Ontology highlight
ABSTRACT:
PROVIDER: PRJNA1158863 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR30616300_1.fastq.gz | Fastqsanger.gz | |||
| SRR30616300_2.fastq.gz | Fastqsanger.gz | |||
| SRR30616301_1.fastq.gz | Fastqsanger.gz | |||
| SRR30616301_2.fastq.gz | Fastqsanger.gz | |||
| SRR30616302_1.fastq.gz | Fastqsanger.gz |
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Project description:Diatom cell walls, made of nanostructured silica, are of interest in diverse areas ranging from cellular structure, to hierarchical organization in biomineralization, to nanotechnology. Thus far, only cell surface proteins and proteins tightly associated with silica matrix have been characterized, and essential components of the silica deposition vesicle (SDV) are unknown, including components of the SDV membrane, cytoskeletal-interacting proteins, and proteins involved in trafficking associated with the SDV. Thus, an understanding of most of the molecular components and the dynamics of cellular processes involved in cell wall synthesis is lacking. In this work we report the first whole-cell response analysis using whole genome microarrays to identify genes potentially involved in diverse aspects of diatom cell division or cell wall synthesis. Thalassiosira pseudonana transcript profiles from precise time points, known to be associated with specific cell wall formation processes in cell-cycle synchronized cultures, suggests that this gene set includes extracellular proteins, silica matrix proteins, and proteins involved in signal transduction, vesicle trafficking, and transport. Protein localization experiments further confirm the first discovery of proteins associated with the SDV membrane. We propose that these proteins provide the interface between extra-SDV organization by the cytoskeleton and intra-SDV organization of silica polymerization determinants, which lead to the higher order organization of diatom silica structure. Analyzed mRNA from 0, 2, 4, 7, 8 and 9 hr of synchronized cell cycle using the Affymetrix GeneChip whole genome tiling array. Initial analysis of gene level expression was performed using Affymetrix Expression Console Software, version 1.1. No biological replicates were performed. 0 hr is used as reference point.
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Project description:modENCODE_submission_3168 Although C. elegans was the first multicellular organism with a completely sequenced genome, how this genome is arranged within the nucleus is not known. By chromatin immunoprecipitation of the nuclear transmembrane protein LEM-2, we determined the regions of the C. elegans genome associated with the nuclear membrane. We found that large regions of several megabases on the left and right arms of each autosome were associated with the nuclear membrane. The center of each autosome was free of such interactions, suggesting these regions are largely looped out from the nuclear membrane. The X chromosome, unlike the autosomes, was associated with the nuclear membrane only at its left end. At a finer scale, these large membrane-associated domains consist of smaller subdomains of LEM-2 associations. These subdomains are characterized by a high density of repetitive sequences, a low density of genes, and high levels of H3K27 trimethylation. The subdomains were punctuated by gaps containing genes with high transcriptional activity. Finally, we found that a chromosome arm translocated to the center of a chromosome retained its association with the nuclear membrane, although there was a decrease of association up to 400 kb from the fusion point. This indicates that local chromatin properties are the main determinant of interaction with the nuclear membrane, but the degree of association can be modulated by position along the chromosome. Our data provide the foundation for a model of the spatial arrangement of C.elegans chromosomes within the nucleus. Supplemental materials are available online at http://www.genome.org . Microarray and high-throughput sequencing data are available online at modENCODE Data Coordinating Center website, http://206.108.121.120/submit/public/list . These dataset are designed to confirm ChIP-chip experiments. The three experiments listed consist of: (1) LEM-2 ChIP-seq (seq-SDQ3891_LEM2_N2_MXemb_1_A_EE8_KI021); (2) control IgG ChIP-seq (seq-AB46540_NIgG_N2_MXemb_2_A_EE1432); and (3)Input-seq (seq-NA_N2_MXemb_3_A_EE1432) For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf
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