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Research: Telomeric repeat evolution in the phylum Nematoda revealed by high-quality genome assemblies and subtelomere structures
- Jiseon Lim,
- Wonjoo Kim,
- Jun Kim,
- and Junho Lee
Genome Res. November 2023 33: 1947-1957; Published in Advance November 2, 2023, doi:10.1101/gr.278124.123
...Telomeric repeat evolution in the phylum Nematoda revealed by high-quality assemblies and subtelomere structures Jiseon Lim1,2, Wonjoo Kim1,2, Jun Kim1,3,4 and Junho Lee1,2,3 1Department of Biological Sciences, Seoul National University, Gwanak-gu, Seoul 08826, South Korea; 2Institute of Molecular...
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Resource: Long-read assembly and comparative evidence-based reanalysis of Cryptosporidium genome sequences reveal expanded transporter repertoire and duplication of entire chromosome ends including subtelomeric regions
- Rodrigo P. Baptista,
- Yiran Li,
- Adam Sateriale,
- Mandy J. Sanders,
- Karen L. Brooks,
- Alan Tracey,
- Brendan R.E. Ansell,
- Aaron R. Jex,
- Garrett W. Cooper,
- Ethan D. Smith,
- Rui Xiao,
- Jennifer E. Dumaine,
- Peter Georgeson,
- Bernard J. Pope,
- Matthew Berriman,
- Boris Striepen,
- James A. Cotton,
- and Jessica C. Kissinger
Genome Res. January 2022 32: 203-213; Published in Advance November 11, 2021, doi:10.1101/gr.275325.121
...Long-read assembly and comparative evidence-based reanalysis of Cryptosporidium sequences reveal expanded transporter repertoire and duplication of entire chromosome ends including subtelomeric regions Rodrigo P. Baptista1,2, Yiran Li2, Adam Sateriale3, Mandy J. Sanders4, Karen L. Brooks4, Alan...
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Research: Chromosome-scale assemblies of Acanthamoeba castellanii genomes provide insights into Legionella pneumophila infection–related chromatin reorganization
- Cyril Matthey-Doret,
- Morgan J. Colp,
- Pedro Escoll,
- Agnès Thierry,
- Pierrick Moreau,
- Bruce Curtis,
- Tobias Sahr,
- Matt Sarrasin,
- Michael W. Gray,
- B. Franz Lang,
- John M. Archibald,
- Carmen Buchrieser,
- and Romain Koszul
Genome Res. September 2022 32: 1698-1710; Published in Advance September 15, 2022, doi:10.1101/gr.276375.121
...Chromosome-scale assemblies of Acanthamoeba castellanii s provide insights into Legionella pneumophila infection–related chromatin reorganization Cyril Matthey-Doret1,2,6, Morgan J. Colp3,6, Pedro Escoll4, Agnès Thierry1, Pierrick Moreau1, Bruce Curtis3, Tobias Sahr4, Matt Sarrasin5, Michael W...
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Research: Expanding heterochromatin reveals discrete subtelomeric domains delimited by chromatin landscape transitions
- Antoine Hocher,
- Myriam Ruault,
- Petra Kaferle,
- Marc Descrimes,
- Mickaël Garnier,
- Antonin Morillon,
- and Angela Taddei
Genome Res. December 2018 28: 1867-1881; Published in Advance October 24, 2018, doi:10.1101/gr.236554.118
...measured by ChIP-chip. Repression was largely independent of initial transcript level (Fig. 2D) and of coding status (e.g., the right subtelomere of Chromosome VI) (Fig. 2C; Supplemental Fig. S2B). These extended silent domains (ESDs) included 100 genes that were not bound by Sir3 in WT cells...
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Research: Natural diversity of telomere length distributions across 100 Saccharomyces cerevisiae strains
- Clotilde Garrido,
- Cintia Gómez-Muñoz,
- Etienne Kornobis,
- Nicolas Agier,
- Oana Ilioaia,
- Gilles Fischer,
- and Zhou Xu
Genome Res. March 2026 36: 522-533; Published in Advance January 16, 2026, doi:10.1101/gr.281132.125
...of Guppy (step 1). Barcodes and adapters were then removed by Porechop (step 2), and candidate sequences mapping to the telomere regions of the corresponding assembly were selected (step 3). The initial reads corresponding to these candidates were scanned for telomere sequences using Telofinder (step 4...
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Resource: Subtelomeric CTCF and cohesin binding site organization using improved subtelomere assemblies and a novel annotation pipeline
- Nicholas Stong,
- Zhong Deng,
- Ravi Gupta,
- Sufen Hu,
- Shiela Paul,
- Amber K. Weiner,
- Evan E. Eichler,
- Tina Graves,
- Catrina C. Fronick,
- Laura Courtney,
- Richard K. Wilson,
- Paul M. Lieberman,
- Ramana V. Davuluri,
- and Harold Riethman
Genome Res. June 2014 24: 1039-1050; Published in Advance March 27, 2014, doi:10.1101/gr.166983.113
...Subtelomeric CTCF and cohesin binding site organization using improved subtelomere assemblies and a novel annotation pipeline Nicholas Stong 1 , 2 , Zhong Deng 2 , Ravi Gupta 2 , Sufen Hu 2 , Shiela Paul 2 , Amber K. Weiner 2...
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Research: The evolution of African great ape subtelomeric heterochromatin and the fusion of human chromosome 2
- Mario Ventura,
- Claudia R. Catacchio,
- Saba Sajjadian,
- Laura Vives,
- Peter H. Sudmant,
- Tomas Marques-Bonet,
- Tina A. Graves,
- Richard K. Wilson,
- and Evan E. Eichler
Genome Res. June 2012 22: 1036-1049; Published in Advance March 14, 2012, doi:10.1101/gr.136556.111
..., to the formation of subtelomeric heterochromatin. Our findings highlight the complex interplay between duplicated sequences and chromosomal rearrangements that rapidly alter the cytogenetic landscape in a short period of evolutionary time. [Supplemental material is available for this article.] Chimpanzee...
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Research: Combination of short-read, long-read, and optical mapping assemblies reveals large-scale tandem repeat arrays with population genetic implications
- Matthias H. Weissensteiner,
- Andy W.C. Pang,
- Ignas Bunikis,
- Ida Höijer,
- Olga Vinnere-Petterson,
- Alexander Suh,
- and Jochen B.W. Wolf
Genome Res. May 2017 27: 697-708; Published in Advance March 30, 2017, doi:10.1101/gr.215095.116
..., our results highlight the importance of adding a layer of information on structure that is inaccessible to each approach independently. [Supplemental material is available for this article.] De novo assembly lies at the core of any -wide investigation. Initiatives such as the Genome 10K Project...
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Research: Telomerase-independent survival leads to a mosaic of complex subtelomere rearrangements in Chlamydomonas reinhardtii
- Frédéric Chaux,
- Nicolas Agier,
- Clotilde Garrido,
- Gilles Fischer,
- Stephan Eberhard,
- and Zhou Xu
Genome Res. September 2023 33: 1582-1598; Published in Advance August 14, 2023, doi:10.1101/gr.278043.123
...of approximately 350 copies corresponding to ∼3 Mb. Two other repeated elements, called Suber and Subtile, were found next to Sultan elements at three subtelomeres, called class C. The Suber element, initially named pTANC (Hails et al. 1993), contains the most abundant interstitial telomere sequence (ITS...
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Method: Complete genetic and epigenetic architecture of D4Z4 macrosatellites in FSHD, BAMS, and reference cohorts with D4Z4End2End
- Lucinda C. Xiao,
- Ayush Semwal,
- Brianna St John,
- Kathleen Zeglinski,
- Shian Su,
- James Lancaster,
- Shifeng Xue,
- Bruno Reversade,
- Matthew E. Ritchie,
- Frédérique Magdinier,
- Marnie E. Blewitt,
- and Quentin Gouil
Genome Res. March 23, 2026 ; Published in Advance March 23, 2026, doi:10.1101/gr.280907.125
...dystrophy worldwide, with an estimated prevalence of between 1/8000 and 20,000 (Mostacciuolo et al. 2009; Deenen et al. 2014; Wang et al. 2022). FSHDhas a complex etiology involving genetic and epigenetic dysregulation of the D4Z4 macrosatellite array in the subtelomere of Chromosome 4 (4q35). The D4Z4...
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