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Single-cell 3D genome structure reveals distinct human pluripotent states (CUT&Tag-seq)

ABSTRACT: Single-cell 3D genome structure reveals distinct human pluripotent states (CUT&Tag-seq)

PROVIDER: PRJNA1084793 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR28244205_1.fastq.gz	Fastqsanger.gz
	SRR28244205_2.fastq.gz	Fastqsanger.gz
	SRR28244206_1.fastq.gz	Fastqsanger.gz
	SRR28244206_2.fastq.gz	Fastqsanger.gz
	SRR28244207_1.fastq.gz	Fastqsanger.gz

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Single-cell 3D genome structure reveals distinct human pluripotent states (CUT&Tag-seq)

Project description:Pluripotent states of embryonic stem cells (ESCs) with distinct transcription profile affect their differentiation capacity and therapeutic potential. By single cell analysis of high-resolution three-dimensional (3D) genome structure, we show that remodeling genome structure is highly associated with pluripotent states of human ESCs (hESCs). Naive pluripotent state is featured with specialized 3D genome structures and clear chromatin compartmentation distinct from primed state. Naive pluripotent state may be achieved by remodeled active euchromatin compartment and less chromatin interaction in the nuclear center. This unique genome organization is linked to elevated chromatin accessibility on enhancers and thus high expression levels of naive pluripotent genes localized in this region. On the contrary, primed state exhibits intermingled genome organization. Moreover, active euchromatin and primed pluripotent genes are distributed in the nuclear periphery and yet repressive heterochromatin densely concentrated in the nuclear center, reducing chromatin accessibility and transcription of naive genes. Thus, inversion or relocation of heterochromatin to euchromatin compartmentation is related to regulating chromatin accessibility and thus define pluripotent states and cell identity.

2024-03-11 | GSE260993 | GEO

Identification of chromatin states during zebrafish gastrulation using CUT&RUN and CUT&Tag

Project description:Here we describe successful implementation of CUT&Tag for profiling protein-DNA interactions in zebrafish embryos. We optimized CUT&Tag protocol to generate high resolution maps of enrichment for the histone variant H2A.Z during zebrafish development. We were able to establish dynamics of H2A.Z genomic patterning from shield stage to 24hpf embryos. Our work demonstrates the power of combining CUT&Tag with the strengths of the zebrafish system to better understand the changing embryonic chromatin landscape and its roles in shaping development.

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HCT116_SMARCA4 CUT&Tag

Project description:HCT116_SMARCA4 CUT&Tag

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Identification of chromatin states in mouse testicular germ cells using CUT&Tag

Project description:Here we describe successful implementation of CUT&Tag sequencing technology for profiling of protein-DNA interactions in mouse testicular germ cells. By performing CUT&Tag sequencing using antibodies against XAP5/XAP5L, we identified numerous common binding sites for both proteins. This work highlights the significant overlap in the genomic targets of XAP5 and XAP5L.

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CUT&TAG of OE19 cell line

Project description:To map the chromatin binding sites for SMC1 in OE19 cells, we performed CUT&TAG.

2024-09-25 | E-MTAB-14090 | biostudies-arrayexpress

CUT&TAG of OE19 cell line

Project description:To map the chromatin binding sites for various factors in OE19 cells, we performed CUT&TAG.

2023-02-24 | E-MTAB-11356 | biostudies-arrayexpress

Bulk Cut&run and Cut&tag

Project description:Bulk Cut&run and Cut&tag

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scNanoSeq-CUT&Tag: a long-read single-cell CUT&Tag sequencing method for efficient chromatin modification profiling within individual cells

Project description:We developed scNanoSeq-CUT&Tag, a streamlined method by adapting a modified CUT&Tag protocol to Oxford Nanopore sequencing platform for efficient chromatin modification profiling at single-cell resolution. We firstly tested the performance of scNanoSeq-CUT&Tag on six human cell lines: K562, 293T, GM12878, HG002, H9, HFF1 and adult mouse blood cells, it showed that scNanoSeq-CUT&Tag can accurately distinguish different cell types in vitro and in vivo. Moreover, scNanoSeq-CUT&Tag enables to effectively map the allele-specific epigenomic modifications in the human genome andallows to analyze co-occupancy of histone modifications. Taking advantage of long-read sequencing,scNanoSeq-CUT&Tag can sensitively detect epigenomic state of repetitive elements. In addition, by applying scNanoSeq-CUT&Tag to testicular cells of adult mouse B6D2F1, we demonstrated that scNanoSeq-CUT&Tag maps dynamic epigenetic state changes during mouse spermatogenesis. Finally, we exploited the epigenetic changes of human leukemia cell line K562 during DNA demethylation, it showed that NanoSeq-CUT&Tag can capture H3K27ac signals changes along DNA demethylation. Overall, we prove that scNanoSeq-CUT&Tag is a valuable tool for efficiently probing chromatin state changes within individual cells.

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Project description:To investigate GLI3 TF targets during organoid fate decisions, we performed Cut&Tag of GLI3 binding

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Project description:To investigate the enrichment of SMARCA4-R1157W mutation on downstream target gene promoters, we performed CUT&Tag experiments in HCT116 cells.

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