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Method: High-throughput and genome-scale targeted mutagenesis using CRISPR in a nonmodel multicellular organism, Bombyx mori
- Sanyuan Ma,
- Tong Zhang,
- Ruolin Wang,
- Pan Wang,
- Yue Liu,
- Jiasong Chang,
- Aoming Wang,
- Xinhui Lan,
- Le Sun,
- Hao Sun,
- Run Shi,
- Wei Lu,
- Dan Liu,
- Na Zhang,
- Wenbo Hu,
- Xiaogang Wang,
- Weiqing Xing,
- Ling Jia,
- and Qingyou Xia
Genome Res. January 2024 34: 134-144; Published in Advance January 8, 2024, doi:10.1101/gr.278297.123
.... (D) Distribution of the deep sequenced reads and sgRNA numbers. (E) Summary of microinjection information for B. mori. (F) Distribution of sgRNAs detected by deep sequencing over the B. mori whole . (G,H) The number of sgRNAs detected in individuals.To construct the mutant library, we designed...
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Resource: Genome-scale targeted mutagenesis in Brassica napus using a pooled CRISPR library
- Jianjie He,
- Kai Zhang,
- Shuxiang Yan,
- Mi Tang,
- Weixian Zhou,
- Yongtai Yin,
- Kang Chen,
- Chunyu Zhang,
- and Maoteng Li
Genome Res. May 2023 33: 798-809; Published in Advance June 8, 2023, doi:10.1101/gr.277650.123
...ligated into the expression cassettes of the CRISPR-Cas9 (Supplemental Fig. S1B). To evaluate the quality, total sgRNAs amplified from the pooled plasmids were sequenced by high-throughput sequencing (HTS). These results showed that 89.74% of the sgRNA (16,228) read counts fell into the range between one...
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Method: 3′-end ligation sequencing is a sensitive method to detect DNA nicks at potential sites of off-target activity induced by prime editors
- Jacob Stewart-Ornstein,
- Matthew J. Irby,
- Marina K. Lilieholm,
- Dylan Laprise,
- Maria D. Collier,
- Thomas Aunins,
- Dewi Harjanto,
- Aaron N. Chang,
- Deepak Reyon,
- and Jeremy S. Duffield
Genome Res. September 2025 35: 2064-2075; Published in Advance August 5, 2025, doi:10.1101/gr.280164.124
...-complemented Illumina read 1 adapter was directly ligated to the 3′ end of a SSB using a randomized splint sequence with a 5′ biotin modification (Supplemental Table S4). This ligation was followed by fragmentation, streptavidin purification, end repair, ligation of an Illumina read 2 adapter, and two rounds of PCR...
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Method: Verkko2 integrates proximity-ligation data with long-read De Bruijn graphs for efficient telomere-to-telomere genome assembly, phasing, and scaffolding
- Dmitry Antipov,
- Mikko Rautiainen,
- Sergey Nurk,
- Brian P. Walenz,
- Steven J. Solar,
- Adam M. Phillippy,
- and Sergey Koren
Genome Res. July 2025 35: 1583-1594; Published in Advance May 19, 2025, doi:10.1101/gr.280383.124
...Verkko2 integrates proximity-ligation data with long-read De Bruijn graphs for efficient telomere-to-telomere assembly, phasing, and scaffolding Dmitry Antipov1,4, Mikko Rautiainen2,4, Sergey Nurk3, Brian P. Walenz1, Steven J. Solar1, Adam M. Phillippy1 and Sergey Koren1 1Genome Informatics Section...
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Research: Distinct types of short open reading frames are translated in plant cells
- Igor Fesenko,
- Ilya Kirov,
- Andrey Kniazev,
- Regina Khazigaleeva,
- Vassili Lazarev,
- Daria Kharlampieva,
- Ekaterina Grafskaia,
- Viktor Zgoda,
- Ivan Butenko,
- Georgy Arapidi,
- Anna Mamaeva,
- Vadim Ivanov,
- and Vadim Govorun
Genome Res. September 2019 29: 1464-1477; Published in Advance August 6, 2019, doi:10.1101/gr.253302.119
...author: fesigor@gmail.comAbstractGenomes contain millions of short (<100 codons) open reading frames (sORFs), which are usually dismissed during gene annotation. Nevertheless, peptides encoded by such sORFs can play important biological roles, and their impact on cellular processes has long been...
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Method: Integration of hyperspectral imaging and transcriptomics from individual cells with SpectralSeq
- Yike Xie,
- Abbas Habibalahi,
- Ayad G. Anwer,
- Kanu Wahi,
- Jacqueline Bailey,
- Francis Lin,
- Catherine Gatt,
- Emma M.V. Johansson,
- Tatyana Chtanova,
- Jeff Holst,
- Ewa Goldys,
- and Fabio Zanini
Genome Res. August 2025 35: 1809-1820; Published in Advance July 8, 2025, doi:10.1101/gr.280014.124
...Seq.Given that spliceosome factors were downregulated in larger cells, we suspected that cells of different size might show preferential usage of specific gene isoforms. To explore this hypothesis, HTSeq 2.0 was employed to subassign reads for individual genes into their exonic components (Putri et al. 2022). Within each...
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Research: Population genomics reveals mechanisms and dynamics of de novo expressed open reading frame emergence in Drosophila melanogaster
- Anna Grandchamp,
- Lucas Kühl,
- Marie Lebherz,
- Kathrin Brüggemann,
- John Parsch,
- and Erich Bornberg-Bauer
Genome Res. June 2023 33: 872-890; Published in Advance July 13, 2023, doi:10.1101/gr.277482.122
...sister s. So far, most studies do not detect noncoding homologs of de novo genes because of incomplete assemblies and annotations, and long evolutionary distances separating s. Here, we overcome these issues by searching for de novo expressed open reading frames (neORFs), the not-yet fixed precursors...
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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
...: sp339@cam.ac.ukAbstractRecent evidence from proteomics and deep massively parallel sequencing studies have revealed that eukaryotic s contain substantial numbers of as-yet-uncharacterized open reading frames (ORFs). We define these uncharacterized ORFs as novel ORFs (nORFs). nORFs in humans...
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Method: Genome-scale identification of cellular pathways required for cell surface recognition
- Sumana Sharma,
- S. Josefin Bartholdson,
- Amalie C.M. Couch,
- Kosuke Yusa,
- and Gavin J. Wright
Genome Res. September 2018 28: 1372-1382; Published in Advance June 18, 2018, doi:10.1101/gr.231183.117
...and C) or technical (D and E) replicate experiments is shown.Genome-scale, cell-based CRISPR-KO screens identify directly interacting receptorsMany extracellular proteins are known to bind HS, and the finding that HS binding in our assay could be additive rather than codependent on other receptors...
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Method: Classification and clustering of RNA crosslink-ligation data reveal complex structures and homodimers
- Minjie Zhang,
- Irena T. Hwang,
- Kongpan Li,
- Jianhui Bai,
- Jian-Fu Chen,
- Tsachy Weissman,
- James Y. Zou,
- and Zhipeng Lu
Genome Res. May 2022 32: 968-985; Published in Advance March 24, 2022, doi:10.1101/gr.275979.121
..., extracting structure information from such data presents unique challenges. Here, we introduce a set of computational tools for the systematic analysis of data from a wide variety of crosslink-ligation methods, specifically focusing on read mapping, alignment classification, and clustering. We design a new...

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