Review
BibTex RIS Cite

İnsan genomlarında gözlenen karmaşık yapısal yeniden düzenlenme kalıpları

Year 2021, Volume: 4 Issue: 2, 33 - 47, 31.08.2021

Abstract

Genom tarama teknolojilerinin ve ileri biyoinformatik yaklaşımların gelişmesi ve genomların daha yüksek çözünürlükte incelenmesi ile son yıllarda yeni ve kompleks kromozomal düzenlenme türleri tanımlanmıştır. Kromoanagenez terimi adı altında toplanan, oluşum mekanizmalarına ve yapısal özelliklerine göre Kromotripsis, Kromoanasentez ve Kromopleksi gibi alt kategoriler altında incelenen bu tip kompleks yapılar, kanser genomlarında ve bazı konjenital hastalıklarda rapor edilmektedirler. Her bir alt kategorinin birbirinden ayrılabilmesi için belirli özellikler belirlenmiş olmasına rağmen bu kromozomal yeniden düzenlenme fenomenlerinin altyapıları henüz net olarak anlaşılamamıştır. Kromoanagenez doğasının ve hastalıklarla ilişkisinin daha iyi anlaşılabilmesi için yeni biyoinformatik algoritmaların özellikle veri görselleştirme araçlarının geliştirilmesine, şu ana kadar elde edilen bulguların bütünsel olarak analiz edilmesine ve ilgili deneysel modellerin geliştirilmesine ihtiyaç bulunmaktadır. Böylece, bu yapısal fenomenlerin hastalık gelişimlerindeki etkileri, tanı, tedavi ve evrelemedeki potansiyelleri keşfedilebilir.

References

  • Aguilera, A. ve Gómez-González, B. (2008). Genome instability: A mechanistic view of its causes and consequences. Nature Reviews Genetics, 9(3), 204–217. doi:10.1038/nrg2268
  • Arlt, M. F., Wilson, T. E. ve Glover, T. W. (2012). Replication stress and mechanisms of CNV formation. Current Opinion in Genetics and Development, 22(3), 204–210. doi:10.1016/j.gde.2012.01.009
  • Baca, S. C., Prandi, D., Lawrence, M. S., Mosquera, J. M., Romanel, A., Drier, Y., … Garraway, L. A. (2013). Punctuated evolution of prostate cancer genomes. Cell, 153(3), 666–677. doi:10.1016/j.cell.2013.03.021
  • Bertelsen, B., Nazaryan-Petersen, L., Sun, W., Mehrjouy, M. M., Xie, G., Chen, W., … Tümer, Z. (2016). A germline chromothripsis event stably segregating in 11 individuals through three generations. Genetics in Medicine, 18(5), 494–500. doi:10.1038/gim.2015.112
  • Chouard, T. (2010). Revenge of the hopeful monster. Nature, 463(7283), 864–867. doi:10.1038/463864a
  • Ciavarra, G. ve Zacksenhaus, E. (2011). Multiple pathways counteract cell death induced by RB1 loss: Implications for cancer. Cell Cycle, 10(10), 1533–1539. doi:10.4161/cc.10.10.15520
  • Crasta, K., Ganem, N. J., Dagher, R., Lantermann, A. B., Ivanova, E. V., Pan, Y., … Pellman, D. (2012). DNA breaks and chromosome pulverization from errors in mitosis. Nature, 482(7383), 53–58. doi:10.1038/nature10802
  • De Pagter, M. S., Van Roosmalen, M. J., Baas, A. F., Renkens, I., Duran, K. J., Van Binsbergen, E., … Kloosterman, W. P. (2015). Chromothripsis in healthy individuals affects multiple protein-coding genes and can result in severe congenital abnormalities in offspring. American Journal of Human Genetics, 96(4), 651–656. doi:10.1016/j.ajhg.2015.02.005
  • Eldredge, N. (2014). APPENDIX: Punctuated Equilibria: An Alternative to Phyletic Gradualism. Time Frames. doi:10.1515/9781400860296.193
  • Feuk, L., MacDonald, J. R., Tang, T., Carson, A. R., Li, M., Rao, G., … Scherer, S. W. (2005). Discovery of human inversion polymorphisms by comparative analysis of human and chimpanzee DNA sequence assemblies. PLoS Genetics, 1(4), 0489–0498. doi:10.1371/journal.pgen.0010056
  • Forment, J. V., Kaidi, A. ve Jackson, S. P. (2012). Chromothripsis and cancer: Causes and consequences of chromosome shattering. Nature Reviews Cancer, 12(10), 663–670. doi:10.1038/nrc3352
  • Fridman, J. S. ve Lowe, S. W. (2003). Control of apoptosis by p53. Oncogene, 22(56 REV. ISS. 8), 9030–9040. doi:10.1038/sj.onc.1207116
  • Fukami, M., Shima, H., Suzuki, E., Ogata, T., Matsubara, K. ve Kamimaki, T. (2017). Catastrophic cellular events leading to complex chromosomal rearrangements in the germline. Clinical Genetics, 91(5), 653–660. doi:10.1111/cge.12928
  • Ghavi-Helm, Y., Jankowski, A., Meiers, S., Viales, R. R., Korbel, J. O. ve Furlong, E. E. M. (2019). Highly rearranged chromosomes reveal uncoupling between genome topology and gene expression. Nature Genetics, 51(8), 1272–1282. doi:10.1038/s41588-019-0462-3
  • Goldschmidt, R. (1915). The material basis of evolution. Nature, 95(2385), 550–551. doi:10.1038/095550b0 GOLDSCHMIDT, R. B. (1951). Chromosomes and genes. Cold Spring Harbor symposia on quantitative biology, 16, 1–11. doi:10.1101/SQB.1951.016.01.003
  • Gonzalez-Sandoval, A. ve Gasser, S. M. (2016). On TADs and LADs: Spatial Control Over Gene Expression. Trends in Genetics, 32(8), 485–495. doi:10.1016/j.tig.2016.05.004
  • Gould, S. J. ve Eldredge, N. (1993). Punctuated equilibrium comes of age. Nature, 366(6452), 223–227. doi:10.1038/366223a0
  • Gu, H., Jiang, J. hui, Li, J. ying, Zhang, Y. nan, Dong, X. sheng, Huang, Y. yu, … Chen, Z. (2013). A Familial Cri-du-Chat/5p Deletion Syndrome Resulted from Rare Maternal Complex Chromosomal Rearrangements (CCRs) and/or Possible Chromosome 5p Chromothripsis. PLoS ONE, 8(10). doi:10.1371/journal.pone.0076985
  • Hadi, K., Yao, X., Behr, J. M., Deshpande, A., Xanthopoulakis, C., Tian, H., … Imielinski, M. (2020). Distinct Classes of Complex Structural Variation Uncovered across Thousands of Cancer Genome Graphs. Cell, 183(1), 197-210.e32. doi:10.1016/j.cell.2020.08.006
  • Haffner, M. C., Aryee, M. J., Toubaji, A., Esopi, D. M., Albadine, R., Gurel, B., … Yegnasubramanian, S. (2010). Androgen-induced TOP2B-mediated double-strand breaks and prostate cancer gene rearrangements. Nature Genetics, 42(8), 668–675. doi:10.1038/ng.613
  • Heng, H. H. Q. (2009). The genome-centric concept: Resynthesis of evolutionary theory. BioEssays, 31(5), 512–525. doi:10.1002/bies.200800182
  • Heng, H. H. Q., Liu, G., Stevens, J. B., Bremer, S. W., Ye, K. J., Abdallah, B. Y., … Ye, C. J. (2011). Decoding the genome beyond sequencing: The new phase of genomic research. Genomics, 98(4), 242–252. doi:10.1016/j.ygeno.2011.05.008
  • Hoelzer, G. A., Smith, E. ve Pepper, J. W. (2006). On the logical relationship between natural selection and self-organization. Journal of Evolutionary Biology, 19(6), 1785–1794. doi:10.1111/j.1420-9101.2006.01177.x
  • Holland, A. J. ve Cleveland, D. W. (2012). Chromoanagenesis and cancer: Mechanisms and consequences of localized, complex chromosomal rearrangements. Nature Medicine, 18(11), 1630–1638. doi:10.1038/nm.2988
  • Huang, Y., Jiang, L., Yi, Q., Lv, L., Wang, Z., Zhao, X., … Shi, Q. (2012). Lagging chromosomes entrapped in micronuclei are not “lost” by cells. Cell Research, 22(5), 932–935. doi:10.1038/cr.2012.26
  • Iliakis, G., Murmann, T. ve Soni, A. (2015). Alternative end-joining repair pathways are the ultimate backup for abrogated classical non-homologous end-joining and homologous recombination repair: Implications for the formation of chromosome translocations. Mutation Research - Genetic Toxicology and Environmental Mutagenesis, 793, 166–175. doi:10.1016/j.mrgentox.2015.07.001
  • Jones, M. J. K. ve Jallepalli, P. V. (2012). Chromothripsis: Chromosomes in Crisis. Developmental Cell, 23(5), 908–917. doi:10.1016/j.devcel.2012.10.010
  • Kass, E. M., Moynahan, M. E. ve Jasin, M. (2016). When Genome Maintenance Goes Badly Awry. Molecular Cell, 62(5), 777–787. doi:10.1016/j.molcel.2016.05.021
  • Kinsella, M., Patel, A. ve Bafna, V. (2014). The elusive evidence for chromothripsis. Nucleic Acids Research, 42(13), 8231–8242. doi:10.1093/nar/gku525
  • Korbel, J. O. ve Campbell, P. J. (2013, 14 Mart). Criteria for inference of chromothripsis in cancer genomes. Cell. Cell. doi:10.1016/j.cell.2013.02.023
  • Leibowitz, M. L., Zhang, C. Z. ve Pellman, D. (2015). Chromothripsis: A New Mechanism for Rapid Karyotype Evolution. Annual Review of Genetics, 49, 183–211. doi:10.1146/annurev-genet-120213-092228
  • Liu, B., Conroy, J. M., Morrison, C. D., Odunsi, A. O., Qin, M., Wei, L., … Wang, J. (2015). Structural variation discovery in the cancer genome using next generation sequencing: Computational solutions and perspectives. Oncotarget, 6(8), 5477–5489. doi:10.18632/oncotarget.3491
  • Liu, G., Stevens, J. B., Horne, S. D., Abdallah, B. Y., Ye, K. J., Bremer, S. W., … Heng, H. H. (2014). Genome chaos: Survival strategy during crisis. Cell Cycle, 13(4), 528–537. doi:10.4161/cc.27378
  • Liu, P., Erez, A., Nagamani, S. C. S., Dhar, S. U., Kołodziejska, K. E., Dharmadhikari, A. V., … Bi, W. (2011). Chromosome catastrophes involve replication mechanisms generating complex genomic rearrangements. Cell, 146(6), 889–903. doi:10.1016/j.cell.2011.07.042
  • Liu, S., Kwon, M., Mannino, M., Yang, N., Renda, F., Khodjakov, A. ve Pellman, D. (2018). Nuclear envelope assembly defects link mitotic errors to chromothripsis. Nature, 561(7724), 551–555. doi:10.1038/s41586-018-0534-z
  • Luijten, M. N. H., Lee, J. X. T. ve Crasta, K. C. (2018). Mutational game changer: Chromothripsis and its emerging relevance to cancer. Mutation Research - Reviews in Mutation Research, 777, 29–51. doi:10.1016/j.mrrev.2018.06.004
  • Lupiáñez, D. G., Spielmann, M. ve Mundlos, S. (2016). Breaking TADs: How Alterations of Chromatin Domains Result in Disease. Trends in Genetics, 32(4), 225–237. doi:10.1016/j.tig.2016.01.003
  • Lupski, J. R. (2007). Structural Variation in the Human Genome. New England Journal of Medicine, 356(11), 1169–1171. doi:10.1056/nejmcibr067658
  • Lupski, J. R. (2015). Structural variation mutagenesis of the human genome: Impact on disease and evolution. Environmental and Molecular Mutagenesis, 56(5), 419–436. doi:10.1002/em.21943
  • Ly, P., Teitz, L. S., Kim, D. H., Shoshani, O., Skaletsky, H., Fachinetti, D., … Cleveland, D. W. (2017). Selective y centromere inactivation triggers chromosome shattering in micronuclei and repair by non-homologous end joining. Nature Cell Biology, 19(1), 68–75. doi:10.1038/ncb3450
  • Maher, C. A. ve Wilson, R. K. (2012). Chromothripsis and human disease: Piecing together the shattering process. Cell, 148(1–2), 29–32. doi:10.1016/j.cell.2012.01.006
  • Malhotra, D. ve Sebat, J. (2012). CNVs: Harbingers of a rare variant revolution in psychiatric genetics. Cell, 148(6), 1223–1241. doi:10.1016/j.cell.2012.02.039
  • Mardin, B. R., Drainas, A. P., Waszak, S. M., Weischenfeldt, J., Isokane, M., Stütz, A. M., … Korbel, J. O. (2015). A cell‐based model system links chromothripsis with hyperploidy. Molecular Systems Biology, 11(9), 828. doi:10.15252/msb.20156505
  • Masset, H., Hestand, M. S., Van Esch, H., Kleinfinger, P., Plaisancié, J., Afenjar, A., … Vermeesch, J. R. (2016). A Distinct Class of Chromoanagenesis Events Characterized by Focal Copy Number Gains. Human Mutation, 37(7), 661–668. doi:10.1002/humu.22984
  • McDermott, D. H., Gao, J. L., Liu, Q., Siwicki, M., Martens, C., Jacobs, P., … Murphy, P. M. (2015). Chromothriptic cure of WHIM syndrome. Cell, 160(4), 686–699. doi:10.1016/j.cell.2015.01.014
  • Morishita, M., Muramatsu, T., Suto, Y., Hirai, M., Konishi, T., Hayashi, S., … Inazawa, J. (2016). Chromothripsis-like chromosomal rearrangements induced by ionizing radiation using proton microbeam Irradiation system. Oncotarget, 7(9), 10182–10192. doi:10.18632/oncotarget.7186
  • Notta, F., Chan-Seng-Yue, M., Lemire, M., Li, Y., Wilson, G. W., Connor, A. A., … Gallinger, S. (2016). A renewed model of pancreatic cancer evolution based on genomic rearrangement patterns. Nature, 538(7625), 378–382. doi:10.1038/nature19823
  • Passerini, V., Ozeri-Galai, E., De Pagter, M. S., Donnelly, N., Schmalbrock, S., Kloosterman, W. P., … Storchová, Z. (2016). The presence of extra chromosomes leads to genomic instability. Nature Communications, 7(1), 1–12. doi:10.1038/ncomms10754
  • Pellestor, F. (y.y.). Chromothripsis : methods and protocols, 367.
  • Pellestor, F. (2019). Chromoanagenesis: Cataclysms behind complex chromosomal rearrangements. Molecular Cytogenetics, 12(1), 1–12. doi:10.1186/s13039-019-0415-7
  • Pellestor, F. ve Gatinois, V. (2018). Chromoanasynthesis: Another way for the formation of complex chromosomal abnormalities in human reproduction. Human Reproduction, 33(8), 1381–1387. doi:10.1093/humrep/dey231
  • Pellestor, F. ve Gatinois, V. (2020, 28 Ocak). Chromoanagenesis: A piece of the macroevolution scenario. Molecular Cytogenetics. BioMed Central. doi:10.1186/s13039-020-0470-0
  • Pellestor, F., Gatinois, V., Puechberty, J., Geneviève, D. ve Lefort, G. (2014). Chromothripsis: Potential origin in gametogenesis and preimplantation cell divisions. A review. Fertility and Sterility, 102(6), 1785–1796. doi:10.1016/j.fertnstert.2014.09.006
  • Rausch, T., Jones, D. T. W., Zapatka, M., Stütz, A. M., Zichner, T., Weischenfeldt, J., … Korbel, J. O. (2012). Genome sequencing of pediatric medulloblastoma links catastrophic DNA rearrangements with TP53 mutations. Cell, 148(1–2), 59–71. doi:10.1016/j.cell.2011.12.013
  • Rode, A., Maass, K. K., Willmund, K. V., Lichter, P. ve Ernst, A. (2016). Chromothripsis in cancer cells: An update. International Journal of Cancer, 138(10), 2322–2333. doi:10.1002/ijc.29888
  • Rubin, M. A., Maher, C. A. ve Chinnaiyan, A. M. (2011). Common gene rearrangements in prostate cancer. Journal of Clinical Oncology, 29(27), 3659–3668. doi:10.1200/JCO.2011.35.1916
  • Shen, M. M. (2013). Chromoplexy: A New Category of Complex Rearrangements in the Cancer Genome. Cancer Cell, 23(5), 567–569. doi:10.1016/j.ccr.2013.04.025
  • Shlien, A. ve Malkin, D. (2009). Copy number variations and cancer. Genome Medicine, 1(6). doi:10.1186/gm62
  • So, A., Le Guen, T., Lopez, B. S. ve Guirouilh-Barbat, J. (2017). Genomic rearrangements induced by unscheduled DNA double strand breaks in somatic mammalian cells. FEBS Journal, 284(15), 2324–2344. doi:10.1111/febs.14053
  • Stankiewicz, P. ve Lupski, J. R. (2010). Structural variation in the human genome and its role in disease. Annual Review of Medicine, 61, 437–455. doi:10.1146/annurev-med-100708-204735
  • Stephens, P. J., Greenman, C. D., Fu, B., Yang, F., Bignell, G. R., Mudie, L. J., … Campbell, P. J. (2011). Massive genomic rearrangement acquired in a single catastrophic event during cancer development. Cell, 144(1), 27–40. doi:10.1016/j.cell.2010.11.055
  • Terradas, M., Martín, M. ve Genescà, A. (2016). Impaired nuclear functions in micronuclei results in genome instability and chromothripsis. Archives of Toxicology, 90(11), 2657–2667. doi:10.1007/s00204-016-1818-4
  • Terradas, M., Martín, M., Tusell, L. ve Genescà, A. (2010). Genetic activities in micronuclei: Is the DNA entrapped in micronuclei lost for the cell? Mutation Research - Reviews in Mutation Research, 705(1), 60–67. doi:10.1016/j.mrrev.2010.03.004
  • Theißen, G. (2006). The proper place of hopeful monsters in evolutionary biology. Theory in Biosciences, 124(3–4), 349–369. doi:10.1016/j.thbio.2005.11.002
  • Theißen, G. (2009). Saltational evolution: Hopeful monsters are here to stay. Theory in Biosciences, 128(1), 43–51. doi:10.1007/s12064-009-0058-z
  • Tommerup, N. (1993). Mendelian cytogenetics. Chromosome rearrangements associated with mendelian disorders. Journal of Medical Genetics, 30(9), 713–727. doi:10.1136/jmg.30.9.713
  • Tubio, J. M. C. ve Estivill, X. (2011). Cancer: When catastrophe strikes a cell. Nature, 470(7335), 476–477. doi:10.1038/470476a Van Binsbergen, E., Hochstenbach, R., Giltay, J. ve Swinkels, M. (2012). Unstable transmission of a familial complex chromosome rearrangement. American Journal of Medical Genetics, Part A, 158 A(11), 2888–2893. doi:10.1002/ajmg.a.35580
  • Venkatesan, S., Natarajan, A. T. ve Hande, M. P. (2015). Chromosomal instability-mechanisms and consequences. Mutation Research - Genetic Toxicology and Environmental Mutagenesis, 793, 176–184. doi:10.1016/j.mrgentox.2015.08.008
  • Vogelstein, B., Lane, D. ve Levine, A. J. (2000). Surfing the p53 network. Nature, 408(6810), 307–310. doi:10.1038/35042675
  • Weckselblatt, B., Hermetz, K. E. ve Rudd, M. K. (2015). Unbalanced translocations arise from diverse mutational mechanisms including chromothripsis. Genome Research, 25(7), 937–947. doi:10.1101/gr.191247.115
  • Willis, N. A., Rass, E. ve Scully, R. (2015). Deciphering the Code of the Cancer Genome: Mechanisms of Chromosome Rearrangement. Trends in Cancer, 1(4), 217–230. doi:10.1016/j.trecan.2015.10.007
  • Xu, B., Sun, Z., Liu, Z., Guo, H., Liu, Q., Jiang, H., … Shao, C. (2011). Replication stress induces micronuclei comprising of aggregated DNA double-strand breaks. PLoS ONE, 6(4), e18618. doi:10.1371/journal.pone.0018618
  • Ye, C. J., Stilgenbauer, L., Moy, A., Liu, G. ve Heng, H. H. (2019). What Is Karyotype Coding and Why Is Genomic Topology Important for Cancer and Evolution? Frontiers in Genetics, 10, 1082. doi:10.3389/fgene.2019.01082
  • Zepeda-Mendoza, C. J. ve Morton, C. C. (2019). The Iceberg under Water: Unexplored Complexity of Chromoanagenesis in Congenital Disorders. American Journal of Human Genetics, 104(4), 565–577. doi:10.1016/j.ajhg.2019.02.024
  • Zhang, C. Z., Leibowitz, M. L. ve Pellman, D. (2013). Chromothripsis and beyond: Rapid genome evolution from complex chromosomal rearrangements. Genes and Development, 27(23), 2513–2530. doi:10.1101/gad.229559.113
Year 2021, Volume: 4 Issue: 2, 33 - 47, 31.08.2021

Abstract

References

  • Aguilera, A. ve Gómez-González, B. (2008). Genome instability: A mechanistic view of its causes and consequences. Nature Reviews Genetics, 9(3), 204–217. doi:10.1038/nrg2268
  • Arlt, M. F., Wilson, T. E. ve Glover, T. W. (2012). Replication stress and mechanisms of CNV formation. Current Opinion in Genetics and Development, 22(3), 204–210. doi:10.1016/j.gde.2012.01.009
  • Baca, S. C., Prandi, D., Lawrence, M. S., Mosquera, J. M., Romanel, A., Drier, Y., … Garraway, L. A. (2013). Punctuated evolution of prostate cancer genomes. Cell, 153(3), 666–677. doi:10.1016/j.cell.2013.03.021
  • Bertelsen, B., Nazaryan-Petersen, L., Sun, W., Mehrjouy, M. M., Xie, G., Chen, W., … Tümer, Z. (2016). A germline chromothripsis event stably segregating in 11 individuals through three generations. Genetics in Medicine, 18(5), 494–500. doi:10.1038/gim.2015.112
  • Chouard, T. (2010). Revenge of the hopeful monster. Nature, 463(7283), 864–867. doi:10.1038/463864a
  • Ciavarra, G. ve Zacksenhaus, E. (2011). Multiple pathways counteract cell death induced by RB1 loss: Implications for cancer. Cell Cycle, 10(10), 1533–1539. doi:10.4161/cc.10.10.15520
  • Crasta, K., Ganem, N. J., Dagher, R., Lantermann, A. B., Ivanova, E. V., Pan, Y., … Pellman, D. (2012). DNA breaks and chromosome pulverization from errors in mitosis. Nature, 482(7383), 53–58. doi:10.1038/nature10802
  • De Pagter, M. S., Van Roosmalen, M. J., Baas, A. F., Renkens, I., Duran, K. J., Van Binsbergen, E., … Kloosterman, W. P. (2015). Chromothripsis in healthy individuals affects multiple protein-coding genes and can result in severe congenital abnormalities in offspring. American Journal of Human Genetics, 96(4), 651–656. doi:10.1016/j.ajhg.2015.02.005
  • Eldredge, N. (2014). APPENDIX: Punctuated Equilibria: An Alternative to Phyletic Gradualism. Time Frames. doi:10.1515/9781400860296.193
  • Feuk, L., MacDonald, J. R., Tang, T., Carson, A. R., Li, M., Rao, G., … Scherer, S. W. (2005). Discovery of human inversion polymorphisms by comparative analysis of human and chimpanzee DNA sequence assemblies. PLoS Genetics, 1(4), 0489–0498. doi:10.1371/journal.pgen.0010056
  • Forment, J. V., Kaidi, A. ve Jackson, S. P. (2012). Chromothripsis and cancer: Causes and consequences of chromosome shattering. Nature Reviews Cancer, 12(10), 663–670. doi:10.1038/nrc3352
  • Fridman, J. S. ve Lowe, S. W. (2003). Control of apoptosis by p53. Oncogene, 22(56 REV. ISS. 8), 9030–9040. doi:10.1038/sj.onc.1207116
  • Fukami, M., Shima, H., Suzuki, E., Ogata, T., Matsubara, K. ve Kamimaki, T. (2017). Catastrophic cellular events leading to complex chromosomal rearrangements in the germline. Clinical Genetics, 91(5), 653–660. doi:10.1111/cge.12928
  • Ghavi-Helm, Y., Jankowski, A., Meiers, S., Viales, R. R., Korbel, J. O. ve Furlong, E. E. M. (2019). Highly rearranged chromosomes reveal uncoupling between genome topology and gene expression. Nature Genetics, 51(8), 1272–1282. doi:10.1038/s41588-019-0462-3
  • Goldschmidt, R. (1915). The material basis of evolution. Nature, 95(2385), 550–551. doi:10.1038/095550b0 GOLDSCHMIDT, R. B. (1951). Chromosomes and genes. Cold Spring Harbor symposia on quantitative biology, 16, 1–11. doi:10.1101/SQB.1951.016.01.003
  • Gonzalez-Sandoval, A. ve Gasser, S. M. (2016). On TADs and LADs: Spatial Control Over Gene Expression. Trends in Genetics, 32(8), 485–495. doi:10.1016/j.tig.2016.05.004
  • Gould, S. J. ve Eldredge, N. (1993). Punctuated equilibrium comes of age. Nature, 366(6452), 223–227. doi:10.1038/366223a0
  • Gu, H., Jiang, J. hui, Li, J. ying, Zhang, Y. nan, Dong, X. sheng, Huang, Y. yu, … Chen, Z. (2013). A Familial Cri-du-Chat/5p Deletion Syndrome Resulted from Rare Maternal Complex Chromosomal Rearrangements (CCRs) and/or Possible Chromosome 5p Chromothripsis. PLoS ONE, 8(10). doi:10.1371/journal.pone.0076985
  • Hadi, K., Yao, X., Behr, J. M., Deshpande, A., Xanthopoulakis, C., Tian, H., … Imielinski, M. (2020). Distinct Classes of Complex Structural Variation Uncovered across Thousands of Cancer Genome Graphs. Cell, 183(1), 197-210.e32. doi:10.1016/j.cell.2020.08.006
  • Haffner, M. C., Aryee, M. J., Toubaji, A., Esopi, D. M., Albadine, R., Gurel, B., … Yegnasubramanian, S. (2010). Androgen-induced TOP2B-mediated double-strand breaks and prostate cancer gene rearrangements. Nature Genetics, 42(8), 668–675. doi:10.1038/ng.613
  • Heng, H. H. Q. (2009). The genome-centric concept: Resynthesis of evolutionary theory. BioEssays, 31(5), 512–525. doi:10.1002/bies.200800182
  • Heng, H. H. Q., Liu, G., Stevens, J. B., Bremer, S. W., Ye, K. J., Abdallah, B. Y., … Ye, C. J. (2011). Decoding the genome beyond sequencing: The new phase of genomic research. Genomics, 98(4), 242–252. doi:10.1016/j.ygeno.2011.05.008
  • Hoelzer, G. A., Smith, E. ve Pepper, J. W. (2006). On the logical relationship between natural selection and self-organization. Journal of Evolutionary Biology, 19(6), 1785–1794. doi:10.1111/j.1420-9101.2006.01177.x
  • Holland, A. J. ve Cleveland, D. W. (2012). Chromoanagenesis and cancer: Mechanisms and consequences of localized, complex chromosomal rearrangements. Nature Medicine, 18(11), 1630–1638. doi:10.1038/nm.2988
  • Huang, Y., Jiang, L., Yi, Q., Lv, L., Wang, Z., Zhao, X., … Shi, Q. (2012). Lagging chromosomes entrapped in micronuclei are not “lost” by cells. Cell Research, 22(5), 932–935. doi:10.1038/cr.2012.26
  • Iliakis, G., Murmann, T. ve Soni, A. (2015). Alternative end-joining repair pathways are the ultimate backup for abrogated classical non-homologous end-joining and homologous recombination repair: Implications for the formation of chromosome translocations. Mutation Research - Genetic Toxicology and Environmental Mutagenesis, 793, 166–175. doi:10.1016/j.mrgentox.2015.07.001
  • Jones, M. J. K. ve Jallepalli, P. V. (2012). Chromothripsis: Chromosomes in Crisis. Developmental Cell, 23(5), 908–917. doi:10.1016/j.devcel.2012.10.010
  • Kass, E. M., Moynahan, M. E. ve Jasin, M. (2016). When Genome Maintenance Goes Badly Awry. Molecular Cell, 62(5), 777–787. doi:10.1016/j.molcel.2016.05.021
  • Kinsella, M., Patel, A. ve Bafna, V. (2014). The elusive evidence for chromothripsis. Nucleic Acids Research, 42(13), 8231–8242. doi:10.1093/nar/gku525
  • Korbel, J. O. ve Campbell, P. J. (2013, 14 Mart). Criteria for inference of chromothripsis in cancer genomes. Cell. Cell. doi:10.1016/j.cell.2013.02.023
  • Leibowitz, M. L., Zhang, C. Z. ve Pellman, D. (2015). Chromothripsis: A New Mechanism for Rapid Karyotype Evolution. Annual Review of Genetics, 49, 183–211. doi:10.1146/annurev-genet-120213-092228
  • Liu, B., Conroy, J. M., Morrison, C. D., Odunsi, A. O., Qin, M., Wei, L., … Wang, J. (2015). Structural variation discovery in the cancer genome using next generation sequencing: Computational solutions and perspectives. Oncotarget, 6(8), 5477–5489. doi:10.18632/oncotarget.3491
  • Liu, G., Stevens, J. B., Horne, S. D., Abdallah, B. Y., Ye, K. J., Bremer, S. W., … Heng, H. H. (2014). Genome chaos: Survival strategy during crisis. Cell Cycle, 13(4), 528–537. doi:10.4161/cc.27378
  • Liu, P., Erez, A., Nagamani, S. C. S., Dhar, S. U., Kołodziejska, K. E., Dharmadhikari, A. V., … Bi, W. (2011). Chromosome catastrophes involve replication mechanisms generating complex genomic rearrangements. Cell, 146(6), 889–903. doi:10.1016/j.cell.2011.07.042
  • Liu, S., Kwon, M., Mannino, M., Yang, N., Renda, F., Khodjakov, A. ve Pellman, D. (2018). Nuclear envelope assembly defects link mitotic errors to chromothripsis. Nature, 561(7724), 551–555. doi:10.1038/s41586-018-0534-z
  • Luijten, M. N. H., Lee, J. X. T. ve Crasta, K. C. (2018). Mutational game changer: Chromothripsis and its emerging relevance to cancer. Mutation Research - Reviews in Mutation Research, 777, 29–51. doi:10.1016/j.mrrev.2018.06.004
  • Lupiáñez, D. G., Spielmann, M. ve Mundlos, S. (2016). Breaking TADs: How Alterations of Chromatin Domains Result in Disease. Trends in Genetics, 32(4), 225–237. doi:10.1016/j.tig.2016.01.003
  • Lupski, J. R. (2007). Structural Variation in the Human Genome. New England Journal of Medicine, 356(11), 1169–1171. doi:10.1056/nejmcibr067658
  • Lupski, J. R. (2015). Structural variation mutagenesis of the human genome: Impact on disease and evolution. Environmental and Molecular Mutagenesis, 56(5), 419–436. doi:10.1002/em.21943
  • Ly, P., Teitz, L. S., Kim, D. H., Shoshani, O., Skaletsky, H., Fachinetti, D., … Cleveland, D. W. (2017). Selective y centromere inactivation triggers chromosome shattering in micronuclei and repair by non-homologous end joining. Nature Cell Biology, 19(1), 68–75. doi:10.1038/ncb3450
  • Maher, C. A. ve Wilson, R. K. (2012). Chromothripsis and human disease: Piecing together the shattering process. Cell, 148(1–2), 29–32. doi:10.1016/j.cell.2012.01.006
  • Malhotra, D. ve Sebat, J. (2012). CNVs: Harbingers of a rare variant revolution in psychiatric genetics. Cell, 148(6), 1223–1241. doi:10.1016/j.cell.2012.02.039
  • Mardin, B. R., Drainas, A. P., Waszak, S. M., Weischenfeldt, J., Isokane, M., Stütz, A. M., … Korbel, J. O. (2015). A cell‐based model system links chromothripsis with hyperploidy. Molecular Systems Biology, 11(9), 828. doi:10.15252/msb.20156505
  • Masset, H., Hestand, M. S., Van Esch, H., Kleinfinger, P., Plaisancié, J., Afenjar, A., … Vermeesch, J. R. (2016). A Distinct Class of Chromoanagenesis Events Characterized by Focal Copy Number Gains. Human Mutation, 37(7), 661–668. doi:10.1002/humu.22984
  • McDermott, D. H., Gao, J. L., Liu, Q., Siwicki, M., Martens, C., Jacobs, P., … Murphy, P. M. (2015). Chromothriptic cure of WHIM syndrome. Cell, 160(4), 686–699. doi:10.1016/j.cell.2015.01.014
  • Morishita, M., Muramatsu, T., Suto, Y., Hirai, M., Konishi, T., Hayashi, S., … Inazawa, J. (2016). Chromothripsis-like chromosomal rearrangements induced by ionizing radiation using proton microbeam Irradiation system. Oncotarget, 7(9), 10182–10192. doi:10.18632/oncotarget.7186
  • Notta, F., Chan-Seng-Yue, M., Lemire, M., Li, Y., Wilson, G. W., Connor, A. A., … Gallinger, S. (2016). A renewed model of pancreatic cancer evolution based on genomic rearrangement patterns. Nature, 538(7625), 378–382. doi:10.1038/nature19823
  • Passerini, V., Ozeri-Galai, E., De Pagter, M. S., Donnelly, N., Schmalbrock, S., Kloosterman, W. P., … Storchová, Z. (2016). The presence of extra chromosomes leads to genomic instability. Nature Communications, 7(1), 1–12. doi:10.1038/ncomms10754
  • Pellestor, F. (y.y.). Chromothripsis : methods and protocols, 367.
  • Pellestor, F. (2019). Chromoanagenesis: Cataclysms behind complex chromosomal rearrangements. Molecular Cytogenetics, 12(1), 1–12. doi:10.1186/s13039-019-0415-7
  • Pellestor, F. ve Gatinois, V. (2018). Chromoanasynthesis: Another way for the formation of complex chromosomal abnormalities in human reproduction. Human Reproduction, 33(8), 1381–1387. doi:10.1093/humrep/dey231
  • Pellestor, F. ve Gatinois, V. (2020, 28 Ocak). Chromoanagenesis: A piece of the macroevolution scenario. Molecular Cytogenetics. BioMed Central. doi:10.1186/s13039-020-0470-0
  • Pellestor, F., Gatinois, V., Puechberty, J., Geneviève, D. ve Lefort, G. (2014). Chromothripsis: Potential origin in gametogenesis and preimplantation cell divisions. A review. Fertility and Sterility, 102(6), 1785–1796. doi:10.1016/j.fertnstert.2014.09.006
  • Rausch, T., Jones, D. T. W., Zapatka, M., Stütz, A. M., Zichner, T., Weischenfeldt, J., … Korbel, J. O. (2012). Genome sequencing of pediatric medulloblastoma links catastrophic DNA rearrangements with TP53 mutations. Cell, 148(1–2), 59–71. doi:10.1016/j.cell.2011.12.013
  • Rode, A., Maass, K. K., Willmund, K. V., Lichter, P. ve Ernst, A. (2016). Chromothripsis in cancer cells: An update. International Journal of Cancer, 138(10), 2322–2333. doi:10.1002/ijc.29888
  • Rubin, M. A., Maher, C. A. ve Chinnaiyan, A. M. (2011). Common gene rearrangements in prostate cancer. Journal of Clinical Oncology, 29(27), 3659–3668. doi:10.1200/JCO.2011.35.1916
  • Shen, M. M. (2013). Chromoplexy: A New Category of Complex Rearrangements in the Cancer Genome. Cancer Cell, 23(5), 567–569. doi:10.1016/j.ccr.2013.04.025
  • Shlien, A. ve Malkin, D. (2009). Copy number variations and cancer. Genome Medicine, 1(6). doi:10.1186/gm62
  • So, A., Le Guen, T., Lopez, B. S. ve Guirouilh-Barbat, J. (2017). Genomic rearrangements induced by unscheduled DNA double strand breaks in somatic mammalian cells. FEBS Journal, 284(15), 2324–2344. doi:10.1111/febs.14053
  • Stankiewicz, P. ve Lupski, J. R. (2010). Structural variation in the human genome and its role in disease. Annual Review of Medicine, 61, 437–455. doi:10.1146/annurev-med-100708-204735
  • Stephens, P. J., Greenman, C. D., Fu, B., Yang, F., Bignell, G. R., Mudie, L. J., … Campbell, P. J. (2011). Massive genomic rearrangement acquired in a single catastrophic event during cancer development. Cell, 144(1), 27–40. doi:10.1016/j.cell.2010.11.055
  • Terradas, M., Martín, M. ve Genescà, A. (2016). Impaired nuclear functions in micronuclei results in genome instability and chromothripsis. Archives of Toxicology, 90(11), 2657–2667. doi:10.1007/s00204-016-1818-4
  • Terradas, M., Martín, M., Tusell, L. ve Genescà, A. (2010). Genetic activities in micronuclei: Is the DNA entrapped in micronuclei lost for the cell? Mutation Research - Reviews in Mutation Research, 705(1), 60–67. doi:10.1016/j.mrrev.2010.03.004
  • Theißen, G. (2006). The proper place of hopeful monsters in evolutionary biology. Theory in Biosciences, 124(3–4), 349–369. doi:10.1016/j.thbio.2005.11.002
  • Theißen, G. (2009). Saltational evolution: Hopeful monsters are here to stay. Theory in Biosciences, 128(1), 43–51. doi:10.1007/s12064-009-0058-z
  • Tommerup, N. (1993). Mendelian cytogenetics. Chromosome rearrangements associated with mendelian disorders. Journal of Medical Genetics, 30(9), 713–727. doi:10.1136/jmg.30.9.713
  • Tubio, J. M. C. ve Estivill, X. (2011). Cancer: When catastrophe strikes a cell. Nature, 470(7335), 476–477. doi:10.1038/470476a Van Binsbergen, E., Hochstenbach, R., Giltay, J. ve Swinkels, M. (2012). Unstable transmission of a familial complex chromosome rearrangement. American Journal of Medical Genetics, Part A, 158 A(11), 2888–2893. doi:10.1002/ajmg.a.35580
  • Venkatesan, S., Natarajan, A. T. ve Hande, M. P. (2015). Chromosomal instability-mechanisms and consequences. Mutation Research - Genetic Toxicology and Environmental Mutagenesis, 793, 176–184. doi:10.1016/j.mrgentox.2015.08.008
  • Vogelstein, B., Lane, D. ve Levine, A. J. (2000). Surfing the p53 network. Nature, 408(6810), 307–310. doi:10.1038/35042675
  • Weckselblatt, B., Hermetz, K. E. ve Rudd, M. K. (2015). Unbalanced translocations arise from diverse mutational mechanisms including chromothripsis. Genome Research, 25(7), 937–947. doi:10.1101/gr.191247.115
  • Willis, N. A., Rass, E. ve Scully, R. (2015). Deciphering the Code of the Cancer Genome: Mechanisms of Chromosome Rearrangement. Trends in Cancer, 1(4), 217–230. doi:10.1016/j.trecan.2015.10.007
  • Xu, B., Sun, Z., Liu, Z., Guo, H., Liu, Q., Jiang, H., … Shao, C. (2011). Replication stress induces micronuclei comprising of aggregated DNA double-strand breaks. PLoS ONE, 6(4), e18618. doi:10.1371/journal.pone.0018618
  • Ye, C. J., Stilgenbauer, L., Moy, A., Liu, G. ve Heng, H. H. (2019). What Is Karyotype Coding and Why Is Genomic Topology Important for Cancer and Evolution? Frontiers in Genetics, 10, 1082. doi:10.3389/fgene.2019.01082
  • Zepeda-Mendoza, C. J. ve Morton, C. C. (2019). The Iceberg under Water: Unexplored Complexity of Chromoanagenesis in Congenital Disorders. American Journal of Human Genetics, 104(4), 565–577. doi:10.1016/j.ajhg.2019.02.024
  • Zhang, C. Z., Leibowitz, M. L. ve Pellman, D. (2013). Chromothripsis and beyond: Rapid genome evolution from complex chromosomal rearrangements. Genes and Development, 27(23), 2513–2530. doi:10.1101/gad.229559.113
There are 75 citations in total.

Details

Primary Language Turkish
Subjects Industrial Biotechnology, Health Care Administration
Journal Section Derlemeler
Authors

Tunç Tuncel

Ayhan Demir This is me

Publication Date August 31, 2021
Published in Issue Year 2021 Volume: 4 Issue: 2

Cite

APA Tuncel, T., & Demir, A. (2021). İnsan genomlarında gözlenen karmaşık yapısal yeniden düzenlenme kalıpları. Türkiye Sağlık Enstitüleri Başkanlığı Dergisi, 4(2), 33-47.