Abstract:
:Protein ADP-ribosylation is a structurally heterogeneous post-translational modification (PTM) that influences the physicochemical and biological properties of the modified protein. ADP-ribosylation of chromatin changes its structural properties, thereby regulating important nuclear functions. A lack of suitable antibodies for chromatin immunoprecipitation (ChIP) has so far prevented a comprehensive analysis of DNA-associated protein ADP-ribosylation. To analyze chromatin ADP-ribosylation, we recently developed a novel ADP-ribose-specific chromatin-affinity purification (ADPr-ChAP) methodology that uses the recently identified ADP-ribose-binding domains RNF146 WWE and Af1521. In this protocol, we describe how to use this robust and versatile method for genome-wide and loci-specific localization of chromatin ADP-ribosylation. ADPr-ChAP enables bioinformatic comparisons of ADP-ribosylation with other chromatin modifications and is useful for understanding how ADP-ribosylation regulates biologically important cellular processes. ADPr-ChAP takes 1 week and requires standard skills in molecular biology and biochemistry. Although not covered in detail here, this technique can also be combined with conventional ChIP or DNA analysis to define the histone marks specifically associated with the ADP-ribosylated chromatin fractions and dissect the molecular mechanism and functional role of chromatin ADP-ribosylation.
journal_name
Nat Protocjournal_title
Nature protocolsauthors
Bisceglie L,Bartolomei G,Hottiger MOdoi
10.1038/nprot.2017.072subject
Has Abstractpub_date
2017-09-01 00:00:00pages
1951-1961issue
9eissn
1754-2189issn
1750-2799pii
nprot.2017.072journal_volume
12pub_type
杂志文章相关文献
Nature Protocols文献大全abstract::Mouse embryonic stem cells (mESCs) are key tools for genetic engineering, development of stem cell-based therapies and basic research on pluripotency and early lineage commitment. However, successful derivation of germline-competent embryonic stem cell lines has, until recently, been limited to a small number of inbre...
journal_title:Nature protocols
pub_type: 杂志文章
doi:10.1038/nprot.2014.030
更新日期:2014-03-01 00:00:00
abstract::Single-cell electroporation allows transfection of plasmid DNA or macromolecules into individual living cells using modified patch electrodes and common electrophysiological equipment. This protocol is optimized for rapid in vivo electroporation of Xenopus laevis tadpole brains with DNA, dextrans, morpholinos and comb...
journal_title:Nature protocols
pub_type: 杂志文章
doi:10.1038/nprot.2006.186
更新日期:2006-01-01 00:00:00
abstract::Reactive oxygen species (ROS) are continuously produced in the cell as a consequence of aerobic metabolism, and are controlled by several antioxidant mechanisms. An accurate measurement of ROS is essential to evaluate the redox status of the cell, or the effects of molecules with the pro-oxidant or antioxidant activit...
journal_title:Nature protocols
pub_type: 杂志文章
doi:10.1038/nprot.2009.189
更新日期:2009-01-01 00:00:00
abstract::A mechanistic understanding of HIV-1 latency depends on a model system that recapitulates the in vivo condition of latently infected, resting CD4(+) T lymphocytes. Latency seems to be established after activated CD4(+) T cells, the principal targets of HIV-1 infection, become productively infected and survive long eno...
journal_title:Nature protocols
pub_type: 杂志文章
doi:10.1038/nprot.2014.188
更新日期:2014-12-01 00:00:00
abstract::The genomic instability of stem cells in culture, caused by their routine in vitro propagation or by their genetic manipulation, is deleterious both for their clinical application and for their use in basic research. Frequent evaluation of the genomic integrity of stem cells is thus required, and it is usually perform...
journal_title:Nature protocols
pub_type: 杂志文章
doi:10.1038/nprot.2013.051
更新日期:2013-05-01 00:00:00
abstract::The human stomach contains two primary domains: the corpus, which contains the fundic epithelium, and the antrum. Each of these domains has distinct cell types and functions, and therefore each presents with unique disease pathologies. Here, we detail two protocols to differentiate human pluripotent stem cells (hPSCs)...
journal_title:Nature protocols
pub_type: 杂志文章
doi:10.1038/s41596-018-0080-z
更新日期:2019-01-01 00:00:00
abstract::Analysis of the sequence and nature of protein N termini has many applications. Defining the termini of proteins for proteome annotation in the Human Proteome Project is of increasing importance. Terminomics analysis of protease cleavage sites in degradomics for substrate discovery is a key new application. Here we de...
journal_title:Nature protocols
pub_type: 杂志文章
doi:10.1038/nprot.2011.382
更新日期:2011-09-22 00:00:00
abstract::Realizing the potential of human embryonic stem cells (hESCs) in research and commercial applications requires generic protocols for culture, expansion and genetic modification that function between multiple lines. Here we describe a feeder-free hESC culture protocol that was tested in 13 independent hESC lines derive...
journal_title:Nature protocols
pub_type: 杂志文章
doi:10.1038/nprot.2008.140
更新日期:2008-01-01 00:00:00
abstract::We describe a step-by-step protocol for measuring the stable products of the nitric oxide (NO) pathway: nitrite, nitrite plus nitrate and nitrate. This described protocol is easy to apply and is about 50 times more sensitive than the commonly used Griess reaction or commercially available assay kits based on the Gries...
journal_title:Nature protocols
pub_type: 杂志文章
doi:10.1038/nprot.2006.341
更新日期:2006-01-01 00:00:00
abstract::Gene tagging with fluorescent proteins is essential for investigations of the dynamic properties of cellular proteins. CRISPR-Cas9 technology is a powerful tool for inserting fluorescent markers into all alleles of the gene of interest (GOI) and allows functionality and physiological expression of the fusion protein. ...
journal_title:Nature protocols
pub_type: 杂志文章
doi:10.1038/nprot.2018.042
更新日期:2018-06-01 00:00:00
abstract::The radial arm water maze (RAWM) contains six swim paths (arms) extending out of an open central area, with an escape platform located at the end of one arm (the goal arm). The goal arm location remains constant for a given mouse. On day 1, mice are trained for 15 trials (spaced over 3 h), with trials alternating betw...
journal_title:Nature protocols
pub_type: 杂志文章
doi:10.1038/nprot.2006.275
更新日期:2006-01-01 00:00:00
abstract::Herein we describe a protocol that uses hollow-fiber flow field-flow fractionation (FFF) coupled with multiangle light scattering (MALS) for hydrodynamic size-based separation and characterization of complex protein aggregates. The fractionation method, which requires 1.5 h to run, was successfully modified from the a...
journal_title:Nature protocols
pub_type: 杂志文章
doi:10.1038/nprot.2015.009
更新日期:2015-01-01 00:00:00
abstract::Most currently available colorectal cancer (CRC) mouse models are not suitable for studying progression toward the metastatic stage. Recently, establishment of tumor organoid lines, either from murine CRC models or patients, and the possibility of engineering them with genome-editing technologies, have provided a larg...
journal_title:Nature protocols
pub_type: 杂志文章
doi:10.1038/nprot.2017.137
更新日期:2018-02-01 00:00:00
abstract::Association studies can focus on candidate gene(s), a particular genomic region, or adopt a genome-wide association approach, each of which has implications for marker selection. The strategy for marker selection will affect the statistical power of the study to detect a disease association and is a crucial element of...
journal_title:Nature protocols
pub_type: 杂志文章
doi:10.1038/nprot.2009.38
更新日期:2009-01-01 00:00:00
abstract::The pig has emerged as an important large animal model in biomedical and pharmaceutical research. We describe a protocol for high-efficiency germline transgenesis and sustained transgene expression in pigs by using the Sleeping Beauty (SB) transposon system. The protocol is based on co-injection of a plasmid encoding ...
journal_title:Nature protocols
pub_type: 杂志文章
doi:10.1038/nprot.2014.010
更新日期:2014-04-01 00:00:00
abstract::Protein digestion using a dedicated protease represents a key element in a typical mass spectrometry (MS)-based shotgun proteomics experiment. Up to now, digestion has been predominantly performed with trypsin, mainly because of its high specificity, widespread availability and ease of use. Lately, it has become appar...
journal_title:Nature protocols
pub_type: 杂志文章
doi:10.1038/nprot.2016.057
更新日期:2016-05-01 00:00:00
abstract::In situ mRNA hybridization is one of the most powerful techniques for analyzing patterns of gene expression. However, its usefulness is limited in complex plant tissues by the need to fix, embed and section samples before localizing the desired mRNA. Here we present a robust whole-mount in situ hybridization method th...
journal_title:Nature protocols
pub_type: 杂志文章
doi:10.1038/nprot.2014.162
更新日期:2014-10-01 00:00:00
abstract::This protocol and the accompanying software program called LEVER (lineage editing and validation) enable quantitative automated analysis of phase-contrast time-lapse images of cultured neural stem cells. Images are captured at 5-min intervals over a period of 5-15 d as the cells proliferate and differentiate. LEVER au...
journal_title:Nature protocols
pub_type: 杂志文章
doi:10.1038/nprot.2011.422
更新日期:2011-11-17 00:00:00
abstract::N-Succinimidyl 3-(di-tert-butyl[(18)F]fluorosilyl)benzoate ([(18)F]SiFB) is a highly reactive prosthetic group for radiolabeling of proteins for use in positron emission tomography (PET). It is similar to N-succinimidyl-4-[(18)F]fluorobenzoate ([(18)F]SFB), the 'gold-standard' prosthetic group for protein (18)F-labeli...
journal_title:Nature protocols
pub_type: 杂志文章
doi:10.1038/nprot.2012.110
更新日期:2012-11-01 00:00:00
abstract::This protocol describes a method for converting short single-stranded and double-stranded DNA into libraries compatible with high-throughput sequencing using Illumina technology. This method has primarily been developed to improve sequence retrieval from ancient DNA, but it is also applicable to the sequencing of shor...
journal_title:Nature protocols
pub_type: 杂志文章
doi:10.1038/nprot.2013.038
更新日期:2013-04-01 00:00:00
abstract::The development of single-molecule switching (SMS) fluorescence microscopy (also called single-molecule localization microscopy) over the last decade has enabled researchers to image cell biological structures at unprecedented resolution. Using two opposing objectives in a so-called 4Pi geometry doubles the available ...
journal_title:Nature protocols
pub_type: 杂志文章
doi:10.1038/s41596-020-00428-7
更新日期:2020-12-16 00:00:00
abstract::More than 400,000 people each year suffer adverse effects following bites from venomous snakes. However, snake venom is also a rich source of bioactive molecules with known or potential therapeutic applications. Manually 'milking' snakes is the most common method to obtain venom. Safer alternative methods to produce v...
journal_title:Nature protocols
pub_type: 杂志文章
doi:10.1038/s41596-020-00463-4
更新日期:2021-01-27 00:00:00
abstract::We describe the implementation and use of an adaptive imaging framework for optimizing spatial resolution and signal strength in a light-sheet microscope. The framework, termed AutoPilot, comprises hardware and software modules for automatically measuring and compensating for mismatches between light-sheet and detecti...
journal_title:Nature protocols
pub_type: 杂志文章
doi:10.1038/s41596-018-0043-4
更新日期:2018-11-01 00:00:00
abstract::This protocol describes a directed evolution method for in vitro mutagenesis and recombination of polynucleotide sequences. The staggered extension process (StEP) is essentially a modified PCR that uses highly abbreviated annealing and extension steps to generate staggered DNA fragments and promote crossover events al...
journal_title:Nature protocols
pub_type: 杂志文章
doi:10.1038/nprot.2006.309
更新日期:2006-01-01 00:00:00
abstract::Here, we describe a simple protocol for the design and construction of a laser-guided direct writing (LGDW) system able to micropattern the self-assembly of liver sinusoid-like structures with micrometer resolution in vitro. To the best of our knowledge, LGDW is the only technique able to pattern cells "on the fly" wi...
journal_title:Nature protocols
pub_type: 杂志文章
doi:10.1038/nprot.2006.386
更新日期:2006-01-01 00:00:00
abstract::The goal of many current studies of neovascularization is to define the phenotype of vascular cell populations of different origins and to determine how such cells promote assembly of vascular channel. Here, we describe a protocol to immunophenotype vascular cells by high-resolution imaging and by fluorescence-activat...
journal_title:Nature protocols
pub_type: 杂志文章
doi:10.1038/nprot.2007.537
更新日期:2008-01-01 00:00:00
abstract::This transformation procedure generates, with high efficiency (70-90%), hairy roots in cultivars, landraces and accessions of Phaseolus vulgaris (common bean) and other Phaseolus spp. Hairy roots rapidly develop after wounding young plantlets with Agrobacterium rhizogenes, at the cotyledon node, and keeping the plants...
journal_title:Nature protocols
pub_type: 杂志文章
doi:10.1038/nprot.2007.259
更新日期:2007-01-01 00:00:00
abstract::Postembryonic development is an important process of organismal maturation after embryonic growth. Despite key progress in recent years in understanding embryonic development via fluorescence time-lapse microscopy, comparatively less live-cell imaging of postembryonic development has been done. Here we describe a prot...
journal_title:Nature protocols
pub_type: 杂志文章
doi:10.1038/nprot.2012.128
更新日期:2012-12-01 00:00:00
abstract::Cap-analysis gene expression (CAGE) provides accurate high-throughput measurement of RNA expression. CAGE allows mapping of all the initiation sites of both capped coding and noncoding RNAs. In addition, transcriptional start sites within promoters are characterized at single-nucleotide resolution. The latter allows t...
journal_title:Nature protocols
pub_type: 杂志文章
doi:10.1038/nprot.2012.005
更新日期:2012-02-23 00:00:00
abstract::Boronic acids and esters have critical roles in the areas of synthetic organic chemistry, molecular sensors, materials science, drug discovery, and catalysis. Many of the current applications of boronic acids and esters require materials with very low levels of transition metal contamination. Most of the current metho...
journal_title:Nature protocols
pub_type: 杂志文章
doi:10.1038/nprot.2016.184
更新日期:2017-03-01 00:00:00