Biology subjects

Harbour, J. W.

Publications and source records attributed to Harbour, J. W..

2 recordsLinked to original sources

bioRxiv2019

SparK: A Publication-quality NGS Visualization Tool

While there are sophisticated resources available for displaying NGS data, including the Integrative Genomics Viewer (IGV) and the UCSC genome browser, exporting regions and assembling figures for publication remains challenging. In particular, customizing track appearance and overlaying track replicates is a manual and time-consuming process. Here, we present SparK, a tool which auto-generates publication-ready, high-resolution, true vector graphic figures from any NGS-based tracks, including RNA-seq, ChIP-seq, and ATAC-seq. Novel functions of SparK include averaging of replicates, plotting standard deviation tracks, and highlighting significantly changed areas. SparK is written in Python 3, making it executable on any major OS platform. Using command line prompts to generate figures allows later changes to be made very easy. For instance, if the genomic region of the plot needs to be changed, or tracks need to be added or removed, the figure can easily be re-generated within seconds without the manual process of re-exporting and re-assembling everything. After plotting with SparK, changes to the output SVG vector graphic files are simple to make, including text, lines, and colors. SparK is publicly available on GitHub: https://github.com/harbourlab/SparK.

bioinformatics↗

bioRxiv2019

Fate of developmental mechanisms of myocardial plasticity in the postnatal heart

Whether the hearts organ-founding, progenitor cell gene regulatory networks (CPC-GRNs) are sustained after birth and can be therapeutically evoked for regeneration in response to disease, remains elusive. Here, we report a spatiotemporally resolved analysis of CPC-GRN deployment dynamics, through the pan-CPC-GRN gene Isl1. We show that the Isl1-CPC-GRNs that are deployed during early cardiogenesis and generate the cardiomyocyte majority from mesoderm, undergo programmed silencing through proteasome- and PRC2-mediated Isl1 repression, selectively in the arterial pole. In contrast, we identify a neural crest (CNC)-specific Wnt/{beta}-catenin/Isl1-CPC-GRN that is deployed through the venous pole during cardiac growth and partitioning, and contributes a minority of cardiomyocytes which, in turn, expand massively to build ~10% of the biventricular myocardium. These "dorsal CNCs" continue to sporadically generate cardiomyocytes throughout postnatal growth which, however, are non-proliferative, suggesting that partitioning-like, fetal proliferation signals could be therapeutically targeted to evoke clonal expansion capacity in postnatal CNC-cardiomyocytes for heart regeneration.

developmental biology↗