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Transcribed germline-limited coding sequences in Oxytricha trifallax.

Richard V Miller1,2, Rafik Neme1,3, Derek M Clay1,2

  • 1Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY 10032, USA.

G3 (Bethesda, Md.)
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Summary

In the ciliate Oxytricha trifallax, transcribed germline-limited open reading frames (TGLOs) are developmental genes. DNA elimination during macronuclear development normally silences these TGLOs, but RNA can reprogram their retention.

Keywords:
DNA eliminationciliategenome rearrangementgermlinemicronucleusnoncoding RNA

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Area of Science:

  • Developmental Biology
  • Microbial Eukaryotes
  • Genetics

Background:

  • The germline-soma distinction is fundamental in metazoan development, with distinct gene expression in germline and somatic cells.
  • Ciliates like Oxytricha trifallax display nuclear dimorphism, possessing both germline (MIC) and somatic (MAC) genomes within one cell.
  • O. trifallax undergoes extensive RNA-guided DNA elimination and genome rearrangement to form the somatic MAC from the germline MIC.

Purpose of the Study:

  • To update the inventory of transcribed germline-limited open reading frames (TGLOs) in O. trifallax.
  • To investigate the expression patterns and regulation of TGLOs during nuclear development.
  • To explore the impact of external RNA on TGLO retention and transcription in the somatic macronucleus.

Main Methods:

  • Massive RNA-guided DNA elimination and genome rearrangement analysis.
  • Identification and characterization of transcribed germline-limited open reading frames (TGLOs).
  • Experimental manipulation using synthetic RNA to probe TGLO retention and subsequent transcription.

Main Results:

  • TGLOs are primarily expressed during nuclear development and are typically absent from the mature somatic macronucleus (MAC).
  • Exposure to synthetic RNA can alter the DNA elimination process, leading to the retention of TGLOs in the MAC.
  • Retention of TGLOs in the MAC results in their transcription outside the standard developmental program.

Conclusions:

  • TGLOs represent a class of developmentally regulated, protein-coding sequences.
  • DNA elimination serves as the primary mechanism for terminating TGLO gene expression during somatic macronuclear development.
  • External RNA interference offers a novel mechanism to reprogram gene expression by influencing DNA elimination and TGLO retention.