GEO series
Repeats mimic pathogen-associated patterns across a vast evolutionary landscape [RIP-Seq]
GSE305618
Homo sapiens
Other; Expression profiling by high throughput sequencing
16 samples
Submitted 2025/08/20
Platform GPL24676
Summary
An emerging hallmark of many human diseases is transcription of typically silenced repetitive DNA containing pathogen-associated molecular patterns (PAMPs). These PAMPs engage the innate immune system via pattern recognition receptors (PRRs) – a phenomenon known as “viral mimicry.” We propose a statistical physics framework to quantify viral mimicry by measuring “selective forces” that enrich PAMPs compared to a genome-wide reference distribution. We validate our predictions by identifying repeats that bind different PRRs and show viral mimicry in different repeat families across eukaryotic genomes, suggesting shared mechanisms drive emergence and retention. We propose two non-exclusive evolutionary hypotheses. The first ‘repeat-centric’ hypothesis posits PAMPs are integral to the repeat lifecycle and are therefore enriched as they mediate repeat expansion. The second ‘organism-centric’ hypothesis proposes viral mimicry functions as a cell-intrinsic feedback mechanism for sensing and reacting to transcriptional dysregulation, which provides a selective pressure to maintain PAMPs in genomes.
Published in
Šulc P, Di Gioacchino A, Solovyov A et al.
· Cell genomics 2025
· PMID 40997813
· doi:10.1016/j.xgen.2025.101011
This dataset
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Direct links to NCBI, no account and no request form: the whole study as GSE305618_RAW.tar, processed values as the series matrix, the supplementary file directory, and per-sample supplementary files for any of the 16 samples. Raw sequencing reads are also available from ENA.
Also filed as BioProject PRJNA1307287 and SRA study SRP609574. Searching any of these in the dataset finder brings you back here.
Study design
8 conditions, mostly in duplicate
RIP-Seq, anti-ZCCHC3 antibody, 300mM salt con… ×2
RIP-Seq, anti-ZCCHC3 antibody, 500mM salt con… ×2
RIP-Seq, mock antibody, 300mM salt concentrat… ×2
RIP-Seq, mock antibody, 500mM salt concentrat… ×2
RIP-Seq, anti-ORFP1p antibody, 300mM salt con… ×2
RIP-Seq, anti-ORFP1p antibody, 500mM salt con… ×2
total RNA control, 300mM salt concentration, ×2
total RNA control, 500mM salt concentration, ×2
Supports a between-group comparison across 16 samples.
8 replicated groups read from 16 sample titles; they account for 16 of them. Check it against the sample list below before relying on it.
Samples in this study
0 selected
- GSM9180698 RIP-Seq, anti-ZCCHC3 antibody, 300mM salt concentration, replicate 1
- GSM9180699 RIP-Seq, anti-ZCCHC3 antibody, 500mM salt concentration, replicate 1
- GSM9180700 RIP-Seq, mock antibody, 300mM salt concentration, replicate 1
- GSM9180701 RIP-Seq, mock antibody, 500mM salt concentration, replicate 1
- GSM9180702 RIP-Seq, anti-ZCCHC3 antibody, 300mM salt concentration, replicate 2
- GSM9180703 RIP-Seq, anti-ZCCHC3 antibody, 500mM salt concentration, replicate 2
- GSM9180704 RIP-Seq, mock antibody, 300mM salt concentration, replicate 2
- GSM9180705 RIP-Seq, mock antibody, 500mM salt concentration, replicate 2
- GSM9180706 RIP-Seq, anti-ORFP1p antibody, 300mM salt concentration, replicate 1
- GSM9180707 RIP-Seq, anti-ORFP1p antibody, 500mM salt concentration, replicate 1
- GSM9180708 total RNA control, 300mM salt concentration, replicate 1
- GSM9180709 total RNA control, 500mM salt concentration, replicate 1
- GSM9180710 RIP-Seq, anti-ORFP1p antibody, 300mM salt concentration, replicate 2
- GSM9180711 RIP-Seq, anti-ORFP1p antibody, 500mM salt concentration, replicate 2
- GSM9180712 total RNA control, 300mM salt concentration, replicate 2
- GSM9180713 total RNA control, 500mM salt concentration, replicate 2
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