Biology subjects

Bakker, M.

Publications and source records attributed to Bakker, M..

3 recordsLinked to original sources

bioRxiv2025

Modulation of archaeal hypernucleosome structure and stability by Mg2+

DNA-wrapping histone proteins play a central role in chromatin organization, gene expression and regulation in most eukaryotes and archaea. While the structure and function of eukaryotic histones are well-characterized, archaeal histones and their complexes with DNA require further scrutiny. Distinct from their eukaryotic counterparts, previously characterized canonical archaeal histones assemble on DNA into an endless superhelical nucleoprotein complex called a hypernucleosome. In this study, we explored whether hypernucleosome formation is a conserved feature of canonical archaeal histones. Moreover, to further elucidate how hypernucleosomes are regulated, we also explored how changes in the physico-chemical conditions, particularly the presence of Mg2+, influence the hypernucleosome. Using a combination of Tethered Particle Motion (TPM) and single-molecule force spectroscopy, we established that T. kodakarensis histones assemble into hypernucleosomes on DNA, similar to the M. fervidus histones HMfA and HMfB, the only canonical histones structurally characterized in previous studies. However, the effects of Mg2+ ions are distinct despite the histones high sequence- and structural similarity. We propose a model in which Mg2+ ions exert a generic effect on hypernucleosome compactness and stability due to electrostatic DNA shielding, with additional differential effects depending on histone identity.

molecular biology↗

bioRxiv2022

FDA-Approved Drug Screening in Patient-Derived Organoids Demonstrates Potential of Drug Repurposing for Rare Cystic Fibrosis Genotypes

BackgroundPreclinical cell-based assays that recapitulate human disease play an important role in drug repurposing. We previously developed a functional forskolin induced swelling (FIS) assay using patient-derived intestinal organoids (PDIOs), allowing functional characterization of CFTR, the gene mutated in people with cystic fibrosis (pwCF). CFTR function-increasing pharmacotherapies have revolutionized treatment for approximately 85% of people with CF, but a large unmet need remains to identify new treatments for all pwCF. MethodsWe used 76 non-homozygous F508del-CFTR PDIOs to test the efficacy of 1400 FDA-approved drugs on improving CFTR function, as measured in FIS assays. ResultsBased on the results of a secondary validation screen, we investigated CFTR elevating function of PDE4 inhibitors and currently existing CFTR modulators in further detail. We show that PDE4 inhibitors are potent CFTR function inducers in PDIOs and that CFTR modulator treatment rescues of CF genotypes that are currently not eligible for this therapy. ConclusionsThis study exemplifies the feasibility of high-throughput compound screening using PDIOs and we show the potential of repurposing drugs for pwCF that are currently not eligible for therapies. One-sentence SummaryWe screened 1400 FDA-approved drugs in CF patient-derived intestinal organoids using the previously established functional FIS assay, and show the potential of repurposing PDE4 inhibitors and CFTR modulators for rare CF genotypes.

molecular biology↗

bioRxiv2016

Easy and Accurate Reconstruction of Whole HIV Genomes from Short-Read Sequence Data

Next-generation sequencing has yet to be widely adopted for HIV. The difficulty of accurately reconstructing the consensus sequence of a quasispecies from reads (short fragments of DNA) in the presence of rapid between- and within-host evolution may have presented a barrier. In particular, mapping (aligning) reads to a reference sequence leads to biased loss of information; this bias can distort epidemiological and evolutionary conclusions. De novo assembly avoids this bias by effectively aligning the reads to themselves, producing a set of sequences called contigs. However contigs provide only a partial summary of the reads, misassembly may result in their having an incorrect structure, and no information is available at parts of the genome where contigs could not be assembled. To address these problems we developed the tool shiver to preprocess reads for quality and contamination, then map them to a reference tailored to the sample using corrected contigs supplemented with existing reference sequences. Run with two commands per sample, it can easily be used for large heterogeneous data sets. We use shiver to reconstruct the consensus sequence and minority variant information from paired-end short-read data produced with the Illumina platform, for 65 existing publicly available samples and 50 new samples. We show the systematic superiority of mapping to shivers constructed reference over mapping the same reads to the standard reference HXB2: an average of 29 bases per sample are called differently, of which 98.5% are supported by higher coverage. We also provide a practical guide to working with imperfect contigs.

bioinformatics↗