Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

Conservation-independent identification of novel miRNAs

ABSTRACT: Motivation: MicroRNAs (miRNAs) are short regulatory RNAs derived from a longer precursor RNA. miRNA biogenesis has been studied in animals and plants, recently elucidating more diverse and complex aspects, such as non-conserved, speciesspecific, and heterogeneous miRNA precursor populations. Small RNA sequencing data can be used to computationally determine genomic loci of miRNA precursors. The challenge is to predict a valid miRNA precursor from inhomogeneous read coverage: while the mature miRNA typically produces hundreds of sequence reads, the remaining part of the precursor is covered very sparsely. Results: We introduce a new conservation-independent method for the identification of miRNA precursors, that allows for speciesspecific heterogeneous precursor populations. The algorithm requires small RNA sequencing data and evaluates precursor secondary structures, with key parameters that can be adjusted based on the specific organism under investigation (within animals, plants, algae). We illustrate the validity of results from our algorithm using sequencing data for the two Volvocine algae Chlamydomonas reinhardtii (Chlamydomonas) and Volvox carteri (Volvox). Both organisms show little cross-species miRNA sequence conservation, and a heterogeneous miRNA precursor population. We validate our list of Chlamydomonas miRNAs with annotated miRNAs, and demonstrate excellent agreement. Furthermore, we are able to identify additional novel miRNA precursors, with structures ranging from simple mammalian-like hairpins to precursor structures indicating the creation of multiple mature/star miRNA duplexes. Novel miRNAs identified in Volvox show no similarity to mature miRNAs in Chlamydomonas. These results confirm the need for conservationindependent miRNA identification methods. Examination of small RNAs of Volvox carteri during different stages of its life cycle

ORGANISM(S): Volvox carteri

SUBMITTER: Anne Dueck

PROVIDER: E-GEOD-58703 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Publications

miRA: adaptable novel miRNA identification in plants using small RNA sequencing data.

Evers Maurits M Huttner Michael M Dueck Anne A Meister Gunter G Engelmann Julia C JC

BMC bioinformatics 20151105

<h4>Background</h4>MicroRNAs (miRNAs) are short regulatory RNAs derived from longer precursor RNAs. miRNA biogenesis has been studied in animals and plants, recently elucidating more complex aspects, such as non-conserved, species-specific, and heterogeneous miRNA precursor populations. Small RNA sequencing data can help in computationally identifying genomic loci of miRNA precursors. The challenge is to predict a valid miRNA precursor from inhomogeneous read coverage from a complex RNA library: ...[more]

PMID: 26542525

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Project description:The green alga Volvox carteri is a model organism for the development of multicellularity. It has a spherical shape with a complete division of labor between around 2000 somatic cells and 16 reproductive cells. When comparing Volvox with its unicellular relative Chlamydomonas rheinhardtii, one striking observation is the similarity in the protein coding genes [1]. Additionally, Baulcombe and colleagues showed that Chlamydomonas contains functional RNAi and miRNA machineries [2]. We deep sequenced small RNAs of the female Volvox strain HK10 in different life stages (asexual reproduction to sexual reproduction), each time dividing the samples into somatic cells and reproductive cells. This allowed for the observation not only of differences in individual life stages, but also for monitoring sRNA content in the two cell types. We show that Volvox expresses miRNAs and that they are 2â??-O-methylated at the 3â?? end. The expression profiles of several miRNAs were validated by Northern blotting showing a differential expression both between cell types and between life stages. Intriguingly, most miRNAs do not seem to be conserved between Volvox and Chlamydomonas, raising the interesting question if this changed miRNome leads to differently targeted mRNAs thus resulting in cell differentiation. Since only little is known about the transcriptome of Volvox, we performed RNASeq in order to analyze potential miRNA targets. In conclusion, most miRNA in Volvox are not conserved in Chlamydomonas although the two species are evolutionary close together. This suggests that dramatic changes in the miRNA expression might be one of the driving forces for the development of multicellularity. 1. Prochnik, S.E., et al., Genomic analysis of organismal complexity in the multicellular green alga Volvox carteri. Science, 2010. 329(5988): p. 223-6. 2. Molnar, A., et al., miRNAs control gene expression in the single-cell alga Chlamydomonas reinhardtii. Nature, 2007. 447(7148): p. 1126-9. Examination of small RNAs of Volvox carteri during different stages of its life cycle

Project description:The green alga Volvox carteri is a model organism for the development of multicellularity. It has a spherical shape with a complete division of labor between around 2000 somatic cells and 16 reproductive cells. When comparing Volvox with its unicellular relative Chlamydomonas rheinhardtii, one striking observation is the similarity in the protein coding genes [1]. Additionally, Baulcombe and colleagues showed that Chlamydomonas contains functional RNAi and miRNA machineries [2]. We deep sequenced small RNAs of the female Volvox strain HK10 in different life stages (asexual reproduction to sexual reproduction), each time dividing the samples into somatic cells and reproductive cells. This allowed for the observation not only of differences in individual life stages, but also for monitoring sRNA content in the two cell types. We show that Volvox expresses miRNAs and that they are 2’-O-methylated at the 3’ end. The expression profiles of several miRNAs were validated by Northern blotting showing a differential expression both between cell types and between life stages. Intriguingly, most miRNAs do not seem to be conserved between Volvox and Chlamydomonas, raising the interesting question if this changed miRNome leads to differently targeted mRNAs thus resulting in cell differentiation. Since only little is known about the transcriptome of Volvox, we performed RNASeq in order to analyze potential miRNA targets. In conclusion, most miRNA in Volvox are not conserved in Chlamydomonas although the two species are evolutionary close together. This suggests that dramatic changes in the miRNA expression might be one of the driving forces for the development of multicellularity. 1. Prochnik, S.E., et al., Genomic analysis of organismal complexity in the multicellular green alga Volvox carteri. Science, 2010. 329(5988): p. 223-6. 2. Molnar, A., et al., miRNAs control gene expression in the single-cell alga Chlamydomonas reinhardtii. Nature, 2007. 447(7148): p. 1126-9.

Dataset Information

Conservation-independent identification of novel miRNAs

Publications

miRA: adaptable novel miRNA identification in plants using small RNA sequencing data.

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