Quadruple 9-mer-based protein binding microarray with DsRed fusion protein

<p>Abstract</p> <p>Background</p> <p>The interaction between a transcription factor and DNA motif (<it>cis</it>-acting element) is an important regulatory step in gene regulation. Comprehensive genome-wide methods have been developed to characterize protein-DNA interactions. Recently, the universal protein binding microarray (PBM) was introduced to determine if a DNA motif interacts with proteins in a genome-wide manner.</p> <p>Results</p> <p>We facilitated the PBM technology using a DsRed fluorescent protein and a concatenated sequence of oligonucleotides. The PBM was designed in such a way that target probes were synthesized as quadruples of all possible 9-mer combinations, permitting unequivocal interpretation of the <it>cis</it>-acting elements. The complimentary DNA strands of the features were synthesized with a primer and DNA polymerase on microarray slides. Proteins were labeled via N-terminal fusion with DsRed fluorescent protein, which circumvents the need for a multi-step incubation. The PBM presented herein confirmed the well-known DNA binding sequences of Cbf1 and CBF1/DREB1B, and it was also applied to elucidate the unidentified <it>cis</it>-acting element of the OsNAC6 rice transcription factor.</p> <p>Conclusion</p> <p>Our method demonstrated PBM can be conveniently performed by adopting: (1) quadruple 9-mers may increase protein-DNA binding interactions in the microarray, and (2) a one-step incubation shortens the wash and hybridization steps. This technology will facilitate greater understanding of genome-wide interactions between proteins and DNA.</p

Additional file 5: Figure S4. of Genome-wide identification of grain filling genes regulated by the OsSMF1 transcription factor in rice

The expression patterns of transcription factors as a putative target of OsSMF1 based on the 300 K Rice Genome Microarray ( www.ggbio.com ). The expression was measured in different sized panicles before heading (1, 3, 5, 8, 10, 15, 20, and 22 cm), at the indicated days after pollination (1, 3, 4, 11, and 21 days) and in the leaf, root, germinating seed, callus, and regenerating callus. (PPTX 75 kb

Additional file 1: Figure S1. of Genome-wide identification of grain filling genes regulated by the OsSMF1 transcription factor in rice

Transcript levels of Wsi18, OsSMF1, and OsREM from 300 K Rice Genome Microarray ( www.ggbio.com ). The transcript levels were measured in different sized panicles before heading (1, 3, 5, 8, 10, 15, 20, and 22 cm), at the indicated days after pollination (1, 3, 4, 11, and 21 days) and in the leaf, root, germinating seed, callus, and regenerating callus. (PPTX 70 kb

Additional file 4: Figure S3. of Genome-wide identification of grain filling genes regulated by the OsSMF1 transcription factor in rice

The query gene, OsSMF1, is marked by an asterisk. Each circle indicates a gene, and the lines represent the correlations between the genes. Eighty-five genes were identified as OsSMF1-related genes, with a minimum correlation value of 0.55 and depth of 1. (PPTX 473 kb

RapaNet: A Web Tool for the Co-Expression Analysis of Brassica rapa Genes

Accumulated microarray data are used for assessing gene function by providing statistical values for co-expressed genes; however, only a limited number of Web tools are available for analyzing the co-expression of genes of Brassica rapa . We have developed a Web tool called RapaNet ( http://bioinfo.mju.ac.kr/arraynet/brassica300k/query/ ), which is based on a data set of 143 B rapa microarrays compiled from various organs and at different developmental stages during exposure to biotic or abiotic stress. RapaNet visualizes correlated gene expression information via correlational networks and phylogenetic trees using Pearson correlation coefficient ( r ). In addition, RapaNet provides hierarchical clustering diagrams, scatterplots of log ratio intensities, related pathway maps, and cis -element lists of promoter regions. To ascertain the functionality of RapaNet, the correlated genes encoding ribosomal protein (L7Ae), photosystem II protein D1 (psbA), and cytochrome P450 monooxygenase in glucosinolate biosynthesis (CYP79F1) were retrieved from RapaNet and compared with their Arabidopsis homologues. An analysis of the co-expressed genes revealed their shared and unique features