Gene Regulatory Networks in human, marmoset and mouse
This tab provides interactive tools to explore GRNs across species
1. Cell label plots
You can pin the plots to keep them visible while scrolling down the page to compare the gene expression and CRE accessibility between the different categories in human, marmoset, and mouse.
Human
Marmoset
Mouse
2. TF to target gene table
- First, select a transcription factor (TF)-target gene pair by clicking on a row in the table below.
- This will display the expression of the TF and the target gene in human and the expression of 1:1 orthologous TFs and target genes marmoset and mouse.
- Additionally, it will create a second table below with the associated CREs connecting the TF to the target gene in human.
3. TF expression plots
Human
Marmoset
Mouse
4. Target gene expression plots
Human
Marmoset
Mouse
5. CRE table
After selecting a TF-target gene pair in the table above, this table displays all CREs mediating TF-target gene interaction in the human GRN. You can select a row in the table below to plot the accessibility of the chosen CRE in human and its 1:1 orthologous CREs in marmoset and mouse.
6. CRE accessibility plots
Human
Marmoset
Mouse
Inferred evolutionary histories of human CREs
This tab enables exploration of the evolutionary histories of human CREs inferred from DeepCeREvo predictions across orthologous regions in 228 mammalian species.
Choose one or multiple NMFs from the dropdown and a CRE from the table below. Then press the button below the table to show the prediction.
Human CREs are classified into the following evolutionary categories:
| ET | Eutherian-conserved |
| BE | Boreoeutheria-shared |
| EG | Euarchontoglires-shared |
| PR | Primate-shared |
| ANT | Anthropoidea (simian)-shared |
| CAT | Catarrhini-shared |
| HOM | Hominoidea (Great Ape)-shared |
| HUM | Human-specific |
To save the plot, right click on it and select 'Save image as...'.
Information & Data
Reference
Ioannis Sarropoulos, Mari Sepp, Tetsuya Yamada, Philipp Schäfer, Nils Trost, Julia Schmidt, Céline Schneider, Charis Drummer, Sophie Mißbach, Ibrahim I. Taskiran, Nikolai Hecker, Carmen Bravo González-Blas, Niklas Kempynck, Robert Frömel, Piyush Joshi, Evgeny Leushkin, Frederik Arnskötter, Kevin Leiss, Konstantin Okonechnikov, Steven Lisgo, Miklós Palkovits, Svante Pääbo, Margarida Cardoso-Moreira, Lena M. Kutscher, Rüdiger Behr, Stefan M. Pfister, Stein Aerts and Henrik Kaessmann. The evolution of gene regulation in mammalian cerebellum development.
Gene regulatory shifts are considered major drivers of evolutionary innovations, including the cerebellum’s expansion during human evolution, yet they remain largely unexplored. In this study, we combined single-nucleus measurements of gene expression and chromatin accessibility from six mammals (human, bonobo, macaque, marmoset, mouse, and opossum) to uncover conserved and diverged regulatory networks in cerebellum development. We identified core regulators of cell identity and developed sequence-based models that revealed conserved regulatory codes. By predicting chromatin accessibility across 240 mammalian species, we reconstructed the evolutionary histories of human cis-regulatory elements, identifying sets associated with positive selection and gene expression changes, including the recent gain of THRB expression in cerebellar progenitor cells. Collectively, our work reveals the shared and mammalian lineage-specific regulatory programs governing cerebellum development.
Data
Raw sequencing data is available at heiData: https://heidata.uni-heidelberg.de/previewurl.xhtml?token=bea0c1aa-3110-4f3a-a98c-f10e65a407d0 (This URL will be updated upon publication).