Abstract:
BACKGROUND:Establishing transcriptional regulatory networks that include protein-protein and protein-DNA interactions has become a key component to better understanding many fundamental biological processes. Although a variety of techniques are available to expose protein-protein and protein-DNA interactions, unequivocally establishing whether two proteins are targeted together to the same promoter or DNA molecule poses a very challenging endeavour. Yet, the recruitment of multiple regulatory proteins simultaneously to the same promoter provides the basis for combinatorial transcriptional regulation, central to the transcriptional regulatory network of eukaryotes. The serial ChIP (sChIP) technology was developed to fill this gap in our knowledge, and we illustrate here its application in plants. RESULTS:Here we describe a modified sChIP protocol that provides robust and quantitative information on the co-association or exclusion of DNA-binding proteins on particular promoters. As a proof of principle, we investigated the association of histone H3 protein variants with modified tails (H3K9ac and H3K9me2) with Arabidopsis RNA polymerase II (RNPII) on the promoter of the constitutively expressed actin gene (At5g09810), and the trichome-expressed GLABRA3 (GL3) gene. As anticipated, our results show a strong positive correlation between H3K9ac and RNPII and a negative correlation between H3K9me2 and RNPII on the actin gene promoter. Our findings also establish a weak positive correlation between both H3K9ac and H3K9me2 and RNPII on the GL3 gene promoter, whose expression is restricted to a discrete number of cell types. We also describe mathematical tools that allow the easy interpretation of sChIP results. CONCLUSION:The sChIP method described here provides a reliable tool to determine whether the tethering of two proteins to the same DNA molecule is positively or negatively correlated. With the increasing need for establishing transcriptional regulatory networks, this modified sChIP method is anticipated to provide an excellent way to explore combinatorial gene regulation in eukaryotes.
journal_name
Plant Methodsjournal_title
Plant methodsauthors
Xie Z,Grotewold Edoi
10.1186/1746-4811-4-25subject
Has Abstractpub_date
2008-10-27 00:00:00pages
25issn
1746-4811pii
1746-4811-4-25journal_volume
4pub_type
杂志文章相关文献
Plant Methods文献大全abstract:BACKGROUND:Simultaneous analysis of multiple functional-related phytohormones and their metabolites will improve our understanding of interactions among different hormones in the same biologic process. RESULTS:A method was developed for simultaneous quantification of multiple phytohormones, abscisic acid, indole-3-ace...
journal_title:Plant methods
pub_type: 杂志文章
doi:10.1186/1746-4811-8-2
更新日期:2012-01-15 00:00:00
abstract::Terahertz technology is still an evolving research field that attracts scientists with very different backgrounds working on a wide range of subjects. In the past two decades, it has been demonstrated that terahertz technology can provide a non-invasive tool for measuring and monitoring the water content of leaves and...
journal_title:Plant methods
pub_type: 杂志文章
doi:10.1186/s13007-015-0057-7
更新日期:2015-03-06 00:00:00
abstract::[This corrects the article DOI: 10.1186/s13007-017-0166-6.]. ...
journal_title:Plant methods
pub_type: 杂志文章,已发布勘误
doi:10.1186/s13007-017-0249-4
更新日期:2017-11-16 00:00:00
abstract:BACKGROUND:In eukaryotic cells, the proteasome maintains homeostasis by selectively degrading regulatory and misfolded proteins, and in doing so contributes to the amino acid pool. Inhibition of the proteasome in yeast and human cells decreases de novo protein synthesis. However, it is not know if proteasome inhibition...
journal_title:Plant methods
pub_type: 杂志文章
doi:10.1186/s13007-016-0120-z
更新日期:2016-03-16 00:00:00
abstract:Background:Chloroplasts are critical organelles that perceive and convey metabolic and stress signals to different cellular components, while remaining the seat of photosynthesis and a metabolic factory. The proteomes of intact leaves, chloroplasts, and suborganellar fractions of plastids have been evaluated in the mod...
journal_title:Plant methods
pub_type: 杂志文章
doi:10.1186/s13007-020-00667-5
更新日期:2020-09-24 00:00:00
abstract:BACKGROUND:Despite increasing demand, imaging the internal structure of plant organs or tissues without the use of transgenic lines expressing fluorescent proteins remains a challenge. Techniques such as magnetic resonance imaging, optical projection tomography or X-ray absorption tomography have been used with various...
journal_title:Plant methods
pub_type: 杂志文章
doi:10.1186/s13007-015-0098-y
更新日期:2015-12-18 00:00:00
abstract:Background:Roses are widely used as garden ornamental plants and cut flowers. Rosa chinensis cv 'Old Blush' has been used as a model genotype in rose studies due to its contribution to recurrent flowering and tea scent traits of modern roses. The deficiency of efficient genetic transformation systems is a handicap limi...
journal_title:Plant methods
pub_type: 杂志文章
doi:10.1186/s13007-017-0268-1
更新日期:2017-12-22 00:00:00
abstract:BACKGROUND:Protoplasts isolated from leaves are useful materials in plant research. One application, the transient expression of recombinant genes using Arabidopsis mesophyll protoplasts (TEAMP), is currently commonly used for studies of subcellular protein localization, promoter activity, and in vivo protein-protein i...
journal_title:Plant methods
pub_type: 杂志文章
doi:10.1186/1746-4811-5-16
更新日期:2009-11-24 00:00:00
abstract:BACKGROUND:Archegoniates (bryophytes, ferns and gymnosperms), such as the moss Physcomitrella patens, possess freely motile sperm cells (spermatozoids) which reach the egg cell via surface water. Although these motile flagellated sperm cells are a traditional botanical subject, they have not been thoroughly analysed in...
journal_title:Plant methods
pub_type: 杂志文章
doi:10.1186/s13007-017-0186-2
更新日期:2017-05-10 00:00:00
abstract:Background:Antirrhinum (snapdragon) species are models for genetic and evolutionary research but recalcitrant to genetic transformation, limiting use of transgenic methods for functional genomics. Transient gene expression from viral vectors and virus-induced gene silencing (VIGS) offer transformation-free alternatives...
journal_title:Plant methods
pub_type: 杂志文章
doi:10.1186/s13007-020-00683-5
更新日期:2020-10-27 00:00:00
abstract:BACKGROUND:Plant breeding and genetics demand fast, exact and reproducible phenotyping. Efficient statistical evaluation of phenotyping data requires standardised data storage ensuring long-term data availability while maintaining intellectual property rights. This is state of the art at phenomics centres, which, howev...
journal_title:Plant methods
pub_type: 杂志文章
doi:10.1186/s13007-015-0069-3
更新日期:2015-04-07 00:00:00
abstract:Background:Herbaria are valuable sources of extensive curated plant material that are now accessible to genetic studies because of advances in high-throughput, next-generation sequencing methods. As an applied assessment of large-scale recovery of plastid and ribosomal genome sequences from herbarium material for plant...
journal_title:Plant methods
pub_type: 杂志文章
doi:10.1186/s13007-019-0534-5
更新日期:2020-01-04 00:00:00
abstract:Background:An effective and expeditious approach to assess plant nitrogen status is urgently needed in rice production and management as the conventional chemical methods are laborious and time-consuming. Results:Fourier transform infrared photoacoustic spectroscopy (FTIR-PAS) was used to record the spectra of rice le...
journal_title:Plant methods
pub_type: 杂志文章
doi:10.1186/s13007-019-0482-0
更新日期:2019-08-19 00:00:00
abstract:Background:Most bacteria are not culturable, but can be identified through molecular methods such as metagenomics studies. Due to specific metabolic requirements and symbiotic relationships, these bacteria cannot survive on typical laboratory media. Many economically and medically important bacteria are unculturable; i...
journal_title:Plant methods
pub_type: 杂志文章
doi:10.1186/s13007-019-0465-1
更新日期:2019-07-31 00:00:00
abstract:BACKGROUND:Suppression subtractive hybridization is a popular technique for gene discovery from non-model organisms without an annotated genome sequence, such as cowpea (Vigna unguiculata (L.) Walp). We aimed to use this method to enrich for genes expressed during drought stress in a drought tolerant cowpea line. Howev...
journal_title:Plant methods
pub_type: 杂志文章
doi:10.1186/1746-4811-6-10
更新日期:2010-04-01 00:00:00
abstract:BACKGROUND:Plant metabolites are commonly functionally classified, as defense- or growth-related phytohormones, primary and specialized metabolites, and so forth. Analytical procedures for the quantifications of these metabolites are challenging because the metabolites can vary over several orders of magnitude in conce...
journal_title:Plant methods
pub_type: 杂志文章
doi:10.1186/s13007-016-0130-x
更新日期:2016-05-26 00:00:00
abstract:Background:Low pollen viability may limit grapevine yield under certain conditions, causing relevant economic losses to grape-growers. It is usually evaluated by the quantification of the number of viable and non-viable pollen grains that are present in a sample after an adequate pollen grain staining procedure. Althou...
journal_title:Plant methods
pub_type: 杂志文章
doi:10.1186/s13007-017-0267-2
更新日期:2018-01-09 00:00:00
abstract:Background:High throughput non-destructive phenotyping is emerging as a significant approach for phenotyping germplasm and breeding populations for the identification of superior donors, elite lines, and QTLs. Detection and counting of spikes, the grain bearing organs of wheat, is critical for phenomics of a large set ...
journal_title:Plant methods
pub_type: 杂志文章
doi:10.1186/s13007-020-00582-9
更新日期:2020-03-18 00:00:00
abstract::[This corrects the article DOI: 10.1186/s13007-019-0478-9.]. ...
journal_title:Plant methods
pub_type: 已发布勘误
doi:10.1186/s13007-019-0495-8
更新日期:2019-10-10 00:00:00
abstract:BACKGROUND:The main aim of this study was to improve fungal resistance in bread wheat via transgenesis. Transgenic wheat plants harboring barley chitinase (chi26) gene, driven by maize ubi promoter, were obtained using biolistic bombardment, whereas the herbicide resistance gene, bar, driven by the CaMV 35S promoter wa...
journal_title:Plant methods
pub_type: 杂志文章
doi:10.1186/s13007-017-0191-5
更新日期:2017-05-22 00:00:00
abstract:: Research in plant molecular biology involves DNA purification on a daily basis. Although different commercial kits enable convenient extraction of high-quality DNA from E. coli cells, PCR and agarose gel samples as well as plant tissues, each kit is designed for a particular type of DNA extraction work, and the cost ...
journal_title:Plant methods
pub_type: 杂志文章
doi:10.1186/1746-4811-6-1
更新日期:2010-01-14 00:00:00
abstract:BACKGROUND:Mitochondria play critical roles in plant growth, development and stress tolerance. Numerous researchers have carried out studies on the plant mitochondrial genome structure, mitochondrial metabolism and nuclear-cytoplasmic interactions. However, classical plant mitochondria extraction methods are time-consu...
journal_title:Plant methods
pub_type: 杂志文章
doi:10.1186/s13007-020-00690-6
更新日期:2020-11-04 00:00:00
abstract:Background:Monitoring the timing of seedling emergence and early development via high-throughput phenotyping with computer vision is a challenging topic of high interest in plant science. While most studies focus on the measurements of leaf area index or detection of specific events such as emergence, little attention ...
journal_title:Plant methods
pub_type: 杂志文章
doi:10.1186/s13007-020-00647-9
更新日期:2020-07-30 00:00:00
abstract:Background:Charcoal rot is a fungal disease that thrives in warm dry conditions and affects the yield of soybeans and other important agronomic crops worldwide. There is a need for robust, automatic and consistent early detection and quantification of disease symptoms which are important in breeding programs for the de...
journal_title:Plant methods
pub_type: 杂志文章
doi:10.1186/s13007-018-0349-9
更新日期:2018-10-03 00:00:00
abstract:BACKGROUND:Allotetraploid white clover (Trifolium repens L.) is an important forage legume widely cultivated in most temperate regions. Only a small number of microsatellite markers are publicly available and can be utilized in white clover breeding programs. The objectives of this study were to develop an integrated a...
journal_title:Plant methods
pub_type: 杂志文章
doi:10.1186/1746-4811-4-19
更新日期:2008-07-16 00:00:00
abstract:Background:Non-contact resonant ultrasound spectroscopy (NC-RUS) has been proven as a reliable technique for the dynamic determination of leaf water status. It has been already tested in more than 50 plant species. In parallel, relative water content (RWC) is highly used in the ecophysiological field to describe the de...
journal_title:Plant methods
pub_type: 杂志文章
doi:10.1186/s13007-019-0511-z
更新日期:2019-11-07 00:00:00
abstract:BACKGROUND:The cultivar Micro-Tom (MT) is regarded as a model system for tomato genetics due to its short life cycle and miniature size. However, efforts to improve tomato genetic transformation have led to protocols dependent on the costly hormone zeatin, combined with an excessive number of steps. RESULTS:Here we re...
journal_title:Plant methods
pub_type: 杂志文章
doi:10.1186/1746-4811-6-23
更新日期:2010-10-07 00:00:00
abstract:BACKGROUND:A multitude of different imaging systems are already available to image genetically altered RNA species; however, only a few of these techniques are actually suitable to visualize endogenous RNA. One possibility is to use fluorescently-labelled and hybridization-sensitive probes. In order to yield more infor...
journal_title:Plant methods
pub_type: 杂志文章
doi:10.1186/1746-4811-10-15
更新日期:2014-05-31 00:00:00
abstract:BACKGROUND:It is well known that preparation of biological (plant and animal) tissues for Scanning Electron Microscopy (SEM) by chemical fixation and critical point drying results in shrinkage of tissues, often by up to 20-30%, depending on the tissue type and fixation protocol used. We sought to identify a protocol th...
journal_title:Plant methods
pub_type: 杂志文章
doi:10.1186/1746-4811-9-36
更新日期:2013-10-02 00:00:00
abstract:BACKGROUND:The data generated during a course of a biological experiment/study can be sometimes be massive and its management becomes quite critical for the success of the investigation undertaken. The accumulation and analysis of such large datasets often becomes tedious for biologists and lab technicians. Most of the...
journal_title:Plant methods
pub_type: 杂志文章
doi:10.1186/1746-4811-5-18
更新日期:2009-12-10 00:00:00