New gene expression switches

Acclimatization is a process that occurs in individual cells to a drastic change in micro and macro environments. When an organism is subjected to a new environment or a change in its normal growing conditions, the cellular mechanisms initiate a warning sign and over a period of time or over generations the acquired, modified traits are being communicated and fixed as a new trait. If there is lack of equilibrium within the cell due to over expression of a single gene or network of associated genes either manmade or due to mutations, the organism or plant tries to fix it by initiating gene regulatory mechanisms. According to our neutral theory of gene expression, always a cell tries to maintain its pH by modifying its cytosol through altered gene expression. In the present investigation, 198 AtMYB genes were analyzed and found to play an intrinsic photosystem linked network of 38 nodes where MYB being regulated by a set of 48 miRNAs. Members of the network have evidence-based link to energy related mechanisms. Altering gene expression to an extent where, the cell may not be able to fix it or a trait, which requires excessive energy loss escorts the organism’s gene regulation by breakdown of the introduced sequence over few generations. Events with constitutive overexpression may suffer poor performance over the years based on gene network prevailing in the crop of interest. Hence, network rewiring with minimal energy expenses is concerned.

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Sodium butyrate induces new gene expression in Friend erythroleukemic cells.

Journal of Biological Chemistry ◽

10.1016/s0021-9258(18)50727-4 ◽

1979 ◽

Vol 254 (10) ◽

pp. 4283-4290 ◽

Cited By ~ 7

Author(s):

R Reeves ◽

P Cserjesi

Keyword(s):

Gene Expression ◽

Sodium Butyrate ◽

New Gene ◽

Friend Erythroleukemic Cells ◽

Erythroleukemic Cells

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Multilayer modelling of the human transcriptome and biological mechanisms of complex diseases and traits

npj Systems Biology and Applications ◽

10.1038/s41540-021-00186-6 ◽

2021 ◽

Vol 7 (1) ◽

Author(s):

Tiago Azevedo ◽

Giovanna Maria Dimitri ◽

Pietro Lió ◽

Eric R. Gamazon

Keyword(s):

Gene Expression ◽

The Cancer Genome Atlas ◽

Human Transcriptome ◽

Reactive Protein ◽

Cancer Genome Atlas ◽

New Gene ◽

Improved Performance ◽

Genomic Resource ◽

The Uk ◽

Genetically Determined

AbstractHere, we performed a comprehensive intra-tissue and inter-tissue multilayer network analysis of the human transcriptome. We generated an atlas of communities in gene co-expression networks in 49 tissues (GTEx v8), evaluated their tissue specificity, and investigated their methodological implications. UMAP embeddings of gene expression from the communities (representing nearly 18% of all genes) robustly identified biologically-meaningful clusters. Notably, new gene expression data can be embedded into our algorithmically derived models to accelerate discoveries in high-dimensional molecular datasets and downstream diagnostic or prognostic applications. We demonstrate the generalisability of our approach through systematic testing in external genomic and transcriptomic datasets. Methodologically, prioritisation of the communities in a transcriptome-wide association study of the biomarker C-reactive protein (CRP) in 361,194 individuals in the UK Biobank identified genetically-determined expression changes associated with CRP and led to considerably improved performance. Furthermore, a deep learning framework applied to the communities in nearly 11,000 tumors profiled by The Cancer Genome Atlas across 33 different cancer types learned biologically-meaningful latent spaces, representing metastasis (p < 2.2 × 10−16) and stemness (p < 2.2 × 10−16). Our study provides a rich genomic resource to catalyse research into inter-tissue regulatory mechanisms, and their downstream consequences on human disease.

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Use of a Beet necrotic yellow vein virus RNA-5-derived replicon as a new tool for gene expression

Journal of General Virology ◽

10.1099/vir.0.80720-0 ◽

2005 ◽

Vol 86 (2) ◽

pp. 463-467 ◽

Cited By ~ 19

Author(s):

Laure Schmidlin ◽

Didier Link ◽

Jérôme Mutterer ◽

Hubert Guilley ◽

David Gilmer

Keyword(s):

Gene Expression ◽

Recombinant Proteins ◽

Expression System ◽

Green Fluorescence Protein ◽

Yellow Vein ◽

Expression Levels ◽

Virus Rna ◽

New Gene ◽

Infected Cells ◽

Fluorescence Protein

A new gene-expression system based on RNA-5 of Beet necrotic yellow vein virus (BNYVV) was constructed to allow the expression of recombinant proteins in virally infected cells. Replication and expression levels of the RNA-5-based replicon containing the green fluorescence protein (GFP) gene were compared with those obtained with the well-characterized RNA-3-derived replicon (Rep-3). When RNA-3 and/or RNA-4 BNYVV RNAs were added to the inoculum, the expression levels of RNA-5-encoded GFP were considerably reduced. To a lesser extent, RNA-3-derived GFP expression was also affected by the presence of RNA-4 and -5. Both RNA-3- and RNA-5-derived molecules were able to express proteins within the same infected cells. Together with Rep-3, the RNA-5-derived replicon thus provides a new tool for the co-expression of different recombinant proteins. In Beta macrocarpa, Rep-5-GFP was able to move in systemic tissues in the presence of RNA-3 and thus provides a new expression system that is not restricted to the inoculated leaves.

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BgeeDB, an R package for retrieval of curated expression datasets and for gene list expression localization enrichment tests

F1000Research ◽

10.12688/f1000research.9973.1 ◽

2016 ◽

Vol 5 ◽

pp. 2748 ◽

Cited By ~ 7

Author(s):

Andrea Komljenovic ◽

Julien Roux ◽

Marc Robinson-Rechavi ◽

Frederic B. Bastian

Keyword(s):

Gene Expression ◽

Gene List ◽

R Package ◽

Rna Seq ◽

Anatomical Structures ◽

Enrichment Test ◽

Expression Of Genes ◽

Affymetrix Microarrays ◽

New Gene

BgeeDB is a collection of functions to import into R re-annotated, quality-controlled and reprocessed expression data available in the Bgee database. This includes data from thousands of wild-type healthy samples of multiple animal species, generated with different gene expression technologies (RNA-seq, Affymetrix microarrays, expressed sequence tags, and in situ hybridizations). BgeeDB facilitates downstream analyses, such as gene expression analyses with other Bioconductor packages. Moreover, BgeeDB includes a new gene set enrichment test for preferred localization of expression of genes in anatomical structures (“TopAnat”). Along with the classical Gene Ontology enrichment test, this test provides a complementary way to interpret gene lists. Availability: http://www.bioconductor.org/packages/BgeeDB/

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GSDMA drives the most replicated association with asthma in naïve CD4+ T cells

10.1101/774760 ◽

2019 ◽

Cited By ~ 1

Author(s):

Anne-Marie Madore ◽

Lucile Pain ◽

Anne-Marie Boucher-Lafleur ◽

Jolyane Meloche ◽

Andréanne Morin ◽

...

Keyword(s):

Gene Expression ◽

Dna Methylation ◽

T Cells ◽

Genetic Variants ◽

Immune Cell ◽

Cell Types ◽

Sequencing Data ◽

Opposite Pattern ◽

Genetic Mechanisms ◽

New Gene

AbstractBackgroundThe 17q12-21 locus is the most replicated association with asthma. However, no study had described the genetic mechanisms underlying this association considering all genes of the locus in immune cell samples isolated from asthmatic and non-asthmatic individuals.ObjectiveThis study takes benefit of samples from naïve CD4+ T cells and eosinophils isolated from the same 200 individuals to describe specific interactions between genetic variants, gene expression and DNA methylation levels for the 17q12-21 asthma locus.Methods and ResultsAfter isolation of naïve CD4+ T cells and eosinophils from blood samples, next generation sequencing was used to measure DNA methylation levels and gene expression counts. Genetic interactions were then evaluated considering genetic variants from imputed genotype data. In naïve CD4+ T cells but not eosinophils, 20 SNPs in the fourth and fifth haplotype blocks modulated both GSDMA expression and methylation levels, showing an opposite pattern of allele frequencies and expression counts in asthmatics compared to controls. Moreover, negative correlations have been measured between methylation levels of CpG sites located within the 1.5 kb region from the transcription start site of GSDMA and its expression counts.ConclusionAvailability of sequencing data from two key cell types isolated from asthmatic and non-asthmatic individuals allowed identifying a new gene in naïve CD4+ T cells that drives the association with the 17q12-21 locus, leading to a better understanding of the genetic mechanisms taking place in it.

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Real-World Data Explores New Gene Expression Profiles in Breast Cancer

Oncology Times ◽

10.1097/01.cot.0000734340.12249.66 ◽

2021 ◽

Vol 43 (3) ◽

pp. 33-33

Author(s):

Sarah LaCorte

Keyword(s):

Breast Cancer ◽

Gene Expression ◽

Real World ◽

Expression Profiles ◽

Gene Expression Profiles ◽

Real World Data ◽

World Data ◽

New Gene

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Frequent EPAS1/HIF2α exons 9 and 12 mutations in non-familial pheochromocytoma

Endocrine Related Cancer ◽

10.1530/erc-13-0384 ◽

2014 ◽

Vol 21 (3) ◽

pp. 495-504 ◽

Cited By ~ 39

Author(s):

Jenny Welander ◽

Adam Andreasson ◽

Michael Brauckhoff ◽

Martin Bäckdahl ◽

Catharina Larsson ◽

...

Keyword(s):

Gene Expression ◽

Copy Number ◽

Gene Expression Pattern ◽

Exon 2 ◽

Dna And Rna ◽

Familial Pheochromocytoma ◽

Predisposing Genes ◽

Adrenal Pheochromocytoma ◽

New Gene ◽

Sporadic Pheochromocytoma

Pheochromocytomas are neuroendocrine tumors arising from the adrenal medulla. While heritable mutations are frequently described, less is known about the genetics of sporadic pheochromocytoma. Mutations in genes involved in the cellular hypoxia response have been identified in tumors, and recentlyEPAS1, encoding HIF2α, has been revealed to be a new gene involved in the pathogenesis of pheochromocytoma and abdominal paraganglioma. The aim of this study was to further characterizeEPAS1alterations in non-familial pheochromocytomas. Tumor DNA from 42 adrenal pheochromocytoma cases with apparently sporadic presentation, without known hereditary mutations in predisposing genes, were analyzed for mutations inEPAS1by sequencing of exons 9 and 12, which contain the two hydroxylation sites involved in HIF2α degradation, and also exon 2. In addition, the copy number at theEPAS1locus as well as transcriptome-wide gene expression were studied by DNA and RNA microarray analyses, respectively. We identified six missenseEPAS1mutations, three in exon 9 and three in exon 12, in five of 42 pheochromocytomas (12%). The mutations were both somatic and constitutional, and had no overlap in 11 cases (26%) with somatic mutations inNF1orRET. One sample had two differentEPAS1mutations, shown by cloning to occur incis, possibly indicating a novel mechanism of HIF2α stabilization through inactivation of both hydroxylation sites. One of the tumors with anEPAS1mutation also had a gain in DNA copy number at theEPAS1locus. AllEPAS1-mutated tumors displayed a pseudo-hypoxic gene expression pattern, indicating an oncogenic role of the identified mutations.

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