Noncoding regulatory elements in the human genome can control gene expression through distinct mechanisms, including acting as enhancers, silencers, or topological elements. However, we lack tools to identify all such classes systematically and quantify their effects on gene expression in an endogenous genomic context....
X. Cai, Michael T. Montgomery, Masahiro Nagano et al.· bioRxiv· 0 citations
Enhancers are drivers of gene regulation thought to act via 3D interactions with promoters. However, genome-wide cohesin depletion causes only limited changes in gene expression, despite widespread loss of contact domains, raising questions about how 3D contacts and cohesin influence enhancer function. Here, we intro...
Philine Guckelberger, Benjamin R. Doughty, Suhas S. P. Rao et al.· Nature Communications· 0 citations
This work presents a variant-agnostic approach to rescue haploinsufficiency by mapping and rationally redesigning the MYBPC3 promoter and identifies synergistic sequence edits that drive robust increases in MYBPC3 expression.
Aaron Renberg, S. Coppersmith, Owen Merritt et al.· bioRxiv· 0 citations
The mV2G atlas provides searchable variant- and gene-centered interfaces, an interactive browser for visualizing variants, target genes, cis-regulatory elements, and chromatin states, as well as downloadable datasets, and a unified tissue-specific V2G prioritization framework.
Dean Y. Zhang, Hufeng Zhou, Maya U. Sheth et al.· bioRxiv· 0 citations
A family of classification models, scE2G, is introduced that predict enhancer–gene regulatory interactions from single-cell datasets and enable mapping of these interactions across diverse cell types and tissues and will enable accurate mapping of enhancer–gene regulatory interactions across thousands of human cell typ...
Maya U. Sheth, Wei-Lin Qiu, X. Ma et al.· Nature Genetics· 1 citation
An encyclopedia of enhancer–gene regulatory interactions in the human genome is built, revealing global properties of enhancer networks, identifying differences in regulatory complexity across genes, and improving analyses linking noncoding variants to target genes and cell types for common, complex diseases.
A. Gschwind, Kristy S. Mualim, Alireza Karbalayghareh et al.· Nature· 6 citations
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