scholarly journals Pipeline to detect the relationship between transposable elements and adjacent genes in host genome

2021 ◽  
Author(s):  
Caroline Meguerditchian ◽  
Ayse Ergun ◽  
Veronique DECROOCQ ◽  
Marie LEFEBVRE ◽  
Quynh Trang Bui
Keyword(s):  
Gene Expression ◽  
Transposable Elements ◽  
Transcriptional Activity ◽  
Potential Role ◽  
Host Genome ◽  
Signalling Pathways ◽  
Adjacent Gene ◽  
Replication Intermediates ◽  
The Relationship ◽  
Affect Gene Expression

Understanding the relationship between transposable elements (TEs) and their associated genes in the host genome is a key point to explore their potential role in genome evolution. Transposable elements can regulate and affect gene expression not only because of their mobility within the genome but also because of its transcriptional activity. Gene expression can be suppressed, decreased or increased and cellular signalling pathways can be activated through the act of the nearby TE expression itself or subsequent TE replication intermediates. We implemented a pipeline which is capable to reveal the relationship between TEs and adjacent gene distribution in the host genome. Our tool is freely available here : https://github.com/marieBvr/TEs_genes_relationship_pipeline

scholarly journals Control of yeast gene expression by transposable elements: maximum expression requires a functional Ty activator sequence and a defective Ty promoter.

1988 ◽  
Vol 8 (10) ◽  
pp. 4009-4017 ◽  
Author(s):  
L R Coney ◽  
G S Roeder
Keyword(s):  
Gene Expression ◽  
Adjacent Gene ◽  
Multiple Sequence ◽  
Sequence Element ◽  
Cis Acting ◽  
Ty Elements ◽  
The Relationship ◽  
Maximum Expression ◽  
Modest Effect

Integration of a transposable element adjacent to a gene frequently results in an alteration in expression of the nearby gene. The purpose of our experiments was to identify cis-acting sequences within a yeast transposon (Ty) that are important for expression of the adjacent gene. The role of these sequences in Ty transcription was also analyzed in order to examine the relationship between Ty and adjacent gene expression. Three naturally occurring Ty elements located at the HIS4 locus were examined. These Ty elements differed by multiple sequence changes and had different effects on HIS4 expression. To determine which sequences were important to Ty and HIS4 expression, Ty::lacZ and Ty::HIS4::lacZ fusion genes were constructed and analyzed. Results of these experiments indicated that a sequence element is present in the Ty epsilon region that is necessary for HIS4 expression but which has only a modest effect on Ty transcription. Additionally, a mutation in the Ty promoter region decreased Ty transcription and increased HIS4 expression. The opposite effects of this mutation on Ty and adjacent gene expression were probably caused by promoter competition.

scholarly journals Impact of Transposable Elements on Methylation and Gene Expression across Natural Accessions of Brachypodium distachyon

2020 ◽  
Vol 12 (11) ◽  
pp. 1994-2001 ◽  
Author(s):  
Michele Wyler ◽  
Christoph Stritt ◽  
Jean-Claude Walser ◽  
Célia Baroux ◽  
Anne C Roulin
Keyword(s):  
Gene Expression ◽  
Dna Methylation ◽  
Transposable Elements ◽  
Brachypodium Distachyon ◽  
Large Fraction ◽  
Expression Patterns ◽  
Specific Gene ◽  
Differential Gene ◽  
The Relationship ◽  
Silent State

Abstract Transposable elements (TEs) constitute a large fraction of plant genomes and are mostly present in a transcriptionally silent state through repressive epigenetic modifications, such as DNA methylation. TE silencing is believed to influence the regulation of adjacent genes, possibly as DNA methylation spreads away from the TE. Whether this is a general principle or a context-dependent phenomenon is still under debate, pressing for studying the relationship between TEs, DNA methylation, and nearby gene expression in additional plant species. Here, we used the grass Brachypodium distachyon as a model and produced DNA methylation and transcriptome profiles for 11 natural accessions. In contrast to what is observed in Arabidopsis thaliana, we found that TEs have a limited impact on methylation spreading and that only few TE families are associated with a low expression of their adjacent genes. Interestingly, we found that a subset of TE insertion polymorphisms is associated with differential gene expression across accessions. Thus, although not having a global impact on gene expression, distinct TE insertions may contribute to specific gene expression patterns in B. distachyon.

scholarly journals Impact of polymorphic transposable elements on transcription in lymphoblastoid cell lines from public data

2019 ◽  
Vol 20 (S9) ◽  
Author(s):  
Giovanni Spirito ◽  
Damiano Mangoni ◽  
Remo Sanges ◽  
Stefano Gustincich
Keyword(s):  
Gene Expression ◽  
Transposable Elements ◽  
Cell Lines ◽  
Dna Sequences ◽  
Host Genome ◽  
Human Populations ◽  
Lymphoblastoid Cell Lines ◽  
Structural Variants ◽  
Public Data ◽  
The Impact

Abstract Background Transposable elements (TEs) are DNA sequences able to mobilize themselves and to increase their copy-number in the host genome. In the past, they have been considered mainly selfish DNA without evident functions. Nevertheless, currently they are believed to have been extensively involved in the evolution of primate genomes, especially from a regulatory perspective. Due to their recent activity they are also one of the primary sources of structural variants (SVs) in the human genome. By taking advantage of sequencing technologies and bioinformatics tools, recent surveys uncovered specific TE structural variants (TEVs) that gave rise to polymorphisms in human populations. When combined with RNA-seq data this information provides the opportunity to study the potential impact of TEs on gene expression in human. Results In this work, we assessed the effects of the presence of specific TEs in cis on the expression of flanking genes by producing associations between polymorphic TEs and flanking gene expression levels in human lymphoblastoid cell lines. By using public data from the 1000 Genome Project and the Geuvadis consortium, we exploited an expression quantitative trait loci (eQTL) approach integrated with additional bioinformatics data mining analyses. We uncovered human loci enriched for common, less common and rare TEVs and identified 323 significant TEV-cis-eQTL associations. SINE-R/VNTR/Alus (SVAs) resulted the TE class with the strongest effects on gene expression. We also unveiled differential functional enrichments on genes associated to TEVs, genes associated to TEV-cis-eQTLs and genes associated to the genomic regions mostly enriched in TEV-cis-eQTLs highlighting, at multiple levels, the impact of TEVs on the host genome. Finally, we also identified polymorphic TEs putatively embedded in transcriptional units, proposing a novel mechanism in which TEVs may mediate individual-specific traits. Conclusion We contributed to unveiling the effect of polymorphic TEs on transcription in lymphoblastoid cell lines.

scholarly journals The enhancer activity of long interspersed nuclear element derived microRNA 625 induced by NF-κB

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Hee-Eun Lee ◽  
Sang-Je Park ◽  
Jae-Won Huh ◽  
Hiroo Imai ◽  
Heui-Soo Kim
Keyword(s):  
Gene Expression ◽  
Transposable Elements ◽  
Human Genome ◽  
Dna Sequences ◽  
Binding Sites ◽  
Luciferase Assay ◽  
Enhancer Activity ◽  
Long Interspersed Nuclear Elements ◽  
Long Interspersed Nuclear Element ◽  
Affect Gene Expression

AbstractTransposable elements (TEs) are DNA sequences that cut or introduced into the genome, and they represent a massive portion of the human genome. TEs generate a considerable number of microRNAs (miRNAs) are derived from TEs (MDTEs). Numerous miRNAs are related to cancer, and hsa-miRNA-625 is a well-known oncomiR derived from long interspersed nuclear elements (LINEs). The relative expression of hsa-miRNA-625-5p differs in humans, chimpanzees, crab-eating monkeys, and mice, and four primers were designed against the 3′UTR of GATAD2B to analyze the different quantities of canonical binding sites and the location of miRNA binding sites. Luciferase assay was performed to score for the interaction between hsa-miRNA-625 and the 3′UTR of GATAD2B, while blocking NF-κB. In summary, the different numbers of canonical binding sites and the locations of miRNA binding sites affect gene expression, and NF-κB induces the enhancer activity of hsa-miRNA-625-5p by sharing the binding sites.

scholarly journals Role of YAP in early ectodermal specification and a Huntington's Disease model of human neurulation

2021 ◽  
Author(s):  
Francesco M Piccolo ◽  
Nathaniel R Kastan ◽  
Tomomi Haremaki ◽  
Qingyun Tian ◽  
Tiago L Laundos ◽  
...  
Keyword(s):  
Transcriptional Activity ◽  
Potential Role ◽  
Hippo Pathway ◽  
Disease Model ◽  
Embryonic Stem ◽  
Ectopic Activation ◽  
Molecular Signals ◽  
The Hippo Pathway ◽  
The Relationship

The Hippo pathway, a highly conserved signaling cascade that functions as an integrator of molecular signals and biophysical states, ultimately impinges upon the transcription coactivator Yes-associated protein 1 (YAP). Hippo-YAP signaling has been shown to play key roles both at the early embryonic stages of implantation and gastrulation, and later during neurogenesis. To explore YAP potential role in neurulation, we used self-organizing neuruloids grown from human embryonic stem cells on micropatterned substrates. We identified YAP activation as a key lineage determinant, first between neuronal ectoderm and non-neuronal ectoderm, and later between epidermis and neural crest, indicating that YAP activity can enhance the effect of BMP4 stimulation and therefore affect ectodermal specification at this developmental stage. Because aberrant Hippo-YAP signaling has been implicated in the pathology of Huntington Disease (HD), we used isogenic mutant neuruloids to explore the relationship between signaling and the disease. We found that HD neuruloids demonstrate ectopic activation of gene targets of YAP and that pharmacological reduction of YAP transcriptional activity can partially rescue the HD phenotype.

scholarly journals Transposon Reactivation in the Germline May Be Useful for Both Transposons and Their Host Genomes

Cells ◽  
2020 ◽  
Vol 9 (5) ◽  
pp. 1172 ◽  
Author(s):  
Stéphanie Maupetit-Mehouas ◽  
Chantal Vaury
Keyword(s):  
Transposable Elements ◽  
Host Genome ◽  
Next Generation ◽  
Mutualistic Interactions ◽  
Transient Relaxation ◽  
The Relationship ◽  
Eukaryotic Genomes ◽  
Developmental Windows

Transposable elements (TEs) are long-term residents of eukaryotic genomes that make up a large portion of these genomes. They can be considered as perfectly fine members of genomes replicating with resident genes and being transmitted vertically to the next generation. However, unlike regular genes, TEs have the ability to send new copies to new sites. As such, they have been considered as parasitic members ensuring their own replication. In another view, TEs may also be considered as symbiotic sequences providing shared benefits after mutualistic interactions with their host genome. In this review, we recall the relationship between TEs and their host genome and discuss why transient relaxation of TE silencing within specific developmental windows may be useful for both.

Control of yeast gene expression by transposable elements: maximum expression requires a functional Ty activator sequence and a defective Ty promoter

1988 ◽  
Vol 8 (10) ◽  
pp. 4009-4017
Author(s):  
L R Coney ◽  
G S Roeder
Keyword(s):  
Gene Expression ◽  
Adjacent Gene ◽  
Multiple Sequence ◽  
Sequence Element ◽  
Cis Acting ◽  
Ty Elements ◽  
The Relationship ◽  
Maximum Expression ◽  
Modest Effect

Integration of a transposable element adjacent to a gene frequently results in an alteration in expression of the nearby gene. The purpose of our experiments was to identify cis-acting sequences within a yeast transposon (Ty) that are important for expression of the adjacent gene. The role of these sequences in Ty transcription was also analyzed in order to examine the relationship between Ty and adjacent gene expression. Three naturally occurring Ty elements located at the HIS4 locus were examined. These Ty elements differed by multiple sequence changes and had different effects on HIS4 expression. To determine which sequences were important to Ty and HIS4 expression, Ty::lacZ and Ty::HIS4::lacZ fusion genes were constructed and analyzed. Results of these experiments indicated that a sequence element is present in the Ty epsilon region that is necessary for HIS4 expression but which has only a modest effect on Ty transcription. Additionally, a mutation in the Ty promoter region decreased Ty transcription and increased HIS4 expression. The opposite effects of this mutation on Ty and adjacent gene expression were probably caused by promoter competition.

Nutrient-regulated gene expression in eukaryotes

2006 ◽  
Vol 73 ◽  
pp. 85-96 ◽  
Author(s):  
Richard J. Reece ◽  
Laila Beynon ◽  
Stacey Holden ◽  
Amanda D. Hughes ◽  
Karine Rébora ◽  
...  
Keyword(s):  
Gene Expression ◽  
Rna Polymerase ◽  
Rna Polymerase Ii ◽  
Transcriptional Control ◽  
Direct Interaction ◽  
Signalling Pathways ◽  
A Cell ◽  
One Step ◽  
Higher Eukaryotes ◽  
Regulated Gene Expression

The recognition of changes in environmental conditions, and the ability to adapt to these changes, is essential for the viability of cells. There are numerous well characterized systems by which the presence or absence of an individual metabolite may be recognized by a cell. However, the recognition of a metabolite is just one step in a process that often results in changes in the expression of whole sets of genes required to respond to that metabolite. In higher eukaryotes, the signalling pathway between metabolite recognition and transcriptional control can be complex. Recent evidence from the relatively simple eukaryote yeast suggests that complex signalling pathways may be circumvented through the direct interaction between individual metabolites and regulators of RNA polymerase II-mediated transcription. Biochemical and structural analyses are beginning to unravel these elegant genetic control elements.

Do the microRNAs we eat affect gene expression?

Nature ◽  
2020 ◽  
Vol 582 (7812) ◽  
pp. S10-S11 ◽  
Author(s):  
Kristina Campbell
Keyword(s):  
Gene Expression ◽  
Affect Gene Expression
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