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Method: An optimized protocol for quality control of gene therapy vectors using nanopore direct RNA sequencing
- Kathleen Zeglinski,
- Christian Montellese,
- Matthew E. Ritchie,
- Monther Alhamdoosh,
- Cédric Vonarburg,
- Rory Bowden,
- Monika Jordi,
- Quentin Gouil,
- Florian Aeschimann,
- and Arthur Hsu
Genome Res. November 2024 34: 1966-1975; Published in Advance October 28, 2024, doi:10.1101/gr.279405.124
..., which is known to recognize such structures as they may resemble those of primary miRNA transcripts (Jin et al. 2020). In the case of the shRNA, another possibility is cleavage mediated by AGO2, a component of the RNA-induced silencing complex (RISC), which can occur if the mature siRNA targets its...
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Research: Characterization of transcript enrichment and detection bias in single-nucleus RNA-seq for mapping of distinct human adipocyte lineages
- Anushka Gupta,
- Farnaz Shamsi,
- Nicolas Altemose,
- Gabriel F. Dorlhiac,
- Aaron M. Cypess,
- Andrew P. White,
- Nir Yosef,
- Mary Elizabeth Patti,
- Yu-Hua Tseng,
- and Aaron Streets
Genome Res. February 2022 32: 242-257; Published in Advance January 18, 2022, doi:10.1101/gr.275509.121
...were snoRNA host genes (SNHGs), which have been shown to have various functions in cytoplasm such as repressing mRNA translation, miRNA sponging, and protein ubiquitination (Zimta et al. 2020). Overall, our results suggest a higher likelihood to deconstruct the functional roles of adipogenic regulatory...
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Research: Multiplex enhancer-reporter assays uncover unsophisticated TP53 enhancer logic
- Annelien Verfaillie,
- Dmitry Svetlichnyy,
- Hana Imrichova,
- Kristofer Davie,
- Mark Fiers,
- Zeynep Kalender Atak,
- Gert Hulselmans,
- Valerie Christiaens,
- and Stein Aerts
Genome Res. July 2016 26: 882-895; Published in Advance May 18, 2016, doi:10.1101/gr.204149.116
...are functional enhancers Having established CHEQ-seq as an accurate multiplex enhancerreporter assay, we turned to all the tested regions covering TP53 ChIP-seq peaks. Of the 1526 targeted peaks, 1010 (66%) were represented by at least one captured sequence and nonambiguous barcode. An additional 49 peaks were...
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Method: Sequencing of individual barcoded cDNAs using Pacific Biosciences and Oxford Nanopore Technologies reveals platform-specific error patterns
- Alla Mikheenko,
- Andrey D. Prjibelski,
- Anoushka Joglekar,
- and Hagen U. Tilgner
Genome Res. April 2022 32: 726-737; Published in Advance March 17, 2022, doi:10.1101/gr.276405.121
...-bp sequences can harbor important elements such as polyadenylation (poly(A)) signals, protein/miRNA-binding sites, microexons, or G-quadruplexes (Lee et al. 2020).View larger version: In this window In a new window Figure 2. Alignment characteristics of RT read pairs. (A) Heatscatter plot showing...
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Method: Comparison of CAGE and RNA-seq transcriptome profiling using clonally amplified and single-molecule next-generation sequencing
- Hideya Kawaji,
- Marina Lizio,
- Masayoshi Itoh,
- Mutsumi Kanamori-Katayama,
- Ai Kaiho,
- Hiromi Nishiyori-Sueki,
- Jay W. Shin,
- Miki Kojima-Ishiyama,
- Mitsuoki Kawano,
- Mitsuyoshi Murata,
- Noriko Ninomiya-Fukuda,
- Sachi Ishikawa-Kato,
- Sayaka Nagao-Sato,
- Shohei Noma,
- Yoshihide Hayashizaki,
- Alistair R.R. Forrest,
- Piero Carninci,
- and The FANTOM Consortium
Genome Res. April 2014 24: 708-717; Published in Advance March 27, 2014, doi:10.1101/gr.156232.113
..., Christodoulou DC, Seidman JG, Church GM, Eisenberg E. 2011. Barcoding bias in high-throughput multiplex sequencing of miRNA. Genome Res 21: 1506–1511. Carninci P, Kvam C, Kitamura A, Ohsumi T, Okazaki Y, Itoh M, Kamiya M, Shibata K, Sasaki N, Izawa M, et al. 1996. High-efficiency fulllength cDNA cloning...
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Research: Landscape of microRNA and target expression variation and covariation in single mouse embryonic stem cells
- Marcel Tarbier,
- Sebastian D. Mackowiak,
- Vaishnovi Sekar,
- Franziska Bonath,
- Etka Yapar,
- Bastian Fromm,
- Omid R. Faridani,
- Inna Biryukova,
- and Marc R. Friedländer
Genome Res. February 2026 36: 291-302; Published in Advance January 12, 2026, doi:10.1101/gr.279914.124
...is a major player in shaping mature miRNA expression profiles.Each single mESC has biases in miRNA arm selectionWe next studied arm biases of miRNA precursors, by correlating the fraction of sequenced miRNAs that originate from the 5′ arms of precursors, across cells (Fig. 3D). It appeared that arm selection...
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Resource: Dynamics of microRNA expression during mouse prenatal development
- Sorena Rahmanian,
- Rabi Murad,
- Alessandra Breschi,
- Weihua Zeng,
- Mark Mackiewicz,
- Brian Williams,
- Carrie A. Davis,
- Brian Roberts,
- Sarah Meadows,
- Dianna Moore,
- Diane Trout,
- Chris Zaleski,
- Alex Dobin,
- Lei-Hoon Sei,
- Jorg Drenkow,
- Alex Scavelli,
- Thomas R. Gingeras,
- Barbara J. Wold,
- Richard M. Myers,
- Roderic Guigó,
- and Ali Mortazavi
Genome Res. November 2019 29: 1900-1909; Published in Advance October 23, 2019, doi:10.1101/gr.248997.119
...gastrulation and proper mesoderm formation. PLoS Genet 3: e227. doi:10.1371/journal.pgen.0030227 ↵Alon S, Vigneault F, Eminaga S, Christodoulou DC, Seidman JG, Church GM, Eisenberg E. 2011. Barcoding bias in high-throughput multiplex sequencing of miRNA. Genome Res 21: 1506–1511. doi:10.1101/gr.121715...
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Method: Systematic identification of edited microRNAs in the human brain
- Shahar Alon,
- Eyal Mor,
- Francois Vigneault,
- George M. Church,
- Franco Locatelli,
- Federica Galeano,
- Angela Gallo,
- Noam Shomron,
- and Eli Eisenberg
Genome Res. August 2012 22: 1533-1540; Published in Advance April 12, 2012, doi:10.1101/gr.131573.111
....A. was supported by a Clore Fellowship. References Alon S, Vigneault F, Eminaga S, Christodoulou DC, Seidman JG, Church GM, Eisenberg E. 2011. Barcoding bias in high-throughput multiplex sequencing of miRNA. Genome Res 21: 1506–1511. Ashburner M, Ball CA, Blake JA, Botstein D, Butler H, Cherry JM, Davis AP...
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Research: Cnidarian microRNAs frequently regulate targets by cleavage
- Yehu Moran,
- David Fredman,
- Daniela Praher,
- Xin Z. Li,
- Liang Meng Wee,
- Fabian Rentzsch,
- Phillip D. Zamore,
- Ulrich Technau,
- and Hervé Seitz
Genome Res. April 2014 24: 651-663; Published in Advance March 18, 2014, doi:10.1101/gr.162503.113
...between bilaterians and cnidarians (Grimson et al. 2008). Here, we identify many new miRNAs inNematostella and show by high-throughput sequencing of nine developmental stages that the majority of miRNAs are developmentally regulated. Nematostella miRNAs are frequently 2014 Moran et al. This article...
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Method: Simple and efficient profiling of transcription initiation and transcript levels with STRIPE-seq
- Robert A. Policastro,
- R. Taylor Raborn,
- Volker P. Brendel,
- and Gabriel E. Zentner
Genome Res. June 2020 30: 910-923; Published in Advance July 6, 2020, doi:10.1101/gr.261545.120
...), their wider adoption is limited by barriers of expense, technical difficulty, and time. To overcome these hurdles, we introduce a new method: Survey of TRanscription Initiation at Promoter Elements with high-throughput sequencing (STRIPE-seq). STRIPE-seq addresses several concerns of efficiency and bias...

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