Supplementary MaterialsAdditional file 1 Duplication numbers of 9 most abundant CREs in top 40 highly expressed genes in sperm cells of rice. table. Frequency graph is also plotted for this distribution as shown in Figure ?Figure22. 1756-0500-4-319-S2.PDF (22K) GUID:?FD5340DB-8193-4AAF-9F75-4F6BFE28F6F9 Additional file 3 A map of 28 abundant CREs and their positions within 1 Kb upstream sequences. SIGNALSCAN program of PLACE database identified the positions of CREs in the upstream regions of top 40 highly expressed genes in sperm cell of rice. These selected CREs were subjected to further extensive analysis for their duplication numbers and distribution across the upstream regions. The figure shows exact location of CREs present in 80% of R547 cost the gene dataset. The blue bars above the horizontal black line indicate CREs on sense strand and the blue bars below the black line designates CREs on anti-sense strand. 1756-0500-4-319-S3.TIFF (1.8M) GUID:?3ACA0317-5351-4813-9718-F40906DCF10F Additional file 4 Unique CREs. The analysis exhibited some unique CREs present in only one of the 40 sperm cell expressing genes with one or two duplications. These CREs were found in these specific sperm cell expressing genes. 1756-0500-4-319-S4.PDF (25K) GUID:?AD7A61CD-EDFC-4515-B634-4C33EF917E26 Additional file 5 Peculiar CREs. Besides abundant CREs present in 80% of the gene dataset, there are few others present in just 5-10% of rice sperm cell expressing genes. 1756-0500-4-319-S5.PDF R547 cost (53K) GUID:?635480D2-9E28-4FC1-9F37-AE79FF323B80 Abstract Background The male germ line in flowering plants is initiated within developing pollen grains via asymmetric division. The smaller cell then becomes totally encased within a much larger vegetative cell, forming a unique “cell within a cell structure”. The generative cell subsequently divides to give rise to two non-motile diminutive sperm cells, which take part in double fertilization and lead to the seed set. Sperm cells are difficult to investigate because of their presence within the confines of the larger vegetative cell. However, recently developed techniques for the isolation of rice sperm cells and the fully annotated rice genome sequence have allowed for the characterization of the transcriptional repertoire of sperm cells. Microarray R547 cost gene expression data has identified a subset of rice genes that show unique or highly preferential expression in sperm cells. This information has led to the identification of em cis /em -regulatory elements (CREs), which are conserved in sperm-expressed genes and are putatively associated with the control of cell-specific expression. Findings We aimed to identify the CREs associated with rice sperm cell-specific gene expression data using em in silico /em prediction tools. We analyzed 1-kb upstream regions of the top 40 sperm cell co-expressed genes for over-represented conserved and novel motifs. Analysis of upstream regions with the SIGNALSCAN program with the PLACE database, MEME R547 cost and the Mclip tool helped to find combinatorial sets of known transcriptional factor-binding sites along with two novel motifs putatively associated with the co-expression of sperm cell-specific genes. Conclusions Our data shows the occurrence of novel motifs, which are putative CREs and are likely targets of transcriptional factors regulating sperm cell gene expression. These motifs can be used to design the experimental verification of regulatory elements and the identification of transcriptional factors that regulate sperm cell-specific gene expression. strong class=”kwd-title” Keywords: em cis /em -regulatory elements, plant reproduction, male gamete, gene expression, em Oryza sativa /em Introduction As in animals, flowering plant sperm cells are small cells Rabbit Polyclonal to MC5R that fuse with the egg during fertilization. The sperm cells produced within developing pollen remain enveloped by much larger vegetative cell. Typically, sperm cells occupy 0.1% of the pollen grain volume. The germination of pollen leads to the extension of the vegetative cell wall to produce a pollen tube, which grows via tip elongation to deliver sperm cells to the embryo sac. Until recently, the condensed appearance of chromatin associated with its small cytoplasmic volume was considered to reflect transcriptional quiescence of sperm cells. Recent developments in techniques to isolate sperm cells from pollen  along with the availability of high-throughput genomic and transcriptomic tools have allowed for the.