Spatial compartmentalization at the nuclear periphery characterized by genome-wide mapping

Feinan Wu,Jie Yao

doi:10.1186/1471-2164-14-591

Abstract

BackgroundHow gene positioning to the nuclear periphery regulates transcription remains largely unclear. By cell imaging, we have previously observed the differential compartmentalization of transcription factors and histone modifications at the nuclear periphery in mouse C2C12 myoblasts. Here, we aim to identify DNA sequences associated with the nuclear lamina (NL) and examine this compartmentalization at the genome-wide level.ResultsWe have integrated high throughput DNA sequencing into the DNA adenine methyltransferase identification (DamID) assay, and have identified ~15, 000 sequencing-based Lamina-Associated Domains (sLADs) in mouse 3T3 fibroblasts and C2C12 myoblasts. These genomic regions range from a few kb to over 1 Mb and cover ~30% of the genome, and are spatially proximal to the NL. Active histone modifications such as H3K4me2/3, H3K9Ac and H3K36me3 are distributed predominantly out of sLADs, consistent with observations from cell imaging that they are localized away from the nuclear periphery. Genomic regions around transcription start sites of expressed sLAD genes display reduced association with the NL; additionally, expressed sLAD genes possess lower levels of active histone modifications than expressed non-sLAD genes.ConclusionsOur work has shown that genomic regions associated with the NL are characterized by the paucity of active histone modifications in mammalian cells, and has revealed novel connections between subnuclear gene positioning, histone modifications and gene expression.

Highlights

How gene positioning to the nuclear periphery regulates transcription remains largely unclear
Detecting DNA sequences associated with the nuclear lamina (NL) by DNA adenine methyltransferase identification (DamID) coupled to high throughput DNA sequencing The published genome-NL interaction maps were constructed using DamID assay followed by analysis on genome tiling arrays [14,15]
This fusion protein was successfully used to identify genomic regions associated with the NL in mouse cells [15], and we have confirmed its localization at the nuclear periphery by immunofluorescence staining

Summary

Introduction

How gene positioning to the nuclear periphery regulates transcription remains largely unclear. DNA adenine methyltransferase identification (DamID) assay has successfully identified large lamina-associated domains (LADs) covering about 40% of the genome in human and mouse cells [14,15]. DamID assay using INM proteins such as Emerin yielded binding profiles that were similar to Lamin B1 [14], indicating that the identified genomic regions largely represent those regions that are preferentially positioned to the nuclear periphery. A recent study has dissected a LAD at the immunoglobulin heavy chain locus and identified DNA sequences that can direct transgenes to the NL in mouse fibroblasts. These sequences are enriched with a GAGA motif and associated with transcription corepressor cKrox and histone deacetylase HDAC3 [16]. While LADs are generally considered as repressive chromatin domains, it is not clear how these domains play regulatory roles on gene transcription

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