scholarly journals Mutation of a major CG methylase in rice causes genome-wide hypomethylation, dysregulated genome expression, and seedling lethality

2014 ◽  
Vol 111 (29) ◽  
pp. 10642-10647 ◽  
Author(s):  
L. Hu ◽  
N. Li ◽  
C. Xu ◽  
S. Zhong ◽  
X. Lin ◽  
...  
Keyword(s):  
Genome Expression ◽  
Genome Wide ◽  
Seedling Lethality

scholarly journals Drosophila primary microRNA-8 encodes a microRNA-encoded peptide acting in parallel of miR-8

2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Audrey Montigny ◽  
Patrizia Tavormina ◽  
Carine Duboe ◽  
Hélène San Clémente ◽  
Marielle Aguilar ◽  
...  
Keyword(s):  
Regulatory Peptides ◽  
Ribosome Profiling ◽  
Small Peptides ◽  
Molecular Approaches ◽  
Genome Expression ◽  
Genome Wide ◽  
Short Orfs ◽  
Regulatory Potential ◽  
Regulatory Feedback Loop ◽  
And Function

Abstract Background Recent genome-wide studies of many species reveal the existence of a myriad of RNAs differing in size, coding potential and function. Among these are the long non-coding RNAs, some of them producing functional small peptides via the translation of short ORFs. It now appears that any kind of RNA presumably has a potential to encode small peptides. Accordingly, our team recently discovered that plant primary transcripts of microRNAs (pri-miRs) produce small regulatory peptides (miPEPs) involved in auto-regulatory feedback loops enhancing their cognate microRNA expression which in turn controls plant development. Here we investigate whether this regulatory feedback loop is present in Drosophila melanogaster. Results We perform a survey of ribosome profiling data and reveal that many pri-miRNAs exhibit ribosome translation marks. Focusing on miR-8, we show that pri-miR-8 can produce a miPEP-8. Functional assays performed in Drosophila reveal that miPEP-8 affects development when overexpressed or knocked down. Combining genetic and molecular approaches as well as genome-wide transcriptomic analyses, we show that miR-8 expression is independent of miPEP-8 activity and that miPEP-8 acts in parallel to miR-8 to regulate the expression of hundreds of genes. Conclusion Taken together, these results reveal that several Drosophila pri-miRs exhibit translation potential. Contrasting with the mechanism described in plants, these data shed light on the function of yet undescribed primary-microRNA-encoded peptides in Drosophila and their regulatory potential on genome expression.

scholarly journals Functional Genomics for the Identification of Modulators of Platelet-Dependent Thrombus Formation

TH Open ◽  
2018 ◽  
Vol 02 (03) ◽  
pp. e272-e279
Author(s):  
Elien Vermeersch ◽  
Benedicte Nuyttens ◽  
Claudia Tersteeg ◽  
Katleen Broos ◽  
Simon De Meyer ◽  
...  
Keyword(s):  
Functional Genomics ◽  
Platelet Reactivity ◽  
Thrombus Formation ◽  
Cell Types ◽  
Correlative Analysis ◽  
Genome Expression ◽  
Genome Wide ◽  
Whole Genome Expression

AbstractDespite the absence of the genome in platelets, transcription profiling provides important insights into platelet function and can help clarify abnormalities in platelet disorders. The Bloodomics Consortium performed whole-genome expression analysis comparing in vitro–differentiated megakaryocytes (MKs) with in vitro–differentiated erythroblasts and different blood cell types. This allowed the identification of genes with upregulated expression in MKs compared with all other cell lineages, among the receptors BAMBI, LRRC32, ESAM, and DCBLD2. In a later correlative analysis of genome-wide platelet RNA expression with interindividual human platelet reactivity, LLRFIP and COMMD7 were additionally identified. A functional genomics approach using morpholino-based silencing in zebrafish identified various roles for all of these selected genes in thrombus formation. In this review, we summarize the role of the six identified genes in zebrafish and discuss how they correlate with subsequently performed mouse experiments.

scholarly journals Drosophila primary microRNA-8 encodes a microRNA encoded peptide acting in parallel of miR-8

2021 ◽  
Author(s):  
Audrey Montigny ◽  
Patrizia Tavormina ◽  
Carine Duboe ◽  
Hélène San Clémente ◽  
Marielle Aguilar ◽  
...  
Keyword(s):  
Regulatory Peptides ◽  
Ribosome Profiling ◽  
Small Peptides ◽  
Molecular Approaches ◽  
Genome Expression ◽  
Genome Wide ◽  
Short Orfs ◽  
Regulatory Potential ◽  
Regulatory Feedback Loop ◽  
And Function

SummaryBackgroundRecent genome-wide studies of many species reveal the existence of a myriad of RNAs differing in size, coding potential and function. Among these are the long non-coding RNAs, some of them producing functional small peptides via the translation of short ORFs. It now appears that any kind of RNA presumably has a potential to encode small peptides. Accordingly, our team recently discovered that plant primary transcripts of microRNAs (pri-miRNAs) produce small regulatory peptides (miPEPs) involved in auto-regulatory feedback loops enhancing their cognate microRNA expression which in turn controls plant development. Here we investigate whether this regulatory feedback loop is present in Drosophila melanogaster.ResultsWe perform a survey of ribosome profiling data and reveal that many pri-miRNAs exhibit ribosome translation marks. Focusing on miR-8, we show that pri-miR-8 can produce a miPEP-8. Functional assays performed in Drosophila reveal that miPEP-8 affects development when overexpressed or knocked down. Combining genetic and molecular approaches as well as genome-wide transcriptomic analyses, we show that miR-8 expression is independent of miPEP-8 activity and that miPEP-8 acts in parallel to miR-8 to regulate the expression of hundreds of genes.ConclusionTaken together, these results reveal that several Drosophila pri-miRNAs exhibit translation potential. Contrasting with the mechanism described in plants, these data shed light on the function of yet un-described pri-microRNA encoded peptides in Drosophila and their regulatory potential on genome expression.

scholarly journals Sex-chromosome dosage effects on gene expression in humans

2018 ◽  
Vol 115 (28) ◽  
pp. 7398-7403 ◽  
Author(s):  
Armin Raznahan ◽  
Neelroop N. Parikshak ◽  
Vijay Chandran ◽  
Jonathan D. Blumenthal ◽  
Liv S. Clasen ◽  
...  
Keyword(s):  
Gene Expression ◽  
Transcription Factor ◽  
Sex Chromosome ◽  
Theoretical Models ◽  
Cellular Functions ◽  
Systematic Map ◽  
Genome Expression ◽  
Dosage Effects ◽  
Genome Wide ◽  
Coexpression Networks

A fundamental question in the biology of sex differences has eluded direct study in humans: How does sex-chromosome dosage (SCD) shape genome function? To address this, we developed a systematic map of SCD effects on gene function by analyzing genome-wide expression data in humans with diverse sex-chromosome aneuploidies (XO, XXX, XXY, XYY, and XXYY). For sex chromosomes, we demonstrate a pattern of obligate dosage sensitivity among evolutionarily preserved X-Y homologs and update prevailing theoretical models for SCD compensation by detecting X-linked genes that increase expression with decreasing X- and/or Y-chromosome dosage. We further show that SCD-sensitive sex-chromosome genes regulate specific coexpression networks of SCD-sensitive autosomal genes with critical cellular functions and a demonstrable potential to mediate previously documented SCD effects on disease. These gene coexpression results converge with analysis of transcription factor binding site enrichment and measures of gene expression in murine knockout models to spotlight the dosage-sensitive X-linked transcription factor ZFX as a key mediator of SCD effects on wider genome expression. Our findings characterize the effects of SCD broadly across the genome, with potential implications for human phenotypic variation.

scholarly journals Available Software for Meta-Analyses of Genome-Wide Expression Studies

2019 ◽  
Vol 20 (5) ◽  
pp. 325-331 ◽  
Author(s):  
Diego A. Forero
Keyword(s):  
Meta Analysis ◽  
Model Organisms ◽  
Online Programs ◽  
Advantages And Disadvantages ◽  
Genome Expression ◽  
Expression Studies ◽  
Genome Wide ◽  
Powerful Approach ◽  
Meta Analyses ◽  
Genome Wide Expression

Advances in transcriptomic methods have led to a large number of published Genome- Wide Expression Studies (GWES), in humans and model organisms. For several years, GWES involved the use of microarray platforms to compare genome-expression data for two or more groups of samples of interest. Meta-analysis of GWES is a powerful approach for the identification of differentially expressed genes in biological topics or diseases of interest, combining information from multiple primary studies. In this article, the main features of available software for carrying out meta-analysis of GWES have been reviewed and seven packages from the Bioconductor platform and five packages from the CRAN platform have been described. In addition, nine previously described programs and four online programs are reviewed. Finally, advantages and disadvantages of these available programs and proposed key points for future developments have been discussed.

scholarly journals Transcriptome and Methylome Analysis Reveal Complex Cross-Talks between Thyroid Hormone and Glucocorticoid Signaling at Xenopus Metamorphosis

Cells ◽  
2021 ◽  
Vol 10 (9) ◽  
pp. 2375
Author(s):  
Nicolas Buisine ◽  
Alexis Grimaldi ◽  
Vincent Jonchere ◽  
Muriel Rigolet ◽  
Corinne Blugeon ◽  
...  
Keyword(s):  
Gene Expression ◽  
Dna Methylation ◽  
Thyroid Hormone ◽  
Biological Networks ◽  
Complex Interactions ◽  
Genome Expression ◽  
Biological Responses ◽  
Genome Wide ◽  
Glucocorticoid Signaling ◽  
Methylome Analysis

Background: Most work in endocrinology focus on the action of a single hormone, and very little on the cross-talks between two hormones. Here we characterize the nature of interactions between thyroid hormone and glucocorticoid signaling during Xenopus tropicalis metamorphosis. Methods: We used functional genomics to derive genome wide profiles of methylated DNA and measured changes of gene expression after hormonal treatments of a highly responsive tissue, tailfin. Clustering classified the data into four types of biological responses, and biological networks were modeled by system biology. Results: We found that gene expression is mostly regulated by either T3 or CORT, or their additive effect when they both regulate the same genes. A small but non-negligible fraction of genes (12%) displayed non-trivial regulations indicative of complex interactions between the signaling pathways. Strikingly, DNA methylation changes display the opposite and are dominated by cross-talks. Conclusion: Cross-talks between thyroid hormones and glucocorticoids are more complex than initially envisioned and are not limited to the simple addition of their individual effects, a statement that can be summarized with the pseudo-equation: TH ∙ GC > TH + GC. DNA methylation changes are highly dynamic and buffered from genome expression.

scholarly journals Available software for meta-analyses of genome-wide expression studies

2019 ◽  
Author(s):  
Diego A Forero
Keyword(s):  
Meta Analysis ◽  
Model Organisms ◽  
Online Programs ◽  
Advantages And Disadvantages ◽  
Genome Expression ◽  
Expression Studies ◽  
Genome Wide ◽  
Powerful Approach ◽  
Meta Analyses ◽  
Genome Wide Expression

Advances in transcriptomic methods have led to a large number of published genome-wide expression studies (GWES), in humans and in model organisms. For several years, GWES involved the use of microarray platforms to compare genome-expression data for two or more groups of samples of interest. Meta-analysis of GWES is a powerful approach for the identification of differentially expressed genes in biological topics or diseases of interest, combining information from multiple primary studies. In this article, I review the main features of available software for carrying out meta-analysis of GWES. I describe seven packages from the Bioconductor platform and 5 packages from the CRAN platform. In addition, nine previously described programs and two online programs are reviewed. Finally, I discuss advantages and disadvantages of these available programs and propose key points for future developments.

scholarly journals MeDIP-Seq and RNA-Seq Releaved TGFB2 Associated with Disease Resistance to ALV-J Infection in Chickens

2020 ◽  
Author(s):  
Yiming Yan ◽  
Huihua Zhang ◽  
Shuang Gao ◽  
Huanmin Zhang ◽  
Xinheng Zhang ◽  
...  
Keyword(s):  
Dna Methylation ◽  
Disease Resistance ◽  
Economic Losses ◽  
Effective Vaccine ◽  
Aberrant Methylation ◽  
Rna Seq ◽  
Genome Expression ◽  
Genome Wide ◽  
Functional Analyses ◽  
Integration Analysis

Abstract BackgroundAvian leukosis virus subgroup J (ALV-J) is an oncogenic virus that causes serious economic losses in the poultry industry; unfortunately, there is no effective vaccine. Therefore, ALV-J-susceptible and -resistant chickens had been screened in this study. DNA methylation plays a crucial role in several biological processes, and an increasing number of diseases were proven to be related to alterations of DNA methylation. Thus, we generated and provide the genome wide genome-expression and DNA-methylation profiles by MeDIP-Seq and RNA-Seq in ALV-J-susceptible and -resistant chickens.Results8304 DMRs were identified by MeDIP-Seq analyses and 515 differentially expressed genes were identified by RNA-Seq analysis. Through the results of integration analysis, we screened six candidate genes for screening ALV-J-resistant chickens that were aberrant methylation in the promoter region. Furthermore, functional analyses showed that overexpression of TGFB2 promoted ALV-J replication, which suggested TGFB2 played an important role in disease resistance to ALV-J infection in chickens.ConclusionsThe present study provides new insights into understanding epigenetic changes in ALV-J-susceptible and -resistant chickens, and results provide a basis for breeding disease-resistant-chicken lines.

scholarly journals Available software for meta-analyses of genome-wide expression studies

2019 ◽  
Author(s):  
Diego A Forero
Keyword(s):  
Meta Analysis ◽  
Model Organisms ◽  
Online Programs ◽  
Advantages And Disadvantages ◽  
Genome Expression ◽  
Expression Studies ◽  
Genome Wide ◽  
Powerful Approach ◽  
Meta Analyses ◽  
Genome Wide Expression

Advances in transcriptomic methods have led to a large number of published genome-wide expression studies (GWES), in humans and in model organisms. For several years, GWES involved the use of microarray platforms to compare genome-expression data for two or more groups of samples of interest. Meta-analysis of GWES is a powerful approach for the identification of differentially expressed genes in biological topics or diseases of interest, combining information from multiple primary studies. In this article, I review the main features of available software for carrying out meta-analysis of GWES. I describe seven packages from the Bioconductor platform and 5 packages from the CRAN platform. In addition, nine previously described programs and two online programs are reviewed. Finally, I discuss advantages and disadvantages of these available programs and propose key points for future developments.

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