Our team as generated several chromatin technologies. The protocols are available in our publications and the reagents are available through Addgene or upon request.
Recombination-Induced Tag Exchange (RITE)
A genetic tag-swap strategy to measure histone protein inheritance and turnover.
- Application of Recombination -Induced Tag Exchange (RITE) to study histone dynamics in human cells. Molenaar TM, Pagès-Gallego M, Meyn V, & van Leeuwen F. Epigenetics, 2020
- Recombination-Induced Tag Exchange (RITE) Cassette Series to Monitor Protein Dynamics in Saccharomyces cerevisiae. Terweij M, van Welsem T, van Deventer S, Verzijlbergen KF, Menendez-Benito V, Ontoso D, … van Leeuwen F. G3 (Bethesda, Md.) 2013
- Spatiotemporal analysis of organelle and macromolecular complex inheritance. Menendez-Benito V, van Deventer SJ, Jimenez-Garcia V, Roy-Luzarraga M, van Leeuwen F, & Neefjes J. PNAS, 2012
- Patterns and Mechanisms of Ancestral Histone Protein Inheritance in Budding Yeast. Radman-Livaja M, Verzijlbergen KF, Weiner A, van Welsem T, Friedman N, … van Leeuwen F. PLoS Biology, 2011
- Recombination-induced tag exchange to track old and new proteins. Verzijlbergen KF, Menendez-Benito V, Van Welsem T, van Deventer SJ, Lindstrom DL, Ovaa H, … van Leeuwen F. PNAS, 2010
Epi-ID
A DNA barcode-based screening system to identify in a genome-wide manner regulators of known chromatin marks or chromatin-binding proteins.
- Epi-ID: Systematic and Direct Screening for Chromatin Regulators in Yeast by Barcode-ChIP-Seq. Poramba-Liyanage DW, Korthout T, & van Leeuwen F. Methods in molecular biology, 2019
- Conserved crosstalk between histone deacetylation and H3K79 methylation generates DOT1L‐dose dependency in HDAC1‐deficient thymic lymphoma. Vlaming H, McLean CM, Korthout T, Alemdehy MF, Hendriks S, Lancini C, … van Leeuwen F. The EMBO Journal, 2019
- Direct screening for chromatin status on DNA barcodes in yeast delineates the regulome of H3K79 methylation by Dot1. Vlaming H, Molenaar TM, van Welsem T, Poramba-Liyanage DW, Smith DE, Velds A, … van Leeuwen F. ELife, 2016
- A Barcode Screen for Epigenetic Regulators Reveals a Role for the NuB4/HAT-B Histone Acetyltransferase Complex in Histone Turnover. Verzijlbergen KF, van Welsem T, Sie D, Lenstra TL, Turner DJ, Holstege, FCP, … van Leeuwen F. PLoS Genetics, 2011
Epi-Decoder
Epi-Decoder is a powerful, versatile, and robust strategy to identify and quantify in an unbiased and systematic manner the proteome of an individual genomic locus by DNA sequencing.
- Inhibition of transcription leads to rewiring of locus-specific chromatin proteomes. Poramba-Liyanage DW, Korthout T, Cucinotta CE, van Kruijsbergen I, van Welsem T, El Atmioui D, … van Leeuwen F. Genome Research, 2020
- Decoding the chromatin proteome of a single genomic locus by DNA sequencing. Korthout T, Poramba-Liyanage DW, van Kruijsbergen I, Verzijlbergen KF, van Gemert FPA, van Welsem T, & van Leeuwen F. PLOS Biology, 2018