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Publications: CV


Below you will find some of our key publications. Bolded names are authors from our lab.

A complete listing of our publications can be found on Pubmed.

RBP Image Database: A resource for the systematic characterization of the subcellular distribution properties of human RNA binding proteins

Louis Philip Benoit BouvretteXiaofeng WangJonathan BoulaisJian KongEasin Uddin SyedSteven M BlueLijun ZhanSara OlsonRebecca StantonXintao WeiBrian YeeEric L Van NostrandXiang-Dong FuChristopher B BurgeBrenton R GraveleyGene W YeoEric Lécuyer 



Localized translation of cell junction mRNAs is required for epithelial cell polarity

Chin A, Bergeman J, Communal L, Boulais J, Mes-Masson A-M, Lécuyer E

Under review.


Persistent mRNA localization defects and cell death in ALS neurons caused by transient cellular stress.

Markmiller S, Sathe S, Server KL, Nguyen TB, Fulzele A, Cody N, Javaherian A, Broski S, Finkbeiner S, Bennett EJ, Lécuyer E, Yeo GW

Cell Reports. 2021, 36: 109685. doi: 10.1016/j.celrep.2021.109685.



Puromycin labeling coupled with proximity ligation assays to define sites of mRNA translation in Drosophila embryos and human cells.

Chin A, Lécuyer E

Methods Mol Biol. 2021, 2381: 267-284.



RNA interference (RNAi) screening in cultured Drosophila cells.

Padilla JA, Chin A, Patel D, Jolivet P, Lécuyer E

Methods Mol Biol. 2021, 2381: 267-284.



Translating messages in different neighbouhoods.

Chin A, Lécuyer E

Dev Cell. 2020, 54: 691-693.



A large-scale binding and functional map of human RNA-binding proteins.

Van Nostrand EL*, Freese P*, Pratt GA*, Wang X*, Wei X*, Xiao R*, Blue SM, Chen JY, Cody NAL, Dominguez D, Olson S, Sundararaman B, Zhan L, Bazile C, Bouvrette LPB, Bergalet J, Duff MO, Garcia KE, Gelboin-Burkhart C, Hochman M, Lambert NJ, Li H, McGurk MP, Nguyen TB, Palden T, Rabano I, Sathe S, Stanton R, Su A, Wang R, Yee BA, Zhou B, Louie AL, Aigner S, Fu XD¶, Lécuyer E¶, Burge CB¶, Graveley BR¶, Yeo GW¶

*=Co-first authors; ¶=Co-corresponding authors.

Nature. 2020, 583: 711-719.



Expanded encyclopaedias of DNA elements in the human and mouse genomes.

ENCODE Project Consortium, Moore JE, Purcaro MJ, Pratt HE, Epstein CB, Shoresh N, Adrian J, Kawli T, Davis CA, Dobin A, Kaul R, Halow J, Van Nostrand EL, Freese P, Gorkin DU, Shen Y, He Y, Mackiewicz M, Pauli-Behn F, Williams BA, Mortazavi A, Keller CA, Zhang XO, Elhajjajy SI, Huey J, Dickel DE, Snetkova V, Wei X, Wang X, Rivera-Mulia JC, Rozowsky J, Zhang J, Chhetri SB, Zhang J, Victorsen A, White KP, Visel A, Yeo GW, Burge CB, Lécuyer E, Gilbert DM, Dekker J, Rinn J, Mendenhall EM, Ecker JR, Kellis M, Klein RJ, Noble WS, Kundaje A, Guigó R, Farnham PJ, Cherry JM, Myers RM, Ren B, Graveley BR, Gerstein MB, Pennacchio LA, Snyder MP, Bernstein BE, Wold B, Hardison RC, Gingeras TR, Stamatoyannopoulos JA, Weng Z

Nature. 2020, 583: 699-710.



Perspectives on ENCODE. 

ENCODE Project Consortium, Snyder MP, Gingeras TR, Moore JE, Weng Z, Gerstein MB, Ren B, Hardison RC, Stamatoyannopoulos JA, Graveley BR, Feingold EA, Pazin MJ, Pagan M, Gilchrist DA, Hitz BC, Cherry JM, Bernstein BE, Mendenhall EM, Zerbino DR, Frankish A, Flicek P, Myers RM

Nature. 2020, 583: 693-698.



Staufen1 localizes to the mitotic spindle and controls the localization of RNA populations to the spindle. 

Hassine S, Bonnet-Magnaval F, Benoit Bouvrette LP, Doran B, Ghram M, Bouthillette M, Lécuyer E, DesGroseillers L

J Cell Sci. 2020, 133: jcs247155. doi: 10.1242/jcs.247155.



Inter-dependent Centrosomal Co-localization of the cen and ik2 cis-Natural Antisense mRNAs in Drosophila. 

Bergalet J, Patel D, Legendre F, Lapointe C, Benoit Bouvrette LP, Chin A, Blanchette M, Kwon E, Lécuyer E

Cell Rep. 2020, 30:3339-3352.



oRNAment: a database of putative RNA binding protein target sites in the transcriptomes of model species. 

Benoit Bouvrette LP, Bovaird S, Blanchette M, Lécuyer E 

Nucleic Acids Res. 2020 , 48(D1):D166-D173. 



Bioinformatics Approaches to Gain Insights into cis-Regulatory Motifs Involved in mRNA Localization. 

Benoit Bouvrette LP, Blanchette M, Lécuyer E 

Adv Exp Med Biol. 2019, 1203:165-194. 



A ribosomal protein S5 isoform is essential for oogenesis and interacts with distinct RNAs in Drosophila melanogaster. 

Kong J, Han H, Bergalet J, Bouvrette LPB, Hernández G, Moon NS, Vali H, Lécuyer E, Lasko P

Sci Rep. 2019, 9:13779. doi: 10.1038/s41598-019-50357-z.



Prediction of mRNA subcellular localization using deep recurrent neural networks. 

Yan Z, Lécuyer E, Blanchette M

Bioinformatics. 2019, 35:i333-i342. 



Small-Molecule Modulation of TDP-43 Recruitment to Stress Granules Prevents Persistent TDP-43 Accumulation in ALS/FTD. 

Fang MY, Markmiller S, Vu AQ, Javaherian A, Dowdle WE, Jolivet P, Bushway PJ, Castello NA, Baral A, Chan MY, Linsley JW, Linsley D, Mercola M, Finkbeiner S, Lécuyer E, Lewcock JW, Yeo GW

Neuron. 2019, 103:802-819.



Pervasive Chromatin-RNA Binding Protein Interactions Enable RNA-Based Regulation of Transcription. 

Xiao R, Chen JY, Liang Z, Luo D, Chen G, Lu ZJ, Chen Y, Zhou B, Li H, Du X, Yang Y, San M, Wei X, Liu W, Lécuyer E, Graveley BR, Yeo GW, Burge CB, Zhang MQ, Zhou Y, Fu XD

Cell. 2019, 178: 107-121.




Optimized FISH methods for visualizing RNA localization properties in Drosophila and human tissues and cultured cells.

Diot C, Chin A, Lécuyer E.

Methods. 2017, 126:156-165. PMID: 28668588

CeFra-seq: Systematic mapping of RNA subcellular distribution properties through cell fractionation coupled to deep-sequencing.

Lefebvre FA, Cody NAL, Benoît Bouvrette LP, Bergalet J, Wang X, Lécuyer E.

Methods. 2017, 126:138-148. PMID: 28579403

RNA localization: Making its way to the center stage.

Chin A, Lécuyer E.

Biochim Biophys Acta. 2017, 1861(11 Pt B):2956-2970. Review. PMID: 28630007

Biochemical Fractionation of Time-Resolved Drosophila Embryos Reveals Similar Transcriptomic Alterations in Replication Checkpoint and Histone mRNA Processing Mutants.

Lefebvre FA, Benoit Bouvrette LP, Bergalet J, Lécuyer E.

J Mol Biol. 2017, 429: 3264-3279. PMID: 28167048

Small Luggage for a Long Journey: Transfer of Vesicle-Enclosed Small RNA in Interspecies Communication.

Lefebvre FA, Lécuyer E.

Front Microbiol. 2017, 8:377.  eCollection Review. PMID: 28360889



A large-scale binding and functional map of human RNA binding proteins.

Van Nostrand EL*, Freese P*, Pratt GA*, Wang X*, Wei X*, Xiao R*, Blue SM, Dominguez D, Cody NAL, Olson S, Sundararaman B, Zhan L, Bazile C, Benoit Bouvrette LPBergalet J, Chen J, Duff MO, Garci KE, Gelboin-Burkhart C, Hochman A, Lambert NJ, Li H, Nguyen TB, Palden T, Rabano I, Sathe S, Stanton R, Zhou B, Su A, Wang R, Yee BA, Louie AL, Aigner S, Fu X-D¶, Lécuyer E¶, Burge CB¶, Graveley BR ¶, Yeo GW¶. * =Co-first authros; ¶ = Co-corresponding authors.

bioRXiv (doi:

Context-Dependent and Disease-Specific Diversity in Protein Interactions within Stress Granules.

Markmiller S, Soltanieh S, Server KL, Mak R, Jin W, Fang MY, Luo EC, Krach F, Yang D, Sen A, Fulzele A, Wozniak JM, Gonzalez DJ, Kankel MW, Gao FB, Bennett EJ, Lécuyer E, Yeo GW.

Cell. 2018, 172(3) :590-604. PMID: 29373831

CeFra-seq reveals broad asymmetric mRNA and noncoding RNA distribution profiles in Drosophila and human cells.

Benoit Bouvrette LP, Cody NAL, Bergalet J, Lefebvre FA, Diot C, Wang X, Blanchette M, Lécuyer E.

RNA. 2018, 24: 98-113. PMID: 29079635

Biological functions, regulatory mechanisms, and disease relevance of RNA localization pathways. 
Bovaird S, Patel D, Padilla JA, Lécuyer E
FEBS Lett. 2018, 592:2948-2972.



Flying the RNA Nest: Drosophila Reveals Novel Insights into the Transcriptome Dynamics of Early Development. 
Lefebvre FA, Lécuyer E

J Dev Biol. 2018, 6: 5. doi: 10.3390/jdb6010005.



Comparative transcriptomic analysis of human and Drosophila extracellular vesicles.

Lefebvre FA, Benoit Bouvrette LP, Perras L, Blanchet-Cohen A, Garnier D, Rak J, Lécuyer E.

Scientific Reports. 2016, 6: 27680. PMID: 27282340

Resources for the Comprehensive Discovery of Functional RNA Elements.

Sundararaman B, Zhan L, Blue SM, Stanton R, Elkins K, Olson S, Wei X, Van Nostrand EL, Pratt GA, Huelga SC, Smalec BM, Wang X, Hong EL, Davidson JM, Lécuyer E, Graveley BR, Yeo GW.

Mol Cell. 2016, 61:903-13. PMID: 26990993

Loss of function of the Drosophila Ninein-related centrosomal protein Bsg25D causes mitotic defects and impairs embryonic development.

Kowanda M, Bergalet J, Wieczorek M, Brouhard G, Lécuyer E, Lasko P.

Biol Open. 2016, 5:1040-51. PMID: 27422905



Subcellular Transcript Localization in Drosophila Embryos and Tissues Visualized by Multiplex-FISH.

Bergalet J, Iampietro C, Chin A, Oré-Rodriguez S, Nguyen X-T, Cody NA, and Lécuyer E. 2015. Edited by Giselbert Hauptmann. Neuromethods. 714: 31-47.



Developmentally regulated elimination of damaged nuclei involves a Chk2-dependent mechanism of mRNA nuclear retention.

Iampietro C, Bergalet J, Wang X, Cody NA, Chin A, Lefebvre FA, Douziech M, Krause HM, Lécuyer E.

Dev Cell. 2014, 29: 468-81. PMID: 24835465

The functions and regulatory principles of mRNA intracellular trafficking.

Bergalet J, Lécuyer E.

Adv Exp Med Biol. 2014, 825: 57-96. Review. PMID: 25201103

SCL, LMO1 and Notch1 reprogram thymocytes into self-renewing cells.

Gerby B, Tremblay CS, Tremblay M, Rojas-Sutterlin S, Herblot S, Hébert J, Sauvageau G, Lemieux S, Lécuyer E, Veiga DF, Hoang T.

PLoS Genet. 2014, 10: e1004768. PMID: 25522233

2013 & Earlier


SPARCS: a web server to analyze (un)structured regions in coding RNA sequences.

Zhang Y, Ponty Y, Blanchette M, Lécuyer E*, Waldispühl J*.

*=co-corresonding authors.

Nucleic Acids Res. 2013, 41(Web Serve r issue): W480-5. PMID: 23748952

The many functions of mRNA localization during normal development and disease: from pillar to post.

Cody NA, Iampietro C, Lécuyer E.

Wiley Interdiscip Rev Dev Biol. 2013, 2: 781-96. PMID: 24123937

Transcriptome-wide regulation of pre-mRNA splicing and mRNA localization by muscleblind proteins.

Wang ET, Cody NA, Jog S, Biancolella M, Wang TT, Treacy DJ, Luo S, Schroth GP, Housman DE, Reddy S, Lécuyer E, Burge CB.

Cell. 2012, 150: 710-24. PMID: 22901804

Global implications of mRNA localization pathways in cellular organization.

Lécuyer E, Yoshida H, Krause HM.

Curr Opin Cell Biol. 2009, 21: 409-15. PMID: 19249199

Global analysis of mRNA localization reveals a prominent role in organizing cellular architecture and function.

Lécuyer E, Yoshida H, Parthasarathy N, Alm C, Babak T, Cerovina T, Hughes TR, Tomancak P, Krause HM.

Cell. 2007, 131: 174-87. PMID: 17923096

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