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Saccharomyces cerevisiae Metabolic Labeling with 4-thiouracil and the Quantification of Newly Synthesized mRNA As a Proxy for RNA Polymerase II Activity
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The coding and noncoding transcriptome of Neurospora crassa.

Ibrahim Avi Cemel1, Nati Ha1,2, Geza Schermann1

  • 1Heidelberg University Biochemistry Center, 69120, Heidelberg, Germany.

BMC Genomics
|December 21, 2017
PubMed
Summary
This summary is machine-generated.

Neurospora crassa has more non-coding RNAs than previously thought. This study identifies 1478 long intergenic noncoding RNAs (lincRNAs) and 1056 antisense transcripts, revealing their distinct features and rapid evolution.

Keywords:
AntisenseNeurosporaNoncoding RNASplicingTranscriptome

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Area of Science:

  • Fungal biology
  • Genomics
  • Molecular biology

Background:

  • Long non-protein coding RNAs (lncRNAs) are crucial but poorly understood.
  • lncRNA annotation and function in Neurospora crassa are incomplete.

Purpose of the Study:

  • To comprehensively analyze and characterize lncRNAs in Neurospora crassa.
  • To understand the prevalence, features, and regulation of lncRNAs in this fungus.

Main Methods:

  • Transcriptome analysis using ChIP-seq, RNA-seq, and polysome fractionation.
  • Annotation and characterization of long intergenic noncoding RNAs (lincRNAs) and natural antisense transcripts.

Main Results:

  • Identified 1478 lincRNAs and 1056 antisense transcripts, comprising 20% of RNA Polymerase II transcripts.
  • lncRNAs are shorter, expressed at lower levels, and have fewer introns than mRNAs.
  • Histone modifications (H3K4me2, H3K27me3) show distinct patterns for lncRNAs compared to mRNAs.
  • lncRNA sequences exhibit rapid evolution, even in closely related species.

Conclusions:

  • Neurospora crassa possesses a higher prevalence of noncoding transcripts than anticipated.
  • lncRNAs and antisense transcripts have unique features compared to mRNAs.
  • This study provides a valuable resource for future lncRNA research in Neurospora.