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Method: Mapping and quantifying nascent transcript start sites using TT-TSS-seq
- Eleanor Elgood Hunt,
- Claudia Vivori,
- Richard Mitter,
- Vedis Agnadottir,
- and Folkert J. van Werven
Genome Res. March 2026 36: 600-610; Published in Advance February 17, 2026, doi:10.1101/gr.280726.125
...://creativecommons.org/licenses/by/4.0/.References ↵Arribere JA, Gilbert WV. 2013. Roles for transcript leaders in translation and mRNA decay revealed by transcript leader sequencing. Genome Res 23: 977–987. doi:10.1101/gr.150342.112 ↵Brown JB, Boley N, Eisman R, May GE, Stoiber MH, Duff MO, Booth BW, Wen J, Park S, Suzuki AM, et al...
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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
...to the inclusion or exclusion of sequence elements such as upstream open reading frames (uORFs), which alter mRNA stability and translational efficiency (Calvo et al. 2009; Barbosa et al. 2013; Wang et al. 2016; Kurihara et al. 2018). Large-scale shifts in TSS usage are also prevalent in various developmental...
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Method: Low-input RNase footprinting for simultaneous quantification of cytosolic and mitochondrial translation
- Qianru Li,
- Haiwang Yang,
- Emily K. Stroup,
- Hongbin Wang,
- and Zhe Ji
Genome Res. March 2022 32: 545-557; Published in Advance February 22, 2022, doi:10.1101/gr.276139.121
...for translation factors (Van Nostrand et al. 2020). High-dose RNase treatment resulted in RNA fragments with decreased lengths, stronger enrichment in coding regions of mRNAs, and depletion of those mapped to 3′ UTRs and introns (Fig. 1C–E; Supplemental Fig. S1B). For example, the binding fragments...
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Research: Prevalence of alternative AUG and non-AUG translation initiators and their regulatory effects across plants
- Ya-Ru Li and
- Ming-Jung Liu
Genome Res. October 2020 30: 1418-1433; Published in Advance September 24, 2020, doi:10.1101/gr.261834.120
...suggests that the LTM treatment performed in this study did not trigger a significant hypoxic response and likely affected the translation initiation of few, if any, transcripts.With the obtained sequencing data sets, we mapped the reads and determined the LTM, CHX, and mRNA read densities per base along...
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Research: Integrated genome and transcriptome sequencing identifies a noncoding mutation in the genome replication factor DONSON as the cause of microcephaly-micromelia syndrome
- Gilad D. Evrony,
- Dwight R. Cordero,
- Jun Shen,
- Jennifer N. Partlow,
- Timothy W. Yu,
- Rachel E. Rodin,
- R. Sean Hill,
- Michael E. Coulter,
- Anh-Thu N. Lam,
- Divya Jayaraman,
- Dianne Gerrelli,
- Diana G. Diaz,
- Chloe Santos,
- Victoria Morrison,
- Antonella Galli,
- Ulrich Tschulena,
- Stefan Wiemann,
- M. Jocelyne Martel,
- Betty Spooner,
- Steven C. Ryu,
- Princess C. Elhosary,
- Jillian M. Richardson,
- Danielle Tierney,
- Christopher A. Robinson,
- Rajni Chibbar,
- Dana Diudea,
- Rebecca Folkerth,
- Sheldon Wiebe,
- A. James Barkovich,
- Ganeshwaran H. Mochida,
- James Irvine,
- Edmond G. Lemire,
- Patricia Blakley,
- and Christopher A. Walsh
Genome Res. August 2017 27: 1323-1335; Published in Advance June 19, 2017, doi:10.1101/gr.219899.116
...exonic coding or canonical splice site impact. In contrast, the lack of highthroughput, unbiased approaches for functional assessment of most noncoding variants has bottlenecked gene discovery. We report the integration of transcriptome sequencing (RNA-seq), which surveys all mRNAs to reveal functional...
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Research: Nutritional control of mRNA isoform expression during developmental arrest and recovery in C. elegans
- Colin S. Maxwell,
- Igor Antoshechkin,
- Nicole Kurhanewicz,
- Jason A. Belsky,
- and L. Ryan Baugh
Genome Res. October 2012 22: 1920-1929; Published in Advance April 26, 2012, doi:10.1101/gr.133587.111
...contain operons that are transcribed to produce poly-cistronic pre-mRNA. Nematodes also use trans-splicing to add a short (22 nt) leader sequence to the 59 end of most (;70%) mRNA transcripts (Blumenthal 2005). There are twomajor types of spliced leader in C. elegans: SL1 and SL2. SL1 is most common...
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Research: Deep small RNA sequencing from the nematode Ascaris reveals conservation, functional diversification, and novel developmental profiles
- Jianbin Wang,
- Benjamin Czech,
- Amanda Crunk,
- Adam Wallace,
- Makedonka Mitreva,
- Gregory J. Hannon,
- and Richard E. Davis
Genome Res. September 2011 21: 1462-1477; Published in Advance June 17, 2011, doi:10.1101/gr.121426.111
...either to unique sequences or to a broad spectrum of different mRNA transcripts (Fig. 6). For the mRNA-matching endosiRNAs, the majority are in the antisense orientation (Fig. 6A,B). Most of these RNAs start with G and are of two distinct lengths, 22 nt and 26 nt (Fig. 6A). Based on the orientation...
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Research: Conserved non-AUG uORFs revealed by a novel regression analysis of ribosome profiling data
- Pieter Spealman,
- Armaghan W. Naik,
- Gemma E. May,
- Scott Kuersten,
- Lindsay Freeberg,
- Robert F. Murphy,
- and Joel McManus
Genome Res. February 2018 28: 214-222; Published in Advance December 18, 2017, doi:10.1101/gr.221507.117
..., Cormican P, Morris DW, Shatsky IN, Baranov PV. 2015. Translation of 5′ leaders is pervasive in genes resistant to eIF2 repression. eLife 4: e03971. ↵Arribere JA, Gilbert WV. 2013. Roles for transcript leaders in translation and mRNA decay revealed by transcript leader sequencing. Genome Res 23: 977...
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Research: The origin and evolution of a distinct mechanism of transcription initiation in yeasts
- Zhaolian Lu and
- Zhenguo Lin
Genome Res. January 2021 31: 51-63; Published in Advance November 20, 2020, doi:10.1101/gr.264325.120
...with those with a pyrimidine (49.2%) (Fig. 3E; Supplemental Fig. S7C).Some uncapped transcripts could be generated by premature reverse transcription (RT) stops or 5′−3′ decay of mRNA, generating “false TSSs.” If uncapped transcripts have more pyrimidines than purines at their first site, it could introduce...
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Resource: Pervasive and dynamic transcription initiation in Saccharomyces cerevisiae
- Zhaolian Lu and
- Zhenguo Lin
Genome Res. July 2019 29: 1198-1210; Published in Advance May 10, 2019, doi:10.1101/gr.245456.118
...length and sequence of 5′ UTR are generated. Different lengths of 5′ UTR may have different mRNA folding structures, which would change their thermostability. Modulation of mRNA stability is a critical step in the regulation of gene expression. In eukaryotic cells, the decay rates of individual mRNAs...

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