## Overview

Model of chromosome organization in interphase, summarizing the main results presented in this paper. Large, discrete chromosomal domains are dynamically associated with the nuclear lamina (NL), in a manner that is dependent on the cell type (Fig. 7, Peric-Hupkes, et al. 2010).

The three-dimensional organization of chromosomes within the nucleus and its dynamics during differentiation are largely unknown. To visualize this process in molecular detail, high-resolution maps of genome-nuclear lamina interactions during subsequent differentiation of mouse embryonic stem cells were generated via lineage-committed neural precursor (or, neural progenitor) cells into terminally differentiated astrocytes. In addition, genome-nuclear lamina interactions for mouse embryonic fibroblasts were profiled.

This revealed that a basal chromosome architecture present in embryonic stem cells is cumulatively altered at hundreds of sites during lineage commitment and subsequent terminal differentiation. This remodeling involves both individual transcription units and multi-gene regions, and affects many genes that determine cellular identity. Often, genes that move away from the lamina are concomitantly activated; many others however remain inactive yet become unlocked for activation in a next differentiation step. These results suggest that lamina-genome interactions are widely involved in the control of gene expression programs during lineage commitment and terminal differentiation.

### NKI mouse LaminB1 ESC track

The mouse LaminB1 ESC track shows a high resolution map of the interaction sites of the entire genome with Lamin B1 (a key NL component) in mouse embryonic stem cells.

### NKI mouse LaminB1 NPC track

The mouse LaminB1 NPC track shows a high resolution map of the interaction sites of the entire genome with Lamin B1 (a key NL component) in mouse neural progenitor cells.

### NKI mouse LaminB1 AC track

The mouse LaminB1 AC track shows a high resolution map of the interaction sites of the entire genome with Lamin B1 (a key NL component) in mouse astrocytes.

### NKI mouse LaminB1 MEF track

The mouse LaminB1 MEF track shows a high resolution map of the interaction sites of the entire genome with Lamin B1 (a key NL component) in mouse embryonic fibroblasts.

## Display Conventions and Configuration

The LaminB1 wiggle tracks values range from -6.00 to 4.93. The default vertical viewing range for the wiggle track was chosen from -1.5 to 1.5 because this is roughly +/- 1.5 standard deviations.

For an example region see genomic location: chr14:92,000 ,000-96,000,000 (Fig 3A, Peric-Hupkes, Meuleman et al., 2010).

## Methods

The DamID technique was applied to generate high-resolution maps of NL interactions for the entire mouse genome. DamID is based on targeted adenine methylation of DNA sequences that interact in vivo with a protein of interest.

DamID was performed as described (Peric-Hupkes, et al. 2010). In short, a fusion protein consisting of Escherichia coli DNA adenine methyltransferase (Dam) fused to mouse LaminB1 was introduced into cultured cells. Dam methylates adenines in the sequence GATC, a mark absent in most eukaryotes. Here, the LaminB1-Dam fusion protein incorporates in the nuclear lamina, as verified by immunofluorescence staining. Hence, the sequences near the nuclear lamina are marked with a unique methylation tag. The adenine methylation pattern was detected with genomic tiling arrays. Unfused Dam was used as a reference. The data shown are the log2-ratio of LaminB1-Dam fusion protein over Dam-only.

Sample labelling and hybridizations were performed as described (Peric-Hupkes, et al. 2010), on a custom-designed Nimblegen HD2 array, with a median probe spacing of ~1kbp. All probes recognize unique (non-repetitive) sequences. The raw data was log2 transformed and loess normalized, followed by quantile normalization across the single channel data of all hybridizations. Replicate arrays were averaged.

## Verification

The data are based on two independent biological replicates for each cell type, performed on separate days. Fluorescence in situ hybridization microscopy confirmed that most of the LaminB1 associated regions are preferentially located at the nuclear periphery. The array platform, the raw and normalized data have been deposited at the NCBI Gene Expression Omnibus (GEO) under accession number GSE17051.

## Credits

The data for this track were generated by Daan Peric-Hupkes, Wouter Meuleman and Bas van Steensel at the Van Steensel Lab, Netherlands Cancer Institute.

## References

Peric-Hupkes D, Meuleman W, Pagie L, Bruggeman SWM, Solovei I, Brugman W, Gräf S, Flicek P, Kerkhoven RM, van Lohuizen M et al. Molecular Maps of the Reorganization of Genome-Nuclear Lamina Interactions during Differentiation. Molecular Cell. 2010 May 28;38(4):603-13.