TY  - JOUR
A1  - Lukoszek, Radoslaw
A1  - Feist, Peter
A1  - Ignatova, Zoya
T1  - Insights into the adaptive response of Arabidopsis thaliana to prolonged thermal stress by ribosomal profiling and RNA-Seq
JF  - BMC plant biology
N2  - 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.
KW  - Translation
KW  - Ribosome profiling
KW  - Transcription
KW  - RNA-Seq
KW  - Secondary structure
KW  - G-quadruplexes
KW  - Heat stress response
Y1  - 2016
U6  - https://doi.org/10.1186/s12870-016-0915-0
SN  - 1471-2229
VL  - 16
PB  - BioMed Central
CY  - London
ER  - 
TY  - JOUR
A1  - Tsukaya, Hirokazu
A1  - Byrne, Mary E.
A1  - Horiguchi, Gorou
A1  - Sugiyama, Munetaka
A1  - Van Lijsebettens, Mieke
A1  - Lenhard, Michael
T1  - How do 'housekeeping' genes control organogenesis?-unexpected new findings on the role of housekeeping genes in cell and organ differentiation
JF  - Journal of plant research
N2  - In recent years, an increasing number of mutations in what would appear to be 'housekeeping genes' have been identified as having unexpectedly specific defects in multicellular organogenesis. This is also the case for organogenesis in seed plants. Although it is not surprising that loss-of-function mutations in 'housekeeping' genes result in lethality or growth retardation, it is surprising when (1) the mutant phenotype results from the loss of function of a 'housekeeping' gene and (2) the mutant phenotype is specific. In this review, by defining housekeeping genes as those encoding proteins that work in basic metabolic and cellular functions, we discuss unexpected links between housekeeping genes and specific developmental processes. In a surprising number of cases housekeeping genes coding for enzymes or proteins with functions in basic cellular processes such as transcription, post-transcriptional modification, and translation affect plant development.
KW  - Development
KW  - Housekeeping genes
KW  - Post-transcriptional modification
KW  - RNAPII
KW  - Pre-mRNA splicing
KW  - Ribosome
KW  - 3 '-end processing
KW  - Transcription
KW  - Translation
Y1  - 2013
U6  - https://doi.org/10.1007/s10265-012-0518-2
SN  - 0918-9440
VL  - 126
IS  - 1
SP  - 3
EP  - 15
PB  - Springer
CY  - Tokyo
ER  - 
TY  - JOUR
A1  - Lukoszek, Radoslaw
A1  - Müller-Röber, Bernd
A1  - Ignatova, Zoya
T1  - Interplay between polymerase II- and polymerase III-assisted expression of overlapping genes
JF  - FEBS letters : the journal for rapid publication of short reports in molecular biosciences
N2  - 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.
KW  - Gene expression
KW  - Transcription
KW  - tRNA
KW  - Nested and overlapping genes
KW  - Arabidopsis thaliana
Y1  - 2013
U6  - https://doi.org/10.1016/j.febslet.2013.09.033
SN  - 0014-5793
SN  - 1873-3468
VL  - 587
IS  - 22
SP  - 3692
EP  - 3695
PB  - Elsevier
CY  - Amsterdam
ER  -