ArticleProceedings of the National Academy of Sciences of the United States of America2016
Model-based transcriptome engineering promotes a fermentative transcriptional state in yeast.
Article in Proceedings of the National Academy of Sciences of the United States of America, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 22 papers.
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Who cites it
22 citing papers in PubMed, 37 citations in OpenAlex.
- Modular deregulation of central carbon metabolism for efficient xylose utilization in Saccharomyces cerevisiae.Nature communications · 2025Article
- 3D Hydrogel Culture System Recapitulates Key Tuberculosis Phenotypes and Demonstrates Pyrazinamide Efficacy.Advanced healthcare materials · 2025Article
- FUN-PROSE: A deep learning approach to predict condition-specific gene expression in fungi.PLoS computational biology · 2023Article
- Engineering ofEngineering microbiology · 2023Review
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- Disrupting the ArcA Regulatory Network Amplifies the Fitness Cost of Tetracycline Resistance in Escherichia coli.mSystems · 2023Article
- Performing in spite of starvation: How Saccharomyces cerevisiae maintains robust growth when facing famine zones in industrial bioreactors.Microbial biotechnology · 2023Article
- Deletion ofFrontiers in microbiology · 2022Article
- Different transcriptional responses of haploid and diploid S. cerevisiae strains to changes in cofactor preference of XR.Microbial cell factories · 2020Article
- Dual threshold optimization and network inference reveal convergent evidence from TF binding locations and TF perturbation responses.Genome research · 2020Article
- Path-seq identifies an essential mycolate remodeling program for mycobacterial host adaptation.Molecular systems biology · 2019Article
- Rewired cellular signaling coordinates sugar and hypoxic responses for anaerobic xylose fermentation in yeast.PLoS genetics · 2019Article
- Integrated Epigenetic Mapping of Human and Mouse Salivary Gene Regulation.Journal of dental research · 2019Article
- A Thi2p Regulatory Network Controls the Post-glucose Effect of Xylose Utilization inFrontiers in microbiology · 2019Article
- Pentose Metabolism in Saccharomyces cerevisiae: The Need to Engineer Global Regulatory Systems.Biotechnology journal · 2019Review
- ATAC2GRN: optimized ATAC-seq and DNase1-seq pipelines for rapid and accurate genome regulatory network inference.BMC genomics · 2018Article
- A semi-synthetic regulon enables rapid growth of yeast on xylose.Nature communications · 2018Article
- NetProphet 2.0: mapping transcription factor networks by exploiting scalable data resources.Bioinformatics (Oxford, England) · 2018Article
- Disruption of the transcription factors Thi2p and Nrm1p alleviates the post-glucose effect on xylose utilization inBiotechnology for biofuels · 2018Article
- Association of improved oxidative stress tolerance and alleviation of glucose repression with superior xylose-utilization capability by a natural isolate ofBiotechnology for biofuels · 2018Article
Corrections and comments
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Authors and funding
7 authors at 1 institution in 1 country.
Funding
Abstract
The ability to rationally manipulate the transcriptional states of cells would be of great use in medicine and bioengineering. We have developed an algorithm, NetSurgeon, which uses genome-wide gene-regulatory networks to identify interventions that force a cell toward a desired expression state. We first validated NetSurgeon extensively on existing datasets. Next, we used NetSurgeon to select transcription factor deletions aimed at improving ethanol production in Saccharomyces cerevisiae cultures that are catabolizing xylose. We reasoned that interventions that move the transcriptional state of cells using xylose toward that of cells producing large amounts of ethanol from glucose might improve xylose fermentation. Some of the interventions selected by NetSurgeon successfully promoted a fermentative transcriptional state in the absence of glucose, resulting in strains with a 2.7-fold increase in xylose import rates, a 4-fold improvement in xylose integration into central carbon metabolism, or a 1.3-fold increase in ethanol production rate. We conclude by presenting an integrated model of transcriptional regulation and metabolic flux that will enable future efforts aimed at improving xylose fermentation to prioritize functional regulators of central carbon metabolism.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.