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Research: Global identification of mammalian host and nested gene pairs reveal tissue-specific transcriptional interplay
- Bertille Montibus,
- James A. Cain,
- Rocio T. Martinez-Nunez,
- and Rebecca J. Oakey
Genome Res. December 2024 34: 2163-2175; Published in Advance November 22, 2024, doi:10.1101/gr.279430.124
...). This was shown for example at two independent imprinted loci, where the expression of a nested gene is associated with “premature” alternative polyadenylation of the host gene upstream of the nested gene, whereas its silencing is associated with polyadenylation at the canonical 3′ UTR (Wood et al. 2008; Cowley...
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Method: Genotyping of selected germline adaptive immune system loci using short-read sequencing data
- Michael K.B. Ford,
- Ananth Hari,
- Meredith Yeager,
- Lisa Mirabello,
- Stephen Chanock,
- Ibrahim Numanagić,
- COVNET Consortium,
- and S. Cenk Sahinalp
Genome Res. September 2025 35: 2076-2086; Published in Advance August 5, 2025, doi:10.1101/gr.280314.124
..., TRB, TRD, TRG) loci using short-read WGS. This comprehensive suite facilitates the use of widely available WGS data for immunogenomic association studies. We performed extensive validation, including (1) analyzing Mendelian concordance in 590 1000 Genomes Project (1kGP) trios (Byrska-Bishop et al...
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Research: Long-read genomics reveal extensive nuclear-specific evolution and allele-specific expression in a dikaryotic fungus
- Rita Tam,
- Mareike Möller,
- Runpeng Luo,
- Zhenyan Luo,
- Ashley Jones,
- Sambasivam Periyannan,
- John P. Rathjen,
- and Benjamin Schwessinger
Genome Res. June 2025 35: 1364-1376; Published in Advance April 11, 2025, doi:10.1101/gr.280359.124
...-to-telomere (T2T) assemblies are revolutionizing our understanding of long-hidden biology “dark matter” such as centromeres, rDNA repeats, inter-haplotype variation, and allele-specific expression (ASE), yet insights into dikaryotic fungi that separate their haploid s into distinct nuclei are limited. Here, we...
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Method: Identification of the shortest species-specific oligonucleotide sequences
- Ioannis Mouratidis,
- Maxwell A. Konnaris,
- Nikol Chantzi,
- Candace S.Y. Chan,
- Michail Patsakis,
- Kimonas Provatas,
- Austin Montgomery,
- Fotis A. Baltoumas,
- Congzhou M. Sha,
- Manvita Mareboina,
- Georgios A. Pavlopoulos,
- Dionysios V. Chartoumpekis,
- and Ilias Georgakopoulos-Soares
Genome Res. February 2025 35: 279-295; Published in Advance January 2, 2025, doi:10.1101/gr.280070.124
...improve our understanding of how genomic regions evolve and can serve as an alternative method for the identification of genomic loci that are changing, at a base pair resolution.k-mer analysis involves counting and comparing substrings of length k in biological sequences. The distribution of nucleotide k...
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Method: Genome-wide maps of CPD deamination in yeast reveal the impact of DNA sequence context and nucleosome architecture on cytosine deamination rates
- Marian F. Laughery,
- Bastian Stark,
- Benjamin Morledge-Hampton,
- Steven A. Roberts,
- and John J. Wyrick
Genome Res. January 2026 36: 183-196; Published in Advance December 9, 2025, doi:10.1101/gr.280384.124
...as panel G, except dCPD enrichment for the 24 h (H) and full (I) deamination sample is plotted.To validate these findings, we analyzed the dCPD-seq data for the cellular and naked DNA 48 h samples that had subsequently undergone full deamination in vitro (i.e., 16 h at 67°C). This analysis revealed...
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Research: Genome-wide nucleosome and transcription factor responses to genetic perturbations reveal chromatin-mediated mechanisms of transcriptional regulation
- Kevin Moyung,
- Yulong Li,
- Heather K. MacAlpine,
- Alexander J. Hartemink,
- and David M. MacAlpine
Genome Res. January 2026 36: 115-128; Published in Advance December 9, 2025, doi:10.1101/gr.279637.124
...with the up- and downregulation of genes and use these signatures to reveal regulatory mechanisms previously unexplored in expression-based studies. Finally, we demonstrate that chromatin features are predictive of transcriptional activity, and we leverage these features to reconstruct chromatin...
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Research: Expanded methylome and quantitative trait loci detection by long-read profiling of personal DNA
- Cristian Groza,
- Bing Ge,
- Warren A. Cheung,
- Tomi Pastinen,
- and Guillaume Bourque
Genome Res. April 2025 35: 644-652; Published in Advance March 20, 2025, doi:10.1101/gr.279240.124
...and detection of modified nucleotides. Also, the extent to which SVs act as methylation quantitative trait loci (SV-mQTLs) is largely unknown. Here, we generated a pan graph summarizing SVs in 782 de novo assemblies obtained from Genomic Answers for Kids, capturing 14.6 million CpG dinucleotides that are absent...
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Method: Accurate fusion transcript identification from long- and short-read isoform sequencing at bulk or single-cell resolution
- Qian Qin,
- Victoria Popic,
- Kirsty Wienand,
- Houlin Yu,
- Emily White,
- Akanksha Khorgade,
- Asa Shin,
- Christophe Georgescu,
- Catarina D. Campbell,
- Arthur Dondi,
- Niko Beerenwinkel,
- Francisca Vazquez,
- Aziz M. Al'Khafaji,
- and Brian J. Haas
Genome Res. April 2025 35: 967-986; Published in Advance March 14, 2025, doi:10.1101/gr.279200.124
...and gene expression regulatory elements of the 5′ gene, or encoding fusion proteins with altered molecular functions, all leading to alterations in the cellular circuitry that ultimately drive uncontrolled cellular proliferation.Identification of gene fusions has been an essential part of charting...
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Research: Identification of the male-specific region on the guppy Y Chromosome from a haplotype-resolved assembly
- Kang Du,
- Oliver Deusch,
- Ilja Bezrukov,
- Christa Lanz,
- Yann Guiguen,
- Margarete Hoffmann,
- Anette Habring,
- Detlef Weigel,
- Manfred Schartl,
- and Christine Dreyer
Genome Res. March 2025 35: 489-498; Published in Advance March 5, 2025, doi:10.1101/gr.279582.124
...of 43 human Y chromosomes reveals extensive complexity and variation. Nature 621: 355–364. doi:10.1038/s41586-023-06425-6 ↵Kapustin Y, Souvorov A, Tatusova T, Lipman D. 2008. Splign: algorithms for computing spliced alignments with identification of paralogs. Biol Direct 3: 20. doi:10...
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Research: Complete genomes of Asgard archaea reveal diverse integrated and mobile genetic elements
- Luis E. Valentin-Alvarado,
- Ling-Dong Shi,
- Kathryn E. Appler,
- Alexander Crits-Christoph,
- Valerie De Anda,
- Benjamin A. Adler,
- Michael L. Cui,
- Lynn Ly,
- Pedro Leão,
- Richard J. Roberts,
- Rohan Sachdeva,
- Brett J. Baker,
- David F. Savage,
- and Jillian F. Banfield
Genome Res. October 2024 34: 1595-1609; Published in Advance October 15, 2024, doi:10.1101/gr.279480.124
...Complete s of Asgard archaea reveal diverse integrated and mobile genetic elements Luis E. Valentin-Alvarado1,2, Ling-Dong Shi1, Kathryn E. Appler3, Alexander Crits-Christoph1,2,11, Valerie De Anda3,4, Benjamin A. Adler1, Michael L. Cui1, Lynn Ly5, Pedro Leão3,12, Richard J. Roberts6, Rohan...
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