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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
...coding gene expression with qPCR-validated targets. Our findings demonstrate that quantifying mRNA fragments from sRNA-seq experiments provides a reliable approach to investigate microRNA–mRNA interactions when total RNA-seq is unavailable.The analysis of gene expression is a cornerstone of functional...
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Method: Parallel analysis of replication timing, gene expression, and copy number with PARTAGE
- Lakshana Sruthi Sadu Murari,
- Quinn Dickinson,
- Silvia Meyer-Nava,
- and Juan Carlos Rivera-Mulia
Genome Res. April 2026 36: 802-813; Published in Advance March 19, 2026, doi:10.1101/gr.281532.125
..., and libraries were prepared for stranded mRNA sequencing. These standard analyses confirmed the close alignment of RT programs with compartmentalization as measured by Hi-C, as well as enrichment of active gene expression in active-early replicating genomic compartments (Fig. 3A). However, these data sets were...
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Method: CodonBERT large language model for mRNA vaccines
- Sizhen Li,
- Saeed Moayedpour,
- Ruijiang Li,
- Michael Bailey,
- Saleh Riahi,
- Lorenzo Kogler-Anele,
- Milad Miladi,
- Jacob Miner,
- Fabien Pertuy,
- Dinghai Zheng,
- Jun Wang,
- Akshay Balsubramani,
- Khang Tran,
- Minnie Zacharia,
- Monica Wu,
- Xiaobo Gu,
- Ryan Clinton,
- Carla Asquith,
- Joseph Skaleski,
- Lianne Boeglin,
- Sudha Chivukula,
- Anusha Dias,
- Tod Strugnell,
- Fernando Ulloa Montoya,
- Vikram Agarwal,
- Ziv Bar-Joseph,
- and Sven Jager
Genome Res. July 2024 34: 1027-1035; Published in Advance July 1, 2024, doi:10.1101/gr.278870.123
...with their corresponding mRNA source and property used for method evaluationThe mRFP expression data set (Nieuwkoop et al. 2023) profiles protein production levels for several gene variants in E. coli. The fungal expression data set (Grigoriev et al. 2014; Wint et al. 2022) includes CDSs >150 bp from a wide range...
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Resource: Exploring the epigenome profiles of repetitive elements with the WashU Repeat Browser
- Jiawei Shen,
- Siyuan Cheng,
- Deepak Purushotham,
- Xiaoyu Zhuo,
- Alan Y Du,
- Wenjin Zhang,
- Daofeng Li,
- and Ting Wang
Genome Res. February 21, 2025 gr.279764.124; Published in Advance February 21, 2025, doi:10.1101/gr.279764.124
.... Epigenetic treatment induces expression of the LTR12 families CAGE-seq (Cap Analysis of Gene Expression sequencing) is a highthroughput sequencing-based technique that quantitatively analyzes the 5' end of mRNA molecules, which addresses technical limitations encountered in conventional RNA-seq methodologies...
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Resource: Binding profiles for 961 Drosophila and C. elegans transcription factors reveal tissue-specific regulatory relationships
- Michelle Kudron,
- Louis Gevirtzman,
- Alec Victorsen,
- Bridget C. Lear,
- Jiahao Gao,
- Jinrui Xu,
- Swapna Samanta,
- Emily Frink,
- Adri Tran-Pearson,
- Chau Huynh,
- Dionne Vafeados,
- Ann Hammonds,
- William Fisher,
- Martha Wall,
- Greg Wesseling,
- Vanessa Hernandez,
- Zhichun Lin,
- Mary Kasparian,
- Kevin White,
- Ravi Allada,
- Mark Gerstein,
- LaDeana Hillier,
- Susan E. Celniker,
- Valerie Reinke,
- and Robert H. Waterston
Genome Res. December 2024 34: 2319-2334; Published in Advance October 22, 2024, doi:10.1101/gr.279037.124
...for further regulatory analysis (Supplemental File S9; modERNresource GitHub, https://github.com/modERNresource).Distribution of peaks and metapeaks relative to protein-coding genesTo evaluate the correlation between TF binding sites and mRNA abundance as measured in other experiments, we assigned the binding...
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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
.... More specialized tools for this approach include the Peak Browser at ChIP Atlas (Oki et al. 2018) or browsing ChIPBase (Huang et al. 2023), which is especially strong for ncRNAs but can also be used for mRNA genes. The Eukaryotic Promoter Database ExPASy has the useful Mass Genome Annotation Archive...
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Research: A gene regulatory element modulates myosin expression and controls cardiomyocyte response to stress
- Taylor Anglen,
- Irene M. Kaplow,
- Baekgyu Choi,
- Enya Dewars,
- Robin M. Perelli,
- Kevin T. Hagy,
- Duc Tran,
- Megan E. Ramaker,
- Svati H. Shah,
- Inkyung Jung,
- Andrew P. Landstrom,
- Ravi Karra,
- Yarui Diao,
- and Charles A. Gersbach
Genome Res. November 2025 35: 2418-2432; Published in Advance October 22, 2025, doi:10.1101/gr.280825.125
...are largely unknown. Here, we profile -wide changes to gene expression and chromatin structure in cardiomyocytes derived from human pluripotent stem cells. We identify and characterize a gene regulatory element essential for regulating MYH6 expression, which encodes human fetal myosin. Using chromatin...
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Resource: Interspecies systems biology links bacterial metabolic pathways to nematode gene expression, chemotaxis behavior, and survival
- Marina Athanasouli,
- Tobias Loschko,
- and Christian Rödelsperger
Genome Res. October 2025 35: 2363-2374; Published in Advance August 5, 2025, doi:10.1101/gr.280848.125
...(PeqLab) and a Qubit 2.0 Fluorometer. The samples were shipped to Novogene for library preparation and messenger RNA (mRNA) sequencing. Libraries were sequenced as 150-bp paired-end reads on an Illumina NovoSeq 6000 platform.RNA-seq and coexpression network analysisFor the coexpression analysis, we...
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Method: Recalibrating differential gene expression by genetic dosage variance prioritizes functionally relevant genes
- Philipp Rentzsch,
- Aaron Kollotzek,
- Kaushik Ram Ganapathy,
- Pejman Mohammadi,
- and Tuuli Lappalainen
Genome Res. October 2025 35: 2316-2325; Published in Advance September 17, 2025, doi:10.1101/gr.280360.124
..., as recently exemplified by the gene encoding the transcription factor SOX9 (Naqvi et al. 2023), these regulatory changes are associated with differences in phenotype and disease risk (Albert and Kruglyak 2015). To our knowledge, there exist currently no assays that measure the viable dosage range of mRNA...
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Research: Historical RNA expression profiles from the extinct Tasmanian tiger
- Emilio Mármol-Sánchez,
- Bastian Fromm,
- Nikolay Oskolkov,
- Zoé Pochon,
- Panagiotis Kalogeropoulos,
- Eli Eriksson,
- Inna Biryukova,
- Vaishnovi Sekar,
- Erik Ersmark,
- Björn Andersson,
- Love Dalén,
- and Marc R. Friedländer
Genome Res. August 2023 33: 1299-1316; Published in Advance July 18, 2023, doi:10.1101/gr.277663.123
...with sheep (Ovis aries) and Tasmanian devil (S. harrisii) tissue atlases, including reliably profiled protein-coding mRNA genes (breadth of coverage >10%), and with shared homologous loci among sheep, Tasmanian devil, and the thylacine (N = 261) (Supplemental Table 27). In this case, both thylacine skeletal...
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