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Method: Recovering gene regulatory networks in single-cell multi-omics data with PRISM-GRN
- Wenhao Zhang,
- Lan Cao,
- Xiaoxuan Gu,
- Yongyu Long,
- and Ying Wang
Genome Res. January 2026 36: 142-158; Published in Advance October 9, 2025, doi:10.1101/gr.280757.125
..., and interpretable exploration of causal GRNs with prior knowledge and multi-omics data.Gene regulatory networks (GRNs), which encapsulate the complex interactions among transcription factors (TFs), target genes, and various regulatory elements, constitute the core machinery of gene regulation (Levine and Davidson...
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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
...fate toward specific lineages at a single-cell level. iTF-seq enables time course monitoring of transcriptome changes, and with biotinylated individual TFs, it provides a multi-omics approach to understanding the mechanisms behind TF-mediated cell fate changes. Our iTF-seq study in mouse embryonic stem...
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Resource: dbEmbryo multi-omics database for analyses of synergistic regulation in early mammalian embryo development
- Xin Huang,
- Xiaohan Tang,
- Xuemei Bai,
- Honglei Li,
- Huan Tao,
- Junting Wang,
- Yaru Li,
- Yu Sun,
- Yang Zheng,
- Xiang Xu,
- Longteng Wang,
- Yang Ding,
- Meisong Lu,
- Pingkun Zhou,
- Xiaochen Bo,
- Hao Li,
- and Hebing Chen
Genome Res. August 2022 32: 1612-1625; Published in Advance August 17, 2022, doi:10.1101/gr.276744.122
...involved in gametogenesis and relate them to experiments, they can choose GED. Methbank 3.0 is a good choice for digging deeper into methylation data. DevOmics is suitable for multi-omics data analyses.Application and summary: a phase-separated model of transcriptional control during early embryo...
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Research: Single-cell multi-omics of human preimplantation embryos shows susceptibility to glucocorticoids
- Cheng Zhao,
- Savana Biondic,
- Katherine Vandal,
- Åsa K. Björklund,
- Michael Hagemann-Jensen,
- Theresa Maria Sommer,
- Jesica Canizo,
- Stephen Clark,
- Pascal Raymond,
- Daniel R. Zenklusen,
- Nicolas Rivron,
- Wolf Reik,
- and Sophie Petropoulos
Genome Res. September 2022 32: 1627-1641; Published in Advance August 10, 2022, doi:10.1101/gr.276665.122
...in dysregulation of metabolic pathways. We examined the direct effect of glucocorticoid exposure, low-dose dexamethasone (DEX), from embryonic day (E) 4 (before lineage specification) until E7 (blastocyst stage after mural–polar specification has initiated). On E7, we used a single-cell multi-omics approach...
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Method: Spatial domain detection using contrastive self-supervised learning for spatial multi-omics technologies
- Jianing Yao,
- Jinglun Yu,
- Brian Caffo,
- Stephanie C. Page,
- Keri Martinowich,
- and Stephanie C. Hicks
Genome Res. July 2025 35: 1621-1632; Published in Advance May 20, 2025, doi:10.1101/gr.279380.124
...in Healthcare, Johns Hopkins University, Baltimore, Maryland 21218, USA Corresponding author: shicks19@jhu.eduAbstractRecent advances in spatially resolved single-omic and multi-omics technologies have led to the emergence of computational tools to detect and predict spatial domains. Additionally, histological...
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Research: Characterization of the distribution and dynamics of chromatin states in the C. elegans germline reveals substantial H3K4me3 remodeling during oogenesis
- Mariateresa Mazzetto,
- Lauren E. Gonzalez,
- Nancy Sanchez,
- and Valerie Reinke
Genome Res. January 2024 34: 57-69; Published in Advance December 26, 2023, doi:10.1101/gr.278247.123
...examples highlight the heterogeneity found in oogenesis genes (Supplemental Fig. S5C–E). For genes found in states 8 (active TSS), 9 (active TSS–gene body), 10 (high transcription), and 12 (euchromatin), GO analysis revealed an enrichment for categories related to gamete generation and reproduction...
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Resource: Pan-cancer multi-omics analysis and orthogonal experimental assessment of epigenetic driver genes
- Andrea Halaburkova,
- Vincent Cahais,
- Alexei Novoloaca,
- Mariana Gomes da Silva Araujo,
- Rita Khoueiry,
- Akram Ghantous,
- and Zdenko Herceg
Genome Res. October 2020 30: 1517-1532; Published in Advance September 22, 2020, doi:10.1101/gr.268292.120
...and multi-omics algorithms, and an orthogonal in vitro screen (CRISPR-Cas9) targeting all ERGs revealed genes with driver roles within and across malignancies and shared driver mechanisms operating across multiple cancer types and hallmarks. This is the largest and most comprehensive analysis thus far...
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Research: Tyrosine 1–phosphorylated RNA polymerase II transcribes PROMPTs to facilitate proximal promoter pausing and induce global transcriptional repression in response to DNA damage
- Kamal Ajit,
- Adele Alagia,
- Kaspar Burger,
- and Monika Gullerova
Genome Res. February 2024 34: 201-216; Published in Advance March 11, 2024, doi:10.1101/gr.278644.123
...-induced transcriptional repression and remains enigmatic.The pausing of newly recruited RNA Pol II at the promoter is a critical step of transcription regulation in mammals (Gressel et al. 2019). RNA Pol II pausing occurs within a 200-bp region downstream from the TSS, where it accumulates until the positive elongation...
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Method: Mapping the regulatory landscape of auditory hair cells from single-cell multi-omics data
- Shuze Wang,
- Mary P. Lee,
- Scott Jones,
- Jie Liu,
- and Joerg Waldhaus
Genome Res. October 2021 31: 1885-1899; Published in Advance April 9, 2021, doi:10.1101/gr.271080.120
...cells and supporting cells after birth. Using an integrative approach, we predicted cell type–specific activating and repressing functions of developmental transcription factors. Furthermore, by integrating gene expression and chromatin accessibility data sets, we reconstructed gene regulatory networks...
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Research: Androgen receptor–mediated assisted loading of the glucocorticoid receptor modulates transcriptional responses in prostate cancer cells
- Johannes Hiltunen,
- Laura Helminen,
- Niina Aaltonen,
- Kaisa-Mari Launonen,
- Hanna Laakso,
- Marjo Malinen,
- Einari A. Niskanen,
- Jorma J. Palvimo,
- and Ville Paakinaho
Genome Res. August 2025 35: 1717-1732; Published in Advance June 2, 2025, doi:10.1101/gr.280224.124
...). Antiandrogen therapy relieves this repression, leading to an increase in GR expression, allowing GR to partially replace AR on chromatin. Although this replacement is incomplete, it is sufficient for GR to regulate critical AR target genes, facilitating drug resistance and cancer progression (Arora et al. 2013...
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