OsHUB2 inhibits function of OsTrx1 in heading date in rice.

Heading date is one of the most pivotal agronomic traits for rice (Oryza sativa) yield and adaptation. Little is known about the crosstalk between histone ubiquitination and histone methylation in rice heading date regulation. Here, we reported HISTONE MONOUBIQUITINATION 1 (OsHUB1) and OsHUB2 are involved in heading date regulation via the Hd1 and Ehd1 pathway. Loss of OsHUB1 and OsHUB2 function resulted in early heading under long-day and short-day photoperiods. The expression of Hd3a, RFT1, and Ehd1 was induced and the transcript levels of Hd1, Ghd7, OsCCA1, OsGI, OsFKF1, and OsTOC1 were reduced under long-day conditions, whereas RFT1 and Ehd1 expression was induced in oshub2 mutants under short-day conditions. OsHUB2 interacted with OsTrx1 and repressed the gene expression of OsTrx1. OsHUB2 directly bound to Ehd1 to ubiquitinate H2B at Ehd1, and H2B ubiquitination levels were reduced in oshub2-2 and oshub2-3 mutants. OsTrx1 were highly enriched at Ehd1, and H3K4me3 levels of Ehd1 were upregulated in oshub2-2. Mutations of OsTrx1 in the oshub2-2 background rescued the early-heading phenotype of oshub2-2. The increases in Ehd1 H3K4me3 levels and transcript levels in oshub2-2 mutants were attenuated in oshub2-2 ostrx1-2 double mutants. Together, our results (i) reveal that OsHUB2 represses the function of OsTrx1 and H3K4me3 levels at Ehd1 and (ii) suggest that OsHUB2-mediated H2B ubiquitination plays critical roles together with H3K4me3 in rice heading date regulation.

Chromatin remodeling factors OsYAF9 and OsSWC4 interact to promote internode elongation in rice.

Deposition of H2A.Z and H4 acetylation by SWI2/SNF2-Related 1 Chromatin Remodeling (SWR1) and Nucleosome Acetyltransferase of H4 (NuA4) complexes in specific regulatory regions modulates transcription and development. However, little is known about these complexes in Oryza sativa (rice) development. Here, we reported that OsYAF9 and OsSWC4, two subunits of SWR1 and NuA4 complexes, are involved in rice vegetative and reproductive development. Loss of OsYAF9 resulted in reduced height, fewer tillers, fewer pollen grains, and defects in embryogenesis and seed filling. OsYAF9 directly interacted with OsSWC4 in vitro and in vivo. Loss of OsSWC4 function exhibited defects in pollen germination and failure to generate seeds, whereas knockdown of OsSWC4 resulted in reduced height and fewer tillers. The reduced height caused by OsYAF9 mutation and OsSWC4 knockdown was due to shorter internodes and defects in cell elongation, and this phenotype was rescued with gibberellin (GA) treatment, suggesting that both OsYAF9 and OsSWC4 are involved in the GA biosynthesis pathway. OsSWC4 was directly bound to the AT-rich region of GA biosynthesis genes, which in turn accomplished H2A.Z deposition and H4 acetylation at the GA biosynthesis genes with OsYAF9. Together, our study provides insights into the mechanisms involving OsSWC4 and OsYAF9 forming a protein complex to promote rice internode elongation with H2A.Z deposition and H4 acetylation.

SDG128 is involved in maize leaf inclination.

Maize leaf angle (LA) is a complex quantitative trait that is controlled by developmental signals, hormones, and environmental factors. However, the connection between histone methylation and LAs in maize remains unclear. Here, we reported that SET domain protein 128 (SDG128) is involved in leaf inclination in maize. Knockdown of SDG128 using an RNA interference approach resulted in an expanded architecture, less large vascular bundles, more small vascular bundles, and larger spacing of large vascular bundles in the auricles. SDG128 interacts with ZmGID2 both in vitro and in vivo. Knockdown of ZmGID2 also showed a larger LA with less large vascular bundles and larger spacing of vascular bundles. In addition, the transcription level of cell wall expansion family genes ZmEXPA1, ZmEXPB2, and GRMZM2G005887; transcriptional factor genes Lg1, ZmTAC1, and ZmCLA4; and auxin pathway genes ZmYUCCA7, ZmYUCCA8, and ZmARF22 was reduced in SDG128 and ZmGID2 knockdown plants. SDG128 directly targets ZmEXPA1, ZmEXPB2, LG1, and ZmTAC1 and is required for H3K4me3 deposition at these genes. Together, the results of the present study suggest that SDG128 and ZmGID2 are involved in the maize leaf inclination.

Phosphorylation of SPT5 by CDKD;2 Is Required for VIP5 Recruitment and Normal Flowering in Arabidopsis thaliana.

The elongation factor suppressor of Ty 5 homolog (Spt5) is a regulator of transcription and histone methylation. In humans, phosphorylation of SPT5 by P-TEFb, a protein kinase composed of Cyclin-dependent kinase 9 (CDK9) and cyclin T, interacts with the RNA polymerase II-associated factor1 (PAF1) complex. However, the mechanism of SPT5 phosphorylation is not well understood in plants. Here, we examine the function of SPT5 in Arabidopsis thaliana and find that spt5 mutant flowers early under long-day and short-day conditions. SPT5 interacts with the CDK-activating kinase 4 (CAK4; CDKD;2) and is specifically phosphorylated by CDKD;2 at threonines. The phosphorylated SPT5 binds VERNALIZATION INDEPENDENCE5 (VIP5), a subunit of the PAF1 complex. Genetic analysis showed that VIP5 acts downstream of SPT5 and CDKD;2 Loss of SPT5 or CDKD;2 function results in early flowering because of decreased amounts of FLOWERING LOCUS C (FLC) transcript. Importantly, CDKD;2 and SPT5 are required for the deposition of VIP5 and the enhancement of trimethylation of histone 3 lysine 4 in the chromatin of the FLC locus. Together, our results provide insight into the mechanism by which the Arabidopsis elongation factor SPT5 recruits the PAF1 complex via the posttranslational modification of proteins and suggest that the phosphorylation of SPT5 by CDKD;2 enables it to recruit VIP5 to regulate chromatin and transcription in Arabidopsis.

SIP1 participates in regulation of flowering time in rice by recruiting OsTrx1 to Ehd1.

Flowering time (heading date) in rice (Oryza sativa) is an important agronomic trait that determines yield. The levels of histone H3 lysine 4 trimethylation (H3K4me3) modulated by TRITHORAX-like proteins regulate gene transcription, flowering time and environmental stress responses. However, plant TRITHORAX-like proteins have no known DNA-binding domain, and therefore the mechanism that gives sequence specificity to these proteins remains unclear. Here, we show that the rice TRITHORAX-like protein OsTrx1 is recruited to its target, Early heading date 1 (Ehd1), by the C2H2 zinc finger protein SDG723/OsTrx1/OsSET33 Interaction Protein 1 (SIP1). SIP1 binds to the promoter of Ehd1 and interacts with OsTrx1. Mutations in SIP1 led to a late heading date under long-day and short-day conditions. Defects in OsTrx1 or SIP1 led to reduced H3K4me3 levels at Ehd1, thus reducing Ehd1 expression. Together, our results show that the transcription factor SIP1 interacts with OxTrx1, allowing OsTrx1 to specifically target Ehd1, altering H3K4me3 levels, increasing Ehd1 expression and thereby promoting flowering.

SDG721 and SDG705 are required for rice growth.

H3K4me3 plays important roles in development, transcription, and environmental responses. Here, we report that SDG721 (SET-domain group protein 721) and SDG705 are involved in regulating rice development. SDG721 and SDG705 encode TRITHORAX-like proteins, which appear to modulate H3K4 methylation levels. Loss of SDG721 and SDG705 function resulted in GA-deficient phenotypes, including semi-dwarfism, reduced cell length, and reduced panicle branching. The transcripts levels and H3K4me3 levels of GA biosynthesis genes and GA signaling pathway genes were downregulated in the sdg721 sdg705 plants. Together, these results suggest that SDG721 and SDG705 regulate H3K4 methylation, which is crucial for plant development in rice.

An epi-allele of SMS causes Sanming dominant genic male sterility in rice.

Male sterility is an important trait in rice for hybrid rice (Oryza sativa) breeding. However, the factors involved in dominant male sterility are largely unknown. Here, we identified a gene from Sanming dominant genic male sterile rice, named Sanming dominant male sterility (SMS), and reported that an epi-allele of this locus contributes to male sterility. Segregation analysis attributed dominant male sterility to a single locus, SMS, which we characterized using a male-sterile near isogenic line (NIL) of rice cultivar 93-11. The SMS locus was heterozygous in the male-sterile 93-11 NIL, containing an epi-allele identical to that in 93-11, and an epi-allele identical to that in rice cultivar Nipponbare, which we refer to as SMS9 and SMSN, respectively. SMS9 is silent and hyper-methylated, whereas SMSN is expressed and hypo-methylated in the 93-11 NIL. Overexpressing SMSN led to male sterility. Mutations in SMS rescued the male sterility of the 93-11 NIL. Interestingly, we observed the duplication of SMSN in Nipponbare, but did not observe the duplication of SMS9 in 93-11. Together, these findings suggest that the reduced methylation and enhanced expression of the SMSN epi-allele in the 93-11 NIL is responsible for its role in conferring dominant male sterility.