Biology subjects

Eriksson, P. R.

Publications and source records attributed to Eriksson, P. R..

6 recordsLinked to original sources

bioRxiv2026

Long-read DNA sequencing reveals global hypomethylation and focal hypermethylation in SDHx-deficient pheochromocytoma and paraganglioma

Pheochromocytomas and paragangliomas (PPGL) are highly heritable neuroendocrine tumors of the autonomic ganglia. Genomic DNA in most cancer cells is hypomethylated. However, DNA in PPGLs secondary to mutations in succinate dehydrogenase complex (SDHx) genes is reportedly hypermethylated due to succinate-mediated inhibition of DNA demethylases. We used nanopore long-read sequencing to characterize the methylome of tumor and white blood cell DNA from SDHx and non-SDHx PPGL patients, alongside normal adrenal medulla. We find that both SDHx and non-SDHx PPGLs are globally hypomethylated, particularly at centromeres. In normal adrenal medulla, CpG islands marked by H3K4 methylation are hypomethylated, whereas CpG islands lacking H3K4 methylation are hypermethylated. In SDHx-related PPGL, some H3K4me-marked CpG islands are hypermethylated, but most are not. We propose that DNA methylation in SDHx-related PPGL reflects the global hypomethylation generally observed in tumors, partly offset by succinate-mediated inhibition of TET DNA demethylases. Opposing effects of succinate may alter the balance between DNA methylation (indirect inhibition of the DNMT3A/B DNA methylases via inhibition of H3K4me demethylases) and DNA demethylation (inhibition of TET DNA demethylases) at active CpG islands.

genomics↗

bioRxiv2025

Sir proteins impede, but do not prevent, access to silent chromatin in living Saccharomyces cerevisiae

Gene silencing at the mating type loci in budding yeast (HMRa and HML) depends on the Sir proteins. Sir2, Sir3 and Sir4 are indispensable for silencing, whereas Sir1 has a more limited role. The Sir proteins are also involved in repression at telomeres and ribosomal DNA (rDNA) repeats. Proposed mechanisms for Sir-mediated silencing include limiting access to silenced DNA and inhibition of transcript initiation and/or elongation. Using an inducible M.SssI DNA methyltransferase expression system, we showed previously that the silenced mating type loci are methylated at a much slower rate than the rest of the genome in vivo. Here, we show that, in the absence of Sir2, Sir3 or Sir4, the silenced loci and the telomeric X elements are methylated at a similar rate to the rest of the genome, indicating that these Sir proteins impede access, but do not prevent it. The rDNA repeats are methylated faster in the absence of Sir2 and, to a lesser extent, of Sir3, but not of Sir4. The methylation rates of adjacent rDNA repeats are not strongly correlated in wild-type cells, suggesting that Sir proteins silence rDNA repeats randomly. Loss of Sir1 increases the methylation rate at HMRa but not at HML, telomeres or rDNA. Our data indicate that steric occlusion is unlikely to be the primary mechanism of silencing, since silenced DNA is accessible in vivo, albeit at a slower rate than elsewhere in the genome.

genetics↗

bioRxiv2025

The ISW1 and CHD1 chromatin remodelers suppress global nucleosome dynamics in living yeast cells

The budding yeast genome is globally accessible to DNA methyltransferases in living cells, unlike in isolated nuclei, where it is mostly inaccessible. Here, we assess the roles of the RSC, ISW1 and CHD1 ATP-dependent chromatin remodelers in generating nucleosome dynamics in vivo. We compare DNA methylation rates in wild type cells and chromatin remodeler mutants by normalizing nuclear methylation rates to the non-nucleosomal mitochondrial DNA methylation rate in each strain. Depletion of subunits of the RSC, ISW1 or CHD1 ATP-dependent chromatin remodelers has little effect on normalized methylation rate. A decaying sine wave model used to fit nucleosome phasing data shows that nucleosome dynamics decrease with distance from the promoter in an Isw1/Chd1-dependent manner. Depletion of both Isw1 and Chd1 increases the methylation rate, suggesting that these remodelers act together to suppress nucleosome dynamics. Furthermore, the TFIIIB and TFIIIC transcription factors exhibit differential dynamics at tRNA genes. Our analysis provides insight into nucleosome and transcription factor dynamics in vivo. TeaserThe budding yeast ISW1 and CHD1 ATP-dependent remodelers organize chromatin on genes, slowing nucleosome dynamics in living cells.

genomics↗

bioRxiv2024

Nucleosome dynamics render heterochromatin accessible in living human cells

The eukaryotic genome is packaged into chromatin, which is composed of a nucleosomal filament that coils up to form more compact structures. Chromatin exists in two main forms: euchromatin, which is relatively decondensed and enriched in transcriptionally active genes, and heterochromatin, which is condensed and transcriptionally repressed 1-10. It is widely accepted that chromatin architecture modulates DNA accessibility, restricting the access of sequence-specific, gene-regulatory, transcription factors to the genome. Here, we measure genome accessibility at all GATC sites in living human MCF7 and MCF10A cells, using an adenovirus vector to express the sequence-specific dam DNA adenine methyltransferase. We find that the human genome is globally accessible in living cells, unlike in isolated nuclei. Active promoters are methylated somewhat faster than gene bodies and inactive promoters. Remarkably, both constitutive and facultative heterochromatic sites are methylated only marginally more slowly than euchromatic sites. In contrast, sites in centromeric chromatin are methylated slowly and are partly inaccessible. We conclude that all nucleosomes in euchromatin and heterochromatin are highly dynamic in living cells, whereas nucleosomes in centromeric -satellite chromatin are static. A dynamic architecture implies that simple occlusion of transcription factor binding sites by chromatin is unlikely to be critical for gene regulation.

genomics↗

bioRxiv2020

The yeast ISW1b ATP-dependent chromatin remodeler is critical for nucleosome spacing and dinucleosome resolution

Isw1 and Chd1 are ATP-dependent nucleosome-spacing enzymes required to establish regular arrays of phased nucleosomes near transcription start sites of yeast genes. Cells lacking both Isw1 and Chd1 have extremely disrupted chromatin, with weak phasing, irregular spacing and a propensity to form closed-packed dinucleosomes. The Isw1 ATPase subunit occurs in two different remodeling complexes: ISW1a (composed of Isw1 and Ioc3) and ISW1b (composed of Isw1, Ioc2 and Ioc4). The Ioc4 subunit of ISW1b binds preferentially to the H3-K36me3 mark. Here we show that ISW1b is primarily responsible for setting nucleosome spacing and resolving close-packed dinucleosomes, whereas ISW1a plays only a minor role. ISW1b and Chd1 make additive contributions to dinucleosome resolution, such that neither enzyme is capable of resolving all dinucleosomes on its own. Loss of the Set2 H3-K36 methyltransferase partly phenocopies loss of Ioc4, resulting in increased dinucleosome levels with only a weak effect on nucleosome spacing, suggesting that Set2-mediated H3-K36 trimethylation contributes to ISW1b-mediated dinucleosome separation. The H4 tail domain is required for normal nucleosome spacing but not for dinucleosome resolution. We conclude that the nucleosome spacing and dinucleosome resolving activities of ISW1b and Chd1 are critical for normal global chromatin organisation.

genomics↗

bioRxiv2019

DNA accessibility is not the primary determinant of chromatin-mediated gene regulation

DNA accessibility is thought to be of major importance in regulating gene expression. We test this hypothesis using a restriction enzyme as a probe of chromatin structure and as a proxy for transcription factors. We measured the digestion rate and the fraction of accessible DNA at all genomic AluI sites in budding yeast and mouse liver nuclei. Hepatocyte DNA is more accessible than yeast DNA, consistent with longer linkers between nucleosomes, and indicating that nucleosome spacing is a major determinant of accessibility. DNA accessibility varies from cell to cell, such that essentially no sites are accessible or inaccessible in every cell. AluI sites in inactive mouse promoters are accessible in some cells, implying that transcription factors could bind without activating the gene. Euchromatin and heterochromatin have very similar accessibilities, suggesting that transcription factors can penetrate heterochromatin. Thus, DNA accessibility is not likely to be the primary determinant of gene regulation.

genomics↗