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Related Experiment Video

Updated: Jul 21, 2025

High-throughput Identification of Gene Regulatory Sequences Using Next-generation Sequencing of Circular Chromosome Conformation Capture 4C-seq
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High-throughput complement component 4 genomic sequence analysis with C4Investigator.

Wesley M Marin1, Danillo G Augusto1,2,3, Kristen J Wade1

  • 1Weill Institute for Neurosciences, Department of Neurology, University of California San Francisco, San Francisco, CA, United States.

Biorxiv : the Preprint Server for Biology
|July 28, 2023
PubMed
Summary
This summary is machine-generated.

We developed C4Investigator, a novel bioinformatic pipeline for analyzing complement component 4 (C4) gene variations. This tool enables comprehensive, high-throughput characterization of C4 sequences from genomic data, revealing significant poly-allelism and functional variants.

Keywords:
C4bioinformatics pipelinecomplement componentcopy numbergenotypingimmunogenetics

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Area of Science:

  • Immunogenetics
  • Bioinformatics
  • Genomics

Background:

  • The complement component 4 (C4) gene locus, comprising C4A and C4B genes on chromosome 6, is crucial for immune system modulation via the classical and lectin complement pathways.
  • C4 exhibits complex genetic variation, including copy number variations (0-5 copies per haplotype) and size variations (C4(L) long-form, C4(S) short-form) due to HERV retrovirus insertion.
  • C4 protein carries human blood group antigens Rodgers and Chido, generally on C4A and C4B, respectively. C4 variations are linked to autoimmune and pathogenic diseases.

Approach:

  • Developed C4Investigator, a novel bioinformatic pipeline for high-throughput characterization of human C4 sequences using short-read sequencing data.
  • C4Investigator analyzes paired-end targeted or whole genome sequencing data to determine gene copy number (C4, C4A, C4B, C4(Rodger), C4(Ch), C4(L), C4(S)).
  • The pipeline also reports the full aligned C4 sequence, enabling nucleotide-level analysis of C4 variations.

Key Points:

  • C4Investigator successfully characterized C4 variation in the 1000 Genomes Project Dataset.
  • Analysis revealed that C4 genes are highly poly-allelic, with numerous variants identified.
  • These identified variants have the potential to significantly impact C4 protein function and immune response.

Conclusions:

  • C4Investigator provides a comprehensive solution for high-throughput genomic analysis of complex C4 variations.
  • The tool facilitates deeper understanding of C4's role in immune function and disease pathogenesis.
  • Further research utilizing C4Investigator can elucidate the functional impact of C4 poly-allelism in various human conditions.