Marek Bartošovič
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View article: G-quadruplex profiling in complex tissues using single-cell CUT&Tag
G-quadruplex profiling in complex tissues using single-cell CUT&Tag Open
G-quadruplexes (G4) are non-canonical DNA structures that gained increasing attention for their potential roles in gene regulation, with implications in neurodegenerative diseases and cancer. Despite their biological significance, G4 struc…
View article: Multiplexed spatial mapping of chromatin features, transcriptome, and proteins in tissues
Multiplexed spatial mapping of chromatin features, transcriptome, and proteins in tissues Open
The phenotypic and functional states of a cell are modulated by a complex interactive molecular hierarchy of multiple omics layers, involving the genome, epigenome, transcriptome, proteome, and metabolome. Spatial omics approaches have ena…
View article: Single-cell mapping of cell-type specific chromatin architecture in the central nervous system
Single-cell mapping of cell-type specific chromatin architecture in the central nervous system Open
Determining how chromatin is structured in the nucleus is critical to studying its role in gene regulation. Recent advances in the analysis of single-cell chromatin architecture have considerably improved our understanding of cell-type-spe…
View article: Single-nuclei histone modification profiling of the adult human central nervous system unveils epigenetic memory of developmental programs
Single-nuclei histone modification profiling of the adult human central nervous system unveils epigenetic memory of developmental programs Open
The adult human central nervous system (CNS) is remarkably complex, with neural cells displaying extensive transcriptional heterogeneity. However, how different layers of epigenetic regulation underpin this heterogeneity is poorly understo…
View article: Spatial epigenome–transcriptome co-profiling of mammalian tissues
Spatial epigenome–transcriptome co-profiling of mammalian tissues Open
Emerging spatial technologies, including spatial transcriptomics and spatial epigenomics, are becoming powerful tools for profiling of cellular states in the tissue context 1–5 . However, current methods capture only one layer of omics inf…
View article: Multimodal chromatin profiling using nanobody-based single-cell CUT&Tag
Multimodal chromatin profiling using nanobody-based single-cell CUT&Tag Open
Probing histone modifications at a single-cell level in thousands of cells has been enabled by technologies such as single-cell CUT&Tag. Here we describe nano-CUT&Tag (nano-CT), which allows simultaneous mapping of up to three epigenomic m…
View article: HITS-CLIP analysis of human ALKBH8 reveals interactions with fully processed substrate tRNAs and with specific noncoding RNAs
HITS-CLIP analysis of human ALKBH8 reveals interactions with fully processed substrate tRNAs and with specific noncoding RNAs Open
Transfer RNAs acquire a large plethora of chemical modifications. Among those, modifications of the anticodon loop play important roles in translational fidelity and tRNA stability. Four human wobble U containing tRNAs obtain 5-methoxycarb…
View article: Nano-CUT&Tag for multimodal profiling of the chromatin v2
Nano-CUT&Tag for multimodal profiling of the chromatin v2 Open
Nano-CUT&Tag is a multimodal technology to profile several histone modifications at the same with single-cell resolution. Nano-CUT&Tag implements a novel Tn5 fusion proteins to anti-mouse and anti-rabbit secondary nanobodies. Optionally, A…
View article: Spatially resolved epigenome-transcriptome co-profiling of mammalian tissues at the cellular level
Spatially resolved epigenome-transcriptome co-profiling of mammalian tissues at the cellular level Open
Emerging spatial technologies including spatial transcriptomics and spatial epigenomics are becoming powerful tools for profiling cellular states in the tissue context. However, current methods capture only one layer of omics information a…
View article: Nano-CUT&Tag for multimodal profiling of the chromatin v1
Nano-CUT&Tag for multimodal profiling of the chromatin v1 Open
Nano-CUT&Tag is a multimodal technology to profile several histone modifications at the same with single-cell resolution. Nano-CUT&Tag implements a novel Tn5 fusion proteins to anti-mouse and anti-rabbit secondary nanobodies. Optionally, A…
View article: Nano-CUT&Tag for multimodal profiling of the chromatin v1
Nano-CUT&Tag for multimodal profiling of the chromatin v1 Open
Nano-CUT&Tag is a multimodal technology to profile several histone modifications at the same with single-cell resolution. Nano-CUT&Tag implements a novel Tn5 fusion proteins to anti-mouse and anti-rabbit secondary nanobodies. Optionally, A…
View article: Multimodal chromatin profiling using nanobody-based single-cell CUT&Tag
Multimodal chromatin profiling using nanobody-based single-cell CUT&Tag Open
Probing epigenomic marks such as histone modifications at a single cell level in thousands of cells has been recently enabled by technologies such as scCUT&Tag. Here we developed a multimodal and optimized iteration of scCUT&Tag called nan…
View article: Spatial-CUT&Tag: Spatially resolved chromatin modification profiling at the cellular level
Spatial-CUT&Tag: Spatially resolved chromatin modification profiling at the cellular level Open
Spatial omics emerged as a new frontier of biological and biomedical research. Here, we present spatial-CUT&Tag for spatially resolved genome-wide profiling of histone modifications by combining in situ CUT&Tag chemistry, microfluidic dete…
View article: Epigenomic priming of immune genes implicates oligodendroglia in multiple sclerosis susceptibility
Epigenomic priming of immune genes implicates oligodendroglia in multiple sclerosis susceptibility Open
Multiple sclerosis (MS) is characterized by a targeted attack on oligodendroglia (OLG) and myelin by immune cells, which are thought to be the main drivers of MS susceptibility. We found that immune genes exhibit a primed chromatin state i…
View article: HITS-CLIP analysis of human ALKBH8 points towards its role in tRNA and noncoding RNA regulation
HITS-CLIP analysis of human ALKBH8 points towards its role in tRNA and noncoding RNA regulation Open
Transfer RNAs acquire a large plethora of chemical modifications. Among those, modifications of the anticodon loop play important roles in translational fidelity and tRNA stability. Four human wobble U containing tRNAs obtain 5-methoxycarb…
View article: Spatial-ATAC-seq: spatially resolved chromatin accessibility profiling of tissues at genome scale and cellular level
Spatial-ATAC-seq: spatially resolved chromatin accessibility profiling of tissues at genome scale and cellular level Open
Cellular function in tissue is dependent upon the local environment, requiring new methods for spatial mapping of biomolecules and cells in the tissue context. The emergence of spatial transcriptomics has enabled genome-scale gene expressi…
View article: Spatial-ATAC-seq: spatially resolved chromatin accessibility profiling of tissues at genome scale and cellular level
Spatial-ATAC-seq: spatially resolved chromatin accessibility profiling of tissues at genome scale and cellular level Open
Cellular function in tissue is dependent upon the local environment, requiring new methods for spatial mapping of biomolecules and cells in the tissue context. The emergence of spatial transcriptomics has enabled genome-scale gene expressi…
View article: Single cell CUT and Tag on 10x genomics platform v1
Single cell CUT and Tag on 10x genomics platform v1 Open
scCU&Tag on 10x platform uses scCUT&Tag protocol from Steven Henikoff's lab (Kaya-Okur et al., 2019), and scATAC-seq chromium platform (10x Genomics) to perform single-cell barcoding. The method can be used to obtain high quality data for …
View article: Single-cell profiling of histone modifications in the mouse brain
Single-cell profiling of histone modifications in the mouse brain Open
The development of the mouse central nervous system (CNS) involves coordinated execution of transcriptional and epigenetic programs. These programs have been extensively studied through single-cell technologies in a pursuit to characterize…
View article: RNA methylation in nuclear pre‐mRNA processing
RNA methylation in nuclear pre‐mRNA processing Open
Eukaryotic RNA can carry more than 100 different types of chemical modifications. Early studies have been focused on modifications of highly abundant RNA, such as ribosomal RNA and transfer RNA, but recent technical advances have made it p…
View article: N6-methyladenosine demethylase FTO targets pre-mRNAs and regulates alternative splicing and 3′-end processing
N6-methyladenosine demethylase FTO targets pre-mRNAs and regulates alternative splicing and 3′-end processing Open
N6-methyladenosine (m6A) is the most abundant base modification found in messenger RNAs (mRNAs). The discovery of FTO as the first m6A mRNA demethylase established the concept of reversible RNA modification. Here, we present a comprehensiv…