ArticleNucleic acids research2012
A workflow for genome-wide mapping of archaeal transcription factors with ChIP-seq.
Article in Nucleic acids research, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 32 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
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.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
32 citing papers in PubMed, 54 citations in OpenAlex.
- Article
- Genomic re-sequencing reveals mutational divergence across genetically engineered strains of model archaea.mSystems · 2025Article
- TbsP and TrmB jointly regulate gapII to influence cell development phenotypes in the archaeon Haloferax volcanii.Molecular microbiology · 2024Article
- Unveiling the repressive mechanism of a PPS-like regulator (PspR) in polyhydroxyalkanoates biosynthesis network.Applied microbiology and biotechnology · 2024Article
- TroR is the primary regulator of the iron homeostasis transcription network in the halophilic archaeon Haloferax volcanii.Nucleic acids research · 2024Article
- A conserved transcription factor controls gluconeogenesis via distinct targets in hypersaline-adapted archaea with diverse metabolic capabilities.PLoS genetics · 2024Article
- Article
- Article
- TrmB Family Transcription Factor as a Thiol-Based Regulator of Oxidative Stress Response.mBio · 2022Article
- ChIP-Seq Occupancy Mapping of the Archaeal Transcription Machinery.Methods in molecular biology (Clifton, N.J.) · 2022Article
- An archaeal histone-like protein regulates gene expression in response to salt stress.Nucleic acids research · 2021Article
- Identifying Components of aFrontiers in microbiology · 2021Article
- The conserved ribonuclease aCPSF1 triggers genome-wide transcription termination of Archaea via a 3'-end cleavage mode.Nucleic acids research · 2020Article
- Article
- PvrA is a novel regulator that contributes to Pseudomonas aeruginosa pathogenesis by controlling bacterial utilization of long chain fatty acids.Nucleic acids research · 2020Article
- DNA mapping and kinetic modeling of the HrdB regulon in Streptomyces coelicolor.Nucleic acids research · 2019Article
- Article
- Internal RNAs overlapping coding sequences can drive the production of alternative proteins in archaea.RNA biology · 2018Article
- The Transcriptional Regulator TFB-RF1 Activates Transcription of a Putative ABC Transporter inFrontiers in microbiology · 2018Article
- Genome-Wide Profiling of DNA Methyltransferases in Mammalian Cells.Methods in molecular biology (Clifton, N.J.) · 2018Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
7 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Deciphering the structure of gene regulatory networks across the tree of life remains one of the major challenges in postgenomic biology. We present a novel ChIP-seq workflow for the archaea using the model organism Halobacterium salinarum sp. NRC-1 and demonstrate its application for mapping the genome-wide binding sites of natively expressed transcription factors. This end-to-end pipeline is the first protocol for ChIP-seq in archaea, with methods and tools for each stage from gene tagging to data analysis and biological discovery. Genome-wide binding sites for transcription factors with many binding sites (TfbD) are identified with sensitivity, while retaining specificity in the identification the smaller regulons (bacteriorhodopsin-activator protein). Chromosomal tagging of target proteins with a compact epitope facilitates a standardized and cost-effective workflow that is compatible with high-throughput immunoprecipitation of natively expressed transcription factors. The Pique package, an open-source bioinformatics method, is presented for identification of binding events. Relative to ChIP-Chip and qPCR, this workflow offers a robust catalog of protein-DNA binding events with improved spatial resolution and significantly decreased cost. While this study focuses on the application of ChIP-seq in H. salinarum sp. NRC-1, our workflow can also be adapted for use in other archaea and bacteria with basic genetic tools.
Indexed as
Identifiers
What OpenQuestion holds
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.