Overview

The human genome is organized in functional compartments that align with the temporal order of DNA replication (Replication Timing). This 3D genome organization is key for gene regulation and its alterations are associated with diseases.

Research in the Rivera-Mulia lab  focusses in understanding how DNA replication timing and large-scale chromosome organization are regulated, maintained in distinct cell types and remodeled during development. We also investigate how alterations in nuclear architecture disrupt gene function in disease. 

To address these questions, we exploit genome-wide characterization of nuclear architecture, replication timing and gene expression as well as computational approaches to construct integrative models of nuclear function.

Pulse-chase-pulse labeling with thymidine analog‎s reveals early and late replication nuclear compartments.

Replication Timing (RT) and 3D genome organization

DNA replication occurs in a defined temporal order known as the replication timing program (RT).

Each chromosome of the human genome is organized into functional domains that align with the RT. These domains  segregate to  distinct nuclear compartments according to their time of replication. Early replicating domains are located at the nuclear interior, while late replicating domains are enriched at the nuclear and nucleolar periphery. 

RT and the spatial organization of the genome are also coordinated with gene expression activity. Genes located within late replicating domains are usually repressed, while highly active genes are located in early replicating domains.

Genome organization, RT and gene regulation in the nucleus. Early replicating compartments are form by active chromatin where genes can be highly expressed. In contrast, late replicating compartments contain more repressive chromatin.

Modeling development with Human Pluripotent Stem Cells

During development, all cell types  differentiate from each other while they acquire specific gene expression programs. RT is also cell type-specific and is remodeled during development in coordination with transcriptional changes and nuclear re-localization.

In our lab, we exploit human embryonic stem cells (hESCs) and optimized differentiation systems to model development and track changes in RT, gene expression and 3D genome organization.


Differentiation systems of human embryonic stem cells (hESCs) towards distinct lineages of endoderm, mesoderm, ectoderm, and neural crest development.

Funding