Document Open Access Logo

Efficient and Accurate Detection of Topologically Associating Domains from Contact Maps

Authors Abbas Roayaei Ardakany, Stefano Lonardi

PDF
Thumbnail PDF

File

LIPIcs.WABI.2017.22.pdf
  • Filesize: 0.55 MB
  • 11 pages

Document Identifiers

Author Details

Abbas Roayaei Ardakany
Stefano Lonardi

Cite As Get BibTex

Abbas Roayaei Ardakany and Stefano Lonardi. Efficient and Accurate Detection of Topologically Associating Domains from Contact Maps. In 17th International Workshop on Algorithms in Bioinformatics (WABI 2017). Leibniz International Proceedings in Informatics (LIPIcs), Volume 88, pp. 22:1-22:11, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2017) https://doi.org/10.4230/LIPIcs.WABI.2017.22

Abstract

Continuous improvements to high-throughput conformation capture (Hi-C) are revealing richerinformation about the spatial organization of the chromatin and its role in cellular functions.Several studies have confirmed the existence of structural features of the genome 3D organiza-tion that are stable across cell types and conserved across species, calledtopological associatingdomains(TADs). The detection of TADs has become a critical step in the analysis of Hi-C data,e.g., to identify enhancer-promoter associations. Here we presentEast, a novel TAD identifi-cation algorithm based on fast 2D convolution of Haar-like features, that is as accurate as thestate-of-the-art method based on the directionality index, but 75-80x faster.Eastis availablein the public domain at https://github.com/ucrbioinfo/EAST.

Subject Classification

Keywords
  • Chromatin
  • TADs
  • 3D genome
  • Hi-C
  • contact maps

Metrics

  • Access Statistics
  • Total Accesses (updated on a weekly basis)
    0
    PDF Downloads
    0
    Metadata Views

References

  1. Giacomo Cavalli and Tom Misteli. Functional implications of genome topology. Nat. Struct. Mol. Biol., 20(3):290-299, 5 March 2013. Google Scholar
  2. Haiming Chen, Jie Chen, Lindsey A. Muir, Scott Ronquist, Walter Meixner, Mats Ljungman, Thomas Ried, Stephen Smale, and Indika Rajapakse. Functional organization of the human 4D nucleome. Proc. Nat'l Acad. Sci. USA, 112(26):8002-8007, 30 June 2015. Google Scholar
  3. Jie Chen, Alfred O. Hero, 3rd, and Indika Rajapakse. Spectral identification of topological domains. Bioinformatics, 32(14):2151-2158, 15 July 2016. Google Scholar
  4. Emily Crane, Qian Bian, Rachel Patton McCord, Bryan R. Lajoie, Bayly S. Wheeler, Edward J. Ralston, Satoru Uzawa, Job Dekker, and Barbara J. Meyer. Condensin-driven remodelling of X chromosome topology during dosage compensation. Nature, 523(7559):240-244, 9 July 2015. Google Scholar
  5. Franklin C. Crow. Summed-area tables for texture mapping. In Proceedings of the 11th Annual Conference on Computer Graphics and Interactive Techniques, SIGGRAPH'84, pages 207-212, New York, NY, USA, 1984. ACM. Google Scholar
  6. Jesse R. Dixon, Inkyung Jung, Siddarth Selvaraj, Yin Shen, Jessica E. Antosiewicz-Bourget, Ah Young Lee, Zhen Ye, Audrey Kim, Nisha Rajagopal, Wei Xie, Yarui Diao, Jing Liang, Huimin Zhao, Victor V. Lobanenkov, Joseph R. Ecker, James A. Thomson, and Bing Ren. Chromatin architecture reorganization during stem cell differentiation. Nature, 518(7539):331-336, 19 February 2015. Google Scholar
  7. Jesse R. Dixon, Siddarth Selvaraj, Feng Yue, Audrey Kim, Yan Li, Yin Shen, Ming Hu, Jun S. Liu, and Bing Ren. Topological domains in mammalian genomes identified by analysis of chromatin interactions. Nature, 485(7398):376-380, 17 May 2012. Google Scholar
  8. Darya Filippova, Rob Patro, Geet Duggal, and Carl Kingsford. Multiscale identification of topological domains in chromatin. In Algorithms in Bioinformatics, pages 300-312. Springer, Berlin, Heidelberg, 2 September 2013. Google Scholar
  9. James Fraser, Carmelo Ferrai, Andrea M. Chiariello, Markus Schueler, Tiago Rito, Giovanni Laudanno, Mariano Barbieri, Benjamin L. Moore, Dorothee C. A. Kraemer, Stuart Aitken, Sheila Q. Xie, Kelly J. Morris, Masayoshi Itoh, Hideya Kawaji, Ines Jaeger, Yoshihide Hayashizaki, Piero Carninci, Alistair R. R. Forrest, FANTOM Consortium, Colin A. Semple, Josée Dostie, Ana Pombo, and Mario Nicodemi. Hierarchical folding and reorganization of chromosomes are linked to transcriptional changes in cellular differentiation. Mol. Syst. Biol., 11(12):852, 23 December 2015. Google Scholar
  10. David U. Gorkin, Danny Leung, and Bing Ren. The 3D genome in transcriptional regulation and pluripotency. Cell Stem Cell, 14(6):762-775, 5 June 2014. Google Scholar
  11. Daniel Jost, Cédric Vaillant, and Peter Meister. Coupling 1D modifications and 3D nuclear organization: data, models and function. Curr. Opin. Cell Biol., 44:20-27, 2017. Google Scholar
  12. Galih Kunarso, Na-Yu Chia, Justin Jeyakani, Catalina Hwang, Xinyi Lu, Yun-Shen Chan, Huck-Hui Ng, and Guillaume Bourque. Transposable elements have rewired the core regulatory network of human embryonic stem cells. Nat. Genet., 42(7):631-634, 6 June 2010. Google Scholar
  13. Erez Lieberman-Aiden, Nynke L van Berkum, Louise Williams, Maxim Imakaev, Tobias Ragoczy, Agnes Telling, Ido Amit, Bryan R. Lajoie, Peter J. Sabo, Michael O. Dorschner, Richard Sandstrom, Bradley Bernstein, M. A. Bender, Mark Groudine, Andreas Gnirke, John Stamatoyannopoulos, Leonid A Mirny, Eric S. Lander, and Job Dekker. Comprehensive mapping of long-range interactions reveals folding principles of the human genome. Science, 326(5950):289-293, 9 October 2009. Google Scholar
  14. Darío G Lupiáñez, Malte Spielmann, and Stefan Mundlos. Breaking TADs: How alterations of chromatin domains result in disease. Trends Genet., 32(4):225-237, 1 April 2016. Google Scholar
  15. Yiqin Ma, Kiriaki Kanakousaki, and Laura Buttitta. How the cell cycle impacts chromatin architecture and influences cell fate. Front. Genet., 6:19, 3 February 2015. Google Scholar
  16. T. Pederson. Chromatin structure and the cell cycle. Proc. Nat'l Acad. Sci. USA, 69(8):2224-2228, August 1972. Google Scholar
  17. Suhas S. P. Rao, Miriam H. Huntley, Neva C. Durand, Elena K. Stamenova, Ivan D. Bochkov, James T. Robinson, Adrian L. Sanborn, Ido Machol, Arina D. Omer, Eric S. Lander, and Erez Lieberman Aiden. A 3D map of the human genome at kilobase resolution reveals principles of chromatin looping. Cell, 159(7):1665-1680, 18 December 2014. Google Scholar
  18. Tom Sexton, Eitan Yaffe, Ephraim Kenigsberg, Frédéric Bantignies, Benjamin Leblanc, Michael Hoichman, Hugues Parrinello, Amos Tanay, and Giacomo Cavalli. Three-dimensional folding and functional organization principles of the drosophila genome. Cell, 148(3):458-472, 3 February 2012. Google Scholar
  19. Yin Shen, Feng Yue, David F. McCleary, Zhen Ye, Lee Edsall, Samantha Kuan, Ulrich Wagner, Jesse Dixon, Leonard Lee, Victor V. Lobanenkov, and Bing Ren. A map of the cis-regulatory sequences in the mouse genome. Nature, 488(7409):116-120, 2 August 2012. Google Scholar
  20. Hanjun Shin, Yi Shi, Chao Dai, Harianto Tjong, Ke Gong, Frank Alber, and Xianghong Jasmine Zhou. TopDom: an efficient and deterministic method for identifying topological domains in genomes. Nucleic Acids Res., 44(7):e70, 20 April 2016. Google Scholar
  21. P. Viola and M. Jones. Rapid object detection using a boosted cascade of simple features. In Proceedings of the 2001 IEEE Computer Society Conference on Computer Vision and Pattern Recognition. CVPR 2001, volume 1, pages I-511-I-518 vol.1, 2001. Google Scholar
Questions / Remarks / Feedback
X

Feedback for Dagstuhl Publishing


Thanks for your feedback!

Feedback submitted

Could not send message

Please try again later or send an E-mail
© 2023-2024 Schloss Dagstuhl – LZI GmbH About DROPS Imprint Privacy Contact