NUCLEAR FACTOR Y, Subunit A (NF-YA) Proteins Positively Regulate Flowering and Act Through FLOWERING LOCUS T

Siriwardana, Chamindika L.; Gnesutta, Nerina; Kumimoto, Roderick W.; Jones, Daniel S.; Myers, Zachary A.; Mantovani, Roberto; Holt, Ben F.

doi:10.1371/journal.pgen.1006496

Cited by 74 publications

(60 citation statements)

References 71 publications

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“…In accordance with many previous reports, we found that Arabidopsis plants grown at 15°C flowers significantly later than at higher ambient temperatures and in their rosette leaves the expression level of FT is lower than at higher ambient temperatures (Figure ). The expression level of FT among other factors is also regulated by another NF‐Y complex (composed of NF‐YA2, NF‐YB2, NF‐YC3; Siriwardana et al, ). The NF‐YA2 transcript is cleaved by miR169h‐n‐5p, according to our degradome analysis (Figure S9).…”

Section: Resultsmentioning

confidence: 99%

Ambient temperature regulates the expression of a small set of sRNAs influencing plant development through NF‐YA2 and YUC2

Gyula

Baksa

Tóth

et al. 2018

Plant Cell & Environment

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Plants substantially alter their developmental programme upon changes in the ambient temperature. The 21-24 nt small RNAs (sRNAs) are important gene expression regulators, which play a major role in development and adaptation. However, little is known about how the different sRNA classes respond to changes in the ambient temperature. We profiled the sRNA populations in four different tissues of Arabidopsis thaliana plants grown at 15°C, 21°C, and 27°C. We found that only a small fraction (0.6%) of the sRNA loci are ambient temperature-controlled. We identified thermoresponsive microRNAs and identified their target genes using degradome libraries. We verified that the target of the thermoregulated miR169, NF-YA2, is also ambient temperature-regulated. NF-YA2, as the component of the conserved transcriptional regulator NF-Y complex, binds the promoter of the flowering time regulator FT and the auxin biosynthesis gene YUC2. Other differentially expressed loci include thermoresponsive phased siRNA loci that target various auxin pathway genes and tRNA fragments. Furthermore, a temperature-dependent 24-nt heterochromatic siRNA locus in the promoter of YUC2 may contribute to the epigenetic regulation of auxin homeostasis. This holistic approach facilitated a better understanding of the role of different sRNA classes in ambient temperature adaptation of plants.

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Section: Resultsmentioning

confidence: 99%

Ambient temperature regulates the expression of a small set of sRNAs influencing plant development through NF‐YA2 and YUC2

Gyula

Baksa

Tóth

et al. 2018

Plant Cell & Environment

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show abstract

“…In addition, the list also contains a number of genes potentially related to the regulation of flowering and flowering time ( supplementary table 6 , Supplementary Material online). These genes include, for example, the one coding for the Ultraviolet-B receptor UVR8, the one encoding a Phosphorylcholine cytidylyltransferase protein and the one encoding a subunit of the Nuclear Factor Y. UV-B regulates photomorphogenesis and flowering ( Yin and Ulm 2017 ), the Nuclear Factor Y transcription factors initiates photoperiod-dependent flowering by cooperatively interacting with CONSTANS to drive the expression of FLOWERING LOCUS T (FT) ( Siriwardana et al. 2016 ).…”

Section: Resultsmentioning

confidence: 99%

Plant Lineage-Specific Amplification of Transcription Factor Binding Motifs by Miniature Inverted-Repeat Transposable Elements (MITEs)

Morata

Marín

Payet³

et al. 2018

Genome Biology and Evolution

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Transposable elements are one of the main drivers of plant genome evolution. Transposon insertions can modify the gene coding capacity or the regulation of their expression, the latter being a more subtle effect, and therefore particularly useful for evolution. Transposons have been show to contain transcription factor binding sites that can be mobilized upon transposition with the potential to integrate new genes into transcriptional networks. Miniature inverted-repeat transposable elements (MITEs) are a type of noncoding DNA transposons that could be particularly suited as a vector to mobilize transcription factor binding sites and modify transcriptional networks during evolution. MITEs are small in comparison to other transposons and can be excised, which should make them less mutagenic when inserting into promoters. On the other hand, in spite of their cut-and-paste mechanisms of transposition, they can reach very high copy numbers in genomes. We have previously shown that MITEs have amplified and redistributed the binding motif of the E2F transcription factor in different Brassicas. Here, we show that MITEs have amplified and mobilized the binding motifs of the bZIP60 and PIF3 transcription factors in peach and Prunus mume, and the TCP15/23 binding motif in tomato. Our results suggest that MITEs could have rewired new genes into transcriptional regulatory networks that are responsible for important adaptive responses and breeding traits in plants, such as stress responses, flowering time, or fruit ripening. The results presented here therefore suggest a general impact of MITEs in the evolution of transcriptional regulatory networks in plants.

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“…Dr1 represses RNAP II transcription by binding to TBP to prevent the formation of an active transcription complex. Members of the heterotrimeric NF-Y transcription factor family in Arabidopsis initiate photoperiod-dependent flowering and also required for activation of the FT promoter by initiating downstream events leading to floral transition ( Siriwardana etal. 2016 ).…”

Section: Discussionmentioning

confidence: 99%

Dominance and Sexual Dimorphism Pervade the Salix purpurea L. Transcriptome

Carlson¹,

Choi²,

Chan³

et al. 2017

Genome Biology and Evolution

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The heritability of gene expression is critical in understanding heterosis and is dependent on allele-specific regulation by local and remote factors in the genome. We used RNA-Seq to test whether variation in gene expression among F1 and F2 intraspecific Salix purpurea progeny is attributable to cis- and trans-regulatory divergence. We assessed the mode of inheritance based on gene expression levels and allele-specific expression for F1 and F2 intraspecific progeny in two distinct tissue types: shoot tip and stem internode. In addition, we explored sexually dimorphic patterns of inheritance and regulatory divergence among F1 progeny individuals. We show that in S. purpurea intraspecific crosses, gene expression inheritance largely exhibits a maternal dominant pattern, regardless of tissue type or pedigree. A significantly greater number of cis- and trans-regulated genes coincided with upregulation of the maternal parent allele in the progeny, irrespective of the magnitude, whereas the paternal allele was higher expressed for genes showing cis × trans or compensatory regulation. Importantly, consistent with previous genetic mapping results for sex in shrub willow, we have delimited sex-biased gene expression to a 2 Mb pericentromeric region on S. purpurea chr15 and further refined the sex determination region. Altogether, our results offer insight into the inheritance of gene expression in S. purpurea as well as evidence of sexually dimorphic expression which may have contributed to the evolution of dioecy in Salix.

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NUCLEAR FACTOR Y, Subunit A (NF-YA) Proteins Positively Regulate Flowering and Act Through FLOWERING LOCUS T

Cited by 74 publications

References 71 publications

Ambient temperature regulates the expression of a small set of sRNAs influencing plant development through NF‐YA2 and YUC2

Ambient temperature regulates the expression of a small set of sRNAs influencing plant development through NF‐YA2 and YUC2

Plant Lineage-Specific Amplification of Transcription Factor Binding Motifs by Miniature Inverted-Repeat Transposable Elements (MITEs)

Dominance and Sexual Dimorphism Pervade the Salix purpurea L. Transcriptome

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