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Gene expression analysis distinguishes tissue specific and gender related functions among adult Ascaris suum tissues.

ABSTRACT: Over a billion people are infected by Ascaris spp. intestinal parasites. We investigated gene expression by various tissues of adult A. suum, and used that information to help resolve basic functions of these tissues, basic biology of parasitism and functional aspects of nematode genomes. The A. suum genome was sequenced and assembled to allow generation of microarray elements. Expression of over 40,000 60-mer elements was investigated in a variety of tissues from both male and female adult worms. Nearly 50 percent of the elements for which signal was detected exhibited differential expression among different tissues. The unique profile of transcripts identified for each tissue clarified functional distinctions among tissues, such as chitin binding in the ovary and peptidase activity in the intestines. Interestingly, hundreds of gender specific elements characterized female or male intestinal tissues, respectively. A. suum genes from the same family were frequently expressed differently among tissues. Transcript abundance for genes specific to A. suum, by comparison to Caenorhabditis elegans, varied to a greater extent among tissues than for genes conserved between A. suum and C. elegans. Analysis using C. elegans protein interaction data identified functional modules conserved between these two nematodes, resulting in identification of functional predictions of essential subnetworks of protein interactions and how these networks may vary among nematode tissues. A notable finding was very high module similarity between adult reproductive tissues and intestine. Our data identified gene and predicted protein determinants that distinguish functions of individual adult A. suum tissues as well those that likely serve all the tissues investigated in our study. The size of A. suum adults (30-40 cm compared to less than 1 cm for many nematodes) enabled this resolution and will facilitate experimental dissection of individual and interactive functions of these tissues in this and other parasitic nematodes.

ORGANISM(S): Ascaris suum

PROVIDER: GSE36690 | GEO | 2012/09/30

SECONDARY ACCESSION(S): PRJNA153609

REPOSITORIES: GEO

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Project description:Over a billion people are infected by Ascaris spp. intestinal parasites. We investigated gene expression by various tissues of adult A. suum, and used that information to help resolve basic functions of these tissues, basic biology of parasitism and functional aspects of nematode genomes. The A. suum genome was sequenced and assembled to allow generation of microarray elements. Expression of over 40,000 60-mer elements was investigated in a variety of tissues from both male and female adult worms. Nearly 50 percent of the elements for which signal was detected exhibited differential expression among different tissues. The unique profile of transcripts identified for each tissue clarified functional distinctions among tissues, such as chitin binding in the ovary and peptidase activity in the intestines. Interestingly, hundreds of gender specific elements characterized female or male intestinal tissues, respectively. A. suum genes from the same family were frequently expressed differently among tissues. Transcript abundance for genes specific to A. suum, by comparison to Caenorhabditis elegans, varied to a greater extent among tissues than for genes conserved between A. suum and C. elegans. Analysis using C. elegans protein interaction data identified functional modules conserved between these two nematodes, resulting in identification of functional predictions of essential subnetworks of protein interactions and how these networks may vary among nematode tissues. A notable finding was very high module similarity between adult reproductive tissues and intestine. Our data identified gene and predicted protein determinants that distinguish functions of individual adult A. suum tissues as well those that likely serve all the tissues investigated in our study. The size of A. suum adults (30-40 cm compared to less than 1 cm for many nematodes) enabled this resolution and will facilitate experimental dissection of individual and interactive functions of these tissues in this and other parasitic nematodes. 10 samples were prepared from the tissues of adult worms of both genders to be analyzed. Two to three replicates were done for each sample, swapping dyes and channel for the test and the control for each sample. The control consisted of pooled worm tissues from both genders with an equal amount being included from each sample. These samples and the control were hybridized against an Agilent 4x44k format custom chip spotted with 42,212 probes. This probeset was created from 38,768 predicted protein coding sequences from an Ascaris suum genome survey sequence (GSS) project, and also from 5,176 EST contigs that were not covered by this predicted GSS gene-set. These 43,944 putative gene sequences from Ascaris suum were filtered for cross-reaction to non-coding sequences using Agilent eArray, and our final set of 42,212 probes was determined.

Project description:A long-standing view of development is that transcription is silenced in the oocyte until early divisions in the embryo. The point at which major transcription is reactivated varies in different organisms, but is usually after the 2-cell stage. However, this model may not be universal. We used RNA-seq and exploited the protracted development of the parasitic nematode Ascaris suum, to provide a comprehensive time course of mRNA expression, degradation, and translation during early development. Surprisingly, we find that ~4,000 genes are transcribed prior to pronuclear fusion and in the 1-4 cell embryos. Intriguingly, we do not detect maternal contribution of many orthologs of maternal C. elegans mRNAs, but instead find these are newly transcribed in the A. suum zygote prior to pronuclear fusion. Ribosome profiling demonstrates that, in general, early embryonic mRNAs are not stored for subsequent translation, but are directly translated following their synthesis. The role of maternally contributed and zygotically transcribed genes differs between the nematodes A. suum and C. elegans despite the fact that the two nematodes appear to exhibit highly similar morphological patterns during early development. Our study indicates that major transcription can occur immediately after fertilization and prior to pronuclear fusion in metazoa, suggesting that newly transcribed genes appear to drive A. suum early development. Furthermore, the mechanisms used for controlling the timing of the expression of key conserved genes has been altered between the two nematodes, illustrating significant plasticity in the regulatory networks that play important roles in developmental outcomes in nematodes. A total of 28 samples are used for this study. The RNAs for the library construction are derived from 0.5 M-bM-^@M-^S 1 ml of synchronized embryo stages corresponding to a minimum of 0.5 billion embryos derived from > 1,000 female worms. The RNAs for polysome analysis are from pooled fractions of polysome gradient. For each sample, the amount of RNA for all polysome fractions is equivalent to the total RNA from the sample. Thus, the data from polysome profiling and RNA transcriptomes are considered as biological replicates. The level of the RNAs between each neighboring stages during development are considered as the reference for each other. Different sequencing strategies were applied for multiple libraries.

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Gene expression analysis distinguishes tissue specific and gender related functions among adult Ascaris suum tissues.

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