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Method: Integration of high-throughput proteomic data and complementary omics layers with PriOmics
- Robin Kosch,
- Katharina Limm,
- Annette M. Staiger,
- Nadine S. Kurz,
- Nicole Seifert,
- Bence Oláh,
- Stefan Solbrig,
- Viola Poeschel,
- Gerhard Held,
- Marita Ziepert,
- Norbert Schmitz,
- Emil Chteinberg,
- Reiner Siebert,
- Rainer Spang,
- Helena U. Zacharias,
- German Ott,
- Peter J. Oefner,
- and Michael Altenbuchinger
Genome Res. January 2026 36: 197-213; Published in Advance November 18, 2025, doi:10.1101/gr.279487.124
...differentiate both ABC and GCB with the same edge sign from unclassified DLBCL, is a peptide proteotypic for DNA methyltransferase 1 (DNMT1). DNMT1, which belongs to a family of DNA methyltransferases that catalyze the transfer of the methyl moiety from S-adenosylmethionine to DNA, plays an important role...
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Method: A high-throughput screening method for selecting feature SNPs to evaluate breed diversity and infer ancestry
- Meilin Zhang,
- Heng Du,
- Yu Zhang,
- Yue Zhuo,
- Zhen Liu,
- Yahui Xue,
- Lei Zhou,
- Sixuan Zhou,
- Wanying Li,
- and Jian-Feng Liu
Genome Res. August 2025 35: 1875-1886; Published in Advance July 15, 2025, doi:10.1101/gr.280176.124
...; Eusebi et al. 2020). Many studies compare and utilize different types of marker techniques, including mitochondrial DNA barcoding (mtDNA) (Guo et al. 2006), the Y-Chromosome technique (Bruford et al. 2003), minisatellite and microsatellite markers (Ćurković et al. 2016), and single...
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Review: A systematic guide for identifying transcription factors that directly regulate the expression of a gene of interest
- Andrew D. Bates,
- Dawid Grzela,
- Maciej Studzian,
- Louise Brennan,
- Moli Williams,
- Conor Fawcett,
- Beth Hammond,
- Manreen Grewal,
- Marcin Ratajewski,
- Lukasz Pulaski,
- and Urszula L. McClurg
Genome Res. March 2026 36: 433-459; Published in Advance February 17, 2026, doi:10.1101/gr.281154.125
...FANTOM5 (Kawaji et al. 2014) or DBTSS (Suzuki et al. 2015). However, for genes expressed at a low level, whole- experiments might not have enough coverage to reliably pinpoint TSS(s).Several databases provide comprehensive DNA methylation data derived from high-throughput sequencing, including single...
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Method: High-throughput and genome-scale targeted mutagenesis using CRISPR in a nonmodel multicellular organism, Bombyx mori
- Sanyuan Ma,
- Tong Zhang,
- Ruolin Wang,
- Pan Wang,
- Yue Liu,
- Jiasong Chang,
- Aoming Wang,
- Xinhui Lan,
- Le Sun,
- Hao Sun,
- Run Shi,
- Wei Lu,
- Dan Liu,
- Na Zhang,
- Wenbo Hu,
- Xiaogang Wang,
- Weiqing Xing,
- Ling Jia,
- and Qingyou Xia
Genome Res. January 2024 34: 134-144; Published in Advance January 8, 2024, doi:10.1101/gr.278297.123
...was extracted. For each sample, 1 μg of RNA was subjected to reverse transcription using the one-step gDNA removal and cDNA synthesis SuperMix kit (TransGen Biotech). Quantitative real-time PCR (qPCR) was performed using SYBR Premix Ex Taq II (Takara), and target gene expression was normalized to the reference...
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Method: Kinetic measurement of gene-specific RNA polymerase II transcription elongation rates
- Haiyue Liu and
- Lea H. Gregersen
Genome Res. November 2025 35: 2550-2562; Published in Advance October 22, 2025, doi:10.1101/gr.280852.125
..., concentration measured by Qubit (DNA high sensitivity assay), and size distribution assessed using TapeStation (high sensitivity D5000 ScreenTape; Agilent, #5067-5592). For the DLD-1 experiment, 10 ng of purified 4sU-labeled RNA was used for high-throughput sequencing library preparation with the NEBNext Ultra...
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Method: CRISPR-Cas9-based repeat depletion for high-throughput genotyping of complex plant genomes
- Marzia Rossato,
- Luca Marcolungo,
- Luca De Antoni,
- Giulia Lopatriello,
- Elisa Bellucci,
- Gaia Cortinovis,
- Giulia Frascarelli,
- Laura Nanni,
- Elena Bitocchi,
- Valerio Di Vittori,
- Leonardo Vincenzi,
- Filippo Lucchini,
- Kirstin E. Bett,
- Larissa Ramsay,
- David James Konkin,
- Massimo Delledonne,
- and Roberto Papa
Genome Res. May 2023 33: 787-797; Published in Advance May 1, 2023, doi:10.1101/gr.277628.122
...-reassociation reaction (Zhulidov et al. 2004). This method has been used in RNA-seq analysis to remove abundant transcripts (Miller et al. 2013; Zhao et al. 2014) and, just occasionally, also to delete repetitive elements in DNA-seq libraries generated from plant s (Matvienko et al. 2013; Ichida and Abe 2019). However...
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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
...author: ryan.lister@uwa.edu.auAbstractIn plants, cytosine DNA methylation (mC) is largely associated with transcriptional repression of transposable elements, but it can also be found in the body of expressed genes, referred to as gene body methylation (gbM). gbM is correlated with ubiquitously expressed...
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Research: Characterization of human transcription factor function and patterns of gene regulation in HepG2 cells
- Belle A. Moyers,
- E. Christopher Partridge,
- Mark Mackiewicz,
- Michael J. Betti,
- Roshan Darji,
- Sarah K. Meadows,
- Kimberly M. Newberry,
- Laurel A. Brandsmeier,
- Barbara J. Wold,
- Eric M. Mendenhall,
- and Richard M. Myers
Genome Res. November 2023 33: 1879-1892; Published in Advance October 18, 2023, doi:10.1101/gr.278205.123
...of the human cell line HepG2 and show the usefulness of large genomic analyses for elucidation of individual TF functions.Gene expression is regulated and modulated by the association, either direct or indirect, of various classes of proteins to DNA, including RNA polymerase and transcription...
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Method: Analysis of coding gene expression from small RNA sequencing
- Aygun Azadova,
- Anthonia Ekperuoh,
- Greg N. Brooke,
- and Antonio Marco
Genome Res. March 2026 36: 611-618; Published in Advance February 10, 2026, doi:10.1101/gr.281364.125
...a sample, reverse-transcribing it into stable cDNA, and finally sequencing using (mostly) Illumina technology (Bentley et al. 2008). RNA-seq has multiple technical variations, either to identify specific types of transcripts or to characterize other RNA products. For instance, small RNA sequencing (s...
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Research: Global characterization of somatic mutations and DNA methylation changes during vegetative propagation in strawberries
- Shaoqiang Hu,
- Xiangguo Zeng,
- Yuguo Liu,
- Yongping Li,
- Minghao Qu,
- Wen-Biao Jiao,
- Yongchao Han,
- and Chunying Kang
Genome Res. October 2024 34: 1582-1594; Published in Advance October 15, 2024, doi:10.1101/gr.279378.124
...for rooting for 3 months and finally planted in soil for characterization.DNA extraction and high-throughput sequencingA total of 3 original plants (CK), 27 regenerated plants under different conditions (LS, LL, HS, HL, CA), and 12 “Beni hoppe” plants were used. For each sample, the young leaves were...

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