scholarly journals The Leaf-Order-Dependent Enhancement of Freezing Tolerance in Cold-Acclimated Arabidopsis Rosettes is not Correlated with the Transcript Levels of the Cold-Inducible Transcription Factors of CBF/DREB1

2003 ◽  
Vol 44 (9) ◽  
pp. 922-931 ◽  
Author(s):  
Taro Takagi ◽  
Masanobu Nakamura ◽  
Hiroaki Hayashi ◽  
Rie Inatsugi ◽  
Ryoichi Yano ◽  
...  
2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Sara Lago ◽  
Matteo Nadai ◽  
Filippo M. Cernilogar ◽  
Maryam Kazerani ◽  
Helena Domíniguez Moreno ◽  
...  

AbstractCell identity is maintained by activation of cell-specific gene programs, regulated by epigenetic marks, transcription factors and chromatin organization. DNA G-quadruplex (G4)-folded regions in cells were reported to be associated with either increased or decreased transcriptional activity. By G4-ChIP-seq/RNA-seq analysis on liposarcoma cells we confirmed that G4s in promoters are invariably associated with high transcription levels in open chromatin. Comparing G4 presence, location and transcript levels in liposarcoma cells to available data on keratinocytes, we showed that the same promoter sequences of the same genes in the two cell lines had different G4-folding state: high transcript levels consistently associated with G4-folding. Transcription factors AP-1 and SP1, whose binding sites were the most significantly represented in G4-folded sequences, coimmunoprecipitated with their G4-folded promoters. Thus, G4s and their associated transcription factors cooperate to determine cell-specific transcriptional programs, making G4s to strongly emerge as new epigenetic regulators of the transcription machinery.


Molecules ◽  
2019 ◽  
Vol 24 (5) ◽  
pp. 932 ◽  
Author(s):  
Dong Cao ◽  
Jiequn Fan ◽  
Xingyuan Xi ◽  
Yuan Zong ◽  
Dongxia Wang ◽  
...  

Red coleoptiles can help crops to cope with adversity and the key genes that are responsible for this trait have previously been isolated from Triticum aestivum, Triticum urartu, and Aegilops tauschii. This report describes the use of transcriptome analysis to determine the candidate gene that controls the trait for white coleoptiles in T. monococcum by screening three cultivars with white coleoptiles and two with red coleoptiles. Fifteen structural genes and two transcription factors that are involved in anthocyanin biosynthesis were identified from the assembled UniGene database through BLAST analysis and their transcript levels were then compared in white and red coleoptiles. The majority of the structural genes reflected lower transcript levels in the white than in the red coleoptiles, which implied that transcription factors related to anthocyanin biosynthesis could be candidate genes. The transcript levels of MYC transcription factor TmMYC-A1 were not significantly different between the white and red coleoptiles and all of the TmMYC-A1s contained complete functional domains. The deduced amino acid sequence of the MYB transcription factor TmMYB-A1 in red coleoptiles was homologous to TuMYB-A1, TaMYB-A1, TaMYB-B1, and TaMYB-D1, which control coleoptile color in corresponding species and contained the complete R2R3 MYB domain and the transactivation domain. TmMYB-a1 lost its two functional domains in white coleoptiles due to a single nucleotide deletion that caused premature termination at 13 bp after the initiation codon. Therefore, TmMYB-A1 is likely to be the candidate gene for the control of the red coleoptile trait, and its loss-of-function mutation leads to the white phenotype in T. monococcum.


2013 ◽  
Vol 75 (3) ◽  
pp. 364-376 ◽  
Author(s):  
YongSig Kim ◽  
Sunchung Park ◽  
Sarah J. Gilmour ◽  
Michael F. Thomashow

2016 ◽  
pp. pp.00051.2016 ◽  
Author(s):  
Zhenqian Zhang ◽  
Xiaona Hu ◽  
Yunqin Zhang ◽  
Zhenyan Miao ◽  
Can Xie ◽  
...  

2004 ◽  
Vol 16 (2) ◽  
pp. 247
Author(s):  
C. Vigneault ◽  
S. McGraw ◽  
G. Bujold ◽  
M.-A. Sirard

During the first stages of bovine embryonic development, until the 8- to 16-cell stage, the zygote is maintained by the mRNA and proteins stored in the oocyte. New embryonic transcription is reported to begin only at the 8- to 16-cell stage even if some minor transcription is detected from the 2-cell stage. In order for this to occur, several factors are required to remodel the chromatin and activate the transcription machinery. Some regulating transcription factors are possibly present in the oocyte in their mRNA form, and their translation could enhance the maternal-to-zygotic transition (MZT). In our study, we observed the expression patterns of five transcription factors (ATF2, HMGN2, HMGB2, HUEL and MSY2) in bovine in vitro-produced embryos. Embryos were produced in vitro using selected cumulus-oocyte complexes from 3-5-mm follicles of slaughterhouse ovaries. Pooled GV or MII oocytes, and 2-, 4-, 8-cell and blastocyst-stage embryos (n=40/stage) were washed in PBS and frozen at −80°C. Each pool was spiked with 1 pg of GFP RNA containing a poly(A) tail. The RNA was extracted using the Absolutely RNA Microprep Kit (Stratagene, La Jolla, CA, USA), co-precipitated with linear acrylamide (Ambion, Austin, TX, USA) and reverse-transcribed with Omniscript (Quiagen). The quantitative amplification of the transcription factors was performed in triplicate using the equivalent of 1 oocyte or embryo per reaction on a Lightcycler (Roche, Indianapolis, IN, USA). Data were normalized with the GFP levels found in each pool and a Least-Significant-Difference method was used for statistical analysis. Immunocytochemistry studies were performed on oocytes and embryos fixed and permeabilized in a solution of paraformaldehyde and Triton X-100, and results were observed on a confocal microscope. Our results show that the transcripts of the transcription factors studied are found at higher levels in pre-MZT embryos and at lower levels in subsequent stages. For HMGN2 and MSY2, there is a decrease in mRNA during oocyte maturation. For both genes, the residual mRNA remains constant up to the 4-cell stage before another loss in transcript levels in the 8-cell stage. In the case of ATF2, HMGB2 and HUEL, the maternal transcript levels are maintained until the 4-cell stage, suggesting that the mRNA is protected from degradation until its possible translation at the MZT. These results, combined to immunolocalization of the proteins, suggest a possible implication of some of these factors in the bovine MZT.


2005 ◽  
Vol 46 (9) ◽  
pp. 1525-1539 ◽  
Author(s):  
Leonid V. Savitch ◽  
Ghislaine Allard ◽  
Motoaki Seki ◽  
Laurian S. Robert ◽  
Nicholas A. Tinker ◽  
...  

2002 ◽  
Vol 99 (17) ◽  
pp. 11507-11512 ◽  
Author(s):  
Z. Gong ◽  
H. Lee ◽  
L. Xiong ◽  
A. Jagendorf ◽  
B. Stevenson ◽  
...  

2009 ◽  
Vol 21 (3) ◽  
pp. 972-984 ◽  
Author(s):  
Colleen J. Doherty ◽  
Heather A. Van Buskirk ◽  
Susan J. Myers ◽  
Michael F. Thomashow

2007 ◽  
Vol 102 (3) ◽  
pp. 1078-1089 ◽  
Author(s):  
Lisa S. Chow ◽  
Laura J. Greenlund ◽  
Yan W. Asmann ◽  
Kevin R. Short ◽  
Shelly K. McCrady ◽  
...  

We hypothesized that enhanced skeletal muscle mitochondrial function following aerobic exercise training is related to an increase in mitochondrial transcription factors, DNA abundance [mitochondrial DNA (mtDNA)], and mitochondria-related gene transcript levels, as well as spontaneous physical activity (SPA) levels. We report the effects of daily treadmill training on 12-wk-old FVB mice for 5 days/wk over 8 wk at 80% peak O2 consumption and studied the training effect on changes in body composition, glucose tolerance, muscle mtDNA muscle, mitochondria-related gene transcripts, in vitro muscle mitochondrial ATP production capacity (MATPC), and SPA levels. Compared with the untrained mice, the trained mice had higher peak O2 consumption (+18%; P < 0.001), lower percentage of abdominal (−25.4%; P < 0.02) and body fat (−19.5%; P < 0.01), improved glucose tolerance ( P < 0.04), and higher muscle mitochondrial enzyme activity (+19.5–43.8%; P < 0.04) and MATPC (+28.9 to +32.4%; P < 0.01). Gene array analysis showed significant differences in mRNAs of mitochondria-related ontology groups between the trained and untrained mice. Training also increased muscle mtDNA (+88.4 to +110%; P < 0.05), peroxisome proliferative-activated receptor-γ coactivator-1α protein (+99.5%; P < 0.04), and mitochondrial transcription factor A mRNA levels (+21.7%; P < 0.004) levels. SPA levels were higher in trained mice ( P = 0.056, two-sided t-test) and significantly correlated with two separate substrate-based measurements of MATPC ( P < 0.02). In conclusion, aerobic exercise training enhances muscle mitochondrial transcription factors, mtDNA abundance, mitochondria-related gene transcript levels, and mitochondrial function, and this enhancement in mitochondrial function occurs in association with increased SPA.


2020 ◽  
Vol 117 (46) ◽  
pp. 28906-28917
Author(s):  
Phillip A. Cleves ◽  
Cory J. Krediet ◽  
Erik M. Lehnert ◽  
Masayuki Onishi ◽  
John R. Pringle

Loss of endosymbiotic algae (“bleaching”) under heat stress has become a major problem for reef-building corals worldwide. To identify genes that might be involved in triggering or executing bleaching, or in protecting corals from it, we used RNAseq to analyze gene-expression changes during heat stress in a coral relative, the sea anemone Aiptasia. We identified >500 genes that showed rapid and extensive up-regulation upon temperature increase. These genes fell into two clusters. In both clusters, most genes showed similar expression patterns in symbiotic and aposymbiotic anemones, suggesting that this early stress response is largely independent of the symbiosis. Cluster I was highly enriched for genes involved in innate immunity and apoptosis, and most transcript levels returned to baseline many hours before bleaching was first detected, raising doubts about their possible roles in this process. Cluster II was highly enriched for genes involved in protein folding, and most transcript levels returned more slowly to baseline, so that roles in either promoting or preventing bleaching seem plausible. Many of the genes in clusters I and II appear to be targets of the transcription factors NFκB and HSF1, respectively. We also examined the behavior of 337 genes whose much higher levels of expression in symbiotic than aposymbiotic anemones in the absence of stress suggest that they are important for the symbiosis. Unexpectedly, in many cases, these expression levels declined precipitously long before bleaching itself was evident, suggesting that loss of expression of symbiosis-supporting genes may be involved in triggering bleaching.


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