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Research: Deciphering the largest disease-associated transcript isoforms in the human neural retina with advanced long-read sequencing approaches
- Merel Stemerdink,
- Tabea Riepe,
- Nick Zomer,
- Renee Salz,
- Michael Kwint,
- Jaap Oostrik,
- Raoul Timmermans,
- Barbara Ferrari,
- Stefano Ferrari,
- Alfredo Dueñas Rey,
- Emma Delanote,
- Suzanne E. de Bruijn,
- Hannie Kremer,
- Susanne Roosing,
- Frauke Coppieters,
- Alexander Hoischen,
- Frans P.M. Cremers,
- Peter A.C. ‘t Hoen,
- Erwin van Wijk,
- and Erik de Vrieze
Genome Res. April 2025 35: 725-739; Published in Advance March 4, 2025, doi:10.1101/gr.280060.124
...by arrows in the overview provided in Figure 5D, with genomic positions provided in Supplemental Table S3. As demonstrated by Reurink et al. (2023), pathogenic deep-intronic variants can induce the inclusion of PEs harboring an in-frame stop codon across all USH2A transcripts. This prompted us to evaluate...
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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
...relevance, integrating the origin of DNA and protein elements (cis and trans) to evaluate false-positive and false-negative risks across experimental systems. Moreover, we explore how perturbation strategies—gain and loss of function—can complement steady-state profiling to establish causality in gene...
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Research: Global loss of cellular m⁶A RNA methylation following infection with different SARS-CoV-2 variants
- Roshan Vaid,
- Akram Mendez,
- Ketan Thombare,
- Rebeca Burgos-Panadero,
- Rémy Robinot,
- Barbara F. Fonseca,
- Nikhil R. Gandasi,
- Johan Ringlander,
- Mohammad Hassan Baig,
- Jae-June Dong,
- Jae Yong Cho,
- Björn Reinius,
- Lisa A. Chakrabarti,
- Kristina Nystrom,
- and Tanmoy Mondal
Genome Res. March 2023 33: 299-313; Published in Advance March 1, 2023, doi:10.1101/gr.276407.121
...%–95% of infected cells for all the variants (Supplemental Fig. S1A). We isolated total RNA 48 h postinfection and evaluated gene expression changes using RNA sequencing (RNA-seq). We first checked viral RNA levels postinfection and observed that RNA-seq reads mapping to the viral were comparable for the three SARS...
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Resource: A platform for curated products from novel open reading frames prompts reinterpretation of disease variants
- Matthew D.C. Neville,
- Robin Kohze,
- Chaitanya Erady,
- Narendra Meena,
- Matthew Hayden,
- David N. Cooper,
- Matthew Mort,
- and Sudhakaran Prabakaran
Genome Res. February 2021 31: 327-336; Published in Advance January 19, 2021, doi:10.1101/gr.263202.120
...have filed patent applications related to the work described here. The title of the patent application is “Treatment of Diseases Associated with Variant Novel Open Reading Frames.” The U.S. Provisional Application was filed on December 9, 2020, application no. 63/123,454.AcknowledgmentsWe thank Rosetta...
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Research: Alternative splicing modulated by genetic variants demonstrates accelerated evolution regulated by highly conserved proteins
- Yun-Hua Esther Hsiao,
- Jae Hoon Bahn,
- Xianzhi Lin,
- Tak-Ming Chan,
- Rena Wang,
- and Xinshu Xiao
Genome Res. April 2016 26: 440-450; Published in Advance February 17, 2016, doi:10.1101/gr.193359.115
..., little is known about the genomic, evolutionary, and regulatory features of genetically modulated alternative splicing (GMAS). Here, we systematically identified intronic tag variants for genetic modulation of alternative splicing using RNA-seq data specific to cellular compartments. Combined with our...
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Research: Post-transcriptional generation of miRNA variants by multiple nucleotidyl transferases contributes to miRNA transcriptome complexity
- Stacia K. Wyman,
- Emily C. Knouf,
- Rachael K. Parkin,
- Brian R. Fritz,
- Daniel W. Lin,
- Lucas M. Dennis,
- Michael A. Krouse,
- Philippa J. Webster,
- and Muneesh Tewari
Genome Res. September 2011 21: 1450-1461; Published in Advance August 3, 2011, doi:10.1101/gr.118059.110
...samples (h1–h9, Supplemental Table S1), as well as several miRNAs of special biological interest because of disease association or tissue specificity. The specific 39 NTA variants for analysis were chosen largely on the basis of being the most common variants for specific miRNAs observed in the human...
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Research: Functional noncoding SNPs in human endothelial cells fine-map vascular trait associations
- Anu Toropainen,
- Lindsey K. Stolze,
- Tiit Örd,
- Michael B. Whalen,
- Paula Martí Torrell,
- Verena M. Link,
- Minna U. Kaikkonen,
- and Casey E. Romanoski
Genome Res. March 2022 32: 409-424; Published in Advance February 22, 2022, doi:10.1101/gr.276064.121
...the attributes and context dependence of functional noncoding SNPs and provide new mechanisms underlying vascular disease risk.Genome-wide association studies (GWASs) have revealed thousands of associations between genetic variants and clinical phenotypes. A large majority of disease-associated loci, and thus...
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Research: Genetic analysis of isoform usage in the human anti-viral response reveals influenza-specific regulation of ERAP2 transcripts under balancing selection
- Chun Jimmie Ye,
- Jenny Chen,
- Alexandra-Chloé Villani,
- Rachel E. Gate,
- Meena Subramaniam,
- Tushar Bhangale,
- Mark N. Lee,
- Towfique Raj,
- Raktima Raychowdhury,
- Weibo Li,
- Noga Rogel,
- Sean Simmons,
- Selina H. Imboywa,
- Portia I. Chipendo,
- Cristin McCabe,
- Michelle H. Lee,
- Irene Y. Frohlich,
- Barbara E. Stranger,
- Philip L. De Jager,
- Aviv Regev,
- Tim Behrens,
- and Nir Hacohen
Genome Res. December 2018 28: 1812-1825; Published in Advance November 16, 2018, doi:10.1101/gr.240390.118
...profound effects on gene regulation by altering protein structure, we jointly analyzed disease-associated variants and local isoQTLs in addition to local eQTLs using two approaches. First, compared with SNPs from the latest GWAS catalog (MacArthur et al. 2017), local eQTLs in stimulated cells were enriched...
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LETTER: Sequence Diversity and Large-Scale Typing of SNPs in the Human Apolipoprotein E Gene
- Deborah A. Nickerson,
- Scott L. Taylor,
- Stephanie M. Fullerton,
- Kenneth M. Weiss,
- Andrew G. Clark,
- Jari H. Stengård,
- Veikko Salomaa,
- Eric Boerwinkle,
- and Charles F. Sing
Genome Res. October 1, 2000 10: 1532-1545; doi:10.1101/gr.146900
...in a large sample those sites observed to vary in a smaller sample. We present results from a systematic investigation of variation at the human apolipoprotein E locus ( APOE ), as well as the evaluation of the two-tiered sampling strategy based on these data. We sequenced 5.5 kb spanning the entire APOE...
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Research: Loss of exon identity is a common mechanism of human inherited disease
- Timothy Sterne-Weiler,
- Jonathan Howard,
- Matthew Mort,
- David N. Cooper,
- and Jeremy R. Sanford
Genome Res. October 2011 21: 1563-1571; Published in Advance July 12, 2011, doi:10.1101/gr.118638.110
...the loss of exonic splicing enhancers but also via the gain of exonic splicing silencers. Disease-associated alterations of the splicing code To determine if specific cis-acting elements are more susceptible to disease-causing mutations than others relative to a background level ascertained by reference...

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