References of "Schudoma, Christian"
     in
Bookmark and Share    
Full Text
Peer Reviewed
See detailGive It AGO: The Search for miRNA-Argonaute Sorting Signals in Arabidopsis thaliana Indicates a Relevance of Sequence Positions Other than the 5'-Position Alone.
Thieme, Christoph J.; Schudoma, Christian; May, Patrick UL et al

in Frontiers in Plant Science (2012), 3

The specific recognition of miRNAs by Argonaute (AGO) proteins, the effector proteins of the RNA-induced silencing complex, constitutes the final step of the biogenesis of miRNAs and is crucial for their ... [more ▼]

The specific recognition of miRNAs by Argonaute (AGO) proteins, the effector proteins of the RNA-induced silencing complex, constitutes the final step of the biogenesis of miRNAs and is crucial for their target interaction. In the genome of Arabidopsis thaliana (Ath), 10 different AGO proteins are encoded and the sorting decision, which miRNA associates with which AGO protein, was reported to depend exclusively on the identity of the 5'-sequence position of mature miRNAs. Hence, with only four different bases possible, a 5'-position-only sorting signal would not suffice to specifically target all 10 different AGOs individually or would suggest redundant AGO action. Alternatively, other and as of yet unidentified sorting signals may exist. We analyzed a dataset comprising 117 Ath-miRNAs with clear sorting preference to either AGO1, AGO2, or AGO5 as identified in co-immunoprecipitation experiments combined with sequencing. While mutual information analysis did not identify any other single position but the 5'-nucleotide to be informative for the sorting at sufficient statistical significance, significantly better than random classification results using Random Forests nonetheless suggest that additional positions and combinations thereof also carry information with regard to the AGO sorting. Positions 2, 6, 9, and 13 appear to be of particular importance. Furthermore, uracil bases at defined positions appear to be important for the sorting to AGO2 and AGO5, in particular. No predictive value was associated with miRNA length or base pair binding pattern in the miRNA:miRNA* duplex. From inspecting available AGO gene expression data in Arabidopsis, we conclude that the temporal and spatial expression profile may also contribute to the fine-tuning of miRNA sorting and function. [less ▲]

Detailed reference viewed: 233 (5 UL)
Full Text
Peer Reviewed
See detailModeling RNA loops using sequence homology and geometric constraints.
Schudoma, Christian; May, Patrick UL; Walther, Dirk

in Bioinformatics (2010), 26(13), 1671-2

SUMMARY: RNA loop regions are essential structural elements of RNA molecules influencing both their structural and functional properties. We developed RLooM, a web application for homology-based modeling ... [more ▼]

SUMMARY: RNA loop regions are essential structural elements of RNA molecules influencing both their structural and functional properties. We developed RLooM, a web application for homology-based modeling of RNA loops utilizing template structures extracted from the PDB. RLooM allows the insertion and replacement of loop structures of a desired sequence into an existing RNA structure. Furthermore, a comprehensive database of loops in RNA structures can be accessed through the web interface. AVAILABILITY AND IMPLEMENTATION: The application was implemented in Python, MySQL and Apache. A web interface to the database and loop modeling application is freely available at http://rloom.mpimp-golm.mpg.de CONTACT: schudoma@mpimp-golm.mpg.de; may@mpimp-golm.mpg.de; walther@mpimp-golm.mpg.de [less ▲]

Detailed reference viewed: 123 (4 UL)
Full Text
Peer Reviewed
See detailSequence-structure relationships in RNA loops: establishing the basis for loop homology modeling.
Schudoma, Christian; May, Patrick UL; Nikiforova, Viktoria et al

in Nucleic Acids Research (2010), 38(3), 970-80

The specific function of RNA molecules frequently resides in their seemingly unstructured loop regions. We performed a systematic analysis of RNA loops extracted from experimentally determined three ... [more ▼]

The specific function of RNA molecules frequently resides in their seemingly unstructured loop regions. We performed a systematic analysis of RNA loops extracted from experimentally determined three-dimensional structures of RNA molecules. A comprehensive loop-structure data set was created and organized into distinct clusters based on structural and sequence similarity. We detected clear evidence of the hallmark of homology present in the sequence-structure relationships in loops. Loops differing by <25% in sequence identity fold into very similar structures. Thus, our results support the application of homology modeling for RNA loop model building. We established a threshold that may guide the sequence divergence-based selection of template structures for RNA loop homology modeling. Of all possible sequences that are, under the assumption of isosteric relationships, theoretically compatible with actual sequences observed in RNA structures, only a small fraction is contained in the Rfam database of RNA sequences and classes implying that the actual RNA loop space may consist of a limited number of unique loop structures and conserved sequences. The loop-structure data sets are made available via an online database, RLooM. RLooM also offers functionalities for the modeling of RNA loop structures in support of RNA engineering and design efforts. [less ▲]

Detailed reference viewed: 149 (1 UL)