Abstract

We apply a single-molecule chromatin fiber sequencing (Fiber-seq) protocol designed for amplification-free cell-type-specific mapping of the regulatory architecture at nucleosome resolution along extended ∼10-kb chromatin fibers to neuronal and non-neuronal nuclei sorted from human brain tissue. Specifically, application of this method enables the resolution of cell-selective promoter and enhancer architectures on single fibers, including transcription factor footprinting and position mapping, with sequence-specific fixation of nucleosome arrays flanking transcription start sites and regulatory motifs. We uncover haplotype-specific chromatin patterns, multiple regulatory elements cis-aligned on individual fibers, and accessible chromatin at 20,000 unique sites encompassing retrotransposons and other repeat sequences hitherto “unmappable” by short-read epigenomic sequencing. Overall, we show that Fiber-seq is applicable to human brain tissue, offering sharp demarcation of nucleosome-depleted regions at sites of open chromatin in conjunction with multi-kilobase nucleosomal positioning at single-fiber resolution on a genome-wide scale.

Original languageEnglish
Article number100911
JournalCell Reports Methods
Volume4
Issue number12
DOIs
StatePublished - 16 Dec 2024

Keywords

  • CP: Biotechnology
  • CP: Neuroscience
  • Hia5 methyltransferase
  • adenine methylation
  • cytosine methylation
  • long-read sequencing
  • nucleosomal array
  • nucleosomal offset
  • postmortem brain
  • transcription factor footprint

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