title: Repeat Composition of CenH3-chromatin and H3K9me2-marked heterochromatin in Sugar Beet (Beta vulgaris).
abstract: Sugar beet (Beta vulgaris) is an important crop of temperate climate zones, which provides nearly 30 % of the world's annual sugar needs. From the total genome size of 758 Mb, only 567 Mb were incorporated in the recently published genome sequence, due to the fact that regions with high repetitive DNA contents (e.g. satellite DNAs) are only partially included. Therefore, to fill these gaps and to gain information about the repeat composition of centromeres and heterochromatic regions, we performed chromatin immunoprecipitation followed by sequencing (ChIP-Seq) using antibodies against the centromere-specific histone H3 variant of sugar beet (CenH3) and the heterochromatic mark of dimethylated lysine 9 of histone H3 (H3K9me2).
  
  
  
  ChIP-Seq analysis revealed that active centromeres containing CenH3 consist of the satellite pBV and the Ty3-gypsy retrotransposon Beetle7, while heterochromatin marked by H3K9me2 exhibits heterogeneity in repeat composition. H3K9me2 was mainly associated with the satellite family pEV, the Ty1-copia retrotransposon family Cotzilla and the DNA transposon superfamily of the En/Spm type. In members of the section Beta within the genus Beta, immunostaining using the CenH3 antibody was successful, indicating that orthologous CenH3 proteins are present in closely related species within this section.
  
  
  
  The identification of repetitive genome portions by ChIP-Seq experiments complemented the sugar beet reference sequence by providing insights into the repeat composition of poorly characterized CenH3-chromatin and H3K9me2-heterochromatin. Therefore, our work provides the basis for future research and application concerning the sugar beet centromere and repeat-rich heterochromatic regions characterized by the presence of H3K9me2.
authors.affiliation: Department of Plant Cell and Molecular Biology, TU Dresden, Dresden, D-01062, Germany.
authors.forename: Teresa
authors.initials: T
authors.lastname: Kowar
authors.affiliation: Department of Plant Cell and Molecular Biology, TU Dresden, Dresden, D-01062, Germany.
authors.forename: Falk
authors.initials: F
authors.lastname: Zakrzewski
authors.affiliation: Biology Centre ASCR, Institute of Plant Molecular Biology, Branišovská 31, Česke Budějovice, CZ-37005, Czech Republic.
authors.forename: Jiří
authors.initials: J
authors.lastname: Macas
authors.affiliation: Biology Centre ASCR, Institute of Plant Molecular Biology, Branišovská 31, Česke Budějovice, CZ-37005, Czech Republic.
authors.forename: Andrea
authors.initials: A
authors.lastname: Kobližková
authors.affiliation: CeBiTec & Faculty of Biology, Bielefeld University, Universitätsstr. 25, Bielefeld, D-33615, Germany.
authors.forename: Prisca
authors.initials: P
authors.lastname: Viehoever
authors.affiliation: CeBiTec & Faculty of Biology, Bielefeld University, Universitätsstr. 25, Bielefeld, D-33615, Germany. bernd.weisshaar@uni-bielefeld.de.
authors.forename: Bernd
authors.initials: B
authors.lastname: Weisshaar
authors.affiliation: Department of Plant Cell and Molecular Biology, TU Dresden, Dresden, D-01062, Germany.
authors.forename: Thomas
authors.initials: T
authors.lastname: Schmidt
mesh_terms: D027461:Beta vulgaris / Q000235:genetics* / Q000378:metabolism; D002503:Centromere / Q000378:metabolism; D002843:Chromatin / Q000235:genetics* / Q000378:metabolism; D047369:Chromatin Immunoprecipitation; D006570:Heterochromatin / Q000235:genetics* / Q000378:metabolism; D006657:Histones / Q000378:metabolism; D008239:Lysine / Q000378:metabolism; D010940:Plant Proteins / Q000235:genetics* / Q000378:metabolism; D017422:Sequence Analysis, DNA
chemical_list: D002843:Chromatin; D006570:Heterochromatin; D006657:Histones; D010940:Plant Proteins; D008239:Lysine
keywords: Beta vulgaris; CenH3; Centromere; ChIP-Seq; H3K9me2; Heterochromatin; Repeats