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. 2008 Apr 22:9:185.
doi: 10.1186/1471-2164-9-185.

Deep sequencing of chicken microRNAs

Joan Burnside  1 , Ming Ouyang, Amy Anderson, Erin Bernberg, Cheng Lu, Blake C Meyers, Pamela J Green, Milos Markis, Grace Isaacs, Emily Huang, Robin W Morgan
Affiliations

Deep sequencing of chicken microRNAs

Joan Burnside et al. BMC Genomics. .

Abstract

Background: The use of new, deep sequencing technologies has greatly accelerated microRNA discovery. We have applied this approach to the identification of chicken microRNAs and to the comparison of microRNAs in chicken embryo fibroblasts (CEF) infected with Marek's disease virus (MDV) to those present in uninfected CEF.

Results: We obtained 125,463 high quality reads that showed an exact match to the chicken genome. The majority of the reads corresponded to previously annotated chicken microRNAs; however, the sequences of many potential novel microsRNAs were obtained. A comparison of the reads obtained in MDV-infected and uninfected CEF indicates that infection does not significantly perturb the expression profile of microRNAs. Frequently sequenced microRNAs include miR-221/222, which are thought to play a role in growth and proliferation. A number of microRNAs (e.g., let-7, miR-199a-1, 26a) are expressed at lower levels in MDV-induced tumors, highlighting the potential importance of this class of molecules in tumorigenesis.

Conclusion: Deep sequencing technology is highly suited for small RNA discovery. This approach is independent of comparative sequence analysis, which has been the primary method used to identify chicken microRNAs. Our results have confirmed the expression of many microRNAs identified by sequence similarity and identified a pool of candidate novel microRNAs.

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Figures

Figure 1
Figure 1
Size distribution of small RNAs.
Figure 2
Figure 2
Sequence and expression of novel chicken microRNAs. A. Sequence and chromosomal location of selected novel microRNAs (location is based on May 2006 build). B. Northern blot analysis of individual microRNAs shows relative expression in different tissues. Blots were hybridized to gga-miR-221 to verify presence of microRNAs in each lane.
Figure 3
Figure 3
Expression of chicken microRNAs in MDV-induced splenic tumors and normal spleens. Small RNA from three individual MDV-induced splenic tumors (T) and normal spleen (Sp) were analyzed by Northern blot analysis and hybridization to probes antisense to indicated microRNAs.
See this image and copyright information in PMC

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