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Massively parallel screen uncovers many rare 3’ UTR variants regulating mRNA abundance of cancer driver genes [rare_cosmic]

ABSTRACT: Massively parallel screen uncovers many rare 3’ UTR variants regulating mRNA abundance of cancer driver genes [rare_cosmic]

PROVIDER: PRJNA972740 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR24575000_1.fastq.gz	Fastqsanger.gz
	SRR24575000_2.fastq.gz	Fastqsanger.gz
	SRR24575001_1.fastq.gz	Fastqsanger.gz
	SRR24575001_2.fastq.gz	Fastqsanger.gz
	SRR24575002_1.fastq.gz	Fastqsanger.gz

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Massively parallel screen uncovers many rare 3’ UTR variants regulating mRNA abundance of cancer driver genes

Project description:Massively parallel screen uncovers many rare 3’ UTR variants regulating mRNA abundance of cancer driver genes

| PRJNA972738 | ENA

Massively parallel screen uncovers many rare 3’ UTR variants regulating mRNA abundance of cancer driver genes [rare_3utr_gnomad.motif_activity]

Project description:Massively parallel screen uncovers many rare 3’ UTR variants regulating mRNA abundance of cancer driver genes [rare_3utr_gnomad.motif_activity]

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Massively parallel screen uncovers many rare 3’ UTR variants regulating mRNA abundance of cancer driver genes [prime_editing_3utr]

Project description:Massively parallel screen uncovers many rare 3’ UTR variants regulating mRNA abundance of cancer driver genes [prime_editing_3utr]

| PRJNA972739 | ENA

Massively parallel screen uncovers many rare 3’ UTR variants regulating mRNA abundance of cancer driver genes [rare_cosmic]

Project description:Understanding the function of rare non-coding genetic variants represents a significant challenge. Here, we developed MapUTR, a screen to identify rare 3’ UTR variants affecting mRNA abundance post-transcriptionally. Among 17,301 rare variants, an average of 24.5% were functional, with 70% in cancer-related genes, many in critical cancer pathways. This observation motivated a further interrogation of 11,929 cancer somatic mutations, uncovering 3,928 (33%) functional mutations in well-established cancer driver genes, such as CDKN2A. Functional MapUTR variants were enriched in miRNA targets and protein-RNA interaction sites. Based on MapUTR, we define a new metric, untranslated tumor mutation burden (uTMB), reflecting the amount of somatic functional MapUTR variants of a tumor. We showed the potential of uTMB in predicting patient survival. Through prime editing, we characterized three variants in cancer-relevant genes (MFN2, FOSL2, and IRAK1), illustrating their cancer-driving potential. Our study elucidates the function of thousands of non-coding variants, nominates non-coding cancer driver mutations, and demonstrates their potential contributions to cancer.

2024-02-06 | GSE232572 | GEO

Massively parallel screen uncovers many rare 3’ UTR variants regulating mRNA abundance of cancer driver genes [rare_3utr_gnomad.motif_activity]

2024-02-06 | GSE232571 | GEO

Massively parallel screen uncovers many rare 3’ UTR variants regulating mRNA abundance of cancer driver genes [prime_editing_3utr]

2024-02-06 | GSE232570 | GEO

Massively parallel screen uncovers many rare 3’ UTR variants regulating mRNA abundance of cancer driver genes

Project description:This SuperSeries is composed of the SubSeries listed below.

2024-02-06 | GSE232573 | GEO

Massively parallel reporter assay of 3’UTR sequences identifies in vivo rules for mRNA degradation

Project description:The stability of mRNAs is regulated by signals within their sequences, but a systematic and predictive understanding of the underlying sequence rules remains elusive. Here, we introduce UTR-Seq, a combination of massively parallel reporter assays and regression models, to survey the dynamics of tens-of-thousands of 3’UTR sequences during early zebrafish embryogenesis. UTR-Seq revealed two temporal degradation programs: a maternally encoded early-onset program and a late-onset program that accelerated degradation after zygotic genome activation. Three signals regulated early-onset rates: stabilizing poly-U and UUAG sequences, and destabilizing GC-rich signals. Three signals explained late-onset degradation: miR-430 seeds, AU-rich sequences and Pumilio recognition sites. Sequence based regression models translated 3’UTRs into their unique decay patterns, and predicted the in vivo impact of sequence signals on mRNA stability. Their application led to the successful design of artificial 3’UTRs that conferred specific mRNA dynamics. UTR-Seq provides a general strategy to uncover the rules of RNA cis-regulation.

2017-12-12 | GSE106677 | GEO

Assessment of Variant Abundance by Massively Parallel Sequencing for PTEN and TPMT

Project description:Determining the pathogenicity of human genetic variants is a critical challenge, and functional assessment is often the only option. Experimentally characterizing millions of possible missense variants in thousands of clinically important genes will likely require generalizable, scalable assays. Here we describe Variant Abundance by Massively Parallel Sequencing (VAMP-seq), which measures the effects of thousands of missense variants of a protein on intracellular abundance in a single experiment. We applied VAMP-seq to quantify the abundance of many thousands of single amino acid variants of two proteins, PTEN and TPMT, in which functional variants are clinically actionable.

2018-03-13 | GSE108727 | GEO

Massively parallel characterization of CYP2C9 variant enzyme activity and abundance

Project description:CYP2C9 encodes a cytochrome P450 enzyme responsible for metabolizing up to 15% of small molecule drugs, and CYP2C9 variants can alter the safety and efficacy of these therapeutics. In particular, the anti-coagulant warfarin is prescribed to over 15 million people annually and polymorphisms in CYP2C9 can affect patient response leading to an increased risk of hemorrhage. We developed Click-seq, a pooled yeast-based activity assay to test thousands of variants. Using Click-seq, we measured the activity of 6,142 missense variants expressed in yeast. We also measured the steady-state cellular abundance of 6,370 missense variants expressed in a human cell line using Variant Abundance by Massively Parallel sequencing (VAMP-seq). These data revealed that almost two-thirds of CYP2C9 variants showed decreased activity, and that protein abundance accounted for half of the variation in CYP2C9 function. We also measured activity scores for 319 previously unannotated human variants, many of which may have clinical relevance.

2021-03-13 | GSE165412 | GEO

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