Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Af-CUT&Tag: An Antibody-Free, High-Resolution Platform for Genome-Wide Profiling of Protein-DNA Interactions in Single Cells and Complex Tissues

ABSTRACT: Traditional antibody-based chromatin profiling methods are limited by antibody availability, cost, cell penetration, and protein modification susceptibility. To address these challenges, we present Af-CUT&Tag, a novel antibody-free approach for high-resolution chromatin profiling. By leveraging engineered binders (LgBiT/NbALFA) fused to Tn5 transposase and targeting CRISPR-integrated tags (HiBiT/ALFA), Af-CUT&Tag eliminates antibody dependence, achieving superior specificity and sensitivity with as few as 500 cells. This method outperforms antibody-based counterparts in signal-to-noise ratio, promoter enrichment, and library quality, while also enabling single-cell resolution (scAf-CUT&Tag). Applying Af-CUT&Tag to Hippo effectors (YAP1/TAZ) during liver regeneration revealed dynamic chromatin remodeling, including YAP1/TAZ-mediated control of lipid metabolism (e.g.,Lpin1, Fasn) and heme clearance (Hpx, Trf). We further identify miR-122 as a critical regulator of these processes, impacting liver regeneration. The versatility of Af-CUT&Tag in cell lines, bulk tissues, and single nuclei establishes it as a transformative tool for studying gene regulation in development, disease, and regeneration.

ORGANISM(S): Mus musculus Homo sapiens

PROVIDER: GSE283706 | GEO | 2024/12/15

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
		Other

Items per page:

1 - 1 of 1

Similar Datasets

Af-CUT&Tag: An Antibody-Free, High-Resolution Platform for Genome-Wide Profiling of Protein-DNA Interactions in Single Cells and Complex Tissues

Project description:Traditional antibody-based chromatin profiling methods are limited by antibody availability, cost, cell penetration, and protein modification susceptibility. To address these challenges, we present Af-CUT&Tag, a novel antibody-free approach for high-resolution chromatin profiling. By leveraging engineered binders (LgBiT/NbALFA) fused to Tn5 transposase and targeting CRISPR-integrated tags (HiBiT/ALFA), Af-CUT&Tag eliminates antibody dependence, achieving superior specificity and sensitivity with as few as 500 cells. This method outperforms antibody-based counterparts in signal-to-noise ratio, promoter enrichment, and library quality, while also enabling single-cell resolution (scAf-CUT&Tag). Applying Af-CUT&Tag to Hippo effectors (YAP1/TAZ) during liver regeneration revealed dynamic chromatin remodeling, including YAP1/TAZ-mediated control of lipid metabolism (e.g.,Lpin1, Fasn) and heme clearance (Hpx, Trf). We further identify miR-122 as a critical regulator of these processes, impacting liver regeneration. The versatility of Af-CUT&Tag in cell lines, bulk tissues, and single nuclei establishes it as a transformative tool for studying gene regulation in development, disease, and regeneration.

2024-12-15 | GSE283705 | GEO

Af-CUT&Tag: A Sensitive and Antibody-Free Chromatin Profiling Method Using Genetically Encoded Tags and High-Affinity Binders I

Project description:Transcription factors and chromatin features play critical roles in regulating gene expression. Experimental methods used for highly sensitive chromatin-binding protein profiling, such as CUT&Tag, are limited due to their high cost and technical restrictions, thereby impeding their widespread application. Therefore, we pioneered an antibody-free and sensitive tool for epigenetic analysis, Af-CUT&Tag. Application of the method requires prior generation of cell expressing a protein of interest (POI) tagged C-terminal short peptides. By leveraging the picomolar affinity between peptide and its binder, Tn5 fused with binder can specifically and highly sensitively recognize the peptide tagging protein. We show that the Af-CUT&Tag method is straightforward and can be applied to different proteins across cell lines and tissues, and extendable to single-cell analysis. With only minimal amounts of cellular or tissue material, it provides high sensitivity and yields abundant chromatin fragments per cell and offers unique insights into the regulation of early liver regeneration by the Hippo signaling pathway at the single-cell level. Together, we demonstrate that Af-CUT&Tag is a universal and comprehensive epigenetic analysis tool that can be extended to peptide and peptide-binding nanobody-Tn5 for epigenetic analysis.

2024-12-15 | GSE283704 | GEO

Identification of ERα AF-1 or AF-2 mediated genes in mouse uterus

Project description:Estrogen receptor alpha (ERα) is a ligand dependent transcription regulator, which contains two transactivation functional domains, AF-1 and AF-2. These activities are regulated differently by the ligands. Specifically, the selective estrogen receptor modulators (SERMs) regulate AF-1 rather than AF-2. It is important to know whether AF-1/AF-2 predominantly regulated genes exist in the tissues for a better understanding of the SERMs functionality. We sought out AF-1 dependent estrogenic genes by using the AF-2 mutated knock-in (KI) mouse model, AF2ERKI. AF2ER is an estrogen-insensitive AF-2 disrupted ERα mutant mouse but unique to this model, AF-1 can be activated by the estrogen-antagonist, fulvestrant (ICI), in vitro and in vivo. The information of ICI-mediated gene expression profile of AF2ERKI could define whether AF-1/AF-2 predominantly regulated genes exist in the tissues.

2020-12-01 | GSE138443 | GEO

Center for Common Disease Genomics [CCDG] - Cardiovascular: SWISS-AF/SWISS-AF-PVI/BEAT-AF

Project description:Center for Common Disease Genomics [CCDG] - Cardiovascular: SWISS-AF/SWISS-AF-PVI/BEAT-AF

| PRJNA671409 | ENA

Center for Common Disease Genomics [CCDG] - Cardiovascular: SWISS-AF/SWISS-AF-PVI/BEAT-AF

Project description:Center for Common Disease Genomics [CCDG] - Cardiovascular: SWISS-AF/SWISS-AF-PVI/BEAT-AF

| PRJNA671410 | ENA

Af-CUT&Tag: A Sensitive and Antibody-Free Chromatin Profiling Method Using Genetically Encoded Tags and High-Affinity Binders I

Project description:Af-CUT&Tag: A Sensitive and Antibody-Free Chromatin Profiling Method Using Genetically Encoded Tags and High-Affinity Binders I

| PRJNA1195068 | ENA

Transcriptional profiles of Tead1/4 Knockout and Unedited CT26 Cells

Project description:The Hippo kinase cascade converges on the transcriptional effectors YAP (Yes-associated protein) and TAZ (transcriptional co-activator with PDZ-binding motif), which regulate gene expression programs by interacting with the transcriptional enhanced associate domain (TEAD) family of transcription factors (TFs). As a key pathway in organ growth, tissue homeostasis, and regeneration, the YAP/TAZ-TEAD complex controls the transcription of genes crucial for replication, S-phase entry, and mitosis. To further elucidate the transcriptional regulatory network, we monitored the target genes of TEAD1 and TEAD4 using CUT&Tag and transcriptome sequencing.

2024-12-31 | GSE236855 | GEO

CUT&Tag for DUX recruitment,domain-influenced chormatin modifications, and a potential binding partner with a member of the SWI/SNF complex

Project description:In order to determine that CUT&Tag is similar to known DUX ChIP-seq, we performed CUT&Tag with a mCherry-tagged DUX (with the mCherry antibody). Once confirmed, we pewrformed CUT&Tag for other DUX derivatives with their mCherry tag Then, we performed CUT&Tag for H3K9ac, which is known to globally increase in 2-cell-like cells, which occurs after DUX expression, and CUT&Tag for SMARCC1, a subunit of the SWI/SNF complex

2023-08-07 | GSE224297 | GEO

YAP/TAZ drives ependymoma-like tumour formation in mice

Project description:YAP1 gene fusions have been observed in a subset of paediatric ependymomas. Here we show that, ectopic expression of active nuclear YAP1 (nlsYAP5SA) in ventricular zone neural progenitor cells using conditionally-induced NEX/NeuroD6-Cre is sufficient to drive brain tumour formation in mice. Neuronal differentiation is inhibited in the hippocampus. Deletion of YAP1’s negative regulators LATS1 and LATS2 kinases in NEX-Cre lineage in double conditional knockout mice also generates similar tumours, which are rescued by deletion of YAP1 and its paralog TAZ. YAP1/TAZ-induced mouse tumours display molecular and ultrastructural characteristics of human ependymoma. RNA sequencing and quantitative proteomics of mouse tumours demonstrate similarities to YAP1-fusion induced supratentorial ependymoma. Finally, we find that transcriptional cofactor HOPX is upregulated in mouse models and in human YAP1-fusion induced ependymoma, supporting their similarity. Our results show that uncontrolled YAP1/TAZ activity in neuronal precursor cells leads to ependymoma-like tumours in mice.

2020-05-26 | PXD018131 | Pride

Af-CUT&Tag: An Antibody-Free, High-Resolution Platform for Genome-Wide Profiling of Protein-DNA Interactions in Single Cells and Complex Tissues

Project description:Af-CUT&Tag: An Antibody-Free, High-Resolution Platform for Genome-Wide Profiling of Protein-DNA Interactions in Single Cells and Complex Tissues

| PRJNA1195075 | ENA

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data