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Related Concept Videos

Cis-regulatory Sequences02:02

Cis-regulatory Sequences

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...
Cis-regulatory Sequences02:02

Cis-regulatory Sequences

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...
Methods of Nuclear Reprogramming01:24

Methods of Nuclear Reprogramming

Nuclear reprogramming is a process of transforming one cell type into an unrelated cell type by epigenetic changes that alter the cell’s original gene expression pattern. Such epigenetic changes force cells to express a different set of genes, which play a significant role in inducing transformation into other cell types. Nuclear reprogramming offers applications in reproductive cloning for livestock propagation and regenerative medicine — developing patient-specific cells for injury repair.
Epigenetic Regulation01:37

Epigenetic Regulation

Epigenetic changes alter the physical structure of the DNA without changing the genetic sequence and often regulate whether genes are turned on or off. This regulation ensures that each cell produces only proteins necessary for its function. For example, proteins that promote bone growth are not produced in muscle cells. Epigenetic mechanisms play an essential role in healthy development. Conversely, precisely regulated epigenetic mechanisms are disrupted in diseases like cancer.
X-chromosome...
Epigenetic Regulation01:46

Epigenetic Regulation

Epigenetic mechanisms play an essential role in healthy development. Conversely, precisely regulated epigenetic mechanisms are disrupted in diseases like cancer.
Epigenetic Regulation01:46

Epigenetic Regulation

Epigenetic mechanisms play an essential role in healthy development. Conversely, precisely regulated epigenetic mechanisms are disrupted in diseases like cancer.

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Related Experiment Video

Updated: Jul 7, 2026

CRISPR-Mediated Reorganization of Chromatin Loop Structure
09:20

CRISPR-Mediated Reorganization of Chromatin Loop Structure

Published on: September 14, 2018

Segmentally Duplicated Regulatory Elements Undergo Human-Specific Rewiring.

Seth Weaver1,2,3, Craig B Lowe1,2,3

  • 1Department of Molecular Genetics and Microbiology, Duke University, Durham, NC 27710, USA.

Molecular Biology and Evolution
|July 6, 2026
PubMed
Summary
This summary is machine-generated.

Segmental duplications create large networks of gene regulatory elements in the human genome. These elements can rewire to regulate new genes, driving evolutionary changes, especially in immune and brain cells.

Keywords:
CRISPRigene regulationhuman evolutionsegmental duplication

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Area of Science:

  • Genomics
  • Evolutionary Biology
  • Gene Regulation

Background:

  • Gene regulatory innovation drives phenotypic changes.
  • Transposable elements form cis-acting element families and co-regulatory networks.
  • Understanding novel mechanisms of co-regulatory network formation is crucial.

Purpose of the Study:

  • To identify mechanisms forming families of noncoding elements with shared sequence similarity and cell type-specific activity.
  • To analyze these families within the human telomere-to-telomere genome assembly and embryonic stem cell chromatin accessibility data.
  • To investigate the role of segmental duplications in creating and modifying gene regulatory networks.

Main Methods:

  • Defining families of noncoding elements based on sequence similarity and cell type-specific activity.
  • Applying this framework to human genome assembly and embryonic stem cell data.
  • Using STARR-seq for functional validation and CRISPRi for target gene identification.

Main Results:

  • Segmental duplications are the primary mechanism creating over a thousand networks of open chromatin elements in embryonic stem cells.
  • Functional validation confirmed these networks as regulatory element families.
  • Post-duplication, regulatory elements either maintained or rewired target gene relationships, with proximal elements regulating distal genes and enhancers targeting genes outside the duplication locus.
  • Many rewiring events are human-specific.
  • Segmental duplications disproportionately expanded regulatory element families in immune cells and specific brain regions.

Conclusions:

  • Segmental duplications are a major source of gene regulatory innovation.
  • Regulatory element rewiring after duplication contributes to gene regulatory evolution, particularly in humans.
  • Placing regulatory elements in new genomic contexts may prime them for neofunctionalization.