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Full-length NF-κB repressing factor contains an XRN2 binding domain.

Jana Alexandrova1, David Piñeiro1, Rebekah Jukes-Jones1

  • 1MRC Toxicology Unit, University of Cambridge, Lancaster Rd, Leicester LE1 9HN, U.K.

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NF-κB repressing factor (NKRF) binds rRNA and contains a conserved domain essential for retaining XRN2 in the nucleolus, regulating early pre-ribosomal RNA processing.

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Area of Science:

  • Molecular Biology
  • RNA Processing
  • Ribosome Biogenesis

Background:

  • NF-κB repressing factor (NKRF) is an RNA binding protein involved in precursor ribosomal RNA processing with XRN2 and DHX15.
  • XRN2, a multifunctional ribonuclease, has its activity and stability regulated by binding partners like PAXT-1, CDKN2AIP, and CDKN2AIPNL via an XRN2 binding domain (XTBD).
  • NKRF's direct interaction with XRN2 was unexplained as NKRF was not predicted to possess an XTBD.

Purpose of the Study:

  • To investigate the structural basis of NKRF's interaction with XRN2.
  • To elucidate the role of NKRF in pre-ribosomal RNA processing and ribosome biogenesis.
  • To understand the mechanism by which NKRF influences XRN2 localization and function.

Main Methods:

  • Identification of an alternative upstream AUG start codon in the NKRF transcript.
  • Demonstration of the presence of a conserved XTBD in the full-length NKRF.
  • Analysis of NKRF's binding to rRNA and its effect on XRN2 retention in the nucleolus.

Main Results:

  • The full-length NKRF protein contains a conserved XRN2 binding domain (XTBD) in its N-terminal extension.
  • NKRF binds directly to ribosomal RNA (rRNA) and is tethered in the nucleolus.
  • The NKRF-XTBD is crucial for retaining XRN2 within the nucleolus, thereby controlling its spatial distribution.

Conclusions:

  • NKRF regulates early pre-rRNA processing steps in ribosome biogenesis by controlling XRN2's localization.
  • The identified XTBD in NKRF is essential for its interaction with XRN2 and its function in the nucleolus.
  • These findings provide further support for the XTBD as a conserved motif mediating XRN2 interactions.