Alfa2-COP is involved in early secretory traffic in Arabidopsis and it is required for plant growth
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ABSTRACT: The loss-of-function mutants of alfa1-COP (alfa1-COP-1) and alfa2-COP (alfa2-COP1), the two alfa-COP isoforms of Arabidopsis. Unlike in alfa1-COP mutant, the alfa2-COP mutant displays defects in plant growth, including small rosettes, stems and roots and mislocalization of p24a5, a protein containing a C-terminal dylisine motif involved in COPI binding. In addition, it exhibited abnormal morphology of the Golgi apparatus. Global expression analyses of the alfa2-COP mutant versus wild-type Arabidopsis plants reveal altered expression of plant cell wall-associated genes. A high expression of the COPII sec31A isoform was observed in the alfa2-COP mutant that also occurs in a mutant of an upstream gene of COPI assembly, the ARF-GEF GNL1
Project description:First we developed a new, simple, and robust assay called CoP (Column Purified chromatin) for profiling of accessible regions by directly purifying fragmentized crosslinked chromatin with DNA purification column. The CoP chromatin regions by CoP-seq are consistent with the accessible regions detected by ATAC-seq and FARIE-seq. Then we integrated CoP-seq and Hi-C technique (Hi-CoP) for interactions of accessible chromatin regions which represent active cis-regulatory elements in cells. Our data showed that Hi-CoP assay can robustly detect interactions of regulatory regions.
Project description:During maturation, eukaryotic precursor RNAs undergo processing events including intron splicing, 3’-end cleavage, and polyadenylation. Here, we describe nanopore analysis of CO-transcriptional Processing (nano-COP), a method for probing the timing and patterns of RNA processing. An extension of native elongating transcript sequencing (NET-seq), which quantifies transcription genome-wide through short-read sequencing of nascent RNA 3’ ends, nano-COP uses long-read nascent RNA sequencing to observe global patterns of RNA processing. First, nascent RNA is stringently purified through a combination of 4-thiouridine metabolic labeling and cellular fractionation. In contrast to cDNA or short-read–based approaches relying on reverse transcription or amplification, the sample is sequenced directly through nanopores to reveal the native context of nascent RNA. nano-COP identifies both active transcription sites and splice isoforms of single RNA molecules during synthesis, providing insight into patterns of intron removal and the physical coupling between transcription and splicing. The nano-COP protocol yields data within 3 days.
Project description:We identified the wt Cop allele of the predicted Fry gene as a mammary carcinoma susceptibility gene. This gene has not been characterized in mammals, so for part of our analysis we conducted microarray experiments to look at the changes in gene expression which occur when the wt Cop Fry allele is ectopically expressed in the MDA-MB-231 breast cancer cell line (a cell line which we identified as having low FRY mRNA expression). We used microarrays to identify the Fry interactome and identified that Fry affects the expression of gene networks that maintain normal cellular and tissue architecture, organization, differentiation of epithelial cells.
Project description:High levels of copper are toxic and therefore bacteria must limit free intracellular levels to prevent cellular damage. In this study, we show that a number of pneumococcal genes are differentially regulated by copper, including an operon encoding a CopY regulator, a protein of unknown function (CupA) and a P1-type ATPase, CopA, which is conserved in all sequenced Streptococcus pneumoniae strains. Transcriptional analysis demonstrated that the cop operon is induced by copper in vitro, repressed by the addition of zinc and is autoregulated by the copper-responsive CopY repressor protein. We also demonstrate that the CopA ATPase is a major pneumococcal copper resistance mechanism and provide the first evidence that the CupA protein plays a role in copper resistance. Our results also show that copper homeostasis is important for pneumococcal virulence as the expression of the cop operon is induced in the lungs and nasopharynx of intranasally infected mice, and a copA(-) mutant strain, which had decreased growth in high levels of copper in vitro, showed reduced virulence in a mouse model of pneumococcal pneumonia. Furthermore, using the copA(-) mutant we observed for the first time in any bacteria that copper homeostasis also appears to be required for survival in the nasopharynx. This SuperSeries is composed of the SubSeries listed below.
Project description:We used high density oligonucleotide arrays to measure the relative expression levels of ~27,000 probe sets in the left ventricles of inbred rat strains; DA (high performing), Copenhagen (COP, low performing), as well as F1(COPxDA) rats bred from these tw
Project description:Gene expression profiles in mammary glands of different rat strains are genetically defined. Experiment Overall Design: 18 Cop rats with or without N-nitrosomethylurea (NMU) treatment at 6h, 1d, and 30 d compared to 18 F344 rats with or without NMU treatment at 6h, 1d, and 30 day
Project description:The objective of this experiment was to determine changes in gene expression upon loss of alfa-1 in C.elegans under well-fed and starvation conditions. The human C9orf72 has an orthologue in C. elegans based on sequence homology, which is the F18A1.6 gene and also recently named as alfa-1 (ALS/FTD-associated gene homolog 1). We analyzed the domain structure of ALFA-1 and found that it shares the same DENN domains as human C9orf72, including the uDENN, cDENN, and dDENN domains. We obtained a mutant strain of the alfa-1 gene, which has a mutant allele (ok3062) of 486 bp deletion and 24 bp insertion in the region of exon 3 and exon 4. To understand the changes in gene expression in the alfa-1 mutant C. elegans, we performed the microarray gene expression profiling experiments under the defined conditions.