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    Wyświetlanie 1-11 z 11
    Tytuł:
    Arabidopsis thaliana microRNA162 level is posttranscriptionally regulated via splicing and polyadenylation site selection
    Autorzy:
    Barciszewska-Pacak, Maria
    Knop, Katarzyna
    Jarmołowski, Artur
    Szweykowska-Kulińska, Zofia
    Powiązania:
    https://bibliotekanauki.pl/articles/1038744.pdf
    Data publikacji:
    2016
    Wydawca:
    Polskie Towarzystwo Biochemiczne
    Tematy:
    miRNA
    pri-miRNA
    abiotic stress
    gene expression
    Opis:
    Arabidopsis microRNA162 (miRNA162) level regulation was studied under abiotic stresses, such as drought and salinity. The TaqMan® microRNA assay proved that A. thaliana miRNA162 level was elevated under these stresses, confirming its salt and drought responsiveness. The promoter region analyses of A. thaliana miRNA162a and b genes (MIR162a and MIR162b) identified numerous salinity and drought responsive elements. However, our results indicated that Arabidopsis MIR162a was presumably the main locus responsible for the mature ath-miRNA162 accumulation under the stresses tested, and the MIR162b was generally rather weakly expressed, both in control and under the stress conditions. The MIR162a structure was confirmed to be complex and the pri-miRNA162a hairpin structure was shown to span an alternative exon and an intron. The MIR162a transcription generated a few pri-miRNA162a splicing isoforms that could be functional and non-functional. Upon drought and salinity stresses, the regulation of the pri-miRNA162a alternative splicing pattern revealed an increase of a functional pri-miR162a isoform and a preferential distal polyA site selection under the stress conditions. Apart from the potential transcriptional regulation of the miRNA genes (MIRs) expression, the data obtained point to an essential role of posttranscriptional regulation of Arabidopsis microRNA162 level.
    Źródło:
    Acta Biochimica Polonica; 2016, 63, 4; 811-816
    0001-527X
    Pojawia się w:
    Acta Biochimica Polonica
    Dostawca treści:
    Biblioteka Nauki
    Artykuł
    Tytuł:
    Barley primary microRNA expression pattern is affected by soil water availability
    Autorzy:
    Swida-Barteczka, Aleksandra
    Kruszka, Katarzyna
    Grabowska, Aleksandra
    Pacak, Andrzej
    Jarmolowski, Artur
    Kurowska, Marzena
    Szarejko, Iwona
    Szweykowska-Kulinska, Zofia
    Powiązania:
    https://bibliotekanauki.pl/articles/1038746.pdf
    Data publikacji:
    2016
    Wydawca:
    Polskie Towarzystwo Biochemiczne
    Tematy:
    pri-miRNA
    miRNA
    drought
    rehydration
    barley genotypes
    Opis:
    MicroRNAs are short molecules of 21-24 nt in length. They are present in all eukaryotic organisms and regulate gene expression by guiding posttranscriptional silencing of mRNAs. In plants, they are key players in signal transduction, growth and development, and in response to abiotic and biotic stresses. Barley (Hordeum vulgare) is an economically important monocotyledonous crop plant. Drought is the world's main cause of loss in cereal production. We have constructed a high-throughput Real-Time RT-qPCR platform for parallel determination of 159 barley primary microRNAs' levels. The platform was tested for two drought-and-rehydration-treated barley genotypes (Rolap and Sebastian). We have determined changes in the expression of primary microRNAs responding to mild drought, severe drought, and rehydration. Based on the results obtained, we conclude that alteration in the primary microRNA expression is relative to the stress's intensity. Mild drought and rehydration mostly decrease the pri-miRNA levels in both of the tested genotypes. Severe drought mainly induces the primary microRNA expression. The main difference between the genotypes tested was a much-stronger induction of pri-miRNAs in Rolap encountering severe drought. The primary microRNAs respond dynamically to mild drought, severe drought, and rehydration treatments. We propose that some of the individual pri-miRNAs could be used as drought stress or rehydration markers. The usage of the platform in biotechnology is also postulated.
    Źródło:
    Acta Biochimica Polonica; 2016, 63, 4; 817-824
    0001-527X
    Pojawia się w:
    Acta Biochimica Polonica
    Dostawca treści:
    Biblioteka Nauki
    Artykuł
    Tytuł:
    Regulatory RNAs in Planarians
    Autorzy:
    Pawlicka, Kamila
    Perrigue, Patrick
    Barciszewski, Jan
    Powiązania:
    https://bibliotekanauki.pl/articles/1038722.pdf
    Data publikacji:
    2016
    Wydawca:
    Polskie Towarzystwo Biochemiczne
    Tematy:
    planarians
    RNAi
    miRNA
    regeneration
    stem cells
    Opis:
    The full scope of regulatory RNA evolution and function in epigenetic processes is still not well understood. The development of planarian flatworms to be used as a simple model organism for research has shown a great potential to address gaps in the knowledge in this field of study. The genomes of planarians encode a wide array of regulatory RNAs that function in gene regulation. Here, we review planarians as a suitable model organism for the identification and function of regulatory RNAs.
    Źródło:
    Acta Biochimica Polonica; 2016, 63, 4; 681-686
    0001-527X
    Pojawia się w:
    Acta Biochimica Polonica
    Dostawca treści:
    Biblioteka Nauki
    Artykuł
    Tytuł:
    Deciphering the soybean molecular stress response via high-throughput approaches
    Autorzy:
    Tyczewska, Agata
    Gracz, Joanna
    Kuczyński, Jakub
    Twardowski, Tomasz
    Powiązania:
    https://bibliotekanauki.pl/articles/1038715.pdf
    Data publikacji:
    2016
    Wydawca:
    Polskie Towarzystwo Biochemiczne
    Tematy:
    soybean
    transcriptome
    miRNA
    proteome
    stress conditions
    Opis:
    As a result of thousands of years of agriculture, humans had created many crop varieties that became the basis of our daily diet, animal feed and also carry industrial application. Soybean is one of the most important crops worldwide and because of its high economic value the demand for soybean products is constantly growing. In Europe, due to unfavorable climate conditions, soybean cultivation is restricted and we are forced to rely on imported plant material. The development of agriculture requires continuous improvements in quality and yield of crop varieties under changing or adverse conditions, namely stresses. To achieve this goal we need to recognize and understand the molecular dependencies underlying plant stress responses. With the advent of new technologies in studies of plant transcriptomes and proteomes, now we have the tools necessary for fast and precise elucidation of desirable crop traits. Here, we present an overview of high-throughput techniques used to analyze soybean responses to different abiotic (drought, flooding, cold stress, salinity, phosphate deficiency) and biotic (infections by F. oxysporum, cyst nematode, SMV) stress conditions at the level of the transcriptome (mRNAs and miRNAs) and the proteome.
    Źródło:
    Acta Biochimica Polonica; 2016, 63, 4; 631-643
    0001-527X
    Pojawia się w:
    Acta Biochimica Polonica
    Dostawca treści:
    Biblioteka Nauki
    Artykuł
    Tytuł:
    MicroRNA-mediated regulation of flower development in grasses
    Autorzy:
    Smoczynska, Aleksandra
    Szweykowska-Kulinska, Zofia
    Powiązania:
    https://bibliotekanauki.pl/articles/1038724.pdf
    Data publikacji:
    2016
    Wydawca:
    Polskie Towarzystwo Biochemiczne
    Tematy:
    miRNA
    grasses
    flower development
    ABCDE model
    Opis:
    Flower structure in grasses is very unique. There are no petals or sepals like in eudicots but instead flowers develop bract-like structures - palea and lemma. Reproductive organs are enclosed by round lodicule that not only protects reproductive organs but also plays an important role during flower opening. The first genetic model for floral organ development was proposed 25 years ago and it was based on the research on model eudicots. Since then, studies have been carried out to answer the question whether this model could be applicable in the case of monocots. Genes from all classes found in eudicots have been also identified in genomes of such monocots like rice, maize or barley. What's more, it seems that miRNA-mediated regulation of floral organ genes that was observed in the case of Arabidopsis thaliana also takes place in monocots. MiRNA172, miRNA159, miRNA171 and miRNA396 regulate expression of floral organ identity genes in barley, rice and maize, affecting various features of the flower structure, ranging from formation of lemma and palea to the development of reproductive organs. A model of floral development in grasses and its genetic regulation is not yet fully characterized. Further studies on both, the model eudicots and grasses, are needed to unravel this topic. This review provides general overview of genetic model of flower organ identity specification in monocots and it's miRNA-mediated regulation.
    Źródło:
    Acta Biochimica Polonica; 2016, 63, 4; 687-692
    0001-527X
    Pojawia się w:
    Acta Biochimica Polonica
    Dostawca treści:
    Biblioteka Nauki
    Artykuł
    Tytuł:
    The role of microRNA in metastatic colorectal cancer and its significance in cancer prognosis and treatment
    Autorzy:
    Tokarz, Paulina
    Blasiak, Janusz
    Powiązania:
    https://bibliotekanauki.pl/articles/1039629.pdf
    Data publikacji:
    2012
    Wydawca:
    Polskie Towarzystwo Biochemiczne
    Tematy:
    prognosis
    colorectal cancer
    metastasis
    prediction
    therapy
    miRNA
    Opis:
    microRNAs (miRNAs) are small, non-coding RNA molecules that regulate gene expression by targeting specific mRNAs. microRNAs play a role in several physiological processes in the cell, including migration, proliferation, differentiation and apoptosis. Apart from their role in regular metabolism, abnormal profiles of miRNA expression accompany cancer transformation, including colorectal cancer (CRC) metastasis. microRNAs may play a role in each phase of CRC metastasis including angiogenesis, invasion, intravasation, circulation, extravasation and metastatic colonization. microRNA levels may serve as a predictive CRC marker, which was confirmed by the serum level of miR-29a targeting KLF4, a marker of cell stemness, and the plasma level of miR-221 down-regulating c-Kit, Stat5A and ETS1, which are signal transducers and transcription factor, respectively. In turn, the level of miR-143 in CRC cells decreasing the amount of MACC1 (metastasis-associated in colon cancer-1) and oncogenic KRAS protein, may be utilized as a prognostic marker. Also, single nucleotide polymorphisms of genes encoding miRNAs, including miR-423 and miR-608, which correlate with tumor recurrence, may be useful as diagnostic, prognostic and predictive indicators in CRC metastasis. Pre-miR-34a and pre-miR-199a decreased the level of Axl, a tyrosine-protein kinase receptor, so they can be considered as drugs in antimetastatic therapy. On the other hand, miR-222 targeting ADAM-17, a disintegrin and metalloproteinase, and miR-328 interacting with ABCG2, an ABC transporter, may overcome drug resistance of cancer cells. microRNAs may be considered in wide-range application to facilitate CRC metastasis diagnosis, prognosis, prediction and therapy, however, further clinical, epidemiological and in vitro studies should be conducted to verify their utility.
    Źródło:
    Acta Biochimica Polonica; 2012, 59, 4; 467-474
    0001-527X
    Pojawia się w:
    Acta Biochimica Polonica
    Dostawca treści:
    Biblioteka Nauki
    Artykuł
    Tytuł:
    New functionality of RNAComposer: an application to shape the axis of miR160 precursor structure
    Autorzy:
    Antczak, Maciej
    Popenda, Mariusz
    Zok, Tomasz
    Sarzynska, Joanna
    Ratajczak, Tomasz
    Tomczyk, Katarzyna
    Adamiak, Ryszard
    Szachniuk, Marta
    Powiązania:
    https://bibliotekanauki.pl/articles/1038732.pdf
    Data publikacji:
    2016
    Wydawca:
    Polskie Towarzystwo Biochemiczne
    Tematy:
    RNA 3D structure prediction
    RNAComposer
    plant miRNA precursor
    Opis:
    RNAComposer is a fully automated, web-interfaced system for RNA 3D structure prediction, freely available at http://rnacomposer.cs.put.poznan.pl/ and http://rnacomposer.ibch.poznan.pl/. Its main components are: manually curated database of RNA 3D structure elements, highly efficient computational engine and user-friendly web application. In this paper, we demonstrate how the latest additions to the system allow the user to significantly affect the process of 3D model composition on several computational levels. Although in general our method is based on the knowledge of secondary structure topology, currently the RNAComposer offers a choice of six incorporated programs for secondary structure prediction. It also allows to apply a conditional search in the database of 3D structure elements and introduce user-provided elements into the final 3D model. This new functionality contributes to a significant improvement of the predicted 3D model reliability and it facilitates a better model adjustment to the experimental data. This is exemplified based on the RNAComposer application for modelling of the 3D structures of precursors of the miR160 family members.
    Źródło:
    Acta Biochimica Polonica; 2016, 63, 4; 737-744
    0001-527X
    Pojawia się w:
    Acta Biochimica Polonica
    Dostawca treści:
    Biblioteka Nauki
    Artykuł
    Tytuł:
    AmiRNA Designer - new method of artificial miRNA design
    Autorzy:
    Mickiewicz, Agnieszka
    Rybarczyk, Agnieszka
    Sarzynska, Joanna
    Figlerowicz, Marek
    Blazewicz, Jacek
    Powiązania:
    https://bibliotekanauki.pl/articles/1038843.pdf
    Data publikacji:
    2016
    Wydawca:
    Polskie Towarzystwo Biochemiczne
    Tematy:
    artificial miRNA
    RNAi
    gene regulation
    sequence specific
    thermodynamic profiles
    Opis:
    MicroRNAs (miRNAs) are small non-coding RNAs that have been found in most of the eukaryotic organisms. They are involved in the regulation of gene expression at the post-transcriptional level in a sequence specific manner. MiRNAs are produced from their precursors by Dicer-dependent small RNA biogenesis pathway. Involvement of miRNAs in a wide range of biological processes makes them excellent candidates for studying gene function or for therapeutic applications. For this purpose, different RNA-based gene silencing techniques have been developed. Artificially transformed miRNAs (amiRNAs) targeting one or several genes of interest represent one of such techniques being a potential tool in functional genomics. Here, we present a new approach to amiRNA*design, implemented as AmiRNA Designer software. Our method is based on the thermodynamic analysis of the native miRNA/miRNA* and miRNA/target duplexes. In contrast to the available automated tools, our program allows the user to perform analysis of natural miRNAs for the organism of interest and to create customized constraints for the design stage. It also provides filtering of the amiRNA candidates for the potential off-targets. AmiRNA Designer is freely available at http://www.cs.put.poznan.pl/arybarczyk/AmiRNA/.
    Źródło:
    Acta Biochimica Polonica; 2016, 63, 1; 71-77
    0001-527X
    Pojawia się w:
    Acta Biochimica Polonica
    Dostawca treści:
    Biblioteka Nauki
    Artykuł
    Tytuł:
    miRNA Multiplayers in glioma. From bench to bedside
    Autorzy:
    Rolle, Katarzyna
    Powiązania:
    https://bibliotekanauki.pl/articles/1038962.pdf
    Data publikacji:
    2015
    Wydawca:
    Polskie Towarzystwo Biochemiczne
    Tematy:
    cancer
    glioblastoma multiforme (GBM)
    miRNA
    anti-cancer therapy
    diagnosis
    prognosis
    Opis:
    Glioblastoma multiforme (GBM) is the most common type of malignant gliomas, characterized by genetic instability, intratumoral histopathological variability and unpredictable clinical behavior. Disappointing results in the treatment of gliomas with surgery, radiation and chemotherapy have fuelled a search for a new therapeutic targets and treatment modalities. A novel small non-coding RNA molecules, microRNAs (miRNAs), appear to represent one of the most attractive target molecules contributing to the pathogenesis of various types of tumors. They play crucial roles in tumorigenesis, angiogenesis, invasion and apoptosis. Some miRNAs are also associated with clinical outcome and chemo- and radiotherapy resistance. Moreover, miRNA have the potential to affect the responses to molecular-targeted therapies and they also might be associated with cancer stem cell properties, affecting tumor maintenance and progression. The expression profiles of miRNAs are also useful for subclassification of GBM, what underscores the heterogeneity of diseases that all share the same WHO histopathological grade. Importantly, molecular subtypes of GBM appear to correlate with clinical phenotypes, tumor characteristic and treatment outcomes. miRNAs are then biological markers with possible diagnostic and prognostic potential. They could also serve as one of the promising treatment targets in human glioblastoma.
    Źródło:
    Acta Biochimica Polonica; 2015, 62, 3; 353-365
    0001-527X
    Pojawia się w:
    Acta Biochimica Polonica
    Dostawca treści:
    Biblioteka Nauki
    Artykuł
    Tytuł:
    Hsa-miR-331-3p inhibits VHL expression by directly targeting its mRNA 3-UTR in HCC cell lines
    Autorzy:
    Cao, Yiyi
    Zhang, Jinnan
    Xiong, Dongmei
    Wang, Dan
    Wu, Ting
    Huang, Ailong
    Tang, Hua
    Powiązania:
    https://bibliotekanauki.pl/articles/1039137.pdf
    Data publikacji:
    2015
    Wydawca:
    Polskie Towarzystwo Biochemiczne
    Tematy:
    HCC
    HBV
    miRNA
    Hsa-miR-331-3p and VHL
    Opis:
    Dysregulation of miRNA is widely involved in human cancers, including hepatocellular carcinoma (HCC). Array data for miRNAs indicated that miR-331-3p might be one of the disorderly expressed miRNAs in HCC cell lines, but the function of miR-331-3p in HCC remains unclear. In this study, quantitative real time polymerase chain reaction (qRT-PCR) results indicated that miR-331-3p was up-regulated in HepG2.2.15 cells, Ad-HBV-HepG2 cells and pCH9/3091transfected SMMC7721 cells compared with their control group, respectively. miRNA target prediction software was used, and VHL was found to be one of the target genes of miR-331-3p. qRT-PCR and western blot analysis indicated VHL expression was decreased when miR-331-3p was over-expressed and increased when miR-331-3p was inhibited in SMMC7721 cells. The luciferase reporter activity was inhibited in SMMC7721 cells when co-transfected with miR-331-3p expression vector and VHL 3'-UTR wild type vector and increased in HepG2.2.15 transfected with miR-331-3p inhibitor compared to its control group respectively. When co-transfected with miR-331-3p expression vector and VHL 3'-UTR mutated type vector in SMMC7721 cells the luciferase reporter activity was recovered. All of these results show that HBV up-regulated miR-331-3p expression in HCC cell lines and miR-331-3p could inhibit VHL expression by directly targeting its 3'-UTR. This provided useful information in exploring the mechanism of HCC induced by HBV infection.
    Źródło:
    Acta Biochimica Polonica; 2015, 62, 1; 77-82
    0001-527X
    Pojawia się w:
    Acta Biochimica Polonica
    Dostawca treści:
    Biblioteka Nauki
    Artykuł
    Tytuł:
    How short RNAs impact the human ribonuclease Dicer activity: putative regulatory feedback-loops and other RNA-mediated mechanisms controlling microRNA processing
    Autorzy:
    Koralewska, Natalia
    Hoffmann, Weronika
    Pokornowska, Maria
    Milewski, Marek
    Lipinska, Andrea
    Bienkowska-Szewczyk, Krystyna
    Figlerowicz, Marek
    Kurzynska-Kokorniak, Anna
    Powiązania:
    https://bibliotekanauki.pl/articles/1038739.pdf
    Data publikacji:
    2016
    Wydawca:
    Polskie Towarzystwo Biochemiczne
    Tematy:
    ribonuclease Dicer
    miRNA processing
    regulatory RNAs
    regulation of Dicer activity
    regulatory feedback-loops
    Opis:
    Ribonuclease Dicer plays a pivotal role in RNA interference pathways by processing long double-stranded RNAs and single-stranded hairpin RNA precursors into small interfering RNAs (siRNAs) and microRNAs (miRNAs), respectively. While details of Dicer regulation by a variety of proteins are being elucidated, less is known about non-protein factors, e.g. RNA molecules, that may influence this enzyme's activity. Therefore, we decided to investigate the question of whether the RNA molecules can function not only as Dicer substrates but also as its regulators. Our previous in vitro studies indicated that the activity of human Dicer can be influenced by short RNA molecules that either bind to Dicer or interact with its substrates, or both. Those studies were carried out with commercial Dicer preparations. Nevertheless, such preparations are usually not homogeneous enough to carry out more detailed RNA-binding studies. Therefore, we have established our own system for the production of human Dicer in insect cells. In this manuscript, we characterize the RNA-binding and RNA-cleavage properties of the obtained preparation. We demonstrate that Dicer can efficiently bind single-stranded RNAs that are longer than ~20-nucleotides. Consequently, we revisit possible scenarios of Dicer regulation by single-stranded RNA species ranging from ~10- to ~60-nucleotides, in the context of their binding to this enzyme. Finally, we show that siRNA/miRNA-sized RNAs may affect miRNA production either by binding to Dicer or by participating in regulatory feedback-loops. Altogether, our studies suggest a broad regulatory role of short RNAs in Dicer functioning.
    Źródło:
    Acta Biochimica Polonica; 2016, 63, 4; 773-783
    0001-527X
    Pojawia się w:
    Acta Biochimica Polonica
    Dostawca treści:
    Biblioteka Nauki
    Artykuł
      Wyświetlanie 1-11 z 11

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