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Resource: MPRAbase a Massively Parallel Reporter Assay database
- Jingjing Zhao,
- Fotis A Baltoumas,
- Maxwell A Konnaris,
- Ioannis Mouratidis,
- Zhe Liu,
- Jasmine Sims,
- Vikram Agarwal,
- Georgios A Pavlopoulos,
- Ilias Georgakopoulos-Soares,
- and Nadav Ahituv
Genome Res. April 22, 2025 gr.280387.124; Published in Advance April 22, 2025, doi:10.1101/gr.280387.124
...MPRAbase A Massively Parallel Reporter Assay database Jingjing Zhao1,2,*, Fotis A. Baltoumas3,*, Maxwell A. Konnaris4,5, Ioannis Mouratidis4, Zhe Liu1,2,6, Jasmine Sims1,2, Vikram Agarwal7, Georgios A. Pavlopoulos3, Ilias Georgakopoulos-Soares4,♱, Nadav Ahituv1,2,♱ 1Department of Bioengineering...
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Research: ISWI1 complex proteins facilitate developmental genome editing in Paramecium
- Aditi Singh,
- Lilia Häußermann,
- Christiane Emmerich,
- Emily Nischwitz,
- Brandon K.B. Seah,
- Falk Butter,
- Mariusz Nowacki,
- and Estienne C. Swart
Genome Res. January 2025 35: 93-108; Published in Advance November 14, 2024, doi:10.1101/gr.278402.123
...ISWI1 complex proteins facilitate developmental editing in Paramecium Aditi Singh1,5, Lilia Häußermann1,5, Christiane Emmerich1, Emily Nischwitz2, Brandon K.B. Seah1, Falk Butter2,3, Mariusz Nowacki4 and Estienne C. Swart1 1Max Planck Institute for Biology, 72076 Tübingen, Germany; 2Institute...
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Research: Developmental transcriptomics in Pristionchus reveals the environmental responsiveness of a plasticity gene-regulatory network
- Shelley Reich,
- Tobias Loschko,
- Julie Jung,
- Samantha Nestel,
- Ralf J. Sommer,
- and Michael S. Werner
Genome Res. July 2025 35: 1560-1573; Published in Advance June 9, 2025, doi:10.1101/gr.279783.124
...Corresponding author: michael.werner@utah.eduAbstractDevelopmental plasticity enables the production of alternative phenotypes in response to different environmental conditions. Although significant advances in understanding the ecological and evolutionary implications of plasticity have been made...
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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
...Embryo covers more developmental stages.Next, we compared dbEmbryo with other databases through characteristic tools. The unique aspect of EMAGE is that it contains standardized spatial representations of the sites of gene expression for each gene, denoted against a set of virtual reference embryo models...
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Research: Single-cell spatial transcriptomics reveals a dystrophic trajectory following a developmental bifurcation of myoblast cell fates in facioscapulohumeral muscular dystrophy
- Lujia Chen,
- Xiangduo Kong,
- Kevin G. Johnston,
- Ali Mortazavi,
- Todd C. Holmes,
- Zhiqun Tan,
- Kyoko Yokomori,
- and Xiangmin Xu
Genome Res. May 2024 34: 665-679; Published in Advance May 22, 2024, doi:10.1101/gr.278717.123
...as the individual nuclei within them. We find myocyte nuclei segregate into two clusters defined by the expression of DUX4 target genes, which is exclusively found in patient/mutant nuclei, whereas MNCs cluster based on developmental states. Patient/mutant myotubes are found in “FSHD-hi” and “FSHD-lo” states...
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Research: Aberrant homeodomain–DNA cooperative dimerization underlies distinct developmental defects in two dominant CRX retinopathy models
- Yiqiao Zheng,
- Gary D. Stormo,
- and Shiming Chen
Genome Res. February 2025 35: 242-256; Published in Advance December 23, 2024, doi:10.1101/gr.279340.124
...Aberrant homeodomain–DNA cooperative dimerization underlies distinct developmental defects in two dominant CRX retinopathy models Yiqiao Zheng1,2,5, Gary D. Stormo3 and Shiming Chen2,4 1Molecular Genetics and Genomics Graduate Program, Division of Biology & Biomedical Sciences, Washington...
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Method: High-throughput single-cell functional elucidation of neurodevelopmental disease–associated genes reveals convergent mechanisms altering neuronal differentiation
- Matthew A. Lalli,
- Denis Avey,
- Joseph D. Dougherty,
- Jeffrey Milbrandt,
- and Robi D. Mitra
Genome Res. September 2020 30: 1317-1331; Published in Advance September 4, 2020, doi:10.1101/gr.262295.120
...studies in discovering thousands of disease-associated genes necessitates developing novel high-throughput functional genomics approaches to elucidate the molecular mechanisms of these genes. Here, we have coupled multiplexed repression of neurodevelopmental disease–associated genes to single...
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Resource: Zebrafish transposable elements show extensive diversification in age, genomic distribution, and developmental expression
- Ni-Chen Chang,
- Quirze Rovira,
- Jonathan Wells,
- Cédric Feschotte,
- and Juan M. Vaquerizas
Genome Res. July 2022 32: 1408-1423; Published in Advance January 5, 2022, doi:10.1101/gr.275655.121
...they have exploited distinct cellular niches to propagate, these activities may also be integrated in normal developmental programs. For example, the expression of the murine long interspersed nuclear element-1 family (LINE-1) can be detected shortly after fertilization and peaks at the two-cell stage...
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Perspective: Ribosome decision graphs for the representation of eukaryotic RNA translation complexity
- Jack A.S. Tierney,
- Michał Świrski,
- Håkon Tjeldnes,
- Jonathan M. Mudge,
- Joanna Kufel,
- Nicola Whiffin,
- Eivind Valen,
- and Pavel V. Baranov
Genome Res. April 2024 34: 530-538; Published in Advance May 7, 2024, doi:10.1101/gr.278810.123
...for the apparent multitude of translated regions within the same molecules. They also do not take into account the stochasticity of the process that allows alternative translations of the same RNA molecules by different ribosomes. There is a need for formal representations of mRNA complexity that would enable...
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Research: Single-cell transcriptome and metagenome profiling reveals the genetic basis of rumen functions and convergent developmental patterns in ruminants
- Juan Deng,
- Ya-Jing Liu,
- Wen-Tian Wei,
- Qi-Xuan Huang,
- Li-Ping Zhao,
- Ling-Yun Luo,
- Qi Zhu,
- Lin Zhang,
- Yuan Chen,
- Yan-Ling Ren,
- Shan-Gang Jia,
- Yu-Luan Lin,
- Ji Yang,
- Feng-Hua Lv,
- Hong-Ping Zhang,
- Feng-E Li,
- Li Li,
- and Meng-Hua Li
Genome Res. October 2023 33: 1690-1707; Published in Advance October 26, 2023, doi:10.1101/gr.278239.123
..., proliferated significantly after the late embryonic stage (E3) in sheep and the middle embryonic stage (E2) in goats (Fig. 1A,B). Similar developmental patterns were also observed in different goat cell types (Fig. 1B). Altogether, we generated a spatial and temporal representation of cellular diversity...
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