Department of Cell Biology

Publications

2022

Chi B, Öztürk MM, Paraggio CL, Leonard CE, Sanita ME, Dastpak M, O’Connell JD, Coady JA, Zhang J, Gygi SP, Lopez-Gonzalez R, Reed R. Three ALS genes regulate expression of the MHC class II antigen presentation pathway [Internet]. bioRxiv; 2022 MayAvailable from: https://www.biorxiv.org/content/10.1101/2022.05.11.489680v1. [Supplementary Figures]

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Dastpak M, Kim H, Paraggio CL, Leonard CE, Yin S, Chi B, Nassar KW, Rowe RG, Hou Z, Zhang J, Cohn EF, Yang N, Marion W, Zhang Y, Daley GQ, Reed R. Chemokine Receptor 1 and its associated immune pathway are downregulated in SF3B1 MT blood and non-blood cancers [Internet]. bioRxiv; 2022 Mar. Available from: https://www.biorxiv.org/content/10.1101/2022.03.31.485699v1. [Supplementary Figures]

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2019
Wang K, Yin C, Du X, Chen S, Wang J, Zhang L, Wang L, Yu Y, Chi B, Shi M, Wang C, Reed R, Zhou Y, Huang J, and Cheng H (2019) A U2-snRNP–independent role of SF3b in promoting mRNA export. PNAS https://doi.org/10.1073/pnas.1818835116 [Epub ahead of print]
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Yin S, Gambe RG, Sun J, Martinez AZ, Cartun ZJ, Regis FFD, Wan Y, Fan J, Brooks AN, Herman SEM, Ten Hacken E, Taylor-Weiner A, Rassenti LZ, Ghia EM, Kipps TJ, Obeng EA, Cibulskis CL, Neuberg D, Campagna DR, Fleming MD, Ebert BL, Wiestner A, Leshchiner I, DeCaprio JA, Getz G, Reed R, Carrasco RD, Wu CJ, Wang L (2019) A Murine Model of Chronic Lymphocytic Leukemia Based on B Cell-Restricted Expression of Sf3b1 Mutation and Atm Deletion. Cancer Cell 35(2): 283–296. PMID: 30712845. [Supplementary Tables]

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2018

Ten Hacken E, Valentin R, Regis FFD, Sun J, Yin S, Werner L, Deng J, Gruber M, Wong J, Zheng M, Gill AL, Seiler M, Smith P, Thomas M, Buonamici S, Ghia EM, Kim E, Rassenti LZ, Burger JA, Kipps TJ, Meyerson ML, Bachireddy P, Wang L, Reed R, Neuberg D, Carrasco RD, Brooks AN, Letai A, Davids MS, Wu CJ (2018) Splicing modulation sensitizes chronic lymphocytic leukemia cells to venetoclax by remodeling mitochondrial apoptotic dependencies. JCI Insight. 3(19):e121438. doi: 10.1172/jci.insight.121438.

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Searchable database for spliceosome associated proteins

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Chi B, O’Connell JD, Iocolano AD, Coady JA, Yu Y, Gangopadhyay J, Gygi SP and Reed R (2018) The neurodegenerative diseases ALS and SMA are linked at the molecular level via the ASC-1 complex. Nucleic Acids Res. 46(22):11939-11951. doi: 10.1093/nar/gky1093. PMID: 30398641, PMCID: PMC6294556

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Yin S, Iocolano A, Yu Y, Gangopadhyay J, Reed R (2018) In Vitro System for Coupling RNAP II Transcription to Primary microRNA Processing and a Three-Way System for RNAP II Transcription/Splicing/microRNA Processing. Methods Mol Biol, 1823. Springer, New York, NY. 43-50. PMID: 29959672 

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Chi B, O’Connell JD, Yamazaki T, Gangopadhyay J , Gygi SP and Reed R (2018) Interactome analyses revealed that the U1 snRNP machinery overlaps extensively with the RNAP II machinery and contains multiple ALS/SMA-causative proteins. Sci Rep 8: 8755-8766

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2017

Yin S, Lopez-Gonzalez R, Kunz RC, Gangopadhyay J, Borufka C, Gygi SP, Gao F-B, Reed R (2017) Evidence that C9ORF72 dipeptide repeat proteins associate with U2 snRNP to cause mis-splicing in ALS/FTD patients. Cell Reports 19: 2244-2256

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NEWS LINKS RELATED TO OUR WORK ON ALS/FTD

https://hms.harvard.edu/news/assembly-failure-0?utm_source=Silverpop&utm_medium=email&utm_term=s1&utm_content=6.19.17.HMS
http://news.harvard.edu/gazette/story/2017/06/harvard-study-shows-link-between-rna-misfires-and-als-dementia/
https://www.eurekalert.org/pub_releases/2017-06/hms-af061217.php
https://medicalxpress.com/news/2017-06-reveals-rna-splicing-errors-als.html

Paolella BR, Gibson WJ, Urbanski LK, Alberta JA, Zack, TI, Bandopadhayay P, Nichols CA, Agarwalla PK, Brown MS, Lamothe R, Yu Y, Choi PS, Obeng EA, Heck D, Wei G, Wang B, Tsherniak A, Vazquez F, Weir BA, Root DE, Cowley GS, Buhrlage SJ, Stiles CD, Ebert BL, Hahn WC, Reed R, Beroukhim R (2017) Copy-number and gene dependency analysis reveals partial copy loss of wild- type SF3B1 as a novel cancer vulnerability. eLIFE 6: e23268

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2016

Wang L, Brooks A, Fan J, Wan Y, Gambe R, Li S, Hergert S, Yin S, Freeman SS, Levin JZ, Fan L, Seiler M, Buonamici S, Smith PG, Chau KF, Cibulskis CL, Zhang W, Rassenti LZ, Ghia EM, Kipps TJ, Fernandes S, Bloch DB, Kotliar D, Landau DA, Shukla S, Aster JC, Reed R, DeLuca DS, Brown JR, Neuberg D, Getz G, Livak KJ, Meyerson MM, Kharchenko PV and Wu CJ (2016) Transcriptomic characterization of SF3B1 mutation reveals its pleiotropic effects in chronic lymphocytic leukemia. Cancer Cell 30: 750-763. PMID: 27818134.

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2015

Kumar R, Corbett MA, van Bon BW, Woenig JA, Weir L, Douglas E, Friend KL, Gardner A, Shaw M, Jolly LA, Tan C, Hunter MF, Hackett A, Field M, Palmer EE, Leffler M, Rogers C, Boyle J, Bienek M, Jensen C, Van Buggenhout G, Van Esch H, Hoffmann K, Raynaud M, Zhao H, Reed R, Hu H, Haas SA, Haan E, Kalscheuer VM and Gecz J (2015) THOC2 mutations implicate mRNA-export pathway in X-linked intellectual disability. Am J Hum Genet. 97(2): 302-310. PMID: 26166480. 

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Yin S, Yu Y and Reed R (2015) Primary microRNA processing is functionally coupled to RNAP II transcription in vitro. Sci Rep. 5: 11992. PMID: 26149087, PMCID: PMC4493704.

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Yu Y, Reed R (2015) FUS functions in coupling transcription to splicing by mediating an interaction between RNAP II and U1 snRNP. Proc Natl Acad Sci USA. 112(28): 8608-8613. PMID: 26124092, PMCID: PMC4507187. 

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Yu Y, Chi B, Xia W, Gangopadhyay J, Yamazaki T, Winkelbauer-Hurt ME, Yin S, Eliasse Y, Adams E, Shaw CE and Reed R (2015) U1 snRNP is mislocalized in ALS patient fibroblasts bearing NLS mutations in FUS and is required for motor neuron outgrowth in zebrafish. Nucleic Acids Res. 43(6):3208-3218. PMID: 25735748, PMCID: PMC4381066.

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Shi M*, Zhang H*, Wang L*, Zhu C, Sheng K, Du Y, Wang K, Dias A, Chen S, Whitman M, Li D, Wang E, Reed R, and Cheng H (2015) Premature Termination Codons Are Recognized in the Nucleus in A Reading-Frame Dependent Manner. Cell Discovery. 1, 15001; doi:10.1038/celldisc.2015.1 *these three authors contributed equally to this work

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2014

Folco EG and Reed R (2014) In vitro systems for coupling RNAP II transcription to splicing and polyadenylation. Methods Mol Biol, 1126Irvine, CA: Humana Press. 169-177. Print. PMID: 24549664.

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2013

Chesi A, Staahl BT, Jovicic A, Couthouis J, Fasolino M, Raphael AR, Yamazaki T, Elias L, Polak M, Kelly C, Williams KL, Fifita JA, Maragakis NJ, Nicholson GA, King OD, Reed R, Crabtree GR, Blair IP, Glass JD, and Gitler AD (2013) Exome sequencing to identify de novo mutations in sporadic ALS trios. Nat Neurosci. 16(7):851-5. PMID: 23708140, PMCID: PMC3709464.

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Di Gregorio E, Bianchi FT, Schiavi A, Chiotto A, Rolando M, Verdun di Cantogno L, Grosso E, Cavalieri S, Calcia A, Lacerenza D, Zuffardi O, Retta SF, Stevanin G, Marelli C, Durr A, Forlani S, Chelly J, Montarolo F, Tempia F, Beggs HE, Reed R, Squadrone S, Abete MC, Migone N, Brussino A, Ventura N, Di Cunto F, and Brusco A (2013) A de novo X;8 translocation creates a PTK2-THOC2 gene fusion with THOC2 expression knockdown in a patient with psychomotor retardation and congenital cerebellar hypoplasia. J Med Genet. 50(8):543-51. PMID: 23749989.

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Lei H, Zhai B, Yin S, Gygi S and Reed R (2013) Evidence that a consensus element found in naturally intronless mRNAs promotes mRNA export. Nucleic Acids Res. 41(4): 2517-25. PMID: 23275560, PMCID: PMC3575797.

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2012

NEWS LINKS RELATED TO OUR WORK ON THE MOTOR NEURON DISEASE ALS:

http://www.alsa.org/research/journal-news/october-2012.html#feature
http://medicalxpress.com/news/2012-09-pathway-links-lou-gehrig-disease.html
http://news.harvard.edu/gazette/story/2012/09/link-found-between-als-and-sma

Yamazaki T, Chen S, Yu Y, Yan B, Haertlein TC, Carrasco MA, Tapia JC, Zhai B, Das R, Lalancette-Hebert M, Sharma A, Chandran S, Sullivan G, Nishimura AL, Shaw CE, Gygi SP, Shneider NA, Maniatis T, and Reed R (2012) FUS-SMN protein interactions link the motor neuron diseases ALS and SMA. Cell Reports. 2(4): 799-806. PMID: 23022481, PMCID: PMC3483417.
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Folco EG, Lee CS, Dufu K,Yamazaki T and Reed R (2012) The proteins PDIP3 and ZC11A associate with the human TREX complex in an ATP-Dependent manner and function in mRNA export PLoS One. 7(8), e43804. PMID: 22928037, PMCID: PMC3426524.

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Folco EG, Lei H, Hsu JL and Reed R (2012) Small-scale nuclear extracts for functional assays of gene expression machineries. J. Vis. Exp. (64), e4140, DOI: 10.3791/4140.(Small Scale Nuclear Extract Method Video)

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Viphakone N, Hautbergue G, Walsh M, Chang C, Holland A, Folco EG, Reed R and Wilson SA (2012) TREX exposes the RNA-binding domain of Nxf1 to enable mRNA export. Nature Comms. 3: 1006. PMID: 22893130, PMCID: PMC3654228.

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2011

Wang L, Lawrence MS, Wan Y, Stojanov P, Sougnez C, Stevenson K, Werner L, Sivachenko A, DeLuca DS, Zhang L, Zhang W, Vartanov AR, Fernandes SM, Goldstein NR, Folco EG, Cibulskis K, Tesar B, Sievers QL, Shefler E, Gabriel S, Hacohen N, Reed R, Meyerson M, Golub TR, Lander ES, Neuberg D, Brown JR, Getz G and Wu CJ (2011) SF3B1 and other novel cancer genes in chronic lymphocytic leukemia. N Engl J Med. 365(26):2497-506. PMID: 22150006, PMCID: PMC3685413.

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Lei H, Dias AP and Reed R (2011) Export and stability of naturally intronless mRNAs require specific coding region sequences and the TREX mRNA export complex. Proc Natl Acad Sci USA. 108(44): 17985-90. PMID: 22010220, PMCID: PMC3207654.

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Folco EG, Coil KE and Reed R (2011) The anti-tumor drug E7107 reveals an essential role for SF3b in remodeling U2 snRNP to expose the branch point-binding region. Genes Dev. 25(5): 440-444. PMID: 21363962, PMCID: PMC3049285.

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2010

Dias AP, Dufu K, Lei H and Reed R (2010) A role for TREX components in the release of spliced mRNA from nuclear speckle domains. Nature Comms. 1: 97-107. PMID: 20981025, PMCID: PMC3793428.

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Dufu K, Livingstone MJ, Seebacher J, Gygi S, Wilson SA and Reed R (2010) ATP is required for interactions between UAP56 and two conserved mRNA export proteins, Aly and CIP29, to assemble the TREX complex. Genes Dev. 24(18): 2043-2053. PMID: 20844015, PMCID: PMC2939366.

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Yu Y, Das R, Folco EG and Reed R (2010) A model in vitro system for co-transcriptional splicing. Nucleic Acids Res. 38(21): 7570-7578. PMID: 20631007, PMCID: PMC2995048.

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2008

Valencia P, Dias AP and Reed R (2008) Splicing promotes rapid and efficient mRNA export in mammalian cells. Proc Natl Acad Sci USA. 105(9): 3386–3391. PMID: 18287003, PMCID: PMC2265164

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Lee CS, Dias AP, Jedrychowski M, Patel AH, Hsu JL and Reed R (2008) Human DDX3 functions in translation and interacts with the translation initiation factor eIF3. Nucleic Acids Res. 36(14): 4708-18. PMID: 18628297, PMCID: PMC2504307.

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2007

Ganapathi KA, Austin KM, Lee CS, Dias A, Malsch MM, Reed R, Shimamura A. The human Shwachman-Diamond syndrome protein, SBDS, associates with ribosomal RNA. Blood. 2007 Sep 1;110(5):1458-65. doi: 10.1182/blood-2007-02-075184. Epub 2007 May 2. PMID: 17475909; PMCID: PMC1975835.

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Das R, Yu J, Zhang Z, Gygi M, Krainer A, Gygi S and Reed R (2007) SR Proteins Function in Coupling RNAP II Transcription to Pre-mRNA Splicing. Mol Cell. 26: 867-881. PMID: 17588520.

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Ibrahim EC, Hims MM, Shomron N, Burge CB, Slaugenhaupt SA and Reed R (2007) Weak definition of IKBKAP exon 20 leads to aberrant splicing in familial dysautonomia. Hum Mutat. 28(1):41-53.PMID: 16964593

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Hims MM, Ibrahim EC, Leyne M, Mull J, Liu L, Lazaro C, Shetty RS, Gill S, Gusella JF, Reed R and Slaugenhaupt SA (2007) Therapeutic potential and mechanism of kinetin as a treatment for the human splicing disease familial dysautonomia. J Mol Med (Berl). 85(2):149-61. PMID: 17206408

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2006

Cheng H, Dufu K, Lee CS, Hsu JL, Dias A and Reed R (2006) Human mRNA export machinery recruited to the 5' end of mRNA. Cell 127: 1389-1400. PMID: 17190602.

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Das R, Dufu K, Romney B, Feldt M, Elenko M, and Reed R (2006) Functional coupling of RNAP II transcription to spliceosome assembly. Genes Dev. 120: 1100-1109. PMID: 16651655, PMCID: PMC1472470.

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2005

Reed R and Cheng H (2005) TREX, SR proteins and export of mRNA. Curr Opin Cell Biol. 17(3):269-73. Review. PMID: 15901496

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Masuda S, Das R, Cheng H, Hurt E, Dorman N and Reed R (2005) Recruitment of the human TREX complex to mRNA during splicing. Genes Dev. 19: 1512-1517. PMID: 15998806, PMCID: PMC1172058.

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Ibrahim EC, Schaal TD, Hertel KJ, Reed R and Maniatis T (2005) Serine/arginine-rich protein-dependent suppression of exon skipping by exonic splicing enhancers. Proc Natl Acad Sci U S A. 102(14):5002-7. PMID: 15753297

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2004

Rodríguez-Navarro S, Fischer T, Luo MJ, Antúnez O, Brettschneider S, Lechner J, Pérez-Ortín JE, Reed R and Hurt E (2004) Sus1, a functional component of the SAGA histone acetylase complex and the nuclear pore-associated mRNA export machinery. Cell. 116(1):75-86. PMID: 14718168

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Hurt E, Luo MJ, Röther S, Reed R and Strässer K (2004) Cotranscriptional recruitment of the serine-arginine-rich (SR)-like proteins Gbp2 and Hrb1 to nascent mRNA via the TREX complex. Proc Natl Acad Sci U S A. 101(7):1858-62. PMID: 14769921

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Ferraiuolo MA, Lee CS, Ler LW, Hsu JL, Costa-Mattioli M, Luo MJ, Reed R and Sonenberg N (2004) A nuclear translation-like factor eIF4AIII is recruited to the mRNA during splicing and functions in nonsense-mediated decay. Proc Natl Acad Sci U S A. 101(12):4118-23. PMID: 15024115

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2003

Reed R (2003) Coupling transcription, splicing and mRNA export. Curr Opin Cell Biol. 15(3):326-31. Review. PMID: 12787775

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Zhou Z and Reed R (2003) Purification of functional RNA-protein complexes using MS2-MBP. Curr Protoc Mol Biol. Chapter 27:Unit 27.3. PMID: 18265330.

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Luo MJ and Reed R (2003) Identification of RNA binding proteins by UV cross-linking. Curr Protoc Mol Biol. Chapter 27:Unit 27.2.PMID: 18265329

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Lee CS, Das R, and Reed R (2003) Agarose gel separation/isolation of RNA-protein complexes. Curr Protoc Mol Biol. Chapter 27:Unit 27.1. PMID: 18265328

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2002

Maniatis T and Reed R (2002) An extensive network of coupling among gene expression machines. Nature. 416(6880):499-506. Review. PMID: 11932736

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Reed R and Hurt E (2002) A conserved mRNA export machinery coupled to pre-mRNA splicing. Cell. 108(4):523-31. Review. PMID: 11909523

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Strässer K, Masuda S, Mason P, Pfannstiel J, Oppizzi M, Rodriguez-Navarro S, Rondón AG, Aguilera A, Struhl K, Reed R and Hurt E (2002) TREX is a conserved complex coupling transcription with messenger RNA export. Nature. 417(6886):304-8. PMID: 11979277

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Zhou Z, Sim J, Griffith J and Reed R (2002) Purification and electron microscopic visualization of functional human spliceosomes. Proc Natl Acad Sci U S A. 99(19):12203-7. PMID: 12215496

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Zhou Z, Licklider LJ, Gygi SP, and Reed R (2002) Comprehensive proteomic analysis of the human spliceosome. Nature. 419(6903):182-5. PMID: 12226669

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Chung S, Zhou Z, Huddleston KA, Harrison DA, Reed R, Coleman TA and Rymond BC (2002) Crooked neck is a component of the human spliceosome and implicated in the splicing process. Biochim Biophys Acta. 1576(3):287-97. PMID: 12084575

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2001

Reed R and Magni K (2001) A new view of mRNA export: separating the wheat from the chaff. Nat Cell Biol. 3(9):E201-4. Review. PMID: 11533670

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Clouse KN, Luo MJ, Zhou Z and Reed R (2001) A Ran-independent pathway for export of spliced mRNA. Nat Cell Biol. 3(1):97-9. PMID: 11146633

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Chua K and Reed R (2001) An upstream AG determines whether a downstream AG is selected during catalytic step II of splicing. Mol Cell Biol. 21(5):1509-14.PMID: 11238888

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Luo ML, Zhou Z, Magni K, Christoforides C, Rappsilber J, Mann M and Reed R (2001) Pre-mRNA splicing and mRNA export linked by direct interactions between UAP56 and Aly. Nature. 413(6856):644-7. PMID: 11675789

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2000

Reed R (2000) Mechanisms of fidelity in pre-mRNA splicing. Curr Opin Cell Biol. 12(3):340-5. Review. PMID: 10801464

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Zhou Z*, Luo MJ*, Straesser K, Katahira J, Hurt E, and Reed R (2000) The protein Aly links pre-messenger-RNA splicing to nuclear export in metazoans. Nature. 407(6802):401-5. PMID: 1101419 *these authors contributed equally to this work

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Das R, Zhou Z and Reed R (2000) Functional association of U2 snRNP with the ATP-independent spliceosomal complex E. Mol Cell. 5(5):779-87. PMID: 10882114

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1999

Will CL, Schneider C, Reed R and Lührmann R (1999) Identification of both shared and distinct proteins in the major and minor spliceosomes. Science. 284:2003-2005. PMID 10373121 

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Chua K and Reed R (1999) The RNA splicing factor hSlu7 is required for correct 3' splice-site choice. Nature. 402(6758):207-10. PMID: 10647016

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Luo MJ and Reed R (1999) Splicing is required for rapid and efficient mRNA export in metazoans. Proc Natl Acad Sci U S A. 96(26):14937-42. PMID: 10611316

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Das R and Reed R (1999) Resolution of the mammalian E complex and the ATP-dependent spliceosomal complexes on native agarose mini-gels. RNA. 5(11):1504-8. PMID: 10580479

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Das BK, Xia L, Palandjian L, Gozani O, Chyung Y and Reed R (1999) Characterization of a protein complex containing spliceosomal proteins SAPs 49, 130, 145, and 155. Mol Cell Biol. 19(10):6796-802. PMID: 10490618

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Chua K and Reed R (1999) Human step II splicing factor hSlu7 functions in restructuring the spliceosome between the catalytic steps of splicing. Genes Dev. 13(7):841-50. PMID: 10197984

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