Biology subjects

Oakes, C. G.

Publications and source records attributed to Oakes, C. G..

5 recordsLinked to original sources

bioRxiv2025

Computational array reconstruction for spatial transcriptomics

Several optics-free spatial transcriptomics assays that make use of diffusion of reads from beads have recently been developed, and provide a proof of principle for high-throughput, untargeted, spatial transcriptomics. These approaches leads to a challenging computational array reconstruction problem. We show that an statistical inference method, which we term accumap, outperforms the current approach which is to run UMAP on the bead count matrix. The accumap method makes use of predicted distances to reconstruct bead positions and can improve the accuracy of reconstruction by a factor of 3 in the diffusible Slide-Tag simulation framework.

bioinformatics↗

bioRxiv2025

Uniform pre-processing of bacterial single-cell RNA-seq

Bacteria are highly heterogeneous, even under controlled conditions, making single-cell RNA sequencing (scRNA-seq) essential for studying microbial diversity and symbiosis. Since its first application in 2015, bacterial scRNA-seq has expanded, but different assays depend on distinct, custom, in-house preprocessing making it difficult to analyze data as part of a unified workflow. The kallisto-bustools suite of tools has enabled uniform pre-processing of eukaryotic scRNA-seq while also reducing time and resource demands for pre-processing, but is not optimized for bacterial scRNA-seq. We adapt kallisto-bustools to be suitable for reads generated from operons, as well as for a much shorter gene length distribution, and show that it can efficiently and accurately quantify bacterial scRNA-seq. Our work provides a scalable foundation for uniform pre-processing and analysis of microbial single-cell transcriptomics.

bioinformatics↗

bioRxiv2025

Transcriptomic responses to endurance exercise training in rats

The bio-molecular changes of exercise, and how to best optimize them for improved performance, are an important human health research question. A recent study by the Molecular Transducers of Physical Activity Consortium (MoTrPAC) used a cohort of Rattus norvegicus to produce a whole-organism molecular map of the temporal effects of endurance exercise training. This dataset, encompassing hundreds of assays across 19 different tissues, can be used to evaluate the predictive power of gene expression, understand isoform-level changes in response to exercise, and with modern tools can be examined for associations with viral infection. Our analysis of the RNA-seq data reveals that gene expression can accurately predict the amount of exercise a rat was trained in. Additionally, we find biologically relevant isoform-level differences in expression that are masked in gene-level analysis. Finally, we find a potential novel virus that may negatively impact physiological measurements. This more comprehensive analysis provides a blueprint for directing similar analyses with respect to physiological perturbations across organisms.

genomics↗

bioRxiv2025

Gene syntax defines supercoiling-mediated transcriptional feedback

Gene syntax--the order and arrangement of genes and their regulatory elements--shapes the dynamic coordination of both natural and synthetic gene circuits. Transcription at one locus profoundly impacts the transcription of nearby adjacent genes, but the molecular basis of this effect remains poorly understood. Here, using integrated reporter circuits in human cells, we show that the reciprocal effects of transcription and DNA supercoiling, which we term supercoiling-mediated feedback, regulates expression of adjacent genes in a syntax-specific manner. Using a suite of chromatin state assays, we measure syntax-and induction-dependent formation of chromatin structures in human induced pluripotent stem cells. Applying syntax as a design parameter and without altering sequence or copy number, we built compact gene circuits, tuning the expression mean, noise, and stoichiometry across diverse delivery methods and cell types. Integrating supercoiling-mediated feedback into models of gene regulation will expand our understanding of native systems and enhance the design of synthetic gene circuits.

synthetic biology↗

bioRxiv2024

Cells transit through a quiescent-like state to convert to neurons at high rates

While transcription factors (TFs) provide essential cues for directing and redirecting cell fate, TFs alone are insufficient to drive cells to adopt alternative fates. Rather, transcription factors rely on receptive cell states to induce novel identities. Cell state emerges from and is shaped by cellular history and the activity of diverse processes. Here, we define the cellular and molecular properties of a highly receptive state amenable to transcription factor-mediated direct conversion from fibroblasts to induced motor neurons. Using a well-defined model of direct conversion to a post-mitotic fate, we identify the highly proliferative, receptive state that transiently emerges during conversion. Through examining chromatin accessibility, histone marks, and nuclear features, we find that cells reprogram from a state characterized by global reductions in nuclear size and transcriptional activity. Supported by globally increased levels of H3K27me3, cells enter a quiescent-like state of reduced RNA metabolism and elevated expression of REST and p27, markers of quiescent neural stem cells. From this transient state, cells convert to neurons at high rates. Inhibition of Ezh2, the catalytic subunit of PRC2 that deposits H3K27me3, abolishes conversion. Our work offers a roadmap to identify global changes in cellular processes that define cells with different conversion potentials that may generalize to other cell-fate transitions. HighlightsO_LIProliferation drives cells to a compact nuclear state that is receptive to TF-mediated conversion. C_LIO_LIIncreased receptivity to TFs corresponds to reduced nuclear volumes. C_LIO_LIReprogrammable cells display global, genome-wide increases in H3K27me3. C_LIO_LIHigh levels of H3K27me3 support cells transits through a state of altered RNA metabolism. C_LIO_LIInhibition of Ezh2 increases nuclear size, reduces the expression of the quiescence marker p27. C_LIO_LIAcute inhibition of Ezh2 abolishes motor neuron conversion. C_LI One Sentence SummaryCells transit through a quiescent-like state characterized by global reductions in nuclear size and transcriptional activity to convert to neurons at high rates. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=143 SRC="FIGDIR/small/624928v1_ufig1.gif" ALT="Figure 1"> View larger version (38K): org.highwire.dtl.DTLVardef@ee2127org.highwire.dtl.DTLVardef@1c2a39dorg.highwire.dtl.DTLVardef@183bf46org.highwire.dtl.DTLVardef@82b98d_HPS_FORMAT_FIGEXP M_FIG C_FIG

systems biology↗