SANe: The Seed Active Network for Discovering Transcriptional Regulatory Programs of Seed Development

AbstractDeveloping seeds undergo coordinated physiological and morphological changes crucial for development of the embryo, dormancy and germination. The metabolic changes that occur during seed development are regulated by interconnected network of Transcription Factors (TFs) that regulate gene expression in a spatiotemporal manner. The complexity of these networks is such that the TFs that play key regulatory roles during seed development are largely unknown. In this study, we created a genome-scale regulatory network dedicated to describing regulation of biological processes within various compartments and developmental stages of Arabidopsis seeds. Differential network analysis revealed key TFs that rewire their targeting patterns specifically during seed development, many of which were already known, and a few novel ones that we verified experimentally. Our method shows that a high-resolution tissue-specific transcriptome dataset can be accurately modeled as a functional regulatory network predictive of related TFs. We provide an easy to use webtool using which researchers can upload a newly generated transcriptome and identify key TFs important to their dataset as well as gauge their regulatory effect on phenotypes observed in the experiment. We refer to this network as Seed Active Network (SANe) and made it accessible athttps://plantstress-pereira.uark.edu/SANe/. We anticipate SANe will facilitate the discovery of TFs yet unknown for their involvement in seed related metabolic pathways and provide an interface to generate new hypothesis for experimentation.

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Construction of Light-Responsive Gene Regulatory Network for Growth, Development and Secondary Metabolite Production in Cordyceps militaris

Biology ◽

10.3390/biology11010071 ◽

2022 ◽

Vol 11 (1) ◽

pp. 71

Author(s):

Ammarin In-on ◽

Roypim Thananusak ◽

Marasri Ruengjitchatchawalya ◽

Wanwipa Vongsangnak ◽

Teeraphan Laomettachit

Keyword(s):

Gene Regulatory Network ◽

Secondary Metabolite ◽

Regulatory Network ◽

Cordyceps Militaris ◽

Secondary Metabolite Production ◽

Metabolite Production ◽

A Genome ◽

Gene Regulatory ◽

Growth Development ◽

Genome Scale

Cordyceps militaris is an edible fungus that produces many beneficial compounds, including cordycepin and carotenoid. In many fungi, growth, development and secondary metabolite production are controlled by crosstalk between light-signaling pathways and other regulatory cascades. However, little is known about the gene regulation upon light exposure in C. militaris. This study aims to construct a gene regulatory network (GRN) that responds to light in C. militaris. First, a genome-scale GRN was built based on transcription factor (TF)-target gene interactions predicted from the Regulatory Sequence Analysis Tools (RSAT). Then, a light-responsive GRN was extracted by integrating the transcriptomic data onto the genome-scale GRN. The light-responsive network contains 2689 genes and 6837 interactions. From the network, five TFs, Snf21 (CCM_04586), an AT-hook DNA-binding motif TF (CCM_08536), a homeobox TF (CCM_07504), a forkhead box protein L2 (CCM_02646) and a heat shock factor Hsf1 (CCM_05142), were identified as key regulators that co-regulate a large group of growth and developmental genes. The identified regulatory network and expression profiles from our analysis suggested how light may induce the growth and development of C. militaris into a sexual cycle. The light-mediated regulation also couples fungal development with cordycepin and carotenoid production. This study leads to an enhanced understanding of the light-responsive regulation of growth, development and secondary metabolite production in the fungi.

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Faculty Opinions recommendation of Genome-Scale Transcriptional Regulatory Network Models of Psychiatric and Neurodegenerative Disorders.

Faculty Opinions – Post-Publication Peer Review of the Biomedical Literature ◽

10.3410/f.735080013.793566184 ◽

2019 ◽

Author(s):

Saikat Chakrabarti

Keyword(s):

Neurodegenerative Disorders ◽

Regulatory Network ◽

Transcriptional Regulatory Network ◽

Network Models ◽

Transcriptional Regulatory ◽

Genome Scale

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

Quantitative Biology ◽

10.1007/s40484-014-0027-5 ◽

2014 ◽

Vol 2 (1) ◽

pp. 30-46 ◽

Cited By ~ 6

Author(s):

Guodong Liu ◽

Antonio Marras ◽

Jens Nielsen

Keyword(s):

Regulatory Network ◽

Transcriptional Regulatory Network ◽

Scale Modeling ◽

Transcriptional Regulatory ◽

The Future ◽

Genome Scale

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Transcriptional regulatory network for the establishment of CD8+ T cell exhaustion

Experimental & Molecular Medicine ◽

10.1038/s12276-021-00568-0 ◽

2021 ◽

Author(s):

Wooseok Seo ◽

Chandsultana Jerin ◽

Hiroyoshi Nishikawa

Keyword(s):

T Cells ◽

T Cell ◽

Immune Responses ◽

Regulatory Network ◽

Intracellular Signaling ◽

Chronic Infection ◽

Developmental Stages ◽

Transcriptional Regulatory Network ◽

Activated T Cells ◽

Transcriptional Regulatory

AbstractChronic infection with persistent antigenic stimulation results in the generation of exhausted CD8+ T cells, which are considered defective effector CD8+ T cells, and thus compromises effective immune responses. However, recent studies have illustrated that exhausted CD8+ T cells may be purposely generated and maintained to provide mild immune responses against chronic infection or cancer, which can be safer over a long period of time than strong immune responses. Indeed, a specific population of exhausted CD8+ T cells that behaves similarly to self-renewing stem cells and provides a continuous supply of exhausted CD8+ T cells has been identified, indicating that this population can be considered progenitors of exhausted CD8+ T cells. Furthermore, several ground-breaking studies in the last few years have shed new light on the transcriptional regulatory network governing the generation and propagation of exhausted CD8+ T cells, which involves T cell receptor (TCR) signaling that leads to NFAT-TCF1 (nuclear factor of activated T cells-T cell factor 1) activity followed by activation of the TOX/NR4A axis. Elucidation of the intracellular signaling pathways will help to define the definitive developmental stages leading to exhausted CD8+ T cells, which can be exploited to advance our never-ending battle against cancer. This review will summarize the recent discoveries that have deepened our understanding of the exhaustion program of cytotoxic CD8+ T cells.

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Genome-scale Transcriptomic Insights Into the Gene-regulatory Network of Seed Abortion in Triploid Siraitia Grosvenorii

10.21203/rs.3.rs-966900/v1 ◽

2021 ◽

Author(s):

Rongchang Wei ◽

Dongping Tu ◽

Xiyang Huang ◽

Zuliang Luo ◽

Xiaohua Huang ◽

...

Keyword(s):

Gene Regulatory Network ◽

Regulatory Network ◽

Developmental Stages ◽

Differentially Expressed ◽

Seed Abortion ◽

Submicroscopic Structure ◽

Medicinal Value ◽

Siraitia Grosvenorii ◽

Gene Regulatory ◽

Genome Scale

Abstract BackgroundSiraitia grosvenorii (Swingle) C. Jeffrey, also known as Luohanguo or monk fruit, is a famous traditional Chinese medicine ingredient with important medicinal value and broad development prospects. Diploid S. grosvenorii has too many seeds. Thus, studying the molecular mechanism of seed abortion in triploid S. grosvenorii, identifying the abortion-related genes, and regulating their expression will be a new direction to obtain seedless S. grosvenorii. Herein, we examined the submicroscopic structure of triploid S. grosvenorii seeds during abortion. ResultsBy measuring the content of endogenous hormones, we found that abscisic acid (ABA) and trans-zeatin (ZR) levels were significantly downregulated at days 15 and 20 after flowering. RNA-seq of triploid seeds at different developmental stages was performed to identify the key genes regulating abortion of triploid S. grosvenorii seeds. Multiple differentially expressed genes between adjacent stages were identified; seven genes were differentially expressed across all stages. Weight gene co-expression network analysis revealed that the enhancement of monoterpene and terpene metabolic processes might lead to seed abortion by reducing substrate flow to ABA and ZR.ConclusionsThese findings provide insights into the gene-regulatory network of seed abortion in triploid S. grosvenorii from different perspectives, thereby facilitating the innovation of the breeding technology of S. grosvenorii.

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Genome-Scale Transcriptional Regulatory Network Models of Psychiatric and Neurodegenerative Disorders

Cell Systems ◽

10.1016/j.cels.2019.01.002 ◽

2019 ◽

Vol 8 (2) ◽

pp. 122-135.e7 ◽

Cited By ~ 14

Author(s):

Jocelynn R. Pearl ◽

Carlo Colantuoni ◽

Dani E. Bergey ◽

Cory C. Funk ◽

Paul Shannon ◽

...

Keyword(s):

Neurodegenerative Disorders ◽

Regulatory Network ◽

Transcriptional Regulatory Network ◽

Network Models ◽

Transcriptional Regulatory ◽

Genome Scale

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Genome-Scale Transcriptional Regulatory Network Models of Psychiatric Disorders

European Neuropsychopharmacology ◽

10.1016/j.euroneuro.2016.09.465 ◽

2017 ◽

Vol 27 ◽

pp. S417

Author(s):

Seth Ament ◽

Jocelynn Pearl ◽

Cory Funk ◽

Dani Bergey ◽

Paul Shannon ◽

...

Keyword(s):

Psychiatric Disorders ◽

Regulatory Network ◽

Transcriptional Regulatory Network ◽

Network Models ◽

Transcriptional Regulatory ◽

Genome Scale

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The reconstruction of the genome‐scale transcriptional regulatory network in e. coli

The FASEB Journal ◽

10.1096/fasebj.22.1_supplement.529.3 ◽

2008 ◽

Vol 22 (S1) ◽

Author(s):

Bernhard O. Palsson

Keyword(s):

Regulatory Network ◽

Transcriptional Regulatory Network ◽

E Coli ◽

Transcriptional Regulatory ◽

Genome Scale

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Genome-scale transcriptional regulatory network models for the mouse and human striatum predict roles for SMAD3 and other transcription factors in Huntington’s disease

10.1101/087114 ◽

2016 ◽

Cited By ~ 1

Author(s):

Seth A. Ament ◽

Jocelynn R. Pearl ◽

Robert M. Bragg ◽

Peter J. Skene ◽

Sydney R. Coffey ◽

...

Keyword(s):

Gene Expression ◽

Huntington's Disease ◽

Huntington’S Disease ◽

Target Genes ◽

Differentially Expressed ◽

Scale Model ◽

Mouse Striatum ◽

Transcriptional Regulatory ◽

A Genome ◽

Genome Scale

AbstractTranscriptional changes occur presymptomatically and throughout Huntington’s Disease (HD), motivating the study of transcriptional regulatory networks (TRNs) in HD. We reconstructed a genome-scale model for the target genes of 718 TFs in the mouse striatum by integrating a model of the genomic binding sites with transcriptome profiling of striatal tissue from HD mouse models. We identified 48 differentially expressed TF-target gene modules associated with age‐ and Htt allele-dependent gene expression changes in the mouse striatum, and replicated many of these associations in independent transcriptomic and proteomic datasets. Strikingly, many of these predicted target genes were also differentially expressed in striatal tissue from human disease. We experimentally validated a key model prediction that SMAD3 regulates HD-related gene expression changes using chromatin immunoprecipitation and deep sequencing (ChIP-seq) of mouse striatum. We found Htt allele-dependent changes in the genomic occupancy of SMAD3 and confirmed our model’s prediction that many SMAD3 target genes are down-regulated early in HD. Importantly, our study provides a mouse and human striatal-specific TRN and prioritizes a hierarchy of transcription factor drivers in HD.

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Female gametogenesis and early seed development in Amaranthus hypochondriacus L.

Botanical Sciences ◽

10.17129/botsci.1875 ◽

2018 ◽

Vol 96 (3) ◽

pp. 383

Author(s):

Angelica Barrales-López ◽

Lorenzo Guevara-Olvera ◽

Eduardo Espitia-Rangel ◽

Mario M. González-Chavira ◽

Aurea Bernardino-Nicanor ◽

...

Keyword(s):

Seed Development ◽

Female Gametophyte ◽

Seed Quality ◽

Developmental Stages ◽

Morphological Changes ◽

Seed Proteins ◽

Amaranthus Hypochondriacus ◽

Type Pattern ◽

Functional Megaspore ◽

Female Gametogenesis

Background: Attention to amaranth grains has increased in recent years due to the nutritional value of their seed proteins, which have high levels of the amino acid lysine. However, there is no detailed study describing the stages of seed development in Amaranthus hypochondriacus. Question: How are the developmental patterns of the female gametophyte and young seed in Amaranthus hypochondriacus?Species studied: Amaranthus hypochondriacus L ’Revancha’ (Amaranthaceae).Study site and years of study: Plants were growth and collected from 2014 to 2016, in a greenhouse at Instituto Tecnológico de Celaya, Guanajuato, Mexico.Methods: Glomerules were collected before pollination and two weeks after anthesis. The ovules at different development stages were fixed and cleared and were analyzed by light microscopy. A clearing protocol was used to observe the developmental stages during female gametogenesis and embryogenesis.Results: We observed that the Amaranthus hypochondriacus ovule has a campylotropous form. The female gametophyte showed a Polygonum-type pattern of development. We were also able to identify all the stages from the megaspore mother cell to the cotyledon embryo stage. After meiosis, the micropylar megaspore differentiates into the functional megaspore. The embryo did not show symmetric divisions, although the final pattern is similar to that of in eudicotyledons. The suspensor showed additional longitudinal divisions, giving rise to a 2-rowed suspensor, while the endosperm showed a helobial development.Conclusions: These results will be used as baseline to identify morphological changes during seed development and to develop new strategies to improve seed quality or increase the yield.

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