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Transcription factors interact with RNA to regulate genes (CUT&Tag)

ABSTRACT: Transcription factors interact with RNA to regulate genes (CUT&Tag)

PROVIDER: PRJNA971181 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR24491812_1.fastq.gz	Fastqsanger.gz
	SRR24491812_2.fastq.gz	Fastqsanger.gz
	SRR24491813_1.fastq.gz	Fastqsanger.gz
	SRR24491813_2.fastq.gz	Fastqsanger.gz
	SRR24491814_1.fastq.gz	Fastqsanger.gz

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Transcription factors interact with RNA to regulate genes

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Transcription factors interact with RNA to regulate genes (CUT&Tag)

Project description:Transcription factors (TFs) orchestrate the gene expression programs that define each cell’s identity. The canonical TF accomplishes this with two domains, one that binds specific DNA sequences and the other that binds protein coactivators or corepressors. We find that at least half of TFs also bind RNA, doing so through a previously unrecognized domain with sequence and functional features analogous to the arginine-rich motif of the HIV transcriptional activator Tat. RNA binding contributes to TF function by promoting the dynamic association between DNA, RNA and TF on chromatin. TF-RNA interactions are a conserved feature essential for vertebrate development and disrupted in disease. We propose that the ability to bind DNA, RNA and protein is a general property of many TFs and is fundamental to their gene regulatory function.

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Project description:c-Fos and c-Jun form activator protein 1 (AP-1) transcription factors that regulate gene expression by binding to specific motifs on the genome. To investigate c-Fos regulating genes in OIR rod photoreceptor cells, we performed CUT&Tag subjecting normoxia P14 and OIR P14 retina using c-Fos, H3K27ac (enhancer maker), H3K4me3 (active promoter maker), and H3K27me3 ( gene repression maker) antibodies.

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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.

2024-09-06 | GSE249799 | GEO

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