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Method: A versatile type VI CRISPR-based approach for targeted m⁶A demethylation in mRNAs
- Panagiotis G. Adamopoulos,
- Konstantina Athanasopoulou,
- and Andreas Scorilas
Genome Res. January 2026 36: 169-182; Published in Advance December 11, 2025, doi:10.1101/gr.280476.125
...information on a target site of interest.The advent of innovative methodologies, such as those integrating CRISPR/Cas systems with RNA-processing approaches, has expedited research in this domain, furnishing novel tools for dissecting the roles of post-transcriptional modifications in gene expression dynamics...
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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
...2018). miRNAs group into seed families that mostly target the same pool of mRNAs through complementary base pairing of their 7-nt seed region (Lai 2002; Bartel 2009). Each family targets hundreds of mRNAs, and together, miRNAs are considered key post-transcriptional regulators (Friedman et al. 2009).It...
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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
...collection established with a pooled CRISPR library consisting of 18,414 sgRNAs that target 10,480 genes. Then, we show the editing efficiency and the strong capability of reverse and forward genetic screening of this transgenic collection.ResultssgRNA design and characteristics of the selected target sites...
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Research: Transcriptomic landscape of transposable elements reveals LTR7-PLAAT4 as a potential oncogene and therapeutic target in pancreatic adenocarcinoma
- Meilong Shi,
- Chuanqi Teng,
- Shan Zhang,
- Xiaobo He,
- Lingyun Xu,
- Fengxian Han,
- Rongqi Wen,
- Ganjun Yu,
- Jingwen Liu,
- Yang Feng,
- Yanfeng Wu,
- Yan Ren,
- Gang Jin,
- and Jing Li
Genome Res. February 2026 36: 275-290; Published in Advance January 8, 2026, doi:10.1101/gr.280528.125
...platform and evaluated the correlation between drug sensitivity and LTR7-PLAAT4 status in the organoids. A bespoke 64 compound library was assembled for screening, including chemotherapy (n = 14) and targeted drugs (n = 23) (Supplemental Table S8). As positive controls, one organoid (DAC78) bearing...
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Method: Systematic mapping of TF-mediated cell fate changes by a pooled induction coupled with scRNA-seq and multi-omics approaches
- Muyoung Lee,
- Qingqing Guo,
- Mijeong Kim,
- Joonhyuk Choi,
- Alia Segura,
- Alper Genceroglu,
- Lucy LeBlanc,
- Nereida Ramirez,
- Yu Jin Jang,
- Yeejin Jang,
- Bum-Kyu Lee,
- Edward M. Marcotte,
- and Jonghwan Kim
Genome Res. March 2024 34: 484-497; Published in Advance April 5, 2024, doi:10.1101/gr.277926.123
..., CRISPR-Cas9-mediated perturbation, and overexpression screens, to address numerous questions in biology and medicine without relying on a limited number of reporter genes (Adamson et al. 2016; Dixit et al. 2016; Jaitin et al. 2016; Aarts et al. 2017; Datlinger et al. 2017).Here, we introduce i...
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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
...the for a complementary sequence. When such a target DNA sequence is identified, the enzyme becomes active and can cleave the DNA backbone at that genomic location. The search and recognition mechanism for CRISPR enzymes is highly specific to the spacer sequence of the provided gRNA, but incomplete base pairing between...
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Method: FocalSV enables target region–based structural variant assembly and refinement using single-molecule long-read sequencing data
- Can Luo,
- Zimeng Jamie Zhou,
- Yichen Henry Liu,
- and Xin Maizie Zhou
Genome Res. October 2025 35: 2252-2272; Published in Advance August 13, 2025, doi:10.1101/gr.280282.124
...these benchmarks, FocalSV(target) used regions of interest defined by SVs identified by GIAB. To avoid biased evaluation, we also measured false positive (FP) counts within regions lacking known SVs. Recognizing that some tools may report fewer SVs—leading to lower recall but artificially high precision—we further...
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Research: Wnt signaling activation induces CTCF binding and loop formation at cis-regulatory elements of target genes
- Anna Nordin,
- Chaitali Chakraborty,
- Mattias Jonasson,
- Orgena Dano,
- Gianluca Zambanini,
- Pierfrancesco Pagella,
- Silvia Remeseiro,
- and Claudio Cantù
Genome Res. August 2025 35: 1701-1716; Published in Advance June 23, 2025, doi:10.1101/gr.279684.124
...identified the exact position of the CTCF and TCF/LEF binding site(s) within these RUW regions and designed CRISPR sgRNAs which would lead Cas9 to disrupt only the core of the CTCF binding motif (Fig. 6A). We transfected cells with Cas9 and either the targeting or a scrambled sgRNA control...
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Method: Rapid SARS-CoV-2 surveillance using clinical, pooled, or wastewater sequence as a sensor for population change
- Apurva Narechania,
- Dean Bobo,
- Kevin Deitz,
- Rob DeSalle,
- Paul J. Planet,
- and Barun Mathema
Genome Res. October 2024 34: 1651-1660; Published in Advance September 25, 2024, doi:10.1101/gr.278594.123
...KHILL measures change in terms of k-mer representation and frequency across days, it is sensitive to uneven coverage and the noise characteristic of metagenomic sequencing in a way that marker-based analysis is not. To screen the noisiest time points and assure even coverage, we calculated the alpha...
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Method: Pooled analysis of radiation hybrids identifies loci for growth and drug action in mammalian cells
- Arshad H. Khan,
- Andy Lin,
- Richard T. Wang,
- Joshua S. Bloom,
- Kenneth Lange,
- and Desmond J. Smith
Genome Res. October 2020 30: 1458-1467; Published in Advance September 2, 2020, doi:10.1101/gr.262204.120
...it is true in mammalian cells is unknown.We tested the first prediction by asking whether there was increased overlap between the growth genes identified using RH-BSA and those identified in loss-of-function CRISPR (Hart et al. 2015; Wang et al. 2015) and CRISPRi screens (Gilbert et al. 2014). Contrary...

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