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Method: Read-level genotyping of short tandem repeats using long reads and single-nucleotide variation with STRkit
- David R. Lougheed,
- Tomi Pastinen,
- and Guillaume Bourque
Genome Res. March 2026 36: 578-588; Published in Advance January 15, 2026, doi:10.1101/gr.280766.125
...disease and complex traits but can be difficult to resolve with short-read sequencing. We present STRkit, a software package for genotyping STRs using long-read sequencing (LRS) that uses proximate single-nucleotide variants to improve genotyping accuracy without a priori haplotype information. We show...
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Research: Characterization of DNA methylation reader proteins in Arabidopsis thaliana
- Jonathan Cahn,
- James P.B. Lloyd,
- Ino D. Karemaker,
- Pascal W.T.C. Jansen,
- Jahnvi Pflueger,
- Owen Duncan,
- Jakob Petereit,
- Ozren Bogdanovic,
- A. Harvey Millar,
- Michiel Vermeulen,
- and Ryan Lister
Genome Res. December 2024 34: 2229-2243; Published in Advance December 4, 2024, doi:10.1101/gr.279379.124
...catalyzing DNA demethylation (erasers). Investigation of DNA methyltransferases in Arabidopsis thaliana has revealed sequence context-specific activity for these enzymes: MET1 is responsible for maintaining mCG, being recruited to hemimethylated sites after replication (Finnegan et al. 1996; Ronemus et al...
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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
...al. 2009). More recently, larger variations in TL across natural isolates have been reported (D'Angiolo et al. 2023; O'Donnell et al. 2023). Using short-read whole- sequencing data, D'Angiolo and colleagues (2023) found that wild strains display shorter telomeres than strains from domesticated...
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Research: Natural variation in C. elegans short tandem repeats
- Gaotian Zhang,
- Ye Wang,
- and Erik C. Andersen
Genome Res. October 2022 32: 1852-1861; Published in Advance October 4, 2022, doi:10.1101/gr.277067.122
...al. 2012; Félix and Duveau 2012; Cook et al. 2017; Crombie et al. 2019, 2022; Lee et al. 2021). The C. elegans Natural Diversity Resource (CeNDR) catalogs and distributes thousands of wild strains, sequence data, and -wide variation data, including SNVs and short indels (Andersen et al. 2012; Cook et...
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Method: Accurate allocation of multimapped reads enables regulatory element analysis at repeats
- Alexis Morrissey,
- Jeffrey Shi,
- Daniela Q. James,
- and Shaun Mahony
Genome Res. June 2024 34: 937-951; Published in Advance July 10, 2024, doi:10.1101/gr.278638.123
...(TEs) and other repetitive regions have been shown to contain gene regulatory elements, including transcription factor binding sites. However, regulatory elements harbored by repeats have proven difficult to characterize using short-read sequencing assays such as ChIP-seq or ATAC-seq. Most regulatory...
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Research: Massive variation of short tandem repeats with functional consequences across strains of Arabidopsis thaliana
- Maximilian O. Press,
- Rajiv C. McCoy,
- Ashley N. Hall,
- Joshua M. Akey,
- and Christine Queitsch
Genome Res. August 2018 28: 1169-1178; Published in Advance July 3, 2018, doi:10.1101/gr.231753.117
...in Arabidopsis thaliana inbred lines. Nature 465: 627–631. ↵Benson G. 1999. Tandem repeats finder: a program to analyze DNA sequences. Nucleic Acids Res 27: 573–580. ↵Bilgin Sonay T, Carvalho T, Robinson M, Greminger M, Krutzen M, Comas D, Highnam G, Mittelman DA, Sharp AJ, Marques-Bonet T, et al. 2015. Tandem...
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Review: Understanding isoform expression by pairing long-read sequencing with single-cell and spatial transcriptomics
- Natan Belchikov,
- Justine Hsu,
- Xiang Jennie Li,
- Julien Jarroux,
- Wen Hu,
- Anoushka Joglekar,
- and Hagen U. Tilgner
Genome Res. November 2024 34: 1735-1746; doi:10.1101/gr.279640.124
..., rely on short reads and offer the ability to transcriptomically compare different cell types but are limited in their ability to measure differential isoform expression. More recently, long-read sequencing methods have been combined with single-cell and spatial technologies in order to characterize...
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Method: Detecting m6A RNA modification from nanopore sequencing using a semisupervised learning framework
- Haotian Teng,
- Marcus Stoiber,
- Ziv Bar-Joseph,
- and Carl Kingsford
Genome Res. November 2024 34: 1987-1999; Published in Advance October 15, 2024, doi:10.1101/gr.278960.124
...or disturb the reverse transcription process. This is followed by short-read cDNA sequencing, which identifies the RNA modifications by comparing the read ends of the cDNA or the base mismatches/deletions in cDNA. Although these methods were able to generate detailed maps of RNA modification sites, they all...
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Research: Nucleosomes and DNA methylation shape meiotic DSB frequency in Arabidopsis thaliana transposons and gene regulatory regions
- Kyuha Choi,
- Xiaohui Zhao,
- Andrew J. Tock,
- Christophe Lambing,
- Charles J. Underwood,
- Thomas J. Hardcastle,
- Heïdi Serra,
- Juhyun Kim,
- Hyun Seob Cho,
- Jaeil Kim,
- Piotr A. Ziolkowski,
- Nataliya E. Yelina,
- Ildoo Hwang,
- Robert A. Martienssen,
- and Ian R. Henderson
Genome Res. April 2018 28: 532-546; Published in Advance March 12, 2018, doi:10.1101/gr.225599.117
..., with hotspots controlled by chromatin and DNA sequence. To map meiotic DSBs throughout a plant , we purified and sequenced Arabidopsis thaliana SPO11-1-oligonucleotides. SPO11-1-oligos are elevated in gene promoters, terminators, and introns, which is driven by AT-sequence richness that excludes nucleosomes...
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Research: Polycomb-dependent differential chromatin compartmentalization determines gene coregulation in Arabidopsis
- Ying Huang,
- Sanchari Sicar,
- Juan S. Ramirez-Prado,
- Deborah Manza-Mianza,
- Javier Antunez-Sanchez,
- Rim Brik-Chaouche,
- Natalia Y. Rodriguez-Granados,
- Jing An,
- Catherine Bergounioux,
- Magdy M. Mahfouz,
- Heribert Hirt,
- Martin Crespi,
- Lorenzo Concia,
- Fredy Barneche,
- Simon Amiard,
- Aline V. Probst,
- Jose Gutierrez-Marcos,
- Federico Ariel,
- Cécile Raynaud,
- David Latrasse,
- and Moussa Benhamed
Genome Res. July 2021 31: 1230-1244; Published in Advance June 3, 2021, doi:10.1101/gr.273771.120
...acts directly or indirectly to regulate chromatin interactions, although how this histone modification modulates 3D chromatin architecture remains elusive. To decipher the impact of the dynamic deposition of H3K27me3 on the Arabidopsis thaliana nuclear interactome, we combined genetics, transcriptomics...

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