title: Data analysis algorithm for DamID-seq profiling of chromatin proteins in Drosophila melanogaster.
abstract: Analysis of gene expression regulation typically requires identification of genomic sites bound by regulatory proteins. For this purpose, chromatin immunoprecipitation (ChIP) and Dam identification (DamID) methods can be applied to cell lines, whole organisms, or enriched cell populations. In this work, we present modifications to the experimental DamID protocol, as well as a custom data processing algorithm, that allow to confidently identify genomic sites enriched with the proteins of interest. This algorithm is implemented in Perl and is also available as executable files, thereby making DamID analysis relatively straightforward. Finally, we demonstrate how this pipeline performs when fed with real experimental data.
authors.affiliation: Institute of Molecular and Cellular Biology SB RAS, Novosibirsk, Russia.
authors.forename: Daniil A
authors.initials: DA
authors.lastname: Maksimov
authors.affiliation: Institute of Molecular and Cellular Biology SB RAS, Novosibirsk, Russia.
authors.forename: Petr P
authors.initials: PP
authors.lastname: Laktionov
authors.affiliation: Institute of Molecular and Cellular Biology SB RAS, Novosibirsk, Russia. belyakin@mcb.nsc.ru.|Novosibirsk State University, Novosibirsk, Russia. belyakin@mcb.nsc.ru.
authors.forename: Stepan N
authors.initials: SN
authors.lastname: Belyakin
mesh_terms: D000465:Algorithms; D000818:Animals; D002843:Chromatin / Q000737:chemistry*; D047369:Chromatin Immunoprecipitation; D004331:Drosophila melanogaster / Q000235:genetics*; D020869:Gene Expression Profiling; D011506:Proteins / Q000235:genetics; D017422:Sequence Analysis, DNA / Q000379:methods*
chemical_list: D002843:Chromatin; D011506:Proteins
keywords: DamID-seq; chromatin profiling; high-throughput sequencing; peak calling; transcription factors