A Predictive Coexpression Network Identifies Novel Genes Controlling the Seed-to-Seedling Phase Transition in <i>Arabidopsis thaliana</i>

Silva, Anderson Tadeu; Ribone, Pamela Anahí; Chan, Raquel L.; Ligterink, Wilco; Hilhorst, Henk W. M.

doi:10.1104/pp.15.01704

Cited by 80 publications

(86 citation statements)

References 55 publications

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“…S4). The changes at the transcriptional level are in agreement (≥ 50% overlap, FC = 2, FDR = 0.05) with recent data describing transcriptional changes during the seed to seedling transition (Silva et al ., ; Table S1c). The upregulated genes were over‐representing processes involved in protein localization, oxygen and reactive oxygen species metabolic process, ribosome biogenesis, translation, stress responses, cell wall organization, photosynthesis, and lipid transport and localization (Fig.…”

Section: Resultsmentioning

confidence: 99%

“… Table S1a qRT‐PCR data for gene expression analysis and primers used Table S1b Total gene set with fold change (FC), adjusted P‐value, for total RNA, polysomal RNA and polysomal occupancy changes across seed germination Table S1c Comparison of the transcriptional difference in the current data set and dataset from Silva et al . () Table S1d Translational regulated genes during seed germination Table S1e Dominant gene groups among the translational regulated shift genes Table S1f Gene set enrichment analysis for the translational shift genes Table S1g Sequence feature analysis for the translational shifts during seed germination Table S1h Literature derived sequence feature analysis for the translational shifts during seed germination Table S1i Ribosomal protein gene transcriptional profile during seed germination …”

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Extensive translational regulation during seed germination revealed by polysomal profiling

et al. 2016

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Summary This work investigates the extent of translational regulation during seed germination.The polysome occupancy of each gene is determined by genome‐wide profiling of total mRNA and polysome‐associated mRNA. This reveals extensive translational regulation during Arabidopsis thaliana seed germination.The polysome occupancy of thousands of individual mRNAs changes to a large extent during the germination process. Intriguingly, these changes are restricted to two temporal phases (shifts) during germination, seed hydration and germination. Sequence features, such as upstream open reading frame number, transcript length, mRNA stability, secondary structures, and the presence and location of specific motifs correlated with this translational regulation. These features differed significantly between the two shifts, indicating that independent mechanisms regulate translation during seed germination.This study reveals substantial translational dynamics during seed germination and identifies development‐dependent sequence features and cis elements that correlate with the translation control, uncovering a novel and important layer of gene regulation during seed germination.

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Section: Resultsmentioning

confidence: 99%

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confidence: 99%

Extensive translational regulation during seed germination revealed by polysomal profiling

et al. 2016

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“…Finally, and regarding root development, AtHB12 , but not its paralogue AtHB7 , was reported to be involved in root growth during early stages of plant development . A similar role was assigned to AtHB13 .…”

Section: Biological Functions Of Hd‐zip I Tfsmentioning

confidence: 90%

Plant transcription factors from the homeodomain‐leucine zipper family I. Role in development and stress responses

2017

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In front of stressful conditions plants display adaptation mechanisms leading to changes in their morphology, physiology, development and molecular composition. Transcription factors (TFs) play crucial roles in these complex adaptation processes. This work is focused in the homeodomain-leucine zipper I (HD-Zip I) family of TFs, unique to plants. First discovered in 1991, they were identified and isolated from monocotyledonous and dicotyledonous plants showing high structural similarity and diversified functions. These TFs have, besides the homeodomain and leucine zipper, conserved motifs in their carboxy-termini allowing the interaction with the basal machinery and with other regulatory proteins. The model dicotyledonous plant Arabidopsis thaliana has 17 HD-Zip I members; most of them regulated by external stimuli and hormones. These TFs are involved in key developmental processes like root and stem elongation, rosette leaves morphology determination, inflorescence stem branching, flowering and pollen hydration. Moreover, they are key players in responses to environmental stresses and illumination conditions. Several HD-Zip I encoding genes from different species were protected in patents because their overexpression or mutation generates improved agronomical phenotypes. Here we discuss many aspects about these TFs including structural features, biological functions and their utilization as biotechnological tools to improve crops. V C 2017 IUBMB Life, 69(5): [280][281][282][283][284][285][286][287][288][289] 2017

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“…Common approaches rely on the clustering of gene expression profiles using a pair-wise grouping strength parameter such as a correlation coefficient followed by a hard or soft thresholding to define the network vertices. This strategy has been widely applied in different biological context and has facilitated the generation of hypothesis on gene functions and gene-gene associations (Angelovici et al, 2009; Bassel et al, 2011; Verdier et al, 2013; Costa et al, 2015; Silva et al, 2016). However, such clustering approaches disregard the edge directionality as well as the non-linearity of the regulatory cascades and are susceptible to overfitting, resulting in high network complexities; hence unsuitable for network re-construction, at least without additional assumptions (Margolin et al, 2006).…”

Section: Introductionmentioning

confidence: 99%

Transcriptome and translatome profiling and translational network analysis during seed maturation reveals conserved transcriptional and distinct translational regulatory patterns

Bai

Horst

Delhomme

et al. 2019

Preprint

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25Seed maturation is an important plant developmental process that follows embryo development. It is 26 associated with a series of physiological changes such as the establishment of desiccation tolerance, 27 seed longevity and seed dormancy. However, the translational dynamics associated with seed 28 maturation, especially its connection with seed germination remains largely elusive. Here 29 transcriptome and translatome profiling were performed during seed maturation. During seed 30 maturation we observed a gradual disappearance of polysomes and a relative increase of monosomes, 31 indicating a gradual reduction of global translation. Comparing the levels of polysomal associated 32 mRNAs with total mRNA levels showed that thousands of genes are translationally regulated at early 33 sates of maturation, as judged by dramatic changes in polysomal occupancy. By including previous 34 published data from germination and seedling establishment, a translational regulatory network: 35SeedTransNet was constructed. Network analysis identified hundreds of gene modules with distinct 36 functions and transcript sequence features indicating the existence of separate translational regulatory 37 circuits possibly acting through specific regulatory elements. The regulatory potential of one such 38 element was confirmed in vivo. The network identified several seed maturation associated genes as 39 central nodes, and we could confirm the importance of many of these hub genes with a maturation 40 associated seed phenotype by mutant analysis. One of the identified regulators an AWPM19 family 41 protein PM19-Like1 (PM19L1) was shown to regulate seed dormancy and longevity. This putative 42 RBP also affects the transitional regulation of one its, by the SeedTransNet identified, target mRNAs. 43Our data shows the usefulness of SeedTransNet in identifying regulatory pathways during seed phase 44 transitions . 45 46

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A Predictive Coexpression Network Identifies Novel Genes Controlling the Seed-to-Seedling Phase Transition in Arabidopsis thaliana

Cited by 80 publications

References 55 publications

Extensive translational regulation during seed germination revealed by polysomal profiling

Extensive translational regulation during seed germination revealed by polysomal profiling

Plant transcription factors from the homeodomain‐leucine zipper family I. Role in development and stress responses

Transcriptome and translatome profiling and translational network analysis during seed maturation reveals conserved transcriptional and distinct translational regulatory patterns

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