AUTHOR=Pathak Rashmi Upadhyay , Phanindhar Kundurthi , Mishra Rakesh K. 

TITLE=Transposable elements as scaffold/matrix attachment regions: shaping organization and functions in genomes

JOURNAL=Frontiers in Molecular Biosciences

VOLUME=Volume 10 - 2023

YEAR=2024

URL=https://www.frontiersin.org/journals/molecular-biosciences/articles/10.3389/fmolb.2023.1326933

DOI=10.3389/fmolb.2023.1326933

ISSN=2296-889X

ABSTRACT=Hierarchical structure of eukaryotic genomes have regulatory layers, one of them being epigenetic 'indexing' of the genome that leads to cell type specific pattern of gene expression.By establishing loops and defining chromatin domains, cells can achieve coordinated control over multi-locus segments of the genome. This is thought to be achieved using Scaffold/Matrix attachment regions (S/MARs) that establish structural and functional loops and topologically associating domains (TADs) that define a self-interacting region of the genome. Large scale genome wide mapping of S/MARs has begun to uncover these aspects of genome organization.A recent genome-wide study shows association of transposable elements (TEs) with a significant fraction of S/MARs, suggesting that multitude of TE derived repeats constitute a class of anchorage sites of chromatin loops to nuclear architecture. Here we provide an insight that TE driven dispersal of S/MARs has the potential to restructure the chromosomes by creating novel loops and domains. The combination of TEs and S/MARs as elements that can hop through the genome along with regulatory capabilities may provide an active mechanism of genome evolution leading to emergence of novel features in biological systems.Significance -Genome-wide study mapping developmental S/MARs reveal an intriguing link between these elements and TEs. This article highlights the potential of TE-S/MAR combination to drive evolution by re-structuring and shaping the genome.