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Research: Transposon insertional mutagenesis in Saccharomyces uvarum reveals trans-acting effects influencing species-dependent essential genes
- Monica R. Sanchez,
- Celia Payen,
- Frances Cheong,
- Blake T. Hovde,
- Sarah Bissonnette,
- Adam P. Arkin,
- Jeffrey M. Skerker,
- Rachel B. Brem,
- Amy A. Caudy,
- and Maitreya J. Dunham
Genome Res. March 2019 29: 396-406; Published in Advance January 11, 2019, doi:10.1101/gr.232330.117
...@uw.eduAbstractTo understand how complex genetic networks perform and regulate diverse cellular processes, the function of each individual component must be defined. Comprehensive phenotypic studies of mutant alleles have been successful in model organisms in determining what processes depend on the normal function of a gene...
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Methods: Inference of RhoGAP/GTPase regulation using single-cell morphological data from a combinatorial RNAi screen
- Oaz Nir,
- Chris Bakal,
- Norbert Perrimon,
- and Bonnie Berger
Genome Res. March 2010 20: 372-380; Published in Advance February 9, 2010, doi:10.1101/gr.100248.109
..., systems-level description is known (Friedman and Perrimon 2007). Recent advances in genomics and proteomics have transformed the field of signal transduction, as large-scale approaches allow systematic interrogation of the using RNAi and mapping of PPIs using mass spectrometry. In turn, computational...
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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
...allows regulator/target coexpression analysis (Tsherniak et al. 2017), and the Xena Browser (Goldman et al. 2015), which can also be used to correlate variation with expression (both of GOI and of candidate TF). It is, however, important to remember that DepMap does not validate successful knockout...
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Method: De novo individualized disease modules reveal the synthetic penetrance of genes and inform personalized treatment regimens
- Taylor M. Weiskittel,
- Choong Y. Ung,
- Cristina Correia,
- Cheng Zhang,
- and Hu Li
Genome Res. January 2022 32: 124-134; Published in Advance December 7, 2021, doi:10.1101/gr.275889.121
....Pooled -omic data from patient samples have enabled construction of cellular interaction modules that provides a system-level understanding of disease etiology. This new conceptualization of disease has led to discoveries of previously unknown mechanisms and has significantly expanded opportunities...
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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
...(Calbo et al. 2011). Similarly, Wnt1-driven mammary gland tumors can evolve two clones, with the Hras-mutated clone acquiring a basal-like proliferative phenotype (Cleary et al. 2014).View larger version: In this window In a new window Figure 2. Cell- and system-level view of intratumor heterogeneity...
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Research: DNA methylation changes induced by long and short photoperiods in Nasonia
- Mirko Pegoraro,
- Akanksha Bafna,
- Nathaniel J. Davies,
- David M. Shuker,
- and Eran Tauber
Genome Res. February 2016 26: 203-210; Published in Advance December 15, 2015, doi:10.1101/gr.196204.115
...complement. Following injection, surviving females were collected and kept in different photoperiods as above. qPCR (SYBR green-based) was carried to determine transcript levels of the targeted gene, using the standard curve method. Aequeorin mRNA (a jellyfish photoreceptor) was spiked to the RNA samples...
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Method: Model-driven mapping of transcriptional networks reveals the circuitry and dynamics of virulence regulation
- Ezekiel J. Maier,
- Brian C. Haynes,
- Stacey R. Gish,
- Zhuo A. Wang,
- Michael L. Skowyra,
- Alyssa L. Marulli,
- Tamara L. Doering,
- and Michael R. Brent
Genome Res. May 2015 25: 690-700; Published in Advance February 2, 2015, doi:10.1101/gr.184101.114
...pattern, these TFs explain much of the transcriptional dynamics of capsule induction. Phenotypic analysis of TF deletion mutants revealed complex relationships among virulence factors and virulence in mice. These resources and analyses provide the first integrated, systems-level view of capsule regulation...
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Method: Bacterial genome reduction using the progressive clustering of deletions via yeast sexual cycling
- Yo Suzuki,
- Nacyra Assad-Garcia,
- Maxim Kostylev,
- Vladimir N. Noskov,
- Kim S. Wise,
- Bogumil J. Karas,
- Jason Stam,
- Michael G. Montague,
- Timothy J. Hanly,
- Nico J. Enriquez,
- Adi Ramon,
- Gregory M. Goldgof,
- R. Alexander Richter,
- Sanjay Vashee,
- Ray-Yuan Chuang,
- Elizabeth A. Winzeler,
- Clyde A. Hutchison III,
- Daniel G. Gibson,
- Hamilton O. Smith,
- John I. Glass,
- and J. Craig Venter
Genome Res. March 2015 25: 435-444; Published in Advance February 5, 2015, doi:10.1101/gr.182477.114
..., La Jolla, California 92093, USA Corresponding author: ysuzuki@jcvi.org Abstract The availability of genetically tractable organisms with simple genomes is critical for the rapid, systems-level understanding of basic biological processes. Mycoplasma bacteria, with the smallest...
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Method: Prioritizing candidate disease genes by network-based boosting of genome-wide association data
- Insuk Lee,
- U. Martin Blom,
- Peggy I. Wang,
- Jung Eun Shim,
- and Edward M. Marcotte
Genome Res. July 2011 21: 1109-1121; Published in Advance May 2, 2011, doi:10.1101/gr.118992.110
...notable, as such genes might be useful as cancer cell-specific drug targets (Luo et al. 2009). More generally, these tests confirm that the human gene network is predictive of a variety of cellular level loss-of-function phenotypes, including specific bigenic traits. Genes linked to specific mouse...
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RECOMB Special/Review: Protein networks in disease
- Trey Ideker and
- Roded Sharan
Genome Res. April 2008 18: 644-652; doi:10.1101/gr.071852.107
...are based on the observation that the chemical–genetic interaction profile of an agent is similar to the genetic interaction profile of genes in its target pathway. Moreover, gene deletions that result in hypersensitivity to a specific drug can identify pathways that buffer the cell against the toxic...
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