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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
...relevance, integrating the origin of DNA and protein elements (cis and trans) to evaluate false-positive and false-negative risks across experimental systems. Moreover, we explore how perturbation strategies—gain and loss of function—can complement steady-state profiling to establish causality in gene...
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Research: tRNA-derived small RNAs are embedded in the gene regulatory network instructing Drosophila metamorphosis
- Junling Shi,
- Jiaqi Xu,
- Jun Ma,
- and Feng He
Genome Res. December 2023 33: 2119-2132; Published in Advance November 16, 2023, doi:10.1101/gr.278128.123
...development of mouse and zebrafish (Chen et al. 2016, 2021a). These diverse and context-dependent functions of tsRNAs suggest a need for a comprehensive profiling and functional analysis of tsRNAs at the systems level within a developmental context.Development is a process in which cells can adaptively...
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Research: Sex differences in human adipose tissue gene expression and genetic regulation involve adipogenesis
- Warren D. Anderson,
- Joon Yuhl Soh,
- Sarah E. Innis,
- Alexis Dimanche,
- Lijiang Ma,
- Carl D. Langefeld,
- Mary E. Comeau,
- Swapan K. Das,
- Eric E. Schadt,
- Johan L.M. Björkegren,
- and Mete Civelek
Genome Res. October 2020 30: 1379-1392; Published in Advance September 23, 2020, doi:10.1101/gr.264614.120
...-biased gene set identified through our analyses.View this table: In this window In a new window Table 1. Cohort sample characteristics: sample sizes, data attributes, and acquisition informationWe next investigated the degree to which the observed sex differences in gene expression were context-dependent. We...
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Research: A high-resolution gene expression atlas links dedicated meristem genes to key architectural traits
- Steffen Knauer,
- Marie Javelle,
- Lin Li,
- Xianran Li,
- Xiaoli Ma,
- Kokulapalan Wimalanathan,
- Sunita Kumari,
- Robyn Johnston,
- Samuel Leiboff,
- Robert Meeley,
- Patrick S. Schnable,
- Doreen Ware,
- Carolyn Lawrence-Dill,
- Jianming Yu,
- Gary J. Muehlbauer,
- Michael J. Scanlon,
- and Marja C.P. Timmermans
Genome Res. December 2019 29: 1962-1973; Published in Advance November 19, 2019, doi:10.1101/gr.250878.119
...that facilitates binding of other TFs to regulate target gene expression in this context-dependent manner (Reiter et al. 2017). However, given that KN1 primarily targets genes that function in organ primordia, an alternative, nonmutually exclusive view for the contribution of KN1 to SAM function...
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Research: Alternative splicing modulated by genetic variants demonstrates accelerated evolution regulated by highly conserved proteins
- Yun-Hua Esther Hsiao,
- Jae Hoon Bahn,
- Xianzhi Lin,
- Tak-Ming Chan,
- Rena Wang,
- and Xinshu Xiao
Genome Res. April 2016 26: 440-450; Published in Advance February 17, 2016, doi:10.1101/gr.193359.115
...exons. We observed that GMAS events are highly cell type independent, indicating that splicing-altering genetic variants could have widespread function across cell types. Interestingly, GMAS genes, exons, and single-nucleotide variants (SNVs) all demonstrated positive selection or accelerated evolution...
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Perspective: Insights into neural crest development and evolution from genomic analysis
- Marcos Simões-Costa and
- Marianne E. Bronner
Genome Res. July 2013 23: 1069-1080; doi:10.1101/gr.157586.113
...and colleagues shows that the zebrafish pax3a gene expression is also controlled by two distinct enhancers. Although manipulations in BMP, Wnt, and FGF signaling disrupt the activity of the individual enhancers, when combined in the same construct, they are less susceptible to environmental perturbations. Thus...
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Research: A systems level predictive model for global gene regulation of methanogenesis in a hydrogenotrophic methanogen
- Sung Ho Yoon,
- Serdar Turkarslan,
- David J. Reiss,
- Min Pan,
- June A. Burn,
- Kyle C. Costa,
- Thomas J. Lie,
- Joseph Slagel,
- Robert L. Moritz,
- Murray Hackett,
- John A. Leigh,
- and Nitin S. Baliga
Genome Res. November 2013 23: 1839-1851; Published in Advance October 2, 2013, doi:10.1101/gr.153916.112
...-state and time-course experiments that were performed in chemostats or batch cultures under a spectrum of environmental perturbations that modulated methanogenesis. Analyses of the EGRIN model have revealed novel components of methanogenesis that included at least three additional protein-coding genes...
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Research: Parallel evolution of transcriptome architecture during genome reorganization
- Sung Ho Yoon,
- David J. Reiss,
- J. Christopher Bare,
- Dan Tenenbaum,
- Min Pan,
- Joseph Slagel,
- Robert L. Moritz,
- Sujung Lim,
- Murray Hackett,
- Angeli Lal Menon,
- Michael W.W. Adams,
- Adam Barnebey,
- Steven M. Yannone,
- John A. Leigh,
- and Nitin S. Baliga
Genome Res. November 2011 21: 1892-1904; Published in Advance July 12, 2011, doi:10.1101/gr.122218.111
...of transcription starts and stops inside operons and coding sequences (Croucher and Thomson 2010; Sorek and Cossart 2010). Importantly, it is now clear that multiple transcriptional units can be generated from the same set of genes in diverse environmental conditions. Such context-dependent modulation of over 40...
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Perspective: Cancer cell states and emergent properties of the dynamic tumor system
- Dalia Barkley,
- Anjali Rao,
- Maayan Pour,
- Gustavo S. França,
- and Itai Yanai
Genome Res. October 2021 31: 1719-1727; doi:10.1101/gr.275308.121
...be genetic or nongenetic (Marusyk et al. 2012). Genetic intra-tumoral heterogeneity has been extensively studied and is one of the prerequisites for tumor evolution resulting in therapeutic failure (Hu et al. 2017; McGranahan and Swanton 2017). However, recent work has revealed the prevalence of nongenetic...
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Method: Identification of determinants of differential chromatin accessibility through a massively parallel genome-integrated reporter assay
- Jennifer Hammelman,
- Konstantin Krismer,
- Budhaditya Banerjee,
- David K. Gifford,
- and Richard I. Sherwood
Genome Res. October 2020 30: 1468-1480; Published in Advance September 24, 2020, doi:10.1101/gr.263228.120
..., which enables changes to gene expression during development or disease or as a response to environmental stimuli. However, the regulation of DNA accessibility via the recruitment of transcription factors is difficult to study in the context of the native because every genomic site is distinct...
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