Biology subjects

Karlsson, O. E.

Publications and source records attributed to Karlsson, O. E..

2 recordsLinked to original sources

bioRxiv2023

DNA methylation governs the sensitivity of repeats to restriction by the HUSH-MORC2 corepressor

The human silencing hub (HUSH) complex binds to transcripts of LINE-1 retrotransposons (L1s) and other genomic repeats, recruiting MORC2 and other effectors to remodel chromatin. However, how HUSH and MORC2 operate alongside DNA methylation, a central epigenetic regulator of repeat transcription, remains poorly understood. Here we interrogate this relationship in human neural progenitor cells (hNPCs), a somatic model of brain development that tolerates removal of DNA methyltransferase DNMT1. Upon loss of MORC2 or HUSH subunit TASOR in hNPCs, L1s remain silenced by robust promoter methylation. However, genome demethylation and activation of evolutionarily-young L1s attracts MORC2 binding. Simultaneous depletion of DNMT1 and MORC2 causes massive accumulation of L1 transcripts. We identify the same mechanistic hierarchy at pericentromeric -satellites and clustered protocadherin genes, repetitive elements important for chromosome structure and neurodevelopment respectively. Our data delineate the independent epigenetic control of repeats in somatic cells, with implications for understanding the vital functions of HUSH-MORC2 in hypomethylated contexts throughout human development.

molecular biology↗

bioRxiv2020

Molecular Ecology of Coral Reef Microorganisms in the Western Indian Ocean coast of Kenya

Coral reefs face increased environmental threats from anthropomorphic climate change and pollution, from agriculture, industries and tourism. They are economically vital for many people worldwide, and harbour a fantastically diverse ecosystem, being the home for many species of fish and algae. Surprisingly little is known about the microbial communities living in and in the surrounding of coral reefs. Here we employ high throughput sequencing for investigating the bacteria living in the water column and upper sediment layer in close proximity to coral reefs on the Kenyan coast of the West Indian Ocean. We show that while the read-level taxonomic distribution of bacteria is similar with ones obtained from 16S metabarcoding, whole metagenome sequencing provides valuable functional insights not available with 16S metabarcoding. We find evidence of pollution, marked by the presence of Vibrio and more importantly the presence of antibiotic resistance notably to vancomycin, that we attribute to the use of avoparcin in agriculture. Additionally, 175 bacterial genomes not previously sequenced were discovered. Our study is the first whole-metagenome study from the West Indian Ocean, provides a much-needed baseline to study microbes surrounding coral reefs under different conditions as well as the microbiome of coral reefs.

ecology↗