scholarly journals A shape-shifting nuclease unravels structured RNA

2021 ◽  
Author(s):  
Katarina Meze ◽  
Armend Axhemi ◽  
Dennis R Thomas ◽  
Ahmet Doymaz ◽  
Leemor Joshua-Tor
Keyword(s):  
Gene Expression ◽  
Rna Processing ◽  
Cold Shock ◽  
Substrate Recognition ◽  
Critical Role ◽  
Rna Degradation ◽  
Rna Turnover ◽  
Linker Region ◽  
Conformational Plasticity ◽  
Gene Expression Levels

RNA turnover pathways ensure appropriate gene expression levels by eliminating unwanted transcripts that may otherwise interfere with cellular programs. The enzyme Dis3-like protein 2 (Dis3L2) is a 3′-5′ exoribonuclease that, through its RNA turnover activity, plays a critical role in human development1. Dis3L2 can independently degrade structured substrates and its targets include many coding and non-coding 3′-uridylated RNAs1-5. While the basis for Dis3L2 substrate recognition has been well-characterized6, the mechanism of structured RNA degradation by this family of enzymes is unknown. We characterized the discrete steps of the degradation cycle by determining electron cryo-microscopy structures representing snapshots along the RNA turnover pathway and measuring kinetic parameters for single-stranded (ss) and double-stranded (ds) RNA processing. We discovered a dramatic conformational change that is triggered by the dsRNA, involving repositioning of two cold shock domains by 70 Å. This movement exposes a trihelix-linker region, which acts as a wedge to separate the two RNA strands. Furthermore, we show that the trihelix linker is critical for dsRNA, but not ssRNA, degradation. These findings reveal the conformational plasticity of this enzyme, and detail a novel mechanism of structured RNA degradation.

Regulated and quality-control mRNA turnover pathways in eukaryotes

2010 ◽  
Vol 38 (6) ◽  
pp. 1506-1510 ◽  
Author(s):  
Boris Reznik ◽  
Jens Lykke-Andersen
Keyword(s):  
Quality Control ◽  
Rna Processing ◽  
Rna Localization ◽  
Rna Degradation ◽  
Eukaryotic Cells ◽  
Mrna Turnover ◽  
Surveillance Systems ◽  
Rna Turnover ◽  
Rna Surveillance ◽  
Multiple Levels

Gene expression can be regulated at multiple levels, including transcription, RNA processing, RNA localization, translation and, finally, RNA turnover. RNA degradation may occur at points along the processing pathway or during translation as it undergoes quality control by RNA surveillance systems. Alternatively, mRNAs may be subject to regulated degradation, often mediated by cis-encoded determinants in the mRNA sequence that, through the recruitment of trans factors, determine the fate of the mRNA. The aim of the present review is to highlight mechanisms of regulated and quality-control RNA degradation in eukaryotic cells, with an emphasis on mammals.

scholarly journals Impact of RNA degradation on measurements of gene expression

2014 ◽  
Author(s):  
Irene Gallego Romero ◽  
Athma A. Pai ◽  
Jenny Tung ◽  
Yoav Gilad
Keyword(s):  
Gene Expression ◽  
Expression Profiling ◽  
Rna Extraction ◽  
Rna Degradation ◽  
Significant Loss ◽  
Whole Genome ◽  
Expression Levels ◽  
Rna Quality ◽  
The Impact ◽  
Gene Expression Levels

The use of low quality RNA samples in whole-genome gene expression profiling remains controversial. It is unclear if transcript degradation in low quality RNA samples occurs uniformly, in which case the effects of degradation can be normalized, or whether different transcripts are degraded at different rates, potentially biasing measurements of expression levels. This concern has rendered the use of low quality RNA samples in whole-genome expression profiling problematic. Yet, low quality samples are at times the sole means of addressing specific questions – e.g., samples collected in the course of fieldwork. We sought to quantify the impact of variation in RNA quality on estimates of gene expression levels based on RNA-seq data. To do so, we collected expression data from tissue samples that were allowed to decay for varying amounts of time prior to RNA extraction. The RNA samples we collected spanned the entire range of RNA Integrity Number (RIN) values (a quality metric commonly used to assess RNA quality). We observed widespread effects of RNA quality on measurements of gene expression levels, as well as a slight but significant loss of library complexity in more degraded samples. While standard normalizations failed to account for the effects of degradation, we found that a simple linear model that controls for the effects of RIN can correct for the majority of these effects. We conclude that in instances where RIN and the effect of interest are not associated, this approach can help recover biologically meaningful signals in data from degraded RNA samples.

XBP1 Expression Is An Important Prognostic Factor for Newly Diagnosed Myeloma Patients.

Blood ◽  
2008 ◽  
Vol 112 (11) ◽  
pp. 1686-1686
Author(s):  
Tina Bagratuni ◽  
Ping Wu ◽  
David Gonzalez de Castro ◽  
Emma L Davenport ◽  
Brian A Walker ◽  
...  
Keyword(s):  
Gene Expression ◽  
Overall Survival ◽  
Plasma Cells ◽  
Critical Role ◽  
Clinical Samples ◽  
Newly Diagnosed ◽  
Expression Levels ◽  
Downstream Target ◽  
Lower Ratio ◽  
Gene Expression Levels

Abstract The immunoglobulin production of myeloma plasma cells means they are dependent on the unfolded protein response process (UPR), which controls protein production and ensures its proper translation and folding. Knockout mouse studies have highlighted the importance of IRE1, a transducer of the UPR signal and XBP1 its downstream target, in B cell development. Gene expression studies show that XBP1 is highly expressed in myeloma plasma cells and it is consistently deregulated in clinical samples. XBP1s, the active moiety, is a known myeloma survival factor and IgVH-XBP1s transgenic mice develop myeloma. In this work we demonstrate that XBP1s levels correlate with survival of myeloma patients and that targeting it with small molecules may be a useful therapeutic strategy. We have re-sequenced IRE1 and determined the gene expression levels of IRE1, total XBP1, XBP1 unspliced (XBP1u), and XBP1 spliced (XBP1s) in a large series of myeloma patients (n=260), and correlated biological findings with clinical characteristics and patient outcome. To quantitatively assess the expression of XBP1s and XBP1u variants, we have designed a novel real time PCR method (Lux Technology, Invitrogen) capable of determining the ratio of these transcripts within a sample. These results show that total IRE1 and XBP1 are highly expressed in all patients. In addition all patients expressed higher levels of XBP1s, the active transcription factor which is anti-apoptotic, compared to the inactive precursor XBP1u. We correlated XBP1s/u gene expression levels with clinical parameters in 159 newly diagnosed patients. This group of patients contained 68 females and 91 males with a median age of 64 years (range 39–89), B2M median = 7.45mg/mL (range 1.1–30mg/mL), haemoglobin median = 10.2g/dL (range 5.7–14.7g/dL) and ISS status stage 1 = 21%, stage 2 = 36%, and stage 3 = 36%. The XBP1s/u ratio demonstrated a statistically significant effect on overall survival (OS) in patients with high B2M (B2M >5), with a cut-off ratio of 2.8 for the XBP1s/u expression (assigned using the quartile method). In this group of patients those with higher XBP1s/u have shorter survival (28 months) compared to those with lower XBP1s/u (not reached, 50+ months). (p = 0.033). The cause for the high and variable XBP1s levels is uncertain but could be mediated by IRE activity. Sequence analysis of the kinase and endoribonuclease domain of IRE1 identified 3/50 patients with an inactivating mutation in the endoribonuclease domain (G923V): patients with this mutation had a lower ratio of XBP1s to XBP1u and a longer survival. In conclusion, this study is the first to demonstrate the clinical significance of high XBP1s levels in myeloma and shows that patients with high levels of XBP1s have a shorter overall survival. Coupled with our previous study highlighting the critical role of the UPR in myeloma and the report of the XBP1s transgenic mouse model, the importance of the IRE1-XBP1 axis myeloma is now established, and its role as a therapeutic target needs to be explored.

scholarly journals The critical role of RNA processing and degradation in the control of gene expression

2010 ◽  
Vol 34 (5) ◽  
pp. 883-923 ◽  
Author(s):  
Cecília M. Arraiano ◽  
José M. Andrade ◽  
Susana Domingues ◽  
Inês B. Guinote ◽  
Michal Malecki ◽  
...  
Keyword(s):  
Gene Expression ◽  
Rna Processing ◽  
Critical Role ◽  
Control Of Gene Expression

scholarly journals MYH9 Inhibition Suppresses TGF-β1-Stimulated Lung Fibroblast-to-Myofibroblast Differentiation

2021 ◽  
Vol 11 ◽  
Author(s):  
Xionghua Sun ◽  
Mei Zhu ◽  
Xihua Chen ◽  
Xiaogang Jiang
Keyword(s):  
Gene Expression ◽  
Pulmonary Fibrosis ◽  
Atpase Activity ◽  
Critical Role ◽  
Lung Fibroblast ◽  
Lung Fibroblasts ◽  
Myofibroblast Differentiation ◽  
Expression Levels ◽  
Tgf Β1 ◽  
Gene Expression Levels

Previous cDNA microarray results showed that MYH9 gene expression levels are increased in TGF-β1-stimulated lung fibroblast. Recently, our proteomic results revealed that the expression levels of MYH9 protein are notably upregulated in lung tissues of bleomycin-treated rats. However, whether MYH9 plays a critical role in the differentiation of fibroblast remains unclear. Herein, we demonstrated that TGF-β1 increased MYH9 expression, and siRNA-mediated knockdown of MYH9 and pharmacological inhibition of MYH9 ATPase activity remarkably repressed TGF-β1-induced lung fibroblast-to-myofibroblast differentiation. TGF-β1-stimulated MYH9 induction might be via ALK5/Smad2/3 pathway but not through noncanonical pathways, including p38 mitogen-activated kinase, and Akt pathways in lung fibroblasts. Our results showed that MYH9 inhibition suppressed TGF-β1-induced lung fibroblast-to-myofibroblast differentiation, which provides valuable information for illuminating the pathological mechanisms of lung fibroblast differentiation, and gives clues for finding new potential target for pulmonary fibrosis treatment.

A Review on Important Histone Acetyltransferase (HAT) Enzymes as Targets for Cancer Therapy

2019 ◽  
Vol 15 (2) ◽  
pp. 120-130
Author(s):  
Mohammad Ghanbari ◽  
Reza Safaralizadeh ◽  
Kiyanoush Mohammadi
Keyword(s):  
Gene Expression ◽  
Histone Acetyltransferase ◽  
Critical Role ◽  
Cancer Treatments ◽  
Control Of Gene Expression ◽  
Post Translational Modifications ◽  
Therapeutic Drugs ◽  
The Status ◽  
Acetyl Group ◽  
Increase Gene Expression

At the present time, cancer is one of the most lethal diseases worldwide. There are various factors involved in the development of cancer, including genetic factors, lifestyle, nutrition, and so on. Recent studies have shown that epigenetic factors have a critical role in the initiation and development of tumors. The histone post-translational modifications (PTMs) such as acetylation, methylation, phosphorylation, and other PTMs are important mechanisms that regulate the status of chromatin structure and this regulation leads to the control of gene expression. The histone acetylation is conducted by histone acetyltransferase enzymes (HATs), which are involved in transferring an acetyl group to conserved lysine amino acids of histones and consequently increase gene expression. On the basis of similarity in catalytic domains of HATs, these enzymes are divided into different groups such as families of GNAT, MYST, P300/CBP, SRC/P160, and so on. These enzymes have effective roles in apoptosis, signaling pathways, metastasis, cell cycle, DNA repair and other related mechanisms deregulated in cancer. Abnormal activation of HATs leads to uncontrolled amplification of cells and incidence of malignancy signs. This indicates that HAT might be an important target for effective cancer treatments, and hence there would be a need for further studies and designing of therapeutic drugs on this basis. In this study, we have reviewed the important roles of HATs in different human malignancies.

scholarly journals Alternative splicing during mammalian organ development

2021 ◽  
Author(s):  
Pavel V. Mazin ◽  
Philipp Khaitovich ◽  
Margarida Cardoso-Moreira ◽  
Henrik Kaessmann
Keyword(s):  
Gene Expression ◽  
Alternative Splicing ◽  
Regulatory Networks ◽  
Organ Development ◽  
Functional Diversification ◽  
Mammalian Genomes ◽  
Species Comparisons ◽  
Time Specific ◽  
The Brain ◽  
Gene Expression Levels

AbstractAlternative splicing (AS) is pervasive in mammalian genomes, yet cross-species comparisons have been largely restricted to adult tissues and the functionality of most AS events remains unclear. We assessed AS patterns across pre- and postnatal development of seven organs in six mammals and a bird. Our analyses revealed that developmentally dynamic AS events, which are especially prevalent in the brain, are substantially more conserved than nondynamic ones. Cassette exons with increasing inclusion frequencies during development show the strongest signals of conserved and regulated AS. Newly emerged cassette exons are typically incorporated late in testis development, but those retained during evolution are predominantly brain specific. Our work suggests that an intricate interplay of programs controlling gene expression levels and AS is fundamental to organ development, especially for the brain and heart. In these regulatory networks, AS affords substantial functional diversification of genes through the generation of tissue- and time-specific isoforms from broadly expressed genes.

scholarly journals Genome-wide CRISPR/Cas9 screening identifies CARHSP1 responsible for radiation resistance in glioblastoma

2021 ◽  
Vol 12 (8) ◽  
Author(s):  
Guo-dong Zhu ◽  
Jing Yu ◽  
Zheng-yu Sun ◽  
Yan Chen ◽  
Hong-mei Zheng ◽  
...  
Keyword(s):  
Cold Shock ◽  
Mrna Level ◽  
Critical Role ◽  
Inflammatory Signaling ◽  
Heat Stable ◽  
Genome Wide ◽  
Attractive Therapeutic Target ◽  
Heat Stable Protein ◽  
Signaling Activation ◽  
Shock Proteins

AbstractGlioblastomas (GBM) is the most common primary malignant brain tumor, and radiotherapy plays a critical role in its therapeutic management. Unfortunately, the development of radioresistance is universal. Here, we identified calcium-regulated heat-stable protein 1 (CARHSP1) as a critical driver for radioresistance utilizing genome-wide CRISPR activation screening. This is a protein with a cold-shock domain (CSD)-containing that is highly similar to cold-shock proteins. CARHSP1 mRNA level was upregulated in irradiation-resistant GBM cells and knockdown of CARHSP1 sensitized GBM cells to radiotherapy. The high expression of CARHSP1 upon radiation might mediate radioresistance by activating the inflammatory signaling pathway. More importantly, patients with high levels of CARHSP1 had poorer survival when treated with radiotherapy. Collectively, our findings suggested that targeting the CARHSP1/TNF-α inflammatory signaling activation induced by radiotherapy might directly affect radioresistance and present an attractive therapeutic target for GBM, particularly for patients with high levels of CARHSP1.

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