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Resource: A systematic analysis of Trypanosoma brucei chromatin factors identifies novel protein interaction networks associated with sites of transcription initiation and termination
- Desislava P. Staneva,
- Roberta Carloni,
- Tatsiana Auchynnikava,
- Pin Tong,
- Juri Rappsilber,
- A. Arockia Jeyaprakash,
- Keith R. Matthews,
- and Robin C. Allshire
Genome Res. November 2021 31: 2138-2154; Published in Advance August 18, 2021, doi:10.1101/gr.275368.121
...that alter gene expression accordingly. The histone tails of the evolutionarily divergent eukaryotic parasite Trypanosoma brucei have atypical sequences and PTMs distinct from those often considered universally conserved. Here we identify 65 predicted readers, writers, and erasers of histone acetylation...
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Method: RAmbler resolves complex repeats in human Chromosomes 8, 19, and X
- Sakshar Chakravarty,
- Glennis Logsdon,
- and Stefano Lonardi
Genome Res. April 2025 35: 863-876; Published in Advance March 4, 2025, doi:10.1101/gr.279308.124
...to close most of the repetitive gaps and achieved 99.9% completeness (Miga et al. 2020; Logsdon et al. 2021; Hoyt et al. 2022; Nurk et al. 2022; Rautiainen et al. 2023). In particular, the method developed to assemble human Chromosome 8 depended on the use of single-copy k-mers (hereafter called unikmers...
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Research: Centromeric instability and chromoanasynthesis observed in nine supernumerary marker chromosomes resolved with long-read genome sequencing
- Kristine Bilgrav Saether,
- Angelo Salazar Mantero,
- Marlene Ek,
- Maria Pettersson,
- Elisabeth Syk Lundberg,
- Christopher M. Grochowski,
- Claudia M.B. Carvalho,
- Jesper Eisfeldt,
- and Anna Lindstrand
Genome Res. April 2026 36: 661-670; Published in Advance March 25, 2026, doi:10.1101/gr.281175.125
...Centromeric instability and chromoanasynthesis observed in nine supernumerary marker chromosomes resolved with long-read sequencing Kristine Bilgrav Saether1,2,6, Angelo Salazar Mantero1,3,6, Marlene Ek1,3, Maria Pettersson1,3, Elisabeth Syk Lundberg1,3, Christopher M. Grochowski4, Claudia M...
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Method: Gapless assembly of complete human and plant chromosomes using only nanopore sequencing
- Sergey Koren,
- Zhigui Bao,
- Andrea Guarracino,
- Shujun Ou,
- Sara Goodwin,
- Katharine M. Jenike,
- Julian Lucas,
- Brandy McNulty,
- Jimin Park,
- Mikko Rautiainen,
- Arang Rhie,
- Dick Roelofs,
- Harrie Schneiders,
- Ilse Vrijenhoek,
- Koen Nijbroek,
- Olle Nordesjo,
- Sergey Nurk,
- Mike Vella,
- Katherine R. Lawrence,
- Doreen Ware,
- Michael C. Schatz,
- Erik Garrison,
- Sanwen Huang,
- William Richard McCombie,
- Karen H. Miga,
- Alexander H.J. Wittenberg,
- and Adam M. Phillippy
Genome Res. November 2024 34: 1919-1930; Published in Advance November 6, 2024, doi:10.1101/gr.279334.124
...assembly, which can then be further resolved using the UL reads, and finally phased into chromosome-scale haplotypes with Pore-C. The resulting assemblies have a base accuracy exceeding 99.999% (Q50) and near-perfect continuity, with most chromosomes assembled as single contigs. We conclude that ONT...
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Research: Extreme heterochiasmy and high rates of sex-reversed recombination result in large yet homomorphic sex chromosomes in the Emei moustache toad
- Siyu Xie,
- Jun Li,
- Wanyan Chen,
- Lydia J.M. Fong,
- Chunhua Huang,
- Yan Feng,
- Qingbo Ai,
- Mian Zhao,
- Judith E. Mank,
- and Hua Wu
Genome Res. June 2025 35: 1325-1336; Published in Advance April 24, 2025, doi:10.1101/gr.280161.124
...of Zoology and Biodiversity Research Centre, University of British Columbia, Vancouver, British Columbia V6T 1Z4, Canada Corresponding author: wuhua@ccnu.edu.cnAbstractUnlike the highly degenerated sex chromosomes in birds and mammals, many amphibians possess homomorphic sex chromosomes, which may result...
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REPORT: Gene Survey of the Pathogenic Protozoan Trypanosoma cruzi
- Betina M. Porcel,
- Anh-Nhi Tran,
- Martti Tammi,
- Zoltan Nyarady,
- Maria Rydåker,
- Turan P. Urmenyi,
- Edson Rondinelli,
- Ulf Pettersson,
- Bj̈orn Andersson,
- and Lena Åslund
Genome Res. August 1, 2000 10: 1103-1107; doi:10.1101/gr.10.8.1103
...is of particular interest. Genome projects for several medically important parasites have therefore been initiated and are in progress. Trypanosoma cruzi , the causative agent of Chagas' disease affecting ∼18 million people in Latin America (WHO; www.who.int/ctd/chagas/burdens.htm ), is a flagellated protozoan...
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Research: Rearrangement of macronucleus chromosomes correspond to TAD-like structures of micronucleus chromosomes in Tetrahymena thermophila
- Zhengyu Luo,
- Tengfei Hu,
- Hong Jiang,
- Ruoyu Wang,
- Qianlan Xu,
- Simo Zhang,
- Jun Cao,
- and Xiaoyuan Song
Genome Res. March 2020 30: 406-414; Published in Advance March 12, 2020, doi:10.1101/gr.241687.118
...for maintaining the TAD-like structure in single cells (Bintu et al. 2018). Thus, the mechanism of TADs formation and maintenance is still largely unknown.Tetrahymena thermophila, a ciliated protozoan, contains two nuclei in the same cell: the transcriptionally active polyploid macronucleus (MAC...
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Perspective: Short arms of human acrocentric chromosomes and the completion of the human genome sequence
- Stylianos E. Antonarakis
Genome Res. April 2022 32: 599-607; Published in Advance March 31, 2022, doi:10.1101/gr.275350.121
...: regulation of RNA polymerase I transcription in the nucleolus. Genes Dev 17: 1691–1702. doi:10.1101/gad.1098503R ↵Guipponi M, Yaspo ML, Riesselman L, Chen H, De Sario A, Roizès G, Antonarakis SE. 2000. Genomic structure of a copy of the human TPTE gene which encompasses 87 kb on the short arm of chromosome...
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Research: Mitotic chromosomes harbor cell type– and species-specific structural features within a universal loop array conformation
- Marlies E. Oomen,
- A. Nicole Fox,
- Inma Gonzalez,
- Amandine Molliex,
- Thaleia Papadopoulou,
- Pablo Navarro,
- and Job Dekker
Genome Res. August 2025 35: 1733-1744; Published in Advance June 6, 2025, doi:10.1101/gr.280648.125
..., Germany Corresponding authors: pnavarro@pasteur.fr, job.dekker@umassmed.eduAbstractMitotic chromosomes are considered to be universally folded as loop arrays across species and cell types. However, some studies suggest that features of mitotic chromosomes might be cell type– or species-specific. We...
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Research: De novo genome assemblies of two cryptodiran turtles with ZZ/ZW and XX/XY sex chromosomes provide insights into patterns of genome reshuffling and uncover novel 3D genome folding in amniotes
- Basanta Bista,
- Laura González-Rodelas,
- Lucía Álvarez-González,
- Zhi-qiang Wu,
- Eugenia E. Montiel,
- Ling Sze Lee,
- Daleen B. Badenhorst,
- Srihari Radhakrishnan,
- Robert Literman,
- Beatriz Navarro-Dominguez,
- John B. Iverson,
- Simon Orozco-Arias,
- Josefa González,
- Aurora Ruiz-Herrera,
- and Nicole Valenzuela
Genome Res. October 2024 34: 1553-1569; Published in Advance October 16, 2024, doi:10.1101/gr.279443.124
...of Staurotypus and Apalone, respectively. We used the Trachemys (Simison et al. 2020) for comparison, as it is an annotated chromosome-level assembly that has been partially mapped physically and some chromosome assignments corrected accordingly (Lee et al. 2020), along with Gopherus evgoodei (Rhie et al. 2021...
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