publication . Preprint . 2018

Contribution of structural variation to genome structure: TAD fusion discovery and ranking

Linh Huynh; Fereydoun Hormozdiari;
Open Access English
  • Published: 09 Mar 2018
  • Publisher: Cold Spring Harbor Laboratory
Abstract
<jats:title>Abstract</jats:title><jats:p>The significant contribution of structural variants to function, disease, and evolution is widely reported. However, in many cases, the mechanism by which these variants contribute to the phenotype is not well understood. Recent studies reported structural variants that disrupted the three-dimensional genome structure by fusing two topologically associating domains (TADs), such that enhancers from one TAD interacted with genes from the other TAD, and could cause severe developmental disorders. However, no computational method exists for directly scoring and ranking structural variations based on their effect on the three-...
49 references, page 1 of 4

[1] J. H. Gibcus and J. Dekker, \The hierarchy of the 3d genome," Molecular cell, vol. 49, no. 5, pp. 773{782, 2013.

[2] H. K. Long, S. L. Prescott, and J. Wysocka, \Ever-changing landscapes: transcriptional enhancers in development and evolution," Cell, vol. 167, no. 5, pp. 1170{1187, 2016.

[3] B. Bonev and G. Cavalli, \Organization and function of the 3D genome," Nature Reviews Genetics, vol. 17, no. 11, pp. 661{678, 2016.

[4] J. R. Dixon, S. Selvaraj, F. Yue, A. Kim, Y. Li, Y. Shen, M. Hu, J. S. Liu, and B. Ren, \Topological domains in mammalian genomes identi ed by analysis of chromatin interactions," Nature, vol. 485, no. 7398, pp. 376{380, 2012.

[5] L. Schermelleh, R. Heintzmann, and H. Leonhardt, \A guide to super-resolution uorescence microscopy," The Journal of cell biology, vol. 190, no. 2, pp. 165{175, 2010. [OpenAIRE]

[6] A. D. Schmitt, M. Hu, and B. Ren, \Genome-wide mapping and analysis of chromosome architecture," Nature Reviews Molecular Cell Biology, vol. 17, no. 12, pp. 743{755, 2016.

[7] D. Bau and M. A. Marti-Renom, \Structure determination of genomic domains by satisfaction of spatial restraints," Chromosome research, vol. 19, no. 1, pp. 25{35, 2011.

[8] E. de Wit and W. de Laat, \A decade of 3c technologies: insights into nuclear organization," Genes & development, vol. 26, no. 1, pp. 11{24, 2012.

[9] O. Hakim and T. Misteli, \Snapshot: chromosome conformation capture," Cell, vol. 148, no. 5, pp. 1068{1068, 2012.

[10] F. Ay, T. L. Bailey, and W. S. Noble, \Statistical con dence estimation for Hi-C data reveals regulatory chromatin contacts," Genome research, vol. 24, no. 6, pp. 999{1011, 2014.

[11] M. Simonis, P. Klous, E. Splinter, Y. Moshkin, R. Willemsen, E. De Wit, B. Van Steensel, and W. De Laat, \Nuclear organization of active and inactive chromatin domains uncovered by chromosome conformation capture{ on-chip (4c)," Nature genetics, vol. 38, no. 11, pp. 1348{1354, 2006.

[12] J. Dostie, T. A. Richmond, R. A. Arnaout, R. R. Selzer, W. L. Lee, T. A. Honan, E. D. Rubio, A. Krumm, J. Lamb, C. Nusbaum, et al., \Chromosome conformation capture carbon copy (5c): a massively parallel solution for mapping interactions between genomic elements," Genome research, vol. 16, no. 10, pp. 1299{1309, 2006. [OpenAIRE]

[13] J.-M. Belton, R. P. McCord, J. H. Gibcus, N. Naumova, Y. Zhan, and J. Dekker, \Hi-C: a comprehensive technique to capture the conformation of genomes," Methods, vol. 58, no. 3, pp. 268{276, 2012.

[14] N. L. Van Berkum, E. Lieberman-Aiden, L. Williams, M. Imakaev, A. Gnirke, L. A. Mirny, J. Dekker, and E. S. Lander, \Hi-C: a method to study the three-dimensional architecture of genomes.," Journal of visualized experiments: JoVE, no. 39, 2010.

[15] Z. Duan, M. Andronescu, K. Schutz, C. Lee, J. Shendure, S. Fields, W. S. Noble, and C. A. Blau, \A genomewide 3C-method for characterizing the three-dimensional architectures of genomes," Methods, vol. 58, no. 3, pp. 277{288, 2012.

49 references, page 1 of 4
Abstract
<jats:title>Abstract</jats:title><jats:p>The significant contribution of structural variants to function, disease, and evolution is widely reported. However, in many cases, the mechanism by which these variants contribute to the phenotype is not well understood. Recent studies reported structural variants that disrupted the three-dimensional genome structure by fusing two topologically associating domains (TADs), such that enhancers from one TAD interacted with genes from the other TAD, and could cause severe developmental disorders. However, no computational method exists for directly scoring and ranking structural variations based on their effect on the three-...
49 references, page 1 of 4

[1] J. H. Gibcus and J. Dekker, \The hierarchy of the 3d genome," Molecular cell, vol. 49, no. 5, pp. 773{782, 2013.

[2] H. K. Long, S. L. Prescott, and J. Wysocka, \Ever-changing landscapes: transcriptional enhancers in development and evolution," Cell, vol. 167, no. 5, pp. 1170{1187, 2016.

[3] B. Bonev and G. Cavalli, \Organization and function of the 3D genome," Nature Reviews Genetics, vol. 17, no. 11, pp. 661{678, 2016.

[4] J. R. Dixon, S. Selvaraj, F. Yue, A. Kim, Y. Li, Y. Shen, M. Hu, J. S. Liu, and B. Ren, \Topological domains in mammalian genomes identi ed by analysis of chromatin interactions," Nature, vol. 485, no. 7398, pp. 376{380, 2012.

[5] L. Schermelleh, R. Heintzmann, and H. Leonhardt, \A guide to super-resolution uorescence microscopy," The Journal of cell biology, vol. 190, no. 2, pp. 165{175, 2010. [OpenAIRE]

[6] A. D. Schmitt, M. Hu, and B. Ren, \Genome-wide mapping and analysis of chromosome architecture," Nature Reviews Molecular Cell Biology, vol. 17, no. 12, pp. 743{755, 2016.

[7] D. Bau and M. A. Marti-Renom, \Structure determination of genomic domains by satisfaction of spatial restraints," Chromosome research, vol. 19, no. 1, pp. 25{35, 2011.

[8] E. de Wit and W. de Laat, \A decade of 3c technologies: insights into nuclear organization," Genes & development, vol. 26, no. 1, pp. 11{24, 2012.

[9] O. Hakim and T. Misteli, \Snapshot: chromosome conformation capture," Cell, vol. 148, no. 5, pp. 1068{1068, 2012.

[10] F. Ay, T. L. Bailey, and W. S. Noble, \Statistical con dence estimation for Hi-C data reveals regulatory chromatin contacts," Genome research, vol. 24, no. 6, pp. 999{1011, 2014.

[11] M. Simonis, P. Klous, E. Splinter, Y. Moshkin, R. Willemsen, E. De Wit, B. Van Steensel, and W. De Laat, \Nuclear organization of active and inactive chromatin domains uncovered by chromosome conformation capture{ on-chip (4c)," Nature genetics, vol. 38, no. 11, pp. 1348{1354, 2006.

[12] J. Dostie, T. A. Richmond, R. A. Arnaout, R. R. Selzer, W. L. Lee, T. A. Honan, E. D. Rubio, A. Krumm, J. Lamb, C. Nusbaum, et al., \Chromosome conformation capture carbon copy (5c): a massively parallel solution for mapping interactions between genomic elements," Genome research, vol. 16, no. 10, pp. 1299{1309, 2006. [OpenAIRE]

[13] J.-M. Belton, R. P. McCord, J. H. Gibcus, N. Naumova, Y. Zhan, and J. Dekker, \Hi-C: a comprehensive technique to capture the conformation of genomes," Methods, vol. 58, no. 3, pp. 268{276, 2012.

[14] N. L. Van Berkum, E. Lieberman-Aiden, L. Williams, M. Imakaev, A. Gnirke, L. A. Mirny, J. Dekker, and E. S. Lander, \Hi-C: a method to study the three-dimensional architecture of genomes.," Journal of visualized experiments: JoVE, no. 39, 2010.

[15] Z. Duan, M. Andronescu, K. Schutz, C. Lee, J. Shendure, S. Fields, W. S. Noble, and C. A. Blau, \A genomewide 3C-method for characterizing the three-dimensional architectures of genomes," Methods, vol. 58, no. 3, pp. 277{288, 2012.

49 references, page 1 of 4
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