Biology subjects

Birkhoff, J. C.

Publications and source records attributed to Birkhoff, J. C..

2 recordsLinked to original sources

bioRxiv2022

Chromatin architecture and cis-regulatory landscape of the DACT2-SMOC2 locus in the developing synovial joint.

BackgroundSynovial joints form in several steps, starting with the formation of an interzone, a condensation of mesenchymal cells at the sites of prospective joints. Despite the identification of multiple factors essential for formation of interzone, little is known about the regulation of their spatio-temporal gene expression during that process in limb development. Here, we investigated the cis- regulatory landscape of the Wnt-modulator encoding genes DACT2 and SMOC2, both expressed in the forming joint interzone. ResultsMechanically collected interzone and phalange samples, respectively, from chick embryos were found to express acknowledged marker genes (GDF5 and MATN1), as well as DACT2 and SMOC2. Using Targeted Chromatin Capture (T2C) we characterized the 3D chromatin structure of a ~3.45 Mb-long region encompassing DACT2 and SMOC2, which revealed differences at sub-TAD level between interzones and phalange. We identified candidate enhancers (CEs) based on H3-histone marks (H3K427ac and H3K4me1) located in close proximity to the promoters of DACT2 and SMOC2, and further documented these CEs in a zebrafish enhancer assay. ConclusionsOur approach yields new insight into the regulation, in dynamic chromatin context, of two Wnt-signaling modulatory genes during synovial joint induction.

developmental biology↗

bioRxiv2021

Zeb2 DNA-binding sites in ES cell derived neuroprogenitor cells reveal autoregulation and align with neurodevelopmental knockout mouse and disease phenotypes.

Perturbation and mechanistic studies have shown that the DNA-binding transcription factor Zeb2 controls cell fate decision and differentiation and/or maturation in multiple cell lineages in embryos and after birth. In cultured embryonic stem cells (ESCs) Zeb2s strong upregulation is necessary for the exit from primed pluripotency and for entering general and neural differentiation. We edited mouse ESCs to produce epitope-tagged Zeb2 from one of its two endogenous alleles. Using ChIP-sequencing, we mapped 2,432 DNA-binding sites of Zeb2 in ESC-derived neuroprogenitor cells (NPCs). A new, major site maps promoter-proximal to Zeb2 itself, and its homozygous removal demonstrates that Zeb2 autoregulation is necessary to elicit proper Zeb2-dependent effects in NPC differentiation. We then cross-referenced all Zeb2 DNA-binding sites with transcriptome data from Zeb2 perturbations in ESCs, ventral forebrain in mouse embryos, and adult neurogenesis from the mouse forebrain V-SVZ. While the characteristics of these neurodevelopmental systems differ, we still find interesting overlaps. This contributes to explaining neurodevelopmental disorders caused by ZEB2 deficiency, including Mowat-Wilson Syndrome.

cell biology↗