Biology subjects

Cox, T. C.

Publications and source records attributed to Cox, T. C..

4 recordsLinked to original sources

bioRxiv2024

Regulatory Functional Landscape of the HMX1 Gene for Normal Ear Development

Enhancers, through the combinatorial action of transcription factors (TFs), dictate both the spatial specificity and the levels of gene expression, and their aberrations can result in diseases. The association between HMX1 and its downstream enhancer with ear deformities has been previously documented. However, the pathogenic variations and molecular mechanisms underlying the bilateral constricted ear (BCE) malformations remain unclear. This study identifies a copy number variation (CNV) encompassing three enhancers that induces BCE. These enhancers, collectively termed the positional identity hierarchical enhancer cluster (PI-HEC), co-regulate spatiotemporal expression of the HMX1 gene in a coordinated and synergistic mode, each displaying unique activity-location-structure characteristics. A thorough exploration of this regulatory locus reveals that specific motif clusters within the PI-HEC variably modulate its activity and specificity, with the high mobility group (HMG) box combined with Coordinator and homeodomain (HD)-TFs notably influencing them respectively. Our findings based on various types of mouse models, reveal that both aberrant Hmx1 expression in the fibroblasts of the basal pinna, originating from neural crest cells, and ectopic expression in the distal pinna structures contribute to the abnormal development of the outer ear, including the cartilage, muscle, and epidermis tissues. This study deepens our understanding of mammalian ear morphogenesis and sheds light on the complexity of gene expression regulation by enhancers and specific sequence motifs.

developmental biology↗

bioRxiv2022

A distant global control region is essential for normal expression of anterior HOXA genes during mouse and human craniofacial development.

Defects in embryonic patterning resulting in craniofacial abnormalities account for approximately 1/3 of birth defects. The regulatory programs that build and shape the face require precisely controlled spatiotemporal gene expression, achieved through tissue-specific enhancers. Large regions with coactivation of enhancer elements and co-regulation of multiple genes, referred to as superenhancers, are important in determining cell identity and perturbation could result in developmental defects. Building upon a previously published epigenomic atlas of human embryonic craniofacial tissue in which we identified over 75,000 putative embryonic craniofacial enhancer regions, we have identified 531 superenhancer regions unique to embryonic craniofacial tissue, including 37 which fall in completely noncoding regions. To demonstrate the utility of this data for the understanding of craniofacial development and the etiology of craniofacial abnormalities, we focused on a craniofacial-specific superenhancer in a [~]600kb noncoding region located between NPVF and NFE2L3. This region harbors over 100 individual putative craniofacial enhancer segments and 7 in vivo validated craniofacial enhancers from primary craniofacial tissue as well as strong enhancer activation signatures in a culture model of cranial neural crest cell (CNCC) development. However, none of the directly adjacent genes have been implicated in neural crest specification, craniofacial development, or abnormalities. To identify potential regulatory targets of this superenhancer region, we characterized three-dimensional chromatin structure of this region in CNCCs and mouse embryonic craniofacial tissues using multiple techniques (4C-Seq, HiC). We identified long range interactions that exclude most intervening genes and specifically target the anterior portion of the HOXA gene cluster located 1.2 to 1.8 Mb away. We demonstrate the specificity of the enhancer region for regulation of anterior HOXA genes through CRISPR/Cas9 editing of human embryonic stem cells. Mice homozygous for deletion of the superenhancer confirm the specificity of the enhancer region and demonstrate that the region is essential for viability. At fetal stages homozygotes develop at the same rate as heterozygous and wild type littermates but die at P0-P1 and have high penetrance of orofacial clefts that phenocopy previously described Hoxa2-/- mice. Moreover, we identified a de novo deletion partially overlapping the superenhancer in a human fetus with severe craniofacial abnormalities. This evidence suggests we have identified a critical noncoding locus control region that specifically regulates anterior HOXA genes and whose deletion is likely pathogenic in human patients.

developmental biology↗

bioRxiv2022

Interferon receptor gene dosage determines multiple hallmarks of Down syndrome

Trisomy 21 causes Down syndrome, a condition characterized by cognitive impairments, immune dysregulation, and atypical morphogenesis. Using whole blood transcriptome analysis, we demonstrate that specific overexpression of four interferon receptors encoded on chromosome 21 associates with chronic interferon hyperactivity and systemic inflammation in Down syndrome. To define the contribution of interferon receptor overexpression to Down syndrome phenotypes, we used genome editing to correct interferon receptor gene dosage in mice carrying triplication of a large genomic region orthologous to human chromosome 21. Normalization of interferon receptor copy number attenuated lethal antiviral responses, prevented heart malformations, decreased developmental delays, improved cognition and normalized craniofacial anomalies. Therefore, interferon receptor gene dosage determines major hallmarks of Down syndrome, indicating that trisomy 21 elicits an interferonopathy amenable to therapeutic intervention. One-Sentence SummaryCorrection of interferon receptor gene dosage rescues multiple key phenotypes in a mouse model of trisomy 21.

genetics↗

bioRxiv2020

The E3 ligase TRIM1 ubiquitinates LRRK2 and controls its localization, degradation, and toxicity

Missense mutations in leucine-rich repeat kinase 2 (LRRK2) are the most common cause of familial Parkinsons Disease (PD); however, pathways regulating LRRK2 subcellular localization, function, and turnover are not fully defined. We performed quantitative mass spectrometry-based interactome studies to identify 48 novel LRRK2 interactors, including the microtubule-associated E3 ubiquitin ligase TRIM1 (Tripartite Motif Family 1). TRIM1 recruits LRRK2 to the microtubule cytoskeleton for ubiquitination and proteasomal degradation by binding LRRK2911-920, a nine amino acid segment within a flexible interdomain region (LRRK2853-981), which we designate the "Regulatory Loop" (RL). Phosphorylation of LRRK2 Ser910/Ser935 within LRRK2 RL serves as a molecular switch controlling LRRK2s association with cytoplasmic 14-3-3 versus microtubule-bound TRIM1. Association with TRIM1 modulates LRRK2s interaction with Rab29 and prevents upregulation of LRRK2 kinase activity by Rab29 in an E3-ligase-dependent manner. Finally, TRIM1 rescues neurite outgrowth deficits caused by PD-driving mutant LRRK2 G2019S. Our data suggest that TRIM1 is a critical regulator of LRRK2, controlling its degradation, localization, binding partners, kinase activity, and cytotoxicity.

molecular biology↗