Independence of chromatin conformation and gene regulation during Drosophila dorsoventral patterning.

TitleIndependence of chromatin conformation and gene regulation during Drosophila dorsoventral patterning.
Publication TypeJournal Article
Year of Publication2021
AuthorsIng-Simmons, E, Vaid, R, Bing, XYang, Levine, M, Mannervik, M, Vaquerizas, JM
JournalNat Genet
Volume53
Issue4
Pagination487-499
Date Published2021/04/30
ISSN1546-1718
KeywordsAnimals, Animals, Genetically Modified, Body Patterning, Cell Differentiation, Cell Lineage, Chromatin, Drosophila melanogaster, Drosophila Proteins, Embryo, Nonmammalian, Enhancer Elements, Genetic, Female, Gene Expression Regulation, Developmental, Genome, High-Throughput Nucleotide Sequencing, Histones, Male, Organ Specificity, Promoter Regions, Genetic, Single-Cell Analysis, Transcription, Genetic
Abstract

The relationship between chromatin organization and gene regulation remains unclear. While disruption of chromatin domains and domain boundaries can lead to misexpression of developmental genes, acute depletion of regulators of genome organization has a relatively small effect on gene expression. It is therefore uncertain whether gene expression and chromatin state drive chromatin organization or whether changes in chromatin organization facilitate cell-type-specific activation of gene expression. Here, using the dorsoventral patterning of the Drosophila melanogaster embryo as a model system, we provide evidence for the independence of chromatin organization and dorsoventral gene expression. We define tissue-specific enhancers and link them to expression patterns using single-cell RNA-seq. Surprisingly, despite tissue-specific chromatin states and gene expression, chromatin organization is largely maintained across tissues. Our results indicate that tissue-specific chromatin conformation is not necessary for tissue-specific gene expression but rather acts as a scaffold facilitating gene expression when enhancers become active.

DOI10.1038/s41588-021-00799-x
Alternate JournalNat Genet
PubMed ID33795866
PubMed Central IDPMC8035076
Grant ListR35 GM118147 / GM / NIGMS NIH HHS / United States
MC_UP_1605/10 / MRC_ / Medical Research Council / United Kingdom