High-throughput methods for the analysis of transcription factors and chromatin modifications: Low input, single cell and spatial genomic technologies

Salma, Mohammad; Andrieu-Soler, Charlotte; Deleuze, Virginie; Soler, Éric

doi:10.1016/j.bcmd.2023.102745

Cited by 12 publications

(4 citation statements)

References 120 publications

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“…We therefore sought to determine whether the MYB-GFP cells could be used to efficiently profile MYB chromatin occupancy by using the GFP moiety as an affinity tag. We performed parallel CUT&RUN (Cleavage Under Target & Release Using Nuclease) 34 , 35 experiments using an anti-MYB or an anti-GFP antibody in MEL cells and in homozygous Myb -GFP MEL cells, respectively. We used an anti-MYB antibody that has been successfully used in landmark studies to detect MYB binding sites in leukemic cells 36 , 37 (see STAR Methods ).…”

Section: Resultsmentioning

confidence: 99%

Efficient genome editing in erythroid cells unveils novel MYB target genes and regulatory functions

Deleuze,

Garcia,

Rouaisnel

et al. 2023

iScience

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Section: Resultsmentioning

confidence: 99%

Efficient genome editing in erythroid cells unveils novel MYB target genes and regulatory functions

Deleuze,

Garcia,

Rouaisnel

et al. 2023

iScience

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“…Genome-wide analysis of histone modifications is essential for shedding light on cellular processes. Alterations in the patterns of histone modifications have been identified at the global level of the genome by using ChIP-chip, ChIP-seq, CUT&RUN and CUT&Tag [ 26 , 27 ].…”

Section: Cutandtag Profiling Of Histone Modificationsmentioning

confidence: 99%

Cut&tag: a powerful epigenetic tool for chromatin profiling

Fu,

Jiang,

Sun

et al. 2023

Epigenetics

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Analysis of transcription factors and chromatin modifications at the genome-wide level provides insights into gene regulatory processes, such as transcription, cell differentiation and cellular response. Chromatin immunoprecipitation is the most popular and powerful approach for mapping chromatin, and other enzyme-tethering techniques have recently become available for living cells. Among these, Cleavage Under Targets and Tagmentation (CUT&Tag) is a relatively novel chromatin profiling method that has rapidly gained popularity in the field of epigenetics since 2019. It has also been widely adapted to map chromatin modifications and TFs in different species, illustrating the association of these chromatin epitopes with various physiological and pathological processes. Scalable single-cell CUT&Tag can be combined with distinct platforms to distinguish cellular identity, epigenetic features and even spatial chromatin profiling. In addition, CUT&Tag has been developed as a strategy for joint profiling of the epigenome, transcriptome or proteome on the same sample. In this review, we will mainly consolidate the applications of CUT&Tag and its derivatives on different platforms, give a detailed explanation of the pros and cons of this technique as well as the potential development trends and applications in the future.

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“…Multiple nucleic acid binding proteins function together to co-regulate specific sets of target genes, which are often called gene regulatory networks (GRNs) (Oksuz et al 2023;Wang et al 2022). High-throughput genomic technologies have generated hundreds of data sets that provide information regarding DNA and RNA targets of individual nucleic acid binding proteins, helping decipher the combinatorial function of TFs and RBPs in regulating specific GRNs (Salma et al 2023;Martin et al 2023;König et al 2012). However, user-friendly analysis tools cannot generate high-throughput comparisons between multiple protein-nucleic acid binding datasets to determine common and unique targets.…”

Section: Introductionmentioning

confidence: 99%

BindCompare: A Novel Integrated Protein-Nucleic Acid Binding Analysis Platform

Mahableshwarkar,

Shum,

Ray

et al. 2024

Preprint

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Advanced genomic technologies have generated thousands of Protein-Nucleic acid binding datasets that have the potential to identify testable gene regulatory network (GRNs) models governed by combinatorial associations between factors. Transcription factors (TFs) and RNA binding proteins (RBPs) are nucleic-acid binding proteins regulating gene expression and are key drivers of GRN function. However, the combinatorial mechanisms by which the interactions between specific TFs and RBPs regulate gene expression remain largely unknown. To identify possible combinations of TFs and RBPs that may function together, developing a tool that compares and contrasts the interactions of multiple TFs and RBPs with nucleic acids to identify their common and unique targets is necessary. Therefore, we introduce BindCompare, a user-friendly tool that can be run locally to predict new combinatorial relationships between TFs and RBPs. BindCompare can analyze data from any organism with known annotated genome information and outputs files with detailed genomic locations and gene information for targets for downstream analysis. Overall, Bindcompare is a new tool that identifies TFs and RBPs that co-bind to the same DNA and/or RNA loci, generating testable hypotheses about their combinatorial regulation of target genes.BindCompare is an open-source package that is available on the Python Packaging Index (PyPI,https://pypi.org/project/bindcompare/) with the source code available on GitHub (https://github.com/pranavmahabs/bindcompare). Complete documentation for the package can be found at both of these links.

show abstract

High-throughput methods for the analysis of transcription factors and chromatin modifications: Low input, single cell and spatial genomic technologies

Cited by 12 publications

References 120 publications

Efficient genome editing in erythroid cells unveils novel MYB target genes and regulatory functions

Efficient genome editing in erythroid cells unveils novel MYB target genes and regulatory functions

Cut&tag: a powerful epigenetic tool for chromatin profiling

BindCompare: A Novel Integrated Protein-Nucleic Acid Binding Analysis Platform

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