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Epigenomic landscape and 3D genome structure in pediatric high-grade glioma

Pediatric high-grade gliomas (pHGGs), including glioblastoma multiforme (GBM) and diffuse intrinsic pontine glioma (DIPG), are morbid brain tumors. Even with treatment survival is poor, making pHGG the number one cause of cancer death in children. Up to 80% of DIPGs harbor a somatic missense mutation in genes encoding histone H3. To investigate whether H3K27M is associated with distinct chromatin structure that alters transcription regulation, we generated the first high-resolution Hi-C maps of pHGG cell lines and tumor tissue. By integrating transcriptome (RNA-seq), enhancer landscape (ChIP-seq), genome structure (Hi-C), and chromatin accessibility (ATAC-seq) datasets from H3K27M and wild-type specimens, we identified tumor-specific enhancers and regulatory networks for known oncogenes. We identified genomic structural variations that lead to potential enhancer hijacking and gene coamplification, including A2M , JAG2 , and FLRT1 . Together, our results imply three-dimensional genome a ....

Northwestern University , United States , Roberth Lurie , Kapa Biosystems , Library Preparation Kit , Cell Signaling Technology , Beckman Coulter , Bristol Myers Squibb , Empire Genomics , Institutional Review Board , Illumina Truseq Stranded Total , Illumina Nextseq , Santa Cruz Biotechnology , Preparation Kit , Bioo Scientific , Agilent High Sensitivity , Arima Genomics , Elute Polymerase Chain Reaction , Purification Kit , Illumina Hiseqx Ten , Thermo Fisher Scientific , Assay Kit , Tris Buffered Saline Tween , Mini Kit , Strand Synthesis System Kit , வடமேற்கு பல்கலைக்கழகம் ,

NanoSINC-seq dissects the isoform diversity in subcellular compartments of single cells


Abstract
Alternative mRNA isoforms play a key role in generating diverse protein isoforms. To dissect isoform usage in the subcellular compartments of single cells, we introduced an novel approach, nanopore sequencing coupled with single-cell integrated nuclear and cytoplasmic RNA sequencing, that couples microfluidic fractionation, which separates cytoplasmic RNA from nuclear RNA, with full-length complementary DNA (cDNA) sequencing using a nanopore sequencer. Leveraging full-length cDNA reads, we found that the nuclear transcripts are notably more diverse than cytoplasmic transcripts. Our findings also indicated that transcriptional noise emanating from the nucleus is regulated across the nuclear membrane and then either attenuated or amplified in the cytoplasm depending on the function involved. Overall, our results provide the landscape that shows how the transcriptional noise arising from the nucleus propagates to the cytoplasm. ....

Grand Island , United States , France General , Takara Bio , Panreac Applichem , Kyoto University , Marubun Research Promotion Foundation Japan , Exchange Research , Cabinet Office , University Of Tokyo , White Rock Foundation , Wako Pure Chemical Industries , Japan Society For The Promotion Of Science , Oxford Nanopore Technologies , Thermo Fisher Scientific , Dojindo Laboratories , Low Input , Preparation Kit , Ligation Sequencing Kit , Creative Commons Attribution Noncommercial , Score Program , Japan Society , Marubun Research Promotion Foundation , மாபெரும் தீவு , ஒன்றுபட்டது மாநிலங்களில் , பிரான்ஸ் ஜநரல் ,