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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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Master transcription regulators are regulatory proteins that are predominantly responsible for regulating the expression of multiple genes. Often these genes work in concert to drive a  complex process. Activation of a master transcription regulator can lead to a cascade of transcriptional activation necessary for that outcome. These regulators can directly bind to the regulatory sequences of the various genes involved, or they can indirectly regulate transcription by binding to regulatory...
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Cellular Differentiation00:57

Cellular Differentiation

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How does a complex organism such as a human develop from a single cell? It all starts from a single fertilized egg which gives rise to a vast array of cell types, such as nerve cells, muscle cells, and epithelial cells that characterize the adult? Throughout development and adulthood, cellular differentiation leads cells to assume their final morphology and physiology. Differentiation is the process by which unspecialized cells become specialized to carry out distinct functions.
A zygote is a...
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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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Combinatorial Gene Control02:33

Combinatorial Gene Control

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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.
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Proteins that regulate transcription can do so either via direct contact with RNA Polymerase or through indirect interactions facilitated by adaptors, mediators, histone-modifying proteins, and nucleosome remodelers. Direct interactions to activate transcription is seen in bacteria as well as in some eukaryotic genes. In these cases, upstream activation sequences are adjacent to the promoters, and the activator proteins interact directly with the transcriptional machinery. For example, in...
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Characterization of Single-Cell Cis-regulatory Elements Informs Implications for Cell Differentiation.

Ying-Ying Ren1,2, Zhen Liu1,2,3

  • 1State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China.

Genome Biology and Evolution
|November 7, 2024
PubMed
Summary
This summary is machine-generated.

Single-cell cis-regulatory elements, active in multiple cell types, are key to cell differentiation. Their genomic features, like transcription factor binding and evolutionary conservation, offer insights into developmental gene regulation.

Keywords:
CREcell differentiationgenomic characteristicspleiotropy

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Area of Science:

  • Genomics
  • Developmental Biology
  • Epigenetics

Background:

  • Cis-regulatory elements control gene expression crucial for cell differentiation during development.
  • Genomic characteristics of single-cell cis-regulatory elements involved in development are not fully understood.

Purpose of the Study:

  • To systematically analyze the genomic features of single-cell cis-regulatory elements in the developing mouse cerebellum.
  • To understand the regulatory mechanisms of cell differentiation governed by these elements.

Main Methods:

  • Analysis of approximately 250,000 putative single-cell cis-regulatory elements using snATAC-seq data from developing mouse cerebellum.
  • Evaluation of pleiotropic effects, transcription factor binding motifs, GC content, distance to transcription start sites, and evolutionary conservation.

Main Results:

  • Over 80% of analyzed elements exhibit pleiotropy, active in multiple cell types.
  • Pleiotropy correlates positively with transcription factor motif density/diversity and GC content, and negatively with distance to transcription start sites.
  • Elements linked to cell differentiation show enhanced evolutionary conservation, motif diversity, GC content, and greater distance from genes.

Conclusions:

  • This study reveals general genomic characteristics of single-cell cis-regulatory elements.
  • Findings provide insights into the genomic and evolutionary basis of how these elements regulate cell differentiation during development.