NOMe-HiC: joint profiling of genetic variants, DNA methylation, chromatin accessibility, and 3D genome in the same DNA molecule
Fu, H.; Zheng, H.; Chen, X.; Weirauch, M. T.; Muglia, L. J.; Wang, L.; Liu, Y.
Show abstract
Cis-regulatory elements coordinate the regulation of their targeted genes expression. However, the joint measurement of cis-regulatory elements activities and their interactions in spatial proximity is limited by the current sequencing approaches. We describe a method, NOMe-HiC, which simultaneously captures single nucleotide polymorphisms, DNA methylation, chromatin accessibility (GpC methyltransferase footprints), and chromosome conformation changes from the same DNA molecule, together with the transcriptome, in a single assay. NOMe-HiC shows high concordance with state-of-the-art mono-omic assays across different molecular measurements and reveals coordinated chromatin accessibility at distal genomic segments in spatial proximity and novel types of long-range allele-specific chromatin accessibility.
Matching journals
The top 5 journals account for 50% of the predicted probability mass.
Similar papers in this journal
Similar papers in this journal
Similar papers in this journal
- A comprehensive catalog of 3D genome organization in diverse human genomes facilitates understanding of the impact of structural variation on chromatin structure 96%
- Prioritization of enhancer mutations by combining allele-specific chromatin accessibility with deep learning 96%
- SEM: sized-based expectation maximization for characterizing nucleosome positions and subtypes 95%
Similar papers in this journal
- Methyl-CODEC enables simultaneous methylation and duplex sequencing 96%
- Graph pangenome reveals functional, evolutionary, and phenotypic significance of human nonreference sequences 95%
- Extensive long-range polycomb interactions and weak compartmentalization are hallmarks of human neuronal 3D genome 95%
Similar papers in this journal
- Z-Flipons conserved between human and mouse are associated with increased transcription initiation rates 96%
- Major cell-types in multiomic single-nucleus datasets impact statistical modeling of links between regulatory sequences and target genes 95%
- Fast Fourier Transform is a training-free, ultrafast, highly efficient, and fully interpretable approach for epigenomic data compression 94%
"Similar papers" are the closest papers from that journal in the model's embedding space. They show what the match is built on, but the ranking comes mostly from a classifier over the whole training set, not from these examples alone.