Zea mays
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA291221 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:Dosage effect on small RNA transcripts in maize copy number alterations
| PRJNA292567 | ENA
Project description:Most angiosperm nuclear DNA is repetitive and derived from silenced transposable elements (TEs). TE silencing requires substantial resources from the plant host, including the production of small interfering RNAs (siRNAs). Thus, the interaction between TEs and siRNAs is a critical aspect of both the function and the evolution of plant genomes. Yet the co-evolutionary dynamics between these two entities remains poorly characterized. Here we studied the organization of TEs within the maize (Zea mays ssp mays) genome, documenting that TEs fall within three groups based on the class and copy numbers. These groups included DNA elements, low copy RNA elements and higher copy RNA elements. The three groups varied statistically in characteristics that included length, location, age, siRNA expression and 24:22 nucleotide (nt) siRNA targeting ratios. In addition, the low copy retroelements encompassed a set of TEs that had previously been shown to decrease expression within a 24 nt siRNA biogenesis mutant (mop1). To investigate the evolutionary dynamics of the three groups, we estimated their abundance in two landraces, one with a genome similar in size to that of the maize reference and the other with a 30% larger genome. For all three accessions, we assessed TE abundance as well as 22 nt and 24 nt siRNA content within leaves. The high copy number retroelements are under targeted similarly by siRNAs among accessions, appear to be born of a rapid bust of activity, and may be currently transpositionally dead or limited. In contrast, the lower copy number group of retrolements are targeted more dynamically and have had a long and ongoing history of transposition in the maize genome
2014-03-11 | GSE55730 | GEO
Project description:Through hierarchical clustering of transcript abundance data across a diverse set of tissues and developmental stages in maize, we have identified a number of coexpression modules which describe the transcriptional circuits of maize development.
2013-03-01 | GSE44743 | GEO
Project description:In many eukaryotes, reproduction involves contributions of genetic material from two parents. At some genes there are parent-of-origin differences in the expression of the maternal and paternal alleles of a gene and this is referred to as imprinting. The analysis of allele-specific expression in several maize hybrids allowed the comprehensive detection of imprinted genes. By comparing allelic expression patterns in multiple crosses, it was possible to observe allelic variation for imprinting in maize. The comparison of genes subject to imprinting in multiple plant species reveals limited conservation for imprinting. The subset of genes that exhibit conserved imprinting in maize and rice may play important, dosage-dependent roles in regulation of seed development. In this study, deep sequencing of RNA isolated from 14 days-after-pollination (DAP) endosperm tissue of five reciprocal hybrid pairs was performed to identify imprinted genes.
2013-11-14 | E-MTAB-4319 | biostudies-arrayexpress
Project description:The prolamin-box binding factor-1 (pbf1) gene encodes a transcription factor that controls the expression of seed storage protein (zein) genes in maize. Prior studies show that pbf1 underwent selection during maize domestication, although how it affected trait change during domestication is unknown. To assay how pbf1 affects phenotypic differences between maize and teosinte, we compared isogenic lines (NILs) that differ for a maize vs.and teosinte alleles of pbf1. Kernel weight for the teosinte NIL (162 mg) is slightly and significantly greater than that for the maize NIL (156 mg). RNAseq data for developing kernels show that the teosinte allele of pbf1 is expressed at about twice the level of the maize allele. However, RNA and protein assays showed no difference in zein profiles between the two NILs. The lower expression for the maize pbf1 allele suggests that selection may have favored this change, however, how reduced pbf1 expression alters phenotype remains unknown. One possibility is that pbf1 regulates genes other than zeins and thereby a domestication trait. The observed drop in seed weight associated with the maize allele of pbf1 is counterintuitive, but could represent a negative pleiotropic effect of selection on some other aspect of kernel composition.
2014-10-10 | E-MTAB-4208 | biostudies-arrayexpress
Project description:Most angiosperm nuclear DNA is repetitive and derived from silenced transposable elements (TEs). TE silencing requires substantial resources from the plant host, including the production of small interfering RNAs (siRNAs). Thus, the interaction between TEs and siRNAs is a critical aspect of both the function and the evolution of plant genomes. Yet the co-evolutionary dynamics between these two entities remains poorly characterized. Here we studied the organization of TEs within the maize (Zea mays ssp mays) genome, documenting that TEs fall within three groups based on the class and copy numbers. These groups included DNA elements, low copy RNA elements and higher copy RNA elements. The three groups varied statistically in characteristics that included length, location, age, siRNA expression and 24:22 nucleotide (nt) siRNA targeting ratios. In addition, the low copy retroelements encompassed a set of TEs that had previously been shown to decrease expression within a 24 nt siRNA biogenesis mutant (mop1). To investigate the evolutionary dynamics of the three groups, we estimated their abundance in two landraces, one with a genome similar in size to that of the maize reference and the other with a 30% larger genome. For all three accessions, we assessed TE abundance as well as 22 nt and 24 nt siRNA content within leaves. The high copy number retroelements are under targeted similarly by siRNAs among accessions, appear to be born of a rapid bust of activity, and may be currently transpositionally dead or limited. In contrast, the lower copy number group of retrolements are targeted more dynamically and have had a long and ongoing history of transposition in the maize genome We compared TE abundances and siRNA profiles among B73 (maize inbred line) and two additional maize landraces, Palomero Toluqueño (PT) and Olote Colorado (OAXA) using HTS
2014-03-11 | E-GEOD-55730 | biostudies-arrayexpress
Project description:Through hierarchical clustering of transcript abundance data across a diverse set of tissues and developmental stages in maize, we have identified a number of coexpression modules which describe the transcriptional circuits of maize development. We examined transcript abundance data at 50 developmental stages/tissues of maize, from embryogenesis to senescence, using a custom Affymetrix Unigene array. The VE stage is germination and emergence Vn leaf stage refers to when the collar of the nth leaf is visible.
2013-03-01 | E-GEOD-44743 | biostudies-arrayexpress
Project description:RNA-directed DNA methylation (RdDM) in plants is a well-characterized example of RNA interference-related transcriptional gene silencing. To determine the relationships between RdDM and heterochromatin in the repeat-rich maize (Zea mays) genome, we performed whole-genome analyses of several heterochromatic features: dimethylation of lysine 9 and lysine 27 (H3K9me2 and H3K27me2), chromatin accessibility, DNA methylation, and small RNAs; we also analyzed two mutants that affect these processes, mediator of paramutation1 and zea methyltransferase2.
2014-12-05 | E-MTAB-4191 | biostudies-arrayexpress
Project description:Maize transgenic event MON810, grown and commercialised worldwide, is the only cultivated GM event in EU. Maize MON810, variety DKC6575, and the corresponding near-isogenic Tietar were studied in different growing conditions, to assess their behaviour in response to drought. Profiling gene expression in water deficit regimes and in generalised water stress showed an up-regulation of different stress- responsive genes. A greater number of differentially expressed genes was observed in Tietar rather than in DKC6575, with genes belonging to transcription factor families and genes encoding HSPs, LEAs and detoxification enzymes. Since these genes have been from literature, indicated as typical of stress responses, their activation in Tietar rather than in DKC6575 may be reminiscent of a more efficient water stress response. DKC6575 was also analysed for the expression of the transgene CryIAb (encoding for the delta-endotoxin insecticidal protein) in water limiting conditions. In all the experiments the CryIAb transcript was not influenced by water stress, but expressed at a constant level. This suggests that though a different pattern of sensitivity to stress, the transgenic variety maintains the same expression level for the transgene.
2015-02-23 | GSE59533 | GEO
Project description:Maize RNA Polymerase D1 (RPD1), the largest subunit of RNA polymerase IV (Pol IV), is required for normal plant development, repression of transposable elements (TEs), and for the regulation of specific alleles associated with TEs. Here, we define the nascent transcriptomes of rpd1 mutant and wild-type (WT) seedlings using global run-on sequencing (GRO-seq) to identify the broader targets of RPD1-based transcriptional regulation. Surprisingly, although TE-like sequences comprise >85% of the maize genome, most TEs are not transcribed at the seedling stage, even in rpd1 mutants. Profile comparisons identify the global set of genes and TEs whose transcription is altered in the absence of RPD1, in some cases in antisense orientation. These results indicate that maize Pol IV specifies Pol II-based transcriptional regulation for certain regions of the maize genome.
2015-02-04 | GSE54166 | GEO