Biology subjects

Gilbertson, E. N.

Publications and source records attributed to Gilbertson, E. N..

5 recordsLinked to original sources

bioRxiv2024

Haplotype editing with CRISPR/Cas9 as a therapeutic approach for dominant-negative missense mutations in NEFL

Inactivation of disease alleles by allele-specific editing is a promising approach to treat dominant-negative genetic disorders, provided the causative gene is haplo-sufficient. We previously edited a dominant NEFL missense mutation with inactivating frameshifts and rescued disease-relevant phenotypes in induced pluripotent stem cell (iPSC)-derived motor neurons. However, a multitude of different NEFL missense mutations cause disease. Here, we addressed this challenge by targeting common single-nucleotide polymorphisms in cis with NEFL disease mutations for gene excision. We validated this haplotype editing approach for two different missense mutations and demonstrated its therapeutic potential in iPSC-motor neurons. Surprisingly, our analysis revealed that gene inversion, a frequent byproduct of excision editing, failed to reliably disrupt mutant allele expression. We deployed alternative strategies and novel molecular assays to increase therapeutic editing outcomes while maintaining specificity for the mutant allele. Finally, population genetics analysis demonstrated the power of haplotype editing to enable therapeutic development for the greatest number of patients. Our data serve as an important case study for many dominant genetic disorders amenable to this approach.

genetics↗

bioRxiv2023

Machine learning reveals the diversity of human 3D chromatin contact patterns

Understanding variation in chromatin contact patterns across human populations is critical for interpreting non-coding variants and their ultimate effects on gene expression and phenotypes. However, experimental determination of chromatin contacts at a population-scale is prohibitively expensive. To overcome this challenge, we develop and validate a machine learning method to quantify the diversity 3D chromatin contacts at 2 kilobase resolution from genome sequence alone. We then apply this approach to thousands of diverse modern humans and the inferred human-archaic hominin ancestral genome. While patterns of 3D contact divergence genome-wide are qualitatively similar to patterns of sequence divergence, we find that 3D divergence in local 1-megabase genomic windows does not follow sequence divergence. In particular, we identify 392 windows with significantly greater 3D divergence than expected from sequence. Moreover, 26% of genomic windows have rare 3D contact variation observed in a small number of individuals. Using in silico mutagenesis we find that most sequence changes to do not result in changes to 3D chromatin contacts. However in windows with substantial 3D divergence, just one or a few variants can lead to divergent 3D chromatin contacts without the individuals carrying those variants having high sequence divergence. In summary, inferring 3D chromatin contact maps across human populations reveals diverse contact patterns. We anticipate that these genetically diverse maps of 3D chromatin contact will provide a reference for future work on the function and evolution of 3D chromatin contact variation across human populations.

genomics↗

bioRxiv2023

Sequence-based machine learning reveals 3D genome differences between bonobos and chimpanzees

Phenotypic divergence between closely related species, including bonobos and chimpanzees (genus Pan), is largely driven by variation in gene regulation. The 3D structure of the genome mediates gene expression; however, genome folding differences in Pan are not well understood. Here, we apply machine learning to predict genome-wide 3D genome contact maps from DNA sequence for 56 bonobos and chimpanzees, encompassing all five extant lineages. We use a pairwise approach to estimate 3D divergence between individuals from the resulting contact maps in 4,420 1 Mb genomic windows. While most pairs were similar,[~] 17% were predicted to be substantially divergent in genome folding. The most dissimilar maps were largely driven by single individuals with rare variants that pro-duce unique 3D genome folding in a region. We also identified 89 genomic windows where bonobo and chimpanzee contact maps substantially diverged, including several windows harboring genes associated with traits implicated in Pan phenotypic divergence. We used in silico mutagenesis to identify 51 3D-modifying variants in these bonobo-chimpanzee diver-gent windows, finding that 34 or 66.67% induce genome folding changes via CTCF binding motif disruption. Our results reveal 3D genome variation at the population-level and identify genomic regions where changes in 3D folding may contribute to phenotypic differences in our closest living relatives.

genomics↗

bioRxiv2022

Reconstructing the 3D genome organization of Neanderthals reveals that chromatin folding shaped phenotypic and sequence divergence

Changes in gene regulation were a major driver of the divergence of archaic hominins (AHs)--Neanderthals and Denisovans--and modern humans (MHs). The three-dimensional (3D) folding of the genome is critical for regulating gene expression; however, its role in recent human evolution has not been explored because the degradation of ancient samples does not permit experimental determination of AH 3D genome folding. To fill this gap, we apply novel deep learning methods for inferring 3D genome organization from DNA sequence to Neanderthal, Denisovan, and diverse MH genomes. Using the resulting 3D contact maps across the genome, we identify 167 distinct regions with diverged 3D genome organization between AHs and MHs. We show that these 3D-diverged loci are enriched for genes related to the function and morphology of the eye, supra-orbital ridges, hair, lungs, immune response, and cognition. Despite these specific diverged loci, the 3D genome of AHs and MHs is more similar than expected based on sequence divergence, suggesting that the pressure to maintain 3D genome organization constrained hominin sequence evolution. We also find that 3D genome organization constrained the landscape of AH ancestry in MHs today: regions more tolerant of 3D variation are enriched for introgression in modern Eurasians. Finally, we identify loci where modern Eurasians have inherited novel 3D genome folding patterns from AH ancestors and validate folding differences in a high-frequency locus using Hi-C, revealing a putative molecular mechanism for phenotypes associated with archaic introgression. In summary, our application of deep learning to predict archaic 3D genome organization illustrates the potential of inferring molecular phenotypes from ancient DNA to reveal previously unobservable biological differences.

evolutionary biology↗

bioRxiv2019

Evidence for rapid phenotypic and behavioral change in a recently established cavefish population

Substantial morphological and behavioral shifts often accompany rapid environmental change, yet, little is known about the early stages of cave colonization. Relative to surface streams, caves are extreme environments with perpetual darkness and low nutrient availability. The Mexican tetra (Astyanax mexicanus), has repeatedly colonized caves throughout Mexico, suggesting an ability to adapt to these conditions. Here, we survey for phenotypic and behavioral differences between a surface population and a cave population of A. mexicanus that has recently colonized Honey Creek Cave, Comal County, Texas, likely within the last century. We found that fish from Honey Creek Cave and fish from Honey Creek surface populations differ significantly in morphological traits including length, coloration, body condition, eye size, and dorsal fin placement. Cavefish also exhibit an increased number of superficial neuromasts relative to surface fish. Behaviorally, cavefish consume fewer worms when trials are performed in both lighted and darkened conditions. Cavefish are more aggressive than surface fish and exhibit fewer behaviors associated with stress. Further in contrast to surface fish, cavefish prefer the edges to the center of an arena and are qualitatively more likely to investigate a novel object placed in the tank. While cavefish and surface fish were wild-caught and developmental environment likely play a role in shaping these differences, our work demonstrates morphological and behavioral shifts for Texas cavefish and offers an exciting opportunity for future work to explore the genetic and environmental contributions to early cave colonization.

animal behavior and cognition↗