TY  - JOUR
A1  - Gassen, Alwine
A1  - Brechtefeld, Doris
A1  - Schandry, Niklas
A1  - Arteaga-Salas, J. Manuel
A1  - Israel, Lars
A1  - Imhof, Axel
A1  - Janzen, Christian J.
T1  - DOT1A-dependent H3K76 methylation is required for replication regulation in Trypanosoma brucei
JF  - Nucleic Acids Research
N2  - Cell-cycle progression requires careful regulation to ensure accurate propagation of genetic material to the daughter cells. Although many cell-cycle regulators are evolutionarily conserved in the protozoan parasite Trypanosoma brucei, novel regulatory mechanisms seem to have evolved. Here, we analyse the function of the histone methyltransferase DOT1A during cell-cycle progression. Over-expression of DOT1A generates a population of cells with aneuploid nuclei as well as enucleated cells. Detailed analysis shows that DOT1A over-expression causes continuous replication of the nuclear DNA. In contrast, depletion of DOT1A by RNAi abolishes replication but does not prevent karyokinesis. As histone H3K76 methylation has never been associated with replication control in eukaryotes before, we have discovered a novel function of DOT1 enzymes, which might not be unique to trypanosomes.
KW  - variants
KW  - cell-cycle regulation
KW  - blood-stream forms
KW  - african trypanosomes
KW  - mammalian cells
KW  - DNA replication
KW  - DOT1
KW  - protein
KW  - transcription
KW  - cultivation
Y1  - 2012
U6  - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-131449
VL  - 40
IS  - 20
ER  - 
TY  - JOUR
A1  - Wolf, Beat
A1  - Kuonen, Pierre
A1  - Dandekar, Thomas
A1  - Atlan, David
T1  - DNAseq workflow in a diagnostic context and an example of a user friendly implementation
JF  - BioMed Research International
N2  - Over recent years next generation sequencing (NGS) technologies evolved from costly tools used by very few, to a much more accessible and economically viable technology. Through this recently gained popularity, its use-cases expanded from research environments into clinical settings. But the technical know-how and infrastructure required to analyze the data remain an obstacle for a wider adoption of this technology, especially in smaller laboratories. We present GensearchNGS, a commercial DNAseq software suite distributed by Phenosystems SA. The focus of GensearchNGS is the optimal usage of already existing infrastructure, while keeping its use simple. This is achieved through the integration of existing tools in a comprehensive software environment, as well as custom algorithms developed with the restrictions of limited infrastructures in mind. This includes the possibility to connect multiple computers to speed up computing intensive parts of the analysis such as sequence alignments. We present a typical DNAseq workflow for NGS data analysis and the approach GensearchNGS takes to implement it. The presented workflow goes from raw data quality control to the final variant report. This includes features such as gene panels and the integration of online databases, like Ensembl for annotations or Cafe Variome for variant sharing.
KW  - next generation sequencing
KW  - genome browser
KW  - mutation
KW  - algorithm
KW  - database
KW  - format
KW  - discovery
KW  - exome
KW  - variants
KW  - alignment
Y1  - 2015
U6  - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-144527
IS  - 403497
ER  -