ArticleDevelopment (Cambridge, England)2016
iDamIDseq and iDEAR: an improved method and computational pipeline to profile chromatin-binding proteins.
Article in Development (Cambridge, England), 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 16 papers.
What it found
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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Who cites it
16 citing papers in PubMed, 27 citations in OpenAlex.
- When RNA goes off script: ensuring transcript fidelity in transgene expression.The EMBO journal · 2026Review
- Mapping SET1B chromatin interactions with DamID using DamMapper, a comprehensive Snakemake workflow.BMC genomics · 2025Article
- Article
- A regulatory loop of JAK/STAT signalling and its downstream targets represses cell fate conversion and maintains male germline stem cell niche homeostasis.Cell proliferation · 2024Article
- Alternative TSS use is widespread in Cryptococcus fungi in response to environmental cues and regulated genome-wide by the transcription factor Tur1.PLoS biology · 2024Article
- Nitrogen sensing and regulatory networks: it's about time and space.The Plant cell · 2024Review
- Ran-GTP assembles a specialized spindle structure for accurate chromosome segregation in medaka early embryos.Nature communications · 2024Article
- A feedforward loop between JAK/STAT downstream target p115 and STAT in germline stem cells.Stem cell reports · 2023Article
- A hierarchical transcription factor cascade regulates enteroendocrine cell diversity and plasticity in Drosophila.Nature communications · 2022Article
- Genome-wide mapping of Piwi association with specific loci in Drosophila ovaries.G3 (Bethesda, Md.) · 2021Article
- Tissue-specific DamID protocol using nanopore sequencing.Journal of biological methods · 2021Article
- Transient genome-wide interactions of the master transcription factor NLP7 initiate a rapid nitrogen-response cascade.Nature communications · 2020Article
- DamID identifies targets of CEH-60/PBX that are associated with neuron development and muscle structure in Caenorhabditis elegans.PloS one · 2020Article
- Dam mutants provide improved sensitivity and spatial resolution for profiling transcription factor binding.Epigenetics & chromatin · 2019Article
- DamID as a versatile tool for understanding gene regulation.Development (Cambridge, England) · 2019Review
- Transient Scute activation via a self-stimulatory loop directs enteroendocrine cell pair specification from self-renewing intestinal stem cells.Nature cell biology · 2018Article
Corrections and comments
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Authors and funding
5 authors at 2 institutions in 1 country.
Funding
Abstract
DNA adenine methyltransferase identification (DamID) has emerged as an alternative method to profile protein-DNA interactions; however, critical issues limit its widespread applicability. Here, we present iDamIDseq, a protocol that improves specificity and sensitivity by inverting the steps DpnI-DpnII and adding steps that involve a phosphatase and exonuclease. To determine genome-wide protein-DNA interactions efficiently, we present the analysis tool iDEAR (iDamIDseq Enrichment Analysis with R). The combination of DamID and iDEAR permits the establishment of consistent profiles for transcription factors, even in transient assays, as we exemplify using the small teleost medaka (Oryzias latipes). We report that the bacterial Dam-coding sequence induces aberrant splicing when it is used with different promoters to drive tissue-specific expression. Here, we present an optimization of the sequence to avoid this problem. This and our other improvements will allow researchers to use DamID effectively in any organism, in a general or targeted manner.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.