Evidence map›Paper›PMID 38862613›Full record

ArticleCommunications biology2024

Multi-omics analysis reveals the dynamic interplay between Vero host chromatin structure and function during vaccinia virus infection.

Vrinda Venu, Cullen Roth, Samantha H Adikari, Eric M Small, Shawn R Starkenburg, Karissa Y Sanbonmatsu, Christina R Steadman

Abstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in Communications biology, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 13 papers.

0numbers the graph read from it
0cells of the map it votes in
13citing papers in PubMed
–field-weighted citation impact
1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

The trial behind it

Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.

Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

13 citing papers in PubMed.

  1. Article
  2. Tuning epigenetics to enhance cancer virotherapy.Acta pharmaceutica Sinica. B · 2026
    Review
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  12. Article
  13. Applying 3D Genome Technology in Virology Research.Methods in molecular biology (Clifton, N.J.) · 2025
    Article
4 · The record

Corrections and comments

PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.

5 · Who and what money

Authors and funding

7 authors.

Vrinda VenuClimate, Ecology & Environment Group, Los Alamos National Laboratory, Los Alamos, NM, USA.ORCID 0000-0001-6131-3340
Cullen RothGenomics & Bioanalytics Group, Los Alamos National Laboratory, Los Alamos, NM, USA.ORCID 0000-0003-4934-6160
Samantha H AdikariBiochemistry & Biotechnology Group, Los Alamos National Laboratory, Los Alamos, NM, USA.
Eric M SmallClimate, Ecology & Environment Group, Los Alamos National Laboratory, Los Alamos, NM, USA.ORCID 0000-0002-6960-4393
Shawn R StarkenburgGenomics & Bioanalytics Group, Los Alamos National Laboratory, Los Alamos, NM, USA.ORCID 0000-0002-8564-1274
Karissa Y SanbonmatsuTheoretical Biology and Biophysics Group, Los Alamos National Laboratory, Los Alamos, NM, USA.ORCID 0000-0002-7965-7392
Christina R SteadmanClimate, Ecology & Environment Group, Los Alamos National Laboratory, Los Alamos, NM, USA. crsteadman@lanl.gov.ORCID 0000-0002-9672-5529

Funding

DOE | LDRD | Los Alamos National Laboratory (Los Alamos Lab) 20210134ER
6 · The paper itself

Abstract

The genome folds into complex configurations and structures thought to profoundly impact its function. The intricacies of this dynamic structure-function relationship are not well understood particularly in the context of viral infection. To unravel this interplay, here we provide a comprehensive investigation of simultaneous host chromatin structural (via Hi-C and ATAC-seq) and functional changes (via RNA-seq) in response to vaccinia virus infection. Over time, infection significantly impacts global and local chromatin structure by increasing long-range intra-chromosomal interactions and B compartmentalization and by decreasing chromatin accessibility and inter-chromosomal interactions. Local accessibility changes are independent of broad-scale chromatin compartment exchange (~12% of the genome), underscoring potential independent mechanisms for global and local chromatin reorganization. While infection structurally condenses the host genome, there is nearly equal bidirectional differential gene expression. Despite global weakening of intra-TAD interactions, functional changes including downregulated immunity genes are associated with alterations in local accessibility and loop domain restructuring. Therefore, chromatin accessibility and local structure profiling provide impactful predictions for host responses and may improve development of efficacious anti-viral counter measures including the optimization of vaccine design.

Indexed as

ChromatinVaccinia virusAnimalsChlorocebus aethiopsHost-Pathogen InteractionsMultiomicsVacciniaVero CellsChromatin

Identifiers

PMID38862613
PMCPMC11166932

What OpenQuestion holds

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LicenceCC BY
Read underepoch 390

Registered trials

None linked

Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.