Arabidopsis FHY3 and FAR1 Regulate Light-Induced myo-Inositol Biosynthesis and Oxidative Stress Responses by Transcriptional Activation of MIPS1

myo-lnositol-l-phosphate synthase （MIPS） catalyzes the limiting step of inositol biosynthesis and has crucial roles in plant growth and development. In response to stress, the transcription of MIPS1 is induced and the biosynthesis of inositol or inositol derivatives is promoted by unknown mechanisms. Here, we found that the light signaling protein FAR-RED ELONGATED HYPOCOTYL3 （FHY3） and its homolog FAR- RED IMPAIRED RESPONSE1 （FAR1） regulate light-induced inositol biosynthesis and oxidative stress re- sponses by activating the transcription of MIPS1. Disruption of FHY3 and FAR1 caused light-induced cell death after dark-light transition, precocious leaf senescence, and increased sensitivity to oxidative stress. Reduction of salicylic acid （SA） accumulation by overexpression of SALICYLIC ACID 3-HYDROXYLASE largely suppressed the cell death phenotype of fhy3 far1 mutant plants, suggesting that FHY3- and FARl-mediated cell death is dependent on SA. Furthermore, comparative analysis of chromatin immuno- precipitation sequencing and microarray results revealed that FHY3 and FAR1 directly target both MIPS1 and MIPS2. The fhy3 far1 mutant plants showed severely decreased MIPS1/2 transcript levels and reduced inositol levels. Conversely, constitutive expression of MIPSl partially rescued the inositol contents, caused reduced transcript levels of SA-biosynthesis genes, and prevented oxidative stress in fhy3 far1. Taken together, our results indicate that the light signaling proteins FHY3 and FAR1 directly bind the promoter of MIPS1 to activate its expression and thereby promote inositol biosynthesis to prevent light-induced oxidative stress and SA-dependent cell death.

Genomic Features and Regulatory Roles of Intermediate-Sized Non-Coding RNAs in Arabidopsis

ABSTRACT Recent advances in genome-wide techniques allowed the identification of thousands of non-coding RNAs with various sizes in eukaryotes, some of which have further been shown to serve important functions in many biologi- cal processes. However, in model plant Arabidopsis, novel intermediate-sized ncRNAs （im-ncRNAs） （50-300 nt） have very limited information. By using a modified isolation strategy combined with deep-sequencing technology, we identified 838 im-ncRNAs in Arabidopsis globally. More than half （58%） are new ncRNA species, mostly evolutionary divergent. Interestingly, annotated protein-coding genes with 5＇-UTR-derived novel im-ncRNAs tend to be highly expressed. For intergenic im-ncRNAs, their average abundances were comparable to mRNAs in seedlings, but subsets exhibited signifi- cantly lower expression in senescing leaves. Further, intergenic im-ncRNAs were regulated by similar genetic and epige- netic mechanisms to those of protein-coding genes, and some showed developmentally regulated expression patterns. Large-scale reverse genetic screening showed that the down-regulation of a number of im-ncRNAs resulted in either obvious molecular changes or abnormal developmental phenotypes in vivo, indicating the functional importance of im-ncRNAs in plant growth and development. Together, our results demonstrate that novel Arabidopsis im-ncRNAs are developmentally regulated and functional components discovered in the transcriptome.

Mechanism of chromosomal DNA replication initiation and replication fork stabilization in eukaryotes

Chromosomal DNA replication is one of the central biological events occurring inside cells.Due to its large size,the replication of genomic DNA in eukaryotes initiates at hundreds to tens of thousands of sites called DNA origins so that the replication could be completed in a limited time.Further,eukaryotic DNA replication is sophisticatedly regulated,and this regulation guarantees that each origin fires once per S phase and each segment of DNA gets duplication also once per cell cycle.The first step of replication initiation is the assembly of pre-replication complex(pre-RC).Since 1973,four proteins,Cdc6/Cdc18,MCM,ORC and Cdt1,have been extensively studied and proved to be pre-RC components.Recently,a novel pre-RC component called Sap1/Girdin was identified.Sap1/Girdin is required for loading Cdc18/Cdc6 to origins for pre-RC assembly in the fission yeast and human cells,respectively.At the transition of G1 to S phase,pre-RC is activated by the two kinases,cyclin-dependent kinase(CDK)and Dbf4-dependent kinase(DDK),and subsequently,RPA,primase-polα,PCNA,topoisomerase,Cdc45,polδ,and polεare recruited to DNA origins for creating two bi-directional replication forks and initiating DNA replication.As replication forks move along chromatin DNA,they frequently stall due to the presence of a great number of replication barriers on chromatin DNA,such as secondary DNA structures,protein/DNA complexes,DNA lesions,gene transcription.Stalled forks must require checkpoint regulation for their stabilization.Otherwise,stalled forks will collapse,which results in incomplete DNA replication and genomic instability.This short review gives a concise introduction regarding the current understanding of replication initiation and replication fork stabilization.