Mechanisms and regulation of alternative pre-mRNA splicing.
Lee, Y. and Rio, D.C. (2015).
Ann. Rev. Biochem., 84, 291-323.
PMID: 25784052
[PubMed – in process]

Protein-Tagging System for Signal Amplification in Gene Expression and Fluorescence Imaging.
Tanenbaum ME, Gilbert LA, Qi LS, Weissman JS, Vale RD. (2014)
Cell, 159: 635-46.
PMC4252608 PMID: 25307933 [PubMed – indexed for MEDLINE] PMCID: PMC4252608 [Available on 2015-10-23]

eIF3 targets cell-proliferation messenger RNAs for translational activation or repression.
Lee AS, Kranzusch PJ, Cate JH.
Nature. 2015 Jun 4;522(7554):111-4. doi: 10.1038/nature14267. Epub 2015 Apr 6.
PubMed PMID: 25849773.

Protein synthesis. Rqc2p and 60S ribosomal subunits mediate mRNA-independent elongation of nascent chains.
Shen PS, Park J, Qin Y, Li X, Parsawar K, Larson MH, Cox J, Cheng Y, Lambowitz AM, Weissman JS, Brandman O, Frost A.
Science. 2015 Jan 2;347(6217):75-8. doi: 10.1126/science.1259724.
PMID: 25554787 [PubMed – indexed for MEDLINE]
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Select item 25378630

Principles of ER cotranslational translocation revealed by proximity-specific ribosome profiling.
Jan CH, Williams CC, Weissman JS.
Science. 2014 Nov 7;346(6210):1257521. doi: 10.1126/science.1257521. Epub 2014 Nov 6.
PMID: 25378630 [PubMed – indexed for MEDLINE] Free PMC Article
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Select item 25378625

Targeting and plasticity of mitochondrial proteins revealed by proximity-specific ribosome profiling.
Williams CC, Jan CH, Weissman JS.
Science. 2014 Nov 7;346(6210):748-51. doi: 10.1126/science.1257522.
PMID: 25378625 [PubMed – indexed for MEDLINE] Free PMC Article
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Select item 25307932

Genome-Scale CRISPR-Mediated Control of Gene Repression and Activation.
Gilbert LA, Horlbeck MA, Adamson B, Villalta JE, Chen Y, Whitehead EH, Guimaraes C, Panning B, Ploegh HL, Bassik MC, Qi LS, Kampmann M, Weissman JS.
Cell. 2014 Oct 23;159(3):647-61. doi: 10.1016/j.cell.2014.09.029. Epub 2014 Oct 9.
PMID: 25307932 [PubMed – indexed for MEDLINE]
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Select item 25274302

Programmable RNA recognition and cleavage by CRISPR/Cas9.
O’Connell MR, Oakes BL, Sternberg SH, East-Seletsky A, Kaplan M, Doudna JA.
Nature. 2014 Dec 11;516(7530):263-6. doi: 10.1038/nature13769. Epub 2014 Sep 28.
PMID: 25274302 [PubMed – indexed for MEDLINE]
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Select item 24789973

A pause sequence enriched at translation start sites drives transcription dynamics in vivo.
Larson MH, Mooney RA, Peters JM, Windgassen T, Nayak D, Gross CA, Block SM, Greenleaf WJ, Landick R, Weissman JS.
Science. 2014 May 30;344(6187):1042-7. doi: 10.1126/science.1251871. Epub 2014 May 1.
PMID: 24789973 [PubMed – indexed for MEDLINE] Free PMC Article
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Quantifying absolute protein synthesis rates reveals principles underlying allocation of cellular resources.
Li GW, Burkhardt D, Gross C, Weissman JS.
Cell. 2014 Apr 24;157(3):624-35. doi: 10.1016/j.cell.2014.02.033.
PMID: 24766808 [PubMed – indexed for MEDLINE]
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A versatile framework for microbial engineering using synthetic non-coding RNAs.
Qi LS, Arkin AP.
Nat Rev Microbiol. 2014 May;12(5):341-54. doi: 10.1038/nrmicro3244. Review.
PMID: 24736794 [PubMed – indexed for MEDLINE]
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Select item 24360272

Dynamic imaging of genomic loci in living human cells by an optimized CRISPR/Cas system.
Chen B, Gilbert LA, Cimini BA, Schnitzbauer J, Zhang W, Li GW, Park J, Blackburn EH, Weissman JS, Qi LS, Huang B.
Cell. 2013 Dec 19;155(7):1479-91. doi: 10.1016/j.cell.2013.12.001. Erratum in: Cell. 2014 Jan 16;156(1-2):373.
PMID: 24360272 [PubMed – indexed for MEDLINE] Free PMC Article
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Genome-wide probing of RNA structure reveals active unfolding of mRNA structures in vivo.
Rouskin S, Zubradt M, Washietl S, Kellis M, Weissman JS.
Nature. 2014 Jan 30;505(7485):701-5. doi: 10.1038/nature12894. Epub 2013 Dec 15.
PMID: 24336214 [PubMed – indexed for MEDLINE] Free PMC Article
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Ribosome profiling reveals pervasive and regulated stop codon readthrough in Drosophila melanogaster.
Dunn JG, Foo CK, Belletier NG, Gavis ER, Weissman JS.
Elife. 2013 Dec 3;2:e01179. doi: 10.7554/eLife.01179.
PMID: 24302569 [PubMed – indexed for MEDLINE] Free PMC Article
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Select item 24250809

Human-like eukaryotic translation initiation factor 3 from Neurospora crassa.
Smith MD, Gu Y, Querol-Audí J, Vogan JM, Nitido A, Cate JH.
PLoS One. 2013 Nov 8;8(11):e78715. doi: 10.1371/journal.pone.0078715. eCollection 2013.
PMID: 24250809 [PubMed – in process] Free PMC Article
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CRISPR-mediated modular RNA-guided regulation of transcription in eukaryotes.
Gilbert LA, Larson MH, Morsut L, Liu Z, Brar GA, Torres SE, Stern-Ginossar N, Brandman O, Whitehead EH, Doudna JA, Lim WA, Weissman JS, Qi LS.
Cell. 2013 Jul 18;154(2):442-51. doi: 10.1016/j.cell.2013.06.044. Epub 2013 Jul 11.
PMID: 23849981 [PubMed – indexed for MEDLINE] Free PMC Article
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Genome-wide annotation and quantitation of translation by ribosome profiling.
Ingolia NT, Brar GA, Rouskin S, McGeachy AM, Weissman JS.
Curr Protoc Mol Biol. 2013 Jul;Chapter 4:Unit 4.18. doi: 10.1002/0471142727.mb0418s103.
PMID: 23821443 [PubMed – indexed for MEDLINE] Free PMC Article
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Two RNA-binding motifs in eIF3 direct HCV IRES-dependent translation.
Sun C, Querol-Audí J, Mortimer SA, Arias-Palomo E, Doudna JA, Nogales E, Cate JH.
Nucleic Acids Res. 2013 Aug;41(15):7512-21. doi: 10.1093/nar/gkt510. Epub 2013 Jun 13.
PMID: 23766293 [PubMed – indexed for MEDLINE] Free PMC Article
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Architecture of human translation initiation factor 3.
Querol-Audi J, Sun C, Vogan JM, Smith MD, Gu Y, Cate JH, Nogales E.
Structure. 2013 Jun 4;21(6):920-8. doi: 10.1016/j.str.2013.04.002. Epub 2013 Apr 25.
PMID: 23623729 [PubMed – indexed for MEDLINE] Free PMC Article
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Other select
publications from
CRSB faculty


Li JJ, Huang H, Bickel PJ, Brenner SE. 2014. Comparison of D. melanogaster and C. elegans developmental stages, tissues, and cells by modENCODE RNA-seq data. Genome Research 24:1086-1101. doi:10.1101/gr.170100.113

Lareau LF, Brenner SE. 2015. Regulation of splicing factors by alternative splicing and NMD is conserved between kingdoms yet evolutionarily flexible. Molecular Biology and Evolution. advance access published online 8 Jan 2015. doi:10.1093/molbev/msv002


Jinek M, East A, Cheng A, Lin S, Ma E, Doudna J. (2013) RNA-programmed genome editing in human cells. eLife. 2:e00471.

Qi LS, Larson MH, Gilbert LA, Doudna JA, Weissman JS, Arkin AP, Lim WA. (2013) Repurposing CRISPR as an RNA-guided platform for sequence-specific control of gene expression.  Cell. 152(5):1173-1183. PMID: 23452860  PMCID: PMC3664290



Aviran S, Trapnell C, Lucks JB, Mortimer SA, Luo S, Schroth GP, Doudna JA, Arkin AP, Pachter L. (2011) Modeling and automation of sequencing-based characterization of RNA structure. Proc Natl Acad Sci USA. 108:11069-11074.

Brooks AN, Aspden JL, Podgornaia AI, Rio DC, Brenner SE. (2011) Identification and experimental validation of splicing regulatory elements in Drosophila melanogaster reveals functionally conserved splicing enhancers in metazoans. RNA. 17:1884-1894.

Brooks AN, Yang L, Duff MO, Hansen KD, Park JW, Dudoit S, Brenner SE, Graveley BR. (2011) Conservation of an RNA regulatory map between Drosophila and mammals. Genome Res. 21:193-202.

Churchman LS and Weissman JS. (2011) Nascent transcript sequencing visualizes transcription at nucleotide resolution. Nature. 469:368-373.

Graveley B, et al. (2011) The developmental transcriptome of Drosophila melanogaster. Nature. 471:473-479.

Hellsten U, Aspden JL, Rio DC, Rokhsar DS. (2011) A segmental genomic duplication generates a functional intron. Nat Comm. 2:454.

Lucks JB, Mortimer SA, Trapnell C, Luo S, Aviran S, Schroth GP, Pachter L, Doudna JA, Arkin AP. (2011) Multiplexed RNA structure characterization with selective 2′-hydroxyl acylation analyzed by primer extension sequencing (SHAPE-Seq). Proc Natl Acad Sci USA. 108:11063-11068.

Sun C, Todorovic A, Querol-Audí J, Bai Y, Villa N, Snyder M, Ashchyan J, Lewis CS, Hartland A, Gradia S, Fraser CS, Doudna JA, Nogales E, Cate JH. (2011) Functional reconstitution of human eukaryotic translation initiation factor 3 (eIF3). Proc Natl Acad Sci USA. 108:20473-20478.



Blanchette M, Green RE, MacArthur S, Brooks AN, Brenner SE, Eisen MB, Rio DC. (2009) Genome-wide analysis of alternative pre-mRNA splicing and RNA binding specificities of the Drosophila hnRNP A/B family members. Mol Cell. 33:438-449.

Hammond MC, Wachter A, Breaker RR. (2009) A plant 5S ribosomal RNA mimic regulates alternative splicing of transcription factor IIIA pre-mRNAs. Nat Struct Mol Biol. 16:541-549.

Ingolia NT, Ghaemmaghami S, Newman JR, Weissman JS. (2009) Genome-wide analysis in vivo of translation with nucleotide resolution using ribosome profiling.Science. 324:218-223.



Olson S, Blanchette M, Park J, Saava Y, Yeo GW, Yeakley JM, Rio DC, Graveley BR. (2007) A regulator of Dscam mutually exclusive splicing fidelity. Nat Struct Mol Biol. 14:1134-1140.