Searching journal content for articles similar to Wong et al. 25 (2): 167.

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Resource: Common and specific gene regulatory programs in zebrafish caudal fin regeneration at single-cell resolution
- Yujie Chen,
- Yiran Hou,
- Qinglin Zeng,
- Irene Wang,
- Meiru Shang,
- Kwangdeok Shin,
- Christopher Hemauer,
- Xiaoyun Xing,
- Junsu Kang,
- Guoyan Zhao,
- and Ting Wang
Genome Res. January 2025 35: 202-218; Published in Advance January 14, 2025, doi:10.1101/gr.279372.124
...-type/lineage-specific marker genes, and characterize transitions of cellular transcriptional states during zebrafish caudal fin regeneration (Hou et al. 2020; Jiang et al. 2021; Tang et al. 2022; Lewis et al. 2023; Cudak et al. 2024). Similar approaches have been applied in other regenerative contexts, such as the zebrafish...
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Research: Sex-biased microRNA expression in mammals and birds reveals underlying regulatory mechanisms and a role in dosage compensation
- Maria Warnefors,
- Katharina Mössinger,
- Jean Halbert,
- Tania Studer,
- John L. VandeBerg,
- Isa Lindgren,
- Amir Fallahshahroudi,
- Per Jensen,
- and Henrik Kaessmann
Genome Res. December 2017 27: 1961-1973; Published in Advance October 27, 2017, doi:10.1101/gr.225391.117
...revealed thousands of sex-biased genes in mammals and birds (Yang et al. 2006; Itoh et al. 2010; Harrison et al. 2015; Melé et al. 2015). Less attention has been given to the potential impact of sex-biased microRNAs (miRNAs)—short regulatory RNAs (∼21 nt) that enable expression fine-tuning of target m...
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Research: Long-range promoter–enhancer contacts are conserved during evolution and contribute to gene expression robustness
- Alexandre Laverré,
- Eric Tannier,
- and Anamaria Necsulea
Genome Res. February 2022 32: 280-296; Published in Advance December 20, 2021, doi:10.1101/gr.275901.121
...a challenging task. Transcription is regulated through complex interactions between trans-acting factors and cis-acting elements. Genes are typically associated with multiple cis-acting elements, which can refine their expression levels, control different expression domains, or confer robustness through partial...
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Research: Independent evolution of transcript abundance and gene regulatory dynamics
- Gat Krieger,
- Offir Lupo,
- Avraham A. Levy,
- and Naama Barkai
Genome Res. July 2020 30: 1000-1011; Published in Advance July 22, 2020, doi:10.1101/gr.261537.120
...expression play key roles in early evolutionary divergence (King and Wilson 1975). In support of that, modifying the expression of a single, differentiation-promoting gene during organism development can give rise to novel body morphologies (Warren et al. 1994; Prud'homme et al. 2006). Although transcription...
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Research: Differences in firing efficiency, chromatin, and transcription underlie the developmental plasticity of the Arabidopsis DNA replication origins
- Joana Sequeira-Mendes,
- Zaida Vergara,
- Ramon Peiró,
- Jordi Morata,
- Irene Aragüez,
- Celina Costas,
- Raul Mendez-Giraldez,
- Josep M. Casacuberta,
- Ugo Bastolla,
- and Crisanto Gutierrez
Genome Res. May 2019 29: 784-797; Published in Advance March 7, 2019, doi:10.1101/gr.240986.118
...,B; Supplemental Fig. S8). This is particularly striking for ORIs in Polycomb chromatin (state 5) and to a lesser extent in the AT-rich heterochromatin (state 8), where a strong enhancement of transcription in 4-d-old seedlings was observed. The opposite happens for the active regions of long genes (state 7...
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Research: Intragenic repeat expansion in the cell wall protein gene HPF1 controls yeast chronological aging
- Benjamin P. Barré,
- Johan Hallin,
- Jia-Xing Yue,
- Karl Persson,
- Ekaterina Mikhalev,
- Agurtzane Irizar,
- Sylvester Holt,
- Dawn Thompson,
- Mikael Molin,
- Jonas Warringer,
- and Gianni Liti
Genome Res. May 2020 30: 697-710; Published in Advance April 10, 2020, doi:10.1101/gr.253351.119
...abundances (eight and three genes changing greater than twofold in calorie-rich and rapamycin media, respectively) (Fig. 5A,B). The known low oxygen responders TIR1 and ANB1 (Lowry and Lieber 1986; Cohen et al. 2001) were repressed by oxygen (i.e., in WA-HPF1). Five of the six transcripts induced...
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Research: The evolution of duplicate gene expression in mammalian organs
- Katerina Guschanski,
- Maria Warnefors,
- and Henrik Kaessmann
Genome Res. September 2017 27: 1461-1474; Published in Advance July 25, 2017, doi:10.1101/gr.215566.116
...generate genomic raw material that allows the emergence of novel functions, likely facilitating adaptive evolutionary innovations. However, global assessments of the functional and evolutionary relevance of duplicate genes in mammals were until recently limited by the lack of appropriate comparative data...
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Research: A quantitative framework for characterizing the evolutionary history of mammalian gene expression
- Jenny Chen,
- Ross Swofford,
- Jeremy Johnson,
- Beryl B. Cummings,
- Noga Rogel,
- Kerstin Lindblad-Toh,
- Wilfried Haerty,
- Federica di Palma,
- and Aviv Regev
Genome Res. January 2019 29: 53-63; Published in Advance December 14, 2018, doi:10.1101/gr.237636.118
...no consensus on a quantitative framework for addressing the functional questions related to evolution of expression levels, due in part to a lack of agreement for how to best model expression evolution in mammals. In Drosophila, studies have found that unlike sequence evolution, divergence of gene expression...
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Research: Conserved microRNA targeting reveals preexisting gene dosage sensitivities that shaped amniote sex chromosome evolution
- Sahin Naqvi,
- Daniel W. Bellott,
- Kathy S. Lin,
- and David C. Page
Genome Res. April 2018 28: 474-483; Published in Advance February 15, 2018, doi:10.1101/gr.230433.117
...autosomes through cross-species sequence alignments. As miRNA targeting occurs post-transcriptionally, reconstruction of its ancestral state is decoupled from transcriptional regulatory mechanisms such as XCI that evolved following X-Y differentiation.ResultsAnalysis of human copy number variation indicates...
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Research: Estrogen-induced chromatin looping changes identify a subset of functional regulatory elements
- Hosiana Abewe,
- Alexandra Richey,
- Jeffery M. Vahrenkamp,
- Matthew Ginley-Hidinger,
- Craig M. Rush,
- Noel Kitchen,
- Xiaoyang Zhang,
- and Jason Gertz
Genome Res. March 2025 35: 393-403; Published in Advance March 3, 2025, doi:10.1101/gr.279699.124
...of Utah, Salt Lake City, Utah 84112, USA; 3Department of Biomedical Engineering, University of Utah, Salt Lake City, Utah 84112, USA Corresponding author: jay.gertz@hci.utah.eduAbstractTranscriptional enhancers can regulate individual or multiple genes through long-range three-dimensional (3D...

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