Journal Article

Sub-kb Hi-C in D. melanogaster reveals conserved characteristics of TADs between insect and mammalian cells

Czajkowsky, Daniel M., Wang, Qi, Shao, Zhifeng, Sun, Qiu

2018

Overview

Topologically associating domains (TADs) are fundamental elements of the eukaryotic genomic structure. However, recent studies suggest that the insulating complexes, CTCF/cohesin, present at TAD borders in mammals are absent from those in Drosophila melanogaster , raising the possibility that border elements are not conserved among metazoans. Using in situ Hi-C with sub-kb resolution, here we show that the D . melanogaster genome is almost completely partitioned into >4000 TADs, nearly sevenfold more than previously identified. The overwhelming majority of these TADs are demarcated by the insulator complexes, BEAF-32/CP190, or BEAF-32/Chromator, indicating that these proteins may play an analogous role in flies as that of CTCF/cohesin in mammals. Moreover, extended regions previously thought to be unstructured are shown to consist of small contiguous TADs, a property also observed in mammals upon re-examination. Altogether, our work demonstrates that fundamental features associated with the higher-order folding of the genome are conserved from insects to mammals. Topologically associating domain (TAD) boundaries in flies seem to be different from those in mammals. Here, the authors use Hi-C with sub-kb resolution to identify about 4000 TADs in flies, most demarcated by the insulator complexes BEAF-32/CP190 or BEAF-32/Chromator like CTCF/cohesin in mammals.

• Publisher: Nature Publishing Group UK,Nature Publishing Group,Nature Portfolio
• Subject: 45/23 / 631/208/726 / 631/337/100/101 / 631/80/103 / Animals / Biological Evolution / CCCTC-Binding Factor - genetics / CCCTC-Binding Factor - metabolism / Cell Cycle Proteins - genetics / Cell Cycle Proteins - metabolism / Chromatin - chemistry / Chromatin - ultrastructure / Chromatin Assembly and Disassembly / Chromosomal Proteins, Non-Histone - genetics / Chromosomal Proteins, Non-Histone - metabolism / Chromosome Mapping - instrumentation / Chromosome Mapping - methods / Chromosomes, Insect - chemistry / Chromosomes, Insect - ultrastructure / Cohesin / Cohesins / DNA-Binding Proteins - genetics / DNA-Binding Proteins - metabolism / Drosophila melanogaster / Drosophila melanogaster - genetics / Drosophila melanogaster - ultrastructure / Drosophila Proteins - genetics / Drosophila Proteins - metabolism / Eye Proteins - genetics / Eye Proteins - metabolism / Gene Expression / Genome, Insect / Genomes / Humanities and Social Sciences / Humans / Insects / Mammalian cells / Mammals / Mammals - genetics / Microtubule-Associated Proteins - genetics / Microtubule-Associated Proteins - metabolism / Molecular Conformation / multidisciplinary / Nuclear Matrix-Associated Proteins - genetics / Nuclear Matrix-Associated Proteins - metabolism / Nuclear Proteins - genetics / Nuclear Proteins - metabolism / Proteins / Science / Science (multidisciplinary)