High-throughput methods for the analysis of transcription factors and chromatin modifications: Low input, single cell and spatial genomic technologies
Résumé
Genome-wide analysis of transcription factors and epigenomic features is instrumental to shed light on DNA-templated regulatory processes such as transcription, cellular differentiation or to monitor cellular responses to environmental cues. Two decades of technological developments have led to a rich set of approaches progressively pushing the limits of epigenetic profiling towards single cells. More recently, disruptive technologies using innovative biochemistry came into play. Assays such as CUT&RUN, CUT&Tag and variations thereof show considerable potential to survey multiple TFs or histone modifications in parallel from a single experiment and in native conditions. These are in the path to become the dominant assays for genome-wide analysis of TFs and chromatin modifications in bulk, single-cell, and spatial genomic applications. The principles together with pros and cons are discussed.
Mots clés
Transcription factors, chromatin, epigenetics, ChIP-Sequencing, CUT&RUN, spatial epigenomics Abbreviations ATAC, Assay of Transposase Accessible Chromatin ChIP, Chromatin ImmunoPrecipitation CUT&RUN, Cleavage Under Target and Release Using Nuclease CUT&Tag, Cleavage Under Targets and Tagmentation DHS, DNAse I hypersensitivity MERFISH, Multiplexed Error Robust Fluorescence In Situ Hybridization, MNase, Micrococcal Nuclease Ser5P-RNAPII, Serine 5 phosphorylated RNA polymerase II TF, Transcription Factor
Transcription factors, chromatin, epigenetics, ChIP-Sequencing, CUT&RUN, spatial epigenomics Abbreviations ATAC, Assay of Transposase Accessible Chromatin
ChIP, Chromatin ImmunoPrecipitation
CUT&RUN, Cleavage Under Target and Release Using Nuclease
CUT&Tag, Cleavage Under Targets and Tagmentation
DHS, DNAse I hypersensitivity
MERFISH, Multiplexed Error Robust Fluorescence In Situ Hybridization, MNase, Micrococcal Nuclease
Ser5P-RNAPII, Serine 5 phosphorylated RNA polymerase II
TF, Transcription Factor
Domaines
Sciences du Vivant [q-bio]Origine | Fichiers produits par l'(les) auteur(s) |
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