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Resource: A high-resolution map of small-scale inversions in the gibbon genome
- Ludovica Mercuri,
- Donato Palmisano,
- Alberto L'Abbate,
- Pietro D'Addabbo,
- Francesco Montinaro,
- Claudia Rita Catacchio,
- Patrick Hasenfeld,
- Mario Ventura,
- Jan O. Korbel,
- Ashley D. Sanders,
- Flavia Angela Maria Maggiolini,
- and Francesca Antonacci
Genome Res. October 2022 32: 1941-1951; Published in Advance September 30, 2022, doi:10.1101/gr.276960.122
...apes, characterized by a diverse chromosome number and rapid rate of large-scale rearrangements. Here we performed single-cell template strand sequencing (Strand-seq), molecular cytogenetics, and deep in silico analysis of a southern white-cheeked gibbon , providing the first comprehensive map of 238...
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Research: Epigenetic maintenance of topological domains in the highly rearranged gibbon genome
- Nathan H. Lazar,
- Kimberly A. Nevonen,
- Brendan O'Connell,
- Christine McCann,
- Rachel J. O'Neill,
- Richard E. Green,
- Thomas J. Meyer,
- Mariam Okhovat,
- and Lucia Carbone
Genome Res. July 2018 28: 983-997; Published in Advance June 18, 2018, doi:10.1101/gr.233874.117
...unexplored. Here, we use the heavily rearranged gibbon to examine how evolutionary chromosomal rearrangements impact -wide chromatin interactions, topologically associating domains (TADs), and their epigenetic landscape. We use high-resolution maps of gibbon–human breaks of synteny (BOS), apply Hi...
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Research: Evolution of gene regulation in ruminants differs between evolutionary breakpoint regions and homologous synteny blocks
- Marta Farré,
- Jaebum Kim,
- Anastasia A. Proskuryakova,
- Yang Zhang,
- Anastasia I. Kulemzina,
- Qiye Li,
- Yang Zhou,
- Yingqi Xiong,
- Jennifer L. Johnson,
- Polina L. Perelman,
- Warren E. Johnson,
- Wesley C. Warren,
- Anna V. Kukekova,
- Guojie Zhang,
- Stephen J. O'Brien,
- Oliver A. Ryder,
- Alexander S. Graphodatsky,
- Jian Ma,
- Harris A. Lewin,
- and Denis M. Larkin
Genome Res. April 2019 29: 576-589; Published in Advance February 13, 2019, doi:10.1101/gr.239863.118
...synteny blocks [HSBs]), often demarcated by evolutionary breakpoint regions (EBRs) where the order of orthologous sequences differs among species. Several studies have shown that HSBs are enriched for evolutionary conserved sequences and genes related to basic organismal development (Larkin et al. 2009...
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RESOURCE: Molecular refinement of gibbon genome rearrangements
- Roberta Roberto,
- Oronzo Capozzi,
- Richard K. Wilson,
- Elaine R. Mardis,
- Mariana Lomiento,
- Eray Tuzun,
- Ze Cheng,
- Alan R. Mootnick,
- Nicoletta Archidiacono,
- Mariano Rocchi,
- and Evan E. Eichler
Genome Res. February 2007 17: 249-257; Published in Advance December 21, 2006, doi:10.1101/gr.6052507
..., many of the intervals associated with translocations were gene-rich, including some genes associated with normal skeletal development. Comparisons of NLE breakpoints with those of other gibbon species reveal variability in the position, suggesting that chromosomal rearrangement has been a longstanding...
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Research: Genome-wide mapping and assembly of structural variant breakpoints in the mouse genome
- Aaron R. Quinlan,
- Royden A. Clark,
- Svetlana Sokolova,
- Mitchell L. Leibowitz,
- Yujun Zhang,
- Matthew E. Hurles,
- Joshua C. Mell,
- and Ira M. Hall
Genome Res. May 2010 20: 623-635; Published in Advance March 22, 2010, doi:10.1101/gr.102970.109
...(relative to the reference), 26% are insertions of unlinked DNA, 9% are tandem duplications, and 6% are inversions. To investigate the origins of SV, we characterized 3316 breakpoint sequences at single-nucleotide resolution. We find that ∼16% of non-transposon SVs have complex breakpoint patterns...
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RESOURCE: Tracking the complex flow of chromosome rearrangements from the Hominoidea Ancestor to extant Hylobates and Nomascus Gibbons by high-resolution synteny mapping
- Doriana Misceo,
- Oronzo Capozzi,
- Roberta Roberto,
- Maria P. Dell’Oglio,
- Mariano Rocchi,
- Roscoe Stanyon,
- and Nicoletta Archidiacono
Genome Res. September 2008 18: 1530-1537; Published in Advance June 13, 2008, doi:10.1101/gr.078295.108
...Tracking the complex flow of chromosome rearrangements from the Hominoidea Ancestor to extant Hylobates and Nomascus Gibbons by high-resolution synteny mapping Doriana Misceo 1 , Oronzo Capozzi 1 , Roberta Roberto 1 , Maria P. Dell’Oglio 1...
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Research: Topologically associating domains and their role in the evolution of genome structure and function in Drosophila
- Yi Liao,
- Xinwen Zhang,
- Mahul Chakraborty,
- and J.J. Emerson
Genome Res. March 2021 31: 397-410; Published in Advance February 9, 2021, doi:10.1101/gr.266130.120
...million years of divergence, showed that ∼30%–40% of their s retain conserved TADs. Comparative genomic analysis of 17 Drosophila species revealed that chromosomal rearrangement breakpoints are enriched at TAD boundaries but depleted within TADs. Additionally, genes within conserved TADs show lower...
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Resource: A comprehensive molecular cytogenetic analysis of chromosome rearrangements in gibbons
- Oronzo Capozzi,
- Lucia Carbone,
- Roscoe R. Stanyon,
- Annamaria Marra,
- Fengtang Yang,
- Christopher W. Whelan,
- Pieter J. de Jong,
- Mariano Rocchi,
- and Nicoletta Archidiacono
Genome Res. December 2012 22: 2520-2528; Published in Advance August 14, 2012, doi:10.1101/gr.138651.112
...sorting and painting on the comparative analysis of primate s. Cytogenet Genome Res 108: 112–121. Girirajan S, Chen L, Graves T, Marques-Bonet T, Ventura M, Fronick C, Fulton L, Rocchi M, Fulton RS, Wilson RK, et al. 2009. Sequencing human-gibbon breakpoints of synteny reveals mosaic new insertions...
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Resource: Inversion variants in human and primate genomes
- Claudia Rita Catacchio,
- Flavia Angela Maria Maggiolini,
- Pietro D'Addabbo,
- Miriana Bitonto,
- Oronzo Capozzi,
- Martina Lepore Signorile,
- Mattia Miroballo,
- Nicoletta Archidiacono,
- Evan E. Eichler,
- Mario Ventura,
- and Francesca Antonacci
Genome Res. May 18, 2018 ; Published in Advance May 18, 2018, doi:10.1101/gr.234831.118
..., sequence, and experimental analyses, we analyzed 109 of these loci and found 67 regions inverted in one ormultiple primates, including 28 newly identified inversions. These events overlap with 81 human genes at their breakpoints, and seven correspond to sites of recurrent rearrangements associated...
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Method: Chromosome assembly of large and complex genomes using multiple references
- Mikhail Kolmogorov,
- Joel Armstrong,
- Brian J. Raney,
- Ian Streeter,
- Matthew Dunn,
- Fengtang Yang,
- Duncan Odom,
- Paul Flicek,
- Thomas M. Keane,
- David Thybert,
- Benedict Paten,
- and Son Pham
Genome Res. November 2018 28: 1720-1732; Published in Advance October 19, 2018, doi:10.1101/gr.236273.118
...of the input sequences into a set of synteny blocks—long and conservative genomic regions with respect to micro-rearrangements. However, RACA reconstructs synteny blocks by aligning all input sequences against a single reference . This approach is biased toward the reference and, in some cases, cannot detect...
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