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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

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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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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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Cell Signaling in Plants01:25

Cell Signaling in Plants

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Plant cells communicate to coordinate their cycle of growth, flowering and fruiting, and activities in roots, shoots, and leaves in response to the changing environmental conditions. Plant signaling is distinct from animal signaling. Plants primarily utilize enzyme-linked receptors, whereas the largest class of cell-surface receptors in animals are G-protein coupled receptors (GPCRs). Unlike animals, receptor tyrosine kinases are rare in plants. Instead, plants have a diverse class of...
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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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Updated: Jan 17, 2026

HOX Loci Focused CRISPR/sgRNA Library Screening Identifying Critical CTCF Boundaries
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Cis-regulatory elements: systematic identification and horticultural applications.

Tian Li1, Wen Zeng1,2, Fangjie Zhu1

  • 1Haixia Institute of Science and Technology, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, College of Horticulture, National Engineering Research Center of JUNCAO, Fujian Agriculture and Forestry University, Fuzhou, 350002 China.

Abiotech
|September 25, 2025
PubMed
Summary
This summary is machine-generated.

Identifying cis-regulatory elements (CREs) is key for understanding gene regulation and improving crops. This review covers methods for CRE identification and their application in horticultural crop breeding for enhanced traits.

Keywords:
BreedingCis-regulatory elementDNA-binding specificityEpigeneticsGene regulatory networkHorticultural crops

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Area of Science:

  • Genomics
  • Molecular Biology
  • Plant Science

Background:

  • Cis-regulatory elements (CREs) are DNA fragments that bind transcription factors (TFs) to control gene expression.
  • CREs act as molecular switches, regulating gene expression dosage, timing, and location.
  • Understanding CREs is crucial for annotating the genome and deciphering gene regulatory networks.

Purpose of the Study:

  • To review high-throughput methodologies for identifying CREs.
  • To illustrate the link between CREs and agronomic traits in horticultural crops.
  • To discuss the exploitation of CREs for crop breeding.

Main Methods:

  • Review of current high-throughput techniques for CRE identification.
  • Analysis of existing literature on CREs and agronomic traits.
  • Discussion of genetic engineering strategies involving CREs.

Main Results:

  • Systematic CRE identification aids functional genome annotation.
  • CREs are associated with various agronomic traits in horticultural crops.
  • CREs offer precise targets for genetic engineering.

Conclusions:

  • High-throughput methods enable comprehensive CRE identification.
  • Harnessing CREs can accelerate the breeding of improved horticultural crops.
  • CREs are valuable targets for precision agriculture and crop enhancement.