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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 conducted a massively parallel reporter assay of 7,160 human duplicated and chimpanzee orthologous sequences in lymphoblastoid (GM12878) and neuroblastoma (SH-SY5Y) cell lines. A large proportion (14–24%) of sequences exhibited 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 correlated with mRNA levels in SH-SY5Y. Differentially active CREs were validated for CHRFAM7A, HYDIN2, and SRGAP2C that may contribute to paralog-specific expression patterns and thereby to human-specific traits. While we find some changes in CRE activity shared between duplicate paralogs likely driving regulatory divergence in gene expression, consideration of non-shared adjacent sequences to duplications suggests a larger role for altered genome positional effects. In all, this work suggests 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.
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This content will become publicly available on February 17, 2027
Profiling the epigenomic landscape of late embryonic and adult mouse hind limb muscles
Skeletal muscles are essential for movement, supporting a wide range of locomotor behaviors. Muscle tissue is composed of multiple cell types including “fast” and “slow” myofibers, whose contractile properties are largely influenced by selective expression of myosin heavy chain (MyHC) isoforms. While ‘super-enhancers’ regulating MyHC gene clusters have been identified, the cis-regulatory elements (CREs) controlling non-MyHC genes important to myofiber physiology remain less defined. Here, we profile the regulatory landscape of two pairs of mouse hind limb muscles differing in MyHC expression at a late embryonic (E18.5) and adult time point to identify candidate CREs that may regulate genes important to myofiber type. Gene expression and chromatin accessibility analyses revealed that epigenetic differences at E18.5 largely reflect limb patterning, whereas adult differences reflect myofiber differentiation. We identified thousands of differentially accessible regions that may regulate genes important for muscle development, muscle biology, and myofiber identity. Among these, twelve conserved, muscle-specific CREs associated with myofiber type were tested for regulatory activity. Nine enhanced and three reduced gene activity in vitro, although their phenotypic effects remain unknown. By profiling multiple muscles across two time points, our study extends current understanding of conserved, muscle-specific CREs that regulate gene expression during myogenesis.
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- Award ID(s):
- 1945809
- PAR ID:
- 10667076
- Publisher / Repository:
- Nature Scientific Reports
- Date Published:
- Journal Name:
- Scientific Reports
- ISSN:
- 2045-2322
- Format(s):
- Medium: X
- Associated Dataset(s):
- View Associated Dataset(s) >>
- Sponsoring Org:
- National Science Foundation
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