NF‐κB‐repressing factor phosphorylation regulates transcription elongation
            <i>via</i>
            its interactions with 5'→3' exoribonuclease 2 and negative elongation factor

Rother, Sascha; Bartels, Myriam; Schweda, Aike Torben; Resch, Klaus; Pallua, Norbert; Nourbakhsh, Mahtab

doi:10.1096/fj.15-270256

Cited by 12 publications

(8 citation statements)

References 43 publications

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“…Interestingly, we observe, however, that the DUF3469 domain of NKRF is not essential for binding of XRN2. Consistent with this, an independent study recently reported that a region downstream of the DUF3469 is important for the interaction between NKRF and XRN2 (77). Our results therefore suggest that although the DUF3469 domain of NKRF may form contacts with XRN2, the nature of the XRN2-NKRF and XRN2-CARF interactions might differ, with other regions of NKRF likely contributing to its association with XRN2.…”

Section: Discussionsupporting

confidence: 60%

The G-patch protein NF-κB-repressing factor mediates the recruitment of the exonuclease XRN2 and activation of the RNA helicase DHX15 in human ribosome biogenesis

et al. 2017

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In eukaryotes, the synthesis of ribosomal subunits, which involves the maturation of the ribosomal (r)RNAs and assembly of ribosomal proteins, requires the co-ordinated action of a plethora of ribosome biogenesis factors. Many of these cofactors remain to be characterized in human cells. Here, we demonstrate that the human G-patch protein NF-κB-repressing factor (NKRF) forms a pre-ribosomal subcomplex with the DEAH-box RNA helicase DHX15 and the 5΄-3΄ exonuclease XRN2. Using UV crosslinking and analysis of cDNA (CRAC), we reveal that NKRF binds to the transcribed spacer regions of the pre-rRNA transcript. Consistent with this, we find that depletion of NKRF, XRN2 or DHX15 impairs an early pre-rRNA cleavage step (A’). The catalytic activity of DHX15, which we demonstrate is stimulated by NKRF functioning as a cofactor, is required for efficient A’ cleavage, suggesting that a structural remodelling event may facilitate processing at this site. In addition, we show that depletion of NKRF or XRN2 also leads to the accumulation of excised pre-rRNA spacer fragments and that NKRF is essential for recruitment of the exonuclease to nucleolar pre-ribosomal complexes. Our findings therefore reveal a novel pre-ribosomal subcomplex that plays distinct roles in the processing of pre-rRNAs and the turnover of excised spacer fragments.

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Section: Discussionsupporting

confidence: 60%

The G-patch protein NF-κB-repressing factor mediates the recruitment of the exonuclease XRN2 and activation of the RNA helicase DHX15 in human ribosome biogenesis

et al. 2017

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“…In agreement with others, we find that NKRF interacts with XRN2 ( Figure 3A) [8,9,29]. However, we also show that efficient binding of NKRF to XRN2 absolutely depends on the integrity of the XTBD ( Figure 5A).…”

Section: Part 1 Ofsupporting

confidence: 92%

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

Alexandrova

Piñeiro

Jukes-Jones

et al. 2020

Biochemical Journal

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NF-κB repressing factor (NKRF) was recently identified as an RNA binding protein that together with its associated proteins, the 5′–3′ exonuclease XRN2 and the helicase DHX15, is required to process the precursor ribosomal RNA. XRN2 is a multi-functional ribonuclease that is also involved in processing mRNAs, tRNAs and lncRNAs. The activity and stability of XRN2 are controlled by its binding partners, PAXT-1, CDKN2AIP and CDKN2AIPNL. In each case, these proteins interact with XRN2 via an XRN2 binding domain (XTBD), the structure and mode of action of which is highly conserved. Rather surprisingly, although NKRF interacts directly with XRN2, it was not predicted to contain such a domain, and NKRF's interaction with XRN2 was therefore unexplained. We have identified an alternative upstream AUG start codon within the transcript that encodes NKRF and demonstrate that the full-length form of NKRF contains an XTBD that is conserved across species. Our data suggest that NKRF is tethered in the nucleolus by binding directly to rRNA and that the XTBD in the N-terminal extension of NKRF is essential for the retention of XRN2 in this sub-organelle. Thus, we propose NKRF regulates the early steps of pre-rRNA processing during ribosome biogenesis by controlling the spatial distribution of XRN2 and our data provide further support for the XTBD as an XRN2 interacting motif.

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“…Experiments on human U-2 OS osteosarcoma cell lines rovide circumstantial evidence for the latter, as XRN2 immunofluorescence staining is observed in both nucleus and nucleoplasms, whereas NKRF locates to the nucleolus, from which the nucleoplasmic CDKN2AIP appears excluded42. As the phosphorylation status of NKRF may modulate the interaction between NKRF and XRN2 43, it will be interesting to see whether it also affects localization of NKRF and/or XRN2.…”

Section: Resultsmentioning

confidence: 99%

Structural basis and function of XRN2 binding by XTB domains

Richter

Katic

Gut

et al. 2016

Nat Struct Mol Biol

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The ribonuclease XRN2 is an essential player in RNA metabolism. In Caenorhabditis elegans, XRN2 functions with PAXT-1, which shares a putative XRN2-binding domain (XTBD) with otherwise unrelated mammalian proteins. Here, we characterize structure and function of an XTBD -XRN2 complex. Although XTBD stably interconnects two XRN2 domains through numerous interacting residues, mutation of a single critical residue suffices to disrupt XTBD -XRN2 complexes in vitro, and recapitulates paxt-1 null mutant phenotypes in vivo. Demonstrating conservation of function, vertebrate XTBD-containing proteins bind XRN2 in vitro, and human CDKN2AIPNL (C2AIL) can substitute for PAXT-1 in vivo. In vertebrates, where three distinct XTBD-containing proteins exist, XRN2 may partition to distinct stable heterodimeric complexes, likely differing in subcellular localization or function. In C. elegans, complex formation with the unique PAXT-1 serves to preserve the stability of XRN2 in the absence of substrate.

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NF‐κB‐repressing factor phosphorylation regulates transcription elongation via its interactions with 5'→3' exoribonuclease 2 and negative elongation factor

Cited by 12 publications

References 43 publications

The G-patch protein NF-κB-repressing factor mediates the recruitment of the exonuclease XRN2 and activation of the RNA helicase DHX15 in human ribosome biogenesis

The G-patch protein NF-κB-repressing factor mediates the recruitment of the exonuclease XRN2 and activation of the RNA helicase DHX15 in human ribosome biogenesis

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

Structural basis and function of XRN2 binding by XTB domains

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