MicroRNA-26a targets ten eleven translocation enzymes and is regulated during pancreatic cell differentiation.

Ten eleven translocation (TET) enzymes (TET1/TET2/TET3) and thymine DNA glycosylase (TDG) play crucial roles in early embryonic and germ cell development by mediating DNA demethylation. However, the molecular mechanisms that regulate TETs/TDG expression and their role in cellular differentiation, including that of the pancreas, are not known. Here, we report that (i) TET1/2/3 and TDG can be direct targets of the microRNA miR-26a, (ii) murine TETs, especially TET2 and TDG, are down-regulated in islets during postnatal differentiation, whereas miR-26a is up-regulated, (iii) changes in 5-hydroxymethylcytosine accompany changes in TET mRNA levels, (iv) these changes in mRNA and 5-hydroxymethylcytosine are also seen in an in vitro differentiation system initiated with FACS-sorted adult ductal progenitor-like cells, and (v) overexpression of miR-26a in mice increases postnatal islet cell number in vivo and endocrine/acinar colonies in vitro.

Protein-protein interactions of tandem affinity purified protein kinases from rice.

Eighty-eight rice (Oryza sativa) cDNAs encoding rice leaf expressed protein kinases (PKs) were fused to a Tandem Affinity Purification tag (TAP-tag) and expressed in transgenic rice plants. The TAP-tagged PKs and interacting proteins were purified from the T1 progeny of the transgenic rice plants and identified by tandem mass spectrometry. Forty-five TAP-tagged PKs were recovered in this study and thirteen of these were found to interact with other rice proteins with a high probability score.

A rice kinase-protein interaction map.

Plants uniquely contain large numbers of protein kinases, and for the vast majority of the 1,429 kinases predicted in the rice (Oryza sativa) genome, little is known of their functions. Genetic approaches often fail to produce observable phenotypes; thus, new strategies are needed to delineate kinase function. We previously developed a cost-effective high-throughput yeast two-hybrid system.

ROS3 is an RNA-binding protein required for DNA demethylation in Arabidopsis.

DNA methylation is an important epigenetic mark for transcriptional gene silencing (TGS) in diverse organisms. Recent studies suggest that the methylation status of a number of genes is dynamically regulated by methylation and demethylation. In Arabidopsis, active DNA demethylation is mediated by the ROS1 (repressor of silencing 1) subfamily of 5-methylcytosine DNA glycosylases through a base excision repair pathway.

Role of Arabidopsis AGO6 in siRNA accumulation, DNA methylation and transcriptional gene silencing.

Argonautes (AGOs) are conserved proteins that contain an RNA-binding PAZ domain and an RNase H-like PIWI domain. In Arabidopsis, except for AGO1, AGO4 and AGO7, the roles of seven other AGOs in gene silencing are not known. We found that a mutation in AGO6 partially suppresses transcriptional gene silencing in the DNA demethylase mutant ros1-1.

A putative Arabidopsis nucleoporin, AtNUP160, is critical for RNA export and required for plant tolerance to cold stress.

To study the genetic control of plant responses to cold stress, Arabidopsis thaliana mutants were isolated by a screen for mutations that impair cold-induced transcription of the CBF3-LUC reporter gene. We report here the characterization and cloning of a mutated gene, atnup160-1, which causes reduced CBF3-LUC induction under cold stress. atnup160-1 mutant plants display altered cold-responsive gene expression and are sensitive to chilling stress and defective in acquired freezing tolerance.

A R2R3 type MYB transcription factor is involved in the cold regulation of CBF genes and in acquired freezing tolerance.

Cold temperatures trigger the expression of the CBF family of transcription factors, which in turn activate many downstream genes that confer freezing tolerance to plants. It has been shown previously that the cold regulation of CBF3 involves an upstream bHLH-type transcription factor, ICE1. ICE1 binds to the Myc recognition sequences in the CBF3 promoter.

Mutations in a conserved replication protein suppress transcriptional gene silencing in a DNA-methylation-independent manner in Arabidopsis.

Mutations in the DNA glycosylase/lyase ROS1 cause transcriptional silencing of the linked RD29A-LUC and 35S-NPTII transgenes in Arabidopsis. We report here that mutations in the Arabidopsis RPA2 locus release the silencing of 35S-NPTII but not RD29A-LUC in the ros1 mutant background. The rpa2 mutation also leads to enhanced expression of some transposons.

Cell-type specific regulation of serotonergic identity by the C. elegans LIM-homeodomain factor LIM-4.

How a common neurotransmitter phenotype specified in neurons of different origins is an outstanding issue in neuronal development and function. In C. elegans larvae, serotonin is synthesized in 2 pairs of neurons, the secretory neurons NSM and the chemosensory neurons ADF.

HOS10 encodes an R2R3-type MYB transcription factor essential for cold acclimation in plants.

We report the identification and characterization of an Arabidopsis mutant, hos10-1 (for high expression of osmotically responsive genes), in which the expression of RD29A and other stress-responsive genes is activated to higher levels or more rapidly activated than in wild-type by low temperature, exogenous abscisic acid (ABA), or salt stress (NaCl). The hos10-1 plants are extremely sensitive to freezing temperatures, completely unable to acclimate to the cold, and are hypersensitive to NaCl. Induction of NCED3 (the gene that encodes the rate-limiting enzyme in ABA biosynthesis) by polyethylene glycol-mediated dehydration and ABA accumulation are reduced by this mutation.

[Analysis and mapping of a rice repeated sequence].

A repeated sequence with a length of 560 bp, termed as DH17, was obtained during PCR amplification of rice NBS-LRR homologues. A repeated unit of 352 bp in the DH17 fragment was revealed through sequence analysis and comparison, which has a high homology with the known sequences of OS48 and TrsA, and belongs to the same repeat family. Southern hybridization displayed that there are higher DH17 copies in the genome of an indica variety, ZYQ8,than that in the genome of japonica variety, JX17.

Isolation and identification of a gene in response to rice blast disease in rice.

We combined cDNA amplified fragment length polymorphism (cDNA-AFLP) with bulked segregant analysis (BSA) to detect genes that control rice blast ( Magnaporthe grisea ) resistance in a double-haploid (DH) population derived from a cross between a blast-resistant variety, Zhai Ye Qing8 (ZYQ8), and a blast-susceptible variety, Jin Xi17 (JX17). In cDNA-AFLP analysis between a blast resistance (R) pool and a blast susceptibility (S) pool from the DH population, 12 transcript-derived fragments (TDFs) that were present in only one of the two pools were detected, 8 of which were from the R pool and 4 from the S pool. Mapping analysis of these TDFs by using the DH mapping population showed that five of them, R1, R8, S9, S16 and S17, were located on chromosome 1.