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Research: Dynamic A-to-I RNA editing in response to gut microbiome in honey bees
- Yuange Duan,
- Min Huang,
- Lin Ye,
- Ling Ma,
- Yashuai Wu,
- Yating Du,
- Jiyao Liu,
- Fan Song,
- Li Tian,
- Wanzhi Cai,
- Hu Li,
- Xin Zhou,
- and Shiqi Luo
Genome Res. March 4, 2026 gr.280291.124; Published in Advance March 4, 2026, doi:10.1101/gr.280291.124
...), demonstrating sufficient depth for a set of 142 reliable editing sites (Supplemental Fig S3). The validation of individual RNA editing 143 sites (and the corresponding positions in DNA) was performed by Sanger sequencing in 144 subsequent sections. 145 In parallel, we also utilized a DNA-free method to identify...
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Research: Yeast genetic interaction screen of human genes associated with amyotrophic lateral sclerosis: identification of MAP2K5 kinase as a potential drug target
- Myungjin Jo,
- Ah Young Chung,
- Nozomu Yachie,
- Minchul Seo,
- Hyejin Jeon,
- Youngpyo Nam,
- Yeojin Seo,
- Eunmi Kim,
- Quan Zhong,
- Marc Vidal,
- Hae Chul Park,
- Frederick P. Roth,
- and Kyoungho Suk
Genome Res. September 2017 27: 1487-1500; Published in Advance June 8, 2017, doi:10.1101/gr.211649.116
...Myungjin Jo,1,7 Ah Young Chung,2,7 Nozomu Yachie,3,7,8 Minchul Seo,1 Hyejin Jeon,1 YoungpyoNam,1 Yeojin Seo,1 Eunmi Kim,2 Quan Zhong,4Marc Vidal,5 Hae Chul Park,2 Frederick P. Roth,3,6 and Kyoungho Suk1 1Department of Pharmacology, Brain Science and Engineering Institute, and Department...
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Research: Experimental and pan-cancer genome analyses reveal widespread contribution of acrylamide exposure to carcinogenesis in humans
- Maria Zhivagui,
- Alvin W.T. Ng,
- Maude Ardin,
- Mona I. Churchwell,
- Manuraj Pandey,
- Claire Renard,
- Stephanie Villar,
- Vincent Cahais,
- Alexis Robitaille,
- Liacine Bouaoun,
- Adriana Heguy,
- Kathryn Z. Guyton,
- Martha R. Stampfer,
- James McKay,
- Monica Hollstein,
- Magali Olivier,
- Steven G. Rozen,
- Frederick A. Beland,
- Michael Korenjak,
- and Jiri Zavadil
Genome Res. April 2019 29: 521-531; Published in Advance March 7, 2019, doi:10.1101/gr.242453.118
..., Adriana Heguy9, Kathryn Z. Guyton10, Martha R. Stampfer11, James McKay12, Monica Hollstein1,13,14, Magali Olivier1, Steven G. Rozen2,3,4, Frederick A. Beland5, Michael Korenjak1 and Jiri Zavadil1 1Molecular Mechanisms and Biomarkers Group, International Agency for Research on Cancer, Lyon 69008, France; 2...
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Method: An extended set of yeast-based functional assays accurately identifies human disease mutations
- Song Sun,
- Fan Yang,
- Guihong Tan,
- Michael Costanzo,
- Rose Oughtred,
- Jodi Hirschman,
- Chandra L. Theesfeld,
- Pritpal Bansal,
- Nidhi Sahni,
- Song Yi,
- Analyn Yu,
- Tanya Tyagi,
- Cathy Tie,
- David E. Hill,
- Marc Vidal,
- Brenda J. Andrews,
- Charles Boone,
- Kara Dolinski,
- and Frederick P. Roth
Genome Res. May 2016 26: 670-680; Published in Advance March 14, 2016, doi:10.1101/gr.192526.115
...Boone,1,2 Kara Dolinski,6 and Frederick P. Roth1,2,3,4,7,9 1Donnelly Centre, 2Department of Molecular Genetics, 3Department of Computer Science, University of Toronto, Toronto, Ontario M5S 3E1, Canada; 4Lunenfeld-Tanenbaum Research Institute, Mt. Sinai Hospital, Toronto, Ontario M5G 1X5, Canada; 5...
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Methods: Quantitative phenotyping via deep barcode sequencing
- Andrew M. Smith,
- Lawrence E. Heisler,
- Joseph Mellor,
- Fiona Kaper,
- Michael J. Thompson,
- Mark Chee,
- Frederick P. Roth,
- Guri Giaever,
- and Corey Nislow
Genome Res. October 2009 19: 1836-1842; Published in Advance July 21, 2009, doi:10.1101/gr.093955.109
...Quantitative phenotyping via deep barcode sequencing Andrew M. Smith 1 , 2 , 3 , Lawrence E. Heisler 3 , 4 , Joseph Mellor 5 , 6 , Fiona Kaper 7 , Michael J. Thompson 7 , Mark Chee 7 , Frederick P. Roth 5 , 6...
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Research: Complete mitochondrial genome phylogeographic analysis of killer whales (Orcinus orca) indicates multiple species
- Phillip A. Morin,
- Frederick I. Archer,
- Andrew D. Foote,
- Julia Vilstrup,
- Eric E. Allen,
- Paul Wade,
- John Durban,
- Kim Parsons,
- Robert Pitman,
- Lewyn Li,
- Pascal Bouffard,
- Sandra C. Abel Nielsen,
- Morten Rasmussen,
- Eske Willerslev,
- M. Thomas P. Gilbert,
- and Timothy Harkins
Genome Res. July 2010 20: 908-916; Published in Advance April 22, 2010, doi:10.1101/gr.102954.109
...Complete mitochondrial genome phylogeographic analysis of killer whales ( Orcinus orca ) indicates multiple species Phillip A. Morin 1 , 2 , 8 , Frederick I. Archer 1 , Andrew D. Foote 3 , 4 , Julia Vilstrup 3 , Eric E. Allen 2...
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Research: Allele-specific alternative splicing and its functional genetic variants in human tissues
- Kofi Amoah,
- Yun-Hua Esther Hsiao,
- Jae Hoon Bahn,
- Yiwei Sun,
- Christina Burghard,
- Boon Xin Tan,
- Ei-Wen Yang,
- and Xinshu Xiao
Genome Res. March 2021 31: 359-371; Published in Advance January 15, 2021, doi:10.1101/gr.265637.120
...was then subcloned into the pZW1 splicing reporter using HindIII and SacII or EcoRI and SacII cloning sites. The candidates for intron retention were cloned into the pcDNA3.1 plasmid. Final constructs were confirmed by Sanger sequencing. Primers used in this study are listed in Supplemental Table S2.Transfection...
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Method: Genome-wide chemical mutagenesis screens allow unbiased saturation of the cancer genome and identification of drug resistance mutations
- Jonathan S. Brammeld,
- Mia Petljak,
- Inigo Martincorena,
- Steven P. Williams,
- Luz Garcia Alonso,
- Alba Dalmases,
- Beatriz Bellosillo,
- Carla Daniela Robles-Espinoza,
- Stacey Price,
- Syd Barthorpe,
- Patrick Tarpey,
- Constantine Alifrangis,
- Graham Bignell,
- Joana Vidal,
- Jamie Young,
- Lucy Stebbings,
- Kathryn Beal,
- Michael R. Stratton,
- Julio Saez-Rodriguez,
- Mathew Garnett,
- Clara Montagut,
- Francesco Iorio,
- and Ultan McDermott
Genome Res. April 2017 27: 613-625; Published in Advance February 8, 2017, doi:10.1101/gr.213546.116
...Stacey Price,1 Syd Barthorpe,1 Patrick Tarpey,1 Constantine Alifrangis,1 Graham Bignell,1 Joana Vidal,5 Jamie Young,1 Lucy Stebbings,1 Kathryn Beal,1 Michael R. Stratton,1 Julio Saez-Rodriguez,2,6 Mathew Garnett,1 Clara Montagut,5 Francesco Iorio,2,7 and Ultan McDermott1,7 1Wellcome Trust Sanger...
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Method: Versatile and robust genome editing with Streptococcus thermophilus CRISPR1-Cas9
- Daniel Agudelo,
- Sophie Carter,
- Minja Velimirovic,
- Alexis Duringer,
- Jean-François Rivest,
- Sébastien Levesque,
- Jeremy Loehr,
- Mathilde Mouchiroud,
- Denis Cyr,
- Paula J. Waters,
- Mathieu Laplante,
- Sylvain Moineau,
- Adeline Goulet,
- and Yannick Doyon
Genome Res. January 2020 30: 107-117; Published in Advance January 3, 2020, doi:10.1101/gr.255414.119
...). EditR (Kluesner et al. 2018) was used to quantify base editing from Sanger sequencing reads with the P-value cutoff set to 0.01. Under these settings, any editing levels ≤5% is considered background. All chromatograms are available as Supplemental Data.Recombinant AAV production...
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Research: A CRISPR knockout screen identifies SETDB1-target retroelement silencing factors in embryonic stem cells
- Kei Fukuda,
- Akihiko Okuda,
- Kosuke Yusa,
- and Yoichi Shinkai
Genome Res. June 2018 28: 846-858; Published in Advance May 4, 2018, doi:10.1101/gr.227280.117
...Saitama 350-1241, Japan; 3Wellcome Sanger Institute, Hinxton, Cambridge, CB10 1SA, United Kingdom Corresponding authors: yshinkai@riken.jp; ky1@sanger.ac.ukAbstractIn mouse embryonic stem cells (mESCs), the expression of provirus and endogenous retroelements is epigenetically repressed. Although many...

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