Proximity Labeling Techniques: A Multi‐Omics Toolbox

Shkel, Olha; Kharkivska, Yevheniia; Kim, Yun Kyung; Lee, Jung Hoon

doi:10.1002/asia.202101240

Cited by 10 publications

(6 citation statements)

References 85 publications

(61 reference statements)

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“…Subsequently, a small-molecule substrate, such as biotin, is added, which initiates the covalent labeling of endogenous proteins within nanometer proximity of the enzyme. The labeled target protein complex or organelle can be affinity purified and enriched using streptavidin-coated magnetic beads, and the results can be analyzed through mass spectrometry or high-throughput sequencing [ 22 ].…”

mentioning

confidence: 99%

The development of proximity labeling technology and its applications in mammals, plants, and microorganisms

Guo,

et al. 2023

Cell Commun Signal

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Protein‒protein, protein‒RNA, and protein‒DNA interaction networks form the basis of cellular regulation and signal transduction, making it crucial to explore these interaction networks to understand complex biological processes. Traditional methods such as affinity purification and yeast two-hybrid assays have been shown to have limitations, as they can only isolate high-affinity molecular interactions under nonphysiological conditions or in vitro. Moreover, these methods have shortcomings for organelle isolation and protein subcellular localization. To address these issues, proximity labeling techniques have been developed. This technology not only overcomes the limitations of traditional methods but also offers unique advantages in studying protein spatial characteristics and molecular interactions within living cells. Currently, this technique not only is indispensable in research on mammalian nucleoprotein interactions but also provides a reliable approach for studying nonmammalian cells, such as plants, parasites and viruses. Given these advantages, this article provides a detailed introduction to the principles of proximity labeling techniques and the development of labeling enzymes. The focus is on summarizing the recent applications of TurboID and miniTurbo in mammals, plants, and microorganisms.

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confidence: 99%

The development of proximity labeling technology and its applications in mammals, plants, and microorganisms

Guo,

et al. 2023

Cell Commun Signal

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“…APEX2 has increased catalytic activity and requires less H 2 O 2 and biotin-phenol, thus reducing the toxic effect on living cells [ 111 ]. In addition to the commonly used PL enzymes, other enzymes have been developed for PL and used in a small range, such as horseradish peroxidase (HRP), transpeptidase sortase A (SrtA) and proteasomal accessory factor A (PafA) [ 112 ].…”

Section: Potential Strategies In Kinase Spatial Assaymentioning

confidence: 99%

Mapping the Protein Kinome: Current Strategy and Future Direction

Hou

Liu²

2023

Cells

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The kinome includes over 500 different protein kinases, which form an integrated kinase network that regulates cellular phosphorylation signals. The kinome plays a central role in almost every cellular process and has strong linkages with many diseases. Thus, the evaluation of the cellular kinome in the physiological environment is essential to understand biological processes, disease development, and to target therapy. Currently, a number of strategies for kinome analysis have been developed, which are based on monitoring the phosphorylation of kinases or substrates. They have enabled researchers to tackle increasingly complex biological problems and pathological processes, and have promoted the development of kinase inhibitors. Additionally, with the increasing interest in how kinases participate in biological processes at spatial scales, it has become urgent to develop tools to estimate spatial kinome activity. With multidisciplinary efforts, a growing number of novel approaches have the potential to be applied to spatial kinome analysis. In this paper, we review the widely used methods used for kinome analysis and the challenges encountered in their applications. Meanwhile, potential approaches that may be of benefit to spatial kinome study are explored.

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“…Proximity ligation is a powerful strategy to address some of these obstacles [71]. Proximity ligation is based on promiscuous non-mammalian enzymes such as the engineered ascorbate peroxidase 2 (APEX2) or the biotin ligase BirA*, which can be expressed in mammalian cells and targeted to specific subcellular localisations or compartments to biotinylate proximal proteins and transcripts in vivo [68,[72][73][74][75][76][77].…”

Section: Assessment Of Ribonucleoprotein Complexes By Proximity Ligationmentioning

confidence: 99%

Compartment-Specific Proximity Ligation Expands the Toolbox to Assess the Interactome of the Long Non-Coding RNA NEAT1

Mamontova

Trifault

Burger

2022

IJMS

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The nuclear paraspeckle assembly transcript 1 (NEAT1) locus encodes two long non-coding (lnc)RNA isoforms that are upregulated in many tumours and dynamically expressed in response to stress. NEAT1 transcripts form ribonucleoprotein complexes with numerous RNA-binding proteins (RBPs) to assemble paraspeckles and modulate the localisation and activity of gene regulatory enzymes as well as a subset of messenger (m)RNA transcripts. The investigation of the dynamic composition of NEAT1-associated proteins and mRNAs is critical to understand the function of NEAT1. Interestingly, a growing number of biochemical and genetic tools to assess NEAT1 interactomes has been reported. Here, we discuss the Hybridisation Proximity (HyPro) labeling technique in the context of NEAT1. HyPro labeling is a recently developed method to detect spatially ordered interactions of RNA-containing nuclear compartments in cultured human cells. After introducing NEAT1 and paraspeckles, we describe the advantages of the HyPro technology in the context of other methods to study RNA interactomes, and review the key findings in mapping NEAT1-associated RNA transcripts and protein binding partners. We further discuss the limitations and potential improvements of HyPro labeling, and conclude by delineating its applicability in paraspeckles-related cancer research.

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Proximity Labeling Techniques: A Multi‐Omics Toolbox

Cited by 10 publications

References 85 publications

The development of proximity labeling technology and its applications in mammals, plants, and microorganisms

The development of proximity labeling technology and its applications in mammals, plants, and microorganisms

Mapping the Protein Kinome: Current Strategy and Future Direction

Compartment-Specific Proximity Ligation Expands the Toolbox to Assess the Interactome of the Long Non-Coding RNA NEAT1

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