NRD1

Summary

Gene Symbol: NRD1
Description: Nrd1 complex RNA-binding subunit
Alias: Nrd1 complex RNA-binding subunit
Species: Saccharomyces cerevisiae S288c

Top Publications

  1. Jamonnak N, Creamer T, Darby M, Schaughency P, Wheelan S, Corden J. Yeast Nrd1, Nab3, and Sen1 transcriptome-wide binding maps suggest multiple roles in post-transcriptional RNA processing. RNA. 2011;17:2011-25 pubmed publisher
    ..RNAs in the yeast Saccharomyces cerevisiae are terminated through a pathway directed by the RNA-binding proteins Nrd1, Nab3, and the RNA helicase Sen1...
  2. Steinmetz E, Brow D. Control of pre-mRNA accumulation by the essential yeast protein Nrd1 requires high-affinity transcript binding and a domain implicated in RNA polymerase II association. Proc Natl Acad Sci U S A. 1998;95:6699-704 pubmed
    b>Nrd1 is an essential yeast protein of unknown function that has an RNA recognition motif (RRM) in its carboxyl half and a putative RNA polymerase II-binding domain, the CTD-binding motif, at its amino terminus...
  3. Vasiljeva L, Kim M, Terzi N, Soares L, Buratowski S. Transcription termination and RNA degradation contribute to silencing of RNA polymerase II transcription within heterochromatin. Mol Cell. 2008;29:313-23 pubmed publisher
    ..These transcripts are terminated by the Nrd1/Sen1 complex and degraded by the exosome...
  4. Thiebaut M, Kisseleva Romanova E, Rougemaille M, Boulay J, Libri D. Transcription termination and nuclear degradation of cryptic unstable transcripts: a role for the nrd1-nab3 pathway in genome surveillance. Mol Cell. 2006;23:853-64 pubmed
    ..Our results suggest an important role for the Nrd1p-Nab3p pathway in the control of gene expression throughout the genome. ..
  5. Conrad N, Wilson S, Steinmetz E, Patturajan M, Brow D, Swanson M, et al. A yeast heterogeneous nuclear ribonucleoprotein complex associated with RNA polymerase II. Genetics. 2000;154:557-71 pubmed
    ..The yeast NRD1 gene encodes an essential RNA-binding protein that shares homology with mammalian CTD-binding proteins and is ..
  6. Tudek A, Porrúa O, Kabzinski T, Lidschreiber M, Kubicek K, Fortova A, et al. Molecular basis for coordinating transcription termination with noncoding RNA degradation. Mol Cell. 2014;55:467-81 pubmed publisher
    The Nrd1-Nab3-Sen1 (NNS) complex is essential for controlling pervasive transcription and generating sn/snoRNAs in S. cerevisiae...
  7. Kubicek K, Cerná H, Holub P, Pasulka J, Hrossova D, Loehr F, et al. Serine phosphorylation and proline isomerization in RNAP II CTD control recruitment of Nrd1. Genes Dev. 2012;26:1891-6 pubmed publisher
    ..Here, we report the solution structure of the Ser5 phosphorylated (pSer5) CTD bound to Nrd1. The structure reveals a direct recognition of pSer5 by Nrd1 that requires the cis conformation of the upstream ..
  8. Arigo J, Carroll K, Ames J, Corden J. Regulation of yeast NRD1 expression by premature transcription termination. Mol Cell. 2006;21:641-51 pubmed
    The yeast RNA binding proteins Nrd1 and Nab3 are required for termination of nonpolyadenylated transcripts from RNA polymerase (Pol) II-transcribed snRNA and snoRNA genes...
  9. Arigo J, Eyler D, Carroll K, Corden J. Termination of cryptic unstable transcripts is directed by yeast RNA-binding proteins Nrd1 and Nab3. Mol Cell. 2006;23:841-51 pubmed
    ..These cryptic unstable transcripts (CUTs) are rapidly degraded by the nuclear exosome. Yeast RNA binding proteins Nrd1 and Nab3 direct termination of sn/snoRNAs and recently have also been implicated in premature transcription ..

More Information

Publications45

  1. Sadowski M, Dichtl B, Hubner W, Keller W. Independent functions of yeast Pcf11p in pre-mRNA 3' end processing and in transcription termination. EMBO J. 2003;22:2167-77 pubmed
    ..We conclude that Pcf11p is a bifunctional protein and that transcript cleavage is not an obligatory step prior to RNAP II termination. ..
  2. Kubicek K, Pasulka J, Cerná H, Lohr F, Stefl R. 1H, 13C, and 15N resonance assignments for the CTD-interacting domain of Nrd1 bound to Ser5-phosphorylated CTD of RNA polymerase II. Biomol NMR Assign. 2011;5:203-5 pubmed publisher
    ..The presented assignment of backbone and side-chain resonances of the Nrd1 CID proton, carbon and nitrogen nuclei will allow studies of the structure and interaction of CID with carboxy-..
  3. Gudipati R, Villa T, Boulay J, Libri D. Phosphorylation of the RNA polymerase II C-terminal domain dictates transcription termination choice. Nat Struct Mol Biol. 2008;15:786-94 pubmed publisher
    ..Similarly to small nucleolar and small nuclear RNAs, transcription of CUT-encoding genes is terminated by the Nrd1 complex pathway...
  4. Leporé N, Lafontaine D. A functional interface at the rDNA connects rRNA synthesis, pre-rRNA processing and nucleolar surveillance in budding yeast. PLoS ONE. 2011;6:e24962 pubmed publisher
    ..We show that this sequence is also required for the interaction between Spt5 and Nrd1, an RNA specific binding protein, and an exosome cofactor...
  5. Hobor F, Pergoli R, Kubicek K, Hrossova D, Bacikova V, Zimmermann M, et al. Recognition of transcription termination signal by the nuclear polyadenylated RNA-binding (NAB) 3 protein. J Biol Chem. 2011;286:3645-57 pubmed publisher
    ..RNA polymerase II transcripts are processed by the poly(A)-independent termination pathway that requires the Nrd1 complex...
  6. Vasiljeva L, Buratowski S. Nrd1 interacts with the nuclear exosome for 3' processing of RNA polymerase II transcripts. Mol Cell. 2006;21:239-48 pubmed
    ..We find that the RNA binding protein Nrd1, complexed with its partners Nab3, Sen1, and cap binding complex, physically interacts with the nuclear form of ..
  7. Mayer A, Heidemann M, Lidschreiber M, Schreieck A, Sun M, Hintermair C, et al. CTD tyrosine phosphorylation impairs termination factor recruitment to RNA polymerase II. Science. 2012;336:1723-5 pubmed publisher
    ..Tyr(1) phosphorylation stimulates binding of elongation factor Spt6 and impairs recruitment of termination factors Nrd1, Pcf11, and Rtt103...
  8. Nedea E, Nalbant D, Xia D, Theoharis N, Suter B, Richardson C, et al. The Glc7 phosphatase subunit of the cleavage and polyadenylation factor is essential for transcription termination on snoRNA genes. Mol Cell. 2008;29:577-87 pubmed publisher
    ..The suppressing fragment, and in a similar manner full-length Sen1, copurifies with the snoRNA termination factors Nrd1 and Nab3, suggesting loss of Glc7 from CPF can be compensated by recruiting Glc7 to Nrd1-Nab3 through Sen1...
  9. Schulz D, Schwalb B, Kiesel A, Baejen C, Torkler P, Gagneur J, et al. Transcriptome surveillance by selective termination of noncoding RNA synthesis. Cell. 2013;155:1075-87 pubmed publisher
    ..cerevisiae is globally restricted by early termination that relies on the essential RNA-binding factor Nrd1. Depletion of Nrd1 from the nucleus results in 1,526 Nrd1-unterminated transcripts (NUTs) that originate from ..
  10. Porrúa O, Hobor F, Boulay J, Kubicek K, d Aubenton Carafa Y, Gudipati R, et al. In vivo SELEX reveals novel sequence and structural determinants of Nrd1-Nab3-Sen1-dependent transcription termination. EMBO J. 2012;31:3935-48 pubmed publisher
    The Nrd1-Nab3-Sen1 (NNS) complex pathway is responsible for transcription termination of cryptic unstable transcripts and sn/snoRNAs...
  11. Wlotzka W, Kudla G, Granneman S, Tollervey D. The nuclear RNA polymerase II surveillance system targets polymerase III transcripts. EMBO J. 2011;30:1790-803 pubmed publisher
    ..To address this, we identified in vivo binding sites for nuclear RNA surveillance factors, Nrd1, Nab3 and the Trf4/5–Air1/2–Mtr4 polyadenylation (TRAMP) complex poly(A) polymerase Trf4, by UV crosslinking...
  12. Heo D, Yoo I, Kong J, Lidschreiber M, Mayer A, Choi B, et al. The RNA polymerase II C-terminal domain-interacting domain of yeast Nrd1 contributes to the choice of termination pathway and couples to RNA processing by the nuclear exosome. J Biol Chem. 2013;288:36676-90 pubmed publisher
    ..differential CTD-CID interactions in the choice of termination pathway, we altered the CTD-binding specificity of Nrd1 by domain swapping...
  13. Honorine R, Mosrin Huaman C, Hervouet Coste N, Libri D, Rahmouni A. Nuclear mRNA quality control in yeast is mediated by Nrd1 co-transcriptional recruitment, as revealed by the targeting of Rho-induced aberrant transcripts. Nucleic Acids Res. 2011;39:2809-20 pubmed publisher
    ..show that the targeting and degradation of Rho-induced aberrant transcripts is associated with a large increase of Nrd1 recruitment to the transcription complex via its CID and RRM domains and a concomitant enrichment of exosome ..
  14. Singh N, Ma Z, Gemmill T, Wu X, Defiglio H, Rossettini A, et al. The Ess1 prolyl isomerase is required for transcription termination of small noncoding RNAs via the Nrd1 pathway. Mol Cell. 2009;36:255-66 pubmed publisher
    ..and upstream regulatory RNAs (uRNAs), that are transcribed by RNA polymerase II (pol II) and terminated by an Nrd1-dependent pathway...
  15. Rondon A, Mischo H, Kawauchi J, Proudfoot N. Fail-safe transcriptional termination for protein-coding genes in S. cerevisiae. Mol Cell. 2009;36:88-98 pubmed publisher
    ..We propose that these alternative Pol II termination pathways serve the dual function of avoiding transcription interference and promoting rapid removal of aberrant transcripts. ..
  16. Noël J, Larose S, Abou Elela S, Wellinger R. Budding yeast telomerase RNA transcription termination is dictated by the Nrd1/Nab3 non-coding RNA termination pathway. Nucleic Acids Res. 2012;40:5625-36 pubmed publisher
    ..Furthermore, the results also demonstrate that the function of this Tlc1 terminator depends on the Nrd1/Nab3 transcription termination pathway...
  17. Vasiljeva L, Kim M, Mutschler H, Buratowski S, Meinhart A. The Nrd1-Nab3-Sen1 termination complex interacts with the Ser5-phosphorylated RNA polymerase II C-terminal domain. Nat Struct Mol Biol. 2008;15:795-804 pubmed publisher
    ..To study how a mechanism is chosen, we analyzed recruitment of Nrd1, which cooperates with Nab3 and Sen1 to terminate small nucleolar RNAs and other short RNAs...
  18. Steinmetz E, Conrad N, Brow D, Corden J. RNA-binding protein Nrd1 directs poly(A)-independent 3'-end formation of RNA polymerase II transcripts. Nature. 2001;413:327-31 pubmed
    ..genes is prevented by a cis-acting element that is recognized, in part, by the essential RNA-binding protein Nrd1. The RNA-binding protein Nab3, the putative RNA helicase Sen1, and the intact C-terminal domain of pol II are also ..
  19. Sheldon K, Mauger D, Arndt K. A Requirement for the Saccharomyces cerevisiae Paf1 complex in snoRNA 3' end formation. Mol Cell. 2005;20:225-36 pubmed
    ..We identified NAB3 as a dosage suppressor of rtf1. Nab3, together with Nrd1, directs 3' end formation of nonpolyadenylated RNA pol II transcripts, such as snoRNAs...
  20. Grzechnik P, Gdula M, Proudfoot N. Pcf11 orchestrates transcription termination pathways in yeast. Genes Dev. 2015;29:849-61 pubmed publisher
    ..short noncoding RNA (ncRNA) generated by RNA polymerase II (Pol II) are terminated by the NRD complex consisting of Nrd1, Nab3, and Sen1...
  21. Lenstra T, Tudek A, Clauder S, Xu Z, Pachis S, van Leenen D, et al. The role of Ctk1 kinase in termination of small non-coding RNAs. PLoS ONE. 2013;8:e80495 pubmed publisher
    ..of shorter cryptic unstable transcripts (CUTs) and small nucleolar/nuclear RNAs (sno/snRNAs) is performed by the Nrd1-Nab3-Sen1 (NNS) complex that binds phosphorylated CTD-Ser5 (Ser5P) via the CTD-interacting domain (CID) of Nrd1p...
  22. Mostovoy Y, Thiemicke A, Hsu T, Brem R. The Role of Transcription Factors at Antisense-Expressing Gene Pairs in Yeast. Genome Biol Evol. 2016;8:1748-61 pubmed publisher
  23. Terzi N, Churchman L, Vasiljeva L, Weissman J, Buratowski S. H3K4 trimethylation by Set1 promotes efficient termination by the Nrd1-Nab3-Sen1 pathway. Mol Cell Biol. 2011;31:3569-83 pubmed publisher
    In Saccharomyces cerevisiae, the Nrd1-Nab3-Sen1 pathway mediates the termination of snoRNAs and cryptic unstable transcripts (CUTs)...
  24. Mitsuzawa H, Kanda E, Ishihama A. Rpb7 subunit of RNA polymerase II interacts with an RNA-binding protein involved in processing of transcripts. Nucleic Acids Res. 2003;31:4696-701 pubmed
    ..The screen identified the S.pombe homolog of the Saccharomyces cerevisiae Nrd1, an RNA-binding protein implicated in 3' end formation of small nucleolar and small nuclear RNAs transcribed by pol ..
  25. Loya T, O Rourke T, Degtyareva N, Reines D. A network of interdependent molecular interactions describes a higher order Nrd1-Nab3 complex involved in yeast transcription termination. J Biol Chem. 2013;288:34158-67 pubmed publisher
    Nab3 and Nrd1 are yeast heterogeneous nuclear ribonucleoprotein (hnRNP)-like proteins that heterodimerize and bind RNA...
  26. Beaufour M, Godin F, Vallee B, Cadene M, Bénédetti H. Interaction proteomics suggests a new role for the Tfs1 protein in yeast. J Proteome Res. 2012;11:3211-8 pubmed publisher
    ..Integration of these results with known functional partners of Tfs1p shows that two subnetworks meet through the Tfs1p node, suggesting that it may act as a bridge between cell signaling and intermediate metabolism in yeast. ..
  27. Webb S, Hector R, Kudla G, Granneman S. PAR-CLIP data indicate that Nrd1-Nab3-dependent transcription termination regulates expression of hundreds of protein coding genes in yeast. Genome Biol. 2014;15:R8 pubmed publisher
    b>Nrd1 and Nab3 are essential sequence-specific yeast RNA binding proteins that function as a heterodimer in the processing and degradation of diverse classes of RNAs...
  28. Bacikova V, Pasulka J, Kubicek K, Stefl R. Structure and semi-sequence-specific RNA binding of Nrd1. Nucleic Acids Res. 2014;42:8024-38 pubmed publisher
    In Saccharomyces cerevisiae, the Nrd1-dependent termination and processing pathways play an important role in surveillance and processing of non-coding ribonucleic acids (RNAs)...
  29. Fox M, Gao H, Smith Kinnaman W, Liu Y, Mosley A. The exosome component Rrp6 is required for RNA polymerase II termination at specific targets of the Nrd1-Nab3 pathway. PLoS Genet. 2015;11:e1004999 pubmed publisher
    ..cryptic unstable transcripts (CUTs), and some stable unannotated transcripts (SUTs) that are terminated by an Nrd1, Nab3, and Sen1 (NNS) dependent mechanism...
  30. Chinchilla K, Rodríguez Molina J, Ursic D, Finkel J, Ansari A, Culbertson M. Interactions of Sen1, Nrd1, and Nab3 with multiple phosphorylated forms of the Rpb1 C-terminal domain in Saccharomyces cerevisiae. Eukaryot Cell. 2012;11:417-29 pubmed publisher
    ..Sen1, along with termination factors Nrd1 and Nab3, is required for the termination of noncoding RNA transcripts, but Sen1 is associated during transcription ..
  31. Fasken M, Laribee R, Corbett A. Nab3 facilitates the function of the TRAMP complex in RNA processing via recruitment of Rrp6 independent of Nrd1. PLoS Genet. 2015;11:e1005044 pubmed publisher
    ..Here, we report that the Nab3 RNA-binding protein of the Nrd1-Nab3-Sen1 (NNS) complex is a potent suppressor of TRAMP mutants...
  32. Kim K, Heo D, Kim I, Suh J, Kim M. Exosome Cofactors Connect Transcription Termination to RNA Processing by Guiding Terminated Transcripts to the Appropriate Exonuclease within the Nuclear Exosome. J Biol Chem. 2016;291:13229-42 pubmed publisher
    The yeast Nrd1 interacts with the C-terminal domain (CTD) of RNA polymerase II (RNApII) through its CTD-interacting domain (CID) and also associates with the nuclear exosome, thereby acting as both a transcription termination and RNA ..
  33. Costello J, Stead J, Feigenbutz M, Jones R, Mitchell P. The C-terminal region of the exosome-associated protein Rrp47 is specifically required for box C/D small nucleolar RNA 3'-maturation. J Biol Chem. 2011;286:4535-43 pubmed publisher
  34. Harel Sharvit L, Eldad N, Haimovich G, Barkai O, Duek L, Choder M. RNA polymerase II subunits link transcription and mRNA decay to translation. Cell. 2010;143:552-63 pubmed publisher
    ..We propose that Rpb4/7, through its interactions at each step in the mRNA lifecycle, represents a class of factors, "mRNA coordinators," which integrate the various stages of gene expression into a system. ..
  35. Glas J, Dümcke S, Zacher B, Poron D, Gagneur J, Tresch A. Simultaneous characterization of sense and antisense genomic processes by the double-stranded hidden Markov model. Nucleic Acids Res. 2016;44:e44 pubmed publisher
    ..Notably, 12% of all transcriptionally active positions showed simultaneous activity on both strands. Furthermore, dsHMM reveals that antisense transcription is specifically suppressed by Nrd1, a yeast termination factor.
  36. Barros M, Tzagoloff A. Aep3p-dependent translation of yeast mitochondrial ATP8. Mol Biol Cell. 2017;28:1426-1434 pubmed publisher