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Preparation of Small RNA Libraries for Sequencing from Early Mouse Embryos
Published on: October 9, 2020
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Antisense RNAs during early vertebrate development are divided in groups with distinct features
Sanjana Pillay1, Hazuki Takahashi2, Piero Carninci2,3
1Department of Cell, Developmental and Regenerative Biology, Mount Sinai School of Medicine, New York, New York 10029, USA.
Genome Research
|April 2, 2021
Summary
Long noncoding RNAs (lncRNAs), specifically natural antisense transcripts (NATs), play a crucial role in zebrafish development. Group 1 NATs are hypothesized to post-transcriptionally silence developmental genes.
Area of Science:
- Developmental Biology
- RNA Biology
- Computational Biology
Background:
- Long noncoding RNAs (lncRNAs) are key regulators, with nearly 50% transcribed antisense to protein-coding genes during zebrafish development.
- The precise function of these natural antisense transcripts (NATs) in early vertebrate development is not well understood.
Purpose of the Study:
- To investigate the role of NATs in early vertebrate development using a computational approach.
- To classify zebrafish NATs based on their expression patterns and functional implications.
Main Methods:
- Computational analysis of existing and novel datasets.
- Transcriptomics to quantify RNA levels in cytoplasmic and nuclear compartments.
- Analysis of NAT coexpression patterns with overlapping protein-coding genes.
Main Results:
- Zebrafish NATs were divided into two groups based on coexpression with protein-coding genes.
- Group 1 NATs, negatively correlated with developmental genes, are abundant in the cytosol and show high complementarity to sense-strand mRNAs.
- Group 2 NATs are coexpressed with housekeeping genes.
Conclusions:
- Group 1 NATs exhibit characteristics suggesting a role in post-transcriptional gene silencing.
- These NATs may function to prevent spurious expression of crucial developmental genes during early development.
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