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ARTICLES

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  Molecular dissection of step 2 catalysis of yeast pre-mRNA splicing investigated in a purified system

  • Thomas Ohrt,
  • Peter Odenwälder,
  • Julia Dannenberg,
  • Mira Prior,
  • Zbigniew Warkocki,
  • Jana Schmitzová,
  • Ramazan Karaduman,
  • Ingo Gregor,
  • Jörg Enderlein,
  • Patrizia Fabrizio,
  • and Reinhard Lührmann

  RNA July 2013 19: 902-915; Published in Advance May 17, 2013, doi:10.1261/rna.039024.113
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  Pre-mRNA splicing occurs in two steps. This paper reports studies of protein factor requirements for step 2 catalysis. The studies reveal that the only remodeling of the spliceosome between step 1 and step 2 is mediated by the DEAH-box ATPase Prp16.

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  Loop–loop interaction in an adenine-sensing riboswitch: A molecular dynamics study

  • Olof Allnér,
  • Lennart Nilsson,
  • and Alessandra Villa

  RNA July 2013 19: 916-926; Published in Advance May 28, 2013, doi:10.1261/rna.037549.112
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  All-atom molecular dynamics simulations of the adenine-sensing add A-riboswitch to study the breaking of the kissing loop, a key tertiary element in the aptamer structure, were performed. A two-step process was observed in all the simulated systems. A general loss of stacking and hydrogen bond interactions is first seen. The junction area is partially organized before the kissing loop formation and one residue, A24, anchors together the loop helices.

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  The Runt domain of AML1 (RUNX1) binds a sequence-conserved RNA motif that mimics a DNA element

  • Junichi Fukunaga,
  • Yusuke Nomura,
  • Yoichiro Tanaka,
  • Ryo Amano,
  • Taku Tanaka,
  • Yoshikazu Nakamura,
  • Gota Kawai,
  • Taiichi Sakamoto,
  • and Tomoko Kozu

  RNA July 2013 19: 927-936; Published in Advance May 24, 2013, doi:10.1261/rna.037879.112
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  AML1 (RUNX1) is a key transcription factor for hematopoiesis. RNA aptamers that bind specifically to the AML1 Runt domain were obtained. All the isolated aptamers contain the conserved sequence motif 5′-NNCCAC-3′ and 5′-GCGMGN′N′-3′ (M:A or C; N and N′ form Watson–Crick base pairs). Three guanines of the motif are directly recognized by three arginine residues of the Runt domain.

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  The roles of 3′-exoribonucleases and the exosome in trypanosome mRNA degradation

  • Abeer Fadda,
  • Valentin Färber,
  • Dorothea Droll,
  • and Christine Clayton

  RNA July 2013 19: 937-947; Published in Advance May 22, 2013, doi:10.1261/rna.038430.113
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  This paper reports results on studies of mRNA decay in Trypanosoma brucei. Surprisingly, mRNA decay of unstable and intermediate stability mRNAs is mediated by different degradative pathways.

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  hnRNP A1 and secondary structure coordinate alternative splicing of Mag

  • N. Ruth Zearfoss,
  • Emily S. Johnson,
  • and Sean P. Ryder

  RNA July 2013 19: 948-957; Published in Advance May 23, 2013, doi:10.1261/rna.036780.112
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  This paper studies the regulation of alternative splicing of the myelin-associated glycoprotein pre-mRNA. The authors show that regulation of exon 12 skipping involves hnRNP A1 interacting with a binding site that overlaps the 5′ splice site. A conserved secondary structure around the binding site contributes to regulation.

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  Thermostable group II intron reverse transcriptase fusion proteins and their use in cDNA synthesis and next-generation RNA sequencing

  • Sabine Mohr,
  • Eman Ghanem,
  • Whitney Smith,
  • Dennis Sheeter,
  • Yidan Qin,
  • Olga King,
  • Damon Polioudakis,
  • Vishwanath R. Iyer,
  • Scott Hunicke-Smith,
  • Sajani Swamy,
  • Scott Kuersten,
  • and Alan M. Lambowitz

  RNA July 2013 19: 958-970; Published in Advance May 22, 2013, doi:10.1261/rna.039743.113
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  This paper describes unusual properties of group II intron-encoded reverse transcriptases. They have higher processivity, fidelity, and thermostability than retroviral enzymes. Moreover, they have an unexpected proclivity for template switching that makes them very useful for a number of cloning applications.

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  The spliceosome catalyzes debranching in competition with reverse of the first chemical reaction

  • Chi-Kang Tseng and
  • Soo-Chen Cheng

  RNA July 2013 19: 971-981; Published in Advance May 16, 2013, doi:10.1261/rna.038638.113
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  This study shows that debranching of lariat intermediates in splicing can be catalyzed by the spliceosome itself and that this reaction is in competition with reverse of the first step of splicing. New parallels between group II intron splicing and spliceosomal splicing are also revealed.

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  Direct evidence for RNA–RNA interactions at the 3′ end of the Hepatitis C virus genome using surface plasmon resonance

  • William Palau,
  • Cyril Masante,
  • Michel Ventura,
  • and Carmelo Di Primo

  RNA July 2013 19: 982-991; Published in Advance May 7, 2013, doi:10.1261/rna.037606.112
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  The 3′ end region of the Hepatitis C virus genome folds into several stem–loops that play important roles in the viral replication cycle. This paper investigates the kinetics of these RNA–RNA interactions using short synthetic RNAs corresponding to the 3′ untranslated region of HCV RNA by surface plasmon resonance (SPR).

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  Cell cycle–dependent transcription factors control the expression of yeast telomerase RNA

  • Isabelle Dionne,
  • Stéphanie Larose,
  • Alain T. Dandjinou,
  • Sherif Abou Elela,
  • and Raymund J. Wellinger

  RNA July 2013 19: 992-1002; Published in Advance May 20, 2013, doi:10.1261/rna.037663.112
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  Because telomere elongation by telomerase is strictly regulated across the cell cycle, occurring only in S phase, it has long been expected that telomerase subunit expression would also be cell cycle regulated. Here the authors contribute the first definitive support for cell cycle regulation of telomerase RNA transcription in budding yeast. Using a modified chromatin immunopurification approach to detect RNA transcripts still at the telomerase RNA locus, the authors show that there is a late G1/S induction and thus cell cycle–dependent regulation of telomerase RNA transcription.