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    • Genomic organization of Polycomb Response Elements and its functional implication in Drosophila and other insects

      ARUMUGAM SRINIVASAN RAKESH K MISHRA

      Article Volume 45 Published: 20 January 2020 Article ID 0012

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      https://www.ias.ac.in/article/fulltext/jbsc/045/0012

    • Keywords

       

      Polycomb Response Elements; PRE Mapper; genome organization; epigenetic memory; insect genomes; Drosophila

    • Abstract

       

      The epigenetic memory is an essential aspect of multicellular organisms to maintain several cell types and their geneexpression pattern. This complex process uses a number of protein factors and specific DNA elements within thedevelopmental cues to achieve this. The protein factors involved in the process are the Polycomb group (PcG)members, and, accordingly, the DNA sequences that interact with these proteins are called Polycomb ResponseElements (PREs). Since the PcG proteins are highly conserved among higher eukaryotes, including insects, andfunction at thousands of sites in the genomes, it is expected that PREs may also be present across the genome.However,the studies on PREs in insect species, other thanDrosophila, is currently lacking.We took a bioinformatics approach todevelop an inclusive PRE prediction tool, ‘PRE Mapper’, to address this need. By applying this tool on the Drosophilamelanogaster genome, we predicted more than 20,000 PREs.When compared with the available PRE prediction methods, thistool shows far better performance by correctly identifying the in vivo binding sites of PcG proteins, identified bygenome-scale ChIP experiments. Further analysis of the predicted PREs shows their cohabitation with chromatindomain boundary elements at several places in the Drosophila genome, possibly defining a composite epigeneticmodule.We analysed 10 insect genomes in this context and find several conserved features in PREs across the insectspecies with some variations in their occurrence frequency. These analyses leading to the identification of PREin insectgenomes contribute to our understanding of epigenetic mechanisms in these organisms.

    • Author Affiliations

       

      ARUMUGAM SRINIVASAN1 RAKESH K MISHRA1

      1. CSIR – Centre for Cellular and Molecular Biology, Uppal Road, Hyderabad 500 007, India

    • Dates

       
      Published
      20 January 2020

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