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The NFkB protein RELA/p65 binds predominantly transcript introns and exons

ABSTRACT: The NFkB protein RELA/p65 binds predominantly transcript introns and exons

PROVIDER: PRJNA811611 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR18185544_1.fastq.gz	Fastqsanger.gz
	SRR18185544_2.fastq.gz	Fastqsanger.gz
	SRR18185545_1.fastq.gz	Fastqsanger.gz
	SRR18185545_2.fastq.gz	Fastqsanger.gz
	SRR18185546_1.fastq.gz	Fastqsanger.gz

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The NFkB protein RELA/p65 binds predominantly transcript introns and exons

Project description:We investigated the ability of the NFkB protein p65 to bind RNA and what its target transcrips were. In this CLIP-seq experiment we demonstrated that p65 is capable of binding RNA and it has a preference to introns and exons, suggesting it binds unspliced RNA.

2022-03-08 | GSE197705 | GEO

Human introns contain conserved tissue-specific cryptic poison exons

Project description:Eukaryotic cells express a large number of transcripts from a single gene due to alternative splicing. Despite hundreds of thousands of splice isoforms being annotated in databases, it has been reported that the current exon catalogs remain incomplete. At the same time, introns of human protein-coding genes contain a large number of evolutionarily conserved elements with unknown function. Here, we explore the possibility that some of them represent cryptic exons that are expressed in rare conditions. We identified a group of cryptic exons that are similar to the annotated exons in terms of evolutionary conservation and RNA-seq read coverage in the GTEx dataset. Most of them were poison, i.e. generated an NMD isoform upon inclusion, and many showed signs of tissue-specific and cancer-specific expression and regulation. We performed RNA-seq in A549 cell line treated with cycloheximide to inactivate NMD, and confirmed using qPCR that seven of eight exons tested are, indeed, expressed. This study shows that introns of human protein-coding genes contain cryptic poison exons, which reside in conserved intronic regions and remain not fully annotated due to insufficient representation in RNA-seq libraries.

2024-11-20 | GSE270310 | GEO

Human introns contain conserved tissue-specific cryptic poison exons

Project description:Human introns contain conserved tissue-specific cryptic poison exons

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Effect of S534A substitution in the p65 subunit of Nfkb on response to 1mg LPS

Project description:WT mice and Nfkb/p65 S534A were exposed to 1mg/kg LPS and their gene expression measured. Affymetrix Mouse 1.0ST chips were used to measure gene expression.

2017-04-05 | GSE67178 | GEO

Effect of S534A substitution in the p65 subunit of Nfkb on response to 1µg LPS

Project description:WT mice and Nfkb/p65 S534A were exposed to 1µg/kg LPS and their gene expression measured. Affymetrix Mouse 1.0ST chips were used to measure gene expression

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Transcription profiling by array of human myometrial cells transfected by NFKB (p65) and CEBP alone and in combination.

Project description:Nuclear factor kappa B and C/EBP are two important transcription factors that independently and synergistically regulate different genes. In this experiment the expression of genes will be examined with the overexpression of NFKB (p65) and CEBP alone and in combination.

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Expression data from fibroblasts expressing p65 variants and depletion of Zbtb7a

Project description:We used microarrays to assess gene expression in p65-knockout 3T3 fibroblasts, after stable reconstitution with normal and engineered forms of NFkB p65, and knock-down of Zbtb7a using stable shRNA interference. Cells were treated with 5ng/ml mouse TNF-alpha to stimulate NFkB pathway activation.

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Coordinated Expression of Retained Introns and Poison Exons in Renal Cell Carcinoma

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Coordinated Expression of Retained Introns and Poison Exons in Renal Cell Carcinoma

Project description:Coordinated intron retention and poison exon inclusion define a subset of kidney tumors by introducing premature stop codons that typically trigger nonsense-mediated decay (NMD). In this study we investigate how mTOR activity modulates these NMD targets, revealing that mTOR inhibition increases the expression of transcripts bearing retained introns and poison exons in certain patient-derived tumors. Our findings show that tumors with low NMD and mTOR activities are more aggressive and have worse outcomes yet display pronounced immune infiltration, highlighting a potential role for these RNA isoforms in shaping tumor progression and immune responses.

2025-05-08 | GSE289050 | GEO

RNase A treatment increases the recruitment of p65 to DNA

Project description:We investigated the ability of the NFkB protein p65 to bind DNA after RNA digestion. In this ChIP-seq experiment, we investigated the genome-wide binding profiles of p65 in Jurkat cells. We demonstrated that p65 binding to promoters and promoter proximal regions is enhanced by digestion of RNA with RNase A.

2022-03-08 | GSE197704 | GEO

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