A suite of enhancer AAVs and transgenic mouse lines for genetic access to cortical cell types

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

Published: June 10, 2024

The mammalian cortex is comprised of cells classified into types according to shared properties. Defining the contribution each cell type processes guided by essential for understanding its function in health and disease. We used transcriptomic epigenomic cortical taxonomies from mouse human define marker genes putative enhancers created a large toolkit transgenic lines enhancer AAVs selective targeting populations. report evaluation fifteen new driver lines, two reporter >800 different covering most subclasses cells. tools reported here as well scaled process tool creation modification enable diverse experimental strategies towards brain function.

Language: Английский

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Regulatory Elements for Gene Therapy of Epilepsy

Cells, Journal Year: 2025, Volume and Issue: 14(3), P. 236 - 236

Published: Feb. 6, 2025

The problem of drug resistance in epilepsy means that many cases, a surgical treatment may be advised. But this is only possible if there an epileptic focus, and resective brain surgery have adverse side effects. One the promising alternatives gene therapy, which allows targeted expression therapeutic genes different regions, even specific cell types. In review, we provide detailed explanations some key terms related to genetic engineering, describe various regulatory elements already been used development approaches treating using viral vectors. We compare few universal promoters for their strength duration transgene expression, our description cell-specific promoters, focus on driving glutamatergic neurons, GABAergic neurons astrocytes. also explore enhancers other cis-regulatory currently vectors consider future perspectives state-of-the-art technologies designing new, stronger more elements. Gene therapy has multiple advantages should become common future, but still lot study invent field.

Language: Английский

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Enhancer Extrachromosomal Circular DNA ANKRD28 Elicits Drug Resistance via POU2F2‐Mediated Transcriptional Network in Multiple Myeloma

Advanced Science, Journal Year: 2025, Volume and Issue: unknown

Published: April 1, 2025

Multiple myeloma (MM) remains an incurable disease primarily due to the emergence of drug resistance, and underlying mechanisms remain unclear. Extrachromosomal circular DNAs (eccDNAs) are prevalent in cancer genomes both coding non-coding regions. However, role eccDNA regions that serve as enhancers has been largely overlooked. Here, genome-wide profiling serum eccDNAs from donors MM patients who responded well or poorly bortezomib-lenalidomide-dexamethasone (VRd) therapy is characterized. A high copy number ANKRD28 (eccANKRD28) predicts poor response prognosis but enhanced transcriptional activity. Established VRd-resistant cell lines exhibit a higher abundance eccANKRD28, CRISPR/Cas9-mediated elevation eccANKRD28 desensitizes bortezomib lenalidomide treatment vitro vivo. Integrated multi-omics analysis (H3K27ac ChIP-seq, scRNA-seq, scATAC-seq, CUT&Tag, et al.) identifies active enhancer involved resistance driven by key transcription factor, POU class 2 homeobox (POU2F2). POU2F2 interacts with sequence-specific RUNX1 RUNX2 motifs form protein complex, which activates promoter oncogenes, including IRF4, JUNB, IKZF3, RUNX3, BCL2. This study elucidates potential network previously unrecognized epigenetic perspective.

Language: Английский

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Deregulated enhancer‐promoter communication in cancer through altered nuclear architecture

International Journal of Cancer, Journal Year: 2025, Volume and Issue: unknown

Published: April 12, 2025

Enhancers are critical regulators of gene expression. Structural variations in cancer genomes can lead to enhancer hijacking, where oncogenes activated by mistargeted activity. Novel enhancer-promoter interactions may also arise through chromosomal rearrangements that create extrachromosomal DNA elements. Additionally, fusion proteins and other mutation-induced alterations protein properties the aberrant assembly into large complexes on size scale 0.1-1 μm termed onco-condensates. Transcription factors co-activators accumulate with cis-regulatory elements these structures, driving oncogenic programs. Here, we review current evidence how altered genome architecture macromolecular result deregulated communication. We discuss emerging strategies exploit mechanisms for clinical applications.

Language: Английский

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Acute Activation of Genes Through Transcriptional Condensates Impact Non-target Genes in a Chromatin Domain

Published: March 19, 2025

Transcription activation of genes by estrogen is driven enhancers, which are often located within the same Topologically Associating Domain (TAD) as non-targeted promoters. We investigated how acute enhancer-driven affects neighbouring non-target TAD. Using single-molecule RNA FISH (smFISH), we tracked transcription TFF1 (enhancer-targeted) and TFF3 (non-targeted) during stimulation. observed mutually exclusive expression patterns: peaked at 1 hour, while reached its peak 3 hours, after ’s had diminished. Chromatin looping data indicated that enhancer loops with but not , suggesting upregulation due to direct enhancer-promoter interactions. CRISPR deletion 1,6-hexanediol (HD) exposure revealed enhancer:promoter undergo Liquid-Liquid Phase Separation (LLPS), sequesters transcriptional machinery inhibits expression. As signalling wanes or LLPS disrupted, declines increases. Our findings reveal can indirectly influence genes, highlighting a dynamic shift in gene progresses.

Language: Английский

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Histone demethylase KDM6B promotes glioma cell proliferation by increasing PDGFRA expression via chromatin loop formation

Neurological Research, Journal Year: 2025, Volume and Issue: unknown, P. 1 - 9

Published: March 25, 2025

Objectives Changes in gene expression pattern play an essential role promoting the process of cancer. For example, platelet-derived growth factor receptor alpha (PDGFRA) is overexpressed many cancers, including gliomas. Abnormal histone methylation a typical characteristics glioma, and our previous studies have shown that lysine demethylase 6B (KDM6B) involved glioma development by regulating specific oncogenes. In this study, regulatory effect underlying mechanism KDM6B on PDGFRA were investigated.

Language: Английский

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Inositol Hexaphosphate (InsP6) Activates the HDAC1/3 Epigenetic Axis to Maintain Intestinal Barrier Function

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

Published: Sept. 16, 2024

HDACs (histone deacetylase) play a crucial role in regulating gene expression, and the inhibition of these enzymes is gaining attention as promising therapeutic approach for cancer treatment. Despite their significant physiological clinical importance, mechanisms HDAC activation remain poorly understood. This study reveals that inositol polyphosphate multikinase (IPMK) essential activating HDAC1 HDAC3 cell lines mice. IPMK deletion or inactivation its kinase activity selectively impairs HDAC1/3's deacetylase activity, significantly influencing expression. Disruption IPMK-HDAC1/3 epigenetic axis results transcriptional upregulation matrix metalloproteinase (MMP) genes, exacerbating intestinal permeability. Remarkably, treatment KO cells with cell-permeable hexaphosphate (InsP6) rescues defects. elucidates IPMK's HDAC1/3 implications barrier function.

Language: Английский

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Acute Activation of Genes Through Transcriptional Condensates Impact Non-target Genes in a Chromatin Domain

Published: Nov. 7, 2024

Transcription activation of genes by estrogens is driven enhancers, which are often located within the same Topologically Associating Domain (TAD) as non-targeted promoters. We investigated how acute enhancer-driven affects neighbouring non-target TAD. Using single-molecule RNA FISH (smFISH), we tracked transcription TFF1 (enhancer-targeted) and TFF3 (non-targeted) during estrogen stimulation. observed mutually exclusive expression patterns: peaked at 1 hour, while reached its peak 3 hours, after ’s had diminished. Chromatin looping data indicated that enhancer loops with but not , suggesting upregulation due to direct enhancer-promoter interactions. CRISPR deletion 1,6-hexanediol (HD) exposure revealed enhancer:promoter undergo Liquid-Liquid Phase Separation (LLPS), sequesters transcriptional machinery inhibits expression. As signalling wanes or LLPS disrupted, declines increases. Our findings reveal can indirectly influence genes, highlighting a dynamic shift in gene progresses.

Language: Английский

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Recruitment of CTCF to the SIRT1 promoter after Oxidative Stress mediates Cardioprotective Transcription

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

Published: May 19, 2024

ABSTRACT Because most DNA-binding transcription factors (dbTFs), including the architectural regulator CTCF, bind RNA and exhibit di-/multimerization, a central conundrum is whether these distinct properties are regulated post-transcriptionally to modulate transcriptional programs. Here, investigating stress-dependent activation of SIRT1, encoding an evolutionarily-conserved protein deacetylase, we show that induced phosphorylation CTCF acts as rheostat permit occupancy low-affinity promoter DNA sites precisely levels necessary. This recruitment SIRT1 eliciting cardioprotective cardiomyocyte program provides resilience against stress beating heart in vivo . Mice harboring mutation conserved binding site altered, cardiomyocyte-specific systolic failure phenotype. role for reveals covalent dbTF modification regulating signal-dependent serves previously unsuspected component oxidative response.

Language: Английский

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Acute Activation of Genes Through Transcriptional Condensates Impact Non-target Genes in a Chromatin Domain

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

Published: Aug. 26, 2024

Abstract Transcription activation of genes by estrogen is driven enhancers, which are often located within the same Topologically Associating Domain (TAD) as non-targeted promoters. We investigated how acute enhancer-driven affects neighbouring non-target TAD. Using single-molecule RNA FISH (smFISH), we tracked transcription TFF1 (enhancer-targeted) and TFF3 (non-targeted) during stimulation. observed mutually exclusive expression patterns: peaked at 1 hour, while reached its peak 3 hours, after ’s had diminished. Chromatin looping data indicated that enhancer loops with but not , suggesting upregulation due to direct enhancer-promoter interactions. CRISPR deletion 1,6-hexanediol (HD) exposure revealed enhancer:promoter undergo Liquid-Liquid Phase Separation (LLPS), sequesters transcriptional machinery inhibits expression. As signalling wanes or LLPS disrupted, declines increases. Our findings reveal can indirectly influence genes, highlighting a dynamic shift in gene progresses.

Language: Английский

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