Journal article
Genome-wide tissue-specific gene expression, co-expression and regulation of co-expressed genes in adult nematode Ascaris suum
PLoS neglected tropical diseases, Vol.8(2), pp.e2678-e2678
02/2014
Handle:
https://hdl.handle.net/2376/104139
PMCID: PMC3916258
PMID: 24516681
Abstract
Caenorhabditis elegans has traditionally been used as a model for studying nematode biology, but its small size limits the ability for researchers to perform some experiments such as high-throughput tissue-specific gene expression studies. However, the dissection of individual tissues is possible in the parasitic nematode Ascaris suum due to its relatively large size. Here, we take advantage of the recent genome sequencing of Ascaris suum and the ability to physically dissect its separate tissues to produce a wide-scale tissue-specific nematode RNA-seq datasets, including data on three non-reproductive tissues (head, pharynx, and intestine) in both male and female worms, as well as four reproductive tissues (testis, seminal vesicle, ovary, and uterus). We obtained fundamental information about the biology of diverse cell types and potential interactions among tissues within this multicellular organism.
Overexpression and functional enrichment analyses identified many putative biological functions enriched in each tissue studied, including functions which have not been previously studied in detail in nematodes. Putative tissue-specific transcriptional factors and corresponding binding motifs that regulate expression in each tissue were identified, including the intestine-enriched ELT-2 motif/transcription factor previously described in nematode intestines. Constitutively expressed and novel genes were also characterized, with the largest number of novel genes found to be overexpressed in the testis. Finally, a putative acetylcholine-mediated transcriptional network connecting biological activity in the head to the male reproductive system is described using co-expression networks, along with a similar ecdysone-mediated system in the female.
The expression profiles, co-expression networks and co-expression regulation of the 10 tissues studied and the tissue-specific analysis presented here are a valuable resource for studying tissue-specific biological functions in nematodes.
Metrics
10 Record Views
Details
- Title
- Genome-wide tissue-specific gene expression, co-expression and regulation of co-expressed genes in adult nematode Ascaris suum
- Creators
- Bruce A Rosa - The Genome Institute, Washington University School of Medicine, St. Louis, Missouri, United States of AmericaDouglas P Jasmer - Department of Veterinary Microbiology and Pathology, Washington State University, Pullman, Washington, United States of AmericaMakedonka Mitreva - The Genome Institute, Washington University School of Medicine, St. Louis, Missouri, United States of America ; Department of Medicine, Division of Infectious Diseases, Washington University School of Medicine, St. Louis, Missouri, United States of America ; Department of Genetics, Washington University School of Medicine, St. Louis, Missouri, United States of America
- Publication Details
- PLoS neglected tropical diseases, Vol.8(2), pp.e2678-e2678
- Academic Unit
- Veterinary Microbiology and Pathology, Department of
- Publisher
- United States
- Grant note
- R01 GM097435 / NIGMS NIH HHS
- Identifiers
- 99900546828001842
- Language
- English
- Resource Type
- Journal article