TY - JOUR
T1 - Using Callus as an Ex Vivo System for Chromatin Analysis
AU - Lavie, Orly
AU - Williams, Leor Eshed
N1 - Publisher Copyright: © 2025. The Author(s), under exclusive license to Springer Science+Business Media, LLC, part of Springer Nature.
PY - 2025
Y1 - 2025
N2 - Next-generation sequencing has revolutionized epigenetics research, enabling a comprehensive analysis of DNA methylation and histone modification profiles to explore complex biological systems at unprecedented depth. Deciphering the intricate epigenetic mechanisms that regulate gene activity presents significant challenges, including the issue of analyzing heterogeneous cell populations in bulk. Bulk analysis introduces bias and can obscure crucial information by averaging readouts from distinct cells. Various approaches have been developed to address this issue, such as cell-type-specific enrichment or single-cell sequencing techniques. However, the need for transgenic lines with fluorescent markers, along with technical challenges such as efficient protoplast isolation and low yield, limits their widespread adoption and use in multi-omic studies. This review discusses the pros and cons of these approaches, providing a valuable basis for selecting the most suitable strategy to minimize heterogeneity. We will also highlight the use of cotyledon-derived callus as an ex vivo system as a simple, accessible, and robust platform for enabling high-throughput multi-omic analyses.
AB - Next-generation sequencing has revolutionized epigenetics research, enabling a comprehensive analysis of DNA methylation and histone modification profiles to explore complex biological systems at unprecedented depth. Deciphering the intricate epigenetic mechanisms that regulate gene activity presents significant challenges, including the issue of analyzing heterogeneous cell populations in bulk. Bulk analysis introduces bias and can obscure crucial information by averaging readouts from distinct cells. Various approaches have been developed to address this issue, such as cell-type-specific enrichment or single-cell sequencing techniques. However, the need for transgenic lines with fluorescent markers, along with technical challenges such as efficient protoplast isolation and low yield, limits their widespread adoption and use in multi-omic studies. This review discusses the pros and cons of these approaches, providing a valuable basis for selecting the most suitable strategy to minimize heterogeneity. We will also highlight the use of cotyledon-derived callus as an ex vivo system as a simple, accessible, and robust platform for enabling high-throughput multi-omic analyses.
KW - ChIP-seq
KW - Epigenome
KW - Multi-omics analysis
KW - Single-cell sequencing
KW - Tissue heterogeneity
KW - Tissue microdissection
KW - Transcriptome
UR - http://www.scopus.com/inward/record.url?scp=85210455215&partnerID=8YFLogxK
U2 - https://doi.org/10.1007/978-1-0716-4228-3_18
DO - https://doi.org/10.1007/978-1-0716-4228-3_18
M3 - مقالة مرجعية
C2 - 39576610
SN - 1064-3745
VL - 2873
SP - 333
EP - 347
JO - Methods in molecular biology
JF - Methods in molecular biology
ER -