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

Overview of attention for article published in BMC Genomics, April 2018
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  • Above-average Attention Score compared to outputs of the same age (60th percentile)
  • Above-average Attention Score compared to outputs of the same age and source (62nd percentile)

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Title
Structure and transcriptional regulation of the major intrinsic protein gene family in grapevine
Published in
BMC Genomics, April 2018
DOI 10.1186/s12864-018-4638-5
Pubmed ID
Authors

Darren Chern Jan Wong, Li Zhang, Isabelle Merlin, Simone D. Castellarin, Gregory A. Gambetta

Abstract

The 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. A 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. Combining 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.

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Mendeley readers

Mendeley readers

The data shown below were compiled from readership statistics for 56 Mendeley readers of this research output. Click here to see the associated Mendeley record.

Geographical breakdown

Country Count As %
Unknown 56 100%

Demographic breakdown

Readers by professional status Count As %
Researcher 11 20%
Student > Ph. D. Student 10 18%
Student > Doctoral Student 5 9%
Student > Bachelor 3 5%
Student > Master 3 5%
Other 8 14%
Unknown 16 29%
Readers by discipline Count As %
Agricultural and Biological Sciences 21 38%
Biochemistry, Genetics and Molecular Biology 12 21%
Unspecified 1 2%
Business, Management and Accounting 1 2%
Engineering 1 2%
Other 0 0%
Unknown 20 36%
Attention Score in Context

Attention Score in Context

This research output has an Altmetric Attention Score of 4. This is our high-level measure of the quality and quantity of online attention that it has received. This Attention Score, as well as the ranking and number of research outputs shown below, was calculated when the research output was last mentioned on 13 April 2018.
All research outputs
#7,306,228
of 23,041,514 outputs
Outputs from BMC Genomics
#3,458
of 10,697 outputs
Outputs of similar age
#127,602
of 329,169 outputs
Outputs of similar age from BMC Genomics
#82
of 223 outputs
Altmetric has tracked 23,041,514 research outputs across all sources so far. This one has received more attention than most of these and is in the 67th percentile.
So far Altmetric has tracked 10,697 research outputs from this source. They receive a mean Attention Score of 4.7. This one has gotten more attention than average, scoring higher than 66% of its peers.
Older research outputs will score higher simply because they've had more time to accumulate mentions. To account for age we can compare this Altmetric Attention Score to the 329,169 tracked outputs that were published within six weeks on either side of this one in any source. This one has gotten more attention than average, scoring higher than 60% of its contemporaries.
We're also able to compare this research output to 223 others from the same source and published within six weeks on either side of this one. This one has gotten more attention than average, scoring higher than 62% of its contemporaries.