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DamID-seq: Genome-wide Mapping of Protein-DNA Interactions by High Throughput Sequencing of Adenine-methylated DNA Fragments.
Wu F, Olson BG, Yao J. Wu F, et al. J Vis Exp. 2016 Jan 27;(107):e53620. doi: 10.3791/53620. J Vis Exp. 2016. PMID: 26862720 Free PMC article.
In this paper, we report the detailed protocol of integrating high throughput DNA sequencing into DamID (DamID-seq). The large number of short reads generated from DamID-seq enables detecting and localizing protein-DNA interactions genome-wide w …
In this paper, we report the detailed protocol of integrating high throughput DNA sequencing into DamID (DamID-seq). Th …
A non-parametric peak calling algorithm for DamID-Seq.
Li R, Hempel LU, Jiang T. Li R, et al. PLoS One. 2015 Mar 18;10(3):e0117415. doi: 10.1371/journal.pone.0117415. eCollection 2015. PLoS One. 2015. PMID: 25785608 Free PMC article.
In order to identify transcription factor binding sites (TFBS) of double sex (DSX)-an important transcription factor in sex determination, we applied the DNA adenine methylation identification (DamID) technology to the fat body tissue of Drosophila, followed by deep sequen …
In order to identify transcription factor binding sites (TFBS) of double sex (DSX)-an important transcription factor in sex determination, w …
Identification of Tox chromatin binding properties and downstream targets by DamID-Seq.
de Jesus Domingues AM, Artegiani B, Dahl A, Calegari F. de Jesus Domingues AM, et al. Genom Data. 2016 Feb 3;7:264-8. doi: 10.1016/j.gdata.2016.02.003. eCollection 2016 Mar. Genom Data. 2016. PMID: 26981424 Free PMC article.
While DamID has been primarily combined with microarray analyses, which limits the spatial resolution and full potential of this technique, our group was the first to combine DamID with sequencing (DamID-Seq) for characterizing the binding loci and pro …
While DamID has been primarily combined with microarray analyses, which limits the spatial resolution and full potential of this tech …
damidseq_pipeline: an automated pipeline for processing DamID sequencing datasets.
Marshall OJ, Brand AH. Marshall OJ, et al. Bioinformatics. 2015 Oct 15;31(20):3371-3. doi: 10.1093/bioinformatics/btv386. Epub 2015 Jun 25. Bioinformatics. 2015. PMID: 26112292 Free PMC article.
Currently, no method exists for automatically processing next-generation sequencing DamID (DamID-seq) data, and the use of DamID-seq datasets with normalization based on read-counts alone can lead to high background and the loss of bound signal. …
Currently, no method exists for automatically processing next-generation sequencing DamID (DamID-seq) data, and the use …
Data analysis algorithm for DamID-seq profiling of chromatin proteins in Drosophila melanogaster.
Maksimov DA, Laktionov PP, Belyakin SN. Maksimov DA, et al. Chromosome Res. 2016 Dec;24(4):481-494. doi: 10.1007/s10577-016-9538-4. Epub 2016 Oct 21. Chromosome Res. 2016. PMID: 27766446
For this purpose, chromatin immunoprecipitation (ChIP) and Dam identification (DamID) methods can be applied to cell lines, whole organisms, or enriched cell populations. In this work, we present modifications to the experimental DamID protocol, as well as a custom …
For this purpose, chromatin immunoprecipitation (ChIP) and Dam identification (DamID) methods can be applied to cell lines, whole org …
DamID profiling of dynamic Polycomb-binding sites in Drosophila imaginal disc development and tumorigenesis.
La Fortezza M, Grigolon G, Cosolo A, Pindyurin A, Breimann L, Blum H, van Steensel B, Classen AK. La Fortezza M, et al. Epigenetics Chromatin. 2018 Jun 5;11(1):27. doi: 10.1186/s13072-018-0196-y. Epigenetics Chromatin. 2018. PMID: 29871666 Free PMC article.
However, limited availability and heterogeneous tissue composition of in vivo source material impose challenges on many experimental approaches. RESULTS: Here we adapt cell-type-specific DamID-seq profiling for use in Drosophila imaginal discs and make FLP/FRT-based …
However, limited availability and heterogeneous tissue composition of in vivo source material impose challenges on many experimental approac …
Mapping transcription factor occupancy using minimal numbers of cells in vitro and in vivo.
Tosti L, Ashmore J, Tan BSN, Carbone B, Mistri TK, Wilson V, Tomlinson SR, Kaji K. Tosti L, et al. Genome Res. 2018 Apr;28(4):592-605. doi: 10.1101/gr.227124.117. Epub 2018 Mar 23. Genome Res. 2018. PMID: 29572359 Free PMC article.
Here we describe an optimized DamID method coupled with next-generation sequencing (DamID-seq) in mouse cells and demonstrate the identification of the binding sites of two TFs, POU5F1 (also known as OCT4) and SOX2, in as few as 1000 embryonic stem cells (ESC …
Here we describe an optimized DamID method coupled with next-generation sequencing (DamID-seq) in mouse cells and demon …
Transient genome-wide interactions of the master transcription factor NLP7 initiate a rapid nitrogen-response cascade.
Alvarez JM, Schinke AL, Brooks MD, Pasquino A, Leonelli L, Varala K, Safi A, Krouk G, Krapp A, Coruzzi GM. Alvarez JM, et al. Nat Commun. 2020 Mar 2;11(1):1157. doi: 10.1038/s41467-020-14979-6. Nat Commun. 2020. PMID: 32123177 Free PMC article.
Here, we capture both stable and transient TF-target interactions genome-wide within minutes after controlled TF nuclear import using time-series chromatin immunoprecipitation (ChIP-seq) and/or DNA adenine methyltransferase identification (DamID-seq). ...
Here, we capture both stable and transient TF-target interactions genome-wide within minutes after controlled TF nuclear import using time-s …
Various modes of HP1a interactions with the euchromatic chromosome arms in Drosophila ovarian somatic cells.
Ilyin AA, Stolyarenko AD, Klenov MS, Shevelyov YY. Ilyin AA, et al. Chromosoma. 2020 Dec;129(3-4):201-214. doi: 10.1007/s00412-020-00738-5. Epub 2020 Jun 5. Chromosoma. 2020. PMID: 32500264
Here, we identified HP1a-interacting domains in the somatic cells of Drosophila ovaries using a DamID-seq approach and compared them with insertion sites of transposable elements (TEs) revealed by genome sequencing. ...
Here, we identified HP1a-interacting domains in the somatic cells of Drosophila ovaries using a DamID-seq approach and compare …
Tools for DNA adenine methyltransferase identification analysis of nuclear organization during C. elegans development.
Sharma R, Ritler D, Meister P. Sharma R, et al. Genesis. 2016 Apr;54(4):151-9. doi: 10.1002/dvg.22925. Genesis. 2016. PMID: 26845390
As an alternative to ChIP, DNA adenine methyltransferase identification by sequencing (DamID-seq) was recently shown to be able to characterize binding sites in single mammalian cells. ...In this report, we present a user-friendly pipeline to analyse DamID- …
As an alternative to ChIP, DNA adenine methyltransferase identification by sequencing (DamID-seq) was recently shown to be abl …
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