Fixed and unalterable Matrix Associated Regions in Drosophila melanogaster genome

ABSTRACT: Eukaryotic genome is compartmentalized into structural and functional domains. One of the concepts of higher order organization of chromatin posits that the DNA is organized in constrained loops that behave as independent functional domains. A predominantly ribo-proteinaceous nucleoskeleton, termed as Nuclear Matrix (NuMat) is proposed to provide the structural platform for attachment of these loops. The DNA sequence located at the base of the loops are known as the Matrix Attachment Regions (MARs). NuMat relates to all nuclear processes and has been shown to be cell type specific in composition. It is a biochemically defined structure and several protocols have been used to isolate the NuMat where some of the steps have been critically evaluated. In the present study we have looked into the dynamics of MARs when the isolation process is varied and also during embryonic development of D. melanogaster. Our results show that a subset of MARs termed here as “Core-MARs” are fixed and unalterable anchor points in the Drosophila genome as they remain associated with NuMat at all developmental stages and do not depend on the isolation procedure used. Core-MARs are abundant in the pericentromeric heterochromatin. On the other hand, MARs in the euchromatin are dynamic and reflect the transcriptomic profile of the developmental stage of the host cell. New MARs are generated by nuclear stabilization (a critical step in the isolation procedure), and during development, mostly at the paused RNA polymerase II (Pol II) promoters. Paused Pol II MARs depend on RNA transcription for NuMat association. RNase A treatment leads to collapse of the NuMat and loss of paused Pol II promoter MARs. Our data reveals the role of MARs in functional compartmentalization of D. melanogaster genome and adds to the current understanding of nuclear architecture and 3D organization of a functionally dynamic nucleus.

INSTRUMENT(S): Q Exactive HF

ORGANISM(S): Drosophila Melanogaster (fruit Fly)

TISSUE(S): Embryo

SUBMITTER: Rahul Sureka  

LAB HEAD: Rakesh Kumar Mishra

PROVIDER: PXD031279 | Pride | 2022-10-25

REPOSITORIES: Pride