Search results for: Andrea Tanzer

Items from 1 to 8 out of 8 results

article

Transcriptome-wide effects of inverted SINEs on gene expression and their impact on RNA polymerase II activity

Mansoureh Tajaddod, Andrea Tanzer, Konstantin Licht, Michael T. Wolfinger, more

Genome Biology > 2016 > 17 > 1 > 1-16

Background Short interspersed elements (SINEs) represent the most abundant group of non-long-terminal repeat transposable elements in mammalian genomes. In primates, Alu elements are the most prominent and homogenous representatives of SINEs. Due to their frequent insertion within or close to coding regions, SINEs have been suggested to play a crucial role during genome evolution. Moreover, Alu elements...

article

Predicting RNA secondary structures from sequence and probing data

Ronny Lorenz, Michael T. Wolfinger, Andrea Tanzer, Ivo L. Hofacker

Methods > 2016 > 103 > C > 86-98

RNA secondary structures have proven essential for understanding the regulatory functions performed by RNA such as microRNAs, bacterial small RNAs, or riboswitches. This success is in part due to the availability of efficient computational methods for predicting RNA secondary structures. Recent advances focus on dealing with the inherent uncertainty of prediction by considering the ensemble of possible...

article

2D Meets 4G: G-Quadruplexes in RNA Secondary Structure Prediction

Ronny Lorenz, Stephan H. Bernhart, Jing Qin, Christian Honer zu Siederdissen, more

IEEE/ACM Transactions on Computational Biology and Bioinformatics > 2013 > 10 > 4 > 832 - 844

G-quadruplexes are abundant locally stable structural elements in nucleic acids. The combinatorial theory of RNA structures and the dynamic programming algorithms for RNA secondary structure prediction are extended here to incorporate G-quadruplexes using a simple but plausible energy model. With preliminary energy parameters, we find that the overwhelming majority of putative quadruplex-forming sequences...

article

Nematode sbRNAs: Homologs of Vertebrate Y RNAs

Ilenia Boria, Andreas R. Gruber, Andrea Tanzer, Stephan H. Bernhart, more

Journal of Molecular Evolution > 2010 > 70 > 4 > 346-358

Stem-bulge RNAs (sbRNAs) are a group of small, functionally yet uncharacterized noncoding RNAs first described in C. elegans, with a few homologous sequences postulated in C. briggsae. In this study, we report on a comprehensive survey of this ncRNA family in the phylum Nematoda. Employing homology search strategies based on both sequence and secondary structure models and a computational promoter...

article

Folding Kinetics of Large RNAs

Michael Geis, Christoph Flamm, Michael T. Wolfinger, Andrea Tanzer, more

Journal of Molecular Biology > 2008 > 379 > 1 > 160-173

We introduce here a heuristic approach to kinetic RNA folding that constructs secondary structures by stepwise combination of building blocks. These blocks correspond to subsequences and their thermodynamically optimal structures. These are determined by the standard dynamic programming approach to RNA folding. Folding trajectories are modeled at base-pair resolution using the Morgan–Higgs heuristic...

article

Evolutionary patterns of non-coding RNAs

Athanasius F. Bompfünewerer, Christoph Flamm, Claudia Fried, Guido Fritzsch, more

Theory in Biosciences > 2005 > 123 > 4 > 301-369

A plethora of new functions of non-coding RNAs (ncRNAs) have been discovered in past few years. In fact, RNA is emerging as the central player in cellular regulation, taking on active roles in multiple regulatory layers from transcription, RNA maturation, and RNA modification to translational regulation. Nevertheless, very little is known about the evolution of this “Modern RNA World” and its components...

article

Molecular Evolution of a MicroRNA Cluster

Andrea Tanzer, Peter F. Stadler

Journal of Molecular Biology > 2004 > 339 > 2 > 327-335

Many of the known microRNAs are encoded in polycistronic transcripts. Here, we reconstruct the evolutionary history of the mir17 microRNA clusters which consist of miR-17, miR-18, miR-19a, miR-19b, miR-20, miR-25, miR-92, miR-93, miR-106a, and miR-106b. The history of this cluster is governed by an initial phase of local (tandem) duplications, a series of duplications of entire clusters and subsequent...

article

Evolutionary patterns of non-coding RNAs

Athanasius F. Bompfünewerer, Christoph Flamm, Claudia Fried, Guido Fritzsch, more

Theory in Biosciences > 2004 > 123 > 4 > 301-369

A plethora of new functions of non-coding RNAs (ncRNAs) have been discovered in past few years. In fact, RNA is emerging as the central player in cellular regulation, taking on active roles in multiple regulatory layers from transcription, RNA maturation, and RNA modification to translational regulation. Nevertheless, very little is known about the evolution of this “Modern RNA World” and its components...

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