Hi-C sequencing data from cortex laboratory rats

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2025, Volume and Issue: unknown

Published: Feb. 11, 2025

Abstract The three-dimensional conformation and packaging of chromosomes modulates the spatial organization nucleus, orchestrating DNA replication repair, maintaining genome stability integrity, regulating gene expression. Hi-C methods provide high-resolution data on chromatin-to-chromatin interactions both within among at a genome-wide scale. resolves topologically-associated domains (TADs) chromatin loops that are linked to cell-specific transcriptional control. We present comprehensive dataset generated from frontal cortex laboratory rats, encompassing diverse group inbred strains (SHR/OlaIpcv, BN-Lx/Cub, BXH6/Cub, HXB2/Ipcv, HXB10/Ipcv, HXB23/Ipcv, HXB31/Ipcv, LE/Stm, F344/Stm) an F1 hybrid (SHR/Olalpcv x BN/NHsdMcwi). This serves as valuable resource for studying mechanisms by which architecture governs expression in brain. Strain-specific variations can illuminate influence structure expression, neuronal functionality, predisposition neurological behavioral disorders.

Language: Английский

---

Genome Restructuring around Innate Immune Genes in Monocytes in Alcohol-associated Hepatitis

Published: Feb. 14, 2025

Many inflammatory genes in the immune system are clustered genome. The 3D genome architecture of these likely plays a critical role their regulation and alterations to this structure may contribute diseases where inflammation is poorly controlled. Alcohol-associated hepatitis (AH) severe disease that contributes significantly morbidity alcohol associated liver disease. Monocytes AH hyper-responsive stimuli inflammation. We performed high throughput chromatin conformation capture (Hi-C) technology on monocytes isolated from 4 patients healthy controls better understand how altered AH. Most chromosomes were dissimilar each other. Comparing HC, many regions contained significant changes contact frequency. While there throughout genome, number hotspots containing higher density structure. A few involved innate immunity including NK-gene receptor complex CXC-chemokines. Finally, we compare results scRNA-seq data with challenged LPS predict impacts transcription genes. Together, reveal perturb expression highly proinflammatory

Language: Английский

---

Genome Restructuring around Innate Immune Genes in Monocytes in Alcohol-associated Hepatitis

Published: Feb. 14, 2025

Many inflammatory genes in the immune system are clustered genome. The 3D genome architecture of these likely plays a critical role their regulation and alterations to this structure may contribute diseases where inflammation is poorly controlled. Alcohol-associated hepatitis (AH) severe disease that contributes significantly morbidity alcohol associated liver disease. Monocytes AH hyper-responsive stimuli inflammation. We performed high throughput chromatin conformation capture (Hi-C) technology on monocytes isolated from 4 patients healthy controls better understand how altered AH. Most chromosomes were dissimilar each other. Comparing HC, many regions contained significant changes contact frequency. While there throughout genome, number hotspots containing higher density structure. A few involved innate immunity including NK-gene receptor complex CXC-chemokines. Finally, we compare results scRNA-seq data with challenged LPS predict impacts transcription genes. Together, reveal perturb expression highly proinflammatory

Language: Английский

---

RNA-Independent Regulatory Functions of lncRNA in Complex Disease

Cancers, Journal Year: 2024, Volume and Issue: 16(15), P. 2728 - 2728

Published: July 31, 2024

During the metagenomics era, high-throughput sequencing efforts both in mice and humans indicate that non-coding RNAs (ncRNAs) constitute a significant fraction of transcribed genome. past decades, regulatory role these transcripts along with their interactions other molecules have been extensively characterized. However, study long (lncRNAs), an ncRNA class transcript lengths exceed 200 nucleotides, revealed certain are transcriptional “by-products”, while loci exert downstream functions through RNA-independent mechanisms. Such mechanisms include, but not limited to, chromatin complex promoter-enhancer competition schemes involve underlying locus or without its nascent transcription, mediating even exclusive roles regulation target genes mammals. Interestingly, such often drive pathological manifestations, including oncogenesis. In this review, we summarize selective examples lncRNAs regulate independently produced transcripts.

Language: Английский

---

Genome Restructuring around Innate Immune Genes in Monocytes in Alcohol-associated Hepatitis

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2024, Volume and Issue: unknown

Published: Aug. 9, 2024

Abstract Many inflammatory genes in the immune system are clustered genome. The 3D genome architecture of these likely plays a critical role their regulation and alterations to this structure may contribute diseases where inflammation is poorly controlled. Alcohol-associated hepatitis (AH) severe disease that contributes significantly morbidity alcohol associated liver disease. Monocytes AH hyper-responsive stimuli inflammation. We performed high throughput chromatin conformation capture (Hi-C) technology on monocytes isolated from 4 patients healthy controls better understand how altered AH. Most chromosomes were dissimilar each other. Comparing HC, many regions contained significant changes contact frequency. While there throughout genome, number hotspots containing higher density structure. A few involved innate immunity including NK-gene receptor complex CXC-chemokines. Finally, we compare results scRNA-seq data with challenged LPS predict impacts transcription genes. Together, reveal perturb expression highly proinflammatory

Language: Английский

---