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Items: 1 to 50 of 97

1.

Neuronal-specific microexon splicing of TAF1 mRNA is directly regulated by SRRM4/nSR100.

Capponi S, Stöffler N, Irimia M, Van Schaik FMA, Ondik MM, Biniossek ML, Lehmann L, Mitschke J, Vermunt MW, Creyghton MP, Graybiel AM, Reinheckel T, Schilling O, Blencowe BJ, Crittenden JR, Timmers HTM.

RNA Biol. 2019 Sep 27:1-13. doi: 10.1080/15476286.2019.1667214. [Epub ahead of print]

PMID:
31559909
2.

Retention of paternal DNA methylome in the developing zebrafish germline.

Skvortsova K, Tarbashevich K, Stehling M, Lister R, Irimia M, Raz E, Bogdanovic O.

Nat Commun. 2019 Jul 11;10(1):3054. doi: 10.1038/s41467-019-10895-6.

3.

Srrm234, but not canonical SR and hnRNP proteins, drive inclusion of Dscam exon 9 variable exons.

Ustaoglu P, Haussmann IU, Liao H, Torres-Mendez A, Arnold R, Irimia M, Soller M.

RNA. 2019 Oct;25(10):1353-1365. doi: 10.1261/rna.071316.119. Epub 2019 Jul 10.

PMID:
31292260
4.

A novel protein domain in an ancestral splicing factor drove the evolution of neural microexons.

Torres-Méndez A, Bonnal S, Marquez Y, Roth J, Iglesias M, Permanyer J, Almudí I, O'Hanlon D, Guitart T, Soller M, Gingras AC, Gebauer F, Rentzsch F, Blencowe BJ, Valcárcel J, Irimia M.

Nat Ecol Evol. 2019 Apr;3(4):691-701. doi: 10.1038/s41559-019-0813-6. Epub 2019 Mar 4.

PMID:
30833759
5.

A novel L1CAM isoform with angiogenic activity generated by NOVA2-mediated alternative splicing.

Angiolini F, Belloni E, Giordano M, Campioni M, Forneris F, Paronetto MP, Lupia M, Brandas C, Pradella D, Di Matteo A, Giampietro C, Jodice G, Luise C, Bertalot G, Freddi S, Malinverno M, Irimia M, Moulton JD, Summerton J, Chiapparino A, Ghilardi C, Giavazzi R, Nyqvist D, Gabellini D, Dejana E, Cavallaro U, Ghigna C.

Elife. 2019 Mar 4;8. pii: e44305. doi: 10.7554/eLife.44305.

6.

ARGLU1 is a transcriptional coactivator and splicing regulator important for stress hormone signaling and development.

Magomedova L, Tiefenbach J, Zilberman E, Le Billan F, Voisin V, Saikali M, Boivin V, Robitaille M, Gueroussov S, Irimia M, Ray D, Patel R, Xu C, Jeyasuria P, Bader GD, Hughes TR, Morris QD, Scott MS, Krause H, Angers S, Blencowe BJ, Cummins CL.

Nucleic Acids Res. 2019 Apr 8;47(6):2856-2870. doi: 10.1093/nar/gkz010.

7.

The Integrator complex regulates differential snRNA processing and fate of adult stem cells in the highly regenerative planarian Schmidtea mediterranea.

Schmidt D, Reuter H, Hüttner K, Ruhe L, Rabert F, Seebeck F, Irimia M, Solana J, Bartscherer K.

PLoS Genet. 2018 Dec 17;14(12):e1007828. doi: 10.1371/journal.pgen.1007828. eCollection 2018 Dec.

8.

Amphioxus functional genomics and the origins of vertebrate gene regulation.

Marlétaz F, Firbas PN, Maeso I, Tena JJ, Bogdanovic O, Perry M, Wyatt CDR, de la Calle-Mustienes E, Bertrand S, Burguera D, Acemel RD, van Heeringen SJ, Naranjo S, Herrera-Ubeda C, Skvortsova K, Jimenez-Gancedo S, Aldea D, Marquez Y, Buono L, Kozmikova I, Permanyer J, Louis A, Albuixech-Crespo B, Le Petillon Y, Leon A, Subirana L, Balwierz PJ, Duckett PE, Farahani E, Aury JM, Mangenot S, Wincker P, Albalat R, Benito-Gutiérrez È, Cañestro C, Castro F, D'Aniello S, Ferrier DEK, Huang S, Laudet V, Marais GAB, Pontarotti P, Schubert M, Seitz H, Somorjai I, Takahashi T, Mirabeau O, Xu A, Yu JK, Carninci P, Martinez-Morales JR, Crollius HR, Kozmik Z, Weirauch MT, Garcia-Fernàndez J, Lister R, Lenhard B, Holland PWH, Escriva H, Gómez-Skarmeta JL, Irimia M.

Nature. 2018 Dec;564(7734):64-70. doi: 10.1038/s41586-018-0734-6. Epub 2018 Nov 21.

9.

Exon Junction Complex Shapes the Transcriptome by Repressing Recursive Splicing.

Blazquez L, Emmett W, Faraway R, Pineda JMB, Bajew S, Gohr A, Haberman N, Sibley CR, Bradley RK, Irimia M, Ule J.

Mol Cell. 2018 Nov 1;72(3):496-509.e9. doi: 10.1016/j.molcel.2018.09.033.

10.

Origin of exon skipping-rich transcriptomes in animals driven by evolution of gene architecture.

Grau-Bové X, Ruiz-Trillo I, Irimia M.

Genome Biol. 2018 Sep 17;19(1):135. doi: 10.1186/s13059-018-1499-9.

11.

Autism-like phenotype and risk gene mRNA deadenylation by CPEB4 mis-splicing.

Parras A, Anta H, Santos-Galindo M, Swarup V, Elorza A, Nieto-González JL, Picó S, Hernández IH, Díaz-Hernández JI, Belloc E, Rodolosse A, Parikshak NN, Peñagarikano O, Fernández-Chacón R, Irimia M, Navarro P, Geschwind DH, Méndez R, Lucas JJ.

Nature. 2018 Aug;560(7719):441-446. doi: 10.1038/s41586-018-0423-5. Epub 2018 Aug 15.

12.

Matt: Unix tools for alternative splicing analysis.

Gohr A, Irimia M.

Bioinformatics. 2019 Jan 1;35(1):130-132. doi: 10.1093/bioinformatics/bty606.

PMID:
30010778
13.

Author Correction: Genome-wide changes in lncRNA, splicing, and regional gene expression patterns in autism.

Parikshak NN, Swarup V, Belgard TG, Irimia M, Ramaswami G, Gandal MJ, Hartl C, Leppa V, de la Torre Ubieta L, Huang J, Lowe JK, Blencowe BJ, Horvath S, Geschwind DH.

Nature. 2018 Aug;560(7718):E30. doi: 10.1038/s41586-018-0295-8.

14.

RES complex is associated with intron definition and required for zebrafish early embryogenesis.

Fernandez JP, Moreno-Mateos MA, Gohr A, Miao L, Chan SH, Irimia M, Giraldez AJ.

PLoS Genet. 2018 Jul 3;14(7):e1007473. doi: 10.1371/journal.pgen.1007473. eCollection 2018 Jul.

15.

Origin and evolution of the chordate central nervous system: insights from amphioxus genoarchitecture.

Albuixech-Crespo B, Herrera-Úbeda C, Marfany G, Irimia M, Garcia-Fernàndez J.

Int J Dev Biol. 2017;61(10-11-12):655-664. doi: 10.1387/ijdb.170258jg. Review.

16.

Absence of Tangentially Migrating Glutamatergic Neurons in the Developing Avian Brain.

García-Moreno F, Anderton E, Jankowska M, Begbie J, Encinas JM, Irimia M, Molnár Z.

Cell Rep. 2018 Jan 2;22(1):96-109. doi: 10.1016/j.celrep.2017.12.032.

17.

Molecular basis of differential 3' splice site sensitivity to anti-tumor drugs targeting U2 snRNP.

Vigevani L, Gohr A, Webb T, Irimia M, Valcárcel J.

Nat Commun. 2017 Dec 13;8(1):2100. doi: 10.1038/s41467-017-02007-z.

18.

Evolutionary recruitment of flexible Esrp-dependent splicing programs into diverse embryonic morphogenetic processes.

Burguera D, Marquez Y, Racioppi C, Permanyer J, Torres-Méndez A, Esposito R, Albuixech-Crespo B, Fanlo L, D'Agostino Y, Gohr A, Navas-Perez E, Riesgo A, Cuomo C, Benvenuto G, Christiaen LA, Martí E, D'Aniello S, Spagnuolo A, Ristoratore F, Arnone MI, Garcia-Fernàndez J, Irimia M.

Nat Commun. 2017 Nov 27;8(1):1799. doi: 10.1038/s41467-017-01961-y.

19.

An atlas of alternative splicing profiles and functional associations reveals new regulatory programs and genes that simultaneously express multiple major isoforms.

Tapial J, Ha KCH, Sterne-Weiler T, Gohr A, Braunschweig U, Hermoso-Pulido A, Quesnel-Vallières M, Permanyer J, Sodaei R, Marquez Y, Cozzuto L, Wang X, Gómez-Velázquez M, Rayon T, Manzanares M, Ponomarenko J, Blencowe BJ, Irimia M.

Genome Res. 2017 Oct;27(10):1759-1768. doi: 10.1101/gr.220962.117. Epub 2017 Aug 30.

20.

Nodal/Activin Pathway is a Conserved Neural Induction Signal in Chordates.

Le Petillon Y, Luxardi G, Scerbo P, Cibois M, Leon A, Subirana L, Irimia M, Kodjabachian L, Escriva H, Bertrand S.

Nat Ecol Evol. 2017 Aug;1(8):1192-1200. doi: 10.1038/s41559-017-0226-3. Epub 2017 Jul 3.

21.

Pica, constipation and cardiorespiratory arrest.

Mourato Nunes I, Pedroso AI, Irimia M, Ramos A.

BMJ Case Rep. 2017 Jul 14;2017. pii: bcr-2017-221066. doi: 10.1136/bcr-2017-221066. No abstract available.

22.

Molecular regionalization of the developing amphioxus neural tube challenges major partitions of the vertebrate brain.

Albuixech-Crespo B, López-Blanch L, Burguera D, Maeso I, Sánchez-Arrones L, Moreno-Bravo JA, Somorjai I, Pascual-Anaya J, Puelles E, Bovolenta P, Garcia-Fernàndez J, Puelles L, Irimia M, Ferran JL.

PLoS Biol. 2017 Apr 19;15(4):e2001573. doi: 10.1371/journal.pbio.2001573. eCollection 2017 Apr.

23.

Major Roles for Pyrimidine Dimers, Nucleotide Excision Repair, and ATR in the Alternative Splicing Response to UV Irradiation.

Muñoz MJ, Nieto Moreno N, Giono LE, Cambindo Botto AE, Dujardin G, Bastianello G, Lavore S, Torres-Méndez A, Menck CFM, Blencowe BJ, Irimia M, Foiani M, Kornblihtt AR.

Cell Rep. 2017 Mar 21;18(12):2868-2879. doi: 10.1016/j.celrep.2017.02.066.

24.

Misregulation of an Activity-Dependent Splicing Network as a Common Mechanism Underlying Autism Spectrum Disorders.

Quesnel-Vallières M, Dargaei Z, Irimia M, Gonatopoulos-Pournatzis T, Ip JY, Wu M, Sterne-Weiler T, Nakagawa S, Woodin MA, Blencowe BJ, Cordes SP.

Mol Cell. 2016 Dec 15;64(6):1023-1034. doi: 10.1016/j.molcel.2016.11.033.

25.

Genome-wide changes in lncRNA, splicing, and regional gene expression patterns in autism.

Parikshak NN, Swarup V, Belgard TG, Irimia M, Ramaswami G, Gandal MJ, Hartl C, Leppa V, Ubieta LT, Huang J, Lowe JK, Blencowe BJ, Horvath S, Geschwind DH.

Nature. 2016 Dec 15;540(7633):423-427. doi: 10.1038/nature20612. Epub 2016 Dec 5. Erratum in: Nature. 2018 Aug;560(7718):E30.

26.

Preferential binding of a stable G3BP ribonucleoprotein complex to intron-retaining transcripts in mouse brain and modulation of their expression in the cerebellum.

Martin S, Bellora N, González-Vallinas J, Irimia M, Chebli K, de Toledo M, Raabe M, Eyras E, Urlaub H, Blencowe BJ, Tazi J.

J Neurochem. 2016 Nov;139(3):349-368. doi: 10.1111/jnc.13768. Epub 2016 Oct 18.

27.

Conserved functional antagonism of CELF and MBNL proteins controls stem cell-specific alternative splicing in planarians.

Solana J, Irimia M, Ayoub S, Orejuela MR, Zywitza V, Jens M, Tapial J, Ray D, Morris Q, Hughes TR, Blencowe BJ, Rajewsky N.

Elife. 2016 Aug 9;5. pii: e16797. doi: 10.7554/eLife.16797.

28.

Evolutionary origin and functional divergence of totipotent cell homeobox genes in eutherian mammals.

Maeso I, Dunwell TL, Wyatt CD, Marlétaz F, Vető B, Bernal JA, Quah S, Irimia M, Holland PW.

BMC Biol. 2016 Jun 13;14:45. doi: 10.1186/s12915-016-0267-0.

29.

Formal linguistics as a cue to demographic history.

Longobardi G, Ceolin A, Ecay A, Ghirotto S, Guardiano C, Irimia MA, Michelioudakis D, Radkevich N, Pettener D, Luiselli D, Barbujani G.

J Anthropol Sci. 2016 Jun 20;94:147-55. doi: 10.4436/JASS.94031. Epub 2015 Apr 11.

30.

Complex transcriptional regulation and independent evolution of fungal-like traits in a relative of animals.

de Mendoza A, Suga H, Permanyer J, Irimia M, Ruiz-Trillo I.

Elife. 2015 Oct 14;4:e08904. doi: 10.7554/eLife.08904.

31.

The alternative splicing factor Nova2 regulates vascular development and lumen formation.

Giampietro C, Deflorian G, Gallo S, Di Matteo A, Pradella D, Bonomi S, Belloni E, Nyqvist D, Quaranta V, Confalonieri S, Bertalot G, Orsenigo F, Pisati F, Ferrero E, Biamonti G, Fredrickx E, Taveggia C, Wyatt CD, Irimia M, Di Fiore PP, Blencowe BJ, Dejana E, Ghigna C.

Nat Commun. 2015 Oct 8;6:8479. doi: 10.1038/ncomms9479.

32.

An alternative splicing event amplifies evolutionary differences between vertebrates.

Gueroussov S, Gonatopoulos-Pournatzis T, Irimia M, Raj B, Lin ZY, Gingras AC, Blencowe BJ.

Science. 2015 Aug 21;349(6250):868-73. doi: 10.1126/science.aaa8381.

33.

Essential roles for the splicing regulator nSR100/SRRM4 during nervous system development.

Quesnel-Vallières M, Irimia M, Cordes SP, Blencowe BJ.

Genes Dev. 2015 Apr 1;29(7):746-59. doi: 10.1101/gad.256115.114.

34.

A highly conserved program of neuronal microexons is misregulated in autistic brains.

Irimia M, Weatheritt RJ, Ellis JD, Parikshak NN, Gonatopoulos-Pournatzis T, Babor M, Quesnel-Vallières M, Tapial J, Raj B, O'Hanlon D, Barrios-Rodiles M, Sternberg MJ, Cordes SP, Roth FP, Wrana JL, Geschwind DH, Blencowe BJ.

Cell. 2014 Dec 18;159(7):1511-23. doi: 10.1016/j.cell.2014.11.035.

35.

Stability depends on positive autoregulation in Boolean gene regulatory networks.

Pinho R, Garcia V, Irimia M, Feldman MW.

PLoS Comput Biol. 2014 Nov 6;10(11):e1003916. doi: 10.1371/journal.pcbi.1003916. eCollection 2014 Nov.

36.

Widespread intron retention in mammals functionally tunes transcriptomes.

Braunschweig U, Barbosa-Morais NL, Pan Q, Nachman EN, Alipanahi B, Gonatopoulos-Pournatzis T, Frey B, Irimia M, Blencowe BJ.

Genome Res. 2014 Nov;24(11):1774-86. doi: 10.1101/gr.177790.114. Epub 2014 Sep 25.

37.

A global regulatory mechanism for activating an exon network required for neurogenesis.

Raj B, Irimia M, Braunschweig U, Sterne-Weiler T, O'Hanlon D, Lin ZY, Chen GI, Easton LE, Ule J, Gingras AC, Eyras E, Blencowe BJ.

Mol Cell. 2014 Oct 2;56(1):90-103. doi: 10.1016/j.molcel.2014.08.011. Epub 2014 Sep 11.

38.

Origin of spliceosomal introns and alternative splicing.

Irimia M, Roy SW.

Cold Spring Harb Perspect Biol. 2014 Jun 2;6(6). pii: a016071. doi: 10.1101/cshperspect.a016071.

39.

[Acute respiratory distress syndrome: case series, two years at an intensive care unit].

Taborda L, Barros F, Fonseca V, Irimia M, Carvalho R, Diogo C, Ramos A.

Acta Med Port. 2014 Mar-Apr;27(2):211-7. Epub 2014 Apr 30. Portuguese.

40.

Functional genomics evidence unearths new moonlighting roles of outer ring coat nucleoporins.

Katsani KR, Irimia M, Karapiperis C, Scouras ZG, Blencowe BJ, Promponas VJ, Ouzounis CA.

Sci Rep. 2014 Apr 11;4:4655. doi: 10.1038/srep04655.

41.

Diversity and evolution of spliceosomal systems.

Roy SW, Irimia M.

Methods Mol Biol. 2014;1126:13-33. doi: 10.1007/978-1-62703-980-2_2.

PMID:
24549653
42.

Elephant shark genome provides unique insights into gnathostome evolution.

Venkatesh B, Lee AP, Ravi V, Maurya AK, Lian MM, Swann JB, Ohta Y, Flajnik MF, Sutoh Y, Kasahara M, Hoon S, Gangu V, Roy SW, Irimia M, Korzh V, Kondrychyn I, Lim ZW, Tay BH, Tohari S, Kong KW, Ho S, Lorente-Galdos B, Quilez J, Marques-Bonet T, Raney BJ, Ingham PW, Tay A, Hillier LW, Minx P, Boehm T, Wilson RK, Brenner S, Warren WC.

Nature. 2014 Jan 9;505(7482):174-9. doi: 10.1038/nature12826. Erratum in: Nature. 2014 Sep 25;513(7519):574.

43.

Regulated aggregative multicellularity in a close unicellular relative of metazoa.

Sebé-Pedrós A, Irimia M, Del Campo J, Parra-Acero H, Russ C, Nusbaum C, Blencowe BJ, Ruiz-Trillo I.

Elife. 2013 Dec 24;2:e01287. doi: 10.7554/eLife.01287.

44.

Deep conservation of cis-regulatory elements in metazoans.

Maeso I, Irimia M, Tena JJ, Casares F, Gómez-Skarmeta JL.

Philos Trans R Soc Lond B Biol Sci. 2013 Nov 11;368(1632):20130020. doi: 10.1098/rstb.2013.0020. Print 2013 Dec 19. Review.

45.

MBNL1 and RBFOX2 cooperate to establish a splicing programme involved in pluripotent stem cell differentiation.

Venables JP, Lapasset L, Gadea G, Fort P, Klinck R, Irimia M, Vignal E, Thibault P, Prinos P, Chabot B, Abou Elela S, Roux P, Lemaitre JM, Tazi J.

Nat Commun. 2013;4:2480. doi: 10.1038/ncomms3480.

PMID:
24048253
46.

A compendium of RNA-binding motifs for decoding gene regulation.

Ray D, Kazan H, Cook KB, Weirauch MT, Najafabadi HS, Li X, Gueroussov S, Albu M, Zheng H, Yang A, Na H, Irimia M, Matzat LH, Dale RK, Smith SA, Yarosh CA, Kelly SM, Nabet B, Mecenas D, Li W, Laishram RS, Qiao M, Lipshitz HD, Piano F, Corbett AH, Carstens RP, Frey BJ, Anderson RA, Lynch KW, Penalva LO, Lei EP, Fraser AG, Blencowe BJ, Morris QD, Hughes TR.

Nature. 2013 Jul 11;499(7457):172-7. doi: 10.1038/nature12311.

47.

Ancient cis-regulatory constraints and the evolution of genome architecture.

Irimia M, Maeso I, Roy SW, Fraser HB.

Trends Genet. 2013 Sep;29(9):521-8. doi: 10.1016/j.tig.2013.05.008. Epub 2013 Jun 18. Review.

PMID:
23791467
48.

MBNL proteins repress ES-cell-specific alternative splicing and reprogramming.

Han H, Irimia M, Ross PJ, Sung HK, Alipanahi B, David L, Golipour A, Gabut M, Michael IP, Nachman EN, Wang E, Trcka D, Thompson T, O'Hanlon D, Slobodeniuc V, Barbosa-Morais NL, Burge CB, Moffat J, Frey BJ, Nagy A, Ellis J, Wrana JL, Blencowe BJ.

Nature. 2013 Jun 13;498(7453):241-5. doi: 10.1038/nature12270. Epub 2013 Jun 5.

49.

Distinct types of disorder in the human proteome: functional implications for alternative splicing.

Colak R, Kim T, Michaut M, Sun M, Irimia M, Bellay J, Myers CL, Blencowe BJ, Kim PM.

PLoS Comput Biol. 2013 Apr;9(4):e1003030. doi: 10.1371/journal.pcbi.1003030. Epub 2013 Apr 25.

50.

Genome of Acanthamoeba castellanii highlights extensive lateral gene transfer and early evolution of tyrosine kinase signaling.

Clarke M, Lohan AJ, Liu B, Lagkouvardos I, Roy S, Zafar N, Bertelli C, Schilde C, Kianianmomeni A, Bürglin TR, Frech C, Turcotte B, Kopec KO, Synnott JM, Choo C, Paponov I, Finkler A, Heng Tan CS, Hutchins AP, Weinmeier T, Rattei T, Chu JS, Gimenez G, Irimia M, Rigden DJ, Fitzpatrick DA, Lorenzo-Morales J, Bateman A, Chiu CH, Tang P, Hegemann P, Fromm H, Raoult D, Greub G, Miranda-Saavedra D, Chen N, Nash P, Ginger ML, Horn M, Schaap P, Caler L, Loftus BJ.

Genome Biol. 2013 Feb 1;14(2):R11. doi: 10.1186/gb-2013-14-2-r11.

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