McGinty, S. P. | bioRxiv Science

bioRxiv2025

Influence of cis-regulatory elements on regulatory divergence in human segmental duplications

Human-specific segmental duplications (HSDs) contain millions of base pairs of sequence unique to the human genome, including genes that shape neurodevelopment. Despite their young age (<6 million years), HSD genes exhibit widespread regulatory divergence, with paralog-specific expression patterns documented across a variety of tissues and cell types. Using long-read expression and epigenomic data, we show that human-specific paralogs tend to have lower activity than the shared, ancestral ones. To systematically characterize the cis-regulatory elements (CREs) within HSDs and understand patterns of regulatory change in recently evolved gene families, we conduct a massively parallel reporter assay of 7,760 human duplicated and chimpanzee orthologous sequences in lymphoblastoid (GM12878) and neuroblastoma (SH-SY5Y) cell lines. A large proportion (14-24%) of sequences exhibit differential activity relative to the chimpanzee ortholog (or between human paralogs), mostly with small fold-differences. Combining measured activity levels across all assayed sequences, predicted differences in cis-regulatory activity correlate with mRNA levels in SH-SY5Y. Differentially active CREs validated for CHRFAM7A, HYDIN2, and SRGAP2C may contribute to paralog-specific expression patterns and thereby to human-specific traits. While we identify some changes in CRE activity within duplicated regions, consideration of adjacent, unique sequences suggests a larger contribution from genome positional effects. In all, this work shows that functional divergence of duplicated CREs contributes moderately to regulatory divergence of HSD genes and uncovers enhancers that are candidate drivers of human-specific regulatory patterns.

genomics↗

bioRxiv2025

CiFi: Accurate long-read chromatin conformation capture with low-input requirements

Hi-C characterizes three-dimensional chromatin organization, facilitates haplotype phasing, and enables genome-assembly scaffolding, but encounters difficulties across complex regions. By coupling chromosome conformation capture (3C) with PacBio HiFi long-read sequencing, here we develop a method (CiFi) that enables analysis of genomic interactions across repetitive regions. Starting with as little as 60,000 cells (sub-microgram DNA), the method produces multi-kilobasepair HiFi reads that contain multiple interacting, concatenated segments ([~]350 bp to 2 kbp). This multiplicity and increase in segment length versus standard short-read-based Hi-C improves read-mapping efficiency and coverage in repetitive regions and enhances haplotype phasing. CiFi pairwise interactions are largely concordant with Hi-C from a human lymphoblastoid cell line, with gains in assigning topologically associating domains across centromeres, segmental duplications, and human disease-associated genomic hotspots. As CiFi requires less input versus established methods, we apply the approach to characterize single small insects: assaying chromatin interactions across the genome from an Anopheles coluzzii mosquito and producing a chromosome-scale scaffolded assembly from a Ceratitis capitata Mediterranean fruit fly. Together, CiFi enables assessment of chromosome-scale interactions of previously recalcitrant low-complexity loci, low-input samples and small organisms.

genomics↗