PendoTMBase: A Database for Plant Endogenous Target Mimics

2020 ◽  
Vol 12 (4) ◽  
pp. 526-529
Author(s):  
Jiacong Deng ◽  
Qingyun Li ◽  
Likun Huang ◽  
Weiqi Tang ◽  
Kehui Zheng ◽  
...  
Keyword(s):  
Endogenous Target

scholarly journals Long Non-Coding RNAs as Endogenous Target Mimics and Exploration of Their Role in Low Nutrient Stress Tolerance in Plants

Genes ◽  
2018 ◽  
Vol 9 (9) ◽  
pp. 459 ◽  
Author(s):  
Priyanka Borah ◽  
Antara Das ◽  
Matthew Milner ◽  
Arif Ali ◽  
Alison Bentley ◽  
...  
Keyword(s):  
Gene Regulation ◽  
Next Generation Sequencing ◽  
Non Coding Rna ◽  
Genome Wide ◽  
Non Coding Rnas ◽  
Endogenous Target ◽  
Long Non Coding Rna ◽  
Nutrient Homeostasis ◽  
Generation Sequencing

Long non-coding RNA (lncRNA) research in plants has recently gained momentum taking cues from studies in animals systems. The availability of next-generation sequencing has enabled genome-wide identification of lncRNA in several plant species. Some lncRNAs are inhibitors of microRNA expression and have a function known as target mimicry with the sequestered transcript known as an endogenous target mimic (eTM). The lncRNAs identified to date show diverse mechanisms of gene regulation, most of which remain poorly understood. In this review, we discuss the role of identified putative lncRNAs that may act as eTMs for nutrient-responsive microRNAs (miRNAs) in plants. If functionally validated, these putative lncRNAs would enhance current understanding of the role of lncRNAs in nutrient homeostasis in plants.

scholarly journals Targeting endogenous proteins for degradation through the affinity-directed protein missile system

Open Biology ◽  
2017 ◽  
Vol 7 (5) ◽  
pp. 170066 ◽  
Author(s):  
Luke J. Fulcher ◽  
Luke D. Hutchinson ◽  
Thomas J. Macartney ◽  
Craig Turnbull ◽  
Gopal P. Sapkota
Keyword(s):  
Tyrosine Phosphatase ◽  
E3 Ligase ◽  
Target Proteins ◽  
Von Hippel Lindau ◽  
Vhl Protein ◽  
Endogenous Target ◽  
Endogenous Proteins ◽  
First Time ◽  
Missile System ◽  
Target Effects

Targeted proteolysis of endogenous proteins is desirable as a research toolkit and in therapeutics. CRISPR/Cas9-mediated gene knockouts are irreversible and often not feasible for many genes. Similarly, RNA interference approaches necessitate prolonged treatments, can lead to incomplete knockdowns and are often associated with off-target effects. Targeted proteolysis can overcome these limitations. In this report, we describe an affinity-directed protein missile (AdPROM) system that harbours the von Hippel–Lindau (VHL) protein, the substrate receptor of the Cullin2 (CUL2) E3 ligase complex, tethered to polypeptide binders that selectively bind and recruit endogenous target proteins to the CUL2-E3 ligase complex for ubiquitination and proteasomal degradation. By using synthetic monobodies that selectively bind the protein tyrosine phosphatase SHP2 and a camelid-derived VHH nanobody that selectively binds the human ASC protein, we demonstrate highly efficient AdPROM-mediated degradation of endogenous SHP2 and ASC in human cell lines. We show that AdPROM-mediated loss of SHP2 in cells impacts SHP2 biology. This study demonstrates for the first time that small polypeptide binders that selectively recognize endogenous target proteins can be exploited for AdPROM-mediated destruction of the target proteins.

scholarly journals Genome-wide analysis of tomato long non-coding RNAs and identification as endogenous target mimic for microRNA in response to TYLCV infection

2015 ◽  
Vol 5 (1) ◽  
Author(s):  
Jinyan Wang ◽  
Wengui Yu ◽  
Yuwen Yang ◽  
Xiao Li ◽  
Tianzi Chen ◽  
...  
Keyword(s):  
Post Inoculation ◽  
Biological Processes ◽  
Virus Induced Gene Silencing ◽  
Dna Virus ◽  
Genome Wide Analysis ◽  
Genome Wide ◽  
Non Coding Rnas ◽  
Endogenous Target ◽  
Leaf Curl Virus ◽  
Insight Into

Abstract Recently, a large number of long noncoding RNAs (lncRNAs) have emerged as important regulators of many biological processes in animals and plants. However, how lncRNAs function during plant DNA virus infection is largely unknown. We performed strand-specific paired-end RNA sequencing of tomato samples infected with Tomato yellow leaf curl virus (TYLCV) with three biological replicates. Overall, we predicted 1565 lncRNAs including long intergenic ncRNAs (lincRNAs) and natural antisense transcripts (lncNATs) and definitively identified lnRNAs that are involved in TYLCV infection by virus-induced gene silencing (VIGS). We also verified the functions of a set of lncRNAs that were differentially expressed between 0 and 7 days post inoculation (dpi). More importantly, we found that several lncRNAs acted as competing endogenous target mimics (eTMs) for tomato microRNAs involved in the TYLCV infection. These results provide new insight into lncRNAs involved in the response to TYLCV infection that are important components of the TYLCV network in tomatoes.

scholarly journals Discovery and Annotation of Plant Endogenous Target Mimicry Sequences from Public Transcriptome Libraries: A Case Study of Prunus persica

2017 ◽  
Vol 14 (4) ◽  
Author(s):  
Gökhan Karakülah
Keyword(s):  
Prunus Persica ◽  
Peach Fruit ◽  
Novel Transcript ◽  
Development Processes ◽  
Plant Transcriptome ◽  
Non Coding Rnas ◽  
Endogenous Target ◽  
Diverse Plant Species ◽  
Transcript Discovery

AbstractNovel transcript discovery through RNA sequencing has substantially improved our understanding of the transcriptome dynamics of biological systems. Endogenous target mimicry (eTM) transcripts, a novel class of regulatory molecules, bind to their target microRNAs (miRNAs) by base pairing and block their biological activity. The objective of this study was to provide a computational analysis framework for the prediction of putative eTM sequences in plants, and as an example, to discover previously un-annotated eTMs in Prunus persica (peach) transcriptome. Therefore, two public peach transcriptome libraries downloaded from Sequence Read Archive (SRA) and a previously published set of long non-coding RNAs (lncRNAs) were investigated with multi-step analysis pipeline, and 44 putative eTMs were found. Additionally, an eTM-miRNA-mRNA regulatory network module associated with peach fruit organ development was built via integration of the miRNA target information and predicted eTM-miRNA interactions. My findings suggest that one of the most widely expressed miRNA families among diverse plant species, miR156, might be potentially sponged by seven putative eTMs. Besides, the study indicates eTMs potentially play roles in the regulation of development processes in peach fruit via targeting specific miRNAs. In conclusion, by following the step-by step instructions provided in this study, novel eTMs can be identified and annotated effectively in public plant transcriptome libraries.

scholarly journals microRNAs Regulate Cell-to-Cell Variability of Endogenous Target Gene Expression in Developing Mouse Thymocytes

PLoS Genetics ◽  
2015 ◽  
Vol 11 (2) ◽  
pp. e1005020 ◽  
Author(s):  
Rory Blevins ◽  
Ludovica Bruno ◽  
Thomas Carroll ◽  
James Elliott ◽  
Antoine Marcais ◽  
...  
Keyword(s):  
Gene Expression ◽  
Target Gene ◽  
Target Gene Expression ◽  
Endogenous Target ◽  
Cell To Cell Variability

scholarly journals A programmable hierarchical-responsive nanoCRISPR elicits robust activation of endogenous target to treat cancer

Theranostics ◽  
2021 ◽  
Vol 11 (20) ◽  
pp. 9833-9846
Author(s):  
Chao Liu ◽  
Ning Wang ◽  
Rui Luo ◽  
Lu Li ◽  
Wen Yang ◽  
...  
Keyword(s):  
Endogenous Target

scholarly journals Optogenetic control of protein binding using light-switchable nanobodies

2019 ◽  
Author(s):  
Agnieszka A. Gil ◽  
Evan M. Zhao ◽  
Maxwell Z. Wilson ◽  
Alexander G. Goglia ◽  
Cesar Carrasco-Lopez ◽  
...  
Keyword(s):  
Protein Binding ◽  
Target Protein ◽  
Size Exclusion ◽  
Light Illumination ◽  
List Type ◽  
Target Proteins ◽  
Wide Range ◽  
Endogenous Target

AbstractA growing number of optogenetic tools have been developed to control binding between two engineered protein domains. In contrast, relatively few tools confer light-switchable binding to a generic target protein of interest. Such a capability would offer substantial advantages, enabling photoswitchable binding to endogenous target proteins in vivo or light-based protein purification in vitro. Here, we report the development of opto-nanobodies (OptoNBs), a versatile class of chimeric photoswitchable proteins whose binding to proteins of interest can be enhanced or inhibited upon blue light illumination. We find that OptoNBs are suitable for a range of applications: modulating intracellular protein localization and signaling pathway activity and controlling target protein binding to surfaces and in protein separation columns. This work represents a first step towards programmable photoswitchable regulation of untagged, endogenous target proteins.HighlightsOpto-Nanobodies (OptoNBs) enable light-regulated binding to a wide range of protein targets.We identify an optimized LOV domain and two loop insertion sites for light-regulated binding.OptoNBs function in vivo: when expressed in cells and fused to signaling domains, OptoNBs enable light-activated and light-inhibited Ras/Erk signaling.OptoNBs function in vitro: Target proteins can be reversibly bound to OptoNB-coated beads and separated through size-exclusion chromatography.

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