Transcriptional circuitry underlying seed coat development in Arabidopsis

Khan, Deirdre; Millar, Jenna L.; Girard, Ian J.; Belmonte, Mark F.

doi:10.1016/j.plantsci.2014.01.004

Cited by 64 publications

(39 citation statements)

References 42 publications

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“…The generation of predictive transcriptional modules can be used to identify specific regulators operating on transcriptional circuitry responsible for coordinating developmental processes Khan et al, 2014). A predictive transcriptional module operative within the funiculus across seed development (Figure 7a) identified two transcription factors interacting with the MYC2 binding site motif: (i) AT1G22490, an uncharacterized bHLH protein; and (ii) BEE2 (BR-ENHANCED EXPRESSION2).…”

Section: Dominant Patterns Of Gene Activity Reveal Similarities and Dmentioning

confidence: 99%

“…ChipEnrich [used according to the methods of Belmonte et al (2013) and Khan et al (2014)] generates a <significant.txt> and <node.txt> file for each DP, which represent the network file and attribute file, respectively. These files were then uploaded into Cytoscape, which allows for the visualization of the transcriptional network.…”

Section: Identification and Visualization Of Predicted Transcriptionamentioning

confidence: 99%

“…These files were then uploaded into Cytoscape, which allows for the visualization of the transcriptional network. For more information regarding these methods, please refer to Belmonte et al (2013) and Khan et al (2014). All network and attribute files can be found in Dataset S3.…”

Section: Identification and Visualization Of Predicted Transcriptionamentioning

confidence: 99%

“…This comprehensive study demonstrated that seed development is a complex process that is coordinated over space and time, and unique mRNA populations accumulate within specific seed regions and subregions. Recently, using the same dataset, Khan et al (2014) found that subregions of the maternal seed coat are transcriptionally distinct from one another as well as from the zygotic regions, and these subregions are predicted to be involved in biological processes that are required for seed development. Although large-scale transcriptome profiling of the seed has provided novel insights about seed development, it was still unclear how all of the maternal structures, including the funiculus, control seed development.…”

Section: Introductionmentioning

confidence: 99%

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Transcriptome atlas of the Arabidopsis funiculus – a study of maternal seed subregions

et al. 2015

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These authors contributed equally to this manuscript. SUMMARYThe funiculus anchors the structurally complex seed to the maternal plant, and is the only direct route of transport for nutrients and maternal signals to the seed. While our understanding of seed development is becoming clearer, current understanding of the genetics and cellular mechanisms that contribute to funiculus development is limited. Using laser microdissection combined with global RNA-profiling experiments we compared the genetic profiles of all maternal and zygotic regions and subregions during seed development. We found that the funiculus is a dynamic region of the seed that is enriched for mRNAs associated with hormone metabolism, molecular transport, and metabolic activities corresponding to biological processes that have yet to be described in this maternal seed structure. We complemented our genetic data with a complete histological analysis of the funiculus from the earliest stages of development through to seed maturation at the light and electron microscopy levels. The anatomy revealed signs of photosynthesis, the endomembrane system, cellular respiration, and transport within the funiculus, all of which supported data from the transcriptional analysis. Finally, we studied the transcriptional programming of the funiculus compared to other seed subregions throughout seed development. Using newly designed in silico algorithms, we identified a number of transcriptional networks hypothesized to be responsible for biological processes like auxin response and glucosinolate biosynthesis found specifically within the funiculus. Taken together, patterns of gene activity and histological observations reveal putative functions of the understudied funiculus region and identify predictive transcriptional circuits underlying these biological processes in space and time.

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Section: Dominant Patterns Of Gene Activity Reveal Similarities and Dmentioning

confidence: 99%

Section: Identification and Visualization Of Predicted Transcriptionamentioning

confidence: 99%

Section: Identification and Visualization Of Predicted Transcriptionamentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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Transcriptome atlas of the Arabidopsis funiculus – a study of maternal seed subregions

et al. 2015

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“…Our comprehensive SC transcriptome analysis identified all of these TF mRNAs in a single analysis (Khan et al, 2014). Not only were all of these known regulators identified in our experiment, we also identified a number of possible gene targets responsible for cell fate specification, the accumulation of mucilage, the deposition of anthocyanin, flavonoid biosynthesis, and SC color.…”

Section: Genomics Of Seed Coat Developmentmentioning

confidence: 99%

Genomic dissection of the seed

et al. 2014

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Seeds play an integral role in the global food supply and account for more than 70% of the calories that we consume on a daily basis. To meet the demands of an increasing population, scientists are turning to seed genomics research to find new and innovative ways to increase food production. Seed genomics is evolving rapidly, and the information produced from seed genomics research has exploded over the past two decades. Advances in modern sequencing strategies that profile every molecule in every cell, tissue, and organ and the emergence of new model systems have provided the tools necessary to unravel many of the biological processes underlying seed development. Despite these advances, the analyses and mining of existing seed genomics data remain a monumental task for plant biologists. This review summarizes seed region and subregion genomic data that are currently available for existing and emerging oilseed models. We provide insight into the development of tools on how to analyze large-scale datasets.

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