Time resolved changes of Adenovirus chromatin structure

Saturday, 29. August 2020
Time resolved changes of Adenovirus chromatin structure

A pVII positioning code determines the dynamics of Adenoviral nucleoprotein structure and primes it for early gene activation Uwe Schwartz et al., (2020) BioRxiv; ID: https://doi.org/10.1101/2020.07.07.190926
Inside the capsid adenovirus DNA is associated with the structural protein pVII. However, the viral DNA organisation, pVII positioning and the dynamic changes of viral packaging upon infection, to form a transcriptional active genome, are not known. We combined MNase-Seq and single genome imaging during early infection to provide the structure and time resolved dynamics of viral chromatin changes, correlated with gene transcription. pVII complexes form nucleosome-like arrays, being precisely positioned on DNA, creating a defined and unique adenoviral nucleoprotein-architecture....

Triple helix structures are stablilized by nucleosomes

Sunday, 29. September 2019
Triple helix structures are stablilized by nucleosomes

Nucleosomes Stabilize ssRNA-dsDNA Triple Helices in Human Cells Rodrigo Maldonado et al., (2019) Molecular Cell; PMID: 30770238
Chromatin-associated non-coding RNAs modulate the epigenetic landscape and its associated gene expression program. The formation of triple helices is one mechanism of sequence-specific targeting of RNA to chromatin. With this study, we show an important role of the nucleosome and its relative positioning to the triplex targeting site (TTS) in stabilizing RNA-DNA triplexes in vitro and in vivo. Triplex stabilization depends on the histone H3 tail and the location of the TTS close to the nucleosomal DNA entry-exit site. Genome-wide analysis of TTS-nucleosome arrangements revealed a defined chromatin organization with an enrichment of...

Transfecting eukaryotic cells with chromatin

Wednesday, 29. May 2019
Transfecting eukaryotic cells with chromatin

Antibody-targeted chromatin enables effective intracellular delivery and functionality of CRISPR/Cas9 expression plasmids Killian et al., (2019) Nucleic Acids Research; PMID: 30809660
We report a novel system for efficient and specific targeted delivery of large nucleic acids to and into cells. Plasmid DNA and core histones were assembled to chromatin by salt gradient dialysis and subsequently connected to bispecific antibody derivatives (bsAbs) via a nucleic acid binding peptide bridge. The resulting reconstituted vehicles termed ‘plasmid-chromatin’ deliver packaged nucleic acids to and into cells expressing antigens that are recognized by the bsAb, enabling intracellular functionality without detectable cytotoxicity. High efficiency of intracellular nucleic...

Functional characterisation of the human chromatin remodeling enzyme BRG1

Tuesday, 12. February 2019
Functional characterisation of the human chromatin remodeling enzyme BRG1

Elucidation of the functional role of the Q- and I-motif in the human chromatin remodeling enzyme BRG1
Helen Hoffmeister et al., (2019) JBC; PMID: 30647132
The Snf2 proteins, comprising 53 different enzymesin humans, belong to the SF2 family. Many Snf2enzymes possess chromatin remodeling activity,requiring a functional ATPase domain consisting ofconserved motifs named Q and I-VII. These motifsform two recA-like domains, creating an ATP-binding pocket. Little is known about the functionof the conserved motifs in chromatin remodelingenzymes. Here, we characterized the function of theQ- and I (Walker I)-motif in hBRG1 (SMARCA4).The motifs are in close proximity to the bound ATP,suggesting a role in nucleotide binding and/orhydrolysis. Unexpectedly, when substituting...

The folding into regular higher order structures of chromatin may not exist

Tuesday, 11. December 2018
The folding into regular higher order structures of chromatin may not exist

Characterizing the nuclease accessibility of DNA in human cells to map higher order structures of chromatin.
Uwe Schwartz et al., (2018) Nucleic Acids Research; PMID: 30496478
Packaging of DNA into chromatin regulates DNA ac-cessibility and consequently all DNA-dependent pro-cesses. The nucleosome is the basic packaging unitof DNA forming arrays that are suggested, by bio-chemical studies, to fold hierarchically into orderedhigher-order structures of chromatin. This organiza-tion has been recently questioned using microscopytechniques, proposing an irregular structure. To ad-dress the principles of chromatin organization, weapplied an in situ differential MNase-seq strategy andanalyzed in silico the results of complete and par-tial digestions of human chromatin....

Purine– and pyrimidine–triple-helix-forming oligonucleotides recognize qualitatively different target sites

Wednesday, 20. December 2017
Purine– and pyrimidine–triple-helix-forming oligonucleotides recognize qualitatively different target sites

Rodrigo Maldonado et al., (2017) RNA; PMID: 29222118
Triplexes are noncanonical DNA structures, which are functionally associated with regulation of gene expression through ncRNAtargeting to chromatin. Based on the rules of Hoogsteen base-pairing, polypurine sequences of a duplex can potentially formtriplex structures with single-stranded oligonucleotides. Prediction of triplex-forming sequences by bioinformatics analyseshave revealed enrichment of potential triplex targeting sites (TTS) at regulatory elements, mainly in promoters and enhancers,suggesting a potential function of RNA–DNA triplexes in transcriptional regulation. Here, we have quantitatively evaluated thepotential of different sequences of human and mouse ribosomal RNA genes (rDNA) to form triplexes...

CHD3 and CHD4 form distinct NuRD complexes with different yet overlapping functionality

Monday, 20. November 2017
CHD3 and CHD4 form distinct NuRD complexes with different yet overlapping functionality

Helen Hoffmeister et al. (2017) Nucleic Acids Research; PMID: 28977666
CHD3 and CHD4 (Chromodomain Helicase DNA bind-ing protein), two highly similar representatives of theMi-2 subfamily of SF2 helicases, are coexpressed inmany cell lines and tissues and have been reportedto act as the motor subunit of the NuRD complex(nucleosome remodeling and deacetylase activities).Besides CHD proteins, NuRD contains several re-pressors like HDAC1/2, MTA2/3 and MBD2/3, argu-ing for a role as a transcriptional repressor. However,the subunit composition varies among cell- and tis-sue types and physiological conditions. In particular,it is unclear if CHD3 and CHD4 coexist in the sameNuRD complex or whether they form distinct NuRDcomplexes with specific functions. We mapped theCHD...

Plasmodium falciparum Nucleosomes Exhibit Reduced Stability and Lost Sequence Dependent Nucleosome Positioning

Friday, 4. November 2016
Plasmodium falciparum Nucleosomes Exhibit Reduced Stability and Lost Sequence Dependent Nucleosome Positioning

Elisabeth Silberhorn et al., (2016) Plos Pathogen; PMID: 28033404
Nucleosomes are not positioned randomly on DNA but on preferential sites with respect to the underlying DNA sequence. Histones belong to the most conserved eukaryotic proteins, as sequence dependent nucleosome positioning is an essential regulatory feature of nucleosomes, determining the accessibility of regulatory factors to DNA. We determined the biochemical properties of plasmodium histones and show that they are distinct from human forms, explaining the accessible chromatin structure of falciparum. Amino acid exchanges in the histones do not present an adaption to the AT-rich genome, but rather reduce the binding affinity to GC-rich DNA sequences, resulting in rather unstable nucleosomes with...

The extended AT-hook is a novel RNA binding motif

Friday, 20. November 2015
The extended AT-hook is a novel RNA binding motif

Michael Filarsky et al., RNA Biol. 2015;12(8):864-76
The AT-hook has been defined as a DNA binding peptide motif that contains a glycine-arginine-proline (G-R-P) tripeptide core flanked by basic amino acids. Recent reports documented variations in the sequence of AT-hooks and revealed RNA binding activity of some canonical AT-hooks, suggesting a higher structural and functional variability of this protein domain than previously anticipated. Here we describe the discovery and characterization of the extended AT-hook peptide motif (eAT-hook), in which basic amino acids appear symmetrical mainly at a distance of 12-15 amino acids from the G-R-P core. We identified 80 human and 60 mouse eAT-hook proteins and biochemically characterized the eAT-hooks of Tip5/BAZ2A,...

A Plasmodium Falciparum Bromodomain Protein Regulates Invasion Gene Expression

Wednesday, 20. May 2015
A Plasmodium Falciparum Bromodomain Protein Regulates Invasion Gene Expression

Josling et al., Cell Host Microbe. 2015 Jun 10;17(6):741-51
During red-blood-cell-stage infection of Plasmodium falciparum, the parasite undergoes repeated rounds of replication, egress, and invasion. Erythrocyte invasion involves specific interactions between host cell receptors and parasite ligands and coordinated expression of genes specific to this step of the life cycle. We show that a parasite-specific bromodomain protein, PfBDP1, binds to chromatin at transcriptional start sites of invasion-related genes and directly controls their expression. Conditional PfBDP1 knockdown causes a dramatic defect in parasite invasion and growth and results in transcriptional downregulation of multiple invasion-related genes at a time point critical for invasion. Conversely,...

TNFα signalling primes chromatin for NF-κB binding and induces rapid and widespread nucleosome repositioning

Saturday, 20. December 2014
TNFα signalling primes chromatin for NF-κB binding and induces rapid and widespread nucleosome repositioning

Sarah Diermeier et al., Genome Biology 2014
Background: The rearrangement of nucleosomes along the DNA fiber profoundly affects gene expression, but little is known about how signalling reshapes the chromatin landscape, in three-dimensional space and over time, to allow establishment of new transcriptional programs. 
Results: Using micrococcal nuclease treatment and high-throughput sequencing, we map genome-wide changes in nucleosome positioning in primary human endothelial cells stimulated with tumour necrosis factor alpha (TNFα) - a proinflammatory cytokine that signals through nuclear factor kappa-B (NF-κB). Within 10 min, nucleosomes reposition at regions both proximal and distal to NF-κB binding sites, before the transcription factor quantitatively...

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EpiGenetics

Chromatin Dynamics and Nuclear Architecture

Prof. Gernot Längst - Biochemistry III  

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