Difference between revisions of "Stusti 2018"
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= Die Sprache der RNA: Von RNA-Schaltern zu CRISPR/ Cas = | = Die Sprache der RNA: Von RNA-Schaltern zu CRISPR/ Cas = | ||
| − | == What makes RNA such a special molecule – specific chemical and structural features of RNA == | + | == What makes RNA such a special molecule – specific chemical and structural features of RNA: Niklas Kehl == |
| − | <pubmed> 21930584 | + | <pubmed> 21930584</pubmed> |
| − | </pubmed> | ||
| − | == RNA synthesis – DNA and RNA dependent RNA polymerases and primase during transcription, replication and repair == | + | == RNA synthesis – DNA and RNA dependent RNA polymerases and primase during transcription, replication and repair: Andrea Lehner == |
| − | <pubmed> 24219496 | + | <pubmed> 24219496 8156586 28979293 26109351</pubmed> |
| − | </pubmed> | ||
| − | == Ribozymes (catalytically active RNAs | + | == Ribozymes (catalytically active RNAs: Christian Thielscher) == |
| − | <pubmed> | + | <pubmed> 21930582 22454536 14730013 10554775 21930585 6297745</pubmed> |
| − | </pubmed> | ||
| − | == The Ribosome - the role and function of ribosomal RNAs | + | == The Ribosome - the role and function of ribosomal RNAs and the central dogma of molecular biology: Matthias Lenz == |
| − | <pubmed> | + | <pubmed> 18292779 21930591 25500179</pubmed> |
| − | </pubmed> | ||
| − | == The Splicosome - the mechanism of mRNA splicing – alternative gene expression, genome size definition and phenotype plasticity == | + | == The Splicosome - the mechanism of mRNA splicing – alternative gene expression, genome size definition and phenotype plasticity: Christian Schneider == |
| − | <pubmed> | + | <pubmed> 24452469,26682498 25798239 </pubmed> |
| − | </pubmed> | ||
| − | + | == Riboregulation and virulence, targeting by antibiotics: Theresia Eisele == | |
| − | |||
| − | |||
| − | |||
| − | |||
| − | |||
| − | == Riboregulation and virulence, targeting by antibiotics == | ||
<pubmed>27651123 26416753 | <pubmed>27651123 26416753 | ||
27120414 27672192 28434876 28529506 28886688</pubmed> | 27120414 27672192 28434876 28529506 28886688</pubmed> | ||
| − | == | + | == Riboswitch modeling: Mark Sinzger == |
| − | <pubmed> | + | <pubmed>19381267 28591515 27378291</pubmed> |
| − | |||
| − | |||
| − | |||
| − | |||
| − | |||
| − | |||
| − | == The RNA world and evolution == | + | == The RNA world and evolution: Roman Doll == |
<pubmed> 25109990 25385129 25734234 25739364 26439358 17540026 29031737 28657884 19117371</pubmed> | <pubmed> 25109990 25385129 25734234 25739364 26439358 17540026 29031737 28657884 19117371</pubmed> | ||
| − | == RNA modification == | + | == RNA modification: Jan Michel Göring == |
<pubmed> 26189113 26832457 27375676 | <pubmed> 26189113 26832457 27375676 | ||
28264529 28624569</pubmed> | 28264529 28624569</pubmed> | ||
| − | == RNA degradation/processing == | + | == RNA degradation/processing: Lena Kricsfalussy-Hrabar == |
<pubmed> 26096689 28202538 19239894 </pubmed> | <pubmed> 26096689 28202538 19239894 </pubmed> | ||
| − | == Regulation by non-coding RNA == | + | == Regulation by non-coding RNA: Maxin Drömer == |
<pubmed> 18981470 24667238 </pubmed> | <pubmed> 18981470 24667238 </pubmed> | ||
| − | == RNA dependent DNA Polymerases - from telomerase to retroviruses== | + | == RNA dependent DNA Polymerases - from telomerase to retroviruses: Ansgar Stenzel== |
| − | <pubmed> 18972389 26830230 28141967 | + | <pubmed> 18972389 26830230 28141967 </pubmed> |
| − | |||
| − | |||
| − | |||
| − | |||
| − | </pubmed> | ||
| − | == CRISPR/Cas: Science – the bacterial “immune” system == | + | == CRISPR/Cas: Science – the bacterial “immune” system: Maximilian Schreier == |
| − | <pubmed> 29358495 29169146 | + | <pubmed> 29358495 29169146 28375731</pubmed> |
| − | |||
| − | == CRISPR/Cas: Application and groundbreaking perspectives == | + | == CRISPR/Cas: Application and groundbreaking perspectives: Johann Liebeton == |
<pubmed> 26771484 </pubmed> | <pubmed> 26771484 </pubmed> | ||
| − | + | == Synthesis, maturation and function of tRNAs – The wobble hypothesis and specific codon usage as a molecular barrier for horizontal gene transfer: Artur Fornol == | |
| − | + | <pubmed> 22016848 26186290 21957054 23166520 21930591</pubmed> | |
| − | |||
| − | |||
| − | == Synthesis, maturation and function of tRNAs – The wobble hypothesis and specific codon usage as a molecular barrier for horizontal gene transfer == | ||
| − | <pubmed> | ||
| − | </pubmed> | ||
== Outlook: Finding function in mystery transcripts – eRNAs, long-non coding (lncRNA) and circular RNA (circRNA) == | == Outlook: Finding function in mystery transcripts – eRNAs, long-non coding (lncRNA) and circular RNA (circRNA) == | ||
| − | <pubmed> | + | <pubmed> 28533025 25561718 26883671 28485684 29182528 21925379</pubmed> |
| − | |||
| − | </pubmed> | ||
== Outlook: RNA and SELEX – new prospects and applications for targeted interference with regulatory pathways == | == Outlook: RNA and SELEX – new prospects and applications for targeted interference with regulatory pathways == | ||
| − | <pubmed> | + | <pubmed> 17627883 19943183 </pubmed> |
| − | </pubmed> | + | |
| + | == RNA-based second messengers: Jörg Stülke == | ||
| + | <pubmed> 28420751 25616065 25682701 25869574 26280533</pubmed> | ||
| + | |||
| + | == Riboswitches: Jörg Stülke == | ||
| + | <pubmed> 27607554 26655897 28121427 29618088 25794618 25794617 25848023 24769284 25571850 25964329 25959893 24816551 25583497 26118534 26494285 28206750 28375729 28396576 28541183 28455443 29537923 27798597 29135333 29420816 28611182</pubmed> | ||
| + | |||
| + | == RNA dependent RNA Polymerases – the RNA replicase == | ||
| + | <pubmed> 29439438 18268843 9878607 </pubmed> | ||
| + | |||
| + | == The mysterious function and role of 6S-RNA and pRNA in bacteria == | ||
| + | <pubmed> 24786589 17383220 24742053 23457253</pubmed> | ||
| + | |||
| + | == RNA thermometers== | ||
| + | <pubmed>25477380 27060146 </pubmed> | ||
Latest revision as of 13:42, 27 July 2018
Contents
- 1 Die Sprache der RNA: Von RNA-Schaltern zu CRISPR/ Cas
- 1.1 What makes RNA such a special molecule – specific chemical and structural features of RNA: Niklas Kehl
- 1.2 RNA synthesis – DNA and RNA dependent RNA polymerases and primase during transcription, replication and repair: Andrea Lehner
- 1.3 Ribozymes (catalytically active RNAs: Christian Thielscher)
- 1.4 The Ribosome - the role and function of ribosomal RNAs and the central dogma of molecular biology: Matthias Lenz
- 1.5 The Splicosome - the mechanism of mRNA splicing – alternative gene expression, genome size definition and phenotype plasticity: Christian Schneider
- 1.6 Riboregulation and virulence, targeting by antibiotics: Theresia Eisele
- 1.7 Riboswitch modeling: Mark Sinzger
- 1.8 The RNA world and evolution: Roman Doll
- 1.9 RNA modification: Jan Michel Göring
- 1.10 RNA degradation/processing: Lena Kricsfalussy-Hrabar
- 1.11 Regulation by non-coding RNA: Maxin Drömer
- 1.12 RNA dependent DNA Polymerases - from telomerase to retroviruses: Ansgar Stenzel
- 1.13 CRISPR/Cas: Science – the bacterial “immune” system: Maximilian Schreier
- 1.14 CRISPR/Cas: Application and groundbreaking perspectives: Johann Liebeton
- 1.15 Synthesis, maturation and function of tRNAs – The wobble hypothesis and specific codon usage as a molecular barrier for horizontal gene transfer: Artur Fornol
- 1.16 Outlook: Finding function in mystery transcripts – eRNAs, long-non coding (lncRNA) and circular RNA (circRNA)
- 1.17 Outlook: RNA and SELEX – new prospects and applications for targeted interference with regulatory pathways
- 1.18 RNA-based second messengers: Jörg Stülke
- 1.19 Riboswitches: Jörg Stülke
- 1.20 RNA dependent RNA Polymerases – the RNA replicase
- 1.21 The mysterious function and role of 6S-RNA and pRNA in bacteria
- 1.22 RNA thermometers
Die Sprache der RNA: Von RNA-Schaltern zu CRISPR/ Cas
What makes RNA such a special molecule – specific chemical and structural features of RNA: Niklas Kehl
David A Hiller, Scott A Strobel
The chemical versatility of RNA.
Philos Trans R Soc Lond B Biol Sci: 2011, 366(1580);2929-35
[PubMed:21930584]
[WorldCat.org]
[DOI]
(I p)
RNA synthesis – DNA and RNA dependent RNA polymerases and primase during transcription, replication and repair: Andrea Lehner
Savio T de Farias, Ariosvaldo P Dos Santos Junior, Thais G Rêgo, Marco V José
Origin and Evolution of RNA-Dependent RNA Polymerase.
Front Genet: 2017, 8;125
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Thomas A Guilliam, Benjamin A Keen, Nigel C Brissett, Aidan J Doherty
Primase-polymerases are a functionally diverse superfamily of replication and repair enzymes.
Nucleic Acids Res: 2015, 43(14);6651-64
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Maria L Kireeva, Mikhail Kashlev, Zachary F Burton
RNA polymerase structure, function, regulation, dynamics, fidelity, and roles in gene expression.
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S Buratowski
The basics of basal transcription by RNA polymerase II.
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Ribozymes (catalytically active RNAs: Christian Thielscher)
Christian Hammann, Andrej Luptak, Jonathan Perreault, Marcos de la Peña
The ubiquitous hammerhead ribozyme.
RNA: 2012, 18(5);871-85
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Sidney Altman
Ribonuclease P.
Philos Trans R Soc Lond B Biol Sci: 2011, 366(1580);2936-41
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David M J Lilley
Mechanisms of RNA catalysis.
Philos Trans R Soc Lond B Biol Sci: 2011, 366(1580);2910-7
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David M J Lilley
The Varkud satellite ribozyme.
RNA: 2004, 10(2);151-8
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K Kruger, P J Grabowski, A J Zaug, J Sands, D E Gottschling, T R Cech
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Cell: 1982, 31(1);147-57
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The Ribosome - the role and function of ribosomal RNAs and the central dogma of molecular biology: Matthias Lenz
The Splicosome - the mechanism of mRNA splicing – alternative gene expression, genome size definition and phenotype plasticity: Christian Schneider
Riboregulation and virulence, targeting by antibiotics: Theresia Eisele
Juan J Quereda, Pascale Cossart
Regulating Bacterial Virulence with RNA.
Annu Rev Microbiol: 2017, 71;263-280
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Petra Dersch, Muna A Khan, Sabrina Mühlen, Boris Görke
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Hao Wang, Paul A Mann, Li Xiao, Charles Gill, Andrew M Galgoci, John A Howe, Artjohn Villafania, Christopher M Barbieri, Juliana C Malinverni, Xinwei Sher, Todd Mayhood, Megan D McCurry, Nicholas Murgolo, Amy Flattery, Matthias Mack, Terry Roemer
Dual-Targeting Small-Molecule Inhibitors of the Staphylococcus aureus FMN Riboswitch Disrupt Riboflavin Homeostasis in an Infectious Setting.
Cell Chem Biol: 2017, 24(5);576-588.e6
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Andreas Matern, Danielle Pedrolli, Stephanie Großhennig, Jörgen Johansson, Matthias Mack
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Aaron M Nuss, Ann Kathrin Heroven, Petra Dersch
RNA Regulators: Formidable Modulators of Yersinia Virulence.
Trends Microbiol: 2017, 25(1);19-34
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Daniel Dar, Maya Shamir, J R Mellin, Mikael Koutero, Noam Stern-Ginossar, Pascale Cossart, Rotem Sorek
Term-seq reveals abundant ribo-regulation of antibiotics resistance in bacteria.
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John A Howe, Hao Wang, Thierry O Fischmann, Carl J Balibar, Li Xiao, Andrew M Galgoci, Juliana C Malinverni, Todd Mayhood, Artjohn Villafania, Ali Nahvi, Nicholas Murgolo, Christopher M Barbieri, Paul A Mann, Donna Carr, Ellen Xia, Paul Zuck, Dan Riley, Ronald E Painter, Scott S Walker, Brad Sherborne, Reynalda de Jesus, Weidong Pan, Michael A Plotkin, Jin Wu, Diane Rindgen, John Cummings, Charles G Garlisi, Rumin Zhang, Payal R Sheth, Charles J Gill, Haifeng Tang, Terry Roemer
Selective small-molecule inhibition of an RNA structural element.
Nature: 2015, 526(7575);672-7
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[DOI]
(I p)
Riboswitch modeling: Mark Sinzger
Christopher Schneider, Leo Bronstein, Jascha Diemer, Heinz Koeppl, Beatrix Suess
ROC'n'Ribo: Characterizing a Riboswitching Expression System by Modeling Single-Cell Data.
ACS Synth Biol: 2017, 6(7);1211-1224
[PubMed:28591515]
[WorldCat.org]
[DOI]
(I p)
Marco Barsacchi, Eva Maria Novoa, Manolis Kellis, Alessio Bechini
SwiSpot: modeling riboswitches by spotting out switching sequences.
Bioinformatics: 2016, 32(21);3252-3259
[PubMed:27378291]
[WorldCat.org]
[DOI]
(I p)
Chase L Beisel, Christina D Smolke
Design principles for riboswitch function.
PLoS Comput Biol: 2009, 5(4);e1000363
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[WorldCat.org]
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(I p)
The RNA world and evolution: Roman Doll
Ádám Kun, Ádám Radványi
The evolution of the genetic code: Impasses and challenges.
Biosystems: 2018, 164;217-225
[PubMed:29031737]
[WorldCat.org]
[DOI]
(I p)
Thomas Fouqueau, Fabian Blombach, Finn Werner
Evolutionary Origins of Two-Barrel RNA Polymerases and Site-Specific Transcription Initiation.
Annu Rev Microbiol: 2017, 71;331-348
[PubMed:28657884]
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(I p)
Abe Pressman, Celia Blanco, Irene A Chen
The RNA World as a Model System to Study the Origin of Life.
Curr Biol: 2015, 25(19);R953-63
[PubMed:26439358]
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[DOI]
(I p)
Jessica C Bowman, Nicholas V Hud, Loren Dean Williams
The ribosome challenge to the RNA world.
J Mol Evol: 2015, 80(3-4);143-61
[PubMed:25739364]
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(I p)
Daniel Lundin, Gustav Berggren, Derek T Logan, Britt-Marie Sjöberg
The origin and evolution of ribonucleotide reduction.
Life (Basel): 2015, 5(1);604-36
[PubMed:25734234]
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(P e)
Paul G Higgs, Niles Lehman
The RNA World: molecular cooperation at the origins of life.
Nat Rev Genet: 2015, 16(1);7-17
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(I p)
Markus Ralser
The RNA world and the origin of metabolic enzymes.
Biochem Soc Trans: 2014, 42(4);985-8
[PubMed:25109990]
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Eugene V Koonin, Artem S Novozhilov
Origin and evolution of the genetic code: the universal enigma.
IUBMB Life: 2009, 61(2);99-111
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Yuri I Wolf, Eugene V Koonin
On the origin of the translation system and the genetic code in the RNA world by means of natural selection, exaptation, and subfunctionalization.
Biol Direct: 2007, 2;14
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(I e)
RNA modification: Jan Michel Göring
Baixing Wu, Li Li, Ying Huang, Jinbiao Ma, Jinrong Min
##Title##
Curr Opin Struct Biol: 2017, 47;67-76
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(I p)
Hiroyuki Hori
Transfer RNA methyltransferases with a SpoU-TrmD (SPOUT) fold and their modified nucleosides in tRNA.
Biomolecules: 2017, 7(1);
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Ajay K Rana, Serge Ankri
Reviving the RNA World: An Insight into the Appearance of RNA Methyltransferases.
Front Genet: 2016, 7;99
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Marcus Fislage, Lina Wauters, Wim Versées
Invited review: MnmE, a GTPase that drives a complex tRNA modification reaction.
Biopolymers: 2016, 105(8);568-79
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(I p)
Clément Dégut, Luc Ponchon, Marcia Folly-Klan, Pierre Barraud, Carine Tisné
The m1A(58) modification in eubacterial tRNA: An overview of tRNA recognition and mechanism of catalysis by TrmI.
Biophys Chem: 2016, 210;27-34
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RNA degradation/processing: Lena Kricsfalussy-Hrabar
John C Zinder, Christopher D Lima
Targeting RNA for processing or destruction by the eukaryotic RNA exosome and its cofactors.
Genes Dev: 2017, 31(2);88-100
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Soraya Aït-Bara, Agamemnon J Carpousis
RNA degradosomes in bacteria and chloroplasts: classification, distribution and evolution of RNase E homologs.
Mol Microbiol: 2015, 97(6);1021-135
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Jonathan Houseley, David Tollervey
The many pathways of RNA degradation.
Cell: 2009, 136(4);763-76
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Regulation by non-coding RNA: Maxin Drömer
Yvonne Göpel, Muna A Khan, Boris Görke
Ménage à trois: post-transcriptional control of the key enzyme for cell envelope synthesis by a base-pairing small RNA, an RNase adaptor protein, and a small RNA mimic.
RNA Biol: 2014, 11(5);433-42
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Boris Görke, Jörg Vogel
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Genes Dev: 2008, 22(21);2914-25
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RNA dependent DNA Polymerases - from telomerase to retroviruses: Ansgar Stenzel
CRISPR/Cas: Science – the bacterial “immune” system: Maximilian Schreier
CRISPR/Cas: Application and groundbreaking perspectives: Johann Liebeton
Addison V Wright, James K Nuñez, Jennifer A Doudna
Biology and Applications of CRISPR Systems: Harnessing Nature's Toolbox for Genome Engineering.
Cell: 2016, 164(1-2);29-44
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Synthesis, maturation and function of tRNAs – The wobble hypothesis and specific codon usage as a molecular barrier for horizontal gene transfer: Artur Fornol
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Codon Bias as a Means to Fine-Tune Gene Expression.
Mol Cell: 2015, 59(2);149-61
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Sibah Alkatib, Lars B Scharff, Marcelo Rogalski, Tobias T Fleischmann, Annemarie Matthes, Stefanie Seeger, Mark A Schöttler, Stephanie Ruf, Ralph Bock
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PLoS Genet: 2012, 8(11);e1003076
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Tamir Tuller
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Mob Genet Elements: 2011, 1(1);75-77
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Richard Giegé, Frank Jühling, Joern Pütz, Peter Stadler, Claude Sauter, Catherine Florentz
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Wiley Interdiscip Rev RNA: 2012, 3(1);37-61
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Ingo Wohlgemuth, Corinna Pohl, Joerg Mittelstaet, Andrey L Konevega, Marina V Rodnina
Evolutionary optimization of speed and accuracy of decoding on the ribosome.
Philos Trans R Soc Lond B Biol Sci: 2011, 366(1580);2979-86
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Outlook: Finding function in mystery transcripts – eRNAs, long-non coding (lncRNA) and circular RNA (circRNA)
Shahnaz Haque, Lorna W Harries
Circular RNAs (circRNAs) in Health and Disease.
Genes (Basel): 2017, 8(12);
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Feng Liu
Enhancer-derived RNA: A Primer.
Genomics Proteomics Bioinformatics: 2017, 15(3);196-200
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Kuei-Yang Hsiao, H Sunny Sun, Shaw-Jenq Tsai
Circular RNA - New member of noncoding RNA with novel functions.
Exp Biol Med (Maywood): 2017, 242(11);1136-1141
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Yiwen Fang, Melissa J Fullwood
Roles, Functions, and Mechanisms of Long Non-coding RNAs in Cancer.
Genomics Proteomics Bioinformatics: 2016, 14(1);42-54
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Tae-Kyung Kim, Martin Hemberg, Jesse M Gray
Enhancer RNAs: a class of long noncoding RNAs synthesized at enhancers.
Cold Spring Harb Perspect Biol: 2015, 7(1);a018622
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Kevin C Wang, Howard Y Chang
Molecular mechanisms of long noncoding RNAs.
Mol Cell: 2011, 43(6);904-14
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Outlook: RNA and SELEX – new prospects and applications for targeted interference with regulatory pathways
Sujin Jeong, Seung Ryul Han, Young Ju Lee, Seong-Wook Lee
Selection of RNA aptamers specific to active prostate-specific antigen.
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Regina Stoltenburg, Christine Reinemann, Beate Strehlitz
SELEX--a (r)evolutionary method to generate high-affinity nucleic acid ligands.
Biomol Eng: 2007, 24(4);381-403
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RNA-based second messengers: Jörg Stülke
Riboswitches: Jörg Stülke
RNA dependent RNA Polymerases – the RNA replicase
The mysterious function and role of 6S-RNA and pRNA in bacteria
Benedikt Steuten, Philipp G Hoch, Katrin Damm, Sabine Schneider, Karen Köhler, Rolf Wagner, Roland K Hartmann
Regulation of transcription by 6S RNAs: insights from the Escherichia coli and Bacillus subtilis model systems.
RNA Biol: 2014, 11(5);508-21
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Amy T Cavanagh, Karen M Wassarman
6S RNA, a global regulator of transcription in Escherichia coli, Bacillus subtilis, and beyond.
Annu Rev Microbiol: 2014, 68;45-60
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Amy T Cavanagh, Karen M Wassarman
6S-1 RNA function leads to a delay in sporulation in Bacillus subtilis.
J Bacteriol: 2013, 195(9);2079-86
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Karen M Wassarman
6S RNA: a small RNA regulator of transcription.
Curr Opin Microbiol: 2007, 10(2);164-8
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RNA thermometers
