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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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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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Bacteria and archaea are susceptible to viral infections just like eukaryotes; therefore, they have developed a unique adaptive immune system to protect themselves. Clustered regularly interspaced short palindromic repeats and CRISPR-associated proteins (CRISPR-Cas) are present in more than 45% of known bacteria and 90% of known archaea.
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Regulation of Expression at Multiple Steps01:23

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The gene expression in cells is regulated at different stages: (i) transcription, (ii) RNA processing, (iii) RNA localization, and (iv) translation. Transcriptional regulation is mediated by regulatory proteins such as transcription factors, activators, or repressors—these control gene expression by initiating or inhibiting the transcription of genes. Once a precursor or pre-mRNA is produced, it undergoes post-transcriptional modification, including 5' capping, splicing, and the...
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Genome editing technologies allow scientists to modify an organism’s DNA via the addition, removal, or rearrangement of genetic material at specific genomic locations. These types of techniques could potentially be used to cure genetic disorders such as hemophilia and sickle cell anemia. One popular and widely used DNA-editing research tool that could lead to safe and effective cures for genetic disorders is the CRISPR-Cas9 system. CRISPR-Cas9 stands for Clustered Regularly Interspaced...
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Dissection of Enhancer Function Using Multiplex CRISPR-based Enhancer Interference in Cell Lines
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Parallel characterization of cis-regulatory elements for multiple genes using CRISPRpath.

Xingjie Ren1, Mengchi Wang2, Bingkun Li1

  • 1Institute for Human Genetics, University of California, San Francisco, San Francisco, CA, USA.

Science Advances
|September 15, 2021
PubMed
Summary
This summary is machine-generated.

CRISPRpath enables scalable, parallel screening of cis-regulatory elements (CREs) for multiple genes within a biological pathway. This method identifies functional enhancers and distinguishes their impact levels on gene expression.

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

  • Genomics
  • Molecular Biology
  • Epigenetics

Background:

  • Current CRISPR screens for cis-regulatory elements (CREs) are limited to single genes.
  • Characterizing CREs across multiple genes in a pathway is challenging.

Purpose of the Study:

  • To develop a scalable screening strategy, CRISPRpath, for parallelly characterizing CREs of multiple genes within the same biological pathway.
  • To identify functional enhancers for genes involved in the 6-thioguanine–induced DNA mismatch repair pathway.

Main Methods:

  • CRISPRpath utilizes pooled CRISPR interference (CRISPRi) and CRISPR nuclease (CRISPRn) approaches.
  • The strategy allows for parallel characterization of CREs linked to genes with converging phenotypes.
  • Different levels of selection pressure were applied to differentiate enhancer impact.

Main Results:

  • CRISPRpath successfully identified functional enhancers for six genes in the DNA mismatch repair pathway.
  • Sixty percent of identified enhancers were known promoters with distinct epigenomic features (e.g., increased chromatin accessibility).
  • The method distinguished between enhancers with strong and weak impacts on gene expression.

Conclusions:

  • CRISPRpath offers a scalable solution for parallel CRE characterization across multiple genes.
  • This approach provides a nuanced understanding of cis-regulation beyond transcriptional output.
  • CRISPRpath can be applied to decipher complex gene regulatory programs at scale.