Search results

Items from 1 to 20 out of 113 results

article

A dual‐luciferase reporter system for characterization of small RNA target genes in both mammalian and insect cells

Zhongyuan Deng, Yuting Zhang, Leyao Li, Xingcheng Xie, more

MicroRNAs (miRNAs) are regulatory RNA molecules that bind to target messenger RNAs (mRNAs) and affect the stability or translational efficiency of the bound mRNAs. Single or dual‐luciferase reporter systems have been successfully used to identify miRNA target genes in mammalian cells. These reporter systems, however, are not sensitive enough to verify miRNA–target gene relationships in insect cell...

article

YTHDF1 promotes mRNA degradation via YTHDF1‐AGO2 interaction and phase separation

Jiong Li, Ke Chen, Xin Dong, Yating Xu, more

Cell Proliferation > 55 > 1 > n/a - n/a

Objectives YTHDF1 is known as a m⁶A reader protein, and many researches of YTHDF1 focused on the regulation of mRNA translation efficiency. However, YTHDF1 is also related to RNA degradation, but how YTHDF1 regulates mRNA degradation is indefinite. Liquid‐liquid phase separation (LLPS) underlies the formation of membraneless compartments in mammal cells, and there are few reports focused on the correlation...

article

Genome‐scale molecular principles of mRNA half‐life regulation in yeast

Sudipto Basu, Saurav Mallik, Suman Hait, Sudip Kundu

The FEBS Journal > 288 > 11 > 3428 - 3447

Precise control of protein and messenger RNA (mRNA) degradation is essential for cellular metabolism and homeostasis. Controlled and specific degradation of both molecular species necessitates their engagements with the respective degradation machineries; this engagement involves a disordered/unstructured segment of the substrate traversing the degradation tunnel of the machinery and accessing the...

article

Regulating Tumor N⁶‐Methyladenosine Methylation Landscape using Hypoxia‐Modulating OsS_x Nanoparticles

Yue Zheng, Yuyi Ling, Dong‐Yang Zhang, Cai‐Ping Tan, more

Small > 17 > 1 > n/a - n/a

The epigenetic dysregulation and hypoxia are two important factors that drive tumor malignancy, and N⁶‐methyladenosine (m⁶A) in mRNA is involved in the regulation of gene expression. Herein, a nanocatalyst OsS_x‐PEG (PEG = poly(ethylene glycol)) nanoparticles (NPs) as O₂ modulator is developed to improve tumor hypoxia. OsS_x‐PEG NPs can significantly downregulate genes involved in hypoxia pathway. Interestingly,...

article

Single molecule approaches for studying gene regulation in metabolic tissues

Lydia Farack, Adi Egozi, Shalev Itzkovitz

Diabetes, Obesity and Metabolism > 20 > S2 > 145 - 156

Gene expression in metabolic tissues can be regulated at multiple levels, ranging from the control of promoter accessibilities, transcription rates, mRNA degradation rates and mRNA localization. Modulating these processes can differentially affect important performance criteria of cells. These include precision, cellular economy, rapid response and maintenance of DNA integrity. In this review we will...

article

Regulation of the ARE-binding proteins, TTP (tristetraprolin) and HuR (human antigen R), in inflammatory response in astrocytes

Alina A. Astakhova, Dmitry V. Chistyakov, Marina G. Sergeeva, Georg Reiser

Neurochemistry International > 2018 > 118 > C > 82-90

Control of decay of mRNA containing the adenine-uridine rich elements (AREs) is an important post-transcriptional mechanism involved in the regulation of inflammatory gene expression. Two widely recognized proteins in this machinery are HuR (human antigen R) – a protein that stabilizes ARE-containing mRNA and TTP (tristetraprolin) – a protein that shortens half-lives of ARE-containing mRNA. Although...

article

Dissecting mRNA decay and translation inhibition during iron deficiency

Lucía Ramos-Alonso, Antonia María Romero, Julio Polaina, Sergi Puig, more

Current Genetics > 2019 > 65 > 1 > 139-145

Iron participates as a vital cofactor in multiple metabolic pathways. Despite its abundance, iron bioavailability is highly restricted in aerobic and alkaline environments. Therefore, living organisms have evolved multiple adaptive mechanisms to respond to iron scarcity. These strategies include a global remodeling of iron metabolism directed to optimize iron utilization. In the baker’s yeast Saccharomyces cerevisiae...

article

Establishment of genetically encoded biosensors for cytosolic boric acid in plant cells

Makiha Fukuda, Shinji Wakuta, Jio Kamiyo, Toru Fujiwara, more

The Plant Journal > 95 > 5 > 763 - 774

Boron (B) is an essential micronutrient for plants. To maintain B concentration in tissues at appropriate levels, plants use boric acid channels belonging to the NIP subfamily of aquaporins and BOR borate exporters. To regulate B transport, these transporters exhibit different cell‐type specific expression, polar localization, and B‐dependent post‐transcriptional regulation. Here, we describe the...

article

Pathogenic Signal Sequence Mutations in Progranulin Disrupt SRP Interactions Required for mRNA Stability

Emile S. Pinarbasi, Andrey L. Karamyshev, Elena B. Tikhonova, I-Hui Wu, more

Cell Reports > 2018 > 23 > 10 > 2844-2851

Cells have evolved quality control pathways to prevent the accumulation of improperly localized proteins, which are often toxic. One of these pathways, regulation of aberrant protein production (RAPP), recognizes aberrant secretory proteins during translation and degrades the associated mRNA. Here, we demonstrate endogenous RAPP substrates. Haploinsufficiency of the secretory protein progranulin (GRN)...

article

Direct measurement of pervasive weak repression by microRNAs and their role at the network level

Fuqiang Ma, Pei Lin, Qingjian Chen, Xuemei Lu, more

BMC Genomics > 2018 > 19 > 1 > 1-12

Background A gene regulatory network (GRN) comprises many weak links that are often regulated by microRNAs. Since miRNAs rarely repress their target genes by more than 30%, doubts have been expressed about the biological relevance of such weak effects. These doubts raise the possibility of under-estimation as miRNA repression is usually estimated indirectly from equilibrium expression levels. Results...

article

Integrative bioinformatics analysis characterizing the role of EDC3 in mRNA decay and its association to intellectual disability

Ute Scheller, Kathrin Pfisterer, Steffen Uebe, Arif B. Ekici, more

BMC Medical Genomics > 2018 > 11 > 1 > 1-11

Background Decapping of mRNA is an important step in the regulation of mRNA turnover and therefore of gene expression, which is a key process controlling development and homeostasis of all organisms. It has been shown that EDC3 plays a role in mRNA decapping, however its function is not well understood. Previously, we have associated a homozygous variant in EDC3 with autosomal recessive intellectual...

article

7-Methylguanosine monophosphate analogues with 5′-(1,2,3-triazoyl) moiety: Synthesis and evaluation as the inhibitors of cNIIIB nucleotidase

Mateusz Kozarski, Dorota Kubacka, Blazej A. Wojtczak, Renata Kasprzyk, more

Bioorganic & Medicinal Chemistry > 2018 > 26 > 1 > 191-199

The hydrolysis of nucleoside 5′-monophosphates to the corresponding nucleosides and inorganic phosphate is catalysed by 5′-nucleotidases, thereby contributing to the control of endogenous nucleotide turnover and affecting the fate of exogenously delivered nucleotide- and nucleoside-derived therapeutics in cells. A recently identified nucleotidase cNIIIB shows preference towards 7-methylguanosine monophosphate...

article

Upf proteins: highly conserved factors involved in nonsense mRNA mediated decay

Puneet Gupta, Yan-Ruide Li

Molecular Biology Reports > 2018 > 45 > 1 > 39-55

Over 10% of genetic diseases are caused by mutations that introduce a premature termination codon in protein-coding mRNA. Nonsense-mediated mRNA decay (NMD) is an essential cellular pathway that degrades these mRNAs to prevent the accumulation of harmful partial protein products. NMD machinery is also increasingly appreciated to play a role in other essential cellular functions, including telomere...

article

Two novel C-terminal frameshift mutations in the β-globin gene lead to rapid mRNA decay

Katarzyna Rawa, Roman J. Szczesny, Ewelina P. Owczarek, Anna Adamowicz-Salach, more

BMC Medical Genetics > 2017 > 18 > 1 > 1-6

Background The thalassemia syndromes are classified according to the globin chain or chains whose production is affected. β-thalassemias are caused by point mutations or, more rarely, deletions or insertions of a few nucleotides in the β-globin gene or its immediate flanking sequences. These mutations interfere with the gene function either at the transcriptional, translational or posttranslational...

article

Regnase-1 Maintains Iron Homeostasis via the Degradation of Transferrin Receptor 1 and Prolyl-Hydroxylase-Domain-Containing Protein 3 mRNAs

Masanori Yoshinaga, Yoshinari Nakatsuka, Alexis Vandenbon, Daisuke Ori, more

Cell Reports > 2017 > 19 > 8 > 1614-1630

Iron metabolism is regulated by transcriptional and post-transcriptional mechanisms. The mRNA of the iron-controlling gene, transferrin receptor 1 (TfR1), has long been believed to be negatively regulated by a yet-unidentified endonuclease. Here, we show that the endonuclease Regnase-1 is critical for the degradation of mRNAs involved in iron metabolism in vivo. First, we demonstrate that Regnase-1...

article

Functional annotation of a novel toxin–antitoxin system Xn-RelT of Xenorhabdus nematophila; a combined in silico and in vitro approach

Lalit Kumar Gautam, Mohit Yadav, Jitendra Singh Rathore

Journal of Molecular Modeling > 2017 > 23 > 6 > 1-9

Toxin–antitoxin (TA) complexes play an important role in stress responses and programmed cell death in bacteria. The RelB-RelE toxin antitoxin system is well studied in Escherichia coli. In this study, we used combined in silico and in vitro approaches to study a novel Xn-RelT toxin from Xenorhabdus nematophila bearing its own antitoxin Xn-RelAT—a RelB homolog of E. coli. The structure for this toxin–antitoxin...

article

LIN41 Post-transcriptionally Silences mRNAs by Two Distinct and Position-Dependent Mechanisms

Florian Aeschimann, Pooja Kumari, Hrishikesh Bartake, Dimos Gaidatzis, more

Molecular Cell > 2017 > 65 > 3 > 476-489.e4

The RNA-binding protein (RBP) LIN41, also known as LIN-41 or TRIM71, is a key regulator of animal development, but its physiological targets and molecular mechanism of action are largely elusive. Here we find that this RBP has two distinct mRNA-silencing activities. Using genome-wide ribosome profiling, RNA immunoprecipitation, and in vitro-binding experiments, we identify four mRNAs, each encoding...

article

Mature maternal mRNAs are longer than zygotic ones and have complex degradation kinetics in sea urchin

Tsvia Gildor, Assaf Malik, Noa Sher, Smadar Ben-Tabou de-Leon

Developmental Biology > 2016 > 414 > 1 > 121-131

Early in embryogenesis, maternally deposited transcripts are degraded and new zygotic transcripts are generated during the maternal to zygotic transition. Recent works have shown that early zygotic transcripts are short compared to maternal transcripts, in zebrafish and Drosophila species. The reduced zygotic transcript length was attributed to the short cell cycle in these organisms that prevents...

article

RNAi pathways in Mucor: A tale of proteins, small RNAs and functional diversity

Santiago Torres-Martínez, Rosa M. Ruiz-Vázquez

Fungal Genetics and Biology > 2016 > 90 > C > 44-52

The existence of an RNA-mediated silencing mechanism in the opportunistic fungal pathogen Mucor circinelloides was first described in the early 2000. Since then, Mucor has reached an outstanding position within the fungal kingdom as a model system to achieve a deeper understanding of regulation of endogenous functions by the RNA interference (RNAi) machinery. M. circinelloides combines diverse components...

chapter

Model-based Inference of Gene Expression Dynamics from Sequence Information

Sabine Arnold, Martin Siemann-Herzberg, Joachim Schmid, Matthias Reuss

Advances in Biochemical Engineering > Biotechnology for the Future > 89-179

A dynamic model of prokaryotic gene expression is developed that makes considerable use of gene sequence information. The main contribution arises from the fact that the combined gene expression model allows us to access the impact of altering a nucleotide sequence on the dynamics of gene expression rates mechanistically. The high level of detail of the mathematical model is considered as an important...

Publication date

Last year (1)
Last 3 years (4)

Close

Date range setting

Set the date range to filter the displayed results. You can set a starting date, ending date or both. You can enter the dates manually or choose them from the calendar.

From:

To:
Set your own date range

Content availability

Available (106)
None (7)

Publication type

article (107)
book (6)

Keywords

MRNA DEGRADATION (113)
GENE EXPRESSION (11)
RNASE E (10)
ESCHERICHIA COLI (6)
TRANSLATION (6)
MRNA STABILITY (5)
INFLAMMATION (4)
QUALITY CONTROL (4)
RIBONUCLEASE (4)
TRANSCRIPTION (4)
TRANSLATIONAL REPRESSION (4)
YEAST (4)
CELLULAR BIOPHYSICS (3)
MICRORNA (3)
MIRNA (3)
MOLECULAR BIOPHYSICS (3)
MRNA INACTIVATION (3)
RNA-BINDING PROTEIN (3)
RNAI (3)
SHINE-DALGARNO SEQUENCE (3)
3′ UTR (2)
ASTROCYTES (2)
BIOLOGY COMPUTING (2)
CAP ANALOGS (2)
CCR4-NOT COMPLEX (2)
CELL-FREE PROTEIN SYNTHESIS (2)
CYCLOHEXIMIDE (2)
DEADENYLASES (2)
DECAPPING (2)
ENDONUCLEASE (2)
ENDORIBONUCLEASE (2)
EXORIBONUCLEASE (2)
FLUORESCENCE SPECTROSCOPY (2)
FUNCTIONAL MRNA HALF-LIFE (2)
HUMAN (2)
MAMMALIAN (2)
MOUSE OOCYTE (2)
MRNA DECAY (2)
MRNA SURVEILLANCE (2)
NONSENSE-MEDIATED MRNA DECAY (2)
NUCLEAR MRNA RETENTION (2)
POSTMORTEM INTERVAL (2)
REGA (2)
RIBOSOME BINDING SITE (2)
RNASE G (2)
RNASE III (2)
RNB (2)
RRP6 (2)
SCAVENGER DECAPPING ENZYMES (2)
SYMBIOTIC NITROGEN FIXATION (2)
TRANSLATION INITIATION (2)
TRYPANOSOMA (2)
GPD1 GENE (1)
CYTOCHROME C 3 (1)
PROSTAGLANDIN E 2 (1)
2P14-P13 (1)
5′ NUCLEOTIDASE CNIIIB (1)
5′ STABILIZER (1)
5′ UTR (1)
5′UTR (1)
7-METHYLGUANOSINE 5′-MONOPHOSPHATE (1)
ADENOVIRUS E4 11K (1)
ADENOVIRUS E4 ORF3 (1)
AGGRESOME (1)
AGING (1)
AGO (1)
AGO2 (1)
ALLOMETRIC SCALING (1)
ALTERNATIVE SPLICING (1)
AMPK (1)
ANAEROBIC DIGESTION (1)
ANEMIA (1)
ANEUPLOIDY (1)
ARABIDOPSIS THALIANA (1)
ARGONAUTE 2 (AGO2) (1)
ASSIGNMENTS (1)
ATP SYNTHASE (1)
AU‐RICH ELEMENTS (1)
BIOELECTRIC PHENOMENA (1)
BIOSENSOR (1)
BLOOD (1)
BODY FLUID IDENTIFICATION (1)
BORIC ACID (1)
BORON (1)
BURSTY TRANSCRIPTION (1)
BY‐2 (1)
CAA/TATC 3′-UTR POLYMORPHISM (1)
CANCER (1)
CAP (1)
CAP‐BINDING PROTEIN (1)
CCCH ZINC FINGER (1)
CCR4-COMPLEX (1)
CCR4-NOT (1)
CDS (1)
CELL FRACTION (1)
CELL MODEL (1)
CELL SIGNALLING TRANSDUCTION NETWORKS (1)
CELL-FREE TRANSLATION (1)
CG (1)
CHANNEL (1)
more

Data set

Elsevier (72)
Springer (19)
Wiley (15)
ieee (5)
Agro (1)
PSJD (1)

INFONA - science communication portal

Search results

A dual‐luciferase reporter system for characterization of small RNA target genes in both mammalian and insect cells

YTHDF1 promotes mRNA degradation via YTHDF1‐AGO2 interaction and phase separation

Genome‐scale molecular principles of mRNA half‐life regulation in yeast

Regulating Tumor N⁶‐Methyladenosine Methylation Landscape using Hypoxia‐Modulating OsS_x Nanoparticles

Single molecule approaches for studying gene regulation in metabolic tissues

Regulation of the ARE-binding proteins, TTP (tristetraprolin) and HuR (human antigen R), in inflammatory response in astrocytes

Dissecting mRNA decay and translation inhibition during iron deficiency

Establishment of genetically encoded biosensors for cytosolic boric acid in plant cells

Pathogenic Signal Sequence Mutations in Progranulin Disrupt SRP Interactions Required for mRNA Stability

Direct measurement of pervasive weak repression by microRNAs and their role at the network level

Integrative bioinformatics analysis characterizing the role of EDC3 in mRNA decay and its association to intellectual disability

7-Methylguanosine monophosphate analogues with 5′-(1,2,3-triazoyl) moiety: Synthesis and evaluation as the inhibitors of cNIIIB nucleotidase

Upf proteins: highly conserved factors involved in nonsense mRNA mediated decay

Two novel C-terminal frameshift mutations in the β-globin gene lead to rapid mRNA decay

Regnase-1 Maintains Iron Homeostasis via the Degradation of Transferrin Receptor 1 and Prolyl-Hydroxylase-Domain-Containing Protein 3 mRNAs

Functional annotation of a novel toxin–antitoxin system Xn-RelT of Xenorhabdus nematophila; a combined in silico and in vitro approach

LIN41 Post-transcriptionally Silences mRNAs by Two Distinct and Position-Dependent Mechanisms

Mature maternal mRNAs are longer than zygotic ones and have complex degradation kinetics in sea urchin

RNAi pathways in Mucor: A tale of proteins, small RNAs and functional diversity

Model-based Inference of Gene Expression Dynamics from Sequence Information

Filter options

Publication date

Content availability

Publication type

Keywords

Data set

INFONA - science communication portal

Search results

Add recipient

Sending message cancelled

Are you sure you want to cancel sending this message?

Send message

Filter options

Publication date

Date range setting

Set the date range to filter the displayed results. You can set a starting date, ending date or both. You can enter the dates manually or choose them from the calendar.

Content availability

Publication type

Keywords

Data set

Reporting an error / abuse

Sending the report failed

Accessibility options