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Funaria hygrometrica sporophyte/gametophyte gene expression

ABSTRACT: Funaria hygrometrica sporophyte/gametophyte gene expression

PROVIDER: PRJEB2156 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	ERR012004.fastq.gz	Fastqsanger.gz
	ERR012005.fastq.gz	Fastqsanger.gz
	ERR012006.fastq.gz	Fastqsanger.gz
	ERR012007.fastq.gz	Fastqsanger.gz

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Transcription profiling by high throughput sequencing of Funaria hygrometrica sporophyte and gametophyte tissue

Project description:Funaria hygrometrica sporophyte/gametophyte gene expression

2011-10-01 | E-MTAB-284 | biostudies-arrayexpress

Genome-wide transcriptomic analysis of the sporophyte of the moss Physcomitrella patens

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Genome-wide transcriptomic analysis of the sporophyte of the moss Physcomitrella patens

Project description:Bryophytes are the most basal of the extant land plants. A major feature of these plants is the biphasic alteration of generations between a dominant haploid gametophyte and a minor diploid sporophyte phase. To analyse the differences in the transcriptome of the early gametophyte (protonema) and early and mid-sporophyte phases of the moss Physcomitrella patens, microarray gene expression profiles were performed using dissected sporophyte tissue. Through further analysis the early and mid-sporophyte phases were compared. RNA isolated from the Gametophytic protonemal tissue was hybridised to six microarrays. Each microarray was hybridised with RNA from a separate biological replicate. Three of these microarrays were co-hybridised with RNA isolated from early sporophytes. With the third gametophyte biological replicate and early sporophyte replicate a dye swap was carried out. The remaining three microarrays hybridised with RNA from the gametophytes were co-hybridised with RNA from mid-sporophytic tissue. A dye swap was carried out on the sixth gametophyte replicate and third mid-sporophyte replicate.To meet the quality requirements for the microarray experiment, at least 400 sporophytes were used per extraction. Three or four RNA extracts were then pooled for further precipitation to maximise purity and concentration. Up to 1600 sporophytes were harvested to prepare sufficient RNA for each microarray replicate. In bioinformatic analysis the channels were split into individual channels and the early and mid-sporophyte were compared.

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Transcription profiling of Ectocarpus strain Esil32 porophyte and gametophyte stages in normal and mutant strains to analyse expression of two sets of genes previously identified as being putatively sporophyte-specific or gametophyte-specific

Project description:The aim of this experiment was to analyse the expression of two sets of genes identified as being putatively sporophyte-specific or gametophyte-specific by a suppressive subtraction hybridisation using cDNA from immature sporophytes and immature gametophytes of the Ectocarpus strain Esil32. The expression of these genes was analysed in the sporophyte and gametophyte generations of the life cycle (again using immature algae that had not yet produces zoidangia) and in the sporophyte generation of a mutant strain, immediate upright, that exhibits gametophyte-like characteristics during the sporophyte generation.

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The DME demethylase regulates sporophyte gene expression, cell proliferation, differentiation, and meristem resurrection

Project description:The flowering plant life cycle consists of alternating haploid (gametophyte) and diploid (sporophyte) generations, where the sporophytic generation begins with fertilization of haploid gametes. In Arabidopsis, genome-wide DNA demethylation is required for normal development, catalyzed by the DEMETER (DME) DNA demethylase in the gamete companion cells of male and female gametophytes. In the sporophyte, postembryonic growth and development are largely dependent on the activity of numerous stem cell niches, or meristems. Analyzing Arabidopsis plants homozygous for a loss-of-function dme-2 allele, we show that DME influences many aspects of sporophytic growth and development. dme-2 mutants exhibited delayed seed germination, variable root hair growth, aberrant cellular proliferation and differentiation followed by enhanced de novo shoot formation, dysregulation of root quiescence and stomatal precursor cells, and inflorescence meristem (IM) resurrection. We also show that sporophytic DME activity exerts a profound effect on the transcriptome of developing Arabidopsis plants, including discrete groups of regulatory genes that are misregulated in dme-2 mutant tissues, allowing us to potentially link phenotypes to changes in specific gene expression pathways. These results show that DME plays a key role in sporophytic development and suggest that DME-mediated active DNA demethylation may be involved in the maintenance of stem cell activities during the sporophytic life cycle in Arabidopsis.

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Epigenetic modifications associated with life cycle transitions in the brown alga Ectocarpus

Project description:In this study, we have carried out a broad census of histone PTMs in Ectocarpus chromatin and have developed a method to evaluate the genome-wide distribution of specific marks. We show that modulation of the expression of sporophyte-biased genes during the life cycle is correlated with marked changes in the pattern of three histone PTMs. In contrast, the expression patterns of gametophyte-biased genes were not correlated with modifications to the histone PTMs assayed, suggesting that gametophyte-biased and sporophyte-biased gene expression are mediated by different epigenetic processes.

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Project description:Determining the sporophyte-to-gametophyte transition in maize

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Analysis of transcript abundances in Ectocarpus life cycle mutants

Project description:The aim of this experiment was to compare transcript abundances in parthenotes (i.e. organisms derived by parthenogenetic development of gametes) of two life cycle mutants of the brown alga Ectocarpus siliculosus with transcript abundances in the wild type sporophyte and gametophyte generations. This is of interest because the two mutations, immediate upright (imm) and ouroboros (oro), cause partial and almost complete hometic conversion, respectively, of the sporophyte into the gametophyte. imm parthenotes exhibit gametophyte-like morphology during early development but remain sporophytes in functional terms (they do not produce gametes) whereas oro parthenotes behave as functional gametophytes and are morphologically indistinguishable from gametophytes apart from the appearance some minor sporophyte-like features very early in development in some individuals. To minimise genetic background effects the samples for this experiment were derived from a segregating population derived from an imm/IMM oro/ORO sporophyte. Four classes of gametophyte were derived from this sporophyte were IMM/ORO (wild type), imm/ORO, IMM/oro and imm/oro. Parthenomes were bulked to provide a wild type sporophyte sample, samples corresponding to the two individual mutants, plus the double mutant. A wild type gametophyte sample was also compared for comparison. Hybridisations with cDNA derived from these five samples were carried out using a NimbleGen expressed-sequence-tag-(EST-)based microarray carrying probes corresponding to 10,600 of the 16,256 genes identified in the Ectocarpus genome.

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A Physcomitrella protein acts in spermatogenesis and sporophyte abortion

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