Looking for Broken TAD Boundaries and Changes on DNA Interactions: Clinical Guide to 3D Chromatin Change Analysis in Complex Chromosomal Rearrangements and Chromothripsis

Kevin Yauy (1) , Vincent Gatinois (1) , Thomas Guignard (2, 1) , Satish Sati (3) , Jacques Puechberty (1) , Jean Baptiste Gaillard (1) , Anouck Schneider (1) , Franck Pellestor (1)

1 Cellules Souches, Plasticité Cellulaire, Médecine Régénératrice et Immunothérapies (IRMB)
2 Département de génétique médicale, maladies rares et médecine personnalisée [CHRU Montpellier]
3 IGH - Institut de génétique humaine

Apparition of next-generation sequencing (NGS) was a breakthrough on knowledge of genome structure. Bioinformatic tools are a key point to analyze this huge amount of data from NGS and characterize the three-dimensional organization of chromosomes. This chapter describes usage of different browsers to explore publicly available online data and to search for possible 3D chromatin changes involved during complex chromosomal rearrangements as chromothripsis. Their pathogenic impact on clinical phenotype and gene misexpression can also be evaluated with annotated databases.

Mots clés: Topologically associated domains; TAD boundaries; Enhancers; Bioinformatics; 3D genome; Genome browser; Chromothripsis

Domaines: Sciences du Vivant [q-bio]

Kevin Yauy, Vincent Gatinois, Thomas Guignard, Satish Sati, Jacques Puechberty, et al.. Looking for Broken TAD Boundaries and Changes on DNA Interactions: Clinical Guide to 3D Chromatin Change Analysis in Complex Chromosomal Rearrangements and Chromothripsis. Franck Pellestor. Chromothripsis. Methods in Molecular Biology, vol 1769., 1769, Humana Press, New York, NY, pp.353--361, 2018, Chromothripsis. Methods in Molecular Biology, Print ISBN 978-1-4939-7779-6 - Online ISBN 978-1-4939-7780-2. ⟨10.1007/978-1-4939-7780-2_22⟩. ⟨hal-02341326⟩