Biology subjects

Falk, J.

Publications and source records attributed to Falk, J..

5 recordsLinked to original sources

bioRxiv2024

Contribution of the neuron-specific ATP1A3 to embryonic spinal circuit emergence

The early neurodevelopmental contributions of ion pumps remain poorly characterized. Combining analysis of public human embryo single-cell transcriptomic datasets and an embryonic chicken model, we found a conserved differentiation sequence whereby spinal cord neurons switch on neuron-specific alpha3 subunit (ATP1A3) of Na+/K+ ATPases. In the chicken model, ATP1A3 is distributed along axons and growth cones. Its knockdown alters axon pathfinding of dorsal interneurons (DIN) that wire spinocerebellar circuits. In mirror of reported electric field (EF)-driven cell migration, we found that DIN axons align in EFs, which was abolished by Na+/K+ ATPase inhibitor Ouabain and ATP1A3 knockdown. We recorded an embryonic trans-neural-epithelial potential generating EF whose pharmacological and surgical manipulation mimicked ATP1A3 knock-down-induced altered DIN axon pathfinding. Using DINs transplantation paradigm, we found that ATP1A3 is required cell-autonomously for EF-mediated long-range guidance. Finally, dominant-negative ATP1A3 mutation causing an early ATP1A3 childhood disease disrupts this fundamental developmental process, revealing unexpected pathogenic mechanisms.

developmental biology↗

bioRxiv2020

Dynamic chromatin accessibility landscape changes following interleukin-1 stimulation

Genome-wide methods for examining chromatin modification provide detailed information on regulatory regions of the genome. Dynamic modifications of chromatin allow rapid access of the gene regulatory machinery to condensed genomic regions facilitating subsequent gene expression. Inflammatory cytokine stimulation of cells can cause rapid gene expression changes through direct signalling pathway-mediated transcription factor activation and regulatory element binding. Here we used the Assay for Transposase Accessible Chromatin with high-throughput sequencing (ATAC-seq) to assess regions of the genome that are differentially accessible following treatment of cells with interleukin-1 (IL-1). We identified 126,483 open chromatin regions, with 241 regions significantly differentially accessible following stimulation, with 64 and 177 more or less accessible, respectively. These differentially accessible regions predominantly correspond to regions of the genome marked as enhancers. Motif searching identified an overrepresentation of a number of transcription factors, most notably RelA in the regions becoming more accessible, with analysis of ChIP-seq data confirmed RelA binding to these regions. A significant correlation in differential chromatin accessibility and gene expression was also observed. Functionality in regulating gene expression was confirmed using CRISPR/Cas9 genome-editing to delete regions for that became more accessible following stimulation in the genes MMP13, IKBKE and C1QTNF1. These same regions were also accessible for activation using a dCas9-transcriptional activator and showed enhancer activity in a cellular model. Together, these data describe and functionally validate a number of dynamically accessible chromatin regions involved in inflammatory signalling.

genomics↗

bioRxiv2019

Histone ChIP-Seq identifies differential enhancer usage during chondrogenesis as critical for defining cell-type specificity

Epigenetic mechanisms are known to regulate gene expression during chondrogenesis. In this study, we have characterised the epigenome during in vitro differentiation of human mesenchymal stem cells (hMSCs) into chondrocytes. Chromatin immunoprecipitation followed by next-generation sequencing (ChIP-seq) was used to assess a range of N-terminal post-transcriptional modifications (marks) to histone H3 lysines (H3K4me3, H3K4me1, H3K27ac, H3K27me3 and H3K36me3) in both hMSCs and differentiated chondrocytes. Chromatin states were characterised using histone ChIP-seq and cis-regulatory elements were identified in chondrocytes. Chondrocyte enhancers were associated with chondrogenesis related gene ontology (GO) terms. In silico analysis and integration of DNA methylation data with chondrogenesis chromatin states revealed that enhancers marked by histone marks H3K4me1 and H3K27ac were de-methylated during in vitro chondrogenesis. Similarity analysis between hMSC and chondrocyte chromatin states defined in this study with epigenomes of cell-types defined by the Roadmap Epigenomics project revealed that enhancers are more distinct between cell-types compared to other chromatin states. Motif analysis revealed that the transcription factor SOX9 is enriched in chondrocyte enhancers. Luciferase reporter assays confirmed that chondrocyte enhancers characterised in this study exhibited enhancer activity which may be modulated by inducing DNA methylation and SOX9 overexpression. Altogether, these integrated data illustrate the cross-talk between different epigenetic mechanisms during chondrocyte differentiation.\n\nSummaryHuman mesenchymal stem cells are able to differentiate into chondrocytes, the cell type found in cartilage, making them an accessible system to study gene regulation during this process. Epigenetic mechanisms such as histone modifications and DNA methylation together with transcription factor binding play a role in activating and repressing gene expression. In this study, we investigated the genome-wide histone modification changes during chondrocyte differentiation. Integration of this data with DNA methylation and SOX9 transcription factor ChIP-seq revealed epigenetic changes at gene enhancer elements. Regions of the genome that transition from non-enhancers to enhancers in chondrocytes are enriched for SOX9 transcription factor binding sites. Luciferase reporter assays revealed that enhancer activity may be modulated by manipulating DNA methylation and SOX9 expression. This study has defined important regulatory elements in chondrocytes which could serve as targets for future mechanistic studies.

genomics↗

bioRxiv2019

Spatial and temporal profiling of receptor membrane insertion controls commissural axon responses to midline repellents

Accurate perception of guidance cues is crucial for axonal pathfinding. During their initial navigation in the spinal cord, commissural axons are kept insensitive to midline repellents. Through yet unclear mechanisms acting during midline crossing in the floor plate, they switch on responsiveness to various repulsive signals, that establish a permanent midline barrier and propel the axons for exit. Whether these gains of response are coupled to occur in synchrony or rather are independently activated through signaling-specific programs is fully unknown. We set-up a paradigm for live imaging and super resolution analysis of guidance receptor dynamics during commissural growth cone navigation in chick and mouse embryos. We uncovered a remarkable program of delivery and allocation of receptors at the growth cone surface, generating receptor-specific spatial and temporal profiles. This reveals a mechanism whereby commissural growth cones can discriminate coincident repulsive signals that they functionalize at different time points of their navigation.

developmental biology↗

bioRxiv2018

How do your genetics compare to the world’s elite marathoners?

Pathway OME (Formerly Pathway Genomics, http://www.pathway.com) has identified a unique set of genetic traits associated with endurance, anxiety and likelihood of hamstring/Achilles injuries in an elite set of marathon runners. To date, this is the largest database of elite marathon athletes to ever have their exomes sequenced. Proprietary SportIQ Artificial Intelligence (AI) algorithms were developed and used to compare genetic traits in these 1,119 elite marathon runners to a normal population enabling us to develop a Marathon Runner profile to assist athletes in training to compete and achieve their athletic goals. Athletes whose genetic profiles differ significantly from the \"Marathon Runner\" profile will gain additional insights on the specific training necessary to prepare their muscles for the demanding conditions of long distance running.

genetics↗