Articles by Biola-Maria Javierre in JoVE
Promoter Capture Hi-C: High-resolution, Genome-wide Profiling of Promoter Interactions Stefan Schoenfelder*1, Biola-Maria Javierre*1,2, Mayra Furlan-Magaril1,3, Steven W. Wingett1,4, Peter Fraser1,5 1Nuclear Dynamics Programme, The Babraham Institute, Babraham Research Campus, 2IJC Building, Campus ICO-Germans Trias i Pujol, Josep Carreras Leukemia Research Institute, 3Departamento de Genética Molecular, Instituto de Fisiología Celular, Universidad Nacional Autónoma de México, 4Bioinformatics Group, The Babraham Institute, Babraham Research Campus, 5Department of Biological Science, Florida State University DNA regulatory elements, such as enhancers, control gene expression by physically contacting target gene promoters, often through long-range chromosomal interactions spanning large genomic distances. Promoter Capture Hi-C (PCHi-C) identifies significant interactions between promoters and distal regions, enabling the assignment of potential regulatory sequences to their target genes.
Other articles by Biola-Maria Javierre on PubMed
Chromosome Contacts in Activated T Cells Identify Autoimmune Disease Candidate Genes Genome Biology. | Pubmed ID: 28870212 Autoimmune disease-associated variants are preferentially found in regulatory regions in immune cells, particularly CD4 T cells. Linking such regulatory regions to gene promoters in disease-relevant cell contexts facilitates identification of candidate disease genes.
The Pluripotent Regulatory Circuitry Connecting Promoters to Their Long-range Interacting Elements Genome Research. Apr, 2015 | Pubmed ID: 25752748 The mammalian genome harbors up to one million regulatory elements often located at great distances from their target genes. Long-range elements control genes through physical contact with promoters and can be recognized by the presence of specific histone modifications and transcription factor binding. Linking regulatory elements to specific promoters genome-wide is currently impeded by the limited resolution of high-throughput chromatin interaction assays. Here we apply a sequence capture approach to enrich Hi-C libraries for >22,000 annotated mouse promoters to identify statistically significant, long-range interactions at restriction fragment resolution, assigning long-range interacting elements to their target genes genome-wide in embryonic stem cells and fetal liver cells. The distal sites contacting active genes are enriched in active histone modifications and transcription factor occupancy, whereas inactive genes contact distal sites with repressive histone marks, demonstrating the regulatory potential of the distal elements identified. Furthermore, we find that coregulated genes cluster nonrandomly in spatial interaction networks correlated with their biological function and expression level. Interestingly, we find the strongest gene clustering in ES cells between transcription factor genes that control key developmental processes in embryogenesis. The results provide the first genome-wide catalog linking gene promoters to their long-range interacting elements and highlight the complex spatial regulatory circuitry controlling mammalian gene expression.