Optimised fluorescence-activated nuclei sorting for epigenomic analysis of cortical cell types
4 affiliations
- 1Department of Clinical & Biomedical Sciences, University of Exeter Medical School, Exeter, United Kingdom
- 2Department of Brain Sciences, Imperial College London, London, United Kingdom
- 3UK Dementia Research Institute, King’s College London, London, United Kingdom
- 4Department of Basic and Clinical Neuroscience, Institute of Psychiatry, Psychology and Neuroscience, King’s College London, London, United Kingdom
Abstract
Increased understanding of the functional complexity of the genome has led to growing recognition of the role of non-sequence-based regulatory variation in disorders of the human central nervous system. Most genomic analyses of the brain are limited by the use of bulk tissue, which comprises a heterogeneous mix of different neural cell types with distinct epigenetic profiles, thereby limiting the ability to attribute regulatory changes to specific cell populations. Given the limited availability of human post-mortem tissue resources and the importance of integrating multi-omic data from the same samples, there is a critical need for methods that enable parallel, cell-type–resolved genomic profiling. We present optimised protocols using fluorescence-activated nuclei sorting (FANS) to isolate nuclei from different human and mouse brain cell types for downstream multi-omic analysis. Our approach enables the robust purification of neuronal, oligodendrocyte, microglial and other glial-origin nuclei from both adult and fetal brain tissue. We demonstrate that FANS-isolated nuclei are compatible with a wide range of genomic assays, including profiling of DNA modifications, histone modifications, chromatin accessibility, and gene expression. This protocol maximises the utility of limited post-mortem tissue resources and provides a unified workflow for comprehensive, cell-type–specific interrogation of molecular mechanisms involved in the brain.
Related
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BibTeX
@article{chioza2026optimised,
title = {{Optimised fluorescence-activated nuclei sorting for epigenomic analysis of cortical cell types}},
author = {Barry Chioza and Stefania Policicchio and Joe Burrage and Georgina E. T. Blake and Rosemary A. Bamford and Alice Franklin and Darren Soanes and Philippa M. Wells and Ann Babtie and Marina Flores Payan and Jonathan P. Davies and Anthony Klokkaris and Emma M. Walker and Joy N. Ismail and Paulina Urbanaviciute and Sarah J. Marzi and Eilis Hannon and Jonathan Mill and Emma L. Dempster},
journal = {PLOS One},
year = {2026},
month = oct,
doi = {10.1371/journal.pone.0359643},
url = {https://doi.org/10.1371/journal.pone.0359643},
note = {CC BY 4.0},
}
RIS
TY - JOUR
TI - Optimised fluorescence-activated nuclei sorting for epigenomic analysis of cortical cell types
AU - Barry Chioza
AU - Stefania Policicchio
AU - Joe Burrage
AU - Georgina E. T. Blake
AU - Rosemary A. Bamford
AU - Alice Franklin
AU - Darren Soanes
AU - Philippa M. Wells
AU - Ann Babtie
AU - Marina Flores Payan
AU - Jonathan P. Davies
AU - Anthony Klokkaris
AU - Emma M. Walker
AU - Joy N. Ismail
AU - Paulina Urbanaviciute
AU - Sarah J. Marzi
AU - Eilis Hannon
AU - Jonathan Mill
AU - Emma L. Dempster
PY - 2026
DA - 2026/10/06
JO - PLOS One
DO - 10.1371/journal.pone.0359643
UR - https://doi.org/10.1371/journal.pone.0359643
AB - Increased understanding of the functional complexity of the genome has led to growing recognition of the role of non-sequence-based regulatory variation in disorders of the human central nervous system. Most genomic analyses of the brain are limited by the use of bulk tissue, which comprises a heterogeneous mix of different neural cell types with distinct epigenetic profiles, thereby limiting the ability to attribute regulatory changes to specific cell populations. Given the limited availability of human post-mortem tissue resources and the importance of integrating multi-omic data from the same samples, there is a critical need for methods that enable parallel, cell-type–resolved genomic profiling. We present optimised protocols using fluorescence-activated nuclei sorting (FANS) to isolate nuclei from different human and mouse brain cell types for downstream multi-omic analysis. Our approach enables the robust purification of neuronal, oligodendrocyte, microglial and other glial-origin nuclei from both adult and fetal brain tissue. We demonstrate that FANS-isolated nuclei are compatible with a wide range of genomic assays, including profiling of DNA modifications, histone modifications, chromatin accessibility, and gene expression. This protocol maximises the utility of limited post-mortem tissue resources and provides a unified workflow for comprehensive, cell-type–specific interrogation of molecular mechanisms involved in the brain.
SN - 1932-6203
ER -