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Gabriele Varani
Department of Biochemistry and Chemistry, University of Washington, Seattle, United States of America

Faculty Member: CELL BIOLOGY > Control of gene expression [ since 9 September 2002 ]
[ Evaluations ]
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Evaluations

RNA-mediated epigenetic programming of a genome-rearrangement pathway.
Nowacki M, Vijayan V, …, Doak TG, Landweber LF
Nature 2008 Jan 10 451(7175):153-8 [abstract on PubMed] [related articles] [full text] [order article]
Selected by | Phillip Newmark / Sui Huang / Chantal Abergel / Gabriele Varani
Evaluated 6 May 2008

A PtdIns4,5P2-regulated nuclear poly(A) polymerase controls expression of select mRNAs.
Mellman DL, Gonzales ML, …, Kendziorski C, Anderson RA
Nature 2008 Feb 21 451(7181):1013-7 [abstract on PubMed] [related articles] [full text] [order article]
Selected by | Tom Misteli / Miles Wilkinson / Susan Wente / Gabriele Varani
Evaluated 6 May 2008

The MC-Fold and MC-Sym pipeline infers RNA structure from sequence data.
Parisien M, Major F
Nature 2008 Mar 6 452(7183):51-5 [abstract on PubMed] [related articles] [full text] [order article]
Selected by | Douglas Turner / Gabriele Varani
Evaluated 6 May 2008

Structure of the RNA-binding domain of telomerase: implications for RNA recognition and binding.
Rouda S, Skordalakes E
Structure 2007 Nov 15(11):1403-12 [abstract on PubMed] [related articles] [full text] [order article]
Selected by | Gabriele Varani
Evaluated 19 Dec 2007

Pin1 modulates RNA polymerase II activity during the transcription cycle.
Xu YX, Manley JL
Genes Dev 2007 Nov 15 21(22):2950-62 [abstract on PubMed] [related articles] [full text] [order article]
Selected by | Gabriele Varani
Evaluated 13 Dec 2007

JMJD6 is a histone arginine demethylase.
Chang B, Chen Y, Zhao Y, Bruick RK
Science 2007 Oct 19 318(5849):444-7 [abstract on PubMed] [related articles] [full text] [order article]
Selected by | Jim Maher / Gabriele Varani
Evaluated 13 Dec 2007

RNA maps reveal new RNA classes and a possible function for pervasive transcription.
Kapranov P, Cheng J, …, Tammana H, Gingeras TR
Science 2007 Jun 8 316(5830):1484-8 [abstract on PubMed] [related articles] [full text] [order article]
Selected by | Ulf Pettersson / Albert La Spada / Sabine Müller / Gabriele Varani
Evaluated 31 Oct 2007

Stepwise protein-mediated RNA folding directs assembly of telomerase ribonucleoprotein.
Stone MD, Mihalusova M, …, Collins K, Zhuang X
Nature 2007 Mar 22 446(7134):458-61 [abstract on PubMed] [related articles] [full text] [order article]
Selected by | Robert Batey / Michael Kiebler / Dehua Pei / Gabriele Varani
Evaluated 14 Aug 2007

Genome-wide mapping of in vivo protein-DNA interactions.
Johnson DS, Mortazavi A, Myers RM, Wold B
Science 2007 Jun 8 316(5830):1497-502 [abstract on PubMed] [related articles] [full text] [order article]
Selected by | Jim Maher / John Jaenike / Deyou Zheng / Ulf Pettersson / Gabriele Varani / Magdalena Zernicka-Goetz
Evaluated 14 Aug 2007

Phosphorylation of HuR by Chk2 regulates SIRT1 expression.
Abdelmohsen K, Pullmann R, …, Furneaux H, Gorospe M
Mol Cell 2007 Feb 23 25(4):543-57 [abstract on PubMed] [related articles] [full text] [order article]
Selected by | Robert Abraham / Gabriele Varani / Megerditch Kiledjian
Evaluated 8 May 2007

TTP and BRF proteins nucleate processing body formation to silence mRNAs with AU-rich elements.
Franks TM, Lykke-Andersen J
Genes Dev 2007 Mar 15 21(6):719-35 [abstract on PubMed] [related articles] [full text] [order article]
Selected by | Gabriele Varani
Evaluated 8 May 2007

Connecting protein structure with predictions of regulatory sites.
Morozov AV, Siggia ED
Proc Natl Acad Sci U S A 2007 Apr 24 104(17):7068-73 [abstract on PubMed] [related articles] [FREE full text]
Selected by | Andras Fiser / Gabriele Varani
Evaluated 8 May 2007

RNA synthetic biology.
Isaacs FJ, Dwyer DJ, Collins JJ
Nat Biotechnol 2006 May 24(5):545-54 [abstract on PubMed] [related articles] [full text] [order article]
Selected by | Gabriele Varani
Evaluated 19 Dec 2006

An RNA gene expressed during cortical development evolved rapidly in humans.
Pollard KS, Salama SR, …, Vanderhaeghen P, Haussler D
Nature 2006 Sep 14 443(7108):167-72 [abstract on PubMed] [related articles] [full text] [order article]
Selected by | Kevan A. Martin / John Abrams / Deyou Zheng / Andrew Feinberg / Rafael Zardoya / Ali H. Brivanlou / Robert Sapolsky / Gabriele Varani / Christopher A. Walsh
Evaluated 15 Dec 2006


A genomic code for nucleosome positioning.
Segal E, Fondufe-Mittendorf Y, …, Wang JP, Widom J
Nature 2006 Aug 17 442(7104):772-8 [abstract on PubMed] [related articles] [order article]
Selected by | Brad Bernstein / Tom Misteli / Kerry Bloom / Nick Rhind / James Bone / Francesc Posas / Michael Meisterernst / Leonie Ringrose / Gabriele Varani
Evaluated 13 Dec 2006

The Xist RNA gene evolved in eutherians by pseudogenization of a protein-coding gene.
Duret L, Chureau C, …, Weissenbach J, Avner P
Science 2006 Jun 16 312(5780):1653-5 [abstract on PubMed] [related articles] [FREE full text]
Selected by | Jim Thomas / Nicolas Galtier / Molly Przeworski / Daniel Gallie / Manyuan Long / Gabriele Varani
Evaluated 10 Oct 2006

Transcript-assisted transcriptional proofreading.
Zenkin N, Yuzenkova Y, Severinov K
Science 2006 Jul 28 313(5786):518-20 [abstract on PubMed] [related articles] [FREE full text]
Selected by | Brent Iverson / Barry Stoddard / Gabriele Varani
Evaluated 10 Oct 2006

Structural basis for gene regulation by a thiamine pyrophosphate-sensing riboswitch.
Serganov A, Polonskaia A, …, Breaker RR, Patel DJ
Nature 2006 Jun 29 441(7097):1167-71 [abstract on PubMed] [related articles] [full text] [order article]
Selected by | Gabriele Varani
Evaluated 1 Aug 2006

Structure of the eukaryotic thiamine pyrophosphate riboswitch with its regulatory ligand.
Thore S, Leibundgut M, Ban N
Science 2006 May 26 312(5777):1208-11 [abstract on PubMed] [related articles] [FREE full text]
Selected by | Peter Unrau / Robert Batey / Gabriele Varani
Evaluated 31 Jul 2006

Structure of the S-adenosylmethionine riboswitch regulatory mRNA element.
Montange RK, Batey RT
Nature 2006 Jun 29 441(7097):1172-5 [abstract on PubMed] [related articles] [full text] [order article]
Selected by | Gabriele Varani
Evaluated 31 Jul 2006

Nrd1 interacts with the nuclear exosome for 3' processing of RNA polymerase II transcripts.
Vasiljeva L, Buratowski S
Mol Cell 2006 Jan 20 21(2):239-48 [abstract on PubMed] [related articles] [full text] [order article]
Selected by | Gabriele Varani
Evaluated 6 Apr 2006

Double chromodomains cooperate to recognize the methylated histone H3 tail.
Flanagan JF, Mi LZ, …, Rastinejad F, Khorasanizadeh S
Nature 2005 Dec 22 438(7071):1181-5 [abstract on PubMed] [related articles] [full text] [order article]
Selected by | Gabriele Varani / Thomas Jenuwein
Evaluated 6 Apr 2006

The RNA-binding protein FCA is an abscisic acid receptor.
Razem FA, El-Kereamy A, Abrams SR, Hill RD
Nature 2006 Jan 19 439(7074):290-4 [abstract on PubMed] [related articles] [full text] [order article]
Selected by | Caren Chang / Martin Robert McAinsh / Michael Blatt / Detlef Weigel / Alistair Hetherington / Judy Callis / Gabriele Varani
Evaluated 6 Apr 2006

Regulation of yeast mRNA 3' end processing by phosphorylation.
He X, Moore C
Mol Cell 2005 Sep 2 19(5):619-29 [abstract on PubMed] [related articles] [full text] [order article]
Selected by | Gabriele Varani
Evaluated 6 Jan 2006

A miniature yeast telomerase RNA functions in vivo and reconstitutes activity in vitro.
Zappulla DC, Goodrich K, Cech TR
Nat Struct Mol Biol 2005 Dec 12(12):1072-7 [abstract on PubMed] [related articles] [full text] [order article]
Selected by | Gabriele Varani
Evaluated 3 Jan 2006

Systematic discovery of regulatory motifs in human promoters and 3' UTRs by comparison of several mammals.
Xie X, Lu J, …, Lander ES, Kellis M
Nature 2005 Mar 17 434(7031):338-45 [abstract on PubMed] [related articles] [full text] [order article]
Selected by | Karin Schmitt / Gabriele Varani
Evaluated 15 Jun 2005

Cotranscriptional recruitment of the pseudouridylsynthetase Cbf5p and of the RNA binding protein Naf1p during H/ACA snoRNP assembly.
Yang PK, Hoareau C, …, Henry Y, Chanfreau G
Mol Cell Biol 2005 Apr 25(8):3295-304 [abstract on PubMed] [related articles] [FREE full text]
Selected by | Gabriele Varani
Evaluated 14 Jun 2005

RNA-guided RNA modification: functional organization of the archaeal H/ACA RNP.
Baker DL, Youssef OA, …, Terns RM, Terns MP
Genes Dev 2005 May 15 19(10):1238-48 [abstract on PubMed] [related articles] [FREE full text]
Selected by | Gabriele Varani
Evaluated 13 Jun 2005

Molecular determinants and guided evolution of species-specific RNA editing.
Reenan RA
Nature 2005 Mar 17 434(7031):409-13 [abstract on PubMed] [related articles] [full text] [order article]
Selected by | Gabriele Varani
Evaluated 3 May 2005

Simultaneous determination of protein structure and dynamics.
Lindorff-Larsen K, Best RB, …, Dobson CM, Vendruscolo M
Nature 2005 Jan 13 433(7022):128-32 [abstract on PubMed] [related articles] [full text] [order article]
Selected by | Volkhard Helms / Gabriele Varani
Evaluated 22 Feb 2005

Structure of a natural guanine-responsive riboswitch complexed with the metabolite hypoxanthine.
Batey RT, Gilbert SD, Montange RK
Nature 2004 Nov 18 432(7015):411-5 [abstract on PubMed] [related articles] [full text] [order article]
Selected by | Reinhard Luehrmann / Eric Westhof / Gabriele Varani
Evaluated 17 Feb 2005

Architecture and assembly of mammalian H/ACA small nucleolar and telomerase ribonucleoproteins.
Wang C, Meier UT
EMBO J 2004 Apr 21 23(8):1857-67 [abstract on PubMed] [related articles] [FREE full text]
Selected by | Gabriele Varani
Evaluated 16 Feb 2005

Assembly and maturation of the U3 snoRNP in the nucleoplasm in a large dynamic multiprotein complex.
Watkins NJ, Lemm I, …, Urlaub H, Lührmann R
Mol Cell 2004 Dec 3 16(5):789-98 [abstract on PubMed] [related articles] [full text] [order article]
Selected by | A. Gregory Matera / Gabriele Varani
Evaluated 16 Feb 2005

Basis for structural diversity in homologous RNAs.
Krasilnikov AS, Xiao Y, Pan T, Mondragón A
Science 2004 Oct 1 306(5693):104-7 [abstract on PubMed] [related articles] [FREE full text]
Selected by | David M.J. Lilley / Gabriele Varani / Douglas Turner
Evaluated 2 Nov 2004

Control of human potassium channel inactivation by editing of a small mRNA hairpin.
Bhalla T, Rosenthal JJ, Holmgren M, Reenan R
Nat Struct Mol Biol 2004 Oct 11(10):950-6 [abstract on PubMed] [related articles] [full text] [order article]
Selected by | Gabriele Varani
Evaluated 1 Nov 2004

Structural basis for template-independent RNA polymerization.
Tomita K, Fukai S, …, Vassylyev DG, Nureki O
Nature 2004 Aug 5 430(7000):700-4 [abstract on PubMed] [related articles] [full text] [order article]
Selected by | Gabriele Varani / Robert Dutnall
Evaluated 1 Nov 2004

Nuclear export of microRNA precursors.
Lund E, Güttinger S, …, Dahlberg JE, Kutay U
Science 2004 Jan 2 303(5654):95-8 [abstract on PubMed] [related articles] [FREE full text]
Selected by | Anita Hopper / James Carrington / Gabriele Varani
Evaluated 11 Aug 2004

An eIF4AIII-containing complex required for mRNA localization and nonsense-mediated mRNA decay.
Palacios IM, Gatfield D, St Johnston D, Izaurralde E
Nature 2004 Feb 19 427(6976):753-7 [abstract on PubMed] [related articles] [full text] [order article]
Selected by | Lynne Maquat / Ilan Davis / Miles Wilkinson / Gabriele Varani
Evaluated 11 Aug 2004

Recognition of RNA polymerase II carboxy-terminal domain by 3'-RNA-processing factors.
Meinhart A, Cramer P
Nature 2004 Jul 8 430(6996):223-6 [abstract on PubMed] [related articles] [full text] [order article]
Selected by | Benoit Coulombe / Gabriele Varani / Elena Conti
Evaluated 11 Aug 2004

MicroRNAs modulate hematopoietic lineage differentiation.
Chen CZ, Li L, Lodish HF, Bartel DP
Science 2004 Jan 2 303(5654):83-6 [abstract on PubMed] [related articles] [FREE full text]
Selected by | Dinah Singer / David States / Shiv Pillai / Gabriele Varani
Evaluated 25 May 2004

Identification of virus-encoded microRNAs.
Pfeffer S, Zavolan M, …, Sander C, Tuschl T
Science 2004 Apr 30 304(5671):734-6 [abstract on PubMed] [related articles] [FREE full text]
Selected by | Lindsey Hutt-Fletcher / Andrew Ellington / Gabriele Varani / Daniel Gallie / James Carrington / Ulf Pettersson / Vishvanath Nene
Evaluated 20 May 2004

Splicing of oskar RNA in the nucleus is coupled to its cytoplasmic localization.
Hachet O, Ephrussi A
Nature 2004 Apr 29 428(6986):959-63 [abstract on PubMed] [related articles] [full text] [order article]
Selected by | Roy Long / Lynne Maquat / Ilan Davis / Gabriele Varani / Reinhard Luehrmann
Evaluated 20 May 2004

Extensive association of functionally and cytotopically related mRNAs with Puf family RNA-binding proteins in yeast.
Gerber AP, Herschlag D, Brown PO
PLoS Biol 2004 Mar 2(3):E79 [abstract on PubMed] [related articles] [FREE full text]
Selected by | Richard Maraia / Gabriele Varani / Jurg Bahler
Evaluated 8 Apr 2004

Ku interacts with telomerase RNA to promote telomere addition at native and broken chromosome ends.
Stellwagen AE, Haimberger ZW, Veatch JR, Gottschling DE
Genes Dev 2003 Oct 1 17(19):2384-95 [abstract on PubMed] [related articles] [FREE full text]
Selected by | Dale Ramsden / Stephen Jackson / Gabriele Varani
Evaluated 27 Jan 2004

CLIP identifies Nova-regulated RNA networks in the brain.
Ule J, Jensen KB, …, Ule A, Darnell RB
Science 2003 Nov 14 302(5648):1212-5 [abstract on PubMed] [related articles] [FREE full text]
Selected by | Gabriele Varani
Evaluated 27 Jan 2004

RNA molecules stimulate prion protein conversion.
Deleault NR, Lucassen RW, Supattapone S
Nature 2003 Oct 16 425(6959):717-20 [abstract on PubMed] [related articles] [full text] [order article]
Selected by | Charles Brenner / Gabriele Varani
Evaluated 23 Jan 2004

Structure and gating mechanism of the acetylcholine receptor pore.
Miyazawa A, Fujiyoshi Y, Unwin N
Nature 2003 Jun 26 423(6943):949-55 [abstract on PubMed] [related articles] [full text] [order article]
Selected by | Wah Chiu / Senyon Choe / Jose Valpuesta / Andreas Engel / Gabriele Varani
Evaluated 24 Nov 2003

Single molecule profiling of alternative pre-mRNA splicing.
Zhu J, Shendure J, Mitra RD, Church GM
Science 2003 Aug 8 301(5634):836-8 [abstract on PubMed] [related articles] [FREE full text]
Selected by | Lee Gehrke / Gabriele Varani
Evaluated 21 Nov 2003

A common sequence motif determines the Cajal body-specific localization of box H/ACA scaRNAs.
Richard P, Darzacq X, …, Verheggen C, Kiss T
EMBO J 2003 Aug 15 22(16):4283-93 [abstract on PubMed] [related articles] [FREE full text]
Selected by | Gabriele Varani
Evaluated 21 Nov 2003

The structure of DNA in the nucleosome core.
Richmond TJ, Davey CA
Nature 2003 May 8 423(6936):145-50 [abstract on PubMed] [related articles] [full text] [order article]
Selected by | Gabriele Varani
Evaluated 17 Jul 2003

An expressed pseudogene regulates the messenger-RNA stability of its homologous coding gene.
Hirotsune S, Yoshida N, …, Wynshaw-Boris A, Yoshiki A
Nature 2003 May 1 423(6935):91-6 [abstract on PubMed] [related articles] [full text] [order article]
Selected by | Herb Arst / Vivian Cheung / Yasushi Okazaki / Alain Prochiantz / Gabriele Varani
Evaluated 17 Jul 2003

Crystal structure of the specificity domain of ribonuclease P.
Krasilnikov AS, Yang X, Pan T, Mondragón A
Nature 2003 Feb 13 421(6924):760-4 [abstract on PubMed] [related articles] [full text] [order article]
Selected by | Peter Qin / David M.J. Lilley / Oliver Weichenrieder / Gabriele Varani / Douglas Turner
Evaluated 2 May 2003

Human and bacterial oxidative demethylases repair alkylation damage in both RNA and DNA.
Aas PA, Otterlei M, …, Seeberg E, Krokan HE
Nature 2003 Feb 20 421(6925):859-63 [abstract on PubMed] [related articles] [full text] [order article]
Selected by | Gabriele Varani
Evaluated 1 May 2003

Small nuclear ribonucleoprotein remodeling during catalytic activation of the spliceosome.
Makarov EM, Makarova OV, …, Wilm M, Lührmann R
Science 2002 Dec 13 298(5601):2205-8 [abstract on PubMed] [related articles] [FREE full text]
Selected by | Gabriele Varani
Evaluated 21 Mar 2003

U1 snRNA associates with TFIIH and regulates transcriptional initiation.
Kwek KY, Murphy S, …, Proudfoot NJ, Akoulitchev A
Nat Struct Biol 2002 Nov 9(11):800-5 [abstract on PubMed] [related articles] [full text] [order article]
Selected by | Michael Meisterernst / Samuel Gunderson / Gabriele Varani
Evaluated 20 Mar 2003

Thiamine derivatives bind messenger RNAs directly to regulate bacterial gene expression.
Winkler W, Nahvi A, Breaker RR
Nature 2002 Oct 31 419(6910):952-6 [abstract on PubMed] [related articles] [full text] [order article]
Selected by | John Burke / Richard Maraia / Richard Gourse / Andrew Ellington / Niles Lehman / Gabriele Varani
Evaluated 22 Jan 2003

Sensing small molecules by nascent RNA: a mechanism to control transcription in bacteria.
Mironov AS, Gusarov I, …, Perumov DA, Nudler E
Cell 2002 Nov 27 111(5):747-56 [abstract on PubMed] [related articles] [order article]
Selected by | Gabriele Varani
Evaluated 22 Jan 2003

Macromolecular architecture in eukaryotic cells visualized by cryoelectron tomography.
Medalia O, Weber I, …, Gerisch G, Baumeister W
Science 2002 Nov 8 298(5596):1209-13 [abstract on PubMed] [related articles] [FREE full text]
Selected by | David Stokes / Carole Parent / Hernando Sosa / Jose Valpuesta / Richard Gomer / Gabriele Varani / Wil Konings
Evaluated 10 Dec 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 5 Nov 2002

A regulatory cytoplasmic poly(A) polymerase in Caenorhabditis elegans.
Wang L, Eckmann CR, …, Wickens M, Kimble J
Nature 2002 Sep 19 419(6904):312-6 [abstract on PubMed] [related articles] [full text] [order article]
Selected by | Jonathan Hodgkin / Elmar Wahle / Talila Volk / Anita Hopper / Gabriele Varani / Samuel Gunderson
Evaluated 4 Nov 2002

Comprehensive proteomic analysis of the human spliceosome.
Zhou Z, Licklider LJ, Gygi SP, Reed R
Nature 2002 Sep 12 419(6903):182-5 [abstract on PubMed] [related articles] [full text] [order article]
Selected by | Michael Rosbash / Gabriele Varani
Evaluated 4 Nov 2002

Single-cell gene expression profiling.
Levsky JM, Shenoy SM, Pezo RC, Singer RH
Science 2002 Aug 2 297(5582):836-40 [abstract on PubMed] [related articles] [FREE full text]
Selected by | Bill Pavan / Gabriele Varani
Evaluated 2 Oct 2002

RNA aptamers as reversible antagonists of coagulation factor IXa.
Rusconi CP, Scardino E, …, Monroe D, Sullenger BA
Nature 2002 Sep 5 419(6902):90-4 [abstract on PubMed] [related articles] [full text] [order article]
Selected by | Gabriele Varani / Ronald Breaker
Evaluated 1 Oct 2002

Modulation of HIV-1 replication by RNA interference.
Jacque JM, Triques K, Stevenson M
Nature 2002 Jul 25 418(6896):435-8 [abstract on PubMed] [related articles]