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U12splicing wiki (internal)

Viikki Biocenter

Institute of Biotechnology

University of Helsinki

Publications

Full list and citation data:
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2018

Oghabian, A. Greco, D. & Frilander, M.J. (2018). IntEREst: Intron-Exon Retention Estimator.
BMC Bioinformatics, 19:130. Software available at Bioconductor and GitHub

Norppa, A.J., Kauppala, T.M., Heikkinen, H.A.,Verma, B., Iwaï, H. & Frilander, M.J. (2018). Mutations in the U11/U12-65K protein associated with isolated growth hormone deficiency lead to structural destabilization and impaired binding of U12 snRNA.
RNA, 24: 396-409.

Jutzi, D., Akinyi, M.V., Mechtersheimer, J., Frilander, M.J. & Ruepp M.-D. (2018). The emerging role of minor intron splicing in neurological disorders.
Cell Stress, 2:40-54

Verma, B., Norppa, A.J., Akinyi, M.V. & Frilander, M.J. (2018). Minor spliceosome and disease.
Seminars in Cell and Developmental Biology, 79:103-112

Martos-Moreno, G.Á., Travieso-Suárez, L., Pozo-Román, J., Muñoz-Calvo, M.T., Chowen, J.A., Frilander, M.J., Pérez-Jurado, L.A., Hawkins, F.G., and Argente, J.(2018). Response to growth hormone in patients with RNPC3 mutations.
EMBO Molecular Medicinde, in press.

Orsini L, Brown J.B., Solari O.S., Li D., He S., Podicheti R., Stoiber M.H., Spanier K.I., Gilbert D., Jansen M., Rusch D., Pfrender M.E, Colbourne J.K., Frilander M.J., Kvist J., Decaestecker E., De Schamphelaere K.A.C, De Meester L. (2018). Early transcriptional response pathways in Daphnia magna are coordinated in networks of crustacean specific genes.
Molecular ecology, 27(4):886-897. (See a Perspective by Stanford & Rogers).

2017

Verbeeren, J., Verma, B., Niemelä, E.H., Yap, K., Makeyev, E.V., and Frilander, M.J. (2017). Alternative exon definition events control the choice between nuclear retention and cytoplasmic export of U11/U12-65K mRNA.
PLoS Genetics, 13(5): e1006824.

Susi, H., Laine, A.-L., Filloux, D., Kraberger, S., Farkas, K., Bernardo, P., Frilander, M.J., Martin, D.P., Varsani, A., and Roumagnac, P. (2017). Genome sequences of a capulavirus infecting Plantago lanceolata in the Åland archipelago of Finland.
Archives of Virology 162:2041–2045.

Ahola, V., Wahlberg, N. & Frilander, M. J. (2017): Butterfly genomics: insights from the genome of Melitaea cinxia.
.Annales Zoologici Fennici 54: 275–291.

2016

Orsini, L., Gilbert, D., Podicheti, R., Jansen, M., Brown, J.B., Solari, O.S., Spanier, K.I., Colbourne, J.K., Rush, D., Decaestecker, E., Asselman, J., De Schamphelaere, K.A.C., Ebert, D., Haag, C.R., Kvist, J., Laforsch, C., Petrusek, A., Beckerman, A.P., Little, T.J., Chaturvedi, A., Pfrender, M.E., De Meester, L., and Frilander, M.J. (2016). Daphnia magna transcriptome by RNA-Seq across 12 environmental stressors.
Scientific Data 3:160030.

Känsäkoski J, Jääskeläinen J, Jääskeläinen T, Tommiska J, Saarinen L, Lehtonen R, Hautaniemi S, Frilander MJ, Palvimo JJ, Toppari J, and Raivio T (2016). Complete androgen insensitivity syndrome caused by a deep intronic pseudoexon-activating mutation in the androgen receptor gene.
Scientific Reports 6:32819
.

2015

Niemelä E.H., Verbeeren, J., Singha, P., Nurmi V. and Frilander, M.J. (2015). Evolutionarily conserved exon definition interactions with U11 snRNP mediate alternative splicing regulation on U11-48K and U11/U12-65K genes.
RNA Biology, 12:1256-1264.

Kvist J., Mattila A.L.K., Somervuo P., Ahola V., Koskinen P., Paulin L., Salmela L., Taipale M., Holm L., Auvinen P., Lehtonen R., Frilander M.J, Hanski I. (2015). Flight-induced changes in gene expression in the Glanville fritillary butterfly.
Molecular Ecology, 24:4886–4900.

Ahola V., Koskinen P., Wong S.C., Kvist J., Paulin L, Auvinen P., Saastamoinen M., Frilander M.J., Lehtonen R., Hanski I. (2015). Temperature and sex related effects of serine protease alleles on larval development in the Glanville fritillary butterfly.
Journal of Evolutionary Biology, 28:2224-2235

2014

Argente, J., Flores, R., Gutiérrez-Arumí, A., Verma, B., Martos-Moreno, G.A., Cuscó, I., Oghabian, A., Chowen, J.A., Frilander, M.J., and Pérez-Jurado, L.A. (2014). Defective minor spliceosome mRNA processing results in isolated familial growth hormone deficiency.
EMBO Molecular Medicine, 6:299–306

Niemelä, E.H., Frilander, M.J. (2014). Regulation of gene expression through inefficient splicing of U12-type introns.
RNA Biology 11: 1325-1329.

Niemelä, E.H., Oghabian, A., Staals, R.H.J., Pruijn, G. and Frilander, M.J. (2014) Global analysis of the nuclear processing of unspliced U12-type introns by the exosome.
Nucleic Acids Research, 42:7358-7369.

Mikkilä, J., Eskelinen, A.-P., Niemelä, E.H., Linko, V., Frilander, M.J., Törmä, P., and Kostiainen, M.A. (2014). Virus-Encapsulated DNA Origami Nanostructures for Cellular Delivery.
Nano Letters, 14:2196–2200.

Turunen, J.J., Pavlova, L.V., Hengesbach, M., Helm, M., Müller, S., Hartmann, R.K. and Frilander, M.J. (2014) RNA ligation. In Hartmann, R. K., Bindereif, A., Schön, A. and Westhof, E. (eds.),
Handbook of RNA biochemistry. 2nd ed. Wiley-VCH GmbH & Co. KGA, Weinheim, Vol. 1, pp. 45-88.

Somervuo P., Kvist J., Ikonen S., Ahonla V., Auvinen P., Paulin L., Koskinen P., Holm L., Taipale M., Ruokolainen A., Saarnio S., Taipale J., Sirén J., Corander J., Frilander M.J., Lehtonen R. & Hanski I. (2014) Transcriptome Analysis Reveals Signature of Adaptation to Landscape Fragmentation.
PLoS ONE, 9(7):e104668.

Ahola V., Lehtonen R., Somervuo P., Salmela L., Koskinen P., Rastas P., Välimäki N., Paulin L., Kvist J., Wahlberg N., Tanskanen J., Hornett E.A., Ferguson L.C., Luo S., Cao Z., de Jong M.A., Duplouy A., Smolander O-P., Vogel H., McCoy R.C., Qian K., Chong W.S., Zhang Q., Ahmad F., Haukka J.K., Josh A., Salojärvi J., Wheat C.W., Grosse-Wilde E., Hughes D., Katainen R., Pitkänen E., Ylinen J., Waterhouse R.M., Turunen M., Vähärautio A., Schulman A.H., Taipale M., Lawson D., Ukkonen E., Mäkinen V., Goldsmith M.R., Holm L., Auvinen P., Frilander M.J. & Hanski I. (2014). The Glanville fritillary genome retains an ancient karyotype and reveals selective chromosomal fusions in Lepidoptera.
Nature Communications, 5:4737
.

2013

Turunen, J.J., Verma, B., Nyman, T.A., and Frilander, M.J. (2013). HnRNPH1/H2, U1 snRNP and U11 snRNP co-operate to regulate the stability of the U11-48K pre-mRNA.
RNA, 19:380-389

Turunen, J.J., Niemelä, E., Verma, B., and Frilander, M.J. (2013). The significant other: Splicing by the Minor Spliceosome.
Wiley Interdisciplinary Reviews - RNA, 4:61-76.
Among the Top10 WIRES-RNA articles!
Download pdf reprint

Qian, K., Pietilä, T., Rönty, M., Michon, F., Frilander, M.J., Ritari, J., Tarkkanen, J., Paulín, L., Auvinen, P., and Auvinen, E. (2013). Identification and Validation of Human Papillomavirus Encoded microRNAs.
PLoS ONE , 8(7):e70202.

Kvist J., Wheat C.W., Kallioniemi E., Saastamoinen M., Hanski I. & Frilander M.J. (2013). Temperature treatments during larval development reveal extensive heritable and plastic variation in gene expression and life history traits.
Molecular Ecology, 22:602–619

2012

Tollenaere, C., Susi, H., Nokso-Koivisto, J., Koskinen, P. Tack, A. J. M., Auvinen, P. Paulin, L., Frilander, M. J., Lehtonen, R. & Laine, A.-L. (2012). SNP Design from 454 Sequencing of Podosphaera plantaginis Transcriptome Reveals a Genetically Diverse Pathogen Metapopulation with High Levels of Mixed-Genotype Infection.
PLoS ONE, 7(12): e52492.

2011

Pessa, H.K.J. & Frilander, M.J. (2011). Minor Splicing, Disrupted.
Science, 332:184-185. (Perspective). Download pdf reprint.

Helenius K, Yang Y, Tselykh TV, Pessa HK, Frilander MJ, Mäkelä TP. (2011). Requirement of TFIIH kinase subunit Mat1 for RNA Pol II C-terminal domain Ser5 phosphorylation, transcription and mRNA turnover.
Nucleic Acids Research, 39:5025-5035.

Saarikangas J, Mattila PK, Varjosalo M, Bovellan M, Hakanen J, Calzada-Wack J, Tost M, Jennen L, Rathkolb B, Hans W, Horsch M, Hyvönen ME, Perälä N, Fuchs H, Gailus-Durner V, Esposito I, Wolf E, de Angelis MH, Frilander MJ, Savilahti H, Sariola H, Sainio K, Lehtonen S, Taipale J, Salminen M, Lappalainen P. (2011). Missing-in-metastasis MIM/MTSS1 promotes actin assembly at intercellular junctions and is required for integrity of kidney epithelia.
Journal of Cell Science, 124:1245-1255.

Wheat CW, Fescemyer HW, Kvist J, Tas E, Vera JC, Frilander MJ, Hanski I, Marden JH. (2011). Functional genomics of life history variation in a butterfly metapopulation.
Molecular Ecology, 20:1813-1828. (See a Perspective by Klepsatel & Flatt).

2010

Verbeeren J., Niemelä E.H., Turunen J.J., Will C.L., Ravantti J.J., Lührmann R. & Frilander M.J. (2010). An ancient mechanism for splicing control: U11 snRNP as an activator of alternative splicing.
Molecular Cell, 37:821-833.

Pessa, H.K.J., Greco D., Kvist J., Wahlström G., Heino T.I., Auvinen P. & Frilander M.J. (2010). Gene Expression Profiling of U12-Type Spliceosome Mutant Drosophila Reveals Widespread Changes in Metabolic Pathways.
PLoS ONE, 5(10): e13215.

Michon F., Kyyrönen M., Tummers M., Frilander M.J. & Thesleff I. (2010).Tooth morphogenesis and ameloblast differentiation are regulated by micro-RNAs.
Developmental Biology, 340:355-368.

Wheat C.W., Haag C., Marden J., Hanski I. & Frilander M.J. (2010). Molecular evidence for balancing selection at a candidate gene (Pgi) influencing ecological dynamics in a butterfly metapopulation.
Molecular Biology and Evolution, 27:267-281.

2009

Sundström J.F., Vaculova A., Smertenko A.P., Savenkov E.I., Golovko A., Minina E., Tiwari B.S., Rodriguez-Nieto S., Zamyatnin A.A. Jr., Välineva T., Saarikettu J., Frilander M.J., Suarez M.F., Zavialov A., Ståhl U., Hussey P.J., Silvennoinen O., Sundberg E., Zhivotovsky B. & Bozhkov P.V. (2009). Tudor staphylococcal nuclease is an evolutionarily conserved component of the programmed cell death degradome.
Nature Cell Biology, 11:1347-1354.

Orsini L., Wheat C.W., Haag C.R., Kvist J., Frilander M.J. & Hanski, I. (2009). Fitness differences associated with Pgi SNP genotypes in the Glanville fritillary butterfly (Melitaea cinxia).
Journal of Evolutionary Biology, 22:367-375.

2008

Pessa, H.K.J., Will, C.L., Meng, X., Schneider, C., Watkins, N.J., Perälä, N., Nymark, M., Turunen, J.J., Lührmann, R. & Frilander, M.J. (2008). Minor spliceosome components are predominantly localized in the nucleus.
PNAS, 105: 8655-8660.    (See a Commentary by Joan Steitz et al.).

Turunen J.J., Will C.L., Grote M., Lührmann R. & Frilander M.J. (2008). The U11-48K protein contacts the 5' splice site of U12-type introns and the U11-59K protein.
Molecular and Cellular Biology, 28:3548-3560.

Paatero A.O., Turakainen H., Happonen L.J., Olsson C., Palomäki T., Pajunen M.I., Meng X., Otonkoski T., Tuuri T., Berry C., Malani N., Frilander M.J., Bushman F.D. & Savilahti H. (2008). Bacteriophage Mu integration in yeast and mammalian genomes.
Nucleic Acids Research, 36:e148.

Marden J.H., Fescemyer H.W., Saastamoinen M., MacFarland S.P., Vera J.C., Frilander M.J., & Hanski I. (2008). Weight and nutrition affect pre-mRNA splicing associated with energetics and life history.
Journal of Experimental Biology, 211:3653-3660.

Vera J.C., Wheat C.W., Fescemyer H.W., Frilander M.J.,Crawford D.L., Hanski I. & Marden J.H. (2008). Rapid transcriptome characterization for a non-model organism using massively parallel 454 pyrosequencing.
Molecular Ecology, 17:1636-1647 (See a Perspective by Hans Ellegren).

2007

Yang, J., Välineva, T., Hong, J., Bu, T., Yao, Z. Jensen, O.N., Frilander, M.J. & Silvennoinen, O. (2007). Transcriptional coactivator protein p100 interacts with snRNP proteins and facilitates the assembly of the spliceosome,
Nucleic Acids Research, 35:4485-4494.

2006

Pessa, H.K.J, Ruokolainen, A., & Frilander M.J. (2006). The abundance of the spliceosomal snRNPs is not limiting the splicing of U12-type introns,
RNA, 12:1883-1892.

2005

Frilander, M.J. & Meng, X. (2005). Proximity of the U12 snRNA with both the 5' splice site and the branch point during early stages of spliceosome assembly,
Molecular and Cellular Biology, 25:4813-4825.

Frilander, M.J. & Turunen J.J. (2005). RNA ligation by T4 DNA ligase. In Handbook of RNA biochemistry (Bindereif, A, Hartmann, R, Schön, A, & Westhof, E. Eds.), pp. 36-52. ISBN 3-527-30826-1. Wiley_VCH, Weinheim, Germany.

2004

Schneider, C., Will, C.L., Watkins, N.J., Brosius, J, Frilander, M.J. & Lührmann, R. (2004). Identification of an evolutionarily divergent U11 small nuclear ribonucleoprotein particle in Drosophila.
PNAS, 101: 9584-9589.

2002

Pirttimaa, M.J., Paatero, A.O., Frilander, M.J., & Bamford, D.H. (2002). Nonspecific NTPase P4 of dsRNA bacteriophage phi6 is required for ssRNA packaging and transcription.
Journal of Virology, 76: 10122-10127.

McConnell, T.S., Cho, S.J., Frilander, M.J. & Steitz, J.A. (2002). Branch point selection in the splicing of U12-dependent introns in vitro.
RNA, 8:579-586.

2001

Frilander, M.J. & Steitz, J.A. (2001). Dynamic exchanges of RNA interactions leading to catalytic core formation in the U12-dependent spliceosome.
Molecular Cell, 7:217-226.

1999

Frilander, M.J. & Steitz, J.A. (1999). Initial recognition of U12-dependent introns requires both U11/5' splice site and U12/branchpoint interactions.
Genes & Development, 13:851-863.



Other

Frilander, M.J. Ribosomi osoittautui RNA-entsyymiksi. (2001). Duodecim, 117, 7-8 (Editorial in Finnish).

Frilander M.J. RNA - elämän alkuperän kemia (2002). Duodecim, 118:2419-2422. (Review in Finnish).

Mikko Frilander & Reetta Kettunen. Vieraskynä: Hiiren perimä kertoo yhtä lailla ihmisestä. Helsingin sanomat 27.12. 2002 (Editorial in a national newspaper)

Sariola H., Frilander M., Heino T., Jernvall J., Partanen J., Sainio K., Salminen M. & Thesleff I. (2003). Kehitysbiologia: Solusta yksilöksi. Kustannus Oy Duodecim, Helsinki. 311 pages. ISBN 951-656-099-7. (Developmental biology textbook in Finnish).

Frilander M. J. (2006). DNA ja geenisäätelyn periaatteet. In Perinnöllisyyslääketiede (P. Aula, H. Kääriäinen and A. Palotie ed.). Vol 3, pp. 1-30. Kustannus Oy Duodecim, Helsinki, Finland. (A chapter in a medical genetic textbook).

Frilander M.J. (2008). Täpläverkkoperhonen liiti genomiaikaan. Duodecim, 124, 2242-2243.

Frilander M.J. (2009). Kemian Nobel-palkinto ribosomien rakenteen selvittäjille. Duodecim, 125, 2476-2477.