Xenopus tropicalis Genome Re-Scaffolding and Re-Annotation Reach the Resolution Required for In Vivo ChIA-PET Analysis

• Published in: PloS one Vol. 10; no. 9; p. e0137526
• Main Authors: Buisine, Nicolas, Ruan, Xiaoan, Bilesimo, Patrice, Grimaldi, Alexis, Alfama, Gladys, Ariyaratne, Pramila, Mulawadi, Fabianus, Chen, Jieqi, Sung, Wing-Kin, Liu, Edison T., Demeneix, Barbara A., Ruan, Yijun, Sachs, Laurent M.
• Format: Journal Article
• Language: English
• Published: United States Public Library of Science 08.09.2015; Public Library of Science (PLoS)
• Subjects: Analysis; Animals; Annotations; Assembly; Binding sites; Bioinformatics; Chromatin - genetics; Consortia; Data processing; Deoxyribonucleic acid; Developmental biology; DNA; DNA methylation; DNA sequencing; Gene expression; Gene Expression Regulation; Gene regulation; Gene Regulatory Networks - genetics; Gene sequencing; Genes; Genetic aspects; Genetics; Genome; Genomes; Genomics; Humans; Identification; Laboratories; Methods; Molecular Sequence Annotation; Networks; Physiological aspects; Physiological responses; Respiration; Ribonucleic acid; RNA; RNA - genetics; RNA polymerase; RNA, Messenger - genetics; Scaffolding; Sequence Analysis, DNA; Thyroid; Thyroid Hormones - genetics; Transcription; Transcription factors; Transcriptome - genetics; Workflow; Xenopus; Xenopus - genetics; France; Singapore; United States > US; Connecticut

Genome-wide functional analyses require high-resolution genome assembly and annotation. We applied ChIA-PET to analyze gene regulatory networks, including 3D chromosome interactions, underlying thyroid hormone (TH) signaling in the frog Xenopus tropicalis. As the available versions of Xenopus tropic...