Abstract
Targeted DamID (TaDa) is a means of profiling the binding of any DNA-associated protein cell-type specifically, including transcription factors, RNA polymerase, and chromatin-modifying proteins. The technique is highly sensitive, highly reproducible, requires no mechanical disruption, cell isolation or antibody purification, and can be performed by anyone with basic molecular biology knowledge. Here, we describe the TaDa method and downstream bioinformatics data processing.
This is a preview of subscription content, log in via an institution to check access.
Access this chapter
Tax calculation will be finalised at checkout
Purchases are for personal use only
Similar content being viewed by others
References
Southall TD, Gold KS, Egger B, Davidson CM, Caygill EE, Marshall OJ, Brand AH (2013) Cell-type-specific profiling of gene expression and chromatin binding without cell isolation: assaying RNA Pol II occupancy in neural stem cells. Dev Cell 26:101–112. https://doi.org/10.1016/j.devcel.2013.05.020
Marshall OJ, Southall TD, Cheetham SW, Brand AH (2016) Cell-type-specific profiling of protein–DNA interactions without cell isolation using targeted DamID with next-generation sequencing. Nat Protoc 11:1586–1598. https://doi.org/10.1038/nprot.2016.084
van Steensel B, Delrow J, Henikoff S (2001) Chromatin profiling using targeted DNA adenine methyltransferase. Nat Genet 27:304–308. https://doi.org/10.1038/85871
van Steensel B, Henikoff S (2000) Identification of in vivo DNA targets of chromatin proteins using tethered dam methyltransferase. Nat Biotechnol 18:424–428. https://doi.org/10.1038/74487
Luo GZ, He C (2017) DNA N 6-methyladenine in metazoans: functional epigenetic mark or bystander? Nat Struct Mol Biol 24:503–506. https://doi.org/10.1038/nsmb.3412
Doupé DP, Marshall OJ, Dayton H, Brand AH, Perrimon N (2018) Drosophila intestinal stem and progenitor cells are major sources and regulators of homeostatic niche signals. Proc Natl Acad Sci 115:12218–12223. https://doi.org/10.1073/pnas.1719169115
Marshall OJ, Brand AH (2017) Chromatin state changes during neural development revealed by in vivo cell-type specific profiling. Nat Commun 8:2271. https://doi.org/10.1038/s41467-017-02385-4
Aughey GN, Estacio Gomez A, Thomson J, Yin H, Southall TD (2018) CATaDa reveals global remodelling of chromatin accessibility during stem cell differentiation in vivo. elife 7:1–22. https://doi.org/10.7554/elife.32341
Guelen L, Pagie L, Brasset E, Meuleman W, Faza MB, Talhout W, Eussen BH, de Klein A, Wessels L, de Laat W, van Steensel B (2008) Domain organization of human chromosomes revealed by mapping of nuclear lamina interactions. Nature 453:948–951. https://doi.org/10.1038/nature06947
Cheetham SW, Brand AH (2018) RNA-DamID reveals cell-type-specific binding of roX RNAs at chromatin-entry sites. Nat Struct Mol Biol 25:109–114. https://doi.org/10.1038/s41594-017-0006-4
Luukkonen BG, Tan W, Schwartz S (1995) Efficiency of reinitiation of translation on human immunodeficiency virus type 1 mRNAs is determined by the length of the upstream open reading frame and by intercistronic distance. J Virol 69:4086–4094
Brand AH, Perrimon N (1993) Targeted gene expression as a means of altering cell fates and generating dominant phenotypes. Development 118:401–415
Marshall OJ, Brand AH (2015) damidseq_pipeline: an automated pipeline for processing DamID sequencing datasets. Bioinformatics 31:3371–3373. https://doi.org/10.1093/bioinformatics/btv386
Delandre C, McMullen JPD, Marshall OJ (2020) Membrane-bound GFP-labelled vectors for Targeted DamID allow simultaneous profiling of expression domains and DNA binding. bioRxiv 1–4. https://doi.org/10.1101/2020.04.17.045948
Aughey GN, Delandre C, Southall TD, Marshall OJ (2020) FlyORF-TaDa allows rapid generation of new lines for in vivo cell-type specific profiling of protein-DNA interactions in Drosophila melanogaster. bioRxiv 2020.08.06.239251. https://doi.org/10.1101/2020.08.06.239251
Tosti L, Ashmore J, Tan BSN, Carbone B, Mistri TK, Wilson V, Tomlinson SR, Kaji K (2018) Mapping transcription factor occupancy using minimal numbers of cells in vitro and in vivo. Genome Res 28:592–605. https://doi.org/10.1101/gr.227124.117
Cheetham SW, Gruhn WH, van den Ameele J, Krautz R, Southall TD, Kobayashi T, Surani MA, Brand AH (2018) Targeted DamID reveals differential binding of mammalian pluripotency factors. Development 145:dev170209. https://doi.org/10.1242/dev.170209
Katsanos D, Barkoulas M (2020) Tissue-specific transcription factor target identification in the Caenorhabditis elegans epidermis using targeted DamID. bioRxiv
Robinson JT, Thorvaldsdóttir H, Winckler W, Guttman M, Lander ES, Getz G, Mesirov JP (2011) Integrative genomics viewer. Nat Biotechnol 29:24–26. https://doi.org/10.1038/nbt.1754
Ramírez F, Bhardwaj V, Arrigoni L, Lam KC, Grüning BA, Villaveces J, Habermann B, Akhtar A, Manke T (2018) High-resolution TADs reveal DNA sequences underlying genome organization in flies. Nat Commun 9(1):189. https://doi.org/10.1038/s41467-017-02525-w
Tarazona S, Furió-Tarí P, Turrà D, Di Pietro A, Nueda MJ, Ferrer A, Conesa A (2015) Data quality aware analysis of differential expression in RNA-seq with NOISeq R/Bioc package. Nucleic Acids Res 43(21):e140. https://doi.org/10.1093/nar/gkv711
Hatch HAM, Belalcazar HM, Marshall OJ, Secombe JA (2021)KDM5-Prospero transcriptional axis functions during early neurodevelopment to regulate mushroom body formation. Elife. 2021 Mar 17;10:e63886. https://doi.org/10.7554/eLife.63886. PMID: 33729157; PMCID: PMC7997662
Author information
Authors and Affiliations
Corresponding author
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2022 The Author(s), under exclusive license to Springer Science+Business Media, LLC, part of Springer Nature
About this protocol
Cite this protocol
Marshall, O.J., Delandre, C. (2022). Profiling Protein–DNA Interactions Cell-Type-Specifically with Targeted DamID. In: Horsfield, J., Marsman, J. (eds) Chromatin. Methods in Molecular Biology, vol 2458. Humana, New York, NY. https://doi.org/10.1007/978-1-0716-2140-0_11
Download citation
DOI: https://doi.org/10.1007/978-1-0716-2140-0_11
Published:
Publisher Name: Humana, New York, NY
Print ISBN: 978-1-0716-2139-4
Online ISBN: 978-1-0716-2140-0
eBook Packages: Springer Protocols