McCarthy, N. | Search bioRxiv

bioRxiv2021

Birth and delineation of the intestinal stem cell niche

Wnt and Rspondin (RSPO) signaling drives proliferation, and bone morphogenetic protein inhibitors (BMPi) impede differentiation, of intestinal stem cells (ISCs). Here we identify the adult mouse ISC niche as a complex, multi-layered structure that encompasses distinct mesenchymal and smooth muscle cell populations. Diverse sub-cryptal cells provide redundant supportive factors, with certain BMPi and the most potent Wnt co-factor, RSPO2, restricted to single cell types. Niche functions refine during a critical period of postnatal crypt morphogenesis, in part to oppose dense aggregation of BMP-expressing sub-epithelial myofibroblasts that promote epithelial differentiation. A specialized muscle layer, the muscularis mucosae, first appears during this period and supplements neighboring RSPO and BMPi sources. In vivo ablation of smooth muscle raises BMP activity and potently limits a pre-weaning burst of crypt fission. Thus, distinct and progressively specialized mesenchymal components together create the milieu required to propagate crypts during rapid organ growth and to sustain adult ISCs.

developmental biology↗

bioRxiv2020

Leveraging a WGS compression and indexing format with dynamic graph references to call structural variants.

We introduce a novel structural variant calling pipeline (BioGraph) that leverages a read compression and indexing format to discover alleles, assess their supporting coverage, and assign useful quality scores. To evaluate BioGraphs performance, we run five sequencing replicates of the individual HG002 through the BioGraph variant calling pipeline, as well as two other short-read sv-calling pipelines. BioGraph detects the GIAB benchmark SVs at a peak sensitivity of {approx}59% compared to {approx}42% sensitivity from the other pipelines. The overall precision of BioGraph is lower than other pipelines ({approx}81% and {approx}90%, respectively), however, adjusting for quality score, BioGraph calls were sensitive to a greater number of SV calls given the same false discovery rate compared to the other pipelines. Cumulatively {approx}77% of GIAB benchmark SVs are discovered by BioGraph in at least one replicate. After merging discovered calls and running BioGraph Coverage to create a squared-off project-level VCF, we find {approx}90% percent of discovered true positive alleles have at least 5x coverage in all replicates, thus increasing per-replicate recall of alleles having at least 1x coverage to {approx}76.9%.

bioinformatics↗