Retrotransposon Alu is enriched in the epichromatin of HL-60 cells.
Epichromatin, the surface of chromatin facing the nuclear envelope in an interphase nucleus, reveals a "rim" staining pattern with specific mouse monoclonal antibodies against histone H2A/H2B/DNA and phosphatidylserine epitopes. Employing a modified ChIP-Seq procedure on undifferentiated and differentiated human leukemic (HL-60/S4) cells,>95% of assembled epichromatin regions overlapped with Alu retrotransposons. They also exhibited enrichment of the AluS subfamily and of Alu oligomers. Furthermore, mapping epichromatin regions to the human chromosomes revealed highly similar localization patterns in the various cell states and with the different antibodies. Comparisons with available epigenetic databases suggested that epichromatin is neither "classical" heterochromatin nor highly expressing genes, implying another function at the surface of interphase chromatin. A modified chromatin immunoprecipitation procedure (xxChIP) was developed because the studied antibodies react generally with mononucleosomes and lysed chromatin. A second fixation is necessary to securely attach the antibodies to the epichromatin epitopes of the intact nucleus.
Department of Pharmaceutical Sciences; College of Pharmacy; University of New England; Portland, ME USA.
Ada L
AL
Olins
Division of Theoretical Bioinformatics; German Cancer Research Center (DKFZ); Heidelberg, Germany; Heidelberg Center for Personalized Oncology; German Cancer Research Center (DKFZ); Heidelberg, Germany.
Naveed
N
Ishaque
German Cancer Research Center; Genomics and Proteomics Core Facility, High Throughput Sequencing Unit; Heidelberg, Germany.
Sasithorn
S
Chotewutmontri
Biophysik der Makromoleküle; German Cancer Research Center; Heidelberg, Germany.
Jörg
J
Langowski
Department of Pharmaceutical Sciences; College of Pharmacy; University of New England; Portland, ME USA.
Donald E
DE
Olins
D020087:Alu Elements / Q000235:genetics*; D000818:Animals; D000911:Antibodies, Monoclonal / Q000276:immunology; D045744:Cell Line, Tumor; D002467:Cell Nucleus / Q000235:genetics; D002843:Chromatin / Q000235:genetics*; D002877:Chromosomes, Human / Q000235:genetics; D044127:Epigenesis, Genetic / Q000235:genetics; D018922:HL-60 Cells; D006570:Heterochromatin / Q000235:genetics; D006801:Humans; D007399:Interphase / Q000235:genetics; D051379:Mice; D009685:Nuclear Envelope / Q000235:genetics; D018626:Retroelements / Q000235:genetics*
D000911:Antibodies, Monoclonal; D002843:Chromatin; D006570:Heterochromatin; D018626:Retroelements
epichromatin; epigenetics; granulocytes; macrophage; myeloid leukemia; nuclear architecture; retrotransposon Alu