Contribution of structural variation to genome structure: TAD fusion discovery and ranking
- Published: 09 Mar 2018
- Publisher: Cold Spring Harbor Laboratory
[1] J. H. Gibcus and J. Dekker, \The hierarchy of the 3d genome," Molecular cell, vol. 49, no. 5, pp. 773{782, 2013. [OpenAIRE]
[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. [OpenAIRE]
[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. [OpenAIRE]
[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.
[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. [OpenAIRE]
[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.
Related research
[1] J. H. Gibcus and J. Dekker, \The hierarchy of the 3d genome," Molecular cell, vol. 49, no. 5, pp. 773{782, 2013. [OpenAIRE]
[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. [OpenAIRE]
[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. [OpenAIRE]
[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.
[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. [OpenAIRE]
[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.