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Direct measurement of RNA Polymerase II hypertranscription in cancer FFPE samples

ABSTRACT: Direct measurement of RNA Polymerase II hypertranscription in cancer FFPE samples

PROVIDER: PRJNA1086538 | ENA |

REPOSITORIES: ENA

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Direct measurement of RNA Polymerase II hypertranscription in cancer FFPE samples

Project description:Hypertranscription occurs at targets of oncogene transcription factors in aggressive human cancers. However, detection relies on mRNAs which are heavily processed and have variable half-lives, and on accurate cell number estimations. Here we apply FFPE-CUTAC on slides and curls to quantify hypertranscription at regulatory elements and replication-coupled histone genes.

2025-01-16 | GSE261351 | GEO

RNA Polymerase II ChipSeq measurement of Pcf11 mutations in yeast

Project description:RNA Polymerase II ChipSeq measurement of Pcf11 mutations in yeast

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The Hippo Pathway Prevents YAP/TAZ–Driven Hypertranscription and Controls Neural Progenitor Number [microarray]

Project description:The Hippo pathway controls the activity of YAP/TAZ transcriptional coactivators through a kinase cascade. Despite the critical role of this pathway in tissue growth and tumorigenesis, it is not fully understood how YAP/TAZ–mediated transcription drives proliferation. By analyzing the effects of inactivating LATS1/2 kinases, the direct upstream inhibitors of YAP/TAZ, on mouse brain development and applying cell-number–normalized transcriptome analysis, we discovered that YAP/TAZ activation causes a global increase in transcription activity, known as hypertranscription, and upregulates many genes associated with increased biosynthetic capacity and proliferation. In contrast, conventional read-depth–normalized RNA-sequencing analysis failed to detect the scope of the transcriptome shift and missed most relevant gene ontologies. Hypertranscription in neural progenitors inhibits differentiation and triggers DNA replication stress, DNA damage, and p53 activation, resulting in massive apoptosis. Our findings reveal the remarkable impact of YAP/TAZ activation on global transcription activity and have important implications for understanding YAP/TAZ function

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The Hippo Pathway Prevents YAP/TAZ–Driven Hypertranscription and Controls Neural Progenitor Number [RNA-seq]

2019-02-19 | GSE120015 | GEO

The Hippo Pathway Prevents YAP/TAZ–Driven Hypertranscription and Controls Neural Progenitor Number [ChIP-seq]

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FFPE DEMOD

Project description:FFPE DEMOD

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Gene expression profiling and RNA Polymerase II ChipSeq measurement of Pcf11 mutations in yeast

Project description:Gene expression profiling and RNA Polymerase II ChipSeq measurement of Pcf11 mutations in yeast

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Absolute Scaling of Single-Cell Transcriptomes Reveals Pervasive Hypertranscription in Adult Stem and Progenitor Cells

Project description:Hypertranscription facilitates biosynthetically demanding cellular state transitions through global upregulation of the nascent transcriptome. Despite its potential widespread relevance, documented examples of hypertranscription remain few and limited predominantly to early development. This limitation is in large part due to the fact that modern sequencing approaches, including single-cell RNA sequencing (scRNA-seq), generally assume similar levels of transcriptional output per cell. Here, we use molecule counting and spike-in normalization to develop absolute scaling of single-cell RNA sequencing data. Absolute scaling enables an estimation of total transcript abundances per cell, which we validate in embryonic stem cell (ESC) and germline data and apply to adult mouse organs at steady-state or during regeneration.

2022-12-21 | GSE221184 | GEO

Expanding epigenomics to archived FFPE tissues: An evaluation of DNA repair methodologies

Project description:A study to evaluate techniques for repairing DNA from formalin-fixed paraffin-embedded (FFPE) tissue samples by direct comparison of FFPE DNA repair methods prior to analysis on genome-wide methylation array to matched fresh frozen (FF) tissues.

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FFPE-ATAC decodes the chromatin accessibility from the clinical archived FFPE tissues

Project description:We present FFPE-ATAC, a new ATAC-seq tool for chromatin accessibility profiling that decodes the chromatin accessibility from mouse FFPE tissue and clinical archived FFPE tissues. The FFPE-ATAC generates the high-quality chromatin accessibility profiles from clinical FFPE tissue sections with 5-20 µm thickness, and reveals the disease-associated regulatory elements in different types of FFPE archived tissue. FFPE-ATAC enables to decode the chromatin states regulating the gene regulation in the cancer and understand the epigenetic regulation in the translational studies.

2021-06-30 | GSE163306 | GEO

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