Abstract
Genome architecture can be drastically modified through a succession of large-scale rearrangements. In the quest to infer these rearrangement scenarios, it is often the case that the parsimony principal alone does not impose enough constraints. In this paper we make an initial effort towards computing scenarios that respect chromosome conformation, by using Hi-C data to guide our computations. We confirm the validity of a model – along with optimization problems Minimum Local Scenario and Minimum Local Parsimonious Scenario – developed in previous work that is based on a partition into equivalence classes of the adjacencies between syntenic blocks. To accomplish this we show that the quality of a clustering of the adjacencies based on Hi-C data is directly correlated to the quality of a rearrangement scenario that we compute between Drosophila melanogaster and Drosophila yakuba. We evaluate a simple greedy strategy to choose the next rearrangement based on Hi-C, and motivate the study of the solution space of Minimum Local Parsimonious Scenario.
This is a preview of subscription content, log in via an institution to check access.
Access this chapter
Tax calculation will be finalised at checkout
Purchases are for personal use only
References
Altenhoff, A.M., Škunca, N., Glover, N., Train, C.-M., Sueki, A., Piližota, I., Gori, K., Tomiczek, B., Müller, S., Redestig, H., et al.: The OMA orthology database in 2015: function predictions, better plant support, synteny view and other improvements. Nucleic acids research, p. gku1158 (2014)
Bergeron, A., Mixtacki, J., Stoye, J.: A unifying view of genome rearrangements. In: Bücher, P., Moret, B.M.E. (eds.) WABI 2006. LNCS, vol. 4175, pp. 163–173. Springer, Heidelberg (2006). doi:10.1007/11851561_16
Campbell, P.J., Stephens, P.J., Pleasance, E.D., O’Meara, S., Li, H., Santarius, T., Stebbings, L.A., Leroy, C., Edkins, S., Hardy, C., et al.: Identification of somatically acquired rearrangements in cancer using genome-wide massively parallel paired-end sequencing. Nat. Genet. 40(6), 722–729 (2008)
Chambers, E.V., Bickmore, W.A., Semple, C.A.: Divergence of mammalian higher order chromatin structure is associated with developmental Loci. PLoS Comput. Biol. 9(4), e1003017 (2013)
Chauve, C., Gavranovic, H., Ouangraoua, A., Tannier, E.: Yeast ancestral genome reconstructions: the possibilities of computational methods II. J. Comput. Biol. 17(9), 1097–1112 (2010)
Chinwalla, A.T., Cook, L.L., Delehaunty, K.D., Fewell, G.A., Fulton, L.A., Fulton, R.S., Graves, T.A., Hillier, L.D.W., Mardis, E.R., McPherson, J.D., et al.: Initial sequencing and comparative analysis of the mouse genome. Nature 420(6915), 520–562 (2002)
Ghiurcuta, C.G., Moret, B.M.E.: Evaluating synteny for improved comparative studies. Bioinformatics 30(12), i9–i18 (2014)
Lieberman-Aiden, E., van Berkum, N.L., Williams, L., Imakaev, M., Ragoczy, T., Telling, A., Amit, I., Lajoie, B.R., Sabo, P.J., Dorschner, M.O., Sandstrom, R., Bernstein, B., Bender, M.A., Groudine, M., Gnirke, A., Stamatoyannopoulos, J., Mirny, L.A., Lander, E.S., Dekker, J.: Comprehensive mapping of long-range interactions reveals folding principles of the human genome. Science 326(5950), 289–293 (2009)
Park, H.-S., Jun, C.-H.: A simple and fast algorithm for k-medoids clustering. Expert Syst. Appl. 36(2, Part 2), 3336–3341 (2009)
Sexton, T., Yaffe, E., Kenigsberg, E., Bantignies, F., Leblanc, B., Hoichman, M., Parrinello, H., Tanay, A., Cavalli, G.: Three-dimensional folding and functional organization principles of the drosophila genome. Cell 148(3), 458–472 (2012)
Simonaitis, P., Swenson, K.M.: Finding Local Genome Rearrangements. Springer, Heidelberg (2017)
Swenson, K.M., Simonaitis, P., Blanchette, M.: Models and algorithms for genome rearrangement with positional constraints. Algorithms Mol. Biol. 11(1), 13 (2016)
Véron, A.S., Lemaitre, C., Gautier, C., Lacroix, V., Sagot, M.-F.: Close 3D proximity of evolutionary breakpoints argues for the notion of spatial synteny. BMC Genom. 12(1), 303 (2011)
Yaffe, E., Tanay, A.: Probabilistic modeling of Hi-C contact maps eliminates systematic biases to characterize global chromosomal architecture. Nat. Genet. 43(11), 1059–1065 (2011)
Yancopoulos, S., Attie, O., Friedberg, R.: Efficient sorting of genomic permutations by translocation, inversion and block interchange. Bioinformatics 21(16), 3340–3346 (2005)
Zeng, X., Nesbitt, M.J., Pei, J., Wang, K., Vergara, I.A., Chen, N.: Orthocluster: a new tool for mining synteny blocks and applications in comparative genomics. In: Proceedings of the 11th International Conference on Extending database technology: Advances in Database Technology, pp. 656–667. ACM (2008)
Zhang, Y., McCord, R.P., Ho, Y.-J., Lajoie, B.R., Hildebrand, D.G., Simon, A.C., Becker, M.S., Alt, F.W., Dekker, J.: Spatial organization of the mouse genome and its role in recurrent chromosomal translocations. Cell 148(5), 908–921 (2012)
Acknowledgements
The authors would like to thank the reviewers for their helpful comments. Sylvain PULICANI is funded by NUMEV grant AAP 2014-2-028 and EPIGENMED grant ANR-10-LABX-12-01. This work is partially supported by the IBC (Institut de Biologie Computationnelle) (ANR-11-BINF-0002) and by the Labex NUMEV flaship project GEM.
Author information
Authors and Affiliations
Corresponding author
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2017 Springer International Publishing AG
About this paper
Cite this paper
Pulicani, S., Simonaitis, P., Rivals, E., Swenson, K.M. (2017). Rearrangement Scenarios Guided by Chromatin Structure. In: Meidanis, J., Nakhleh, L. (eds) Comparative Genomics. RECOMB-CG 2017. Lecture Notes in Computer Science(), vol 10562. Springer, Cham. https://doi.org/10.1007/978-3-319-67979-2_8
Download citation
DOI: https://doi.org/10.1007/978-3-319-67979-2_8
Published:
Publisher Name: Springer, Cham
Print ISBN: 978-3-319-67978-5
Online ISBN: 978-3-319-67979-2
eBook Packages: Computer ScienceComputer Science (R0)