guidedNOMe-seq quantifies chromatin states at single allele resolution for hundreds of custom regions in parallel.

Publisher: BioMed Central Country of Publication: England NLM ID: 100965258 Publication Model: Electronic Cited Medium: Internet ISSN: 1471-2164 (Electronic) Linking ISSN: 14712164 NLM ISO Abbreviation: BMC Genomics Subsets: MEDLINE

Original Publication: London : BioMed Central, [2000-

Chromatin*/genetics ; Chromatin*/metabolism ; Alleles* ; Nucleosomes*/genetics ; Nucleosomes*/metabolism ; High-Throughput Nucleotide Sequencing*/methods; Humans ; Sequence Analysis, DNA/methods

Since the introduction of next generation sequencing technologies, the field of epigenomics has evolved rapidly. However, most commonly used assays are enrichment-based methods and thus only semi-quantitative. Nucleosome occupancy and methylome sequencing (NOMe-seq) allows for quantitative inference of chromatin states with single locus resolution, but this requires high sequencing depth and is therefore prohibitively expensive to routinely apply to organisms with large genomes. To overcome this limitation, we introduce guidedNOMe-seq, where we combine NOMe profiling with large scale sgRNA synthesis and Cas9-mediated region-of-interest (ROI) liberation. To facilitate quantitative comparisons between multiple samples, we additionally develop an R package to standardize differential analysis of any type of NOMe-seq data. We extensively benchmark guidedNOMe-seq in a proof-of-concept study, dissecting the interplay of ChAHP and CTCF on chromatin. In summary we present a cost-effective, scalable, and customizable target enrichment extension to the existing NOMe-seq protocol allowing genome-scale quantification of nucleosome occupancy and transcription factor binding at single allele resolution.
(© 2024. The Author(s).)

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Keywords: CTCF; Cas9 enrichment; ChAHP; Chromatin; NOMe-Seq

0 (Chromatin)
0 (Nucleosomes)

Date Created: 20240729 Date Completed: 20240729 Latest Revision: 20240801

20240801

PMC11288131

10.1186/s12864-024-10625-3

39075377