Ontology highlight
ABSTRACT:
PROVIDER: PRJNA764041 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR15946800_1.fastq.gz | Fastqsanger.gz | |||
| SRR15946800_2.fastq.gz | Fastqsanger.gz | |||
| SRR15946801_1.fastq.gz | Fastqsanger.gz | |||
| SRR15946801_2.fastq.gz | Fastqsanger.gz | |||
| SRR15946802_1.fastq.gz | Fastqsanger.gz |
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Project description:<p>Non-coding elements in our genomes that play critical roles in complex disease are frequently marked by highly unstable RNA species. Sequencing nascent RNAs attached to an actively transcribing RNA polymerase complex can identify unstable RNAs, including those templated from gene-distal enhancers (eRNAs). However, nascent RNA sequencing techniques remain challenging to apply in some cell lines and especially to intact tissues, limiting broad applications in fields such as cancer genomics and personalized medicine. Here we report the development of chromatin run-on and sequencing (ChRO-seq), a novel run-on technology that maps the location of RNA polymerase using virtually any frozen tissue sample, including samples with degraded RNA that are intractable to conventional RNA-seq. We used ChRO-seq to develop the first maps of nascent transcription in 23 human glioblastoma (GBM) brain tumors and patient derived xenografts. Remarkably, >90,000 distal enhancers discovered using the signature of eRNA biogenesis within primary GBMs closely resemble those found in the normal human brain, and diverge substantially from GBM cell models. Despite extensive overall similarity, 12% of enhancers in each GBM distinguish normal and malignant brain tissue. These enhancers drive regulatory programs similar to the developing nervous system and are enriched for transcription factor binding sites that specify a stem-like cell fate. These results demonstrate that GBMs largely retain the enhancer landscape associated with their tissue of origin, but selectively adopt regulatory programs that are responsible for driving stem-like cell properties. We also identified enhancers and their associated transcription factors that regulate genes characteristic of each known GBM subtype, and discovered a core group of transcription factors that control the expression of genes associated with clinical outcomes. This study uncovers new insights into the molecular etiology of GBM and introduces ChRO-seq which can now be used to map regulatory programs contributing to a variety of complex diseases.</p>
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Project description:Transcriptional profiling to identify physical-chemical properties detrimental to nanomaterial-induced pulmonary response
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Project description:Transcriptional profiling to identify physical-chemical properties detrimental to nanomaterial-induced pulmonary response (part 1)
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Project description:Transcriptional profiling to identify physical-chemical properties detrimental to nanomaterial-induced pulmonary response (part 3)
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Project description:Transcriptional profiling to identify physical-chemical properties detrimental to nanomaterial-induced pulmonary response (part 4)
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Project description:Transcriptional profiling to identify physical-chemical properties detrimental to nanomaterial-induced pulmonary response (part 2)
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Project description:Chemical communication is crucial in ecosystems with complex microbial assemblages. However, due to archaeal cultivation challenges, our understanding of the structure diversity and function of secondary metabolites (SMs) within archaeal communities is limited compared to the extensively studied and well-documented bacterial counterparts. Our comprehensive investigation into the biosynthetic potential of archaea, combined with metabolic analyses and the first report of heterologous expression in archaea, has unveiled the previously unexplored biosynthetic capabilities and chemical diversity of archaeal ribosomally synthesized and post-translationally modified peptide (RiPP). We have identified twenty-four new lanthipeptides of RiPPs exhibiting unique chemical characteristics, including a novel subfamily featuring an unexplored type with diamino-dicarboxylic (DADC) termini, largely expanding the chemical landscape of archaeal SMs. This sheds light on the chemical novelty of archaeal metabolites and emphasizes their potential as an untapped resource for natural product discovery. Additionally, archaeal lanthipeptides demonstrate specific antagonistic activity against haloarchaea, mediating the unique biotic interaction in the halophilic niche. Furthermore, they showcased a unique ecological role in enhancing the host's motility by inducing the rod-shaped cell morphology and upregulating the archaellum gene flgA1, facilitating the archaeal interaction with abiotic environments. These discoveries broaden our understanding of archaeal chemical language and provide promising prospects for future exploration of SM-mediated interaction.
2024-11-09 | GSE281021 | GEO