ONLINE RESOURCE

Mapping the invisible chromatin transactions of prophase chromosome remodelling

Itaru Samejima, Christos Spanos, Kumiko Samejima, Juri Rappsilber, Georg Kustatscher and William C. Earnshaw

Molecular Cell, 2022, Feb 3;82(3):696-708 (Open Access)

This is an R Shiny app designed to interactively explore the data presented in our manuscript. For best results it should be viewed on a laptop or PC, though an iPad can function in horizontal mode.

SUMMARY. We have used a combination of chemical genetics, chromatin proteomics and imaging to map the earliest chromatin transactions during vertebrate cell entry into mitosis. Chicken DT40 Cdk1as cells undergo synchronous mitotic entry within 15 minutes following release from a 1NM-PP1-induced arrest in late G2. In addition to changes in chromatin association with nuclear pores and the nuclear envelope, earliest prophase is dominated by changes in the association of ribonucleoproteins with chromatin, particularly in the nucleolus, where pre-rRNA processing factors leave chromatin significantly before RNA polymerase I. Nuclear envelope barrier function is lost early in prophase and cytoplasmic proteins begin to accumulate on the chromatin. As a result, outer kinetochore assembly appears complete by nuclear envelope breakdown (NEBD). Most interphase chromatin proteins remain associated with chromatin until NEBD, after which their levels drop sharply. This website presents an interactive proteomic map of these chromatin transactions during mitotic entry.


A brief introduction: How to use this app


The purpose of this app is to enable users to analyse our data on chromatin transactions during mitotic entry in a straightforward manner. There are two main options: One can search for some proteins of interest and find out how their chromatin association changes as cell enter mitotis. Alternatively, it is possible to interactively analyse the results of our hierarchical clustering analysis. Watch the brief video below to find out more, and please have a look at our manuscript for additional information.




Additional plotting options:

Info How to find your proteins of interest

Use the search mask in the top left to find your proteins of interest and display their behaviour during the mitotic time course. You can search by gene name, protein name or UniProt ID. Choose a display colour and click `Show selected`. Alternatively, it is also possible to click on a protein (or select groups of proteins) in the t-SNE map. Note that gene and protein names are displayed when your mouse hovers over these points. You can also zoom into these plots and download images by clicking on the - - icon. Our database currently covers ~2,500 chicken chromatin proteins, so it is possible that your protein of interest may not have been detected in our experiments. For more information, please have a look at our instruction video in the Help section.

Set cluster granularity

Select clusters to display

Gene Ontology enrichment in selected clusters

Proteins belonging to selected clusters (click to show proteins in plot)

Info How to explore this hierarchical clustering analysis of the proteomics timecourse

Firstly, select the `granularity` of the clustering analysis. This setting corresponds to the height at which the clustering dendrogram is cut. You can choose to display few, but relatively large clusters, many small clusters, or something in between. Secondly, use the dropdown menu options to select which clusters to display. Clusters can be selected in two ways: by their ID or through the proteins that they contain. Once selected, clusters will be shown on the t-SNE map and the corresponding line plots. The GO terms enriched in the selected clusters will be shown in the table at the bottom left, whereas the proteins assigned to each cluster can be found in the bottom right table. Click on those proteins to make them appear in the line plots. You can also zoom into these plots and download images by clicking on the - - icon. For more information, please have a look at our instruction video in the Help section.

Download section

Click on the buttons below to download the data used to populate this app


Chromatin proteomics data (incl. cluster assignments)

Gene Ontology enrichment analysis of clusters