Abstract
BackgroundEukaryotic genome acquires functionality upon proper packaging within the nucleus. This process is facilitated by the structural framework of Nuclear Matrix, a nucleo-proteinaceous meshwork. Matrix Attachment Regions (MARs) in the genome serve as anchoring sites to this framework.ResultsHere we report direct sequencing of the MAR preparation from Drosophila melanogaster embryos and identify >7350 MARs. This amounts to ~2.5% of the fly genome and often coincide with AT rich non-coding regions. We find significant association of MARs with the origins of replication, transcription start sites, paused RNA Polymerase II sites and exons, but not introns, of highly expressed genes. We also identified sequence motifs and repeats that constitute MARs.ConclusionOur data reveal the contact points of genome to the nuclear architecture and provide a link between nuclear functions and genomic packaging.Electronic supplementary materialThe online version of this article (doi:10.1186/1471-2164-15-1022) contains supplementary material, which is available to authorized users.
Highlights
Eukaryotic genome acquires functionality upon proper packaging within the nucleus
We find Matrix Attachment Regions (MARs) cohabiting with regulatory functions, viz., ORI sequences, paused Pol II sites, domain boundaries, etc
These observations reflect the structural perspective of nuclear architecture in context of functioning of these elements
Summary
Eukaryotic genome acquires functionality upon proper packaging within the nucleus. This process is facilitated by the structural framework of Nuclear Matrix, a nucleo-proteinaceous meshwork. Eukaryotic nucleus is a complex organelle, where DNA is highly compacted but still is accessible for nuclear processes in a precisely controlled manner. The structural basis for such compact but orderly organization is provided by a proteinaceous meshwork known as Nuclear Matrix (NuMat), [1,2] that has been visualized by electron microscopy [3,4]. The presence of actin, myosin and several cytoskeletal proteins in the nucleus and NuMat further strengthens this view [8,9]. NuMat as a framework offers potential basis for compartmentalization of the nucleus and explains
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