Biology subjects

Cotney, J.

Publications and source records attributed to Cotney, J..

4 recordsLinked to original sources

bioRxiv2018

A bipartite boundary element restricts UBE3A imprinting to mature neurons.

Angelman syndrome (AS) is a severe neurodevelopmental disorder caused by the loss of function from the maternal allele of UBE3A, a gene encoding an E3 ubiquitin ligase. UBE3A is only expressed from the maternally-inherited allele in mature human neurons due to tissue-specific genomic imprinting. Imprinted expression of UBE3A is restricted to neurons by expression of UBE3A antisense transcript (UBE3A-ATS) from the paternally-inherited allele, which silences the paternal allele of UBE3A in cis. However, the mechanism restricting UBE3A-ATS expression and UBE3A imprinting to neurons is not understood. We used CRISPR/Cas9-mediated genome editing to functionally define a bipartite boundary element critical for neuron-specific expression of UBE3A-ATS in humans. Removal of this element led to upregulation of UBE3A-ATS without repressing paternal UBE3A. However, increasing expression of UBE3A-ATS in the absence of the boundary element resulted in full repression of paternal UBE3A, demonstrating that UBE3A imprinting requires both the loss of function from the boundary element as well as upregulation of UBE3A-ATS. These results suggest that manipulation of the competition between UBE3A-ATS and UBE3A may provide a potential therapeutic approach for AS.\n\nSIGNIFICANCE STATEMENTAngelman syndrome is a neurodevelopmental disorder caused by loss of function from the maternal allele of UBE3A, an imprinted gene. The paternal allele of UBE3A is silenced by a long, non-coding antisense transcript in mature neurons. We have identified a boundary element that stops the transcription of the antisense transcript in human pluripotent stem cells, and thus restricts UBE3A imprinted expression to neurons. We further determined that UBE3A imprinting requires both the loss of the boundary function and sufficient expression of the antisense transcript to silence paternal UBE3A. These findings provide essential details about the mechanisms of UBE3A imprinting that may suggest additional therapeutic approaches for Angelman syndrome.

genetics↗

bioRxiv2018

The marked diversity of unique cortical enhancers enables the generation of neuron-specific tools by Enhancer-Driven Gene Expression (EDGE)

Understanding neural circuit function requires individually addressing their component parts: specific neuronal cell types. However, not only do the precise genetic mechanisms specifying neuronal cell types remain obscure, access to these neuronal cell types by transgenic techniques also remains elusive. While most genes are expressed in the brain, the vast majority are expressed in many different kinds of neurons, suggesting that promoters alone are not sufficiently specific to distinguish cell types. However, there are orders of magnitude more distal genetic cis-regulatory elements controlling transcription (i.e. enhancers), so we screened for enhancer activity in microdissected samples of mouse cortical subregions. This identified thousands of novel putative enhancers, many unique to particular cortical subregions. Pronuclear injection of expression constructs containing such region-specific enhancers resulted in transgenic lines driving expression in distinct sets of cells specifically in the targeted cortical subregions, even though the parent genes promoter was relatively nonspecific. These data showcase the promise of utilizing the genetic mechanisms underlying the specification of diverse neuronal cell types for the development of genetic tools potentially capable of targeting any neuronal circuit of interest, an approach we call Enhancer-Driven Gene Expression (EDGE).\n\nHighlightsO_LIEnhancer ChIP-seq of cortical subregions reveals 59372 putative enhancers.\nC_LIO_LI3740 of these are specific to particular cortical subregions.\nC_LIO_LIThis reflects the remarkable anatomical diversity of the adult cortex.\nC_LIO_LIUnique enhancers provide a means to make targeted cell-type specific genetic tools.\nC_LI

neuroscience↗

bioRxiv2017

Evidence against tetrapod-wide digit identities and for a limited frame shift in bird wings

In crown group tetrapods, individual digits are homologized in relation to a pentadactyl ground plan. However, testing hypotheses of digit homology is challenging because it is unclear whether digits develop with distinct and conserved gene regulatory states. Here we show dramatic evolutionary dynamism in the gene expression profiles of digits, challenging the notion that five digit identities are conserved across amniotes. Transcriptomics of developing limbs shows diversity in the patterns of genetic differentiation of digits, although the anterior-most digit of the pentadactyl limb has a unique, conserved expression profile. Further, we identify a core set of transcription factors that are differentially expressed among the digits of amniote limbs; their spatial expression domains, however, vary between species. In light of these results, we reevaluate the frame shift hypothesis of avian wing evolution and conclude that only the identity of the anterior-most digit has shifted position, suggesting a 1,3,4 digit identity in the bird wing.

evolutionary biology↗

bioRxiv2017

High Resolution Epigenomic Atlas of Early Human Craniofacial Development

Defects in embryonic patterning resulting in craniofacial abnormalities are common birth defects affecting up to 1 in 500 live births worldwide, and are mostly non-syndromic. The regulatory programs that build and shape the craniofacial complex are thought to be controlled by information encoded in the genome between genes and within intronic sequences. Early stages of human craniofacial development have not been interrogated with modern functional genomics techniques, preventing systematic analysis of genetic associations with craniofacial-specific regulatory sequences. Here we describe a comprehensive resource of craniofacial epigenomic annotations and systematic, integrative analysis with a variety of human tissues and cell types. We identified thousands of novel craniofacial enhancers and provide easily accessible genome annotations for craniofacial researchers and clinicians. We demonstrate the utility of our data to find likely causal variants for craniofacial abnormalities and identify a large enhancer cluster that interacts with HOXA genes during craniofacial development.

genomics↗