A Novel Quantitative Evaluation of Bone Formation After Opening Wedge High Tibial Osteotomy Using Tomosynthesis.

This study aimed to establish and validate a novel evaluation method using digital tomosynthesis to quantify bone formation in the gap after opening wedge high tibial osteotomy (OW-HTO). We retrospectively analyzed bone formation in the gap in 22 patients who underwent OW-HTO using digital tomosynthesis at 1, 2, 3, 6, 9, and 12 months postoperatively. Bone formation was semi-quantitatively assessed using the modified van Hemert's score and density measurements on digital tomosynthesis images. The gap filling value (GFV) was calculated as the ratio of the intensities of the opening gap and the tibial shaft. In addition, the relationship between the modified van Hemert's score and GFV was evaluated. The reproducibility of GFV had an interclass correlation coefficient (ICC [1,2]) of 0.958 for intraobserver reliability and an ICC (2,1) of 0.975 for interobserver reliability. The GFV increased in a time-dependent manner and was moderately correlated with the modified van Hemert's score (r = 0.630, p < 0.001). The GFV plateaued at 6 months postoperatively. In addition, the GFV was higher in patients with a modified van Hemert's score of 2 than in patients with a modified van Hemert's score of 3 (p = 0.008). The GFVs obtained using digital tomosynthesis can be used to assess postoperative bone formation in the opening gap after OW-HTO with high accuracy and reproducibility.

Longitudinal Single-Cell Transcriptomics Reveals a Role for Serpina3n-Mediated Resolution of Inflammation in a Mouse Colitis Model.

BACKGROUND & AIMS: Proper resolution of inflammation is essential to maintaining homeostasis, which is important as a dysregulated inflammatory response has adverse consequences, even being regarded as a hallmark of cancer. However, our picture of dynamic changes during inflammation remains far from comprehensive. METHODS: Here we used single-cell transcriptomics to elucidate changes in distinct cell types and their interactions in a mouse model of chemically induced colitis. RESULTS: Our analysis highlights the stromal cell population of the colon functions as a hub with dynamically changing roles over time. Importantly, we found that Serpina3n, a serine protease inhibitor, is specifically expressed in stromal cell clusters as inflammation resolves, interacting with a potential target, elastase. Indeed, genetic ablation of the Serpina3n gene delays resolution of induced inflammation. Furthermore, systemic Serpina3n administration promoted the resolution of inflammation, ameliorating colitis symptoms. CONCLUSIONS: This study provides a comprehensive, single-cell understanding of cell-cell interactions during colorectal inflammation and reveals a potential therapeutic target that leverages inflammation resolution.

Contribution of PDGFRα lineage cells in adult mouse hematopoiesis.

Platelet-derived growth factor receptor alpha (PDGFRα) is a dominant marker of mesodermal mesenchymal cells in mice. Previous studies demonstrated that PDGFRα-positive (PDGFRα+) mesodermal cells develop not only into mesenchymal cells but also into a subset of total hematopoietic cells (HCs) in the limited period during mouse embryogenesis. However, the precise characteristics of the PDGFRα lineage positive (PDGFRα Lin+) HCs in adult mouse hematopoiesis are largely unknown. In this study, we systematically evaluated the characteristics of PDGFRα Lin+ HCs in the bone marrow and peripheral blood using PDGFRα-CRE; ROSAtdTomato mice. Flow cytometry analysis revealed that PDGFRα Lin+ HCs accounted for approximately 20% of total HCs in both the bone marrow and peripheral blood in adult mice. Compositions of myeloid and lymphoid subpopulations among CD45+ mononuclear cells were almost identical in both PDGFRα Lin+ and PDGFRα Lin- cells. Single-cell RNA-sequencing analysis also demonstrated that the transcriptomic signatures of the PDGFRα Lin+ HCs in the peripheral blood largely overlapped with those of the PDGFRα Lin- HCs, suggesting equivalent functions of the PDGFRα Lin+ and PDGFRα Lin- HCs. Although pathophysiological activities of the PDGFRα Lin + HCs were not evaluated, our data clearly demonstrate a significant role of the PDGFRα Lin + HCs in physiological hematopoiesis in adult mice.

Cut-C: cleavage under tethered nuclease for conformational capture.

BACKGROUND: Deciphering the 3D structure of the genome is essential for elucidating the regulatory mechanisms of gene expression in detail. Existing methods, such as chromosome conformation capture (3C) and Hi-C have enabled the identification of novel aspects of chromatin structure. Further identification of protein-centric chromatin conformation is enabled by coupling the Hi-C procedure with a conventional chromatin immunoprecipitation assay. However, these methods are time-consuming and require independent methods for validation. RESULTS: To simultaneously identify protein-centric chromatin conformation and target protein localization, we have developed Cut-C, a method that combines antibody-mediated cleavage by tethered nuclease with chromosome conformation capture to identify chromatin interactions mediated by a protein of interest. Applying Cut-C to H3K4me3, a histone modification enriched at active gene promoters, we have successfully identified chromatin loops mediated by H3K4me3 along with the genome-wide distribution of H3K4me3. Cut-C also identified chromatin loops mediated by CTCF, validating the general applicability of the method. CONCLUSIONS: Cut-C identifies protein-centric chromatin conformations along with the genome-wide distribution of target proteins using simple procedures. The simplified protocol will improve the efficiency of analysing chromatin conformation using precious materials, such as clinical samples.

Chromatin accessibility identifies diversity in mesenchymal stem cells from different tissue origins.

Mesenchymal stem cells (MSCs), which can differentiate into tri-lineage (osteoblast, adipocyte, and chondrocyte) and suppress inflammation, are promising tools for regenerative medicine. MSCs are phenotypically diverse based on their tissue origins. However, the mechanisms underlying cell-type-specific gene expression patterns are not fully understood due to the lack of suitable strategy to identify the diversity. In this study, we investigated gene expression programs and chromatin accessibilities of MSCs by whole-transcriptome RNA-seq analysis and an assay for transposase-accessible chromatin using sequencing (ATAC-seq). We isolated MSCs from four tissues (femoral and vertebral bone marrow, adipose tissue, and lung) and analysed their molecular signatures. RNA-seq identified the expression of MSC markers and both RNA-seq and ATAC-seq successfully clustered the MSCs based on their tissue origins. Interestingly, clustering based on tissue origin was more accurate with chromatin accessibility signatures than with transcriptome profiles. Furthermore, we identified transcription factors potentially involved in establishing cell-type specific chromatin structures. Thus, epigenome analysis is useful to analyse MSC identity and can be utilized to characterize these cells for clinical use.

Quantifying the relative immune cell activation from whole tissue/organ-derived differentially expressed gene data.

Evaluation of immune responses in individual immune cell types is important for the development of new medicines. Here, we propose a computational method designated ICEPOP (Immune CEll POPulation) to estimate individual immune cell type responses from bulk tissue and organ samples. The relative gene responses are scored for each cell type by using the data from differentially expressed genes derived from control- vs drug-treated sample pairs, and the data from public databases including ImmGen and IRIS, which contain gene expression profiles of a variety of immune cells. By ICEPOP, we analysed cell responses induced by vaccine-adjuvants in the mouse spleen, and extended the analyses to human peripheral blood mononuclear cells and gut biopsy samples focusing on human papilloma virus vaccination and inflammatory bowel disease treatment with Infliximab. In both mouse and human datasets, our method reliably quantified the responding immune cell types and provided insightful information, demonstrating that our method is useful to evaluate immune responses from bulk sample-derived gene expression data. ICEPOP is available as an interactive web site ( https://vdynamics.shinyapps.io/icepop/ ) and Python package ( https://github.com/ewijaya/icepop ).

Transcriptomics analysis of salt stress tolerance in the roots of the mangrove Avicennia officinalis.

Salinity affects growth and development of plants, but mangroves exhibit exceptional salt tolerance. With direct exposure to salinity, mangrove roots possess specific adaptations to tolerate salt stress. Therefore, studying the early effects of salt on mangrove roots can help us better understand the tolerance mechanisms. Using two-month-old greenhouse-grown seedlings of the mangrove tree Avicennia officinalis subjected to NaCl treatment, we profiled gene expression changes in the roots by RNA-sequencing. Of the 6547 genes that were differentially regulated in response to salt treatment, 1404 and 5213 genes were significantly up- and down-regulated, respectively. By comparative genomics, 93 key salt tolerance-related genes were identified of which 47 were up-regulated. Upon placing all the differentially expressed genes (DEG) in known signaling pathways, it was evident that most of the DEGs involved in ethylene and auxin signaling were up-regulated while those involved in ABA signaling were down-regulated. These results imply that ABA-independent signaling pathways also play a major role in salt tolerance of A. officinalis. Further, ethylene response factors (ERFs) were abundantly expressed upon salt treatment and the Arabidopsis mutant aterf115, a homolog of AoERF114 is characterized. Overall, our results would help in understanding the possible molecular mechanism underlying salt tolerance in plants.

Mapping circulating serum miRNAs to their immune-related target mRNAs.

PURPOSE: Evidence suggests that circulating serum microRNAs (miRNAs) might preferentially target immune-related mRNAs. If this were the case, we hypothesized that immune-related mRNAs would have more predicted serum miRNA binding sites than other mRNAs and, reciprocally, that serum miRNAs would have more immune-related mRNA targets than non-serum miRNAs. MATERIALS AND METHODS: We developed a consensus target predictor using the random forest framework and calculated the number of predicted miRNA-mRNA interactions in various subsets of miRNAs (serum, non-serum) and mRNAs (immune related, nonimmune related). RESULTS: Immune-related mRNAs were predicted to be targeted by serum miRNA more than other mRNAs. Moreover, serum miRNAs were predicted to target many more immune-related mRNA targets than non-serum miRNAs; however, these two biases in immune-related mRNAs and serum miRNAs appear to be completely independent. CONCLUSION: Immune-related mRNAs have more miRNA binding sites in general, not just for serum miRNAs; likewise, serum miRNAs target many more mRNAs than non-serum miRNAs overall, regardless of whether they are immune related or not. Nevertheless, these two independent phenomena result in a significantly larger number of predicted serum miRNA-immune mRNA interactions than would be expected by chance.

Advax, a Delta Inulin Microparticle, Potentiates In-built Adjuvant Property of Co-administered Vaccines.

Advax, a delta inulin-derived microparticle, has been developed as an adjuvant for several vaccines. However, its immunological characteristics and potential mechanism of action are yet to be elucidated. Here, we show that Advax behaves as a type-2 adjuvant when combined with influenza split vaccine, a T helper (Th)2-type antigen, but behaves as a type-1 adjuvant when combined with influenza inactivated whole virion (WV), a Th1-type antigen. In addition, an adjuvant effect was not observed when Advax-adjuvanted WV vaccine was used to immunize toll-like receptor (TLR) 7 knockout mice which are unable to respond to RNA contained in WV antigen. Similarly, no adjuvant effect was seen when Advax was combined with endotoxin-free ovalbumin, a neutral Th0-type antigen. An adjuvant effect was also not seen in tumor necrosis factor (TNF)-α knockout mice, and the adjuvant effect required the presences of dendritic cells (DCs) and phagocytic macrophages. Therefore, unlike other adjuvants, Advax potentiates the intrinsic or in-built adjuvant property of co-administered antigens. Hence, Advax is a unique class of adjuvant which can potentiate the intrinsic adjuvant feature of the vaccine antigens through a yet to be determined mechanism.

Transcriptional regulatory mechanism of alcohol dehydrogenase 1-deficient mutant of rice for cell survival under complete submergence.

BACKGROUND: Rice is the only crop that germinates and elongates the coleoptile under complete submergence. It has been shown that alcohol dehydrogenase 1 (ADH1)-deficient mutant of rice with reduced alcohol dehydrogenase activity (rad) and reduced ATP level, is viable with much reduced coleoptile elongation under such condition. To understand the altered transcriptional regulatory mechanism of this mutant, we aimed to establish possible relationships between gene expression and cis-regulatory information content. FINDINGS: We performed promoter analysis of the publicly available differentially expressed genes in ADH1 mutant. Our results revealed that a crosstalk between a number of key transcription factors (TFs) and different phytohormones altered transcriptional regulation leading to the survival of the mutant. Amongst the key TFs identified, we suggest potential involvement of MYB, bZIP, ARF and ERF as transcriptional activators and WRKY, ABI4 and MYC as transcriptional repressors of coleoptile elongation to maintain metabolite levels for the cell viability. Out of the repressors, WRKY TF is most likely playing a major role in the alteration of the physiological implications associated with the cell survival. CONCLUSIONS: Overall, our analysis provides a possible transcriptional regulatory mechanism underlying the survival of the rad mutant under complete submergence in an energy crisis condition and develops hypotheses for further experimental validation.

Hydroxypropyl-ß-cyclodextrin spikes local inflammation that induces Th2 cell and T follicular helper cell responses to the coadministered antigen.

Cyclodextrins are commonly used as a safe excipient to enhance the solubility and bioavailability of hydrophobic pharmaceutical agents. Their efficacies and mechanisms as drug-delivery systems have been investigated for decades, but their immunological properties have not been examined. In this study, we reprofiled hydroxypropyl-ß-cyclodextrin (HP-ß-CD) as a vaccine adjuvant and found that it acts as a potent and unique adjuvant. HP-ß-CD triggered the innate immune response at the injection site, was trapped by MARCO(+) macrophages, increased Ag uptake by dendritic cells, and facilitated the generation of T follicular helper cells in the draining lymph nodes. It significantly enhanced Ag-specific Th2 and IgG Ab responses as potently as did the conventional adjuvant, aluminum salt (alum), whereas its ability to induce Ag-specific IgE was less than that of alum. At the injection site, HP-ß-CD induced the temporary release of host dsDNA, a damage-associated molecular pattern. DNase-treated mice, MyD88-deficient mice, and TBK1-deficient mice showed significantly reduced Ab responses after immunization with this adjuvant. Finally, we demonstrated that HP-ß-CD-adjuvanted influenza hemagglutinin split vaccine protected against a lethal challenge with a clinically isolated pandemic H1N1 influenza virus, and the adjuvant effect of HP-ß-CD was demonstrated in cynomolgus macaques. Our results suggest that HP-ß-CD acts as a potent MyD88- and TBK1-dependent T follicular helper cell adjuvant and is readily applicable to various vaccines.

A hormone-responsive C1-domain-containing protein At5g17960 mediates stress response in Arabidopsis thaliana.

Phytohormones play a critical role in mediating plant stress response. They employ a variety of proteins for coordinating such processes. In Arabidopsis thaliana, some members of a Cys-rich protein family known as C1-clan proteins were involved in stress response, but the actual function of the protein family is largely unknown. We studied At5g17960, a C1-clan protein member that possesses three unique C1 signature domains viz. C1_2, C1_3 and ZZ/PHD type. Additionally, we identified 72 other proteins in A. thaliana that contain all three unique signature domains. Subsequently, the 73 proteins were phylogenetically classified into IX subgroups. Promoter motif analysis of the 73 genes identified the presence of hormone-responsive and stress-responsive putative cis-regulatory elements. Furthermore, we observed that transcript levels of At5g17960 were induced in response to different hormones and stress treatments. At1g35610 and At3g13760, two other members of subgroup IV, also showed upregulation upon GA3, biotic and abiotic stress treatments. Moreover, seedlings of independent transgenic A. thaliana lines ectopically expressing or suppressing At5g17960 also showed differential regulation of several abiotic stress-responsive marker genes. Thus, our data suggest that C1-domain-containing proteins have a role to play in plant hormone-mediated stress responses, thereby assigning a putative function for the C1-clan protein family.

Identification of salt gland-associated genes and characterization of a dehydrin from the salt secretor mangrove Avicennia officinalis.

BACKGROUND: Salt stress is a major challenge for growth and development of plants. The mangrove tree Avicennia officinalis has evolved salt tolerance mechanisms such as salt secretion through specialized glands on its leaves. Although a number of structural studies on salt glands have been done, the molecular mechanism of salt secretion is not clearly understood. Also, studies to identify salt gland-specific genes in mangroves have been scarce. RESULTS: By subtractive hybridization (SH) of cDNA from salt gland-rich cell layers (tester) with mesophyll tissues as the driver, several Expressed Sequence Tags (ESTs) were identified. The major classes of ESTs identified include those known to be involved in regulating metabolic processes (37%), stress response (17%), transcription (17%), signal transduction (17%) and transport functions (12%). A visual interactive map generated based on predicted functional gene interactions of the identified ESTs suggested altered activities of hydrolase, transmembrane transport and kinases. Quantitative Real-Time PCR (qRT-PCR) was carried out to validate the expression specificity of the ESTs identified by SH. A Dehydrin gene was chosen for further experimental analysis, because it is significantly highly expressed in salt gland cells, and dehydrins are known to be involved in stress remediation in other plants. Full-length Avicennia officinalis Dehydrin1 (AoDHN1) cDNA was obtained by Rapid Amplification of cDNA Ends. Phylogenetic analysis and further characterization of this gene suggested that AoDHN1 belongs to group II Late Embryogenesis Abundant proteins. qRT-PCR analysis of Avicennia showed up-regulation of AoDHN1 in response to salt and drought treatments. Furthermore, some functional insights were obtained by growing E. coli cells expressing AoDHN1. Growth of E. coli cells expressing AoDHN1 was significantly higher than that of the control cells without AoDHN1 under salinity and drought stresses, suggesting that the mangrove dehydrin protein helps to mitigate the abiotic stresses. CONCLUSIONS: Thirty-four ESTs were identified to be enriched in salt gland-rich tissues of A. officinalis leaves. qRT-PCR analysis showed that 10 of these were specifically enriched in the salt gland-rich tissues. Our data suggest that one of the selected genes, namely, AoDHN1 plays an important role to mitigate salt and drought stress responses.

Reference-free prediction of rearrangement breakpoint reads.

MOTIVATION: Chromosome rearrangement events are triggered by atypical breaking and rejoining of DNA molecules, which are observed in many cancer-related diseases. The detection of rearrangement is typically done by using short reads generated by next-generation sequencing (NGS) and combining the reads with knowledge of a reference genome. Because structural variations and genomes differ from one person to another, intermediate comparison via a reference genome may lead to loss of information. RESULTS: In this article, we propose a reference-free method for detecting clusters of breakpoints from the chromosomal rearrangements. This is done by directly comparing a set of NGS normal reads with another set that may be rearranged. Our method SlideSort-BPR (breakpoint reads) is based on a fast algorithm for all-against-all comparisons of short reads and theoretical analyses of the number of neighboring reads. When applied to a dataset with a sequencing depth of 100×, it finds ∼ 88% of the breakpoints correctly with no false-positive reads. Moreover, evaluation on a real prostate cancer dataset shows that the proposed method predicts more fusion transcripts correctly than previous approaches, and yet produces fewer false-positive reads. To our knowledge, this is the first method to detect breakpoint reads without using a reference genome. AVAILABILITY AND IMPLEMENTATION: The source code of SlideSort-BPR can be freely downloaded from https://code.google.com/p/slidesort-bpr/.

Finding protein-coding genes through human polymorphisms.

Human gene catalogs are fundamental to the study of human biology and medicine. But they are all based on open reading frames (ORFs) in a reference genome sequence (with allowance for introns). Individual genomes, however, are polymorphic: their sequences are not identical. There has been much research on how polymorphism affects previously-identified genes, but no research has been done on how it affects gene identification itself. We computationally predict protein-coding genes in a straightforward manner, by finding long ORFs in mRNA sequences aligned to the reference genome. We systematically test the effect of known polymorphisms with this procedure. Polymorphisms can not only disrupt ORFs, they can also create long ORFs that do not exist in the reference sequence. We found 5,737 putative protein-coding genes that do not exist in the reference, whose protein-coding status is supported by homology to known proteins. On average 10% of these genes are located in the genomic regions devoid of annotated genes in 12 other catalogs. Our statistical analysis showed that these ORFs are unlikely to occur by chance.

Patterns of cis-element enrichment reveal potential regulatory modules involved in the transcriptional regulation of anoxia response of japonica rice.

Unlike other cereal species, rice is able to germinate and elongate under anoxia. The regulatory mechanism that configures the transcriptome of rice during anaerobic germination is yet to be established. In this study, the major regulatory modules among anoxia-responsive genes in rice identified from published microarray data were predicted by ab initio analysis of cis-regulatory information content. Statistically overrepresented sequence motifs were detected from bona fide promoter sequences [-1000 to +200], revealing various patterns of cis-element enrichment that are highly correlated with bZIP, ERF and MYB types of transcription factors. As implied by the cis-element enrichment patterns, combinatorial mechanisms configure the overall changes in gene expression during anoxic germination and coleoptile elongation. High enrichment of cis-elements associated with ARF, bZIP, ERF, MYB and WRKY (SUSIBA2) transcription factors was also detected among the glycolytic and fermentative associated genes that were upregulated during anoxia. The patterns established from the global analysis of cis-element distribution for upregulated and downregulated genes and their associations with potential cognate regulatory transcription factors indicate the significant roles of ethylene and abscisic acid mediated signaling during coleoptile elongation under anoxia. In addition, the regulation of genes encoding enzymes in the glycolytic and fermentative metabolism could be associated with abscisic acid and auxin in rice coleoptiles to maintain sugar and ATP levels for longer survival.

RecountDB: a database of mapped and count corrected transcribed sequences.

The field of gene expression analysis continues to benefit from next-generation sequencing generated data, which enables transcripts to be measured with unmatched accuracy and resolution. But the high-throughput reads from these technologies also contain many errors, which can compromise the ability to accurately detect and quantify rare transcripts. Fortunately, techniques exist to ameliorate the affects of sequencer error. We present RecountDB, a secondary database derived from primary data in NCBI's short read archive. RecountDB holds sequence counts from RNA-seq and 5' capped transcription start site experiments, corrected and mapped to the relevant genome. Via a searchable and browseable interface users can obtain corrected data in formats useful for transcriptomic analysis. The database is currently populated with 2265 entries from 45 organisms and continuously growing. RecountDB is publicly available at: http://recountdb.cbrc.jp.

Probabilistic alignments with quality scores: an application to short-read mapping toward accurate SNP/indel detection.

MOTIVATION: Recent studies have revealed the importance of considering quality scores of reads generated by next-generation sequence (NGS) platforms in various downstream analyses. It is also known that probabilistic alignments based on marginal probabilities (e.g. aligned-column and/or gap probabilities) provide more accurate alignment than conventional maximum score-based alignment. There exists, however, no study about probabilistic alignment that considers quality scores explicitly, although the method is expected to be useful in SNP/indel callers and bisulfite mapping, because accurate estimation of aligned columns or gaps is important in those analyses. RESULTS: In this study, we propose methods of probabilistic alignment that consider quality scores of (one of) the sequences as well as a usual score matrix. The method is based on posterior decoding techniques in which various marginal probabilities are computed from a probabilistic model of alignments with quality scores, and can arbitrarily trade-off sensitivity and positive predictive value (PPV) of prediction (aligned columns and gaps). The method is directly applicable to read mapping (alignment) toward accurate detection of SNPs and indels. Several computational experiments indicated that probabilistic alignments can estimate aligned columns and gaps accurately, compared with other mapping algorithms e.g. SHRiMP2, Stampy, BWA and Novoalign. The study also suggested that our approach yields favorable precision for SNP/indel calling.

Supra-optimal expression of the cold-regulated OsMyb4 transcription factor in transgenic rice changes the complexity of transcriptional network with major effects on stress tolerance and panicle development.

The R2R3-type OsMyb4 transcription factor of rice has been shown to play a role in the regulation of osmotic adjustment in heterologous overexpression studies. However, the exact composition and organization of its underlying transcriptional network has not been established to be a robust tool for stress tolerance enhancement by regulon engineering. OsMyb4 network was dissected based on commonalities between the global chilling stress transcriptome and the transcriptome configured by OsMyb4 overexpression. OsMyb4 controls a hierarchical network comprised of several regulatory sub-clusters associated with cellular defense and rescue, metabolism and development. It regulates target genes either directly or indirectly through intermediary MYB, ERF, bZIP, NAC, ARF and CCAAT-HAP transcription factors. Regulatory sub-clusters have different combinations of MYB-like, GCC-box-like, ERD1-box-like, ABRE-like, G-box-like, as1/ocs/TGA-like, AuxRE-like, gibberellic acid response element (GARE)-like and JAre-like cis-elements. Cold-dependent network activity enhanced cellular antioxidant capacity through radical scavenging mechanisms and increased activities of phenylpropanoid and isoprenoid metabolic processes involving various abscisic acid (ABA), jasmonic acid (JA), salicylic acid (SA), ethylene and reactive oxygen species (ROS) responsive genes. OsMyb4 network is independent of drought response element binding protein/C-repeat binding factor (DREB/CBF) and its sub-regulons operate with possible co-regulators including nuclear factor-Y. Because of its upstream position in the network hierarchy, OsMyb4 functions quantitatively and pleiotrophically. Supra-optimal expression causes misexpression of alternative targets with costly trade-offs to panicle development.

Transcriptional regulatory network triggered by oxidative signals configures the early response mechanisms of japonica rice to chilling stress.

BACKGROUND: The transcriptional regulatory network involved in low temperature response leading to acclimation has been established in Arabidopsis. In japonica rice, which can only withstand transient exposure to milder cold stress (10 degrees C), an oxidative-mediated network has been proposed to play a key role in configuring early responses and short-term defenses. The components, hierarchical organization and physiological consequences of this network were further dissected by a systems-level approach. RESULTS: Regulatory clusters responding directly to oxidative signals were prominent during the initial 6 to 12 hours at 10 degrees C. Early events mirrored a typical oxidative response based on striking similarities of the transcriptome to disease, elicitor and wounding induced processes. Targets of oxidative-mediated mechanisms are likely regulated by several classes of bZIP factors acting on as1/ocs/TGA-like element enriched clusters, ERF factors acting on GCC-box/JAre-like element enriched clusters and R2R3-MYB factors acting on MYB2-like element enriched clusters.Temporal induction of several H2O2-induced bZIP, ERF and MYB genes coincided with the transient H2O2 spikes within the initial 6 to 12 hours. Oxidative-independent responses involve DREB/CBF, RAP2 and RAV1 factors acting on DRE/CRT/rav1-like enriched clusters and bZIP factors acting on ABRE-like enriched clusters. Oxidative-mediated clusters were activated earlier than ABA-mediated clusters. CONCLUSION: Genome-wide, physiological and whole-plant level analyses established a holistic view of chilling stress response mechanism of japonica rice. Early response regulatory network triggered by oxidative signals is critical for prolonged survival under sub-optimal temperature. Integration of stress and developmental responses leads to modulated growth and vigor maintenance contributing to a delay of plastic injuries.