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RNA-seq03:21

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In humans, more than 80% of the genome gets transcribed. However, only around 2% of the genome codes for proteins. The remaining part produces non-coding RNAs which includes ribosomal RNAs, transfer RNAs, telomerase RNAs, and regulatory RNAs, among other types. A large number of regulatory non-coding RNAs have been classified into two groups depending upon their length – small non-coding RNAs, such as microRNA, which are less than 200 nucleotides in length, and long non-coding RNA...
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Finding noncoding RNA transcripts from low abundance expressed sequence tags.

Chenghai Xue1, Fei Li, Fei Li

  • 1Department of Entomology, Nanjing Agricultural University, Nanjing 210095, China.

Cell Research
|May 28, 2008
PubMed
Summary
This summary is machine-generated.

Researchers discovered 118 novel noncoding RNA (ncRNA) genes using a computational strategy on human expressed sequence tags (ESTs). This method mines low-abundance ESTs, revealing a valuable resource for identifying new ncRNA genes.

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Area of Science:

  • Genomics
  • Bioinformatics
  • Molecular Biology

Background:

  • Noncoding RNA (ncRNA) genes are abundant but difficult to identify.
  • Intergenic expressed sequence tags (ESTs) are underutilized for ncRNA discovery due to low abundance and poor annotation.

Purpose of the Study:

  • To develop a computational strategy for discovering novel ncRNA genes from human ESTs.
  • To investigate the potential of intergenic ESTs as a source for novel ncRNA identification.

Main Methods:

  • Collected and filtered intergenic ESTs lacking detailed annotations.
  • Utilized PhastCons scores to identify conserved genomic windows (seeds).
  • Assembled ESTs into contigs and applied criteria (ORF length < 300 nt, Pol-II promoter presence) to screen for ncRNA transcripts.

Main Results:

  • Identified 118 novel ncRNA genes from low-abundance human ESTs.
  • Experimental validation (RT-PCR) confirmed transcription of 6 out of 7 selected candidates in human 2BS cells.

Conclusions:

  • The developed computational strategy effectively identifies novel ncRNA genes from ESTs.
  • Expressed sequence tags represent a valuable, largely untapped resource for ncRNA gene discovery.