@article{LukoszekFeistIgnatova2016,
  author    = {Lukoszek, Radoslaw and Feist, Peter and Ignatova, Zoya},
  title     = {Insights into the adaptive response of Arabidopsis thaliana to prolonged thermal stress by ribosomal profiling and RNA-Seq},
  series = {BMC plant biology},
  volume    = {16},
  journal   = {BMC plant biology},
  publisher = {BioMed Central},
  address   = {London},
  issn      = {1471-2229},
  doi       = {10.1186/s12870-016-0915-0},
  pages     = {13},
  year      = {2016},
  abstract  = {Background: Environmental stress puts organisms at risk and requires specific stress-tailored responses to maximize survival. Long-term exposure to stress necessitates a global reprogramming of the cellular activities at different levels of gene expression. Results: Here, we use ribosome profiling and RNA sequencing to globally profile the adaptive response of Arabidopsis thaliana to prolonged heat stress. To adapt to long heat exposure, the expression of many genes is modulated in a coordinated manner at a transcriptional and translational level. However, a significant group of genes opposes this trend and shows mainly translational regulation. Different secondary structure elements are likely candidates to play a role in regulating translation of those genes. Conclusions: Our data also uncover on how the subunit stoichiometry of multimeric protein complexes in plastids is maintained upon heat exposure.},
  language  = {en}
}
@misc{LukoszekFeistIgnatova2016,
  author    = {Lukoszek, Radoslaw and Feist, Peter and Ignatova, Zoya},
  title     = {Insights into the adaptive response of Arabidopsis thaliana to prolonged thermal stress by ribosomal profiling and RNA-Seq},
  series = {BMC plant biology},
  journal   = {BMC plant biology},
  url       = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-407262},
  pages     = {13},
  year      = {2016},
  abstract  = {Background: Environmental stress puts organisms at risk and requires specific stress-tailored responses to maximize survival. Long-term exposure to stress necessitates a global reprogramming of the cellular activities at different levels of gene expression. Results: Here, we use ribosome profiling and RNA sequencing to globally profile the adaptive response of Arabidopsis thaliana to prolonged heat stress. To adapt to long heat exposure, the expression of many genes is modulated in a coordinated manner at a transcriptional and translational level. However, a significant group of genes opposes this trend and shows mainly translational regulation. Different secondary structure elements are likely candidates to play a role in regulating translation of those genes. Conclusions: Our data also uncover on how the subunit stoichiometry of multimeric protein complexes in plastids is maintained upon heat exposure.},
  language  = {en}
}
@article{ZhangLukoszekMuellerRoeberetal.2011,
  author    = {Zhang, Gong and Lukoszek, Radoslaw and M{\"u}ller-R{\"o}ber, Bernd and Ignatova, Zoya},
  title     = {Different sequence signatures in the upstream regions of plant and animal tRNA genes shape distinct modes of regulation},
  series = {Nucleic acids research},
  volume    = {39},
  journal   = {Nucleic acids research},
  number    = {8},
  publisher = {Oxford Univ. Press},
  address   = {Oxford},
  issn      = {0305-1048},
  doi       = {10.1093/nar/gkq1257},
  pages     = {3331 -- 3339},
  year      = {2011},
  abstract  = {In eukaryotes, the transcription of tRNA genes is initiated by the concerted action of transcription factors IIIC (TFIIIC) and IIIB (TFIIIB) which direct the recruitment of polymerase III. While TFIIIC recognizes highly conserved, intragenic promoter elements, TFIIIB binds to the non-coding 5'-upstream regions of the tRNA genes. Using a systematic bioinformatic analysis of 11 multicellular eukaryotic genomes we identified a highly conserved TATA motif followed by a CAA-motif in the tRNA upstream regions of all plant genomes. Strikingly, the 5'-flanking tRNA regions of the animal genomes are highly heterogeneous and lack a common conserved sequence signature. Interestingly, in the animal genomes the tRNA species that read the same codon share conserved motifs in their upstream regions. Deep-sequencing analysis of 16 human tissues revealed multiple splicing variants of two of the TFIIIB subunits, Bdp1 and Brf1, with tissue-specific expression patterns. These multiple forms most likely modulate the TFIIIB-DNA interactions and explain the lack of a uniform signature motif in the tRNA upstream regions of animal genomes. The anticodon-dependent 5'-flanking motifs provide a possible mechanism for independent regulation of the tRNA transcription in various human tissues.},
  language  = {en}
}
@article{LukoszekMuellerRoeberIgnatova2013,
  author    = {Lukoszek, Radoslaw and M{\"u}ller-R{\"o}ber, Bernd and Ignatova, Zoya},
  title     = {Interplay between polymerase II- and polymerase III-assisted expression of overlapping genes},
  series = {FEBS letters : the journal for rapid publication of short reports in molecular biosciences},
  volume    = {587},
  journal   = {FEBS letters : the journal for rapid publication of short reports in molecular biosciences},
  number    = {22},
  publisher = {Elsevier},
  address   = {Amsterdam},
  issn      = {0014-5793},
  doi       = {10.1016/j.febslet.2013.09.033},
  pages     = {3692 -- 3695},
  year      = {2013},
  abstract  = {Up to 15\% of the genes in different genomes overlap. This architecture, although beneficial for the genome size, represents an obstacle for simultaneous transcription of both genes. Here we analyze the interference between RNA-polymerase II (Pol II) and RNA-polymerase III (Pol III) when transcribing their target genes encoded on opposing strands within the same DNA fragment in Arabidopsis thaliana. The expression of a Pol II-dependent protein-coding gene negatively correlated with the transcription of a Pol III-dependent, tRNA-coding gene set. We suggest that the architecture of the overlapping genes introduces an additional layer of control of gene expression. (C) 2013 Federation of European Biochemical Societies. Published by Elsevier B.V. All rights reserved.},
  language  = {en}
}
@phdthesis{Lukoszek2013,
  author    = {Lukoszek, Radoslaw},
  title     = {Global analysis of tRNA expression and translation in arabidopsis thaliana},
  address   = {Potsdam},
  pages     = {97 S.},
  year      = {2013},
  language  = {en}
}