{
  "abstract": "As part of the CFIm complex, CPSF6 regulates cellular gene expression via alternative polyadenylation. CPSF6 binds primate lentiviral capsids and has been implicated in HIV-1 reverse transcription, nuclear import, and integration targeting. However, interpretations of the role(s) of CPSF6 during HIV-1 replication are complicated by the transcriptional changes that occur when the protein is depleted from cells. To disentangle the role of CPSF6 in HIV-1 replication from alternative polyadenylation, we selectively recoded its capsid-binding phenylalanine-glycine motif to alanine-alanine in CD4-positive Jurkat T cells, CEM12D7 T cells, and THP-1 myeloid/macrophage cells using CRISPR/Cas9-based homology-directed repair. While large variations in single-round HIV-1 infection were observed among isolated T cell clones, en masse comparisons of recoded T cells to cloned control T cells failed to reveal any significant differences in infection levels. Consistent with an overall fitness advantage provided by DNA integration in speckle-associated domains, which was ablated by recoding across cell types, HIV-1 replicated more robustly in control T cell populations. Single-round infection, in addition to spreading replication, was reduced in recoded myeloid/macrophage cells, which correlated with reductions in reverse transcription, and more robust blocks to HIV-1 nuclear import. Recoded monocytes/macrophages, however, did not reveal any evidence for enhanced type I interferon production or sensing of HIV-1 nucleic acids. Altogether, we define endogenously recoded cell lines to uncouple capsid binding from CPSF6’s role in RNA metabolism, which highlights a global fitness advantage of targeted DNA integration and cell type-specific roles for CPSF6 in HIV-1 reverse transcription, nuclear import, and virus replication proficiency.\n\nIMPORTANCE: HIV-1 usurps cellular factors to effectively replicate and avoid innate immune sensing. HIV-1 capsid binds CPSF6, but the consequences of this virus-host interaction on HIV-1 biology are necessarily complicated by the cellular role of CPSF6 in pre-RNA processing. By endogenously recoding CPSF6 to selectively disrupt capsid binding while preserving its RNA-processing activity, we demonstrate in two different T cell lines that CPSF6-mediated targeting of HIV-1 DNA integration into nuclear speckle-associated domains correlates with optimal viral replication. Recoded THP-1 myeloid/macrophage cells revealed additional single-round and multi-round infection defects, which correlated with reductions in reverse transcription and HIV-1 nuclear import. These defects, however, did not correlate with enhanced type I interferon production or detection of HIV-1 nucleic acids by known innate immune sensors. Our work clarifies diverse roles for the capsid-CPSF6 interaction in HIV-1 infection of T lymphocytic versus myeloid cell lines and provides novel cell reagents for future research studies.",
  "abstract_shown": true,
  "affiliations": [
    "Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute",
    "Department of Medicine, Harvard Medical School",
    "Department of Immunology and Microbiology, Scripps Research"
  ],
  "article_type": null,
  "arxiv": null,
  "author_total": 8,
  "authors": [
    {
      "affs": [
        0,
        1
      ],
      "name": "Sooin Jang"
    },
    {
      "affs": [
        0
      ],
      "name": "Rajalingam Radhakrishnan"
    },
    {
      "affs": [
        0
      ],
      "name": "Juliet Greenwood"
    },
    {
      "affs": [
        0,
        1
      ],
      "name": "Parmit K. Singh"
    },
    {
      "affs": [
        0,
        1
      ],
      "name": "Gregory J. Bedwell"
    },
    {
      "affs": [
        2
      ],
      "name": "Refugio Robles-Sikisaka"
    },
    {
      "affs": [
        2
      ],
      "name": "Andrew L. Routh",
      "orcid": "0000-0002-2874-5990"
    },
    {
      "affs": [
        0,
        1
      ],
      "name": "Alan N. Engelman",
      "orcid": "0000-0002-9709-2591"
    }
  ],
  "bibtex": "https://research.draconitic.com/paper/6hmd03pq7bqqw.bib",
  "cited_by": 0,
  "doi": "10.1128/mbio.02276-26",
  "fulltext_url": null,
  "id": "6hmd03pq7bqqw",
  "issns": [
    "2150-7511"
  ],
  "landing_url": "https://journals.asm.org/doi/10.1128/mbio.02276-26",
  "language": null,
  "licence": "CC-BY-4.0",
  "licence_label": "CC BY 4.0",
  "licence_source": "article",
  "licence_url": "https://creativecommons.org/licenses/by/4.0/",
  "metadata_licence": null,
  "native_subjects": [],
  "openalex": null,
  "pdf_url": "https://journals.asm.org/doi/pdf/10.1128/mbio.02276-26",
  "pmcid": null,
  "pmid": null,
  "published": "2026-10-29",
  "publisher": "American Society for Microbiology",
  "ris": "https://research.draconitic.com/paper/6hmd03pq7bqqw.ris",
  "sources": [
    {
      "first_seen": "2026-10-30T12:19:28Z",
      "native_id": "10.1128/mbio.02276-26",
      "source": "crossref",
      "url": "https://journals.asm.org/doi/10.1128/mbio.02276-26"
    }
  ],
  "subjects": [
    {
      "field": "biology",
      "origin": "issn:2150-7511",
      "subfield": "microbiology"
    }
  ],
  "title": "Targeted CPSF6 recoding reveals global fitness advantages of SPAD integration targeting and cell type-specific roles for capsid binding in HIV-1 DNA synthesis and nuclear import",
  "title_text": "Targeted CPSF6 recoding reveals global fitness advantages of SPAD integration targeting and cell type-specific roles for capsid binding in HIV-1 DNA synthesis and nuclear import",
  "type": "peer-reviewed",
  "updated_at": "2026-10-31T00:21:00Z",
  "url": "https://research.draconitic.com/paper/6hmd03pq7bqqw",
  "venue": "mBio",
  "versions": []
}