129: NPIP — Structural variation, selection, and paralog diversification

Dishuck PC et al., Cell Genomics - Using 169 long-read human haplotypes and 1.4 billion full-length cDNA reads, Dishuck et al. resolve the complex NPIP gene family on chromosome 16, revealing extreme copy-number and structural variation, widespread interlocus gene conversion and inversions, ongoing positive selection at specific paralogs, and paralog-specific full-length gene models with tissue-biased expression. Key terms: NPIP, segmental duplications, positive selection, long-read sequencing, gene conversion.

Study Highlights:
The authors use haplotype-resolved long-read assemblies and Iso-Seq to catalog 4,665 NPIP copies across 169 haplotypes and define 28 paralogs. They detect frequent interlocus gene conversion and multiple large inversion polymorphisms mediated by NPIP duplications. Population-level tests (Tajima’s D, nSL) reveal ongoing positive selection at several paralogs while Iso-Seq uncovers paralog-specific ORFs and tissue-biased expression, with 56% of common isoforms previously unreported. VNTR expansion in a human-specific NPIPB subfamily predicts a β-helix domain and novel signal peptide evolution.

Conclusion:
High-resolution pangenomic sequencing shows NPIP is an exceptionally dynamic, human-specific gene family with structural rearrangements, gene conversion, and positive selection shaping paralog-specific gene models and expression; these resolved paralogs now provide targets for functional and clinical follow-up.

Music:
Enjoy the music based on this article at the end of the episode.

Article title:
Structural variation, selection, and diversification of the NPIP gene family from the human pangenome

First author:
Dishuck PC

Journal:
Cell Genomics

DOI:
10.1016/j.xgen.2025.100977

Reference:
Dishuck PC, Munson KM, Lewis AP, Dougherty ML, Underwood JG, Harvey WT, Hsieh P, Pastinen T, Eichler EE. Structural variation, selection, and diversification of the NPIP gene family from the human pangenome. Cell Genomics. 2025;5:100977. doi:10.1016/j.xgen.2025.100977

License:
This episode is based on an open-access article published under the Creative Commons Attribution 4.0 International License (CC BY 4.0) – https://creativecommons.org/licenses/by/4.0/

Support:
Base by Base is independent and ad-free — no sponsors, no paywall. If an episode was worth your time, chip in and keep the papers audited and the original songs coming:
❤️ Support monthly: https://buy.stripe.com/cNifZhclVebvagk2JDgEg01
☕ One-time donation: https://donate.stripe.com/7sY4gz71B2sN3RWac5gEg00
More at basebybase.com

On PaperCast Base by Base you'll discover the latest in genomics, functional genomics, structural genomics, and proteomics.

Episode link: https://basebybase.com/episodes/structural-variation-and-diversification-of-the-npip-gene-family-from-the-human-pangenome

QC:
This episode was checked against the original article PDF and publication metadata for the episode release published on 2025-09-06.

QC Scope:
- article metadata and core scientific claims from the narration
- excludes analogies, intro/outro, and music
- transcript coverage: Audited transcript sections describing NPIP copy-number variation, long-read pangenome mapping, interlocus gene conversion (IGC) and inversion polymorphisms, resurrection/open reading frames of paralogs, brain/testis protein innovations, NPIP-PKD1 fusion transcripts, and population-genetic selection signals (Tajima's D
- transcript topics: NPIP copy-number variation across humans and primates; Long-read sequencing and pangenome mapping of NPIP; Interlocus gene conversion (IGC) and inversion polymorphisms; Resurrection of NPIP pseudogenes and open reading frames; Human-specific protein innovations: signal peptide and VNTR beta-helix; NPIP-PKD1 fusion transcripts

QC Summary:
- factual score: 10/10<...