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Related Concept Videos

Cis-regulatory Sequences02:02

Cis-regulatory Sequences

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Cis-regulatory sequences are short fragments of non-coding DNA that are present on the same chromosomes as the genes that they regulate. These fragments serve as binding sites for transcriptional regulators, proteins that are responsible for controlling gene transcription and differential gene expression across cell types in eukaryotes. Cis-regulatory sequences can be close to the gene of interest or thousands of bases away in the DNA sequence; however, those sequences that are further away are...
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Overview of Transposition and Recombination02:13

Overview of Transposition and Recombination

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Transposons make up a significant part of genomes of various organisms. Therefore, it is believed that transposition played a major evolutionary role in speciation by changing genome sizes and modifying gene expression patterns. For example, in bacteria, transposition can lead to conferring antibiotic resistance. Movement of transposable elements within the genetic pool of pathogenic bacteria can aid in transfer of antibiotic-resistant genetic elements. In eukaryotes, transposons can carry out...
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Cooperative Binding of Transcription Regulators02:13

Cooperative Binding of Transcription Regulators

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Transcriptional regulators bind to specific cis-regulatory sequences in the DNA to regulate gene transcription. These cis-regulatory sequences are very short, usually less than ten nucleotide pairs in length. The short length means that there is a high probability of the exact same sequence randomly occurring throughout the genome.  Since regulators can also bind to groups of similar sequences, this further increases the chances of random binding. Transcriptional regulators form...
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DNA-only Transposons02:57

DNA-only Transposons

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DNA-only transposons are called autonomous transposons since they code for the enzyme transposase that is required for the transposition mechanism. Insertion of transposons can alter gene functions in multiple ways. They can mutate the gene, alter gene expression by introducing a novel promoter or insulator sequence, introduce new splice sites, and change the mRNA transcripts produced, or remodel chromatin structure.
The donor site from where the transposon is excised is either degraded or...
14.5K
Transposons01:24

Transposons

38
Transposons, or "jumping genes," are small mobile genetic elements (MGEs) that range from 700 to 40,000 base pairs in length. They are found in all organisms and can move within the same chromosome or transfer to different chromosomes. In some cases, transposons can also jump between different host DNA molecules, such as plasmids or viruses, contributing to genetic variability.Barbara McClintock first discovered these mobile genetic elements in the 1940s while studying maize genetics, and she...
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Combinatorial Gene Control02:33

Combinatorial Gene Control

8.4K
Combinatorial gene control is the synergistic action of several transcriptional factors to regulate the expression of a single gene. The absence of one or more of these factors may lead to a significant difference in the level of gene expression or repression.
The expression of more than 30,000 genes is controlled by approximately 2000-3000 transcription factors. This is possible because a single transcription factor can recognize more than one regulatory sequence. The specificity in gene...
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Related Experiment Video

Updated: Jul 11, 2025

Quantitative Comparison of cis-Regulatory Element CRE Activities in Transgenic Drosophila melanogaster
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Quantitative Comparison of cis-Regulatory Element CRE Activities in Transgenic Drosophila melanogaster

Published on: December 19, 2011

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Statistical learning quantifies transposable element-mediated cis-regulation.

Cyril Pulver1, Delphine Grun1, Julien Duc1

  • 1School of Life Sciences, Swiss Federal Institute of Technology Lausanne (EPFL), CH-1015, Lausanne, Switzerland.

Genome Biology
|November 11, 2023
PubMed
Summary
This summary is machine-generated.

Transposable elements (TEs) contain cis-regulatory elements (CREs) that influence gene expression. Mathematical modeling shows these TE-derived CREs regulate genes genome-wide, aiding in developmental processes.

Keywords:
CRISPRaCRISPRiCis-regulatory elementsEOMESEmbryogenesisEndodermEpigenomicsGATA6GastrulationGene regulationGene regulatory networksGerm layerLTR5LTR6MER4AMER4DMesendodermPRIMA4-LTRRNA-seqRegulatory motif activitySOX15SVATranscription factorsTranscriptomicsTransposable elements

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Real-Time Quantification of the Effects of IS200/IS605 Family-Associated TnpB on Transposon Activity
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Real-Time Quantification of the Effects of IS200/IS605 Family-Associated TnpB on Transposon Activity

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Quantifying the Activity of cis-Regulatory Elements in the Mouse Retina by Explant Electroporation
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Quantifying the Activity of cis-Regulatory Elements in the Mouse Retina by Explant Electroporation

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Related Experiment Videos

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Quantitative Comparison of cis-Regulatory Element CRE Activities in Transgenic Drosophila melanogaster
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Quantitative Comparison of cis-Regulatory Element CRE Activities in Transgenic Drosophila melanogaster

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Real-Time Quantification of the Effects of IS200/IS605 Family-Associated TnpB on Transposon Activity
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Quantifying the Activity of cis-Regulatory Elements in the Mouse Retina by Explant Electroporation
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Quantifying the Activity of cis-Regulatory Elements in the Mouse Retina by Explant Electroporation

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Area of Science:

  • Genomics
  • Molecular Biology
  • Bioinformatics

Background:

  • Transposable elements (TEs) are prevalent in metazoan genomes.
  • Many TEs contain cis-regulatory elements (CREs) crucial for gene regulation.
  • TEs can form CRE platforms for coordinated gene regulation by transcription factors (TFs).

Purpose of the Study:

  • To mathematically model and test the hypothesis of TE-contributed cis-regulatory activities.
  • To quantify the influence of TE-embedded CREs on gene expression.
  • To investigate the role of TEs in the gene regulatory network of human embryonic stem cells.

Main Methods:

  • Mathematical modeling to estimate TE cis-regulatory activity.
  • Analysis of hundreds of overexpression experiments.
  • Leveraging RNA-seq and epigenomic data.

Main Results:

  • Gene expression differences alone can estimate TE-contributed cis-regulatory activities.
  • TE-embedded CREs influence gene expression within approximately 500kb of promoters.
  • Pluripotency-specific and young TE subfamilies can be reactivated by specific TFs.

Conclusions:

  • TE-embedded CREs contribute to gene regulation during and after gastrulation.
  • A statistical tool is provided to infer TE-dependent cis-regulation from RNA-seq data.
  • Facilitates the study of TEs in the next-generation sequencing era.