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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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Protein domains are small structurally independent units that are part of a single amino acid chain.  Although these domains are often structurally independent, they may rely on synergistic effects to perform their functions as part of a larger protein. Protein domains may be conserved within the same organism, as well as across different organisms.
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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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Drug binding to proteins is a key aspect of pharmacokinetics and can influence a drug's distribution, absorption, and elimination in the body. Several factors, including the drug's physiochemical properties, protein concentration, disease states, and the number of binding sites on the protein, influence this process.
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Proteins undergo chemical modifications that trigger changes in the charge, structure, and conformation of the proteins. Phosphorylation, acetylation, glycosylation, nitrosylation, ubiquitination, lipidation, methylation, and proteolysis are various protein modifications that regulate protein activity. Such modifications are usually enzyme-driven.
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Exploring Sequence Space to Identify Binding Sites for Regulatory RNA-Binding Proteins
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A CRISPR-based sequence proximity binding protein labelling system for scanning upstream regulatory proteins.

Lei Zhang1, Chengcheng Cai1, Qiujie Chen1

  • 1State Key Laboratory of Vegetable Biobreeding, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agriculture and Rural Affairs, Sino-Dutch Joint Laboratory of Horticultural Genomics, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, China.

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Researchers developed a CRISPR-based system (CSPL) to identify proteins binding to plant DNA. This new method successfully detected known and novel proteins on the PIF4 promoter in multiple plant species.

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Area of Science:

  • Plant molecular biology
  • Genetics
  • Biotechnology

Background:

  • Transcriptional regulation relies on dynamic protein-DNA interactions influencing gene expression.
  • Existing technologies struggle to capture transiently DNA-binding proteins, particularly transcription factors, in plants.

Purpose of the Study:

  • To develop a novel CRISPR-based system for detecting promoter-binding proteins in plants.
  • To overcome limitations of current methods in capturing dynamic protein-DNA interactions.

Main Methods:

  • Developed a CRISPR-based sequence proximity binding protein labelling system (CSPL).
  • Leveraged dead Cas9 for specific DNA binding and TurboID for proximity-based protein labeling.
  • Applied CSPL to identify proteins binding to the PIF4 promoter.

Main Results:

  • Successfully identified both known and novel upstream binding proteins on the PIF4 promoter.
  • Demonstrated the efficacy of CSPL in Arabidopsis, cabbage, and rice.
  • Validated CSPL's capability to detect promoter-binding proteins.

Conclusions:

  • CSPL is a powerful tool for identifying promoter-binding proteins in plants.
  • The system has broad potential applications in plant research.
  • CSPL advances the study of transcriptional regulation in diverse plant species.