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Research: Single-cell discovery of m⁶A RNA modifications in the hippocampus
- Shuangshuang Feng,
- Maitena Tellaetxe-Abete,
- Yujie Zhang,
- Yan Peng,
- Han Zhou,
- Mingjie Dong,
- Erika Larrea,
- Liang Xue,
- Li Zhang,
- and Magdalena J. Koziol
Genome Res. June 2024 34: 822-836; Published in Advance July 15, 2024, doi:10.1101/gr.278424.123
..., facilitating the development of future targeted therapeutics.In this study, we aim to address the knowledge gap by performing single-cell RNA sequencing to profile m6A RNA methylation patterns in individual cells of the hippocampus. A myriad of different m6A sequencing detection methods exist, such as m6A RNA...
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Method: Detecting m6A RNA modification from nanopore sequencing using a semisupervised learning framework
- Haotian Teng,
- Marcus Stoiber,
- Ziv Bar-Joseph,
- and Carl Kingsford
Genome Res. November 2024 34: 1987-1999; Published in Advance October 15, 2024, doi:10.1101/gr.278960.124
...processes including mRNA expression, splicing, nuclear exporting, translation efficiency, RNA stability, and miRNA processing (Boulias and Greer 2023). Accurate detection and quantification of m6A modifications is crucial for understanding their impact on gene regulation and cellular processes (Fu et al...
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Method: Resolving the chromatin impact of mosaic variants with targeted Fiber-seq
- Stephanie C. Bohaczuk,
- Zachary J. Amador,
- Chang Li,
- Benjamin J. Mallory,
- Elliott G. Swanson,
- Jane Ranchalis,
- Mitchell R. Vollger,
- Katherine M. Munson,
- Tom Walsh,
- Morgan O. Hamm,
- Yizi Mao,
- Andre Lieber,
- and Andrew B. Stergachis
Genome Res. December 2024 34: 2269-2278; Published in Advance December 9, 2024, doi:10.1101/gr.279747.124
...-in of an illustrative locus showing m6A events (purple ticks) across individual fibers.ResultsTo assess the chromatin impact of variants across extended genomic loci, we designed targeted Fiber-seq to simultaneously capture multiple 100–250 kb genomic loci using a CRISPR–Cas9 targeting approach. Specifically, four...
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Review: Leveraging the power of long reads for targeted sequencing
- Shruti V. Iyer,
- Sara Goodwin,
- and William Richard McCombie
Genome Res. November 2024 34: 1701-1718; doi:10.1101/gr.279168.124
...–Cas-based tools are constantly evolving with an expanding repertoire of Cas proteins and continuing efforts to minimize off-targets, making this an exciting avenue for sequence-specific targeting and enrichment (Adli 2018).CRISPR-based long-read targeting strategies typically begin with HMW DNA extraction...
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Method: Single-cell Rapid Capture Hybridization sequencing reliably detects isoform usage and coding mutations in targeted genes
- Hongke Peng,
- Jafar S. Jabbari,
- Luyi Tian,
- Changqing Wang,
- Yupei You,
- Chong Chyn Chua,
- Natasha S. Anstee,
- Noorul Amin,
- Andrew H. Wei,
- Nadia M. Davidson,
- Andrew W. Roberts,
- David C.S. Huang,
- Matthew E. Ritchie,
- and Rachel Thijssen
Genome Res. April 2025 35: 942-955; Published in Advance January 10, 2025, doi:10.1101/gr.279322.124
.... While single-cell DNA sequencing, such as Mission Bio Tapestri, provides insight into clonality upon drug resistance (Thompson et al. 2022), it lacks transcriptome profiling per cell. In contrast, scRaCH-seq offers short-read whole transcriptomic data and mutation status if the mRNA of the targeted gene...
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Research: The predicted RNA-binding protein regulome of axonal mRNAs
- Raphaëlle Luisier,
- Catia Andreassi,
- Lisa Fournier,
- and Antonella Riccio
Genome Res. September 2023 33: 1497-1512; Published in Advance August 15, 2023, doi:10.1101/gr.277804.123
.... The targeting of RNA transcripts to axons is one of the mechanisms that allows rapid local translation of proteins in response to extracellular signals. 3′ Untranslated regions (UTRs) of mRNA are noncoding sequences that play a critical role in determining transcript localization and translation by interacting...
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Research: Global loss of cellular m⁶A RNA methylation following infection with different SARS-CoV-2 variants
- Roshan Vaid,
- Akram Mendez,
- Ketan Thombare,
- Rebeca Burgos-Panadero,
- Rémy Robinot,
- Barbara F. Fonseca,
- Nikhil R. Gandasi,
- Johan Ringlander,
- Mohammad Hassan Baig,
- Jae-June Dong,
- Jae Yong Cho,
- Björn Reinius,
- Lisa A. Chakrabarti,
- Kristina Nystrom,
- and Tanmoy Mondal
Genome Res. March 2023 33: 299-313; Published in Advance March 1, 2023, doi:10.1101/gr.276407.121
...in these four mRNAs (Fig. 5K). Therefore, rescuing nuclear localization of METTL3 by selinexor promoted stress granule formation in infected cells, restored cellular gene expression, and inhibited SARS-CoV-2 infection in vitro, highlighting the possibility of targeting the m6A pathway as an antiviral strategy...
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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
...detection of target sites was performed using CRISPResso (v.2.0.45) (Clement et al. 2019). Barcode sequences associated with each sample are listed in Supplemental Tables S2 and S3. The m6A data set of silkworm was downloaded from the NCBI BioProject database (https://www.ncbi.nlm.nih.gov/bioproject/) under...
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Method: DNA-m6A calling and integrated long-read epigenetic and genetic analysis with fibertools
- Anupama Jha,
- Stephanie C. Bohaczuk,
- Yizi Mao,
- Jane Ranchalis,
- Benjamin J. Mallory,
- Alan T. Min,
- Morgan O. Hamm,
- Elliott Swanson,
- Danilo Dubocanin,
- Connor Finkbeiner,
- Tony Li,
- Dale Whittington,
- William Stafford Noble,
- Andrew B. Stergachis,
- and Mitchell R. Vollger
Genome Res. November 2024 34: 1976-1986; Published in Advance June 7, 2024, doi:10.1101/gr.279095.124
...(upper left) indicates the value of the Pearson correlation coefficient and the P-value from a two-sided t-test without adjustment for multiple comparisons. (D) Enrichment of m6A calls within targeted motifs of three motif-specific methyltransferases (Dam [purple], EcoRI [red], and TaqI [blue...
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Method: CRISPR-based modular assembly of a UAS-cDNA/ORF plasmid library for more than 5500 Drosophila genes conserved in humans
- Ping Wei,
- Wen Xue,
- Yun Zhao,
- Guang Ning,
- and Jiwu Wang
Genome Res. January 2020 30: 95-106; Published in Advance November 13, 2019, doi:10.1101/gr.250811.119
...CRISPR-based modular assembly (CRISPRmass) for the high-throughput construction of a -wide UAS-cDNA/ORF library from publicly available cDNA/ORF resources. Through cleavage of shared vector sequences of cDNA/ORF plasmids by CRISPR/Cas9 and subsequent insertion of UAS modules by Gibson assembly...

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