title: New bioinformatic tool for quick identification of functionally relevant endogenous retroviral inserts in human genome.
abstract: Endogenous retroviruses (ERVs) and LTR retrotransposons (LRs) occupy ∼8% of human genome. Deep sequencing technologies provide clues to understanding of functional relevance of individual ERVs/LRs by enabling direct identification of transcription factor binding sites (TFBS) and other landmarks of functional genomic elements. Here, we performed the genome-wide identification of human ERVs/LRs containing TFBS according to the ENCODE project. We created the first interactive ERV/LRs database that groups the individual inserts according to their familial nomenclature, number of mapped TFBS and divergence from their consensus sequence. Information on any particular element can be easily extracted by the user. We also created a genome browser tool, which enables quick mapping of any ERV/LR insert according to genomic coordinates, known human genes and TFBS. These tools can be used to easily explore functionally relevant individual ERV/LRs, and for studying their impact on the regulation of human genes. Overall, we identified ∼110,000 ERV/LR genomic elements having TFBS. We propose a hypothesis of "domestication" of ERV/LR TFBS by the genome milieu including subsequent stages of initial epigenetic repression, partial functional release, and further mutation-driven reshaping of TFBS in tight coevolution with the enclosing genomic loci.
authors: a Group for Genomic Regulation of Cell Signaling Systems ; Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry ; Moscow , Russia.
authors: Andrew
authors: A
authors: Garazha
authors: Alena
authors: A
authors: Ivanova
authors: Maria
authors: M
authors: Suntsova
authors: Galina
authors: G
authors: Malakhova
authors: Sergey
authors: S
authors: Roumiantsev
authors: Alex
authors: A
authors: Zhavoronkov
authors: Anton
authors: A
authors: Buzdin
mesh_terms: D001665:Binding Sites; D003001:Cloning, Molecular; D019295:Computational Biology; D004252:DNA Mutational Analysis / Q000379:methods*; D004279:DNA, Viral / Q000235:genetics* / Q000378:metabolism; D030541:Databases, Genetic; D020077:Endogenous Retroviruses / Q000235:genetics* / Q000378:metabolism; D044127:Epigenesis, Genetic; D005786:Gene Expression Regulation; D015894:Genome, Human; D056945:Hep G2 Cells; D006801:Humans; D016254:Mutagenesis, Insertional; D018626:Retroelements; D020079:Terminal Repeat Sequences; D014157:Transcription Factors / Q000235:genetics / Q000378:metabolism; D014158:Transcription, Genetic; D014162:Transfection
chemical_list: D004279:DNA, Viral; D018626:Retroelements; D014157:Transcription Factors
keywords: Database; LTR retrotransposon; endogenous retrovirus; genome browser; human genome; transcription factor binding site