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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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Riboswitches are RNA elements that regulate gene expression by altering their secondary structures in response to specific effector molecules. These elements, located in the leader regions of certain mRNAs, act as transcriptional regulators by toggling between alternative conformations to control downstream gene expression. Riboswitch-mediated regulation is a precise mechanism for modulating biosynthetic pathways, as exemplified by the riboflavin biosynthesis pathway in Bacillus...
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Identification of Circular RNAs using RNA Sequencing
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The human TRAM1 locus expresses circular RNAs.

Josephine Dubois1,2, Georg Sczakiel3

  • 1Institut für Molekulare Medizin, Universität zu Lübeck and UKSH, Campus Lübeck, Ratzeburger Allee 160, 23538, Lübeck, Germany.

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Summary

This study provides experimental proof for two circular RNAs (circRNAs) derived from the TRAM1 gene in human bladder cancer cell lines. These findings establish a foundation for future research on circular RNAs in cancer biology.

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Area of Science:

  • Molecular Biology
  • Genomics
  • Cancer Research

Background:

  • Circular RNAs (circRNAs) are increasingly recognized but experimentally validated examples in mammals remain scarce.
  • Biological studies necessitate the use of experimentally confirmed circRNAs.

Purpose of the Study:

  • To provide conclusive experimental evidence for the existence of TRAM1-specific circRNAs.
  • To investigate the expression patterns of TRAM1 circRNAs and their linear counterparts in bladder cancer cell lines.

Main Methods:

  • Transcriptome analysis of urine RNA from bladder cancer patients and healthy donors.
  • PCR-based methodology, cloning, and sequencing to confirm circular RNA topology.
  • RNase R and antisense oligonucleotide treatments to validate circRNA structure.

Main Results:

  • Identified and experimentally confirmed two TRAM1-specific circRNAs in human bladder cancer cell lines (ECV-304 and RT-4).
  • Demonstrated low expression levels of TRAM1 circRNAs with minor differences between cell lines.
  • Observed down-regulated expression of linear TRAM1 transcripts in a higher-stage cancer model (ECV-304) compared to a more differentiated model (RT-4).

Conclusions:

  • Conclusive experimental evidence supports the existence of TRAM1-specific circRNAs in human bladder cancer cell lines.
  • TRAM1 circRNAs exhibit low expression, while linear TRAM1 transcripts show differential expression related to cancer stage.