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Promoter Capture Hi-C: High-resolution, Genome-wide Profiling of Promoter Interactions
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Genome organization and definition of the Penaeus monodon viral responsive protein 15 (PmVRP15) promoter

Phattarunda Jaree1, Taro Kawai2, Chu-Fang Lo3

  • 1Center of Excellence for Molecular Biology and Genomics of Shrimp, Department of Biochemistry, Faculty of Science, Chulalongkorn University, Phayathai Rd., Bangkok, Thailand.

Fish & Shellfish Immunology
|August 15, 2019
PubMed

Insights

The PmVRP15 gene in shrimp is crucial for fighting white spot syndrome virus (WSSV). Researchers identified key regulatory elements and transcription factors, including interferon regulatory factor (IRF), octamer transcription factor 1 (Oct-1), and nuclear factor of activated T-cells transcription factor (NFAT), that control its expression.

Area of Science:

  • Aquaculture
  • Molecular Biology
  • Immunology

Background:

  • The viral responsive protein 15 (PmVRP15) in black tiger shrimp (Penaeus monodon) is vital for defense against white spot syndrome virus (WSSV).
  • PmVRP15 is expressed in hemocytes and plays a role in WSSV trafficking and assembly.
  • Limited information exists regarding the regulatory mechanisms of the PmVRP15 gene.

Purpose of the Study:

  • To investigate the genome organization and 5' upstream promoter sequences of the PmVRP15 gene.
  • To identify the active promoter region and key transcription factor binding sites involved in PmVRP15 gene regulation.

Main Methods:

  • Genomic DNA analysis to determine gene structure (exons and introns).
  • 5' upstream sequence analysis to identify the transcription start site and TATA box.
  • Promoter deletion assays to pinpoint the active promoter region.
  • Site-directed mutagenesis to investigate the function of putative transcription factor binding sites.

Main Results:

  • The PmVRP15 gene comprises 4 exons and 3 introns, with the start codon in exon 2.
  • The active promoter region was localized between nucleotide positions -525 and +612.
  • Mutagenesis studies revealed that the interferon regulatory factor (IRF) binding site acts as a repressor, while octamer transcription factor 1 (Oct-1) and nuclear factor of activated T-cells transcription factor (NFAT) binding sites function as activators.

Conclusions:

  • This study elucidates the genomic structure and promoter characteristics of the PmVRP15 gene.
  • Identified specific transcription factors (IRF, Oct-1, NFAT) that modulate PmVRP15 gene expression, providing insights into shrimp antiviral immunity.
  • Further research is needed to fully understand the complex regulatory network governing PmVRP15 expression.

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