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The future of genome-scale modeling of yeast through integration of a transcriptional regulatory network

Frontiers of Electrical and Electronic Engineering in China 2014年第1期9卷 30-46页

作者： Guodong Liu Antonio Marras Jens Nielsen Novo Nordisk Foundation Center for Biosustainability Department of Chemical and Biological Engineering Chalmers University of Technology Gothenburg SE41296 Sweden Novo Nordisk Foundation Center for Biosustainability Technical University of Denmark Hфrsholm DK2970 Denmark

Metabolism is regulated at multiple levels in response to the changes of internal or external conditions. transcriptional regulation plays an important role in regulating many metabolic reactions by altering the concentrations of metabolic enzymes. Thus, integration of the transcriptional regulatory information is necessary to improve the accuracy and predictive ability of metabolic models. Here we review the strategies for the reconstruction of a transcriptional regulatory network （TRN） for yeast and the integration of such a reconstruction into a flux balance analysis-based metabolic model. While many large-scale TRN reconstructions have been reported for yeast, these reconstructions still need to be improved regarding the functionality and dynamic property of the regulatory interactions. In addition, mathematical modeling approaches need to be further developed to efficiently integrate transcriptional regulatory interactions to genome-scale metabolic models in a quantitative manner.

关键词： transcriptional regulatory network metabolic model Saccharomyces cerevisiae integration

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transcriptional regulatory networks Activated by PI3K and ERK Transduced Growth Signals in Human Glioblastoma Cells

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Journal of Computer Science & Technology 2005年第4期20卷 439-445页

作者： PeterM.Haverty 翁志萍 UllaHansen BioinformaticsProgram BostonUniversity44CummingtonStreetBostonMA02215U.S.A. BioinformaticsProgram BostonUniversity44CummingtonStreetBostonMA02215U.S.A.／／BiomedicalEngineeringDepartmentBostonUniversity44CummingtonStreetBostonMA02215U.S.A. BioinformaticsProgram BostonUniversity44CummingtonStreetBostonMA02215U.S.A.／／BiologyDepartmentBostonUniversity44CummingtonStreetBostonMA02215U.S.A.

Determining how cells regulate their transcriptional response toextracellular signals is key to the understanding of complex eukaryotic systems. This study wasinitiated with the goals of furthering the study of mammalian transcriptional regulation andanalyzing the relative benefits of related computational methodologies. One dataset available forsuch an analysis involved gene expression profiling of the early growth factor response to plateletderived growth factor (PDGF) in a human glioblastoma cell line; this study differentiated geneswhose expression was regulated by signaling through the phosphoinositide-3-kinase (PI3K) versus theextracellular-signal regulated kinase (ERK) pathways. We have compared the inferred transcriptionfactors from this previous study with additional predictions of regulatory transcription factorsusing two alternative promoter sequence analysis techniques. This comparative analysis, in which thealgorithms predict overlapping, although not identical, sets of factors, argues for meticulousbenchmarking of promoter sequence analysis methods to determine the positive and negative attributesthat contribute to their varying results. Finally, we inferred transcriptional regulatory networksderiving from various signaling pathways using the CARRIE program suite. These networks not onlyincluded previously described transcriptional features of the response to growth signals, but alsopredicted new regulatory features for the propagation and modulation of the growth signal.

关键词： PI3K ERK PDGF transcriptional regulatory network cis-element

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Core transcriptional signatures of phase change in the migratory locust

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Protein & Cell 2019年第12期10卷 883-901页

作者： Pengcheng Yang Li Hou Xianhui Wang Le Kang Beijing Institutes of Life Science Chinese Academy of SciencesBeijing 100101China State Key Laboratory of Integrated Management of Pest Insects and Rodents Institute of ZoologyChinese Academy of SciencesBeijing 100101China

Phenotypic plasticity plays fundamental roles in successful adaptation of animals in response to environmental ***,to reveal the transcriptome reprogramming in locust phase change,a typical phenotypic plasticity,we conducted a comprehensive analysis of multiple phase-related transcriptomic datasets of the migratory *** defined PhaseCore genes according to their contribution to phase differentiation by the adjustment for confounding principal components analysis algorithm(AC-PCA).Compared with other genes,PhaseCore genes predicted phase status with over 87.5%accuracy and displayed more unique gene attributes including the faster evolution rate,higher CpG content and higher specific expression ***,we identified 20 transcription factors(TFs)named PhaseCoreTF genes that are associated with the regulation of PhaseCore ***,we experimentally verified the regulatory roles of three representative TFs(Hr4,Hr46,and grh)in phase change by *** findings revealed that core transcriptional signatures are involved in the global regulation of locust phase changes,suggesting a potential common mechanism underlying phenotypic plasticity in *** expression and network data are accessible in an online resource called LocustMine(http://***:8080/locustmine).

关键词： phenotypic plasticity transcriptional regulatory network RNA interference

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Maize endosperm development

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Journal of Integrative Plant Biology 2021年第4期63卷 613-627页

作者： Dawei Dai Zeyang Ma Rentao Song State Key Laboratory of Plant Physiology and Biochemistry National Maize Improvement CenterBeijing Key Laboratory of Crop Genetic ImprovementJoint International Research Laboratory of Crop Molecular BreedingCollege of Agronomy and BiotechnologyChina Agricultural UniversityBeijing 100193China Shanghai Key Laboratory of Bio-Energy Crops Plant Science CenterSchool of Life SciencesShanghai UniversityShanghai 200444China

Recent breakthroughs in transcriptome analysis and gene characterization have provided valuable resources and information about the maize endosperm developmental *** high temporal-resolution transcriptome analysis has yielded unprecedented access to information about the genetic control of seed *** spatial transcriptome analysis using laser-capture microdissection has revealed the expression patterns of specific populations of genes in the four major endosperm compartments:the basal endosperm transfer layer(BETL),aleurone layer(AL),starchy endosperm(SE),and embryo-surrounding region(ESR).Although the overall picture of the transcriptional regulatory network of endosperm development remains fragmentary,there have been some exciting advances,such as the identification of OPAQUE11(O11)as a central hub of the maize endosperm regulatory network connecting endosperm development,nutrient metabolism,and stress responses,and the discovery that the endosperm adjacent to scutellum(EAS)serves as a dynamic interface for endosperm-embryo *** addition,several genes that function in BETL development,AL differentiation,and the endosperm cell cycle have been identified,such as ZmSWEET4c,Thk1,and Dek15,***,we focus on current advances in understanding the molecular factors involved in BETL,AL,SE,ESR,and EAS development,including the specific transcriptional regulatory networks that function in each compartment during endosperm development.

关键词： endosperm development maize transcriptional regulatory network

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A PtrLBD39-mediated transcriptional network regulates tension wood formation in Populus trichocarpa

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Plant Communications 2022年第1期3卷 85-99页

作者： Jing Yu Chenguang Zhou Danning Li Shuang Li Ying-Chung Jimmy Lin Jack P.Wang Vincent L.Chiang Wei Li State Key Laboratory of Tree Genetics and Breeding Northeast Forestry UniversityHarbin 150040China Department of Life Sciences and Institute of Plant Biology College of Life ScienceNational Taiwan UniversityTaipeiTaiwan 10617China Department of Forestry and Environmental Resources Forest Biotechnology GroupNorth Carolina State UniversityRaleighNC 27695USA

Tension wood(TW)is a specialized xylem tissue formed in angiosperm trees under gravitational stimulus or mechanical stresses(e.g.,bending).The genetic regulation that underlies this important mechanism remains poorly ***,we used laser capture microdissection of stem xylem cells coupled with full transcriptome RNA-sequencing to analyze TW formation in Populus *** tree bending,PtrLBD39 was the most significantly induced transcription factor gene;it has a phylogenetically paired homolog,***-based knockout of PtrLBD39/22 severely inhibited TW formation,reducing cellulose and increasing lignin *** analyses of CRISPR-based PtrLBD39/22 double mutants showed that these two genes regulate a set of TW-related *** immunoprecipitation sequencing(ChIP-seq)was used to identify direct targets of *** integrated transcriptomic analyses and ChIP-seq assays to construct a transcriptional regulatory network(TRN)mediated by *** this TRN,PtrLBD39 directly regulates 26 novel TW-responsive transcription factor *** work suggests that PtrLBD39 and PtrLBD22 specifically control TW formation by mediating a TW-specific TRN in Populus.

关键词： tension wood cellulose lignin transcriptional regulatory network transcriptomics chromatin immunoprecipitation sequencing

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Single-cell analysis of transcription factor regulatory networks reveals molecular basis for subtype-specific dysregulation in acute myeloid leukemia

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Blood Science 2022年第2期4卷 65-75页

作者： Ruixia Sun Lina Sun Xiaowei Xie Xuan Li Peng Wu Lu Wang Ping Zhu State Key Laboratory of Experimental Hematology National Clinical Research Center for Blood DiseasesHaihe Laboratory of Cell EcosystemInstitute of Hematology&Blood Diseases HospitalChinese Academy of Medical Sciences&Peking Union Medical CollegeTianjinChina Center for Stem Cell Medicine and Department of Stem Cell&Regenerative Medicine Chinese Academy of Medical Sciences&Peking Union Medical CollegeTianjinChina

Highly heterogeneous acute myeloid leukemia(AML)exhibits dysregulated transcriptional *** factor(TF)regulatory networks underlying AML subtypes have not been elucidated at single-cell ***,we comprehensively mapped malignancy-related TFs activated in different AML subtypes by analyzing single-cell RNA sequencing data from AMLs and healthy *** first identified six modules of regulatory networks which were prevalently dysregulated in all AML *** subtypes featured with different malignant cellular composition possessed subtype-specific regulatory TFs associated with differentiation suppression or immune *** last,we validated that ERF was crucial for the development of hematopoietic stem/progenitor cells by performing loss-and gain-of-function experiments in zebrafish ***,our work thoroughly documents an abnormal spectrum of transcriptional regulatory networks in AML and reveals subtype-specific dysregulation basis,which provides a prospective view to AML pathogenesis and potential targets for both diagnosis and therapy.

关键词： Acute myeloid leukaemia Co-expression analysis Single-cell RNA-sequencing Transcription factor transcriptional regulatory network

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