Kirstin S. Meyer

Chromatin Composition Is Changed by Poly(ADP-ribosyl)ation during Chromatin Immunoprecipitation

Chromatin-immunoprecipitation (ChIP) employs generally a mild formaldehyde cross-linking step, which is followed by isolation of specific protein-DNA complexes and subsequent PCR testing, to analyze DNA-protein interactions. Poly(ADP-ribosyl)ation, a posttranslational modification involved in diverse cellular functions like repair, replication, transcription, and cell death regulation, is most prominent after DNA damage. Poly(ADP-ribose)polymerase-1 is activated upon binding to DNA strand-breaks and coordinates repair by recruitment or displacement of proteins. Several proteins involved in different nuclear pathways are directly modified or contain poly(ADP-ribose)-interaction motifs. Thus, poly(ADP-ribose) regulates chromatin composition. In immunofluorescence experiments, we noticed artificial polymer-formation after formaldehyde-fixation of undamaged cells. Therefore, we analyzed if the formaldehyde applied during ChIP also induces poly(ADP-ribosyl)ation and its impact on chromatin composition. We observed massive polymer-formation in three different ChIP-protocols tested independent on the cell line. This was due to induction of DNA damage signaling as monitored by γH2AX formation. To abrogate poly(ADP-ribose) synthesis, we inhibited this enzymatic reaction either pharmacologically or by increased formaldehyde concentration. Both approaches changed ChIP-efficiency. Additionally, we detected specific differences in promoter-occupancy of tested transcription factors as well as the in the presence of histone H1 at the respective sites. In summary, we show here that standard ChIP is flawed by artificial formation of poly(ADP-ribose) and suppression of this enzymatic activity improves ChIP-efficiency in general. Also, we detected specific changes in promoter-occupancy dependent on poly(ADP-ribose). By preventing polymer synthesis with the proposed modifications in standard ChIP protocols it is now possible to analyze the natural chromatin-composition.

High Biodiversity on a Deep-Water Reef in the Eastern Fram Strait

We report on the distribution and abundance of megafauna on a deep-water rocky reef (1796–2373 m) in the Fram Strait, west of Svalbard. Biodiversity and population density are high, with a maximum average of 26.7±0.9 species m−2 and 418.1±49.6 individuals m−2 on the east side of the reef summit. These figures contrast with the surrounding abyssal plain fauna, with an average of only 18.1±1.4 species and 29.4±4.3 individuals m−2 (mean ± standard error). The east side of the reef summit, where the highest richness and density of fauna are found, faces into the predominant bottom current, which likely increases in speed to the summit and serves as a source of particulate food for the numerous suspension feeders present there. We conclude that the observed faunal distribution patterns could be the result of hydrodynamic patterns and food availability above and around the reef. To our knowledge, this study is the first to describe the distribution and diversity of benthic fauna on a rocky reef in deep water.

Environmental factors structuring Arctic megabenthos—a case study from a shelf and two fjords

From photographic samples, we describe the benthic megafaunal communities in two north Svalbard fjords and on the adjacent continental shelf. We analyze the fauna in relation to abiotic factors of depth, bottom water temperature, percent cover of hard substratum, heterogeneity of stone size, and bottom-water turbidity to explore how these factors might affect the fauna and how they are related to the functional traits (size, morphology, mobility, colonial/solitary, and feeding type) of the megabenthos. Depth and bottom water temperature were consistently the strongest correlates with faunal composition and functional traits of the constituent species. A greater proportion of the variability in the functional traits of the megabenthos could be explained by abiotic factors rather than faunal composition, indicating that the abiotic factors of depth and temperature were strongly related to the functional traits of the megabenthos. On a local scale, stone size heterogeneity explained most variation in the functional traits of the megabenthos in one fjord. The results of this case study show a significant relationship between bottom water temperature and the functioning of north Svalbard megabenthic communities. Warming temperatures in the Arctic will likely decrease the variety of functional traits represented in Svalbard megabentos, resulting in scavenger-dominated communities. A reduction in megabenthic biomass may also result, reducing energy availability to higher trophic levels.

Observation of a living macroalga at 166 m in a high Arctic fjord

Still photos of the seafloor in Raudfjorden, Spitsbergen, recorded in 2011, showed an abundant macroalga at a depth of 166 m. The macroalga was observed attached to stones of varying size and streaming in the bottom current, which would imply that the alga was alive and growing in situ . The alga likely experiences very low-light conditions, as it is present in a turbid fjord influenced by glacial sedimentation. Arctic macroalgae are often adapted to low-light conditions, but to the authors’ knowledge, the present report is the deepest record of living macroalgae in the high Arctic.