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Method: The SeqSplice multiplexed minigene splicing assay for characterization and quantitation of variant-induced BRCA1 and BRCA2 splice isoforms
- Daffodil M. Canson,
- Michael T. Parsons,
- Gemma Moir-Meyer,
- Troy Dumenil,
- Gemma Montalban,
- Erica Lin,
- Terri P. McVeigh,
- Aimee L. Davidson,
- Shaun M. Bouckaert,
- Matt Trau,
- Darren Korbie,
- and Amanda B. Spurdle
Genome Res. September 2025 35: 2104-2115; Published in Advance August 6, 2025, doi:10.1101/gr.279557.124
...including targeted RT-PCR analysis and RNA sequencing-based tests (Casadei et al. 2019; Wai et al. 2020; Bournazos et al. 2022). Bioinformatic splicing predictions and RNA splicing assay data are then used as evidence in variant pathogenicity assessment models, including the widely adopted American College...
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Research: Promoter architecture determines cotranslational regulation of mRNA
- Lorena Espinar,
- Miquel Àngel Schikora Tamarit,
- Júlia Domingo,
- and Lucas B. Carey
Genome Res. April 2018 28: 509-518; Published in Advance March 22, 2018, doi:10.1101/gr.230458.117
.... Error bars are standard deviation, calculated with bootstrapping.DiscussionWe used a pooled library of random mRNAs under the control of either the TATA+ inducible GALL promoter or the TATA-less constitutive RPL4A promoter to identify features inside of transcripts that exhibit quantitatively different...
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Resource: Tracking pre-mRNA maturation across subcellular compartments identifies developmental gene regulation through intron retention and nuclear anchoring
- Kyu-Hyeon Yeom,
- Zhicheng Pan,
- Chia-Ho Lin,
- Han Young Lim,
- Wen Xiao,
- Yi Xing,
- and Douglas L. Black
Genome Res. June 2021 31: 1106-1119; Published in Advance April 8, 2021, doi:10.1101/gr.273904.120
..., Los Angeles, California 90095, USA; 5Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA ↵6 These authors contributed equally to this work. Corresponding authors: xingyi@email.chop.edu, dougb@microbio.ucla.eduAbstractSteps of mRNA...
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Research: Genome-wide, integrative analysis of circular RNA dysregulation and the corresponding circular RNA-microRNA-mRNA regulatory axes in autism
- Yen-Ju Chen,
- Chia-Ying Chen,
- Te-Lun Mai,
- Chih-Fan Chuang,
- Yu-Chen Chen,
- Sachin Kumar Gupta,
- Laising Yen,
- Yi-Da Wang,
- and Trees-Juen Chuang
Genome Res. March 2020 30: 375-391; Published in Advance March 3, 2020, doi:10.1101/gr.255463.119
...) Experimental validation of the circRNA (or back-spliced) junction of circARID1A. The figure shows the expression fold changes (as determined by qRT-PCR) for circARID1A, ARID1A mRNA, and GAPDH (negative control) in the indicated tissues/cell lines before and after RNase R treatment. (C) Experimental examination...
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Method: Dynamics of intronic polyadenylation in the hematopoietic lineage and its regulation by DNA methylation
- Richa Rashmi,
- Abhinaya Muruganandham,
- Pranita Borkar,
- Sumana Mallick,
- Taylor Hubbs,
- Ari Aviles,
- Daniel Chung,
- and Irtisha Singh
Genome Res. April 13, 2026 gr.281044.125; Published in Advance April 13, 2026, doi:10.1101/gr.281044.125
...using widely 26 available bulk RNA-seq data. These IPA events can be further integrated with other regulatory 27 datasets to elucidate their interplay and functional significance. 28 Introduction 29 Cleavage and polyadenylation are a central step in mRNA biogenesis that determines transcript 30 3′ ends...
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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: Cooperative target mRNA destabilization and translation inhibition by miR-58 microRNA family in C. elegans
- Deni Subasic,
- Anneke Brümmer,
- Yibo Wu,
- Sérgio Morgado Pinto,
- Jochen Imig,
- Martin Keller,
- Marko Jovanovic,
- Helen Louise Lightfoot,
- Sara Nasso,
- Sandra Goetze,
- Erich Brunner,
- Jonathan Hall,
- Ruedi Aebersold,
- Mihaela Zavolan,
- and Michael O. Hengartner
Genome Res. November 2015 25: 1680-1691; Published in Advance July 31, 2015, doi:10.1101/gr.183160.114
.... 2001). Since the mir-80; mir-58.1; mir-81-82 quadruple mutant showed a reduced DNA damage–induced germ cell apoptosis response, we tested if CEP-1 activation following irradiationwas altered in thesemutants by essaying egl-1 induction with quantitative RT-PCR (Fig. 5C). We found no difference in egl-1...
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ARTICLE: Quantitative analysis of CD34+ stem cells using RT-PCR on whole cells.
- D A Molesh and
- J M Hall
Genome Res. April 1994 3: 278-284
...of rare cells expressing a unique mRNA in a large, mixed population of cells. We have demonstrated that RT-PCR can be done on whole cells without the need for extraction of the RNA. This allows for a great saving of time and effort, as well as allowing quantitative analysis to be based on the total number...
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Research: Regeneration alters open chromatin and cis-regulatory landscape of erythroid precursors
- Yichao Zhou,
- Venkatasai Rahul Dogiparthi,
- Hannah L. Harris,
- Suhita Ray,
- Avik Choudhuri,
- Song Yang,
- Yi Zhou,
- Leonard I. Zon,
- M. Jordan Rowley,
- and Kyle J. Hewitt
Genome Res. July 2025 35: 1518-1529; Published in Advance June 2, 2025, doi:10.1101/gr.279949.124
...). (F) Flow cytometry analysis of shRNA-infected cells after 3 days culture, stained with the erythroid-specific cell surface marker LY76 (also known as TER-119). (G) Quantitative RT-PCR of Jun mRNA expression in LIN− cells isolated from spleens of PHZ-treated mice and cultured for 3 days, followed...
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ARTICLES: Long RT-PCR of the entire 8.5-kb NF1 open reading frame and mutation detection on agarose gels.
- J M Martinez,
- H H Breidenbach,
- and R Cawthon
Genome Res. January 1996 6: 58-66; doi:10.1101/gr.6.1.58
...from normal fragments, resulting from other muta- tions, were identifiable on careful quantitation with Molecular Dynamics ImageQuaNT software. However, this approach will not succeed in all cases, because of the very low abundance of some patients' mutant NF1 mRNAs. DISCUSSION Long RT-PCR...

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