Co-expression network analysis and cis-regulatory element enrichment determine putative functions and regulatory mechanisms of grapevine ATL E3 ubiquitin ligases

Wong, D.; Ariani, Pietro; Castellarin, Simone D.; Polverari, Annalisa; Vandelle, Elodie

doi:10.1038/s41598-018-21377-y

Cited by 8 publications

(10 citation statements)

References 106 publications

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“…Transcriptional co-expression networks can be probabilistically inferred from highthroughput gene expression data (Basso et al 2005;Margolin et al 2006;Hernández-Lemus and Siqueiros-García 2013;Hernández-Lemus and Rangel-Escareño 2011;Delgado and Gómez-Vela 2018;Kuzmanovski et al 2018;Wong et al 2018;Manem et al 2018;Liu et al 2018), and provide a representation of the expression landscape of a given phenotype. These type of regulatory networks consist of nodes representing genes and links representing co-expression (i.e.…”

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confidence: 99%

Functional and transcriptional connectivity of communities in breast cancer co-expression networks

et al. 2019

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Transcriptional co-expression networks represent the concerted gene regulation programs by means of statistical inference of co-expression patterns. The rich phenomenology of transcriptional processes behind complex phenotypes such as cancer, is often captured (at least partially) in the connectivity structure of transcriptional co-expression networks. By analyzing the community structure of these networks, we may develop a deeper understanding of that phenomenology. We identified the modular structure of a transcriptional co-expression network obtained from breast cancer gene expression as well as a non-cancer adjacent breast tissue network as a control. We then analyzed the biological functions associated to the resulting communities by means of enrichment analysis. We also generated two projected networks for both, tumor and control networks: The first one is a projection to a network in which nodes are communities and edges represent topologically adjacent communities, indicating co-expression patterns between them. For the second projection, a bipartite network was generated containing a layer of modules and a layer of biological processes, with links between modules and the functions in which they are enriched; from this bipartite network, a projection to the community layer was obtained. From the analysis of the communities and projections, we were able to discern distinctive patterns of regulation between tumors and controls. Even though the connectivity structure of transcriptional co-expression networks is quite different, the topology of the projected networks is somehow similar, indicating functional compartmentalization, in both tumor and control conditions. However, the biological functions represented in the corresponding modules resulted notably different, with the tumor network comprising functional modules enriched for well-known hallmarks of cancer.

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confidence: 99%

Functional and transcriptional connectivity of communities in breast cancer co-expression networks

et al. 2019

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“…Based on the ‘guilt-by-association’ principle, genes involved in related processes often share parallel expression dynamics across a wide range conditions including different organ/cell types, developmental stages, stress, and hormonal perturbations [ 61 ]. Gene co-expression networks (GCNs) analyses, which are built upon the ‘guilt-by-association’ principle, have been particularly useful for ascribing the most representative biological functions to both individual gene(s) [ 62 – 65 ] and large gene families [ 39 , 66 ] in grapevine. This study highlights the strong co-expression relationships within the MIP family itself, and between MIP family members and genes involved various processes such as growth, cell-division, and cell redox homeostasis.…”

Section: Discussionmentioning

confidence: 99%

Structure and transcriptional regulation of the major intrinsic protein gene family in grapevine

et al. 2018

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BackgroundThe major intrinsic protein (MIP) family is a family of proteins, including aquaporins, which facilitate water and small molecule transport across plasma membranes. In plants, MIPs function in a huge variety of processes including water transport, growth, stress response, and fruit development. In this study, we characterize the structure and transcriptional regulation of the MIP family in grapevine, describing the putative genome duplication events leading to the family structure and characterizing the family’s tissue and developmental specific expression patterns across numerous preexisting microarray and RNAseq datasets. Gene co-expression network (GCN) analyses were carried out across these datasets and the promoters of each family member were analyzed for cis-regulatory element structure in order to provide insight into their transcriptional regulation.ResultsA total of 29 Vitis vinifera MIP family members (excluding putative pseudogenes) were identified of which all but two were mapped onto Vitis vinifera chromosomes. In this study, segmental duplication events were identified for five plasma membrane intrinsic protein (PIP) and four tonoplast intrinsic protein (TIP) genes, contributing to the expansion of PIPs and TIPs in grapevine. Grapevine MIP family members have distinct tissue and developmental expression patterns and hierarchical clustering revealed two primary groups regardless of the datasets analyzed. Composite microarray and RNA-seq gene co-expression networks (GCNs) highlighted the relationships between MIP genes and functional categories involved in cell wall modification and transport, as well as with other MIPs revealing a strong co-regulation within the family itself. Some duplicated MIP family members have undergone sub-functionalization and exhibit distinct expression patterns and GCNs. Cis-regulatory element (CRE) analyses of the MIP promoters and their associated GCN members revealed enrichment for numerous CREs including AP2/ERFs and NACs.ConclusionsCombining phylogenetic analyses, gene expression profiling, gene co-expression network analyses, and cis-regulatory element enrichment, this study provides a comprehensive overview of the structure and transcriptional regulation of the grapevine MIP family. The study highlights the duplication and sub-functionalization of the family, its strong coordinated expression with genes involved in growth and transport, and the putative classes of TFs responsible for its regulation.Electronic supplementary materialThe online version of this article (10.1186/s12864-018-4638-5) contains supplementary material, which is available to authorized users.

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“…Sequence ABF [21] CACGTGGC ABRE [35] TACGTGGC ABRE-LIKE [54] ACGTGTC CBF [55] TGGCCGAC E2F-VARIANT [56] TCTCCCGCC G-BOX [57] CACGTG GCC-BOX [58] GCCGCC MYB1 [59] TCCTACC MYB4 [60] ACCTACC RAV1-A [61] CAACA RAV1-B [ synthetic module both at upstream and downstream of the 35S minimal promoter region. SynP18 is the third set of cis motifs active against drought stress.…”

Section: Namementioning

confidence: 99%

Tinkering Cis Motifs Jigsaw Puzzle Led to Root-Specific Drought-Inducible Novel Synthetic Promoters

Jameel

Noman

Liu

et al. 2020

IJMS

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Following an in-depth transcriptomics-based approach, we first screened out and analyzed (in silico) cis motifs in a group of 63 drought-inducible genes (in soybean). Six novel synthetic promoters (SynP14-SynP19) were designed by concatenating 11 cis motifs, ABF, ABRE, ABRE-Like, CBF, E2F-VARIANT, G-box, GCC-Box, MYB1, MYB4, RAV1-A, and RAV1-B (in multiple copies and various combination) with a minimal 35s core promoter and a 222 bp synthetic intron sequence. In order to validate their drought-inducibility and root-specificity, the designed synthetic assemblies were transformed in soybean hairy roots to drive GUS gene using pCAMBIA3301. Through GUS histochemical assay (after a 72 h 6% PEG6000 treatment), we noticed higher glucuronidase activity in transgenic hairy roots harboring SynP15, SynP16, and SynP18. Further screening through GUS fluorometric assay flaunted SynP16 as the most appropriate combination of efficient drought-responsive cis motifs. Afterwards, we stably transformed SynP15, SynP16, and SynP18 in Arabidopsis and carried out GUS staining as well as fluorometric assays of the transgenic plants treated with simulated drought stress. Consistently, SynP16 retained higher transcriptional activity in Arabidopsis roots in response to drought. Thus the root-specific drought-inducible synthetic promoters designed using stimulus-specific cis motifs in a definite fashion could be exploited in developing drought tolerance in soybean and other crops as well. Moreover, the rationale of design extends our knowledge of trial-and-error based cis engineering to construct synthetic promoters for transcriptional upgradation against other stresses.

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Co-expression network analysis and cis-regulatory element enrichment determine putative functions and regulatory mechanisms of grapevine ATL E3 ubiquitin ligases

Cited by 8 publications

References 106 publications

Functional and transcriptional connectivity of communities in breast cancer co-expression networks

Functional and transcriptional connectivity of communities in breast cancer co-expression networks

Structure and transcriptional regulation of the major intrinsic protein gene family in grapevine

Tinkering Cis Motifs Jigsaw Puzzle Led to Root-Specific Drought-Inducible Novel Synthetic Promoters

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