XRN1 chromatin-binding exonuclease XRN1 [Saccharomyces cerevisiae S288C] - Gene

Summary

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Official Symbol: XRN1
Official Full Name: chromatin-binding exonuclease XRN1
Primary source: SGD:S000003141
Locus tag: YGL173C
See related: AllianceGenome:SGD:S000003141; FungiDB:YGL173C; VEuPathDB:YGL173C
Gene type: protein coding
RefSeq status: REVIEWED
Organism: Saccharomyces cerevisiae S288C (strain: S288C)
Lineage: Eukaryota; Fungi; Dikarya; Ascomycota; Saccharomycotina; Saccharomycetes; Saccharomycetales; Saccharomycetaceae; Saccharomyces
Also known as: DST2; KEM1; RAR5; SEP1; SKI1
Summary: Enables 5'-3' RNA exonuclease activity; chromatin binding activity; and eukaryotic initiation factor 4G binding activity. Involved in several processes, including RNA metabolic process; positive regulation of RNA metabolic process; and traversing start control point of mitotic cell cycle. Acts upstream of or within nuclear-transcribed mRNA catabolic process, no-go decay. Located in cytoplasmic ribonucleoprotein granule; eisosome membrane domain/MCC; and nucleus. Is active in cytoplasm. Human ortholog(s) of this gene implicated in Alzheimer's disease. Orthologous to human XRN1 (5'-3' exoribonuclease 1). [provided by Alliance of Genome Resources, Dec 2024]
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Genomic context

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See XRN1 in Genome Data Viewer

Location:: chromosome: VII

Exon count:: 1

Sequence:: Chromosome: VII; NC_001139.9 (175527..180113, complement)

Chromosome VII - NC_001139.9 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:: NC_001139.9

Go to nucleotide: Graphics FASTA GenBank

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Recruitment of Xrn1 to stress-induced genes allows efficient transcription by controlling RNA polymerase II backtracking.
Title: Recruitment of Xrn1 to stress-induced genes allows efficient transcription by controlling RNA polymerase II backtracking.
The yeast exoribonuclease Xrn1 and associated factors modulate RNA polymerase II processivity in 5' and 3' gene regions.
Title: The yeast exoribonuclease Xrn1 and associated factors modulate RNA polymerase II processivity in 5' and 3' gene regions.
Biochemical Characterization of Yeast Xrn1.
Title: Biochemical Characterization of Yeast Xrn1.
We also found that the relative influence of Xrn1 and Ccr4 is different in the genes encoding ribosomal proteins as compared to the rest of the genome.
Title: The mRNA degradation factor Xrn1 regulates transcription elongation in parallel to Ccr4.
The exonuclease Xrn1 activates transcription and translation of mRNAs encoding membrane proteins.
Title: The exonuclease Xrn1 activates transcription and translation of mRNAs encoding membrane proteins.
Phosphorylation of Xrn1 by Rad53 does not appear to affect Xrn1's intrinsic nuclease activity in vitro, but may affect its activity or specificity in vivo.
Title: The Yeast DNA Damage Checkpoint Kinase Rad53 Targets the Exoribonuclease, Xrn1.
In cells lacking the eisosome organizer Pil1, Xrn1 does not associate with the plasma membrane and its activity is preserved till the stationary phase. Thus, properly assembled eisosome is necessary for this kind of Xrn1 regulation, which occurs in a liquid culture as well as in a differentiated colony.
Title: mRNA decay is regulated via sequestration of the conserved 5'-3' exoribonuclease Xrn1 at eisosome in yeast.
Xrn1 facilitates the generation of ssDNA and checkpoint activation at uncapped telomeres. Xrn1 also maintains telomere length independently of ssDNA generation by downregulating the amount of Rif1.
Title: Regulation of telomere metabolism by the RNA processing protein Xrn1.
Studies indicate important roles of the exoribonucleases DIS3L2 and XRN1 in cellular function, viability and disease.
Title: The roles of the exoribonucleases DIS3L2 and XRN1 in human disease.
Xrn1p co-evolves with totiviruses to maintain its potent antiviral activity and limit viral propagation in Saccharomyces yeasts
Title: XRN1 Is a Species-Specific Virus Restriction Factor in Yeasts.

Submit: New GeneRIF Correction See all GeneRIFs (20)

Pathways from PubChem

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Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Homology

Orthologs from OrthoDB

Gene Ontology Provided by SGD

Function	Evidence Code	Pubs
enables 5'-3' RNA exonuclease activity	IBA Inferred from Biological aspect of Ancestor more info
enables 5'-3' RNA exonuclease activity	IDA Inferred from Direct Assay more info	PubMed
enables 5'-3' RNA exonuclease activity	IEA Inferred from Electronic Annotation more info
enables 5'-3' RNA exonuclease activity	IMP Inferred from Mutant Phenotype more info	PubMed
enables 5'-3' exonuclease activity	IEA Inferred from Electronic Annotation more info
enables RNA binding	IBA Inferred from Biological aspect of Ancestor more info
enables RNA binding	IEA Inferred from Electronic Annotation more info
enables chromatin binding	IDA Inferred from Direct Assay more info	PubMed
enables eukaryotic initiation factor 4G binding	IDA Inferred from Direct Assay more info	PubMed
enables exonuclease activity	IEA Inferred from Electronic Annotation more info
enables mRNA binding	HDA more info	PubMed
enables nucleic acid binding	IEA Inferred from Electronic Annotation more info

Process	Evidence Code	Pubs
involved_in NAD-cap decapping	IDA Inferred from Direct Assay more info	PubMed
involved_in cellular response to nitrogen starvation	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in karyogamy	IEA Inferred from Electronic Annotation more info
involved_in mRNA destabilization	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in negative regulation of macroautophagy	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in nonfunctional rRNA decay	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in nuclear-transcribed mRNA catabolic process	IBA Inferred from Biological aspect of Ancestor more info
involved_in nuclear-transcribed mRNA catabolic process	IEA Inferred from Electronic Annotation more info
involved_in nuclear-transcribed mRNA catabolic process	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in nuclear-transcribed mRNA catabolic process, 5'-3' exonucleolytic nonsense-mediated decay	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within nuclear-transcribed mRNA catabolic process, no-go decay	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in nuclear-transcribed mRNA catabolic process, nonsense-mediated decay	IEA Inferred from Electronic Annotation more info
involved_in nuclear-transcribed mRNA catabolic process, nonsense-mediated decay	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in positive regulation of transcription elongation by RNA polymerase II	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within positive regulation of transcription initiation by RNA polymerase II	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in positive regulation of transcription initiation by RNA polymerase II	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in rRNA catabolic process	IBA Inferred from Biological aspect of Ancestor more info
involved_in rRNA processing	IEA Inferred from Electronic Annotation more info
involved_in rRNA processing	IGI Inferred from Genetic Interaction more info	PubMed
involved_in rRNA processing	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in regulation of telomere maintenance	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in sno(s)RNA processing	IGI Inferred from Genetic Interaction more info	PubMed
involved_in tRNA decay	IDA Inferred from Direct Assay more info	PubMed
involved_in translational initiation	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in traversing start control point of mitotic cell cycle	IMP Inferred from Mutant Phenotype more info	PubMed

Component	Evidence Code	Pubs
located_in P-body	IDA Inferred from Direct Assay more info	PubMed
located_in P-body	IEA Inferred from Electronic Annotation more info
located_in P-body	IMP Inferred from Mutant Phenotype more info	PubMed
located_in cytoplasm	HDA more info	PubMed
is_active_in cytoplasm	IDA Inferred from Direct Assay more info	PubMed
located_in cytoplasm	IDA Inferred from Direct Assay more info	PubMed
located_in cytoplasm	IEA Inferred from Electronic Annotation more info
located_in cytoplasmic stress granule	IDA Inferred from Direct Assay more info	PubMed
located_in eisosome membrane domain/MCC	IDA Inferred from Direct Assay more info	PubMed
located_in microtubule	IEA Inferred from Electronic Annotation more info
is_active_in nucleus	IBA Inferred from Biological aspect of Ancestor more info
located_in nucleus	IDA Inferred from Direct Assay more info	PubMed
located_in perinuclear region of cytoplasm	IEA Inferred from Electronic Annotation more info

General protein information

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Preferred Names: chromatin-binding exonuclease XRN1

NP_011342.1

Evolutionarily-conserved 5'-3' exonuclease; deNADing enzyme that modulates mitochondrial NAD-capped RNA; component of cytoplasmic P-bodies involved in mRNA decay; positively regulates transcription initiation and elongation; involved in microtubule-mediated processes, filamentous growth, rRNA maturation, telomere maintenance, tRNA intron turnover; negative regulator of autophagy; activated by glycolytic flux and scavenger decapping enzyme Dcs1p; role in preventing L-A mycovirus pathogenesis

NCBI Reference Sequences (RefSeq)

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Genome Annotation

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference assembly

Genomic

NC_001139.9 Reference assembly

Range

175527..180113 complement

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

NM_001181038.1 → NP_011342.1 TPA: chromatin-binding exonuclease XRN1 [Saccharomyces cerevisiae S288C]

See identical proteins and their annotated locations for NP_011342.1

Status: REVIEWED

UniProtKB/Swiss-Prot

D6VTX9, P22147

UniProtKB/TrEMBL

C7GPN4, N1P4M8

Conserved Domains (4) summary

COG5049
Location:1 → 955

XRN1; 5'-3' exonuclease [Replication, recombination and repair]

pfam18129
Location:1163 → 1233

SH3_12; Xrn1 SH3-like domain

pfam18194
Location:1087 → 1156

Xrn1_D3; Exoribonuclease 1 Domain-3

pfam18334
Location:918 → 1005

XRN1_D2_D3; Exoribonuclease Xrn1 D2/D3 domain