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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
...target expression variation and covariation, but these observations have been limited to a few microRNAs. Here we systematically study microRNA alternative functions in mouse embryonic stem cells (mESCs) by genetically deleting Drosha, leading to global loss of microRNAs. We apply complementary single...
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Method: Multicondition and multimodal temporal profile inference during mouse embryonic development
- Ran Zhang,
- Chengxiang Qiu,
- Galina N. Filippova,
- Gang Li,
- Jay Shendure,
- Jean-Philippe Vert,
- Xinxian Deng,
- William Stafford Noble,
- and Christine M. Disteche
Genome Res. October 2025 35: 2339-2351; Published in Advance August 14, 2025, doi:10.1101/gr.279997.124
..., systematically characterized sex-biased expression patterns during mouse embryonic development. Besides recapitulating well-known sex-biased genes, we generated various data-driven hypotheses for downstream experimental validation in the future.Sunbear also identifies dynamic associations between chromatin...
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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: Cell-type- and chromosome-specific chromatin landscapes and DNA replication programs of Drosophila testis tumor stem cell–like cells
- Jennifer A. Urban,
- Daniel Ringwalt,
- John M. Urban,
- Wingel Xue,
- Ryan Gleason,
- Keji Zhao,
- and Xin Chen
Genome Res. January 2026 36: 83-101; Published in Advance December 10, 2025, doi:10.1101/gr.280809.125
...SCs surround the stem-cell niche, called the hub (Fas3; blue cell cluster). Individual spermatogonial (SG) cysts are identified by the spectrosome/fusome (Hts) and the extracellular adhesion protein, armadillo (Arm), both blue in the confocal image. Scale bar = 10 µm. (B) A schematic and single z...
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Research: H3K36 dimethylation shapes the epigenetic interaction landscape by directing repressive chromatin modifications in embryonic stem cells
- Haifen Chen,
- Bo Hu,
- Cynthia Horth,
- Eric Bareke,
- Phillip Rosenbaum,
- Sin Young Kwon,
- Jacinthe Sirois,
- Daniel N. Weinberg,
- Faith M. Robison,
- Benjamin A. Garcia,
- Chao Lu,
- William A. Pastor,
- and Jacek Majewski
Genome Res. May 2022 32: 825-837; Published in Advance April 8, 2022, doi:10.1101/gr.276383.121
...(Streubel et al. 2018). Here, we used CRISPR-Cas9 editing to create a full KO of Nsd1. We did not observe any increase in the numbers of dead cells or propensity to differentiate. However, we noted a slightly reduced proliferation in the Nsd1-KO mESCs. To study the effects of the deletion of this important...
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Research: Delayed DNA replication in haploid human embryonic stem cells
- Matthew M. Edwards,
- Michael V. Zuccaro,
- Ido Sagi,
- Qiliang Ding,
- Dan Vershkov,
- Nissim Benvenisty,
- Dieter Egli,
- and Amnon Koren
Genome Res. December 2021 31: 2155-2169; Published in Advance November 22, 2021, doi:10.1101/gr.275953.121
...in human haploid embryonic stem cells. The replication delays we describe are among the most profound alterations to the otherwise highly stable eukaryotic DNA replication timing program. The ability to identify replication delays that transcend S-phase was enabled by our approach of directly sequencing...
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Research: Characterization of the role of spatial proximity of DNA double-strand breaks in the formation of CRISPR-Cas9-induced large structural variations
- Mikkel Dahl-Jessen,
- Thorkild Terkelsen,
- Rasmus O. Bak,
- and Uffe Birk Jensen
Genome Res. February 2025 35: 231-241; Published in Advance January 13, 2025, doi:10.1101/gr.278575.123
...by differences in ddPCR sensitivity.Effect of DSB proximity in human embryonic stem cellsHaving observed that spatial proximity affected the formation of CRISPR-Cas9-induced SVs in K562 cells, we subsequently investigated if spatial proximity also affected the formation of SVs in noncancer cells. Hence, we...
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Research: ZNF91 deletion in human embryonic stem cells leads to ectopic activation of SVA retrotransposons and up-regulation of KRAB zinc finger gene clusters
- Nina L. Haring,
- Elisabeth J. van Bree,
- Whitney S. Jordaan,
- Judith R.E. Roels,
- Gonzalo Congrains Sotomayor,
- Tiziana M. Hey,
- Fred T.G. White,
- Marc D. Galland,
- Marten P. Smidt,
- and Frank M.J. Jacobs
Genome Res. April 2021 31: 551-563; Published in Advance March 15, 2021, doi:10.1101/gr.265348.120
...elusive. We analyzed the -wide binding profile for ZNF91 in human cells and found that ZNF91 interacts with the VNTR region of SVAs. Through CRISPR-Cas9-mediated deletion of ZNF91 in human embryonic stem cells, we established that loss of ZNF91 results in increased transcriptional activity of SVAs...
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Method: A novel assay to screen siRNA libraries identifies protein kinases required for chromosome transmission
- Mikhail Liskovykh,
- Nikolay V. Goncharov,
- Nikolai Petrov,
- Vasilisa Aksenova,
- Gianluca Pegoraro,
- Laurent L. Ozbun,
- William C. Reinhold,
- Sudhir Varma,
- Mary Dasso,
- Vadim Kumeiko,
- Hiroshi Masumoto,
- William C. Earnshaw,
- Vladimir Larionov,
- and Natalay Kouprina
Genome Res. October 2019 29: 1719-1732; Published in Advance September 12, 2019, doi:10.1101/gr.254276.119
...-by-side comparison of CRISPR/Cas9 and RNAi screens (Deans et al. 2016; Morgens et al. 2016; Schuster et al. 2019), indicating that the two screening technologies may identify different biological categories of genes or showed little correlation, which can be partially explained by the identification of distinct...
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Method: QuadST identifies cell–cell interaction–changed genes in spatially resolved transcriptomics data
- Xiaoyu Song,
- Yuqing Shang,
- Michelle E. Ehrlich,
- Panos Roussos,
- Guo-Cheng Yuan,
- and Pei Wang
Genome Res. August 2025 35: 1821-1831; Published in Advance June 23, 2025, doi:10.1101/gr.279859.124
...QuadST identifies cell–cell interaction–changed genes in spatially resolved transcriptomics data Xiaoyu Song1, Yuqing Shang1, Michelle E. Ehrlich2, Panos Roussos3,4, Guo-Cheng Yuan5 and Pei Wang6 1Centre for Quantitative Medicine, Duke-NUS Medical School, Singapore 169857; 2Departments of Neurology...
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