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

Wednesday, 20. December 2017

Maldonado,R., Filarski,M., Grummt,I. and Längst,G. (2017) RNA, 10.1261/rna.063800.117.

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...

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

Monday, 20. November 2017

Hoffmeister,H., Fuchs,A.,  et al. (2017) Nucleic Acids Res, 45, 10534–10554.

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...

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

Friday, 4. November 2016

Elisabeth Silberhorn et al., Plos Pathogens (2016)

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...

The extended AT-hook is a novel RNA binding motif

Friday, 20. November 2015

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...

A Plasmodium Falciparum Bromodomain Protein Regulates Invasion Gene Expression

Wednesday, 20. May 2015

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...

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

Saturday, 20. December 2014

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...

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EpiGenetics

Chromatin Dynamics and Nuclear Architecture

Prof. Gernot Längst - Biochemistry III  

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