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Thomas Blumenthal
Department of Molecular, Cellular, and Developmental Biology, University of Colorado, Boulder, United States of America

Faculty Member: DEVELOPMENTAL BIOLOGY > Developmental molecular mechanisms [ since 5 July 2001 ]
[ Biography ] [ Homepage ] [ Evaluations ]
Biography

Tom Blumenthal received his PhD in Genetics from Johns Hopkins in 1970, where he worked on bacteriophage. He was a Whitney Foundation postdoc with James Watson at Harvard, where he showed that bacteriophage QB replicase contains protein synthesis elongation factors. In 1973, he became an Assistant Professor at Indiana University, where he remained until 1996, rising through the ranks to professor and Chairman of Biological Sciences. In 1980, as a Guggenheim fellow, he did a sabbatical with Sydney Brenner at the MRC in Cambridge, where he began work on C. elegans. He studied developmental gene regulation and later began his current projects on mechanisms of trans-splicing and chromosomal gene organization. In 1993 he did a sabbatical with Barbara Meyer in Berkeley where he worked on C. elegans 3? splice site recognition. In 1997, he moved to the University of Colorado School of Medicine as chairman of Biochemistry and Molecular Genetics. In 2006, he moved to the University of Colorado at Boulder where he is Chair of Molecular, Cellular, and Developmental Biology.

Home page

http://mcdb.colorado.edu/faculty/blumenthal.htm

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Evaluations

Splicing promotes rapid and efficient mRNA export in mammalian cells.
Valencia P, Dias AP, Reed R
Proc Natl Acad Sci U S A 2008 Mar 4 105(9):3386-91 [abstract on PubMed] [related articles] [full text] [order article]
Selected by | Thomas Blumenthal
Evaluated 19 Mar 2008

DEPS-1 promotes P-granule assembly and RNA interference in C. elegans germ cells.
Spike CA, Bader J, Reinke V, Strome S
Development 2008 Mar 135(5):983-93 [abstract on PubMed] [related articles] [full text] [order article]
Selected by | Thomas Blumenthal
Evaluated 17 Mar 2008

Spliced leader trans-splicing in the nematode Trichinella spiralis uses highly polymorphic, noncanonical spliced leaders.
Pettitt J, Müller B, Stansfield I, Connolly B
RNA 2008 Feb 6 [abstract on PubMed] [related articles] [full text]
Selected by | Thomas Blumenthal
Evaluated 17 Mar 2008

Control of pre-mRNA splicing by the general splicing factors PUF60 and U2AF65.
Hastings ML, Allemand E, …, Myers MP, Krainer AR
PLoS ONE 2007 2(6):e538 [abstract on PubMed] [related articles] [FREE full text]
Selected by | Thomas Blumenthal
Evaluated 17 Mar 2008

Transcription-dependent gene looping of the HIV-1 provirus is dictated by recognition of pre-mRNA processing signals.
Perkins KJ, Lusic M, …, Giacca M, Proudfoot NJ
Mol Cell 2008 Jan 18 29(1):56-68 [abstract on PubMed] [related articles] [FREE full text]
Selected by | Thomas Blumenthal
Evaluated 17 Mar 2008

Evolutionary dynamics of nematode operons: Easy come, slow go.
Qian W, Zhang J
Genome Res 2008 Mar 18(3):412-21 [abstract on PubMed] [related articles] [full text] [order article]
Selected by | Thomas Blumenthal
Evaluated 14 Mar 2008

STAR family RNA-binding protein ASD-2 regulates developmental switching of mutually exclusive alternative splicing in vivo.
Ohno G, Hagiwara M, Kuroyanagi H
Genes Dev 2008 Feb 1 22(3):360-74 [abstract on PubMed] [related articles] [full text] [order article]
Selected by | Thomas Blumenthal
Evaluated 14 Mar 2008

Splicing factors SF1 and U2AF associate in extra-spliceosomal complexes.
Rino J, Desterro JM, …, Gadella TW, Carmo-Fonseca M
Mol Cell Biol 2008 Feb 19 [abstract on PubMed] [related articles] [full text]
Selected by | Thomas Blumenthal
Evaluated 14 Mar 2008

The multifunctional protein p54nrb/PSF recruits the exonuclease XRN2 to facilitate pre-mRNA 3' processing and transcription termination.
Kaneko S, Rozenblatt-Rosen O, Meyerson M, Manley JL
Genes Dev 2007 Jul 15 21(14):1779-89 [abstract on PubMed] [related articles] [full text] [order article]
Selected by | Thomas Blumenthal
Evaluated 14 Mar 2008

Splicing factors stimulate polyadenylation via USEs at non-canonical 3' end formation signals.
Danckwardt S, Kaufmann I, …, Hentze MW, Kulozik AE
EMBO J 2007 Jun 6 26(11):2658-69 [abstract on PubMed] [related articles] [full text] [order article]
Selected by | Thomas Blumenthal
Evaluated 22 May 2007

The bursicon gene in mosquitoes: an unusual example of mRNA trans-splicing.
Robertson HM, Navik JA, Walden KK, Honegger HW
Genetics 2007 Jun 176(2):1351-3 [abstract on PubMed] [related articles] [FREE full text]
Selected by | Thomas Blumenthal
Evaluated 22 May 2007

Mutations in the SF1-U2AF59-U2AF23 complex cause exon skipping in Schizosaccharomyces pombe.
Haraguchi N, Andoh T, Frendewey D, Tani T
J Biol Chem 2007 Jan 26 282(4):2221-8 [abstract on PubMed] [related articles] [full text] [order article]
Selected by | Thomas Blumenthal
Evaluated 4 Apr 2007

Clustered DNA motifs mark X chromosomes for repression by a dosage compensation complex.
McDonel P, Jans J, Peterson BK, Meyer BJ
Nature 2006 Nov 30 444(7119):614-8 [abstract on PubMed] [related articles] [full text] [order article]
Selected by | Thomas Blumenthal
Evaluated 6 Dec 2006

Operon conservation and the evolution of trans-splicing in the phylum Nematoda.
Guiliano DB, Blaxter ML
PLoS Genet 2006 Nov 24 2(11):e198 [abstract on PubMed] [related articles] [FREE full text]
Selected by | Thomas Blumenthal / Helen Chamberlin
Evaluated 6 Dec 2006

Genomic overview of mRNA 5'-leader trans-splicing in the ascidian Ciona intestinalis.
Satou Y, Hamaguchi M, …, Hastings KE, Satoh N
Nucleic Acids Res 2006 34(11):3378-88 [abstract on PubMed] [related articles] [FREE full text]
Selected by | Thomas Blumenthal
Evaluated 30 Nov 2006

Sm core variation in spliceosomal small nuclear ribonucleoproteins from Trypanosoma brucei.
Wang P, Palfi Z, …, Kambach C, Bindereif A
EMBO J 2006 Oct 4 25(19):4513-23 [abstract on PubMed] [related articles] [FREE full text]
Selected by | Kiyoshi Nagai / Thomas Blumenthal
Evaluated 30 Nov 2006

An interaction between U2AF 65 and CF I(m) links the splicing and 3' end processing machineries.
Millevoi S, Loulergue C, …, Antoniou M, Vagner S
EMBO J 2006 Oct 18 25(20):4854-64 [abstract on PubMed] [related articles] [FREE full text]
Selected by | Thomas Blumenthal / Lynne Maquat
Evaluated 30 Nov 2006

Conservation and functional significance of gene topology in the genome of Caenorhabditis elegans.
Chen N, Stein LD
Genome Res 2006 May 16(5):606-17 [abstract on PubMed] [related articles] [FREE full text]
Selected by | Thomas Blumenthal
Evaluated 18 May 2006

Effective translation of the second cistron in two Drosophila dicistronic transcripts is determined by the absence of in-frame AUG codons in the first cistron.
Wall AA, Phillips AM, Kelly LE
J Biol Chem 2005 Jul 29 280(30):27670-8 [abstract on PubMed] [related articles] [FREE full text]
Selected by | Thomas Blumenthal
Evaluated 17 May 2006

The snoRNA HBII-52 regulates alternative splicing of the serotonin receptor 2C.
Kishore S, Stamm S
Science 2006 Jan 13 311(5758):230-2 [abstract on PubMed] [related articles] [FREE full text]
Selected by | Thomas Blumenthal / James Gusella / Tom Misteli / Andrea Barta / Laurence H. Tecott
Evaluated 26 Jan 2006

Polypyrimidine tract binding protein blocks the 5' splice site-dependent assembly of U2AF and the prespliceosomal E complex.
Sharma S, Falick AM, Black DL
Mol Cell 2005 Aug 19 19(4):485-96 [abstract on PubMed] [related articles] [FREE full text]
Selected by | Thomas Blumenthal / Samuel Gunderson
Evaluated 19 Sep 2005

Delay in synthesis of the 3' splice site promotes trans-splicing of the preceding 5' splice site.
Takahara T, Tasic B, …, Akanuma H, Yanagisawa S
Mol Cell 2005 Apr 15 18(2):245-51 [abstract on PubMed] [related articles] [full text] [order article]
Selected by | Thomas Blumenthal
Evaluated 10 Aug 2005

Exploring functional relationships between components of the gene expression machinery.
Burckin T, Nagel R, …, Hartzog G, Ares M
Nat Struct Mol Biol 2005 Feb 12(2):175-82 [abstract on PubMed] [related articles] [full text] [order article]
Selected by | Thomas Blumenthal
Evaluated 7 Apr 2005

Newly Initiated RNA encounters a factor involved in splicing immediately upon emerging from within RNA polymerase II.
Ujvári A, Luse DS
J Biol Chem 2004 Nov 26 279(48):49773-9 [abstract on PubMed] [related articles] [FREE full text]
Selected by | Thomas Blumenthal / Charles Query
Evaluated 7 Apr 2005

Steroid hormone receptor coactivation and alternative RNA splicing by U2AF65-related proteins CAPERalpha and CAPERbeta.
Dowhan DH, Hong EP, …, Berget SM, O'Malley BW
Mol Cell 2005 Feb 4 17(3):429-39 [abstract on PubMed] [related articles] [full text] [order article]
Selected by | Thomas Blumenthal
Evaluated 6 Apr 2005

A novel method for accurate operon predictions in all sequenced prokaryotes.
Price MN, Huang KH, Alm EJ, Arkin AP
Nucleic Acids Res 2005 33(3):880-92 [abstract on PubMed] [related articles] [FREE full text]
Selected by | Thomas Blumenthal
Evaluated 6 Apr 2005

Spliced leader RNA-mediated trans-splicing in phylum Rotifera.
Pouchkina-Stantcheva NN, Tunnacliffe A
Mol Biol Evol 2005 Jun 22(6):1482-9 [abstract on PubMed] [related articles] [FREE full text]
Selected by | Thomas Blumenthal
Evaluated 5 Apr 2005

Splicing of U12-type introns deposits an exon junction complex competent to induce nonsense-mediated mRNA decay.
Hirose T, Shu MD, Steitz JA
Proc Natl Acad Sci U S A 2004 Dec 28 101(52):17976-81 [abstract on PubMed] [related articles] [FREE full text]
Selected by | Thomas Blumenthal
Evaluated 5 Apr 2005

Novel and essential subunits in the 300-kilodalton nuclear cap binding complex of Trypanosoma brucei.
Li H, Tschudi C
Mol Cell Biol 2005 Mar 25(6):2216-26 [abstract on PubMed] [related articles] [FREE full text]
Selected by | Thomas Blumenthal
Evaluated 5 Apr 2005

Spliced-leader RNA trans splicing in a chordate, Oikopleura dioica, with a compact genome.
Ganot P, Kallesøe T, …, Chourrout D, Thompson EM
Mol Cell Biol 2004 Sep 24(17):7795-805 [abstract on PubMed] [related articles] [FREE full text]
Selected by | Thomas Blumenthal
Evaluated 20 Sep 2004

Genetic suppression of intronic +1G mutations by compensatory U1 snRNA changes in Caenorhabditis elegans.
Zahler AM, Tuttle JD, Chisholm AD
Genetics 2004 Aug 167(4):1689-96 [abstract on PubMed] [related articles] [FREE full text]
Selected by | Thomas Blumenthal
Evaluated 20 Sep 2004

Trans-splicing and polyadenylation of let-7 microRNA primary transcripts.
Bracht J, Hunter S, …, Weeks P, Pasquinelli AE
RNA 2004 Oct 10(10):1586-94 [abstract on PubMed] [related articles] [FREE full text]
Selected by | Thomas Blumenthal / Elsebet Lund
Evaluated 20 Sep 2004

A probabilistic model of 3' end formation in Caenorhabditis elegans.
Hajarnavis A, Korf I, Durbin R
Nucleic Acids Res 2004 32(11):3392-9 [abstract on PubMed] [related articles] [FREE full text]
Selected by | Thomas Blumenthal
Evaluated 31 Aug 2004

Human Fip1 is a subunit of CPSF that binds to U-rich RNA elements and stimulates poly(A) polymerase.
Kaufmann I, Martin G, …, Langen H, Keller W
EMBO J 2004 Feb 11 23(3):616-26 [abstract on PubMed] [related articles] [FREE full text]
Selected by | Thomas Blumenthal
Evaluated 12 Feb 2004

Operon structure and trans-splicing in the nematode Pristionchus pacificus.
Lee KZ, Sommer RJ
Mol Biol Evol 2003 Dec 20(12):2097-103 [abstract on PubMed] [related articles] [FREE full text]
Selected by | Thomas Blumenthal
Evaluated 28 Jan 2004

Alternative trans-splicing of constant and variable exons of a Drosophila axon guidance gene, lola.
Horiuchi T, Giniger E, Aigaki T
Genes Dev 2003 Oct 15 17(20):2496-501 [abstract on PubMed] [related articles] [FREE full text]
Selected by | Richard L. Stevens / Thomas Blumenthal
Evaluated 28 Jan 2004

Extensive exon reshuffling over evolutionary time coupled to trans-splicing in Drosophila.
Labrador M, Corces VG
Genome Res 2003 Oct 13(10):2220-8 [abstract on PubMed] [related articles] [FREE full text]
Selected by | Thomas Blumenthal
Evaluated 28 Jan 2004

Intrinsic differences between authentic and cryptic 5' splice sites.
Roca X, Sachidanandam R, Krainer AR
Nucleic Acids Res 2003 Nov 1 31(21):6321-33 [abstract on PubMed] [related articles] [FREE full text]
Selected by | Thomas Blumenthal
Evaluated 28 Jan 2004

Human immunodeficiency virus type 1 hnRNP A/B-dependent exonic splicing silencer ESSV antagonizes binding of U2AF65 to viral polypyrimidine tracts.
Domsic JK, Wang Y, …, Krainer AR, Stoltzfus CM
Mol Cell Biol 2003 Dec 23(23):8762-72 [abstract on PubMed] [related articles] [FREE full text]
Selected by | Thomas Blumenthal
Evaluated 28 Jan 2004

Protein composition of human prespliceosomes isolated by a tobramycin affinity-selection method.
Hartmuth K, Urlaub H, …, Wilm M, Lührmann R
Proc Natl Acad Sci U S A 2002 Dec 24 99(26):16719-24 [abstract on PubMed] [related articles] [FREE full text]
Selected by | Thomas Blumenthal
Evaluated 20 Jun 2003

REF1/Aly and the additional exon junction complex proteins are dispensable for nuclear mRNA export.
Gatfield D, Izaurralde E
J Cell Biol 2002 Nov 25 159(4):579-88 [abstract on PubMed] [related articles] [FREE full text]
Selected by | Thomas Blumenthal
Evaluated 20 Jun 2003

Pre-spliceosome formation in S.pombe requires a stable complex of SF1-U2AF(59)-U2AF(23).
Huang T, Vilardell J, Query CC
EMBO J 2002 Oct 15 21(20):5516-26 [abstract on PubMed] [related articles] [order article]
Selected by | Thomas Blumenthal
Evaluated 20 Jun 2003

Independent functions of yeast Pcf11p in pre-mRNA 3' end processing and in transcription termination.
Sadowski M, Dichtl B, Hübner W, Keller W
EMBO J 2003 May 1 22(9):2167-77 [abstract on PubMed] [related articles] [FREE full text]
Selected by | Thomas Blumenthal
Evaluated 20 Jun 2003

Molecular mechanisms governing Pcdh-gamma gene expression: evidence for a multiple promoter and cis-alternative splicing model.
Wang X, Su H, Bradley A
Genes Dev 2002 Aug 1 16(15):1890-905 [abstract on PubMed] [related articles] [FREE full text]
Selected by | Thomas Blumenthal
Evaluated 7 Oct 2002

Yhh1p/Cft1p directly links poly(A) site recognition and RNA polymerase II transcription termination.
Dichtl B, Blank D, …, Weiser S, Keller W
EMBO J 2002 Aug 1 21(15):4125-35 [abstract on PubMed] [related articles] [order article]
Selected by | Thomas Blumenthal
Evaluated 7 Oct 2002

Promoter choice determines splice site selection in protocadherin alpha and gamma pre-mRNA splicing.
Tasic B, Nabholz CE, …, Axel R, Maniatis T
Mol Cell 2002 Jul 10(1):21-33 [abstract on PubMed] [related articles] [order article]
Selected by | Thomas Blumenthal
Evaluated 7 Oct 2002

Expression of the essential mRNA export factor Yra1p is autoregulated by a splicing-dependent mechanism.
Preker PJ, Kim KS, Guthrie C
RNA 2002 Aug 8(8):969-80 [abstract on PubMed] [related articles] [FREE full text]
Selected by | Thomas Blumenthal
Evaluated 7 Oct 2002

The U1 snRNP protein U1C recognizes the 5' splice site in the absence of base pairing.
Du H, Rosbash M
Nature 2002 Sep 5 419(6902):86-90 [abstract on PubMed] [related articles] [full text] [order article]
Selected by | Thomas Blumenthal / Gabriele Varani
Evaluated 7 Oct 2002

A misspliced form of the cholecystokinin-B/gastrin receptor in pancreatic carcinoma: role of reduced sellular U2AF35 and a suboptimal 3'-splicing site leading to retention of the fourth intron.
Ding WQ, Kuntz SM, Miller LJ
Cancer Res 2002 Feb 1 62(3):947-52 [abstract on PubMed] [related articles] [FREE full text]
Selected by | Thomas Blumenthal
Evaluated 11 Jul 2002

Removal of a single alpha-tubulin gene intron suppresses cell cycle arrest phenotypes of splicing factor mutations in Saccharomyces cerevisiae.
Burns CG, Ohi R, …, Ares M, Gould KL
Mol Cell Biol 2002 Feb 22(3):801-15 [abstract on PubMed] [related articles] [FREE full text]
Selected by | Thomas Blumenthal
Evaluated 11 Jul 2002

Trans-splicing as a novel mechanism to explain interallelic complementation in Drosophila.
Mongelard F, Labrador M, …, Gerasimova TI, Corces VG
Genetics 2002 Apr 160(4):1481-7 [abstract on PubMed] [related articles] [FREE full text]
Selected by | Thomas Blumenthal
Evaluated 11 Jul 2002

Regulation of the different chromatin states of autosomes and X chromosomes in the germ line of C. elegans.
Fong Y, Bender L, Wang W, Strome S
Science 2002 Jun 21 296(5576):2235-8 [abstract on PubMed] [related articles] [FREE full text]
Selected by | Thomas Blumenthal / Jane Hubbard / Robert K Herman / Mitzi Kuroda / Bruce Bowerman
Evaluated 11 Jul 2002

Regulation of alternative splicing by a transcriptional enhancer through RNA pol II elongation.
Kadener S, Fededa JP, Rosbash M, Kornblihtt AR
Proc Natl Acad Sci U S A 2002 Jun 11 99(12):8185-90 [abstract on PubMed] [related articles] [FREE full text]
Selected by | Thomas Blumenthal
Evaluated 11 Jul 2002

New components of the spliced leader RNP required for nematode trans-splicing.
Denker JA, Zuckerman DM, Maroney PA, Nilsen TW
Nature 2002 Jun 6 417(6889):667-70 [abstract on PubMed] [related articles] [full text] [order article]
Selected by | Thomas Blumenthal
Evaluated 10 Jul 2002

On the role of RNA amplification in dsRNA-triggered gene silencing.
Sijen T, Fleenor J, …, Plasterk RH, Fire A
Cell 2001 Nov 16 107(4):465-76 [abstract on PubMed] [related articles] [order article]
Selected by | Carl Thummel / Thomas Blumenthal
Evaluated 21 Dec 2001

An isoform of eIF4E is a component of germ granules and is required for spermatogenesis in C. elegans.
Amiri A, Keiper BD, …, Rhoads RE, Strome S
Development 2001 Oct 128(20):3899-912 [abstract on PubMed] [related articles] [FREE full text]
Selected by | Thomas Blumenthal
Evaluated 21 Dec 2001

A gene expression map for Caenorhabditis elegans.
Kim SK, Lund J, …, Wylie BN, Davidson GS
Science 2001 Sep 14 293(5537):2087-92 [abstract on PubMed] [related articles] [FREE full text]
Selected by | Jonathan Hodgkin / Michel Labouesse / Thomas Blumenthal
Evaluated 21 Dec 2001

Herpes simplex virus ICP27 protein provides viral mRNAs with access to the cellular mRNA export pathway.
Koffa MD, Clements JB, …, Mattaj IW, Kuersten S
EMBO J 2001 Oct 15 20(20):5769-78 [abstract on PubMed] [related articles] [FREE full text]
Selected by | Thomas Blumenthal
Evaluated 21 Dec 2001

Splicing-related catalysis by protein-free snRNAs.
Valadkhan S, Manley JL
Nature 2001 Oct 18 413(6857):701-7 [abstract on PubMed] [related articles] [full text] [order article]
Selected by | Anita Hopper / Thomas Blumenthal
Evaluated 21 Dec 2001

Conserved Wat1/Pop3 WD-repeat protein of fission yeast secures genome stability through microtubule integrity and may be involved in mRNA maturation.
Ochotorena IL, Hirata D, …, Vardy L, Toda T
J Cell Sci 2001 Aug 114(Pt 16):2911-20 [abstract on PubMed] [related articles] [FREE full text]
Selected by | Thomas Blumenthal
Evaluated 21 Dec 2001

Modulation of P-element pre-mRNA splicing by a direct interaction between PSI and U1 snRNP 70K protein.
Labourier E, Adams MD, Rio DC
Mol Cell 2001 Aug 8(2):363-73 [abstract on PubMed] [related articles] [order article]
Selected by | Thomas Blumenthal / Kiyoshi Nagai
Evaluated 22 Oct 2001

Transgene analysis proves mRNA trans-splicing at the complex mod(mdg4) locus in Drosophila.
Dorn R, Reuter G, Loewendorf A
Proc Natl Acad Sci U S A 2001 Aug 14 98(17):9724-9 [abstract on PubMed] [related articles] [FREE full text]
Selected by | Thomas Blumenthal
Evaluated 22 Oct 2001

Precursor RNAs harboring nonsense codons accumulate near the site of transcription.
Mühlemann O, Mock-Casagrande CS, …, Wilkinson MF, Moore MJ
Mol Cell 2001 Jul 8(1):33-43 [abstract on PubMed] [related articles] [order article]
Selected by | Lynne Maquat / Thomas Blumenthal
Evaluated 22 Oct 2001

dpl-1 DP and efl-1 E2F act with lin-35 Rb to antagonize Ras signaling in C. elegans vulval development.
Ceol CJ, Horvitz HR
Mol Cell 2001 Mar 7(3):461-73 [abstract on PubMed] [related articles] [order article]
Selected by | Thomas Blumenthal
Evaluated 22 Oct 2001

The fate of dsRNA in the nucleus: a p54(nrb)-containing complex mediates the nuclear retention of promiscuously A-to-I edited RNAs.
Zhang Z, Carmichael GG
Cell 2001 Aug 24 106(4):465-75 [abstract on PubMed] [related articles] [order article]
Selected by | Marjori Matzke / Thomas Blumenthal / Brenda Bass
Evaluated 22 Oct 2001