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Research: Epigenetic and evolutionary features of ape subterminal heterochromatin
- DongAhn Yoo,
- Katherine M. Munson,
- and Evan E. Eichler
Genome Res. January 2026 36: 38-49; Published in Advance October 22, 2025, doi:10.1101/gr.280987.125
.... The availability of two fully resolved haplotype assemblies from each ape species allowed for investigations into patterns of allelic variation and between-species comparisons of subterminal organization and differences in methylation patterns. We examined the telomeric transition regions from heterochromatin...
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Method: Multisample motif discovery and visualization for tandem repeats
- Yaran Zhang,
- Marc Hulsman,
- Alex Salazar,
- Niccolò Tesi,
- Lydian Knoop,
- Sven van der Lee,
- Sanduni Wijesekera,
- Jana Krizova,
- Erik-Jan Kamsteeg,
- and Henne Holstege
Genome Res. April 2025 35: 850-862; Published in Advance November 13, 2024, doi:10.1101/gr.279278.124
...Nijmegen, The Netherlands; 5Alzheimer Center Amsterdam, Neurology, Vrije Universiteit Amsterdam, Amsterdam UMC location VUmc, 1081HV Amsterdam, The Netherlands Corresponding author: h.holstege@amsterdamumc.nlAbstractTandem repeats (TRs) occupy a significant portion of the human and are a source...
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Resource: High-quality assembly of the Chinese white truffle genome and recalibrated divergence time estimate provide insight into the evolutionary dynamics of Tuberaceae
- Jacopo Martelossi,
- Jacopo Vujovic,
- Yue Huang,
- Alessia Tatti,
- Kaiwei Xu,
- Federico Puliga,
- Yuanxue Chen,
- Omar Rota Stabelli,
- Fabrizio Ghiselli,
- Xiaoping Zhang,
- and Alessandra Zambonelli
Genome Res. November 2025 35: 2601-2616; Published in Advance August 21, 2025, doi:10.1101/gr.280368.124
...contigs, except for contigs 16 and 17, which show enrichment only at one end (Supplemental Fig. S2). These two contigs carry 45S rDNA loci at the ends lacking telomeric repeats (see Results section “45S rDNA genes are organized as a single tandem array with only one diverging locus dispersed throughout...
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Research: Genetic variation in recalcitrant repetitive regions of the Drosophila melanogaster genome
- Harsh G. Shukla,
- Mahul Chakraborty,
- and J.J. Emerson
Genome Res. September 2025 35: 2023-2040; Published in Advance July 16, 2025, doi:10.1101/gr.280728.125
...examples like histone genes (Maxson et al. 1983), rDNA arrays (Hall et al. 2022), and immunoglobulin genes (Watson and Breden 2012). Tandem repeats are prone to rapid copy number changes mediated through mechanisms such as unequal crossing over, replication slippage, gene conversion, and intrachromatid...
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Resource: Chromosome-level subgenome-aware de novo assembly provides insight into Saccharomyces bayanus genome divergence after hybridization
- Cory Gardner,
- Junhao Chen,
- Christina Hadfield,
- Zhaolian Lu,
- David Debruin,
- Yu Zhan,
- Maureen J. Donlin,
- Tae-Hyuk Ahn,
- and Zhenguo Lin
Genome Res. November 2024 34: 2133-2146; Published in Advance September 17, 2024, doi:10.1101/gr.279364.124
...to leverage high-quality protein sequences from closely related species. The output revealed a total of 11,545 protein-coding genes identified across both haplotypes, with 5737 genes in haplotype-a and 5808 genes in haplotype-b (Table 1; Fig. 2; Supplemental Data Set S3). The variation in gene count between...
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Research: The motif composition of variable number tandem repeats impacts gene expression
- Tsung-Yu Lu,
- Paulina N. Smaruj,
- Geoffrey Fudenberg,
- Nicholas Mancuso,
- and Mark J.P. Chaisson
Genome Res. April 2023 33: 511-524; Published in Advance April 10, 2023, doi:10.1101/gr.276768.122
...@usc.eduAbstractUnderstanding the impact of DNA variation on human traits is a fundamental question in human genetics. Variable number tandem repeats (VNTRs) make up ∼3% of the human but are often excluded from association analysis owing to poor read mappability or divergent repeat content. Although methods exist to estimate VNTR length...
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Research: Differences in activity and stability drive transposable element variation in tropical and temperate maize
- Shujun Ou,
- Armin Scheben,
- Tyler Collins,
- Yinjie Qiu,
- Arun S. Seetharam,
- Claire C. Menard,
- Nancy Manchanda,
- Jonathan I. Gent,
- Michael C. Schatz,
- Sarah N. Anderson,
- Matthew B. Hufford,
- and Candice N. Hirsch
Genome Res. August 2024 34: 1140-1153; Published in Advance September 9, 2024, doi:10.1101/gr.278131.123
...of transposable elements (TEs). For example, 46% of the human consists of TEs (Hoyt et al. 2022). In maize, in which TEs were first discovered, the is 85% TE sequences, of which 75% are long terminal repeat (LTR) retrotransposons (Schnable et al. 2009). In many species, TEs are intertwined with genes and...
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Research: Large tandem duplications affect gene expression, 3D organization, and plant–pathogen response
- Ariadna Picart-Picolo,
- Stefan Grob,
- Nathalie Picault,
- Michal Franek,
- Christel Llauro,
- Thierry Halter,
- Tom R. Maier,
- Edouard Jobet,
- Julie Descombin,
- Panpan Zhang,
- Vijayapalani Paramasivan,
- Thomas J. Baum,
- Lionel Navarro,
- Martina Dvořáčková,
- Marie Mirouze,
- and Frédéric Pontvianne
Genome Res. November 2020 30: 1583-1592; Published in Advance October 8, 2020, doi:10.1101/gr.261586.120
...thaliana, a significant loss of ribosomal RNA (rRNA) genes with a past history of a mutation for the chromatin assembly factor 1 (CAF1) complex causes rapid changes in the structure. Using long-read sequencing and microscopic approaches, we have identified up to 15 independent large tandem duplications...
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Resource: Transposable element variants and their potential adaptive impact in urban populations of the malaria vector Anopheles coluzzii
- Carlos Vargas-Chavez,
- Neil Michel Longo Pendy,
- Sandrine E. Nsango,
- Laura Aguilera,
- Diego Ayala,
- and Josefa González
Genome Res. January 2022 32: 189-202; Published in Advance December 29, 2021, doi:10.1101/gr.275761.121
...observed two MITEs similar to one of the insertions in the proximal breakpoint, in agreement with the findings by Sharakhov et al. (2006) (Fig. 4). We also observed similar TE content in the 2Rb breakpoints as the one described by Lobo et al. (2010): tandem repeats flanking the inversion in the standard...
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Research: Intragenic repeat expansion in the cell wall protein gene HPF1 controls yeast chronological aging
- Benjamin P. Barré,
- Johan Hallin,
- Jia-Xing Yue,
- Karl Persson,
- Ekaterina Mikhalev,
- Agurtzane Irizar,
- Sylvester Holt,
- Dawn Thompson,
- Mikael Molin,
- Jonas Warringer,
- and Gianni Liti
Genome Res. May 2020 30: 697-710; Published in Advance April 10, 2020, doi:10.1101/gr.253351.119
...controlling cell-extracellular matrix interactions, these tandem repeat variations tune human gene expression (Gymrek et al. 2016; Quilez et al. 2016), control nucleosome positioning (Volle and Delaney 2012), regulate circadian clocks (Sawyer et al. 1997), affect organismal morphology (Fondon and Garner 2004...
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