Human genomic DNA is widely interspersed with i-motif structures

Pena Martinez, C. D.; Zeraati, M.; Rouet, R.; Mazigi, O.; Gloss, B.; Chan, C.-L.; Bryan, T. M.; Smith, N. M.; Dinger, M. E.; Kummerfeld, S. K.; Christ, D.

doi:10.1101/2022.04.14.488274

bioRxiv · 10.1101/2022.04.14.488274

Human genomic DNA is widely interspersed with i-motif structures

Pena Martinez, C. D.·Zeraati, M.·Rouet, R.·Mazigi, O.·Gloss, B.·Chan, C.-L.·Bryan, T. M.·Smith, N. M.·Dinger, M. E.·Kummerfeld, S. K.·Christ, D.

View original source ↗Export metadata ↓

Abstract

DNA i-motif structures are formed in the nucleus of human cells and are believed to provide critical genomic regulation. While the existence of i-motif structures in human cells has been demonstrated by immunofluorescent staining and by characterisation of select model genes, the abundance and distribution of such structures in the human genome has remained unclear. Here we utilize high affinity i-motif immunoprecipitation followed by sequencing to map i-motifs in human genomic DNA. Validated by biolayer interferometry and circular dichroism spectroscopy, our approach identified over 650,000 i-motif structures in human genomic DNA. The i-motif structures are widely distributed throughout the human genome and are common among highly expressed genes and in genes upregulated in G0/G1 cell cycle phase. Our findings provide experimental evidence for the widespread formation of i-motif structures in human genomic DNA.

Source connections

Published article ↗

Explore related subjects

genetics Preprint

Keep this discovery

Explore connections, maps & timelines

BibTeX RIS

Pena Martinez, C. D., Zeraati, M., Rouet, R., Mazigi, O., Gloss, B., Chan, C.-L., Bryan, T. M., Smith, N. M., Dinger, M. E., Kummerfeld, S. K., Christ, D.. 2022-04-14. Human genomic DNA is widely interspersed with i-motif structures. https://doi.org/10.1101/2022.04.14.488274

Cite the original work for its findings. Save a collection to share your selection of sources.

KEEP EXPLORING

Related preprints

bioRxiv2026

Integrated exome-transcriptome analysis of a schizophrenia case with an exceptionally low polygenic risk score

Schizophrenia liability reflects both common polygenic variation and rarer variants of larger effect. We investigated a post-mortem schizophrenia case (SZ07) with a schizophrenia polygenic risk score below the first percentile among ancestry-matched cases, asking whether individual-level genomic and transcriptomic analyses could help identify potentially novel schizophrenia-relevant variants. We used exome analysis with multiple variant-prediction tools to generate a panel of variants and corresponding candidate genes potentially implicated in the pathological process in SZ07. The prioritised variants were then assessed using RNA sequencing of three cortical regions. Of these, only an IZUMO4 splice-acceptor variant showed direct RNA-level support. Beyond variant-specific analyses, we characterised broader transcriptomic abnormalities in the SZ07 brain. Pathway analysis of gene-level expression deviations implicated innate immune processes, calcium signalling, synaptic biology, and axon remodelling. Notably, compared with conventional single-sample biological pathway analysis, the analysis we used showed only a weak association with neuronal specificity, suggesting their reduced sensitivity to the main axis of variation related to cellular composition in bulk brain tissue gene expression data. Although the candidate genes showed no significant pathway-level convergence, the broader transcriptomic profile revealed coherent biological alterations largely compatible with the documented history of cerebrovascular disease in SZ07. These results demonstrate how the integration of exome and transcriptome data at the individual level enables the formulation and constraint of hypotheses regarding patient-specific genetic features and their molecular consequences, while highlighting important limitations related to tissue composition, comorbidity, and the choice of reference cohort.

genetics↗

bioRxiv2026

A genetic screen to identify host factors required for commensal bacterial adherence to the gut epithelia

Bacterial adherence to gut epithelial cells likely involves host genetic components. We isolated a gut commensal bacterium, Lelliottia jeotgali, that can robustly colonize C. elegans through attachment to intestinal epithelial cells. Here, we developed a novel screen in C. elegans to identify host genes required for microbiome bacterial colonization. Using transgenic L. jeotgali strain expressing tdTomato, we conducted forward genetic screens in C. elegans to select for mutants that completely lost colonization. We identified multiple allelic mutations in five different C. elegans genes, termed knockout of Lelliottia adherence (kola) mutants, with a near complete loss of adherence. Each of kola-1-5 is uncharacterized and predicted to encode for a secreted or membrane-bound protein. We also identified gly-5, a GalNAc transferase that initiates O-linked glycosylation. Overall, we describe the first C. elegans screen to identify host factors that control microbiome bacterial colonization in the gut.

genetics↗

bioRxiv2026

Male-specific genome sequences for non-invasive sex identification in Nishikigoi (Cyprinus carpio)

Nishikigoi, ornamental cultivars of the common carp (Cyprinus carpio), are economically valuable aquaculture teleosts in which mature females command significantly higher market prices due to superior body conformation and coloration. Consequently, early and non-invasive sex identification is highly desirable for commercial breeding. Although sex determination in common carp follows an XX/XY system, sex-chromosome-specific markers and field-applicable diagnostic methods for Nishikigoi have remained limited. In this study, we conducted sequence-based bulked segregant analysis using whole-genome shotgun sequencing of female and male pools in Kohaku, a representative Nishikigoi lineage. We identified male-specific candidate contigs and successfully developed PCR-based male-specific markers. Validation across multiple Nishikigoi varieties and wild common carp demonstrated that primary primer pairs achieved high diagnostic accuracy. Comparative genomic analysis revealed that these candidate contigs mapped to the genomic region on chromosome 25B containing the male-determining gene Pangu, with the primary marker located in immediate physical proximity to the gene. To enable field diagnostics, we combined non-invasive epidermal mucus DNA extraction, loop-mediated isothermal amplification (LAMP), and chromatography-printed array strip (C-PAS) technology, establishing a rapid on-site detection workflow. Overall, this study provides highly reliable PCR markers associated with the sex-determination locus and establishes a non-invasive, field-applicable diagnostic platform to streamline commercial Nishikigoi breeding and sex-selected stock management.

genetics↗