Identifying the target genes of SUPPRESSOR OF GAMMA RESPONSE 1, a master transcription factor controlling DNA damage response in Arabidopsis

In mammalian cells, the transcription factor p53 plays a crucial role in transmitting DNA damage signals to maintain genome integrity. However, in plants, orthologous genes for p53 and checkpoint proteins are absent. Instead, the plant-specific transcription factor SUPPRESSOR OF GAMMA RADIATION 1 (SOG1) controls most of the genes induced by gamma irradiation and promotes DNA repair, cell cycle arrest, and stem cell death. Thus far, the genes directly controlled by SOG1 remain largely unknown, limiting the understanding of DNA damage signaling in plants. Here, we conducted a microarray analysis and chromatin immunoprecipitation (ChIP)-sequencing, and identified 146 Arabidopsis genes as direct targets of SOG1. By using the ChIP-sequencing data, we extracted the palindromic motif [CTT(N)7AAG] as a consensus SOG1-binding sequence, which mediates target gene induction in response to DNA damage. Furthermore, DNA damage-triggered phosphorylation of SOG1 is required for efficient binding to SOG1-binding sequence. Comparison between SOG1 and p53 target genes showed that both transcription factors control genes responsible for cell cycle regulation, such as CDK inhibitors, and DNA repair proteins, whereas SOG1 preferentially targets genes involved in homologous recombination. We also found that defense-related genes were enriched in the SOG1 target genes. Consistent with this, SOG1 is required for resistance against the hemi-biotrophic fungus Colletotrichum higginsianum, suggesting that SOG1 has a unique function in controlling immune response. This article is protected by copyright. All rights reserved

Extracellular nanovesicles for packaging of CRISPR-Cas9 protein and sgRNA to induce therapeutic exon skipping

Prolonged expression of the CRISPR-Cas9 nuclease and gRNA from viral vectors may cause off-target mutagenesis and immunogenicity. Thus, a transient delivery system is needed for therapeutic genome editing applications. Here, we develop an extracellular nanovesicle-based ribonucleoprotein delivery system named NanoMEDIC by utilizing two distinct homing mechanisms. Chemical induced dimerization recruits Cas9 protein into extracellular nanovesicles, and then a viral RNA packaging signal and two self-cleaving riboswitches tether and release sgRNA into nanovesicles. We demonstrate efficient genome editing in various hard-to-transfect cell types, including human induced pluripotent stem (iPS) cells, neurons, and myoblasts. NanoMEDIC also achieves over 90% exon skipping efficiencies in skeletal muscle cells derived from Duchenne muscular dystrophy (DMD) patient iPS cells. Finally, single intramuscular injection of NanoMEDIC induces permanent genomic exon skipping in a luciferase reporter mouse and in mdx mice, indicating its utility for in vivo genome editing therapy of DMD and beyond

ARTADE2DB: Improved Statistical Inferences for Arabidopsis Gene Functions and Structure Predictions by Dynamic Structure-Based Dynamic Expression (DSDE) Analyses

Recent advances in technologies for observing high-resolution genomic activities, such as whole-genome tiling arrays and high-throughput sequencers, provide detailed information for understanding genome functions. However, the functions of 50% of known Arabidopsis thaliana genes remain unknown or are annotated only on the basis of static analyses such as protein motifs or similarities. In this paper, we describe dynamic structure-based dynamic expression (DSDE) analysis, which sequentially predicts both structural and functional features of transcripts. We show that DSDE analysis inferred gene functions 12% more precisely than static structure-based dynamic expression (SSDE) analysis or conventional co-expression analysis based on previously determined gene structures of A. thaliana. This result suggests that more precise structural information than the fixed conventional annotated structures is crucial for co-expression analysis in systems biology of transcriptional regulation and dynamics. Our DSDE method, ARabidopsis Tiling-Array-based Detection of Exons version 2 and over-representation analysis (ARTADE2-ORA), precisely predicts each gene structure by combining two statistical analyses: a probe-wise co-expression analysis of multiple transcriptome measurements and a Markov model analysis of genome sequences. ARTADE2-ORA successfully identified the true functions of about 90% of functionally annotated genes, inferred the functions of 98% of functionally unknown genes and predicted 1,489 new gene structures and functions. We developed a database ARTADE2DB that integrates not only the information predicted by ARTADE2-ORA but also annotations and other functional information, such as phenotypes and literature citations, and is expected to contribute to the study of the functional genomics of A. thaliana. URL: http://artade.org

各地の深海底に存在する褐色変色域での微生物調査

BE11-P72ポスター要旨 / ブルーアース2011（2011年3月7日～8日, 東京海洋大学品川キャンパス）http://www.godac.jamstec.go.jp/darwin/cruise/natsushima/nt05-18/ehttp://www.godac.jamstec.go.jp/darwin/cruise/natsushima/nt10-06_leg2/ehttp://www.godac.jamstec.go.jp/darwin/cruise/natsushima/nt10-13_leg2/ehttp://www.godac.jamstec.go.jp/darwin/cruise/yokosuka/yk10-10/

イリド イミノホスホラン ノ ゴウセイ ト ハンノウ オヨビ ハンノウ キコウ ノ カイメイ

博士(工学)中部大

Factors Affecting Survival and Local Control in Patients with Bone Metastases Treated with Radiotherapy

The aim of this study was to evaluate the expected prognosis and factors affecting local control (LC) of the bone metastatic sites treated with palliative external beam radiotherapy (RT). Between December 2010 and April 2019, 420 cases (male/female = 240/180; median age [range]: 66 [12–90] years) with predominantly osteolytic bone metastases received RT and were evaluated. LC was evaluated by follow-up computed tomography (CT) image. Median RT doses (BED10) were 39.0 Gy (range, 14.4–71.7 Gy). The 0.5-year overall survival and LC of RT sites were 71% and 84%, respectively. Local recurrence on CT images was observed in 19% (n = 80) of the RT sites, and the median recurrence time was 3.5 months (range, 1–106 months). In univariate analysis, abnormal laboratory data before RT (platelet count, serum albumin, total bilirubin, lactate dehydrogenase, or serum calcium level), high-risk primary tumor sites (colorectal, esophageal, hepatobiliary/pancreatic, renal/ureter, and non-epithelial cancers), no antineoplastic agents (ATs) administration after RT, and no bone modifying agents (BMAs) administration after RT were significantly unfavorable factors for both survival and LC of RT sites. Sex (male), performance status (≥3), and RT dose (BED10) (<39.0 Gy) were significantly unfavorable factors for only survival, and age (≥70 years) and bone cortex destruction were significantly unfavorable factors for only LC of RT sites. In multivariate analysis, only abnormal laboratory data before RT influenced both unfavorable survival and LC of RT sites. Performance status (≥3), no ATs administration after RT, RT dose (BED10) (<39.0 Gy), and sex (male) were significantly unfavorable factors for survival, and primary tumor sites and BMAs administration after RT were significantly unfavorable factors for LC of RT sites. In conclusion, laboratory data before RT was important factor both prognosis and LC of bone metastases treated with palliative RT. At least in patients with abnormal laboratory data before RT, palliative RT seemed to be focused on the only pain relief