Biology subjects

Wolfe, G.

Publications and source records attributed to Wolfe, G..

3 recordsLinked to original sources

bioRxiv2023

Characterization of the RBM15 protein binding with XCI-escaping long noncoding RNAs

The RNA binding motif 15 protein (RBM15) plays a critical role in post-transcriptional regulation. Its role in facilitating N6-methyladenosine (m6A) modification, specifically through guiding the writer complex (WTAP METTL13 METTL14) to DRACH sequence motifs, has been demonstrated for several classes of RNA, including long noncoding RNAs (lncRNAs). The structural mechanism that underlies how RBM15 interacts with RNA has yet to be elucidated. In this study, we mined and bioinformatically assessed publicly available genome-wide RNA 2D structural probing and RBP cross-linking and immunoprecipitation data to investigate how RBM15 interacts with RNA, with a focus on lncRNA transcripts. RBM15, which possesses three RNA recognition motifs (RRMs), primarily interacts with stem-loop structured RNA motifs. Structural modeling reveals RRMs 2 and 3 are coaxially stacked in solution; these two RRMs are responsible for driving RBM15s interaction with RNA. We further demonstrate this experimentally with two RNA hairpins, revealing low micromolar binding affinities. Altogether, this work provides insight into the structural mechanism by which RBM15 interacts with RNAs to govern biological function.

biochemistry↗

bioRxiv2022

Multi-scale observations of mangrove blue carbon fluxes; the NASA Carbon Monitoring System BlueFlux field campaign

The BlueFlux field campaign is supported by NASAs Carbon Monitoring System (CMS) and will develop prototype blue carbon products to inform coastal carbon management. Blue carbon is included in carbon-dioxide removal actions proposed to reduce atmospheric CO2 concentrations to mitigate climate change. Due to their high productivity and carbon storage, combined with historic losses and a wide-range of beneficial ecosystem services, the restoration and conservation of mangrove ecosystems features prominently in blue-carbon planning. The goal of BlueFlux is to carry out multi-scale measurements of CO2 and CH4 fluxes using chambers, flux towers, and aircraft and scale these to gridded products using space-based observations of forest structure and surface reflectance. The measurements cover gradients in disturbance, mainly from the history of hurricanes in the region that drive the dieback of mangroves and the formation of ghost forests. The fluxes of CH4 emissions will be contrasted with CO2 uptake to provide a more complete budget of radiative forcing and to understand the net climate benefits of blue carbon. BlueFlux demonstrates that quantifying the removals of CO2 and emissions of CH4 using a multi-scale approach can provide increased confidence in regional greenhouse-gas accounting, contribute to process-understanding, and help inform restoration and conservation efforts in the context of climate mitigation.

ecology↗

bioRxiv2022

Cotranscriptional folding of the lncRNA Xist A-repeats indicates a modular structure

LncRNAs are emerging to play crucial roles in the regulation of many essential cellular processes and have been linked to human disease, but a detailed understanding of their structure and how this relates to underlying molecular mechanisms is still limited. The structure that a lncRNA adopts can interconvert between multiple conformations. However, characterizing the structure and dynamics is challenging given their large size. Here, we present an integrated approach, combining biochemical and biophysical techniques to investigate the core structural elements and conformational dynamics of the A-repeats of the lncRNA Xist. We combine chemical RNA structure probing, SAXS, NMR-spectroscopy and cryo-EM to comprehensively describe the conformational landscape of the Xist A-repeats. We show that under native-like conditions, the A-repeats are modular, comprising building blocks made from stable AUCG tetraloop hairpins and inter-repeat dimers separated by flexible uracil-rich regions. The structural core of the A-repeats involves dimerization of sequential repeats to form two subdomains, comprising repeats 1-4 and 5-8. The overall topology of the A-repeats is dynamic, with structural variability linked to the uracil-rich linker regions. Our results rationalize context and buffer-dependent structural variations of the Xist lncRNA. The integrative approach presented here establishes a general pipeline for investigating lncRNA structure and dynamics. GRAPHICAL ABSTRACT O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=98 SRC="FIGDIR/small/501616v2_ufig1.gif" ALT="Figure 1"> View larger version (25K): org.highwire.dtl.DTLVardef@1761cbeorg.highwire.dtl.DTLVardef@15905e0org.highwire.dtl.DTLVardef@190bf0corg.highwire.dtl.DTLVardef@1eeca5a_HPS_FORMAT_FIGEXP M_FIG C_FIG

biochemistry↗