TY - JOUR
T1 - Single chromatin fiber profiling and nucleosome position mapping in the human brain
AU - Peter, Cyril J.
AU - Agarwal, Aman
AU - Watanabe, Risa
AU - Kassim, Bibi S.
AU - Wang, Xuedi
AU - Lambert, Tova Y.
AU - Javidfar, Behnam
AU - Evans, Viviana
AU - Dawson, Travis
AU - Fridrikh, Maya
AU - Girdhar, Kiran
AU - Roussos, Panos
AU - Nageshwaran, Sathiji K.
AU - Tsankova, Nadejda M.
AU - Sebra, Robert P.
AU - Vollger, Mitchell R.
AU - Stergachis, Andrew B.
AU - Hasson, Dan
AU - Akbarian, Schahram
N1 - Publisher Copyright:
© 2024 The Author(s)
PY - 2024/12/16
Y1 - 2024/12/16
N2 - 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.
AB - 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.
KW - CP: Biotechnology
KW - CP: Neuroscience
KW - Hia5 methyltransferase
KW - adenine methylation
KW - cytosine methylation
KW - long-read sequencing
KW - nucleosomal array
KW - nucleosomal offset
KW - postmortem brain
KW - transcription factor footprint
UR - http://www.scopus.com/inward/record.url?scp=85212099779&partnerID=8YFLogxK
U2 - 10.1016/j.crmeth.2024.100911
DO - 10.1016/j.crmeth.2024.100911
M3 - Article
C2 - 39631398
AN - SCOPUS:85212099779
SN - 2667-2375
VL - 4
JO - Cell Reports Methods
JF - Cell Reports Methods
IS - 12
M1 - 100911
ER -