NAB3 Nab3p [Saccharomyces cerevisiae S288C] - Gene

Summary

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Official Symbol: NAB3
Official Full Name: Nab3p
Primary source: SGD:S000006111
Locus tag: YPL190C
See related: AllianceGenome:SGD:S000006111; FungiDB:YPL190C; VEuPathDB:YPL190C
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: HMD1
Summary: Enables transcription regulatory region RNA binding activity. Involved in RNA metabolic process. Located in cytoplasm and nucleus. Part of Nrd1 complex. Human ortholog(s) of this gene implicated in autosomal dominant intellectual developmental disorder. Orthologous to several human genes including RALYL (RALY RNA binding protein like); RALY (RALY heterogeneous nuclear ribonucleoprotein); and HNRNPC (heterogeneous nuclear ribonucleoprotein C). [provided by Alliance of Genome Resources, Nov 2024]
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Genomic context

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See NAB3 in Genome Data Viewer

Location:: chromosome: XVI

Exon count:: 1

Sequence:: Chromosome: XVI; NC_001148.4 (185317..187725, complement)

Chromosome XVI - NC_001148.4 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:: NC_001148.4

Go to nucleotide: Graphics FASTA GenBank

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Nab3 nuclear granule accumulation is driven by respiratory capacity.
Title: Nab3 nuclear granule accumulation is driven by respiratory capacity.
Variable penetrance of Nab3 granule accumulation quantified by a new tool for high-throughput single-cell granule analysis.
Title: Variable penetrance of Nab3 granule accumulation quantified by a new tool for high-throughput single-cell granule analysis.
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.
Nab3 is targeted to intranuclear granules in response to glucose starvation by Nab3's proline/glutamine-rich, prion-like domain (PrLD). Localization to the granule is reversible and sensitive to the chemical probe 1,6 hexanediol suggesting condensation is driven by phase separation. Nab3's RNA recognition motif is also required for localization as seen for other PrLD-containing RNA-binding proteins that phase separate.
Title: Nab3's localization to a nuclear granule in response to nutrient deprivation is determined by its essential prion-like domain.
Kinetic cross-linking and analysis of cDNAs uncovers a role for Nab3 in determining gene expression profiles during stress.
Title: Kinetic CRAC uncovers a role for Nab3 in determining gene expression profiles during stress.
Study analyzed the functional role of the prion-like low complexity domains (LCDs) of Nab3, which can assemble into a robust amyloid form. Results show that Nab3 LCD can be exchanged for the low complexity regions of other proteins as the prion protein Sup35, or the RNA-binding protein, Hrp1. Also, its C-terminus seems more complex than previously appreciated.
Title: The hnRNP-like Nab3 termination factor can employ heterologous prion-like domains in place of its own essential low complexity domain.
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(Nrd1, Nab3, and Sen1 ) 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.
a multiplicity of interactions is needed to assemble a higher order Nrd1-Nab3 complex that coats specific nascent RNAs in preparation for termination.
Title: A network of interdependent molecular interactions describes a higher order Nrd1-Nab3 complex involved in yeast transcription termination.

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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 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 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	IDA Inferred from Direct Assay more info	PubMed
located_in cytoplasm	IDA Inferred from Direct Assay more info	PubMed
located_in nucleoplasm	IEA Inferred from Electronic Annotation more info
located_in nucleus	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: Nab3p

NP_015134.1

RNA-binding protein, subunit of Nrd1 complex (Nrd1p-Nab3p-Sen1p); complex interacts with exosome to mediate 3'-end formation of some mRNAs, snRNAs, snoRNAs, and CUTs; required for termination of non-poly(A) transcripts and efficient splicing; Nrd1-Nab3 pathway appears to have a role in rapid suppression of some genes when cells are shifted to poor growth conditions, indicating role for Nrd1-Nab3 in regulating cellular response to nutrient availability

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_001148.4 Reference assembly

Range

185317..187725 complement

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

NM_001184004.1 → NP_015134.1 TPA: Nab3p [Saccharomyces cerevisiae S288C]

See identical proteins and their annotated locations for NP_015134.1

Status: REVIEWED

UniProtKB/Swiss-Prot

D6W3H8, P38996, Q07034

UniProtKB/TrEMBL

B3LKN8, N1NWA5

Conserved Domains (2) summary

COG0724
Location:295 → 439

RRM; RNA recognition motif (RRM) domain [Translation, ribosomal structure and biogenesis]

cd12342
Location:331 → 401

RRM_Nab3p; RNA recognition motif (RRM) found in yeast nuclear polyadenylated RNA-binding protein 3 (Nab3p) and similar proteins