title: BioTAP-XL: Cross-linking/Tandem Affinity Purification to Study DNA Targets, RNA, and Protein Components of Chromatin-Associated Complexes.
abstract: In order to understand how chromatin complexes function in the nucleus, it is important to obtain a comprehensive picture of their protein, DNA, and RNA components, as well as their mutual interactions. This unit presents a chromatin cross-linking approach (BioTAP-XL) that utilizes a special BioTAP-tagged transgenic protein bait along with mass spectrometry to identify protein complex components, and high-throughput sequencing to identify RNA components and DNA binding sites. Full protocols are provided for Drosophila cells and for human cells in culture, along with an additional protocol for Drosophila embryos as the source material. A key element of the approach in all cases is the generation of control data from input chromatin samples.
authors.affiliation: Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts.|Department of Genetics, Harvard Medical School, Boston, Massachusetts.
authors.forename: Artyom A
authors.initials: AA
authors.lastname: Alekseyenko
authors.affiliation: Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts.|Department of Genetics, Harvard Medical School, Boston, Massachusetts.|Department of Molecular and Cellular Biology, Harvard University, Cambridge, Massachusetts.
authors.forename: Kyle A
authors.initials: KA
authors.lastname: McElroy
authors.affiliation: Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts.|Department of Genetics, Harvard Medical School, Boston, Massachusetts.
authors.forename: Hyuckjoon
authors.initials: H
authors.lastname: Kang
authors.affiliation: Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts.|Department of Genetics, Harvard Medical School, Boston, Massachusetts.
authors.forename: Barry M
authors.initials: BM
authors.lastname: Zee
authors.affiliation: Center for Biomedical Informatics, Harvard Medical School, Boston, Massachusetts.|Hematology/Oncology Program, Children's Hospital, Boston, Massachusetts.
authors.forename: Peter V
authors.initials: PV
authors.lastname: Kharchenko
authors.affiliation: Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts.|Department of Genetics, Harvard Medical School, Boston, Massachusetts.
authors.forename: Mitzi I
authors.initials: MI
authors.lastname: Kuroda
mesh_terms: D000818:Animals; D001665:Binding Sites; D002460:Cell Line; D002843:Chromatin / Q000235:genetics / Q000378:metabolism*; D003584:Cytological Techniques / Q000379:methods*; D004247:DNA / Q000235:genetics / Q000378:metabolism*; D004330:Drosophila; D006801:Humans; D008967:Molecular Biology / Q000379:methods*; D011506:Proteins / Q000378:metabolism*; D012313:RNA / Q000378:metabolism*
chemical_list: D002843:Chromatin; D011506:Proteins; D012313:RNA; D004247:DNA
keywords: LC-MS/MS; chromatin; formaldehyde cross-linking; next-generation sequencing