scholarly journals Control of seed dormancy inArabidopsisby acis-acting noncoding antisense transcript

2016 ◽  
Vol 113 (48) ◽  
pp. E7846-E7855 ◽  
Author(s):  
Halina Fedak ◽  
Malgorzata Palusinska ◽  
Katarzyna Krzyczmonik ◽  
Lien Brzezniak ◽  
Ruslan Yatusevich ◽  
...  
Keyword(s):  
Seed Dormancy ◽  
Antisense Rna ◽  
Noncoding Rna ◽  
Major Quantitative Trait Locus ◽  
Antisense Transcript ◽  
Evolutionary Conservation ◽  
Allele Specific ◽  
Trait Locus ◽  
High Level ◽  
Do So

Seed dormancy is one of the most crucial process transitions in a plant’s life cycle. Its timing is tightly controlled by the expression level of the Delay of Germination 1 gene (DOG1).DOG1is the major quantitative trait locus for seed dormancy inArabidopsisand has been shown to control dormancy in many other plant species. This is reflected by the evolutionary conservation of the functional short alternatively polyadenylated form of theDOG1mRNA. Notably, the 3′ region ofDOG1, including the last exon that is not included in this transcript isoform, shows a high level of conservation at the DNA level, but the encoded polypeptide is poorly conserved. Here, we demonstrate that this region ofDOG1contains a promoter for the transcription of a noncoding antisense RNA,asDOG1, that is 5′ capped, polyadenylated, and relatively stable. This promoter is autonomous andasDOG1has an expression profile that is different from knownDOG1transcripts. Using several approaches we show thatasDOG1strongly suppressesDOG1expression during seed maturation incis, but is unable to do so intrans. Therefore, the negative regulation of seed dormancy byasDOG1incisresults in allele-specific suppression ofDOG1expression and promotes germination. Given the evolutionary conservation of theasDOG1promoter, we propose that thiscis-constrained noncoding RNA-mediated mechanism limiting the duration of seed dormancy functions across the Brassicaceae.

scholarly journals Natural Antisense Transcript PEBP1P3 Regulates the RNA Expression, DNA Methylation and Histone Modification of CD45 Gene

Genes ◽  
2021 ◽  
Vol 12 (5) ◽  
pp. 759
Author(s):  
Zhongjing Su ◽  
Guangyu Liu ◽  
Bin Zhang ◽  
Ze Lin ◽  
Dongyang Huang
Keyword(s):  
Dna Methylation ◽  
Alternative Splicing ◽  
Histone Modification ◽  
Antisense Rna ◽  
Noncoding Rna ◽  
Antisense Transcript ◽  
Natural Antisense Transcript ◽  
Regulation Of Expression ◽  
Splicing Isoforms ◽  
Intron 2

The leukocyte common antigen CD45 is a transmembrane phosphatase expressed on all nucleated hemopoietic cells, and the expression levels of its splicing isoforms are closely related to the development and function of lymphocytes. PEBP1P3 is a natural antisense transcript from the opposite strand of CD45 intron 2 and is predicted to be a noncoding RNA. The genotype-tissue expression and quantitative PCR data suggested that PEBP1P3 might be involved in the regulation of expression of CD45 splicing isoforms. To explore the regulatory mechanism of PEBP1P3 in CD45 expression, DNA methylation and histone modification were detected by bisulfate sequencing PCR and chromatin immunoprecipitation assays, respectively. The results showed that after the antisense RNA PEBP1P3 was knocked down by RNA interference, the DNA methylation of CD45 intron 2 was decreased and histone H3K9 and H3K36 trimethylation at the alternative splicing exons of CD45 DNA was increased. Knockdown of PEBP1P3 also increased the binding levels of chromatin conformation organizer CTCF at intron 2 and the alternative splicing exons of CD45. The present results indicate that the natural antisense RNA PEBP1P3 regulated the alternative splicing of CD45 RNA, and that might be correlated with the regulation of histone modification and DNA methylation.

Seed dormancy in barley: identifying superior genotypes through incorporating epistatic interactions

2008 ◽  
Vol 59 (6) ◽  
pp. 517 ◽  
Author(s):  
Y. Bonnardeaux ◽  
C. Li ◽  
R. Lance ◽  
X. Q. Zhang ◽  
K. Sivasithamparam ◽  
...  
Keyword(s):  
Seed Dormancy ◽  
Quantitative Trait ◽  
Major Quantitative Trait Locus ◽  
Specific Gene ◽  
Phenotypic Variance ◽  
Epistatic Interactions ◽  
Minor Qtls ◽  
Superior Genotypes ◽  
Gene Complexes ◽  
Trait Locus

A genetic linkage map of barley with 128 molecular markers was constructed using a doubled haploid (DH) mapping population derived from a cross between barley (Hordeum vulgare) cvv. Stirling and Harrington. Quantitative trait loci controlling seed dormancy were characterised in the population. A major quantitative trait locus (QTL) controlling seed dormancy and accounting for over half the phenotypic variation (52.17%) was identified on the distal end of the long arm of chromosome 5H. Minor QTLs were also detected near the centromeric region of 5H and on chromosomes 1H and 3H. These minor QTLs with additive effects accounted for 7.52% of the phenotypic variance measured. Examination of epistatic interactions further detected additional minor QTLs near the centromere of 2H and on the long arm and short arms of 4H. Combinations of parental alleles at the QTL locations in predictive analyses indicated dramatic differences in germination. These results emphasise the potential differences in dormancy that can be achieved through the use of specific gene combinations and highlights the importance of minor genes and the epistatic interactions that occur between them. This study found that the combination of Stirling alleles at the two QTL locations on the 5H chromosome and Harrington alleles at the 1H and 3H QTL locations significantly produced the greatest dormancy. Uncovering gene complexes controlling the trait may enable breeders to produce superior genotypes with the desirable allele combinations necessary for manipulating seed dormancy in barley.

scholarly journals Mapping of affordability levels for photovoltaic-based electricity generation in the solar belt of sub-Saharan Africa, East Asia and South Asia

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Sándor Szabó ◽  
Irene Pinedo Pascua ◽  
Daniel Puig ◽  
Magda Moner-Girona ◽  
Mario Negre ◽  
...  
Keyword(s):  
East Asia ◽  
South Asia ◽  
Electricity Generation ◽  
Sub Saharan Africa ◽  
Solar Photovoltaic ◽  
Term Operation ◽  
Sub Saharan ◽  
High Level ◽  
Do So

AbstractLack of access to modern forms of energy hampers efforts to reduce poverty. The provision of electricity to off-grid communities is therefore a long-standing developmental goal. Yet, many off-grid electrification projects neglect mid- and long-term operation and maintenance costs. When this is the case, electricity services are unlikely to be affordable to the communities that are the project’s primary target. Here we show that, compared with diesel-powered electricity generation systems, solar photovoltaic systems are more affordable to no less than 36% of the unelectrified populations in East Asia, South Asia, and sub-Saharan Africa. We do so by developing geo-referenced estimates of affordability at a high level of resolution (1 km2). The analysis illustrates the differences in affordability that may be found at the subnational level, which underscores that electrification investments should be informed by subnational data.

scholarly journals An antisense noncoding RNA enhances translation via localised structural rearrangements of its cognate mRNA

2021 ◽  
Author(s):  
Rodrigo S Reis ◽  
Jules Deforges ◽  
Romy R Schmidt ◽  
Jos H M Schippers ◽  
Yves Poirier
Keyword(s):  
Antisense Rna ◽  
Noncoding Rna ◽  
Regulatory Region ◽  
Structural Rearrangement ◽  
Start Codon ◽  
Structural Rearrangements ◽  
Eukaryotic Genes ◽  
Inhibitory Region ◽  
Rna Interaction

Abstract A large portion of eukaryotic genes are associated with noncoding, natural antisense transcripts (NATs). Despite sharing extensive sequence complementarity with their sense mRNAs, mRNA-NAT pairs elusively often evade dsRNA-cleavage and siRNA-triggered silencing. More surprisingly, some NATs enhance translation of their sense mRNAs by yet unknown mechanism(s). Here we show that translation enhancement of the rice (Oryza sativa) PHOSPHATE1.2 (PHO1.2) mRNA is enabled by specific structural rearrangements guided by its noncoding antisense RNA (cis-NATpho1.2). Their interaction in vitro revealed no evidence of widespread intermolecular dsRNA formation, but rather specific local changes in nucleotide base-pairing, leading to higher flexibility of PHO1.2 mRNA at a key high GC regulatory region inhibiting translation, approximately 350 nucleotides downstream of the start codon. Sense-antisense RNA interaction increased formation of the 80S complex in PHO1.2, possibly by inducing structural rearrangement within this inhibitory region, thus making this mRNA more accessible to 60S. This work presents a framework for nucleotide-resolution studies of functional mRNA-antisense pairs. One-sentence summary: Interaction between PHO1.2 mRNA and its cis-natural antisense transcript enhances translation via a mechanism involving a local conformational shift and disruption of a key inhibitory region.

scholarly journals Idiosyncratic volatility, option-based measures of informed trading, and investor attention

2021 ◽  
Author(s):  
Hannes Mohrschladt ◽  
Judith C. Schneider
Keyword(s):  
Stock Returns ◽  
Idiosyncratic Volatility ◽  
Investor Attention ◽  
Intuitive Idea ◽  
Joint Examination ◽  
Stock Market Investors ◽  
Private Investors ◽  
High Level ◽  
Do So ◽  
Option Market

AbstractWe establish a direct link between sophisticated investors in the option market, private stock market investors, and the idiosyncratic volatility (IVol) puzzle. To do so, we employ three option-based volatility spreads and attention data from Google Trends. In line with the IVol puzzle, the volatility spreads indicate that sophisticated investors indeed consider high-IVol stocks as being overvalued. Moreover, the option measures help to distinguish overpriced from fairly priced high-IVol stocks. Thus, these measures are able to predict the IVol puzzle’s magnitude in the cross-section of stock returns. Further, we link the origin of the IVol puzzle to the trading activity of irrational private investors as the return predictability only exists among stocks that receive a high level of private investor attention. Overall, our joint examination of option and stock markets sheds light on the behavior of different investor groups and their contribution to the IVol puzzle. Thereby, our analyses support the intuitive idea that noise trading leads to mispricing, which is identified by sophisticated investors and exploited in the option market.

Differential effects of Cdc68 on cell cycle-regulated promoters in Saccharomyces cerevisiae

1994 ◽  
Vol 14 (11) ◽  
pp. 7455-7465 ◽  
Author(s):  
D Lycan ◽  
G Mikesell ◽  
M Bunger ◽  
L Breeden
Keyword(s):  
Cell Cycle ◽  
Chromatin Structure ◽  
Gene Activation ◽  
High Level Expression ◽  
Specific Component ◽  
Allele Specific ◽  
High Level ◽  
Cyclin Genes ◽  
Regulated Promoters

Swi4 and Swi6 form a complex which is required for Start-dependent activation of HO and for high-level expression of G1 cyclin genes CLN1 and CLN2. To identify other regulators of this pathway, we screened for dominant, recessive, conditional, and allele-specific suppressors of swi4 mutants. We isolated 16 recessive suppressors that define three genes, SSF1, SSF5, and SSF9 (suppressor of swi four). Mutations in all three genes bypass the requirement for both Swi4 and Swi6 for HO transcription and activate transcription from reporter genes lacking upstream activating sequences (UASs). SSF5 is allelic with SIN4 (TSF3), a gene implicated in global repression of transcription and chromatin structure, and SSF9 is likely to be a new global repressor of transcription. SSF1 is allelic with CDC68 (SPT16). cdc68 mutations have been shown to increase expression from defective promoters, while preventing transcription from other intact promoters, including CLN1 and CLN2. We find that CDC68 is a required activator of both SWI4 and SWI6, suggesting that CDC68's role at the CLN promoters may be indirect. The target of CDC68 within the SWI4 promoter is complex in that known activating elements (MluI cell cycle boxes) in the SWI4 promoter are required for CDC68 dependence but only within the context of the full-length promoter. This result suggests that there may be both a chromatin structure and a UAS-specific component to Cdc68 function at SWI4. We suggest that Cdc68 functions both in the assembly of repressive complexes that form on many intact promoters in vivo and in the relief of this repression during gene activation.

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