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Microfluidic technology for low-input mapping of genome-wide lncRNA-chromatin interactions using tissue samples

ABSTRACT: Long noncoding RNAs (lncRNAs) regulate gene expression through binding to DNA, various RNAs, and proteins, playing potentially important but poorly understood roles in development and diseases. Existing approaches for profiling lncRNA–chromatin interactions at the genome scale require large quantities of input material (e.g., 100 million cells per assay). Applying these technologies to tissue samples has been challenging especially when examination of a specific cell type is desired. Here we demonstrate a low-input microfluidic technology based on Chromatin Isolation by RNA purification (ChIRP) process for mapping lncRNA–chromatin interactions using as few as 50,000 cells. We validate our technology on two lncRNAs of different sizes in human and mouse cell lines and brain tissue. We apply our technology muChIRP-seq to neuronal nuclei from postmortem human brain tissues and integrate our data with histone and RNA-seq data to understand the role of lncRNA in the epigenomic and transcriptomic landscape of schizophrenia. MuChIRP-seq enables the mapping of lncRNA–chromatin interactions in tissue samples and in a cell-type-specific fashion, unlocking new opportunities to study lncRNA-mediated gene regulations.

ORGANISM(S): Mus musculus Homo sapiens

PROVIDER: GSE316123 | GEO | 2026/03/22

REPOSITORIES: GEO

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