Uwe Schwartz
YOU?
Author Swipe
View article: Adenovirus maturation establishes the transcription competent packaging of its genome
Adenovirus maturation establishes the transcription competent packaging of its genome Open
Adenoviruses are human pathogens that more recently have gathered interest as tools for human gene therapy and vaccination. The maturation of the viral genome with associated proteins (core) remains largely unexplored. Here, we show that a…
View article: Deciphering chromatin architecture and dynamics in <i>Plasmodium falciparum</i> using the nucDetective pipeline
Deciphering chromatin architecture and dynamics in <i>Plasmodium falciparum</i> using the nucDetective pipeline Open
High-resolution analysis of cellular chromatin structure is crucial for uncovering developmental and cell-type-specific regulatory networks. We developed the nucDetective pipeline to provide a comprehensive evaluation of chromatin organisa…
View article: Mago nashi controls auxin‐mediated embryo patterning in Arabidopsis by regulating transcript abundance
Mago nashi controls auxin‐mediated embryo patterning in Arabidopsis by regulating transcript abundance Open
View article: Adenovirus maturation establishes the transcription competent packaging of its genome
Adenovirus maturation establishes the transcription competent packaging of its genome Open
Adenoviruses are human pathogens that, more recently have gathered interest as tools for human gene therapy and vaccination. During their replication, adenoviruses undergo a critical maturation step culminating in the infectious particle. …
View article: LoDEI: a robust and sensitive tool to detect transcriptome-wide differential A-to-I editing in RNA-seq data
LoDEI: a robust and sensitive tool to detect transcriptome-wide differential A-to-I editing in RNA-seq data Open
RNA editing is a highly conserved process. Adenosine deaminase acting on RNA (ADAR) mediated deamination of adenosine (A-to-I editing) is associated with human disease and immune checkpoint control. Functional implications of A-to-I editin…
View article: nucMACC: An MNase-seq pipeline to identify structurally altered nucleosomes in the genome
nucMACC: An MNase-seq pipeline to identify structurally altered nucleosomes in the genome Open
Micrococcal nuclease sequencing is the state-of-the-art method for determining chromatin structure and nucleosome positioning. Data analysis is complex due to the AT-dependent sequence bias of the endonuclease and the requirement for high …
View article: The Long Non-Coding RNA MALAT1 Modulates NR4A1 Expression through a Downstream Regulatory Element in Specific Cancer Cell Types
The Long Non-Coding RNA MALAT1 Modulates NR4A1 Expression through a Downstream Regulatory Element in Specific Cancer Cell Types Open
Long non-coding RNAs (lncRNAs) have been shown to modulate gene expression and are involved in the initiation and progression of various cancer types. Despite the wealth of studies describing transcriptome changes upon lncRNA knockdown, th…
View article: <i>Arabidopsis</i> <scp>mRNA</scp> export factor <scp>MOS11</scp>: molecular interactions and role in abiotic stress responses
<i>Arabidopsis</i> <span>mRNA</span> export factor <span>MOS11</span>: molecular interactions and role in abiotic stress responses Open
Summary Transcription and export (TREX) is a multi‐subunit complex that links synthesis, processing and export of mRNAs. It interacts with the RNA helicase UAP56 and export factors such as MOS11 and ALYs to facilitate nucleocytosolic trans…
View article: lncRNA LINC00941 modulates MTA2/NuRD occupancy to suppress premature human epidermal differentiation
lncRNA LINC00941 modulates MTA2/NuRD occupancy to suppress premature human epidermal differentiation Open
Numerous long non-coding RNAs (lncRNAs) were shown to have a functional impact on cellular processes such as human epidermal homeostasis. However, the mechanism of action for many lncRNAs remains unclear to date. Here, we report that lncRN…
View article: Biochemical and cellular insights into the Baz2B protein, a non-catalytic subunit of the chromatin remodeling complex
Biochemical and cellular insights into the Baz2B protein, a non-catalytic subunit of the chromatin remodeling complex Open
Baz2B is a regulatory subunit of the ATP-dependent chromatin remodeling complexes BRF1 and BRF5, which control access to DNA during DNA-templated processes. Baz2B has been implicated in several diseases and also in unhealthy ageing, howeve…
View article: Functional involvement of septal miR-132 in extinction and oxytocin-mediated reversal of social fear
Functional involvement of septal miR-132 in extinction and oxytocin-mediated reversal of social fear Open
View article: Epigenetic deregulation of IFN and WNT pathways in AT2 cells impairs alveolar regeneration (in COPD)
Epigenetic deregulation of IFN and WNT pathways in AT2 cells impairs alveolar regeneration (in COPD) Open
Chronic lung diseases, including chronic obstructive pulmonary disease (COPD), affect over 500 million people and are a leading cause of death worldwide. A common feature of both chronic and acute lung diseases is altered respiratory barri…
View article: Epigenetic deregulation of IFN and WNT pathways in AT2 cells impairs alveolar regeneration (in COPD)
Epigenetic deregulation of IFN and WNT pathways in AT2 cells impairs alveolar regeneration (in COPD) Open
Data-sets RNAseq_CountTable.tsv: Raw count table from RNA-seq experiments WGBS_MethylationTable.tsv: Total read coverage and number of methylated sites at CpG positions (reference genome: hg19) Abstract Chronic lung diseases, including chr…
View article: Epigenetic deregulation of IFN and WNT pathways in AT2 cells impairs alveolar regeneration (in COPD)
Epigenetic deregulation of IFN and WNT pathways in AT2 cells impairs alveolar regeneration (in COPD) Open
Data-setsRNAseq_CountTable.tsv: Raw count table from RNA-seq experimentsWGBS_MethylationTable.tsv: Total read coverage and number of methylated sites at CpG positions (reference genome: hg19) AbstractChronic lung diseases, including chron…
View article: Different elongation factors distinctly modulate RNA polymerase II transcription in Arabidopsis
Different elongation factors distinctly modulate RNA polymerase II transcription in Arabidopsis Open
Various transcript elongation factors (TEFs) including modulators of RNA polymerase II (RNAPII) activity and histone chaperones tune the efficiency of transcription in the chromatin context. TEFs are involved in establishing gene expressio…
View article: Changes in adenoviral chromatin organization precede early gene activation upon infection
Changes in adenoviral chromatin organization precede early gene activation upon infection Open
View article: The long non-coding RNA LINC00941 modulates MTA2/NuRD occupancy to suppress premature human epidermal differentiation
The long non-coding RNA LINC00941 modulates MTA2/NuRD occupancy to suppress premature human epidermal differentiation Open
Numerous long non-coding RNAs (lncRNAs) were shown to have functional impact on cellular processes such as human epidermal homeostasis. However, the mechanism of action for many lncRNAs remains unclear to date. Here, we report that lncRNA …
View article: High‐resolution transcriptomic and epigenetic profiling identifies novel regulators of COPD
High‐resolution transcriptomic and epigenetic profiling identifies novel regulators of COPD Open
Patients with chronic obstructive pulmonary disease (COPD) are still waiting for curative treatments. Considering its environmental cause, we hypothesized that COPD will be associated with altered epigenetic signaling in lung cells. We gen…
View article: The long non-coding RNA MALAT1 modulates NR4A1 expression through a downstream regulatory element in specific cancer-cell-types
The long non-coding RNA MALAT1 modulates NR4A1 expression through a downstream regulatory element in specific cancer-cell-types Open
Summary Chromatin-associated long non-coding RNAs (lncRNAs) have been shown to define chromatin density, regulate gene expression, and are involved in the initiation and progression of various cancer types. Despite the wealth of studies de…
View article: nucMACC: A MNase-seq pipeline to identify structurally altered nucleosomes in the genome
nucMACC: A MNase-seq pipeline to identify structurally altered nucleosomes in the genome Open
Micrococcal nuclease sequencing (MNase-seq) is the state-of-the-art method for determining chromatin structure and nucleosome positioning. Data analysis is complex due to the AT-dependent sequence bias of the endonuclease, and the requirem…
View article: Distinct role of subunits of the Arabidopsis RNA polymerase II elongation factor PAF1C in transcriptional reprogramming
Distinct role of subunits of the Arabidopsis RNA polymerase II elongation factor PAF1C in transcriptional reprogramming Open
Transcript elongation by RNA polymerase II (RNAPII) is dynamic and highly regulated, thereby contributing to the implementation of gene expression programs during plant development or in response to environmental cues. The heterohexameric …
View article: Pronounced sequence specificity of the TET enzyme catalytic domain guides its cellular function
Pronounced sequence specificity of the TET enzyme catalytic domain guides its cellular function Open
TET (ten-eleven translocation) enzymes catalyze the oxidation of 5-methylcytosine bases in DNA, thus driving active and passive DNA demethylation. Here, we report that the catalytic domain of mammalian TET enzymes favor CGs embedded within…
View article: HMGN5, an RNA or Nucleosome binding protein - potentially switching between the substrates to regulate gene expression
HMGN5, an RNA or Nucleosome binding protein - potentially switching between the substrates to regulate gene expression Open
The packaging of DNA into chromatin and its compaction within cells renders the underlying DNA template un-accessible for processes like transcription, replication and repair. Active mechanisms as chromatin modifying activities or the asso…
View article: Phosphorylation of the FACT histone chaperone subunit SPT16 affects chromatin at RNA polymerase II transcriptional start sites in <i>Arabidopsis</i>
Phosphorylation of the FACT histone chaperone subunit SPT16 affects chromatin at RNA polymerase II transcriptional start sites in <i>Arabidopsis</i> Open
The heterodimeric histone chaperone FACT, consisting of SSRP1 and SPT16, contributes to dynamic nucleosome rearrangements during various DNA-dependent processes including transcription. In search of post-translational modifications that ma…
View article: High-resolution transcriptomic and epigenetic profiling identifies novel regulators of COPD phenotypes in human lung fibroblasts
High-resolution transcriptomic and epigenetic profiling identifies novel regulators of COPD phenotypes in human lung fibroblasts Open
Patients with chronic obstructive pulmonary disease (COPD) are still waiting for curative treatments. Considering the environmental cause of COPD (e.g., cigarette smoke) and disease phenotypes, including stem-cell senescence and impaired d…
View article: Versatile workflow for cell type–resolved transcriptional and epigenetic profiles from cryopreserved human lung
Versatile workflow for cell type–resolved transcriptional and epigenetic profiles from cryopreserved human lung Open
Complexity of lung microenvironment and changes in cellular composition during disease make it exceptionally hard to understand molecular mechanisms driving development of chronic lung diseases. Although recent advances in cell type-resolv…
View article: Adenoviral chromatin organization primes for early gene activation
Adenoviral chromatin organization primes for early gene activation Open
SUMMARY Within the virion, adenovirus DNA associates with the virus-encoded, protamine-like structural protein pVII. Whether this association is organized, and how genome packaging changes during infection and subsequent transcriptional ac…
View article: Versatile workflow for cell type resolved transcriptional and epigenetic profiles from cryopreserved human lung
Versatile workflow for cell type resolved transcriptional and epigenetic profiles from cryopreserved human lung Open
The complexity of the lung microenvironment together with changes in cellular composition during disease progression make it exceptionally hard to understand the molecular mechanisms leading to the development of chronic lung diseases. Alt…
View article: Nucleosomes Stabilize ssRNA-dsDNA Triple Helices in Human Cells
Nucleosomes Stabilize ssRNA-dsDNA Triple Helices in Human Cells Open
View article: Characterizing the nuclease accessibility of DNA in human cells to map higher order structures of chromatin
Characterizing the nuclease accessibility of DNA in human cells to map higher order structures of chromatin Open
Packaging of DNA into chromatin regulates DNA accessibility and consequently all DNA-dependent processes. The nucleosome is the basic packaging unit of DNA forming arrays that are suggested, by biochemical studies, to fold hierarchically i…