TY  - JOUR
A1  - Omidbakhshfard, Mohammad Amin
A1  - Winck, Flavia Vischi
A1  - Arvidsson, Samuel Janne
A1  - Riano-Pachon, Diego M.
A1  - Müller-Röber, Bernd
T1  - A step-by-step protocol for formaldehyde-assisted isolation of regulatory elements from Arabidopsis thaliana
JF  - Journal of integrative plant biology
N2  - The control of gene expression by transcriptional regulators and other types of functionally relevant DNA transactions such as chromatin remodeling and replication underlie a vast spectrum of biological processes in all organisms. DNA transactions require the controlled interaction of proteins with DNA sequence motifs which are often located in nucleosome-depleted regions (NDRs) of the chromatin. Formaldehyde-assisted isolation of regulatory elements (FAIRE) has been established as an easy-to-implement method for the isolation of NDRs from a number of eukaryotic organisms, and it has been successfully employed for the discovery of new regulatory segments in genomic DNA from, for example, yeast, Drosophila, and humans. Until today, however, FAIRE has only rarely been employed in plant research and currently no detailed FAIRE protocol for plants has been published. Here, we provide a step-by-step FAIRE protocol for NDR discovery in Arabidopsis thaliana. We demonstrate that NDRs isolated from plant chromatin are readily amenable to quantitative polymerase chain reaction and next-generation sequencing. Only minor modification of the FAIRE protocol will be needed to adapt it to other plants, thus facilitating the global inventory of regulatory regions across species.
KW  - Arabidopsis thaliana
KW  - chromatin
KW  - cis-regulatory elements
KW  - epigenomics
KW  - FAIRE-qPCR
KW  - FAIRE-seq
KW  - gene expression
KW  - gene regulatory network
KW  - transcription factor
Y1  - 2014
U6  - https://doi.org/10.1111/jipb.12151
SN  - 1672-9072
SN  - 1744-7909
VL  - 56
IS  - 6
SP  - 527
EP  - 538
PB  - Wiley-Blackwell
CY  - Hoboken
ER  - 
TY  - JOUR
A1  - Mettler, Tabea
A1  - Mühlhaus, Timo
A1  - Hemme, Dorothea
A1  - Schöttler, Mark Aurel
A1  - Rupprecht, Jens
A1  - Idoine, Adam
A1  - Veyel, Daniel
A1  - Pal, Sunil Kumar
A1  - Yaneva-Roder, Liliya
A1  - Winck, Flavia Vischi
A1  - Sommer, Frederik
A1  - Vosloh, Daniel
A1  - Seiwert, Bettina
A1  - Erban, Alexander
A1  - Burgos, Asdrubal
A1  - Arvidsson, Samuel Janne
A1  - Schoenfelder, Stephanie
A1  - Arnold, Anne
A1  - Guenther, Manuela
A1  - Krause, Ursula
A1  - Lohse, Marc
A1  - Kopka, Joachim
A1  - Nikoloski, Zoran
A1  - Müller-Röber, Bernd
A1  - Willmitzer, Lothar
A1  - Bock, Ralph
A1  - Schroda, Michael
A1  - Stitt, Mark
T1  - Systems analysis of the response of photosynthesis, metabolism, and growth to an increase in irradiance in the photosynthetic model organism chlamydomonas reinhardtii
JF  - The plant cell
N2  - We investigated the systems response of metabolism and growth after an increase in irradiance in the nonsaturating range in the algal model Chlamydomonas reinhardtii. In a three-step process, photosynthesis and the levels of metabolites increased immediately, growth increased after 10 to 15 min, and transcript and protein abundance responded by 40 and 120 to 240 min, respectively. In the first phase, starch and metabolites provided a transient buffer for carbon until growth increased. This uncouples photosynthesis from growth in a fluctuating light environment. In the first and second phases, rising metabolite levels and increased polysome loading drove an increase in fluxes. Most Calvin-Benson cycle (CBC) enzymes were substrate-limited in vivo, and strikingly, many were present at higher concentrations than their substrates, explaining how rising metabolite levels stimulate CBC flux. Rubisco, fructose-1,6-biosphosphatase, and seduheptulose-1,7-bisphosphatase were close to substrate saturation in vivo, and flux was increased by posttranslational activation. In the third phase, changes in abundance of particular proteins, including increases in plastidial ATP synthase and some CBC enzymes, relieved potential bottlenecks and readjusted protein allocation between different processes. Despite reasonable overall agreement between changes in transcript and protein abundance (R-2 = 0.24), many proteins, including those in photosynthesis, changed independently of transcript abundance.
Y1  - 2014
U6  - https://doi.org/10.1105/tpc.114.124537
SN  - 1040-4651
SN  - 1532-298X
VL  - 26
IS  - 6
SP  - 2310
EP  - 2350
PB  - American Society of Plant Physiologists
CY  - Rockville
ER  -