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Genetic Engineering of Dictyostelium discoideum Cells Based on Selection and Growth on Bacteria
Published on: January 25, 2019
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The Long Noncoding RNA Transcriptome of Dictyostelium discoideum Development
Rafael D Rosengarten1, Balaji Santhanam2, Janez Kokosar3
1Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas 77030 rafael@genialis.com gadi@bcm.edu.
G3 (Bethesda, Md.)
|December 10, 2016
Summary
This study surveys long noncoding RNAs (lncRNAs) in Dictyostelium discoideum development, revealing their prevalence and distinct expression patterns. These noncoding RNAs likely play a crucial role in the organism's developmental transitions.
Area of Science:
- Molecular Biology
- Developmental Biology
- Genomics
Background:
- Dictyostelium discoideum exists as single cells but aggregates and differentiates upon starvation.
- Significant changes occur in protein-coding transcripts during D. discoideum development.
- A comprehensive analysis of long noncoding RNAs (ncRNAs) in D. discoideum development was previously lacking.
Purpose of the Study:
- To globally characterize the antisense and long intergenic noncoding RNA (lncRNA) transcriptome during D. discoideum development.
- To investigate the expression profiles and potential functions of ncRNAs in relation to protein-coding RNAs.
- To explore novel mitochondrial antisense transcripts and tRNA polymorphisms.
Main Methods:
- RNA-sequencing (RNA-seq) on developmental time course samples.
- Selective ribosomal RNA (rRNA) depletion library preparation.
- Analysis of coding and noncoding RNA transcriptomes, including mitochondrial and tRNA transcripts.
Main Results:
- Detection of 9833 protein-coding mRNAs, 621 lncRNAs, and 162 antisense RNAs (asRNAs).
- Noncoding RNAs exhibited distinct genomic distribution, expression levels, length, and nucleotide composition.
- Temporal expression profiles of ncRNAs mirrored coding RNAs, with some correlated to known coding RNAs, suggesting functional roles.
- Identification of two novel mitochondrial antisense transcripts and tRNA anticodon polymorphisms.
Conclusions:
- The characterized noncoding RNA transcriptome is prevalent and distinct in D. discoideum.
- ncRNAs display dynamic expression patterns during development, correlating with coding RNAs.
- These findings indicate that lncRNAs are integral to the progression of molecular and cellular phenotypes during D. discoideum development.
Keywords:
Dictyostelium discoideumdevelopmentnoncoding RNAribosomal RNA depletionslime moldtranscriptome time courseMore Related Videos
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