Publications

• Who let the DoGs out? - biogenesis of stress-induced readthrough transcripts.Rosa-Mercado NA, Steitz JA. Trends Biochem Sci. 2022 Mar; 2021 Sep 3. PMID: 34489151.
• Modulation of mRNA 3'-End Processing and Transcription Termination in Virus-Infected Cells.Vijayakumar A, Park A, Steitz JA. Front Immunol. 2022; 2022 Feb 10. PMID: 35222412.
• SARS-CoV-2 expresses a microRNA-like small RNA able to selectively repress host genes.Pawlica P, Yario TA, White S, Wang J, Moss WN, Hui P, Vinetz JM, Steitz JA. Proc Natl Acad Sci U S A. 2021 Dec 28; 2021 Dec 13. PMID: 34903581.
• STL-seq reveals pause-release and termination kinetics for promoter-proximal paused RNA polymerase II transcripts.Zimmer JT, Rosa-Mercado NA, Canzio D, Steitz JA, Simon MD. Mol Cell. 2021 Nov 4; 2021 Sep 13. PMID: 34520723.
• tRNA-like leader-trailer interaction promotes 3'-end maturation of MALAT1.Torabi SF, DeGregorio SJ, Steitz JA. RNA. 2021 Oct; 2021 Jul 12. PMID: 34253686.
• Structural analyses of an RNA stability element interacting with poly(A).Torabi SF, Chen YL, Zhang K, Wang J, DeGregorio SJ, Vaidya AT, Su Z, Pabit SA, Chiu W, Pollack L, Steitz JA. Proc Natl Acad Sci U S A. 2021 Apr 6. PMID: 33785601.
• RNA stabilization by a poly(A) tail 3'-end binding pocket and other modes of poly(A)-RNA interaction.Torabi SF, Vaidya AT, Tycowski KT, DeGregorio SJ, Wang J, Shu MD, Steitz TA, Steitz JA. Science. 2021 Feb 5; 2021 Jan 7. PMID: 33414189.
• Hyperosmotic stress alters the RNA polymerase II interactome and induces readthrough transcription despite widespread transcriptional repression.Rosa-Mercado NA, Zimmer JT, Apostolidi M, Rinehart J, Simon MD, Steitz JA. Mol Cell. 2021 Feb 4; 2021 Jan 4. PMID: 33400923.
• Idiosyncrasies of Viral Noncoding RNAs Provide Insights into Host Cell Biology.Withers JB, Mondol V, Pawlica P, Rosa-Mercado NA, Tycowski KT, Ghasempur S, Torabi SF, Steitz JA. Annu Rev Virol. 2019 Sep 29; 2019 Apr 30. PMID: 31039329.
• Structural Basis for Target-Directed MicroRNA Degradation.Sheu-Gruttadauria J, Pawlica P, Klum SM, Wang S, Yario TA, Schirle Oakdale NT, Steitz JA, MacRae IJ. Mol Cell. 2019 Sep 19; 2019 Jul 25. PMID: 31353209.
• Quantitative Fluorescence In Situ Hybridization (FISH) and Immunofluorescence (IF) of Specific Gene Products in KSHV-Infected Cells.Vallery TK, Steitz JA. J Vis Exp. 2019 Aug 27; 2019 Aug 27. PMID: 31524859.
• How Complementary Targets Expose the microRNA 3' End for Tailing and Trimming during Target-Directed microRNA Degradation.Pawlica P, Sheu-Gruttadauria J, MacRae IJ, Steitz JA. Cold Spring Harb Symp Quant Biol. 2019; 2020 Feb 4. PMID: 32019864.
• Two herpesviral noncoding PAN RNAs are functionally homologous but do not associate with common chromatin loci.Withers JB, Li ES, Vallery TK, Yario TA, Steitz JA. PLoS Pathog. 2018 Nov; 2018 Nov 1. PMID: 30383841.
• Kaposi's Sarcoma-Associated Herpesvirus mRNA Accumulation in Nuclear Foci Is Influenced by Viral DNA Replication and Viral Noncoding Polyadenylated Nuclear RNA.Vallery TK, Withers JB, Andoh JA, Steitz JA. J Virol. 2018 Jul 1; 2018 Jun 13. PMID: 29643239.
• Caution needs to be taken when assigning transcription start sites to ends of protein-coding genes: a rebuttal.Sabath N, Vilborg A, Steitz JA, Shalgi R. Hum Genomics. 2018 Jun 27; 2018 Jun 27. PMID: 29945683.
• Immunoprecipitation of Tri-methylated Capped RNA.Hayes KE, Barr JA, Xie M, Steitz JA, Martinez I. Bio Protoc. 2018 Feb 5. PMID: 29527542.
• Comparative analysis reveals genomic features of stress-induced transcriptional readthrough.Vilborg A, Sabath N, Wiesel Y, Nathans J, Levy-Adam F, Yario TA, Steitz JA, Shalgi R. Proc Natl Acad Sci U S A. 2017 Oct 3; 2017 Sep 19. PMID: 28928151.
• An Exportin-1-dependent microRNA biogenesis pathway during human cell quiescence.Martinez I, Hayes KE, Barr JA, Harold AD, Xie M, Bukhari SIA, Vasudevan S, Steitz JA, DiMaio D. Proc Natl Acad Sci U S A. 2017 Jun 20; 2017 Jun 5. PMID: 28584122.
• Settling the m(6)A debate: methylation of mature mRNA is not dynamic but accelerates turnover.Rosa-Mercado NA, Withers JB, Steitz JA. Genes Dev. 2017 May 15. PMID: 28637691.
• Readthrough transcription: How are DoGs made and what do they do?Vilborg A, Steitz JA. RNA Biol. 2017 May 4; 2016 Feb 9. PMID: 26861889.
• Fluorescence Amplification Method for Forward Genetic Discovery of Factors in Human mRNA Degradation.Alexandrov A, Shu MD, Steitz JA. Mol Cell. 2017 Jan 5; 2016 Dec 22. PMID: 28017590.
• Methyltransferase-like protein 16 binds the 3'-terminal triple helix of MALAT1 long noncoding RNA.Brown JA, Kinzig CG, DeGregorio SJ, Steitz JA. Proc Natl Acad Sci U S A. 2016 Dec 6; 2016 Nov 21. PMID: 27872311.
• A proximity-dependent assay for specific RNA-protein interactions in intact cells.Zhang W, Xie M, Shu MD, Steitz JA, DiMaio D. RNA. 2016 Nov; 2016 Sep 22. PMID: 27659050.
• Host miRNA degradation by Herpesvirus saimiri small nuclear RNA requires an unstructured interacting region.Pawlica P, Moss WN, Steitz JA. RNA. 2016 Aug; 2016 Jun 22. PMID: 27335146.
• Myriad Triple-Helix-Forming Structures in the Transposable Element RNAs of Plants and Fungi.Tycowski KT, Shu MD, Steitz JA. Cell Rep. 2016 May 10; 2016 Apr 28. PMID: 27134163.
• Hoogsteen-position pyrimidines promote the stability and function of the MALAT1 RNA triple helix.Brown JA, Kinzig CG, DeGregorio SJ, Steitz JA. RNA. 2016 May; 2016 Mar 7. PMID: 26952103.
• EBV noncoding RNA EBER2 interacts with host RNA-binding proteins to regulate viral gene expression.Lee N, Yario TA, Gao JS, Steitz JA. Proc Natl Acad Sci U S A. 2016 Mar 22; 2016 Mar 7. PMID: 26951683.
• A heterotrimer model of the complete Microprocessor complex revealed by single-molecule subunit counting.Herbert KM, Sarkar SK, Mills M, Delgado De la Herran HC, Neuman KC, Steitz JA. RNA. 2016 Feb; 2015 Dec 18. PMID: 26683315.
• Calcium signaling and transcription: elongation, DoGs, and eRNAs.Vilborg A, Passarelli MC, Steitz JA. Receptors Clin Investig. 2016; 2016 Feb 1. PMID: 29147672.
• Intronless β-Globin Reporter: A Tool for Studying Nuclear RNA Stability Elements.Brown JA, Steitz JA. Methods Mol Biol. 2016. PMID: 27236793.
• In silico discovery and modeling of non-coding RNA structure in viruses.Moss WN, Steitz JA. Methods. 2015 Dec; 2015 Jun 23. PMID: 26116541.
• Herpesvirus saimiri MicroRNAs Preferentially Target Host Cell Cycle Regulators.Guo YE, Oei T, Steitz JA. J Virol. 2015 Nov; 2015 Aug 19. PMID: 26292323.
• Noncoding RNA-guided recruitment of transcription factors: A prevalent but undocumented mechanism?Lee N, Steitz JA. Bioessays. 2015 Sep; 2015 Jul 22. PMID: 26200477.
• Widespread Inducible Transcription Downstream of Human Genes.Vilborg A, Passarelli MC, Yario TA, Tycowski KT, Steitz JA. Mol Cell. 2015 Aug 6; 2015 Jul 16. PMID: 26190259.
• The host Integrator complex acts in transcription-independent maturation of herpesvirus microRNA 3' ends.Xie M, Zhang W, Shu MD, Xu A, Lenis DA, DiMaio D, Steitz JA. Genes Dev. 2015 Jul 15. PMID: 26220997.
• Proteomics and Transcriptomics of BJAB Cells Expressing the Epstein-Barr Virus Noncoding RNAs EBER1 and EBER2.Pimienta G, Fok V, Haslip M, Nagy M, Takyar S, Steitz JA. PLoS One. 2015; 2015 Jun 29. PMID: 26121143.
• Viral noncoding RNAs: more surprises.Tycowski KT, Guo YE, Lee N, Moss WN, Vallery TK, Xie M, Steitz JA. Genes Dev. 2015 Mar 15. PMID: 25792595.
• EBV noncoding RNA binds nascent RNA to drive host PAX5 to viral DNA.Lee N, Moss WN, Yario TA, Steitz JA. Cell. 2015 Feb 12; 2015 Feb 5. PMID: 25662012.
• Virus meets host microRNA: the destroyer, the booster, the hijacker.Guo YE, Steitz JA. Mol Cell Biol. 2014 Oct; 2014 Jul 21. PMID: 25047834.
• Structural insights into the stabilization of MALAT1 noncoding RNA by a bipartite triple helix.Brown JA, Bulkley D, Wang J, Valenstein ML, Yario TA, Steitz TA, Steitz JA. Nat Struct Mol Biol. 2014 Jul; 2014 Jun 22. PMID: 24952594.
• 3'-Biotin-tagged microRNA-27 does not associate with Argonaute proteins in cells.Guo YE, Steitz JA. RNA. 2014 Jul; 2014 May 12. PMID: 24821854.
• Alternative capture of noncoding RNAs or protein-coding genes by herpesviruses to alter host T cell function.Guo YE, Riley KJ, Iwasaki A, Steitz JA. Mol Cell. 2014 Apr 10. PMID: 24725595.
• The noncoding RNA revolution-trashing old rules to forge new ones.Cech TR, Steitz JA. Cell. 2014 Mar 27. PMID: 24679528.
• Versatile microRNA biogenesis in animals and their viruses.Xie M, Steitz JA. RNA Biol. 2014; 2014 May 7. PMID: 24823351.
• RNA families in Epstein-Barr virus.Moss WN, Lee N, Pimienta G, Steitz JA. RNA Biol. 2014; 2013 Dec 20. PMID: 24441309.
• Mammalian 5'-capped microRNA precursors that generate a single microRNA.Xie M, Li M, Vilborg A, Lee N, Shu MD, Yartseva V, Šestan N, Steitz JA. Cell. 2013 Dec 19. PMID: 24360278.
• Phosphorylation of DGCR8 increases its intracellular stability and induces a progrowth miRNA profile.Herbert KM, Pimienta G, DeGregorio SJ, Alexandrov A, Steitz JA. Cell Rep. 2013 Nov 27; 2013 Nov 14. PMID: 24239349.
• Genome-wide analyses of Epstein-Barr virus reveal conserved RNA structures and a novel stable intronic sequence RNA.Moss WN, Steitz JA. BMC Genomics. 2013 Aug 9; 2013 Aug 9. PMID: 23937650.
• Human spliceosomal protein CWC22 plays a role in coupling splicing to exon junction complex deposition and nonsense-mediated decay.Alexandrov A, Colognori D, Shu MD, Steitz JA. Proc Natl Acad Sci U S A. 2012 Dec 26; 2012 Dec 10. PMID: 23236153.
• Formation of triple-helical structures by the 3'-end sequences of MALAT1 and MENβ noncoding RNAs.Brown JA, Valenstein ML, Yario TA, Tycowski KT, Steitz JA. Proc Natl Acad Sci U S A. 2012 Nov 20; 2012 Nov 5. PMID: 23129630.
• AUF1/hnRNP D is a novel protein partner of the EBER1 noncoding RNA of Epstein-Barr virus.Lee N, Pimienta G, Steitz JA. RNA. 2012 Nov; 2012 Sep 25. PMID: 23012480.
• Tracking expression and subcellular localization of RNA and protein species using high-throughput single cell imaging flow cytometry.Borah S, Nichols LA, Hassman LM, Kedes DH, Steitz JA. RNA. 2012 Aug; 2012 Jun 28. PMID: 22745225.
• Conservation of a triple-helix-forming RNA stability element in noncoding and genomic RNAs of diverse viruses.Tycowski KT, Shu MD, Borah S, Shi M, Steitz JA. Cell Rep. 2012 Jul 26; 2012 Jul 5. PMID: 22840393.
• EBV and human microRNAs co-target oncogenic and apoptotic viral and human genes during latency.Riley KJ, Rabinowitz GS, Yario TA, Luna JM, Darnell RB, Steitz JA. EMBO J. 2012 May 2; 2012 Mar 30. PMID: 22473208.
• Tri-snRNP-associated proteins interact with subunits of the TRAMP and nuclear exosome complexes, linking RNA decay and pre-mRNA splicing.Nag A, Steitz JA. RNA Biol. 2012 Mar; 2012 Mar 1. PMID: 22336707.
• A viral nuclear noncoding RNA binds re-localized poly(A) binding protein and is required for late KSHV gene expression.Borah S, Darricarrère N, Darnell A, Myoung J, Steitz JA. PLoS Pathog. 2011 Oct; 2011 Oct 13. PMID: 22022268.
• A primate herpesvirus uses the integrator complex to generate viral microRNAs.Cazalla D, Xie M, Steitz JA. Mol Cell. 2011 Sep 16. PMID: 21925386.
• Human eIF4AIII interacts with an eIF4G-like partner, NOM1, revealing an evolutionarily conserved function outside the exon junction complex.Alexandrov A, Colognori D, Steitz JA. Genes Dev. 2011 May 15. PMID: 21576267.
• miR-29 and miR-30 regulate B-Myb expression during cellular senescence.Martinez I, Cazalla D, Almstead LL, Steitz JA, DiMaio D. Proc Natl Acad Sci U S A. 2011 Jan 11; 2010 Dec 27. PMID: 21187425.
• Poly(A) tail recognition by a viral RNA element through assembly of a triple helix.Mitton-Fry RM, DeGregorio SJ, Wang J, Steitz TA, Steitz JA. Science. 2010 Nov 26. PMID: 21109672.
• Down-regulation of a host microRNA by a Herpesvirus saimiri noncoding RNA.Cazalla D, Yario T, Steitz JA. Science. 2010 Jun 18. PMID: 20558719.
• Comprehensive analysis of Rhesus lymphocryptovirus microRNA expression.Riley KJ, Rabinowitz GS, Steitz JA. J Virol. 2010 May; 2010 Mar 10. PMID: 20219930.
• Down-regulation of a host microRNA by a viral noncoding RNA.Cazalla D, Steitz JA. Cold Spring Harb Symp Quant Biol. 2010; 2010 Dec 7. PMID: 21139068.
• Nuclear networking fashions pre-messenger RNA and primary microRNA transcripts for function.Pawlicki JM, Steitz JA. Trends Cell Biol. 2010 Jan; 2009 Dec 11. PMID: 20004579.
• miRNPs: versatile regulators of gene expression in vertebrate cells.Steitz JA, Vasudevan S. Biochem Soc Trans. 2009 Oct. PMID: 19754429.
• A conserved WD40 protein binds the Cajal body localization signal of scaRNP particles.Tycowski KT, Shu MD, Kukoyi A, Steitz JA. Mol Cell. 2009 Apr 10; 2009 Mar 12. PMID: 19285445.
• Drosophila hnRNP A1 homologs Hrp36/Hrp38 enhance U2-type versus U12-type splicing to regulate alternative splicing of the prospero twintron.Borah S, Wong AC, Steitz JA. Proc Natl Acad Sci U S A. 2009 Feb 24; 2009 Feb 5. PMID: 19196985.
• Subnuclear compartmentalization of transiently expressed polyadenylated pri-microRNAs: processing at transcription sites or accumulation in SC35 foci.Pawlicki JM, Steitz JA. Cell Cycle. 2009 Feb 1; 2009 Feb 21. PMID: 19177009.
• Flexibility in the site of exon junction complex deposition revealed by functional group and RNA secondary structure alterations in the splicing substrate.Mishler DM, Christ AB, Steitz JA. RNA. 2008 Dec; 2008 Oct 24. PMID: 18952819.
• Conserved motifs in both CPSF73 and CPSF100 are required to assemble the active endonuclease for histone mRNA 3'-end maturation.Kolev NG, Yario TA, Benson E, Steitz JA. EMBO Rep. 2008 Oct; 2008 Aug 8. PMID: 18688255.
• Primary microRNA transcript retention at sites of transcription leads to enhanced microRNA production.Pawlicki JM, Steitz JA. J Cell Biol. 2008 Jul 14. PMID: 18625843.
• Where in the cell is the minor spliceosome?Steitz JA, Dreyfuss G, Krainer AR, Lamond AI, Matera AG, Padgett RA. Proc Natl Acad Sci U S A. 2008 Jun 24; 2008 Jun 17. PMID: 18562285.
• Cell-cycle control of microRNA-mediated translation regulation.Vasudevan S, Tong Y, Steitz JA. Cell Cycle. 2008 Jun 1; 2008 Mar 25. PMID: 18469529.
• Switching from repression to activation: microRNAs can up-regulate translation.Vasudevan S, Tong Y, Steitz JA. Science. 2007 Dec 21; 2007 Nov 29. PMID: 18048652.
• U2 snRNP binds intronless histone pre-mRNAs to facilitate U7-snRNP-dependent 3' end formation.Friend K, Lovejoy AF, Steitz JA. Mol Cell. 2007 Oct 26. PMID: 17964263.
• Mutational analysis of a viral RNA element that counteracts rapid RNA decay by interaction with the polyadenylate tail.Conrad NK, Shu MD, Uyhazi KE, Steitz JA. Proc Natl Acad Sci U S A. 2007 Jun 19; 2007 Jun 11. PMID: 17563387.
• Target mRNAs are repressed as efficiently by microRNA-binding sites in the 5' UTR as in the 3' UTR.Lytle JR, Yario TA, Steitz JA. Proc Natl Acad Sci U S A. 2007 Jun 5; 2007 May 29. PMID: 17535905.
• AU-rich-element-mediated upregulation of translation by FXR1 and Argonaute 2.Vasudevan S, Steitz JA. Cell. 2007 Mar 23. PMID: 17382880.
• Identification of a rapid mammalian deadenylation-dependent decay pathway and its inhibition by a viral RNA element.Conrad NK, Mili S, Marshall EL, Shu MD, Steitz JA. Mol Cell. 2006 Dec 28. PMID: 17189195.
• Epstein-Barr virus noncoding RNAs are confined to the nucleus, whereas their partner, the human La protein, undergoes nucleocytoplasmic shuttling.Fok V, Friend K, Steitz JA. J Cell Biol. 2006 May 8. PMID: 16682524.
• Multiple domains of EBER 1, an Epstein-Barr virus noncoding RNA, recruit human ribosomal protein L22.Fok V, Mitton-Fry RM, Grech A, Steitz JA. RNA. 2006 May; 2006 Mar 23. PMID: 16556938.
• In vivo assembly of functional U7 snRNP requires RNA backbone flexibility within the Sm-binding site.Kolev NG, Steitz JA. Nat Struct Mol Biol. 2006 Apr; 2006 Mar 19. PMID: 16547514.
• Metazoan oocyte and early embryo development program: a progression through translation regulatory cascades.Vasudevan S, Seli E, Steitz JA. Genes Dev. 2006 Jan 15. PMID: 16418480.
• The challenge of viral snRNPs.Conrad NK, Fok V, Cazalla D, Borah S, Steitz JA. Cold Spring Harb Symp Quant Biol. 2006. PMID: 17381320.
• Symplekin and multiple other polyadenylation factors participate in 3'-end maturation of histone mRNAs.Kolev NG, Steitz JA. Genes Dev. 2005 Nov 1; 2005 Oct 17. PMID: 16230528.
• Molecular basis for RNA kink-turn recognition by the h15.5K small RNP protein.Szewczak LB, Gabrielsen JS, Degregorio SJ, Strobel SA, Steitz JA. RNA. 2005 Sep. PMID: 16120832.
• Small nuclear RNAs encoded by Herpesvirus saimiri upregulate the expression of genes linked to T cell activation in virally transformed T cells.Cook HL, Lytle JR, Mischo HE, Li MJ, Rossi JJ, Silva DP, Desrosiers RC, Steitz JA. Curr Biol. 2005 May 24. PMID: 15916956.
• A Kaposi's sarcoma virus RNA element that increases the nuclear abundance of intronless transcripts.Conrad NK, Steitz JA. EMBO J. 2005 May 18; 2005 Apr 28. PMID: 15861127.
• SRprises along a messenger's journey.Huang Y, Steitz JA. Mol Cell. 2005 Mar 4. PMID: 15749011.
• An embryonic poly(A)-binding protein (ePAB) is expressed in mouse oocytes and early preimplantation embryos.Seli E, Lalioti MD, Flaherty SM, Sakkas D, Terzi N, Steitz JA. Proc Natl Acad Sci U S A. 2005 Jan 11; 2005 Jan 3. PMID: 15630085.
• Splicing of U12-type introns deposits an exon junction complex competent to induce nonsense-mediated mRNA decay.Hirose T, Shu MD, Steitz JA. Proc Natl Acad Sci U S A. 2004 Dec 28; 2004 Dec 17. PMID: 15608055.
• Guide RNAs with 5' caps and novel box C/D snoRNA-like domains for modification of snRNAs in metazoa.Tycowski KT, Aab A, Steitz JA. Curr Biol. 2004 Nov 23. PMID: 15556860.
• Evidence for reassociation of RNA-binding proteins after cell lysis: implications for the interpretation of immunoprecipitation analyses.Mili S, Steitz JA. RNA. 2004 Nov; 2004 Sep 23. PMID: 15388877.
• A molecular link between SR protein dephosphorylation and mRNA export.Huang Y, Yario TA, Steitz JA. Proc Natl Acad Sci U S A. 2004 Jun 29; 2004 Jun 21. PMID: 15210956.
• The Herpesvirus saimiri small nuclear RNAs recruit AU-rich element-binding proteins but do not alter host AU-rich element-containing mRNA levels in virally transformed T cells.Cook HL, Mischo HE, Steitz JA. Mol Cell Biol. 2004 May. PMID: 15121869.
• Premature termination codons do not affect the rate of splicing of neighboring introns.Lytle JR, Steitz JA. RNA. 2004 Apr. PMID: 15037775.
• Transportins 1 and 2 are redundant nuclear import factors for hnRNP A1 and HuR.Rebane A, Aab A, Steitz JA. RNA. 2004 Apr. PMID: 15037768.
• An intronic enhancer regulates splicing of the twintron of Drosophila melanogaster prospero pre-mRNA by two different spliceosomes.Scamborova P, Wong A, Steitz JA. Mol Cell Biol. 2004 Mar. PMID: 14966268.
• Splicing double: insights from the second spliceosome.Patel AA, Steitz JA. Nat Rev Mol Cell Biol. 2003 Dec. PMID: 14685174.
• Commentary: Bio2010--new challenges for biology educators.Steitz JA. Cell Biol Educ. 2003 Summer. PMID: 12888841.