scholarly journals Genome-Wide Expression and Alternative Splicing in Domesticated Sunflowers (Helianthus annuus L.) under Flooding Stress

Agronomy ◽  
2021 ◽  
Vol 11 (1) ◽  
pp. 92
Author(s):  
Joon Seon Lee ◽  
Lexuan Gao ◽  
Laura Melissa Guzman ◽  
Loren H. Rieseberg
Keyword(s):  
Gene Expression ◽  
Alternative Splicing ◽  
Mixed Model ◽  
Agricultural Land ◽  
Alcohol Fermentation ◽  
Expression Levels ◽  
Flooding Stress ◽  
Genome Wide ◽  
And Control ◽  
Gene Expression Levels

Approximately 10% of agricultural land is subject to periodic flooding, which reduces the growth, survivorship, and yield of most crops, reinforcing the need to understand and enhance flooding resistance in our crops. Here, we generated RNA-Seq data from leaf and root tissue of domesticated sunflower to explore differences in gene expression and alternative splicing (AS) between a resistant and susceptible cultivar under both flooding and control conditions and at three time points. Using a combination of mixed model and gene co-expression analyses, we were able to separate general responses of sunflower to flooding stress from those that contribute to the greater tolerance of the resistant line. Both cultivars responded to flooding stress by upregulating expression levels of known submergence responsive genes, such as alcohol dehydrogenases, and slowing metabolism-related activities. Differential AS reinforced expression differences, with reduced AS frequencies typically observed for genes with upregulated expression. Significant differences were found between the genotypes, including earlier and stronger upregulation of the alcohol fermentation pathway and a more rapid return to pre-flooding gene expression levels in the resistant genotype. Our results show how changes in the timing of gene expression following both the induction of flooding and release from flooding stress contribute to increased flooding tolerance.

scholarly journals Intra- and inter-specific variations of gene expression levels in yeast are largely neutral

2016 ◽  
Author(s):  
Jian-Rong Yang ◽  
Calum Maclean ◽  
Chungoo Park ◽  
Huabin Zhao ◽  
Jianzhi Zhang
Keyword(s):  
Gene Expression ◽  
Genome Sequence ◽  
Large Fraction ◽  
General Role ◽  
Expression Levels ◽  
Genome Wide ◽  
Sequence Variations ◽  
Expression Evolution ◽  
Molecular Phenotypes ◽  
Gene Expression Levels

ABSTRACTIt is commonly, although not universally, accepted that most intra- and inter-specific genome sequence variations are more or less neutral, whereas a large fraction of organism-level phenotypic variations are adaptive. Gene expression levels are molecular phenotypes that bridge the gap between genotypes and corresponding organism-level phenotypes. Yet, it is unknown whether natural variations in gene expression levels are mostly neutral or adaptive. Here we address this fundamental question by genome-wide profiling and comparison of gene expression levels in nine yeast strains belonging to three closely related Saccharomyces species and originating from five different ecological environments. We find that the transcriptome-based clustering of the nine strains approximates the genome sequence-based phylogeny irrespective of their ecological environments. Remarkably, only ∼0.5% of genes exhibit similar expression levels among strains from a common ecological environment, no greater than that among strains with comparable phylogenetic relationships but different environments. These and other observations strongly suggest that most intra- and inter-specific variations in yeast gene expression levels result from the accumulation of random mutations rather than environmental adaptations. This finding has profound implications for understanding the driving force of gene expression evolution, genetic basis of phenotypic adaptation, and general role of stochasticity in evolution.

P1-229: Genome-Wide Association Study of Brain Gene Expression Levels (eGWAS)

2011 ◽  
Vol 7 ◽  
pp. S184-S184
Author(s):  
Nilufer Ertekin-Taner ◽  
Fanggeng Zou ◽  
High Chai ◽  
Curtis Younkin ◽  
Julia Crook ◽  
...  
Keyword(s):  
Gene Expression ◽  
Association Study ◽  
Genome Wide Association Study ◽  
Genome Wide Association ◽  
Expression Levels ◽  
Brain Gene Expression ◽  
Genome Wide ◽  
Gene Expression Levels

Genome-wide Association of Haplotype Markers to Gene Expression Levels

2003 ◽  
Vol 68 (0) ◽  
pp. 89-108
Author(s):  
A. WINDEMUTH ◽  
M. KUMAR ◽  
K. NANDABALAN ◽  
B. KOSHY ◽  
C. XU ◽  
...  
Keyword(s):  
Gene Expression ◽  
Genome Wide Association ◽  
Expression Levels ◽  
Genome Wide ◽  
Gene Expression Levels

scholarly journals A Genome-Wide Study of DNA Methylation Patterns and Gene Expression Levels in Multiple Human and Chimpanzee Tissues

PLoS Genetics ◽  
2011 ◽  
Vol 7 (2) ◽  
pp. e1001316 ◽  
Author(s):  
Athma A. Pai ◽  
Jordana T. Bell ◽  
John C. Marioni ◽  
Jonathan K. Pritchard ◽  
Yoav Gilad
Keyword(s):  
Gene Expression ◽  
Dna Methylation ◽  
Expression Levels ◽  
Genome Wide ◽  
A Genome ◽  
Methylation Patterns ◽  
Genome Wide Study ◽  
Gene Expression Levels

scholarly journals Gene expression levels as endophenotypes in genome-wide association studies of Alzheimer disease

Neurology ◽  
2010 ◽  
Vol 74 (6) ◽  
pp. 480-486 ◽  
Author(s):  
F. Zou ◽  
M. M. Carrasquillo ◽  
V. S. Pankratz ◽  
O. Belbin ◽  
K. Morgan ◽  
...  
Keyword(s):  
Gene Expression ◽  
Alzheimer Disease ◽  
Association Studies ◽  
Genome Wide Association ◽  
Genome Wide Association Studies ◽  
Expression Levels ◽  
Genome Wide ◽  
Gene Expression Levels

scholarly journals Integrative genomic strategies applied to a lymphoblast cell line model reveal specific transcriptomic signatures associated with clozapine response

2020 ◽  
Author(s):  
SAJ de With ◽  
APS Ori ◽  
T Wang ◽  
SL Pulit ◽  
E Strengman ◽  
...  
Keyword(s):  
Gene Expression ◽  
Dna Methylation ◽  
Adverse Effects ◽  
Drug Targets ◽  
Molecular Mechanisms ◽  
Disease Risk ◽  
Density Lipoprotein ◽  
Expression Levels ◽  
Genome Wide ◽  
Gene Expression Levels

AbstractClozapine is an important antipsychotic drug. However, its use is often accompanied by metabolic adverse effects and, in rare instances, agranulocytosis. The molecular mechanisms underlying these adverse events are unclear. To gain more insights into the response to clozapine at the molecular level, we exposed lymphoblastoid cell lines (LCLs) to increasing concentrations of clozapine and measured genome-wide gene expression and DNA methylation profiles. We observed robust and significant changes in gene expression levels due to clozapine (n = 463 genes at FDR < 0.05) affecting cholesterol and cell cycle pathways. At the level of DNA methylation, we find significant changes upstream of the LDL receptor, in addition to global enrichments of regulatory, immune and developmental pathways. By integrating these data with human tissue gene expression levels obtained from the Genotype-Tissue Expression project (GTEx), we identified specific tissues, including liver and several tissues involved in immune, endocrine and metabolic functions, that clozapine treatment may disproportionately affect. Notably, differentially expressed genes were not enriched for genome-wide disease risk of schizophrenia or for known psychotropic drug targets. However, we did observe a nominally significant association of genetic signals related to total cholesterol and low-density lipoprotein levels. Together, these results shed light on the biological mechanisms through which clozapine functions. The observed associations with cholesterol pathways, its genetic architecture and specific tissue effects may be indicative of the metabolic adverse effects observed in clozapine users. LCLs may thus serve as a useful tool to study these molecular mechanisms further.

scholarly journals Evaluation of microphthalmia associated transcription factor (MITF) expression in peripheral blood of a population with malign melanoma and control population and cell lines

1969 ◽  
Vol 40 (1) ◽  
pp. 16-33
Author(s):  
Nelson Rangel ◽  
Milena Rondón ◽  
Sandra Ramírez
Keyword(s):  
Gene Expression ◽  
Transcription Factor ◽  
Cell Lines ◽  
Peripheral Blood ◽  
Housekeeping Genes ◽  
Expression Levels ◽  
Free People ◽  
And Control ◽  
Mitf Expression ◽  
Gene Expression Levels

Background: The incidence of malign melanoma tumours has increased more rapidly than any other type of cancer; this has intensified the searching for tools that facilitate early detection of melanoma. Microphthalmia associated transcription factor (MITF) is currently known as being a master melanocyte regulator. The article analyses MITF gene expression in peripheral blood of individuals suffering from melanoma, compared to people without any type of cancer and some cell lines. Materials and methods: Thirty one samples of peripheral blood were used: 19 from patients having melanoma and 12 from healthy people. Then RNA was extracted from these samples. MITF and housekeeping genes (b2M and GAPDH) expression levels were then quantified by real-time PCR. Five cell lines were also used to determine the MITF expression. Results: MITF gene expression could be observed in all individuals, though no statistical significant differences were found among expression levels in the groups studied (p=0.09). Even so, MITF expression in the group of patients suffering from melanoma was much more variable than that observed in the group of cancer-free people. Expression was detected in the cell line AGS (gastric adenocarcinoma), not yet described. Conclusions: MITF gene expression levels were detected in the peripheral blood from both people suffering from melanoma and people without any type of cancer. However, variability in the number of molecules in MITF gene expression was observed in people with melanoma, this suggests the presence of tumour cells in circulation.

scholarly journals Xylitol and capsular gene expression in Streptococcus pneumoniae

2009 ◽  
Vol 58 (11) ◽  
pp. 1470-1473 ◽  
Author(s):  
Paula Kurola ◽  
Terhi Tapiainen ◽  
Tarja Kaijalainen ◽  
Matti Uhari ◽  
Annika Saukkoriipi
Keyword(s):  
Gene Expression ◽  
Streptococcus Pneumoniae ◽  
Otitis Media ◽  
Acute Otitis Media ◽  
Brain Heart Infusion ◽  
Rrna Gene ◽  
Expression Levels ◽  
Atcc Strain ◽  
And Control ◽  
Gene Expression Levels

Xylitol is a sugar alcohol that inhibits the growth and adherence of Streptococcus pneumoniae. In clinical trials, xylitol has been shown to decrease the occurrence of acute otitis media in day-care children but did not decrease nasopharyngeal carriage of the pneumococci. It has also been shown that xylitol affects the ultrastructure of the pneumococcal capsule. Here, it was hypothesized that xylitol might affect the expression of pneumococcal capsular genes. Capsule gene expression levels were studied in 24 clinical pneumococcal isolates and one ATCC strain (49619) by using a real-time RT-PCR method targeting the mRNA of the second gene of the pneumococcal capsular locus, the cpsB gene. The isolates were exposed to 5 % glucose, 5 % xylitol and control medium (brain heart infusion medium containing 10 % fetal bovine serum) for 2 h. cpsB gene expression levels were measured by using a relative quantification method with calibrator normalization where the 16S rRNA gene of pneumococcus was used as a reference. Exposure to xylitol lowered cpsB gene expression levels significantly compared with those in the control (P=0.035) and glucose (P=0.011) media. This finding supports previous results where exposure to xylitol changed the ultrastructure of the pneumococcal capsule and could explain further the high clinical efficacy of xylitol in preventing otitis media.

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