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Research: Primate segmental duplication creates novel promoters for the LRRC37 gene family within the 17q21.31 inversion polymorphism region
- Cemalettin Bekpen,
- Ibrahim Tastekin,
- Priscillia Siswara,
- Cezmi A. Akdis,
- and Evan E. Eichler
Genome Res. June 2012 22: 1050-1058; Published in Advance March 14, 2012, doi:10.1101/gr.134098.111
..., Hubley R, Smit A, Eichler EE. 2008. DupMasker: A tool for annotating primate segmental duplications.Genome Res 18: 1362–1368. Johnson ME, Viggiano L, Bailey JA, Abdul-Rauf M, Goodwin G, Rocchi M, Eichler EE. 2001. Positive selection of a gene family during the emergence of humans and African apes. Nature...
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LETTER: Evolutionary dynamics of segmental duplications from human Y-chromosomal euchromatin/heterochromatin transition regions
- Stefan Kirsch,
- Claudia Münch,
- Zhaoshi Jiang,
- Ze Cheng,
- Lin Chen,
- Christiane Batz,
- Evan E. Eichler,
- and Werner Schempp
Genome Res. July 2008 18: 1030-1042; Published in Advance April 29, 2008, doi:10.1101/gr.076711.108
...duplicon (colored bars) state (see Methods). ( B ) Duplicated sequences simultaneously subjected to DupMasker analysis ( Jiang et al. 2008 ) for prediction of ancestral duplicons are compared against experimentally determined loci. Phylogenetic analysis of human Y-chromosomal SDs We performed phylogenetic...
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Research: Independent expansion, selection, and hypervariability of the TBC1D3 gene family in humans
- Xavi Guitart,
- David Porubsky,
- DongAhn Yoo,
- Max L. Dougherty,
- Philip C. Dishuck,
- Katherine M. Munson,
- Alexandra P. Lewis,
- Kendra Hoekzema,
- Jordan Knuth,
- Stephen Chang,
- Tomi Pastinen,
- and Evan E. Eichler
Genome Res. November 2024 34: 1798-1810; Published in Advance August 6, 2024, doi:10.1101/gr.279299.124
...annotated with DupMasker (Jiang et al. 2008).These findings suggest that the evolution of TBC1D3 may have contributed to human cranial expansion over the past two million years (Stringer 2016). Investigations of the sequence evolution and variation among humans and nonhuman primates (NHPs) would help test...
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LETTER: Sequencing human–gibbon breakpoints of synteny reveals mosaic new insertions at rearrangement sites
- Santhosh Girirajan,
- Lin Chen,
- Tina Graves,
- Tomas Marques-Bonet,
- Mario Ventura,
- Catrina Fronick,
- Lucinda Fulton,
- Mariano Rocchi,
- Robert S. Fulton,
- Richard K. Wilson,
- Elaine R. Mardis,
- and Evan E. Eichler
Genome Res. February 2009 19: 178-190; Published in Advance November 24, 2008, doi:10.1101/gr.086041.108
...of these sites provides a model for a replication-dependent repair mechanism for double-strand breaks (DSBs) at rearrangement sites and insights into the structure and formation of primate segmental duplications at sites of genomic rearrangements during evolution. Footnotes ↵ 5 Corresponding...
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Research: Interchromosomal core duplicons drive both evolutionary instability and disease susceptibility of the Chromosome 8p23.1 region
- Kiana Mohajeri,
- Stuart Cantsilieris,
- John Huddleston,
- Bradley J. Nelson,
- Bradley P. Coe,
- Catarina D. Campbell,
- Carl Baker,
- Lana Harshman,
- Katherine M. Munson,
- Zev N. Kronenberg,
- Milinn Kremitzki,
- Archana Raja,
- Claudia Rita Catacchio,
- Tina A. Graves,
- Richard K. Wilson,
- Mario Ventura,
- and Evan E. Eichler
Genome Res. November 2016 26: 1453-1467; Published in Advance October 7, 2016, doi:10.1101/gr.211284.116
.... The centromeric breakpoint maps to a ∼18-kbp core duplicon (Xiao element) that contains OR7E, a gene flanked by SATR2, SATR1, and ERV1 repeat sequences. (D) A schematic description of the DA core duplicon. DupMasker annotation maps the ancestral duplicons to Chr 16p13.3 and Chr 21q22.11; these duplicons form part...
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Method: The origin, global distribution, and functional impact of the human 8p23 inversion polymorphism
- Maximilian P.A. Salm,
- Stuart D. Horswell,
- Claire E. Hutchison,
- Helen E. Speedy,
- Xia Yang,
- Liming Liang,
- Eric E. Schadt,
- William O. Cookson,
- Anthony S. Wierzbicki,
- Rossi P. Naoumova,
- and Carol C. Shoulders
Genome Res. June 2012 22: 1144-1153; Published in Advance March 7, 2012, doi:10.1101/gr.126037.111
...LCR subunits. TMRCA analysis of a nonduplicated LCR section in orangutans that is duplicated in humans and chimpanzees dates the divergence of human REPP/REPD to ;9.5 mya (Supplemental Fig. S10A,B), suggesting REPP was formed prior to the emergence of gorillas during primate speciation. Moreover...

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