Protein ubiquitination is involved in most cellular processes. In Arabidopsis (Arabidopsis thaliana), ubiquitin-mediated protein degradation regulates the stability of key components of the circadian clock feedback loops and the photoperiodic flowering pathway. Here, we identified two ubiquitin-specific proteases, UBP12 and UBP13, involved in circadian clock and photoperiodic flowering regulation. Double mutants of ubp12 and ubp13 display pleiotropic phenotypes, including early flowering and short periodicity of circadian rhythms. In ubp12 ubp13 double mutants, CONSTANS (CO) transcript rises earlier than that of wild-type plants during the day, which leads to increased expression of FLOWERING LOCUS T. This, and analysis of ubp12 co mutants, indicates that UBP12 and UBP13 regulate photoperiodic flowering through a CO-dependent pathway. In addition, UBP12 and UBP13 regulate the circadian rhythm of clock genes, including LATE ELONGATED HYPOCOTYL, CIRCADIAN CLOCK ASSOCIATED1, and TIMING OF CAB EXPRESSION1. Furthermore, UBP12 and UBP13 are circadian controlled. Therefore, our work reveals a role for two deubiquitinases, UBP12 and UBP13, in the control of the circadian clock and photoperiodic flowering, which extends our understanding of ubiquitin in daylength measurement in higher plants.
Human p300 is a transcriptional co-activator and a major acetyltransferase that acetylates histones and other proteins facilitating gene transcription. The activity of p300 relies on the fine-tuned interactome that involves a dozen p300 domains and hundreds of binding partners and links p300 to a wide range of vital signaling events. Here, we report a novel function of the ZZ-type zinc finger (ZZ) of p300 as a reader of histone H3. We show that the ZZ domain and acetyllysine-recognizing bromodomain of p300 play critical roles in modulating p300 enzymatic activity and its association with chromatin. The acetyllysine binding function of bromodomain is essential for acetylation of histones H3 and H4, whereas interaction of the ZZ domain with H3 promotes selective acetylation of the histone H3K27 and H3K18 sites.
Transposable elements (TEs) are ubiquitously present in plant genomes and often account for significant fractions of the nuclear DNA. For example, roughly 40% of the rice genome consists of TEs, many of which are retrotransposons, including 14% LTR-and ∼1% non-LTR retrotransposons. Despite their wide distribution and abundance, very few TEs have been found to be transpositional, indicating that TE activities may be tightly controlled by the host genome to minimize the potentially mutagenic effects associated with active transposition. Consistent with this notion, a growing body of evidence suggests that epigenetic silencing pathways such as DNA methylation, RNA interference, and H3K9me2 function collectively to repress TE activity at the transcriptional and posttranscriptional levels. It is not yet clear, however, whether the removal of histone modifications associated with active transcription is also involved in TE silencing. Here, we show that the rice protein JMJ703 is an active H3K4-specific demethylase required for TEs silencing. Impaired JMJ703 activity led to elevated levels of H3K4me3, the misregulation of numerous endogenous genes, and the transpositional reactivation of two families of non-LTR retrotransposons. Interestingly, loss of JMJ703 did not affect TEs (such as Tos17) previously found to be silenced by other epigenetic pathways. These results indicate that the removal of active histone modifications is involved in TE silencing and that different subsets of TEs may be regulated by distinct epigenetic pathways. R etrotransposons are RNA-mediated transposable elements (TEs), which are abundant in the genomes of both plants and animals (1, 2). Retrotransposons are classified into long terminal repeat (LTR) or non-LTR types, and they are mobilized in a "copy and paste" manner (3-5). The integration of a newly transposed copy might disrupt local gene structure and affect the expression of nearby genes. In humans, misregulation of retrotransposons causes numerous diseases (3, 6, 7).Although transposition of TEs is a major driving force for genome evolution, host genomes have evolved diverse mechanisms to limit harmful mobilization (1, 7). DNA methylation and histone methylation are two reversible epigenetic modifications that control transposon activity (8-13). In plants, histone H3 that is dimethylated at residue K9 (H3K9me2) associates with methylated DNA sequences such as CpG, CHG, and CHH (where H = A, T, or C) and correlates with gene silencing, whereas H3 trimethylated at K4 (H3K4me3) is linked to active transcription (14-16). Histone methylation is highly dynamic. Lysine methylation is catalyzed by SET domain group (SDG) proteins and reversed by a family of Jumonji C (JmjC) domain-containing proteins, which use Fe (II) and α-ketoglutarate (αKG) as cofactors (17,18). In Arabidopsis, JMJ25/IBM1 (increase in BONSAI methylation) encodes an H3K9 demethylase (19,20). Mutation of IBM1 results in increased levels of H3K9me2 and DNA methylation in genes but not in transposons, indicating that IBM1 disti...
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