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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
...and protein profiling in the same single human embryonic stem cells (Reimegard et al. 2021). (Lower left) Estimated translational efficiency and expression noise. The normalized RNA variation was for select genes subtracted from the normalized protein variation, and the genes were divided into three groups...
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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
...identity factors from the original Sunbear model (Supplemental Fig. S8). These results suggest the importance of explicitly encoding condition and batch factors and representing time with a sinusoidal encoding.Sunbear reveals sexual dimorphism in gene expression during mouse embryonic development...
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Review: A systematic guide for identifying transcription factors that directly regulate the expression of a gene of interest
- Andrew D. Bates,
- Dawid Grzela,
- Maciej Studzian,
- Louise Brennan,
- Moli Williams,
- Conor Fawcett,
- Beth Hammond,
- Manreen Grewal,
- Marcin Ratajewski,
- Lukasz Pulaski,
- and Urszula L. McClurg
Genome Res. March 2026 36: 433-459; Published in Advance February 17, 2026, doi:10.1101/gr.281154.125
..., hinging on the precise binding of transcription factors (TFs) and cofactors to gene regulatory elements such as promoters and enhancers. Although it is relatively routine to profile -wide DNA binding landscapes of proteins, identifying the specific proteins that bind to, and regulate the transcription of...
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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
...and lose potency, these broad H3K4me3 domains become refined (Zhang et al. 2021). Further, broad H3K27me3 enrichment across gene bodies is associated with gene repression (Young et al. 2011). To investigate whether broad histone modification patterns are present in the two populations of stem cells...
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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
...depleted of genes compared to the rest of the (Hannibal et al. 2014). The genes that were found in mouse UR regions were enriched for cell adhesion and neurogenesis annotations, similar to haploid-delayed variants, which contained both cell-adhesion genes and several categories of genes related...
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Method: Kinetic measurement of gene-specific RNA polymerase II transcription elongation rates
- Haiyue Liu and
- Lea H. Gregersen
Genome Res. November 2025 35: 2550-2562; Published in Advance October 22, 2025, doi:10.1101/gr.280852.125
...point mutations or factor perturbations followed by average RNAPII rate estimation have associated RNAPII speed with functionality, direct measurements of RNAPII transcription elongation rates for individual genes and their correlation with chromatin modifications, RNAPII-associated cofactors, or 3′end...
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Research: Xist upstream deletion leads to dysregulation of Xist and autosomal gene expression
- Sudeshna Majumdar,
- Lakshmi Sowjanya Bammidi,
- Hemant C. Naik,
- Avinchal Manhas,
- Runumi Baro,
- Akash Kalita,
- Amlan Jyoti Naskar,
- Sundarraj Nidharshan,
- Girija S. Bariha,
- Dimple Notani,
- and Srimonta Gayen
Genome Res. September 2025 35: 1992-2010; Published in Advance August 6, 2025, doi:10.1101/gr.279822.124
...) lying between Tsix and Jpx in the regulation of Xist and XCI in mouse extra-embryonic endoderm stem cells (XEN), which represent the maintenance phase of imprinted XCI. Here, we show that the deletion of this Xist upstream sequence in the inactive X leads to the upregulation of Xist expression...
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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
...sample, and the rest was used for chromatin immunoprecipitation (ChIP). Fifty microliters of Dynabeads M-280 sheep anti-rabbit IgG (Invitrogen) were washed three times with 0.5% BSA in PBS before incubating with 5 μg rabbit anti-GFP (Abcam ab290), 3.75 μL rabbit anti-H3K4me3 (Millipore 07-473, lot...
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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
...interactions. Here, we use the mouse embryonic stem cell (mESC) model to describe in detail the relationships within the H3K27-H3K36-DNA methylation subnetwork. In particular, we focus on the major epigenetic reorganization caused by deletion of the histone 3 lysine 36 methyltransferase NSD1, which in m...
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Method: A scalable computational framework for predicting gene expression from candidate cis-regulatory elements
- Qinhu Zhang,
- Siguo Wang,
- Zhipeng Li,
- Wenzheng Bao,
- Wenjian Liu,
- and De-Shuang Huang
Genome Res. February 2026 36: 361-374; Published in Advance January 16, 2026, doi:10.1101/gr.281219.125
...that are grouped by TF family and are often enriched in proximal or distal regulatory regions. For instance, SP1-like TFs activate or repress basal transcription by usually binding to the GC box (GGGCGG) or GT/CACC box in the promoter region of many genes. CTCF-like TFs not only function as transcriptional...
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