Single-cell CRISPR activation screens in primary B cells discover gene regulatory mechanisms for hundreds of autoimmune risk loci.

Kriachkov, V.; Ching, J. W. H.; Lancaster, J.; Vespasiani, D.; Denny, N.; Hamley, J. C.; Gubbels, L.; Bandala Sanchez, E.; Neeland, M.; Levi, E.; Davies, K.; Shanthikumar, S.; Shevchenko, G.; Bryant, V. L.; Hodson, D. J.; Davies, J. O. J.; King, H. W.

doi:10.64898/2026.03.01.708923

bioRxiv · 10.64898/2026.03.01.708923

Single-cell CRISPR activation screens in primary B cells discover gene regulatory mechanisms for hundreds of autoimmune risk loci.

Kriachkov, V.·Ching, J. W. H.·Lancaster, J.·Vespasiani, D.·Denny, N.·Hamley, J. C.·Gubbels, L.·Bandala Sanchez, E.·Neeland, M.·Levi, E.·Davies, K.·Shanthikumar, S.·Shevchenko, G.·Bryant, V. L.·Hodson, D. J.·Davies, J. O. J.·King, H. W.

View original source ↗Export metadata ↓

Abstract

Genome-wide association studies (GWAS) have discovered thousands of genetic variants linked to autoimmune disease, and yet the molecular pathways underlying autoimmunity have remained elusive. A key challenge is that >90% of identified GWAS risk loci are in non-coding genomic regions making it difficult to predict their relevance to disease. Here, we have curated fine-mapped non-coding risk variants from over 30 different autoimmune traits including common conditions such as systemic lupus erythematosus (SLE), Crohns disease, and multiple sclerosis, and reveal shared genetic signatures between diverse autoimmune diseases. We subsequently performed a high-throughput single-cell multi-omic CRISPR activation screen targeting 763 autoimmune risk loci in primary human B cells (a highly relevant cell type to autoimmune diseases) and discover 524 cis-regulatory target gene effects for 378 risk loci, with many risk loci regulating multiple gene targets. This Single Cell Analysis of Non-coding Distal Autoimmune Loci (SCANDAL) provides a powerful experimental resource linking non-coding risk loci to many disease-relevant genes, including lowly-expressed cytokines and transcription factors for which perturbation effects can be difficult to quantify with other CRISPR-based strategies. We reveal how increased transcriptional activity at one non-coding risk locus can drive transcription at other risk loci within the same regulatory landscape that may be relevant to understand genetic pleiotropy of autoimmune diseases. Finally, we quantified allele-specific effects on target gene expression with massive parallel reporter assays and prime editing to discover a gain-of-function variant associated with SLE that controls expression of the transcription factor REL/cREL which subsequently binds dozens of risk loci and target genes associated with different autoimmune diseases. Our study provides a valuable resource linking non-coding risk loci with their cis-regulatory target genes and advances our understanding of the shared genetic networks and mechanisms involved in autoimmunity.

Explore related subjects

genomics Preprint

Keep this discovery

Explore connections, maps & timelines

BibTeX RIS

Kriachkov, V., Ching, J. W. H., Lancaster, J., Vespasiani, D., Denny, N., Hamley, J. C., Gubbels, L., Bandala Sanchez, E., Neeland, M., Levi, E., Davies, K., Shanthikumar, S., Shevchenko, G., Bryant, V. L., Hodson, D. J., Davies, J. O. J., King, H. W.. 2026-03-02. Single-cell CRISPR activation screens in primary B cells discover gene regulatory mechanisms for hundreds of autoimmune risk loci.. https://doi.org/10.64898/2026.03.01.708923

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

KEEP EXPLORING

Related preprints

bioRxiv2026

Genome-wide diversity across 130 years reveals drastic post-bottleneck genetic erosion in a recovering population of golden eagles (Aquila chrysaetos)

Many wild populations have experienced severe human-induced declines, but the genetic consequences of such bottlenecks are often poorly understood. In Finland, as well as in many other countries, golden eagles were heavily persecuted during the 19th-20th centuries, disappearing from southern regions and reaching their lowest population size in the 1950-1960s. Although conservation efforts facilitated demographic recovery, the long-term genomic consequences of the bottleneck remained unknown. Here, we used whole-genome sequencing data spanning 136 years to evaluate patterns of genetic diversity in 26 Finnish golden eagles before, during, and after the mid-20th century bottleneck. We found substantial loss of genetic variation, including an 82% reduction in genome-wide heterozygosity, a 42% decline in nucleotide diversity, a 67% reduction in Watterson's theta, and a substantial loss of variable sites. Analyses of the site frequency spectrum and Tajima's D confirmed historical population contraction, and runs of homozygosity analysis indicated elevated post-bottleneck inbreeding. These results indicate strong genetic erosion in Finnish golden eagles despite the census size recovery. Therefore, incorporating genomic indicators in conservation monitoring and performing regional assessments are necessary to guide management and preserve biodiversity in line with the Global Biodiversity Framework's goal of maintaining genetic variation.

genomics↗

bioRxiv2026

Long-read analysis of complete human 5S rDNA arrays reveals a zoned organization with two-state unit methylation linked to chromatin architecture

Despite the fundamental importance of the 5S ribosomal DNA (rDNA) to all cellular life, the landscape of its units by position along its array has remained poorly understood. Here, recent telomere-to-telomere long-read sequencing is used to resolve 5S rDNA arrays from flank to flank and to follow the state of each unit along single molecules. The array is zoned at both the sequence and the epigenetic level. Notably, methylation is bimodal at the level of the unit, and the combination of low-methylation and high-methylation units gives rise to the overall methylation pattern of the array. Moreover, the average number of low-methylation units remains relatively constant regardless of array length. Chromatin fiber sequencing (Fiber-seq) data further show that low-methylation units are more accessible, have lower nucleosome occupancy and are more frequently footprinted at the TFIIIB-binding site, consistent with analyses of ATAC-seq and ChIP-seq data from cell lines. Across species, this pattern is shared among apes, whereas other species show diverse patterns. These results provide a unit-resolved view of the human 5S rDNA array and reveal a zone-specific organization of unit methylation that is associated with chromatin architecture.

genomics↗

bioRxiv2026

Using Oyster Genomics to Understand Human Health

As sessile filter feeders that experience continuous environmental exposure, oysters, particularly Crassostrea virginica, offer a unique opportunity to understand how environmental exposure alters the genome and influence health. Furthermore, oysters must be sorted by size for market value for premium size and taste. However, it requires intensive labor, specialized equipment (tumblers), and is susceptible to environmental risks like pollution. Therefore, it is desirable to produce uniform oysters without machines. However, limitations in the previous reference genome [2] have constrained our understanding of how genes are organized and maintained in oyster populations. To this end, we harvested 240 adult oysters in same location, 120 extremely large size and 120 extremely small, controlled with all confounding factors such as age and water temperature. We perform a genome wise associate study (GWAS) using next generation whole genome sequencing, aiming to discover genomic regions associated with oyster size. Using PacBio HiFi, Illumina, and Hi-C technologies, we generated a 99.7% complete chromosome-level genome assembly for C. virginica (NCBI RefSeq GCF_053477285.1) [75]. We identified a ~13 Mb region on chromosome 1 uniquely expanded in C. virginica and enriched for innate immune and stress-response genes. To evaluate whether these structural features are reflected at the population level, we then conducted a k-mer analysis. This revealed differential sequence patterns by size, including enrichment of bacterial DNA in smaller individuals and host variation at the RNF213 locus within this region. By highlighting genome structure as a mediator of immune resilience, this work supports the use of oysters as sentinels to advance out understanding of how the dynamic reassembly of the genome due to environmental exposures influence health in human populations.

genomics↗