Global expression profiling of Physcomitrella patens Hydroxyproline O-arabinosylatransferases (hpat) mutants
ABSTRACT: Hydroxyproline O-arabinosylatransferases (HPATs) are members of a small, deeply conserved family of plant-specific glycosyltransferases that add arabinose sugars to diverse proteins such as cell wall-associated extensins and small signaling peptides. We used a custom designed NimbleGene microarray based on genome version 1.6 to perform transcriptome profiling on Physcomitrella patens protonema tissue from wild type and two hpat mutants.
Project description:***This experiment was updated on 26-02-2016 to correct the accidental mis-labelling of some raw data files. For data downloaded before this date, please note that the file labelled as Caulonema_a.pair contains the raw data for Chloronema A and the file labelled as Chloronema_a.pair contains the data for Caulonema A. ***** We analyzed the transcriptional profile of all phases in the life cycle of P. patens, including all major tissues and 4 different sporophyte developmental stages. For this analysis we took advantage of a custom designed NimbleGene microarray based on genome version 1.6, and developed adequate protocols for the isolation and purification of mRNA directly from mechanically purified cells of chloronema, caulonema, rhizoids, gametophores, sporophytes, spores, archegonia and protoplasts.
Project description:Physcomitrella patens reproductive organs (archegonia and antheridia) were mechanically isolated for transcriptome profiling. Comparison between wt and Ppglr1/2, a glutamate receptor double knock-out mutant, was done to identify deferentially expressed genes. A custom designed NimbleGene microarray based on genome version 1.6 was used for this study.
Project description:At least six histone H1 variants exist in mammalian somatic cells that bind to the linker DNA and stabilize the nucleosome particle contributing to higher order chromatin compaction. In addition, H1 seems to be involved in the active regulation of gene expression. It is not well known whether the different variants have specific roles, are distributed differentially along the genome, or regulate specific promoters. By taking advantage of specific antibodies to H1 variants and HA-tagged recombinant H1 variants expressed in a breast cancer-derived cell line, we have investigated the distribution of the different somatic H1 variants (H1.2 to H1.5, H1.0 and H1X) in particular promoters and genome-wide. Analysis of H1 (H1.0, H1.2, H1.3, H1.4, H1.5 and H1X) and H3 abundance in promoter regions
Project description:Chromosomes and genes are non-randomly arranged within the mammalian cell nucleus. Clustering of genes is of great significance in transcriptional regulation. However, the relevance of gene clustering in their expression during differentiation of neural precursor cells (NPCs) into astrocytes remains unclear. We performed a genome-wide enhanced circular chromosomal conformation capture (e4C) to screen genes associated with an astrocyte-specific gene, glial fibrillary acidic protein (Gfap), during astrocyte differentiation. We identified 13 genes that were specifically associated with Gfap and expressed in NPC-derived astrocytes. These results provide evidence for functional significance of gene clustering in transcriptional regulation during NPCs differentiation. comparison of NPCs vs LIF+ vs LIF- cells.
Project description:7 days old protonema of Physcomitrella patens Wildtype and two transgenic lines, ΔPpcmt line 281 (Noy-Malka et al. 2014; IMSC accession 40738) and ΔPpmet line 5 (Yaari et al. 2015; IMSC accession 40758) grown on BCDAT solid medium.
Project description:To investigate the disruption effect of Group A PP2C on global gene expression in Physcomitrella patens, we performed microarray analysis of wildtype plant and PpABI1 disruptants using a custom Physcomitrella oligonucleotide microarray, which carries probes for 33,942 gene models of Physcomitrella genome version 1.1. on a 4 x 44 K Agilent platform. Gene expression in wildtype plant and ppabi1 disruptants were measured at 0, 1, 3, 6 and 12 hours after exposure to 10 μM ABA. Three biologically independent experiments were performed at 0 hour. Also to discover the early ABA-responsive genes, gene expression in wildtype was measured at 0 and 3 hours after exposure to 1 μM ABA.
Project description:Hyperthermophilic bacteria of the genus Thermotoga are known to utilize a wide range of simple and complex polysaccharides. T. maritima's transcriptional response to a variety of mono- and poly-saccharides was previously studied to assign functions to genes involved in carbohydrate uptake and utilization. To compare and contrast closely-related members of the Thermotoga genus, a four-species microarray was developed by expanding a whole genome T. maritima array to include unique genes from three other species (T. neapolitana, T. petrophila, and T. sp. RQ2). This multi-species array was used to investigate the diversity of the genus, specifically the response of each of the four species to a mixture of polysaccharides (galactomannan, glucomannan, xylan, pectin, lichenan, and carboxymethyl cellulose). RNA derived from glucose-grown cultures (glu) was compared to RNA derived from polysaccharide-grown cultures (poly) using a dye swap setup.
Project description:Transcriptional profiling with next-generation sequencing methods demonstrated that a Neurospora crassa mutant with the three most highly expressed beta-glucosidase genes deleted had a transcriptional response to cellobiose similair to that of wild type N. crassa exposed to cellulose. N. crassa was pregrown in Sucrose and transferred to Avicel (cellulose), Cellobiose, Sucrose or media with no carbon added. Biological triplicates used to identify differentially expressed genes in WT on Avicel. Single libraries for mutant strains identify which genes show similair expression on cellobiose as in the WT on cellulose.
Project description:Transcriptional profiling with next-generation sequencing methods refined our understanding of the N. crassa transcriptional response to cellulose and demonstrated that the newly characterized transcription factors clr-1 and clr-2 were required for the bulk of that response including induction all major cellulase and some major hemicellulase genes. N. crassa pregrown in Sucrose and transferred to Avicel (cellulose), Sucrose or media with no carbon added. Biological triplicates used to identify differentially expressed genes in WT. Single libraries for mutant strains identify which genes show deficient regulation in response to Avicel. Note: Samples named "cdr1" and "cdr2" correspond to the genes clr-1 and clr-2 respectively.