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The histone proteins in the nucleosomes are post-translationally modified (PTM) to increase or decrease access to DNA. The commonly observed PTMs are methylation, acetylation, phosphorylation, and ubiquitination of lysine amino acids in the histone H3 tail region. These histone modifications have specific meaning for the cell. Hence, they are called "histone code". The protein complex involved in histone modification is termed as "reader-writer" complex.
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Chromatin modification alters gene expression; therefore, scientists can add histone-modifying enzymes, histone variants, and chromatin remodeling complexes to somatic cells to aid reprogramming into pluripotent stem (iPS) cells.
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ALTRE: workflow for defining ALTered Regulatory Elements using chromatin accessibility data.

Elizabeth Baskin, Rick Farouni, Ewy A Mathé

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    |December 25, 2016
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    Summary
    This summary is machine-generated.

    This study introduces ALTRE, a new R package and web app for analyzing regulatory elements in DNA. ALTRE simplifies the comparison of chromatin accessibility data across cell types to understand gene regulation.

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    Area of Science:

    • Genomics
    • Computational Biology
    • Epigenetics

    Background:

    • Regulatory elements control gene transcription, with cell-type specific locations and accessibility.
    • Understanding these differences is crucial for cellular development and disease research.
    • Chromatin accessibility data (e.g., DNase-seq, ATAC-seq) provides insights into regulatory element function.

    Purpose of the Study:

    • To develop a streamlined tool for differential analysis of regulatory elements genome-wide.
    • To simplify the comparison of chromatin accessibility data across diverse cell types.
    • To make advanced regulatory element analysis accessible to a broader user base.

    Main Methods:

    • Development of ALTRE, an R package and R Shiny web application.
    • Utilizes chromatin accessibility data, including DNase-seq and ATAC-seq.
    • Facilitates genome-wide differential analysis of regulatory elements.

    Main Results:

    • ALTRE provides an accessible platform for analyzing altered regulatory elements.
    • The tool simplifies complex differential accessibility analyses.
    • Enables identification of cell-type specific regulatory element changes.

    Conclusions:

    • ALTRE enhances the ability to study gene regulation across different cell types.
    • The package democratizes the analysis of regulatory element accessibility.
    • Facilitates discoveries in cellular development and disease mechanisms through accessible bioinformatics tools.