NRD1 Nrd1 complex RNA-binding subunit [Saccharomyces cerevisiae S288C] - Gene

Summary

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Gene symbol: NRD1
Gene description: Nrd1 complex RNA-binding subunit
Primary source: FungiDB:YNL251C
Locus tag: YNL251C
See related: SGD:S000005195; AllianceGenome:SGD:S000005195; VEuPathDB:YNL251C
Gene type: protein coding
RefSeq status: REVIEWED
Organism: Saccharomyces cerevisiae S288C (strain: S288C)
Lineage: Eukaryota; Fungi; Dikarya; Ascomycota; Saccharomycotina; Saccharomycetes; Saccharomycetales; Saccharomycetaceae; Saccharomyces
Summary: Enables protein domain specific binding activity and transcription regulatory region RNA binding activity. Involved in RNA metabolic process. Part of Nrd1 complex. Orthologous to human SCAF4 (SR-related CTD associated factor 4) and SCAF8 (SR-related CTD associated factor 8). [provided by Alliance of Genome Resources, Apr 2022]
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Genomic context

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See NRD1 in Genome Data Viewer

Location:: chromosome: XIV

Exon count:: 1

Sequence:: Chromosome: XIV; NC_001146.8 (172588..174315, complement)

Chromosome XIV - NC_001146.8 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:: NC_001146.8

Go to nucleotide: Graphics FASTA GenBank

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Nrd1p identifies aberrant and natural exosomal target messages during the nuclear mRNA surveillance in Saccharomyces cerevisiae.
Title: Nrd1p identifies aberrant and natural exosomal target messages during the nuclear mRNA surveillance in Saccharomyces cerevisiae.
Termination of non-coding transcription in yeast relies on both an RNA Pol II CTD interaction domain and a CTD-mimicking region in Sen1.
Title: Termination of non-coding transcription in yeast relies on both an RNA Pol II CTD interaction domain and a CTD-mimicking region in Sen1.
Three sequence motifs in Sen1 that mediate direct interactions with the RNA polymerase II CTD interaction domain (CID) of Nrd1 have been identified.
Title: Identification of Three Sequence Motifs in the Transcription Termination Factor Sen1 that Mediate Direct Interactions with Nrd1.
RNA polymerase II CTD tyrosine 1 is required for efficient termination by the Nrd1-Nab3-Sen1 pathway by slowing down transcription and suppressing termination defects.
Title: RNA Polymerase II CTD Tyrosine 1 Is Required for Efficient Termination by the Nrd1-Nab3-Sen1 Pathway.
Antisense transcription is specifically suppressed by Nrd1, a yeast termination factor.
Title: Simultaneous characterization of sense and antisense genomic processes by the double-stranded hidden Markov model.
Nrd1 and Nab3 function is tightly integrated with the nutrient response, and indicates a role for these proteins in the regulation of many mRNA coding genes.
Title: PAR-CLIP data indicate that Nrd1-Nab3-dependent transcription termination regulates expression of hundreds of protein coding genes in yeast.
The data raise the intriguing possibility that Nab3 and Nrd1 can function independently to recruit Rrp6 to ncRNA targets, providing combinatorial flexibility in RNA processing.
Title: Nab3 facilitates the function of the TRAMP complex in RNA processing via recruitment of Rrp6 independent of Nrd1.
Rrp6 acts with the NNS complex globally to promote transcription termination in addition to 3' end RNA processing and/or degradation at specific targets
Title: The exosome component Rrp6 is required for RNA polymerase II termination at specific targets of the Nrd1-Nab3 pathway.
Results show that the Nrd1-Trf4 interaction is required for optimal exosome activity in vivo and for the stimulation of polyadenylation of NNS targets by TRAMP in vitro.
Title: Molecular basis for coordinating transcription termination with noncoding RNA degradation.
Determination of the solution structure of a two-domain RNA-binding fragment of Nrd1.
Title: Structure and semi-sequence-specific RNA binding of Nrd1.

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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 RNA binding	IBA Inferred from Biological aspect of Ancestor more info
enables RNA binding	IDA Inferred from Direct Assay more info	PubMed
enables RNA binding	IEA Inferred from Electronic Annotation more info
enables mRNA binding	HDA more info	PubMed
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed
enables protein domain specific binding	IDA Inferred from Direct Assay more info	PubMed
enables transcription regulatory region RNA binding	IDA Inferred from Direct Assay more info	PubMed

Process	Evidence Code	Pubs
involved_in CUT catabolic process	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in antisense RNA transcript catabolic process	IDA Inferred from Direct Assay more info	PubMed
involved_in antisense RNA transcript catabolic process	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in mRNA 3'-end processing	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in nuclear mRNA surveillance	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in snRNA 3'-end processing	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in sno(s)RNA 3'-end processing	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in tRNA 3'-end processing	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in termination of RNA polymerase II transcription, exosome-dependent	IDA Inferred from Direct Assay more info	PubMed

Component	Evidence Code	Pubs
part_of Nrd1 complex	IBA Inferred from Biological aspect of Ancestor more info
part_of Nrd1 complex	IDA Inferred from Direct Assay more info	PubMed
located_in nucleus	IEA Inferred from Electronic Annotation more info

General protein information

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Preferred Names: Nrd1 complex RNA-binding subunit

NP_014148.1

RNA-binding subunit of Nrd1 complex; complex interacts with exosome to mediate 3'-end formation of some mRNAs, snRNAs, snoRNAs, and CUTs; interacts with CTD of RNA pol II large subunit Rpo21p at phosphorylated Ser5 to direct transcription termination of non-polyadenylated transcripts; H3K4 trimethylation of transcribed regions by Set1p enhances recruitment of Nrd1p to those sites; role in regulation of mitochondrial abundance and cell size

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_001146.8 Reference assembly

Range

172588..174315 complement

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

NM_001183089.1 → NP_014148.1 TPA: Nrd1 complex RNA-binding subunit [Saccharomyces cerevisiae S288C]

See identical proteins and their annotated locations for NP_014148.1

Status: REVIEWED

UniProtKB/Swiss-Prot

D6W0U2, P53617

UniProtKB/TrEMBL

A0A7I9G4M2, A6ZRJ2, B3LP95, C7GPB0, C8ZFY6, G2WLL5, N1NZY7

Conserved Domains (2) summary

cd16984
Location:8 → 149

CID_Nrd1_like; CID (CTD-Interacting Domain) of Nrd1 and similar proteins

cd12331
Location:336 → 412

RRM_NRD1_SEB1_like; RNA recognition motif (RRM) found in Saccharomyces cerevisiae protein Nrd1, Schizosaccharomyces pombe Rpb7-binding protein seb1 and similar proteins