Zea mays
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA407211 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR6033030.fastq.gz | Fastqsanger.gz | |||
| SRR6033031.fastq.gz | Fastqsanger.gz | |||
| SRR6033022.fastq.gz | Fastqsanger.gz | |||
| SRR6033032.fastq.gz | Fastqsanger.gz | |||
| SRR6033033.fastq.gz | Fastqsanger.gz |
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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: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
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Project description:Mu killer contains a partial inverted duplication of the mudrA transposase gene and two copies of the terminal inverted repeat A region of MuDR. Mu killer can effectively silence single copy MuDR/Mu lines but failed to silence about 25% of the time in multiple copy lines. Mu killer was partially sequenced and shown to be collinear with mudrA. Mu killer individuals that silenced MuDR contained two short antisense transcripts, while individuals that failed to silence MuDR contained multiple sense transcripts but no antisense transcripts. Transcriptomes from Mu killer-silenced individuals were compared to epigenetically silenced lines; the 2 silencing mechanisms were shown to affect different pathways.
2012-07-28 | GSE38314 | 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: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:Mu killer contains a partial inverted duplication of the mudrA transposase gene and two copies of the terminal inverted repeat A region of MuDR. Mu killer can effectively silence single copy MuDR/Mu lines but failed to silence about 25% of the time in multiple copy lines. Mu killer was partially sequenced and shown to be collinear with mudrA. Mu killer individuals that silenced MuDR contained two short antisense transcripts, while individuals that failed to silence MuDR contained multiple sense transcripts but no antisense transcripts. Transcriptomes from Mu killer-silenced individuals were compared to epigenetically silenced lines; the 2 silencing mechanisms were shown to affect different pathways. 4 replicates of the Mu-active and Mu-inactive lines at 2 anther stages (1.0mm, 2.00mm) with a balanced dye-swap design. Normalized intensities for each channel are provided.
2012-07-27 | E-GEOD-38314 | biostudies-arrayexpress
Project description:Small RNAs (21-24 nt) are pivotal regulators of gene expression that guide both transcriptional and post-transcriptional silencing mechanisms in diverse eukaryotes, including most if not all plants. MicroRNAs (miRNAs) and short interfering RNAs (siRNAs) are the two major types, both of which have a demonstrated and important role in plant development, stress responses and pathogen resistance. In this work, we used a deep sequencing approach (Sequencing-By-Synthesis, or SBS) to develop sequence resources of small RNAs from different maize tissues (including leaves, ears and tassels) collected from wild-type plants of the B73 variety. The high depth of the resulting datasets enabled us to examine in detail critical small RNA features as size distribution, tissue-specific regulation and sequence conservation between different organs in this species. We also developed database resources and a dedicated website (http://smallrna.udel.edu/) with computational tools for allowing other users to identify new miRNAs or siRNAs involved in specific regulatory pathways, verify the degree of conservation of these sequences in other plant species and map small RNAs on genes or larger regions of the maize genome under study.
2009-12-31 | GSE17339 | GEO
Project description:Transposable elements (TEs) comprise a substantial portion of many eukaryotic genomes and are typically transcriptionally silenced. RNA–dependent RNA polymerase 2 (RDR2) is a component of the RNA–directed DNA methylation (RdDM) silencing pathway. In maize, loss of mediator of paramutation1 (mop1) encoded RDR2 function results in reactivation of transcriptionally silenced Mu transposons and a substantial reduction in the accumulation of 24 nt short-interfering RNAs (siRNAs) that recruit RNA silencing components. An RNA–seq experiment conducted on shoot apical meristems (SAMs) revealed that, as expected based on a model in which RDR2 generates 24 nt siRNAs that suppress expression, most differentially expressed DNA TEs (78%) were up-regulated in the mop1 mutant. In contrast, most differentially expressed retrotransposons (68%) were down-regulated. This striking difference suggests that distinct silencing mechanisms are applied to different silencing templates. In addition, 6,000 genes (24% of analyzed genes), including nearly 80% (286/361) of genes in chromatin modification pathways, were differentially expressed. Overall, two-thirds of differentially regulated genes were down-regulated in the mop1 mutant. This finding suggests that RDR2 plays a significant role in regulating the expression of not only transposons, but also of genes. A re-analysis of existing small RNA data identified both RDR2–sensitive and RDR2–resistant species of 24 nt siRNAs that we hypothesize may at least partially explain the complex changes in the expression of genes and transposons observed in the mop1 mutant. Single sequencing library was constructed for mop1 mutant and non-mutant. Each library was sequenced using 2 lanes on a Solexa flow cell. Processed data file 'ZmB73_4a.53_filtered_genes.fasta' and its README file are linked below as supplementary files. The fasta file contains the gene model ID and corresponding sequence generated from maize genome project. This fasta file was used for the following samples: GSM418173, GSM418174, GSM420173, GSM420174, GSM422828, GSM422829.
2009-11-20 | E-GEOD-16789 | biostudies-arrayexpress
Project description:Small RNAs (21-24 nt) are pivotal regulators of gene expression that guide both transcriptional and post-transcriptional silencing mechanisms in diverse eukaryotes, including most if not all plants. MicroRNAs (miRNAs) and short interfering RNAs (siRNAs) are the two major types, both of which have a demonstrated and important role in plant development, stress responses and pathogen resistance. In this work, we used a deep sequencing approach (Sequencing-By-Synthesis, or SBS) to develop sequence resources of small RNAs from different maize tissues (including leaves, ears and tassels) collected from wild-type plants of the B73 variety. The high depth of the resulting datasets enabled us to examine in detail critical small RNA features as size distribution, tissue-specific regulation and sequence conservation between different organs in this species. We also developed database resources and a dedicated website (http://smallrna.udel.edu/) with computational tools for allowing other users to identify new miRNAs or siRNAs involved in specific regulatory pathways, verify the degree of conservation of these sequences in other plant species and map small RNAs on genes or larger regions of the maize genome under study. Small RNA libraries were derived from leaves, ears and tassels of maize variety B73 (wild-type). Plants were grown in a flood irrigated plot at the University of Arizona (Tucson, AZ, USA) in 2007 and organs were pooled from several plants for each library. Young leaves were collected from 6-weeks-old seedlings. Post-meiotic immature ears were harvested from 10- and 11-week old plants while pre-meiotic tassels were collected from 8-week old plants. Total RNA was isolated using the Plant RNA Purification Reagent (Invitrogen) and submitted to Illumina (Hayward, CA, http://www.illumina.com) for small RNA library construction using approaches described in (Lu et al., 2007) with minor modifications. The small RNA libraries were sequenced with the Sequencing-By-Synthesis (SBS) technology by Illumina. PERL scripts were designed to remove the adapter sequences and determine the abundance of each distinct small RNA. We thank Lyudmila Sidorenko and Vicki Chandler for providing the plant material and Kan Nobuta for assistance with the computational methods.
2009-12-31 | E-GEOD-17339 | biostudies-arrayexpress
Project description:We report the role of sRNAs populations during the induction of callus tissues from VS-535 maize embryos displaying contrasting in vitro embryogenic potential; characterized through Next-generation sequencing (NGS). We conclude that the Embryogenic Response during Maize Somatic Embryogenesis induction is closely related to sRNAs regulation and depends on the developmental stage of the explant.
2019-10-21 | GSE120436 | GEO