genetic and epigenetic features. We obtained similar correlations if considering the spatial compactness of the DNA segments containing transcription start sites, RNA polymerase II, and H3K4me3 peaks. Moreover, we designed a new objective function for reconstructing chromosome 3D structures using multidimensional scaling and compared it with two existent objective functions. The three objective functions have been implemented as web-based and standalone tools. The web server and source code are available at http://dna.cs.miami.edu/3DChrom/.
KW - 3D genome
KW - Hi-C
KW - Structural Properties.
KW - Topologically Associating Domains
UR - http://www.scopus.com/inward/record.url?scp=85062532012&partnerID=8YFLogxK
UR - http://www.scopus.com/inward/citedby.url?scp=85062532012&partnerID=8YFLogxK
U2 - 10.1109/BIBM.2018.8621459
DO - 10.1109/BIBM.2018.8621459
M3 - Conference contribution
T3 - Proceedings - 2018 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2018
SP - 21
EP - 28
BT - Proceedings - 2018 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2018
A2 - Schmidt, Harald
A2 - Griol, David
A2 - Wang, Haiying
A2 - Baumbach, Jan
A2 - Zheng, Huiru
A2 - Callejas, Zoraida
A2 - Hu, Xiaohua
A2 - Dickerson, Julie
A2 - Zhang, Le
PB - Institute of Electrical and Electronics Engineers Inc.
ER -