Long intergenic noncoding RNAs (lincRNAs) transcribed from intergenic regions of yeast and animal genomes play important roles in key biological processes. Yet, plant lincRNAs remain poorly characterized and how lincRNA biogenesis is regulated is unclear. Using a reproducibility-based bioinformatics strategy to analyze 200 Arabidopsis thaliana transcriptome data sets, we identified 13,230 intergenic transcripts of which 6480 can be classified as lincRNAs. Expression of 2708 lincRNAs was detected by RNA sequencing experiments. Transcriptome profiling by custom microarrays revealed that the majority of these lincRNAs are expressed at a level between those of mRNAs and precursors of miRNAs. A subset of lincRNA genes shows organ-specific expression, whereas others are responsive to biotic and/or abiotic stresses. Further analysis of transcriptome data in 11 mutants uncovered SERRATE, CAP BINDING PROTEIN20 (CBP20), and CBP80 as regulators of lincRNA expression and biogenesis. RT-PCR experiments confirmed these three proteins are also needed for splicing of a small group of introncontaining lincRNAs.

MYC2 is an important regulator for jasmonic acid (JA) signaling, but little is known about its posttranslational regulation. Here, we show that the MYC2 C-terminal region interacted with the PLANT U-BOX PROTEIN10 (PUB10) armadillo repeats in vitro. MYC2 was efficiently polyubiquitinated by PUB10 with UBC8 as an E2 enzyme and the conserved C249 in PUB10 was required for activity. The inactive PUB10(C249A) mutant protein retained its ability to heterodimerize with PUB10, thus blocking PUB10 E3 activity as a dominant-negative mutant. Both MYC2 and PUB10 were nucleus localized and coimmunoprecipitation experiments confirmed their interaction in vivo. Although unstable in the wild type, MYC2 stability was enhanced in pub10, suggesting destabilization by PUB10. Moreover, MYC2 half-life was shortened or prolonged by induced expression of PUB10 or the dominant-negative PUB10(C249A) mutant, respectively. Root growth of pub10 seedlings phenocopied 35S:MYC2 seedlings and was hypersensitive to methyl jasmonate, whereas 35S:PUB10 and jin1-9 (myc2) seedlings were hyposensitive. In addition, the root phenotype conferred by MYC2 overexpression in double transgenic plants was reversed or enhanced by induced expression of PUB10 or PUB10(C249A), respectively. Similar results were obtained with three other JA-regulated genes, TAT, JR2, and PDF1.2. Collectively, our results show that MYC2 is targeted by PUB10 for degradation during JA responses.

The transition from vegetative growth to floral meristems in higher plants is regulated through the integration of internal cues and environmental signals. We were interested to examine the molecular mechanism of flowering in the day-neutral plant tomato (Solanum lycopersicum L.) and the effect of environmental conditions on tomato flowering. Analysis of the tomato genome uncovered 13 PEBP (phosphatidylethanolamine-binding protein) genes, and found six of them were FT-like genes which named as SlSP3D, SlSP6A, SlSP5G, SlSP5G1, SlSP5G2, and SlSP5G3. Six FT-like genes were analyzed to clarify their functional roles in flowering using transgenic and expression analyses. We found that SlSP5G, SlSP5G2, and SlSP5G3 proteins were floral inhibitors whereas only SlSP3D/SFT (SINGLE FLOWER TRUSS) was a floral inducer. SlSP5G was expressed at higher levels in long day (LD) conditions compared to short day (SD) conditions while SlSP5G2 and SlSP5G3 showed the opposite expression patterns. The silencing of SlSP5G by VIGS (Virus induced gene silencing) resulted in tomato plants that flowered early under LD conditions and the silencing of SlSP5G2 and SlSP5G3 led to early flowering under SD conditions. The higher expression levels of SlSP5G under LD conditions were not seen in phyB1 mutants, and the expression levels of SlSP5G2 and SlSP5G3 were increased in phyB1 mutants under both SD and LD conditions compared to wild type plants. These data suggest that SlSP5G, SlSP5G2, and SlSP5G3 are controlled by photoperiod, and the different expression patterns of FT-like genes under different photoperiod may contribute to tomato being a day neutral plant. In addition, PHYB1 mediate the expression of SlSP5G, SlSP5G2, and SlSP5G3 to regulate flowering in tomato.

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Dispersed H3K27 trimethylation (H3K27me3) of the AGAMOUS (AG) genomic locus is mediated by CURLY LEAF (CLF), a component of the Polycomb Repressive Complex (PRC) 2. Previous reports have shown that the AG second intron, which confers AG tissue-specific expression, harbors sequences targeted by several positive and negative regulators. Using RACE reverse transcription polymerase chain reaction, we found that the AG intron 2 encodes several noncoding RNAs. RNAi experiment showed that incRNA4 is needed for CLF repressive activity. AG-incRNA4RNAi lines showed increased leaf AG mRNA levels associated with a decrease of H3K27me3 levels; these plants displayed AG overexpression phenotypes. Genetic and biochemical analyses demonstrated that the AG-incRNA4 can associate with CLF to repress AG expression in leaf tissues through H3K27me3-mediated repression and to autoregulate its own expression level. The mechanism of AG-incRNA4-mediated repression may be relevant to investigations on tissue-specific expression of Arabidopsis MADS-box genes.