Natural antisense transcripts and long non-coding RNA in Neurospora crassa

Area of Science:

• Genomics
• Molecular Biology
• Fungal Biology

Background:

• Long non-coding RNAs (lncRNAs) and natural antisense transcripts (NATs) are increasingly recognized for their roles in gene regulation.
• Their functional significance and prevalence across diverse organisms are still under investigation.
• Neurospora crassa serves as a model organism for studying fungal gene expression.

Purpose of the Study:

• To identify and characterize lncRNAs and NATs in Neurospora crassa using RNA sequencing.
• To investigate the overlap and regulatory potential between sense and antisense transcripts.
• To explore the influence of environmental stimuli (light and temperature) on lncRNA and NAT expression.

Main Methods:

• RNA sequencing (ABI SOLiD platform) was employed to analyze transcriptomes.
• Bioinformatic analyses were used to identify novel lncRNAs and NATs, including their overlap patterns.
• Quantitative PCR (qPCR) was utilized to validate the expression of selected transcript pairs.
• Comparative analysis of transcript features (length, introns) was performed based on antisense expression.

Main Results:

• 939 novel lncRNAs were identified, with 477 being antisense to annotated genes.
• Extensive overlap was observed between sense and antisense transcripts, with many complementary over significant lengths.
• 11 lncRNAs showed upregulation in response to light.
• Differences in transcript length and intron positioning were noted between transcripts with and without antisense expression.
• Expression of sense/antisense transcript pairs was confirmed by qPCR.

Conclusions:

• Neurospora crassa possesses a significant repertoire of lncRNAs and NATs.
• These transcripts exhibit substantial overlap and are regulated by environmental factors like light.
• The findings highlight the potential functional roles of lncRNAs and NATs in fungal gene regulation and response to stimuli.
• This study provides a foundation for further research into the specific functions of NATs in N. crassa.