Characterising open chromatin identifies novel cis-regulatory elements important for paraxial mesoderm formation and axis extension

Abstract

The development of multicellular organisms is exquisitely regulated through differential gene activity, which governs cell differentiation programs. However, many details of spatiotemporal control of gene regulation are still poorly understood. We used the accessibility of chick embryos to examine genome-wide signatures characterizing the progressive differentiation of paraxial mesoderm along the head-to-tail axis. Paraxial mesoderm becomes organized into repetitive units, termed somites, the hallmark of the segmented vertebrate body plan. New somite pairs form periodically as the axis extends at the posterior end. This process generates a developmental gradient within a single embryo, with anterior somites more advanced in their differentiation compared to posterior somites. Following somite formation, cell rearrangements generate compartments, comprising lineages of the musculoskeletal system, including cartilage of the vertebral column and ribs, and skeletal muscle cells of the trunk and limbs. To examine how paraxial mesoderm becomes regionalized and patterned to eventually generate these discrete lineages, we investigated dynamic changes of the transcriptome and of chromatin accessibility using RNA-seq and ATAC-seq across a spatiotemporal series along the embryonic axis. Footprint analysis uncovers differential coverage of binding sites for a number of key transcription factors known to be involved in axial patterning and differentiation, including HOX genes. Furthermore, associating accessible chromatin with nearby expressed genes identifies candidate cis-regulatory elements (CRE). As exemplars we use TCF15 and MEOX1, which are crucial for somite formation and differentiation, to experimentally validate CREs in vivo using fluorescent reporters. Time-lapse microscopy reveals CRE spatiotemporal activity and mutation analysis uncovers necessary upstream regulators. The CRE for MEOX1 is conserved and recognized in Xenopus. In addition, a human element is active in chicken.In vivo epigenome editing of TCF15 and MEOX1 CREs disrupts gene expression regulation and recapitulates phenotypic abnormalities of anterior-posterior axis extension.3

Engineered Peptide-Functionalized Hydrogels Modulate the RNA Transcriptome of Human Nucleus Pulposus Cells In Vitro

“…AFAP1L2 (also known as XB130), one of the most highly downregulated genes in this data set, codes for an adaptor protein that mediates intracellular signal transduction through the PI3K/AKT signaling pathway to regulate proliferation, motility and cell survival as well as having implications in inflammation through Src and IL-8 signaling 76,77 . LRRC17 is a known negative regulator of RANKL (receptor activator of NF-kappaB ligand) 78 that has also been shown to be differentially regulated in the context of both nucleus pulposus and chondrocytes, and was also downregulated by culture on the LMP gel 72,79 . Likewise, a marker of angiogenesis, ESM1, has been shown to be differentially regulated in this work and in a study that directed the differentiation of human pluripotent stem cells towards notochord- and nucleus pulposus-like populations 72 .…”

The transcripts of a gastrula-premarked enhancer prime posterior tissue development through cross-talk with morphogen effector

“…A substantial body of work on various enhancers have proposed mechanisms of enhancer function by regulating adjacent genes (53)(54)(55)(56)(57). Considering that p-Enh is located in the first intron of Cdx2 and crucial role of Cdx2 in body axis development (32,(58)(59)(60), we examined whether the expression of Cdx2 was affected in p-Enh-KO embryos.…”

Fine-tuning of the PAX-SIX-EYA-DACH network by multiple microRNAs controls embryo myogenesis

“…The biochemical interactions and complex feedback loops between PSED members have been dissected (Kumar, 2009). In paraxial mesoderm, the expression of PSED members (PAX1/6/7/9, SIX1/2, EYA2) is upregulated during the transition from presegmented mesoderm to epithelial somites (Mok et al, 2020). In addition, SIX1/4, EYA1/2/4 and DACH1/2 have been shown to initiate myogenesis through activation of the MRF genes, similar to PAX3 and PAX7 (Grifone et al, 2007;Heanue et al, 1999;Maroto et al, 1997;Relaix et al, 2013;Relaix et al, 2005;Spitz et al, 1998;Tajbakhsh et al, 1997;Tapscott, 2005).…”