Biology subjects

Ness, J.

Publications and source records attributed to Ness, J..

3 recordsLinked to original sources

bioRxiv2026

Genome architecture shapes the evolutionary origins of redundant enhancers in fly and mouse

Shadow enhancers are groups of DNA regulatory elements that control the same target gene and drive overlapping expression patterns. Large-scale surveys have found shadow enhancers control most developmental genes in animal genomes. The way in which shadow enhancers arise and how they subsequently evolve may further illuminate their regulatory logic and mechanisms of action. To investigate the evolutionary origins of shadow enhancers, we searched for sequence signatures of three birth mechanisms: duplication of existing enhancers, transposable element (TE) co-option, and TE-mediated splitting of ancestral regulatory elements in the Drosophila melanogaster and mouse genomes. Using 420 fly shadow enhancer sets and 9,051 mouse shadow enhancer sets, we found detectable duplication evidence in 18.3% of fly shadow enhancer sets and 33.9% of mouse sets. Duplication signatures were more frequent in larger shadow sets, suggesting that repeated duplication can expand regulatory landscapes. TE-derived enhancers were present in both species but were not enriched in shadow enhancers relative to single enhancers, suggesting that TE co-option contributes to enhancer evolution generally rather than preferentially generating redundant enhancer architectures. Finally, TE-mediated enhancer splitting was rare in both genomes. These results indicate that shadow enhancer birth is mechanistically heterogeneous, reflecting a mixture of duplication, TE co-option, and other mechanisms, whose contributions are shaped by genome architecture and evolutionary time. Therefore, we find that overlapping regulatory functions can arise through multiple evolutionary routes and that birth mechanisms can influence, but do not strictly determine, the regulatory logic of the resulting enhancer set.

genetics↗

bioRxiv2026

Novel Drosophila cis-regulatory elements can be uncovered by footprinting transcription factor binding sites in ATAC-seq data

Developmental processes depend on carefully coordinated gene expression. Expression is modulated by the binding of transcription factors (TFs) to cis-regulatory elements (CREs), like enhancers and promoters. Many computational and experimental approaches have been developed to find CREs, particularly enhancers, in the genome, each with strengths and caveats. Given the increasing availability of ATAC-seq data and methods to find TF binding therein, we hypothesized that we could use TF footprinting tools to find clusters of TF binding events within accessible chromatin that may act as CREs. Using Drosophila anterior-posterior patterning network as a test bed, we used a digital genomic footprinting tool (DGT), TOBIAS, on previously published early embryo ATAC-seq data to characterize the TF footprint landscape of 16 TFs essential for embryonic patterning. Even in this system, with its extensive enhancer annotation, most footprinted TF binding sites lie outside of known enhancers, with intergenic and intronic regions hosting the highest TF footprint count, albeit at low density. To find potential novel enhancers, we identified high-density TF footprint clusters that are highly conserved and overlap with active enhancer histone mark signals. Five high confidence candidates were selected for reporter assay validation and all five were found to drive spatially patterned expression in the embryo. This study shows that even in a highly characterized system, the analysis of footprinted TF binding sites in ATAC-seq data can uncover new regulatory regions and suggests this approach may be helpful in using existing ATAC-seq data to find novel CREs. ARTICLE SUMMARYGiven the increasing availability of ATAC-seq datasets, workflows to exploit the data to uncover new cis-regulatory elements (CREs), including enhancers, are valuable. Using early anterior-posterior patterning in the Drosophila embryo as a test case, we find that previously published transcription factor footprinting tools and ATAC-seq data can be analyzed to yield new candidate CREs. Experimental validation confirms the activity of selected candidate CREs, suggesting that existing data can be analyzed to find novel regulatory elements.

genomics↗

bioRxiv2019

μECoG Recordings Through a Thinned Skull

The studies described in this paper for the first time characterize the acute and chronic performance of optically transparent thin-film {micro}ECoG grids implanted on a thinned skull as both an electrophysiological complement to existing thinned skull preparation for optical recordings/manipulations, and a less invasive alternative to epidural or subdurally placed {micro}ECoG arrays. In a longitudinal chronic study, {micro}ECoG grids placed on top of a thinned skull maintain impedances comparable to epidurally placed {micro}ECoG grids that are stable for periods of at least one month. Optogenetic activation of cortex is also reliably demonstrated through the optically transparent ECoG grids acutely placed on the thinned skull. Finally, spatially distinct electrophysiological recordings were evident on {micro}ECoG electrodes placed on a thinned skull separated by 500-750{micro}m, as assessed by stimulation evoked responses using optogenetic activation of cortex as well as invasive and epidermal stimulation of the sciatic and median nerve at chronic time points. Neural signals were collected through a thinned skull in multiple species, demonstrating potential utility in neuroscience research applications such as in vivo imaging, optogenetics, calcium imaging, and neurovascular coupling.

neuroscience↗