Ovcharenko Group Wiki

Transcriptional regulation (Nature review)

• https://www.nature.com/articles/s41586-019-1517-4

Enhancer mutations

• a regulatory mutation of a TF with a hair pigmentation phenotype; F. Imsland et al., Nature Genetics, 48, 152-158, (2016)

Scoring enhancer mutations

• (better than CADD?) I.Ionita-Laza A spectral approach integrating functional genomic annotations for coding and noncoding variants, Nature Genetics, 48, 214-220, (2016)

Noncoding mutations in Cancer

• X. Zhang et al., Identification of focally amplified lineage-specific super-enhancers in human epithelial cancers, Nature Genetics, 48, 176-182, (2016)
• A.Fujimoto et al., Whole-genome mutational landscape and characterization of noncoding and structural mutations in liver cancer, Nature Genetics 48, 500-509 (2016)

Regulatory landscape

• M.M.Pradeepa et al., Histone H3 globular domain acetylation identifies a new class of enhancers, Nature Genetics, 48, 681-686 (2016)
• R.D.Acemel et al., A single three-dimensional chromatin compartment in amphioxus indicates a stepwise evolution of vertebrate Hox bimodal regulation, Nature Genetics, 48, 336-341 (2016)
• S.Whalen et al., Enhancer-promoter interactions are encoded by complex genomic signatures on looping chromatin, Nature Genetics, (2016)

Enhancer, evolution & development

• Lan and Pritchard, Coregulation of tandem duplicate genes slows evolution of subfunctionalization in mammals, Science 352(6288), 1009-1013 (2016)
• Y Yao et al., Cis-regulatory architecture of a brain signaling center predates the origin of chordates, Nature Genetics 48, 575-580 (2016)
• Taskiran et al., Cell-type-directed design of synthetic enhancers, Nature, (2023)
• Kim et al., DNA-guided transcription factor cooperativity shapes face and limb mesenchyme, Cell, 2023

Enhancer (bidirectional) transcription

• DN Bagchi et al., The Determinants of Directionality in Transcriptional Initiation, Trends in Genetics 32, 322-333 (2016)