Jennifer A. Akiyama

Oct 9, 2024 | nature.com | Samuel Abassah-Oppong |Raquel Rouco |Cailyn H. Spurrell |Fabrice Darbellay |Jennifer A. Akiyama |Javier Lopez-Rios | +5 more

AbstractApproximately a quarter of the human genome consists of gene deserts, large regions devoid of genes often located adjacent to developmental genes and thought to contribute to their regulation. However, defining the regulatory functions embedded within these deserts is challenging due to their large size.

Mar 5, 2024 | nature.com | Sudha Rajderkar |Maria Amaral |Laura Cook |Fabrice Darbellay |Cailyn H. Spurrell |Marco Osterwalder | +9 more

AbstractThe genetic basis of human facial variation and craniofacial birth defects remains poorly understood. Distant-acting transcriptional enhancers control the fine-tuned spatiotemporal expression of genes during critical stages of craniofacial development. However, a lack of accurate maps of the genomic locations and cell type-resolved activities of craniofacial enhancers prevents their systematic exploration in human genetics studies.

Apr 20, 2023 | nature.com | Sudha Rajderkar |Iros Barozzi |Yiwen Zhu |Ana Alcaina Caro |Matthew Blow |Jennifer A. Akiyama | +3 more

ENCODE ChIP-seq data analysis and prioritization of TAD boundary deletion lociPreviously published chromosome conformation capture data was used for combined analyses and selection of TAD boundary deletion loci in this study, wherein TAD boundary calls were based on the maximum enrichment of CTCF at the TAD borders and their consistency across cell-types10. Over 3300 genome-wide annotated TAD boundaries5,10 were then ranked on a weighted score (see Supplementary Fig.