Measuring the three-dimensional structural properties of topologically associating domains

Tong Liu, Zheng Wang

Research output: Chapter in Book/Report/Conference proceedingConference contribution

1 Citation (Scopus)

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 languageEnglish (US)
Title of host publicationProceedings - 2018 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2018
EditorsHarald Schmidt, David Griol, Haiying Wang, Jan Baumbach, Huiru Zheng, Zoraida Callejas, Xiaohua Hu, Julie Dickerson, Le Zhang
PublisherInstitute of Electrical and Electronics Engineers Inc.
Pages21-28
Number of pages8
ISBN (Electronic)9781538654880
DOIs
StatePublished - Jan 21 2019
Event2018 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2018 - Madrid, Spain
Duration: Dec 3 2018Dec 6 2018

Publication series

NameProceedings - 2018 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2018

Conference

Conference2018 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2018
CountrySpain
CityMadrid
Period12/3/1812/6/18

Fingerprint

Epigenomics
Structural properties
Genes
Genome
Chromosome Structures
RNA Polymerase II
Transcription Initiation Site
Transcription
Chromosomes
RNA
Base Pairing
DNA
Servers

Keywords

  • 3D genome
  • Hi-C
  • Structural Properties.
  • Topologically Associating Domains

ASJC Scopus subject areas

  • Biomedical Engineering
  • Health Informatics

Cite this

Liu, T., & Wang, Z. (2019). Measuring the three-dimensional structural properties of topologically associating domains. In H. Schmidt, D. Griol, H. Wang, J. Baumbach, H. Zheng, Z. Callejas, X. Hu, J. Dickerson, ... L. Zhang (Eds.), Proceedings - 2018 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2018 (pp. 21-28). [8621459] (Proceedings - 2018 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2018). Institute of Electrical and Electronics Engineers Inc.. https://doi.org/10.1109/BIBM.2018.8621459

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 proceedingConference contribution

Liu, T & Wang, Z 2019, Measuring the three-dimensional structural properties of topologically associating domains. in H Schmidt, D Griol, H Wang, J Baumbach, H Zheng, Z Callejas, X Hu, J Dickerson & L Zhang (eds), Proceedings - 2018 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2018., 8621459, Proceedings - 2018 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2018, Institute of Electrical and Electronics Engineers Inc., pp. 21-28, 2018 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2018, Madrid, Spain, 12/3/18. https://doi.org/10.1109/BIBM.2018.8621459
Liu T, Wang Z. Measuring the three-dimensional structural properties of topologically associating domains. In Schmidt H, Griol D, Wang H, Baumbach J, Zheng H, Callejas Z, Hu X, Dickerson J, Zhang L, editors, Proceedings - 2018 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2018. Institute of Electrical and Electronics Engineers Inc. 2019. p. 21-28. 8621459. (Proceedings - 2018 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2018). https://doi.org/10.1109/BIBM.2018.8621459
Liu, Tong ; Wang, Zheng. / Measuring the three-dimensional structural properties of topologically associating domains. Proceedings - 2018 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2018. editor / 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. pp. 21-28 (Proceedings - 2018 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2018).
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