Abstract：
:Gene regulatory grids (GRGs) encompass the space of all the possible transcription factor (TF)-target gene interactions that regulate gene expression, with gene regulatory networks (GRNs) representing a temporal and spatial manifestation of a portion of the GRG, essential for the specification of gene expression. Thus, understanding GRG architecture provides a valuable tool to explain how genes are expressed in an organism, an important aspect of synthetic biology and essential toward the development of the "in silico" cell. Progress has been made in some unicellular model systems (eg, yeast), but significant challenges remain in more complex multicellular organisms such as plants. Key to understanding the organization of GRGs is therefore identifying the genes that TFs bind to, and control. The application of sensitive and high-throughput methods to investigate genome-wide TF-target gene interactions is providing a wealth of information that can be linked to important agronomic traits. We describe here the methods and resources that have been developed to investigate the architecture of plant GRGs and GRNs. We also provide information regarding where to obtain clones or other resources necessary for synthetic biology or metabolic engineering.
journal_name
Methods Enzymoljournal_title
Methods in enzymologyauthors
Yang F,Ouma WZ,Li W,Doseff AI,Grotewold Edoi
10.1016/bs.mie.2016.03.003subject
Has Abstractpub_date
2016-01-01 00:00:00pages
251-304eissn
0076-6879issn
1557-7988pii
S0076-6879(16)00115-4journal_volume
576pub_type
杂志文章abstract：:In principle, the long emission lifetimes of lanthanide chelates should enable their ultrasensitive detection in biological systems by time-resolved optical microscopy. However, most lanthanide-imaging systems cannot achieve sensitivities that exceed those of conventional fluorescence microscopes, since they are limit...
journal_title：Methods in enzymology
pub_type： 杂志文章
doi：10.1016/bs.mie.2020.04.030
更新日期：2020-01-01 00:00:00
abstract：:Nonsense-mediated mRNA decay (NMD) is an evolutionarily conserved mechanism of specific degradation of transcripts with a premature stop codon. NMD eliminates aberrant mRNAs arising from mutations, alternative splicing, and other events in cells. In addition, many normal transcripts undergo NMD. Recent studies demonst...
journal_title：Methods in enzymology
pub_type： 杂志文章
doi：10.1016/bs.mie.2016.02.008
更新日期：2016-01-01 00:00:00
abstract：:The breakthrough discovery that double-stranded RNA of 21 nucleotides in length (referred to as short or small interfering RNA; siRNA) can trigger sequence-specific gene silencing in mammalian cells has led to the development of a powerful new approach to study gene function (Dillon et al., 2005; Dykxhoorn et al., 200...
journal_title：Methods in enzymology
pub_type： 杂志文章
doi：10.1016/S0076-6879(06)06046-0
更新日期：2006-01-01 00:00:00
abstract：:Staphylococcus aureus is a Gram-positive major human pathogen involved in a wide range of human infectious diseases (from minor skin infections to septicemia, endocarditis or toxic shock syndrome). The treatment of S. aureus infections is very challenging due to the emergence of multiple antibiotic-resistant isolates....
journal_title：Methods in enzymology
pub_type： 杂志文章
doi：10.1016/bs.mie.2018.08.022
更新日期：2018-01-01 00:00:00
abstract：:Fluorescence-based imaging regimes require exposure of living samples under study to high intensities of focused incident illumination. An often underestimated, overlooked, or simply ignored fact in the design of any experimental imaging protocol is that exposure of the specimen to these excitation light sources must ...
journal_title：Methods in enzymology
pub_type： 杂志文章
doi：10.1016/B978-0-12-391856-7.00039-1
更新日期：2012-01-01 00:00:00
abstract：:Autophagy is an extremely dynamic process that mediates the rapid degradation of intracellular components in response to different stress conditions. The autophagic response is executed by specific protein complexes, whose function is regulated by posttranslational modifications and interactions with positive and nega...
journal_title：Methods in enzymology
pub_type： 杂志文章
doi：10.1016/bs.mie.2016.09.069
更新日期：2017-01-01 00:00:00
abstract：:The breaking of RNA strands by 2'-O-transphosphorylation is a ubiquitous reaction in biology, and enzymes that catalyze this reaction play key roles in RNA metabolism. The mechanisms of 2'-O-transphosphorylation in solution are relatively well studied, but complex and can involve different transition states depending ...
journal_title：Methods in enzymology
pub_type： 杂志文章
doi：10.1016/bs.mie.2017.07.017
更新日期：2017-01-01 00:00:00
abstract：:The gasdermin (GSDM) family consists of gasdermin A (GSDMA), B (GSDMB), C (GSDMC), D (GSDMD), E or DNFA5 (GSDME), and DFNB59 in human. Expressed in the skin, gastrointestinal tract, and various immune cells, GSDMs mediate homeostasis and inflammation upon activation by caspases and unknown proteases. In particular, GS...
journal_title：Methods in enzymology
pub_type： 杂志文章
doi：10.1016/bs.mie.2019.04.024
更新日期：2019-01-01 00:00:00
abstract：:Intraflagellar transport (IFT) involves the movement of large proteinaceous particles or trains along the length of ciliary and flagellar axonemal microtubules. The particles contain multiple copies of two protein complexes. As isolated from the flagellated model organism, Chlamydomonas reinhardtii, IFT A contains 6 d...
journal_title：Methods in enzymology
pub_type： 杂志文章
doi：10.1016/B978-0-12-397945-2.00010-X
更新日期：2013-01-01 00:00:00
abstract：:PRA2 was found to interact with the ER-localized protein VAMP-associated protein of 33 kDa or VAP-33 by a yeast two-hybrid screen. We describe here the purification of PRA2 and VAP-33 as well as an in vitro pull-down procedure to verify the interaction. PRA2 was found to form a large sodium dodecyl sulfate (SDS)-insol...
journal_title：Methods in enzymology
pub_type： 杂志文章
doi：10.1016/S0076-6879(05)03069-7
更新日期：2005-01-01 00:00:00
abstract：:The yeast Saccharomyces cerevisiae is an ideal model system for examining fundamental nitrogen oxide biochemistry. The utility of this model system lies in both the similarities and the differences between yeast and mammalian cells. The similarities between the two systems, with regards to many of the fundamental bioc...
journal_title：Methods in enzymology
pub_type： 杂志文章
doi：10.1016/S0076-6879(05)96025-4
更新日期：2005-01-01 00:00:00
abstract：:The above methodology has been used to prepare a variety of PE-immunotoxins. These reagents are potent cytotoxic agents for cells in culture that bind the appropriate antibody and nontoxic when cells do not bind the antibody. PE-immunotoxins can be used to select for mutant cultured cells which lack the target of the ...
journal_title：Methods in enzymology
pub_type： 杂志文章
doi：10.1016/s0076-6879(87)51015-1
更新日期：1987-01-01 00:00:00
abstract：:Histone variants and posttranslational modifications (PTMs) are essential for epigenetic regulation of transcriptional expression. Single and/or combinatorial PTMs of histones play important roles in development and disease formation. Mass spectrometry (MS) has been a powerful tool to study histone variants and PTMs, ...
journal_title：Methods in enzymology
pub_type： 杂志文章
doi：10.1016/B978-0-12-391940-3.00001-9
更新日期：2012-01-01 00:00:00
abstract：:Peptides are multidentate chiral ligands capable of coordinating different metal ions. Nowadays, they can be obtained with high yield and purity, thanks to the advances on peptide/protein chemistry as well as in equipment (peptide synthesizers). Based on the identity and length of their amino acid sequences, peptides ...
journal_title：Methods in enzymology
pub_type： 杂志文章
doi：10.1016/bs.mie.2016.04.007
更新日期：2016-01-01 00:00:00
abstract：:Cell-free (CF) protein expression has emerged as one of the most efficient production platforms for membrane proteins. Central bottlenecks prevalent in conventional cell-based expression systems such as mistargeting, inclusion body formation, degradation as well as product toxicity can be addressed by taking advantage...
journal_title：Methods in enzymology
pub_type： 杂志文章
doi：10.1016/bs.mie.2014.12.016
更新日期：2015-01-01 00:00:00
abstract：:Dynamin I is a large GTPase enzyme required in membrane constriction and fission during multiple forms of endocytosis. The first method described here is for the rapid purification of native dynamin from peripheral membrane extracts of sheep brain using ammonium sulfate precipitation and affinity purification on recom...
journal_title：Methods in enzymology
pub_type： 杂志文章
doi：10.1016/S0076-6879(05)04049-8
更新日期：2005-01-01 00:00:00
abstract：:Methane production and consumption in anaerobic marine sediments is catalyzed by a series of reversible tetrahydromethanopterin (H(4)MPT)-linked C1 transfer reactions. Although many of these reactions are conserved between one-carbon compound utilizing microorganisms, two remain diagnostic for archaeal methane metabol...
journal_title：Methods in enzymology
pub_type： 杂志文章
doi：10.1016/B978-0-12-385112-3.00004-4
更新日期：2011-01-01 00:00:00
abstract：:Respiration is widely used for evaluation of the metabolic capabilities or physiological state of the microbial culture. This chapter describes novel approaches for characterization of respiration at a single cell level: (1) flow cytometry-based redox sensing (FCRS) of actively metabolizing microbes; (2) respiration r...
journal_title：Methods in enzymology
pub_type： 杂志文章
doi：10.1016/B978-0-12-386905-0.00010-3
更新日期：2011-01-01 00:00:00
abstract：:Genetically encoded fluorescent sensors are essential tools in modern biological research, and recent advances in fluorescent proteins (FPs) have expanded the scope of sensor design and implementation. In this review we compare different sensor platforms, including Förster resonance energy transfer (FRET) sensors, flu...
journal_title：Methods in enzymology
pub_type： 杂志文章,评审
doi：10.1016/bs.mie.2017.01.019
更新日期：2017-01-01 00:00:00
abstract：:A procedure for an in vitro signaling assay is described for the MAPK and NFkappaB pathways. The method uses a membrane-cleared lysate that contains all the soluble components required for activating these signaling cascades. The pathways can be activated by variety of molecules, including kinases, G-proteins, and E3 ...
journal_title：Methods in enzymology
pub_type： 杂志文章
doi：10.1016/S0076-6879(07)38024-5
更新日期：2008-01-01 00:00:00
abstract：:Critical to the advancement of tumor immunotherapy is the reliable identification of responders and the quantification of the tumor-specific immune response elicited by treatments. In this regard, Enzyme-Linked Immunospot assay (ELISpot) is an ideal monitoring technique due to its high sensitivity, ease of execution a...
journal_title：Methods in enzymology
pub_type： 杂志文章
doi：10.1016/bs.mie.2019.05.058
更新日期：2020-01-01 00:00:00
abstract：:Posttranslational modification of circadian clock proteins by phosphorylation is an essential regulatory process in the control of eukaryotic circadian clocks. In the Neurospora circadian clock, the key clock protein FREQUENCY (FRQ) is progressively phosphorylated. The phosphorylation of FRQ is regulated by both kinas...
journal_title：Methods in enzymology
pub_type： 杂志文章
doi：10.1016/S0076-6879(05)93017-6
更新日期：2005-01-01 00:00:00
abstract：:Complex I is the major entry point in the bacterial and mitochondrial respiratory chain. Structural knowledge of the enzyme is still limited because of its large size and complicated architecture. Only the structure of the hydrophilic domain of a bacterial Complex I has been solved to high resolution by X-ray crystall...
journal_title：Methods in enzymology
pub_type： 杂志文章
doi：10.1016/S0076-6879(08)04401-7
更新日期：2009-01-01 00:00:00
abstract：:Circadian rhythms generated by cell autonomous biological clocks allow for the appropriate temporal synchronization of physiology and behavior, optimizing the efficiency of biological systems. Circadian oscillators and functions have been uncovered in both central and peripheral tissues. This article describes methodo...
journal_title：Methods in enzymology
pub_type： 杂志文章
doi：10.1016/S0076-6879(05)93027-9
更新日期：2005-01-01 00:00:00
abstract：:The enzymes involved in mitochondrial oxidative phosphorylation (OXPHOS) are coassembled into higher ordered supercomplexes within the mitochondrial inner membrane. The cytochrome bc(1)-cytochrome c oxidase (COX) supercomplex is formed by the coassociation of the two electron transport chain complexes, the cytochrome ...
journal_title：Methods in enzymology
pub_type： 杂志文章
doi：10.1016/S0076-6879(08)04411-X
更新日期：2009-01-01 00:00:00
abstract：:A simple and convenient method is described to determine primary deuterium kinetic isotope effects (1°DKIEs) on reactions where the hydron incorporated into the reaction product is derived from solvent water. The 1°DKIE may be obtained by 1H NMR analyses as the ratio of the yields of H- and D-labeled products from a r...
journal_title：Methods in enzymology
pub_type： 杂志文章
doi：10.1016/bs.mie.2017.06.043
更新日期：2017-01-01 00:00:00
abstract：:Extracellular thiol/disulfide redox environments are highly regulated in healthy individuals and become oxidized in disease. This oxidation affects the function of cell surface receptors, ion channels, and structural proteins. Downstream signaling due to changes in extracellular redox potential can be studied using a ...
journal_title：Methods in enzymology
pub_type： 杂志文章
doi：10.1016/S0076-6879(10)74010-6
更新日期：2010-01-01 00:00:00
abstract：:Optogenetic systems enable unmatched precision for controlling molecular biological processes but require the use of specialized electrical and optical hardware. In an effort to make working with optogenetic systems more accessible, we recently described an open-source hardware platform called the Light Plate Apparatu...
journal_title：Methods in enzymology
pub_type： 杂志文章
doi：10.1016/bs.mie.2019.04.018
更新日期：2019-01-01 00:00:00
abstract：:Glycosylphosphatidylinositol-anchored proteins can be specifically identified by several methods. PI-PLC digestion analyses, the most widely used technique, can be performed more reliably when conducted with purified protein and phase partitioning to exclude steric effects and when combined with alkaline hydrolysis to...
journal_title：Methods in enzymology
pub_type： 杂志文章
doi：10.1016/0076-6879(95)50099-5
更新日期：1995-01-01 00:00:00
abstract：:Genetic modifier screens offer a powerful, indeed a uniquely powerful tool for the analysis and identification of elements capable of modulating specific cellular functions in development. Here, we describe the methodology that allowed us to explore the genetic circuitry that affects a Notch mutant phenotype caused by...
journal_title：Methods in enzymology
pub_type： 杂志文章
doi：10.1016/B978-0-12-397926-1.00016-0
更新日期：2014-01-01 00:00:00
