An RNA-Seq Bioinformatics Pipeline for Data Processing of Arabidopsis Thaliana Datasets

Deshpande, Sumukh; James, Anne; Franklin, Chris; Leach, Lindsey; Taramonli, Sandy; Yang, Jianhua

doi:10.1145/3175587.3175592

Cited by 2 publications

(1 citation statement)

References 42 publications

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“…Proper ETR function is dependent upon the activity of RAN1, which utilizes a copper ion cofactor, and CONSTITUITIVE-TRIPLE-RESPONSE 1 (CTR1 )which mediates transduction of the ethylene signal via ethylene insensitive 2 (EIN2) and ethylene insensitive-like (EIL) family proteins [33][34][35][36]. Receptor function has also been shown to involve association with reversion-to-ethylene-sensitivity 1 (RTE1), a negative regulator of ethylene response, and cytochrome b5 proteins [37][38][39]. Following successful perception of ethylene, the hormone signal is transduced via a series of messengers to the nucleus where ethylene responsive transcription factors activate downstream ripening-associated genes involved in cell wall softening, and starch to sugar conversion ( Figure 2) [1, 4,40].…”

Section: Classical Model For Ethylene-dependent Ripeningmentioning

confidence: 99%

Beyond Ethylene: New Insights Regarding the Role of AOX in the Respiratory Climacteric

Hewitt¹,

Dhingra²

2019

Preprint

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Climacteric fruits are characterized by a dramatic increase in autocatalytic ethylene production, which is accompanied by a spike in respiration, at the onset of ripening. The change in the mode of ethylene production from autoinhibitory to auto-stimulatory is known as the system 1 (S1) to system 2 (S2) transition. Existing physiological models explain the basic and overarching genetic, hormonal, and transcriptional regulatory mechanisms governing the S1 to S2 transition of climacteric fruit. However, the links between ethylene and respiration, the two main factors that characterize the respiratory climacteric, have been largely understudied at the molecular level. Results of recent studies indicate that the AOX respiratory pathway may play an important role in mediating cross talk between ethylene response, carbon metabolism, ATP production, and ROS signaling during climacteric ripening. New genomic, metabolic, and epigenetic information sheds light on the interconnectedness of ripening-associated metabolic pathways, necessitating expanding the current, ethylene-centric physiological models. Understanding points at which ripening responses can be manipulated may reveal key, speciesand cultivar-specific targets for regulation of ripening enabling superior strategies for reducing postharvest wastage.

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Section: Classical Model For Ethylene-dependent Ripeningmentioning

confidence: 99%

Beyond Ethylene: New Insights Regarding the Role of AOX in the Respiratory Climacteric

Hewitt¹,

Dhingra²

2019

Preprint

View full text Add to dashboard Cite

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Characterizing the impact of CPSF30 gene disruption on TuMV infection in Arabidopsis thaliana

Wei,

Yuan,

Alshaya

et al. 2024

GM Crops & Food

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CPSF30, a key polyadenylation factor, also serves as an m 6 A reader, playing a crucial role in determining RNA fate post-transcription. While its homologs mammals are known to be vital for viral replication and immune evasion, the full scope of CPSF30 in plant, particular in viral regulation, remains less explored. Our study demonstrates that CPSF30 significantly facilitates the infection of turnip mosaic virus (TuMV) in Arabidopsis thaliana , as evidenced by infection experiments on the engineered cpsf30 mutant. Among the two isoforms, CPSF30-L, which were characterized with m 6 A binding activity, emerged as the primary isoform responding to TuMV infection. Analysis of m 6 A components revealed potential involvement of the m 6 A machinery in regulating TuMV infection. In contrast, CPSF30-S exhibited distinct subcellular localization, coalescing with P-body markers (AtDCP1 and AtDCP2) in cytoplasmic granules, suggesting divergent regulatory mechanisms between the isoforms. Furthermore, comprehensive mRNA-Seq and miRNA-Seq analysis of Col-0 and cpsf30 mutants revealed global transcriptional reprogramming, highlighting CPSF30’s role in selectively modulating gene expression during TuMV infection. In conclusion, this research underscores CPSF30’s critical role in the TuMV lifecycle and sets the stage for further exploration of its function in plant viral regulation.

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An RNA-Seq Bioinformatics Pipeline for Data Processing of Arabidopsis Thaliana Datasets

Cited by 2 publications

References 42 publications

Beyond Ethylene: New Insights Regarding the Role of AOX in the Respiratory Climacteric

Beyond Ethylene: New Insights Regarding the Role of AOX in the Respiratory Climacteric

Characterizing the impact of CPSF30 gene disruption on TuMV infection in Arabidopsis thaliana

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