scholarly journals MicroRNA Profiling: From Dark Matter to White Matter, or Identifying New Players in Neurobiology

2007 ◽  
Vol 7 ◽  
pp. 155-166 ◽  
Author(s):  
Anna M. Krichevsky
Keyword(s):  
Dark Matter ◽  
Mirna Expression ◽  
Regulatory Networks ◽  
Expression Patterns ◽  
Basic Principles ◽  
Protein Coding ◽  
Rna Molecules ◽  
Coding Regions ◽  
Small Regulatory Rna ◽  
Mirna Expression Profiling

Contemporary biology has been revolutionized by a recently discovered class of small regulatory RNA molecules, microRNAs (miRNAs). Missed by researchers for decades due to their tiny size, usually mapping to non-protein-coding regions of genomes, miRNAs and miRNA-mediated regulatory networks have been the “dark matter” of molecular biology. Deciphering miRNA pathways and functions in the CNS of complex organisms is tightly linked to understanding miRNA expression patterns. To facilitate these emerging studies, I here review the basic principles of medium- and high-throughput technologies available for miRNA expression profiling.

scholarly journals Left-Sided Colorectal Cancer Distinct in Indigenous African Patients Compared to Other Ethnic Groups in South Africa.

2021 ◽  
Author(s):  
M. McCabe ◽  
C. Penny ◽  
P. Magangane ◽  
S. Mirza ◽  
Y. Perner
Keyword(s):  
Colorectal Cancer ◽  
South Africa ◽  
Ethnic Groups ◽  
Mirna Expression ◽  
Expression Profiling ◽  
Expression Patterns ◽  
Molecular Characteristics ◽  
Anatomical Site ◽  
Molecular Features ◽  
Mirna Expression Profiling

Abstract Introduction: A large proportion of indigenous African (IA) colorectal cancer (CRC) patients in South Africa are young (<50years), with no unique histopathological or molecular characteristics. Anatomical site as well as microsatellite instability (MSI) status have shown to be associated with different clinicopathological and molecular features. This study aimed to ascertain key histopathological and miRNA expression patterns in microsatellite stable (MSS) and low-frequency MSI (MSI-L) patients, to provide insight into the mechanism of the disease. Methods: A retrospective cohort (2011-2015) of MSS/MSI-L CRC patient samples diagnosed at Charlotte Maxeke Johannesburg Academic Hospital was analyzed. Samples were categorized by site [Right colon cancer (RCC) versus left (LCC)], ethnicity [IA versus other ethnic groups (OEG)] and MSI status (MSI-L vs MSS). T-test, Fischer’s exact and Chi-square tests were conducted. Additional miRNA expression profiling was performed on IA patient samples. Results: IA patients with LCC demonstrated an increased prevalence in males, sigmoid colon, signet-ring-cell morphology, MSI-L with BAT25/26 marker instability and advanced disease association. MiRNA expression profiling revealed unique clustering, with dysregulation of let-7 and miRNA-125. Conclusion: This study revealed distinct histopathological features for LCC, and suggests BAT25/26, miRNAs let-7a-5p and miRNA-125a/b-5p as negative prognostic markers in African CRC patients. Larger confirmatory studies are recommended.

scholarly journals Emerging Roles of Estrogen-Regulated Enhancer and Long Non-Coding RNAs

2020 ◽  
Vol 21 (10) ◽  
pp. 3711
Author(s):  
Melina J. Sedano ◽  
Alana L. Harrison ◽  
Mina Zilaie ◽  
Chandrima Das ◽  
Ramesh Choudhari ◽  
...  
Keyword(s):  
Rna Sequencing ◽  
Expression Patterns ◽  
Biological Significance ◽  
Rna Seq ◽  
Biological Functions ◽  
Protein Coding ◽  
Rna Molecules ◽  
Non Coding Rna ◽  
Genome Wide ◽  
Non Coding Rnas

Genome-wide RNA sequencing has shown that only a small fraction of the human genome is transcribed into protein-coding mRNAs. While once thought to be “junk” DNA, recent findings indicate that the rest of the genome encodes many types of non-coding RNA molecules with a myriad of functions still being determined. Among the non-coding RNAs, long non-coding RNAs (lncRNA) and enhancer RNAs (eRNA) are found to be most copious. While their exact biological functions and mechanisms of action are currently unknown, technologies such as next-generation RNA sequencing (RNA-seq) and global nuclear run-on sequencing (GRO-seq) have begun deciphering their expression patterns and biological significance. In addition to their identification, it has been shown that the expression of long non-coding RNAs and enhancer RNAs can vary due to spatial, temporal, developmental, or hormonal variations. In this review, we explore newly reported information on estrogen-regulated eRNAs and lncRNAs and their associated biological functions to help outline their markedly prominent roles in estrogen-dependent signaling.

MYC stimulates EZH2 expression by repression of its negative regulator miR-26a

Blood ◽  
2008 ◽  
Vol 112 (10) ◽  
pp. 4202-4212 ◽  
Author(s):  
Sandrine Sander ◽  
Lars Bullinger ◽  
Kay Klapproth ◽  
Katja Fiedler ◽  
Hans A. Kestler ◽  
...  
Keyword(s):  
Mirna Expression ◽  
Cell Cycle Progression ◽  
Ectopic Expression ◽  
Negative Regulator ◽  
Protein Coding ◽  
Myc Oncogene ◽  
Polycomb Protein ◽  
Ezh2 Expression ◽  
Mirna Expression Profiling ◽  
The Impact

Abstract The MYC oncogene, which is commonly mutated/amplified in tumors, represents an important regulator of cell growth because of its ability to induce both proliferation and apoptosis. Recent evidence links MYC to altered miRNA expression, thereby suggesting that MYC-regulated miRNAs might contribute to tumorigenesis. To further analyze the impact of MYC-regulated miRNAs, we investigated a murine lymphoma model harboring the MYC transgene in a Tet-off system to control its expression. Microarray-based miRNA expression profiling revealed both known and novel MYC targets. Among the miRNAs repressed by MYC, we identified the potential tumor suppressor miR-26a, which possessed the ability to attenuate proliferation in MYC-dependent cells. Interestingly, miR-26a was also found to be deregulated in primary human Burkitt lymphoma samples, thereby probably being of clinical relevance. Although today only few miRNA targets have been identified in human disease, we could show that ectopic expression of miR-26a influenced cell cycle progression by targeting the bona fide oncogene EZH2, a Polycomb protein and global regulator of gene expression yet unknown to be regulated by miRNAs. Thus, in addition to directly targeting protein-coding genes, MYC modulates genes important to oncogenesis via deregulation of miRNAs, thereby vitally contributing to MYC-induced lymphomagenesis.

scholarly journals Bacterial Noncoding RNAs Excised from within Protein-Coding Transcripts

mBio ◽  
2018 ◽  
Vol 9 (5) ◽  
Author(s):  
Daniel Dar ◽  
Rotem Sorek
Keyword(s):  
Expression Patterns ◽  
Noncoding Rnas ◽  
Large Set ◽  
Rna Structures ◽  
Protein Coding ◽  
Small Noncoding Rnas ◽  
Coding Regions ◽  
Protein Coding Genes ◽  
Evolutionarily Conserved ◽  
Intergenic Regions

ABSTRACT Prokaryotic genomes encode a plethora of small noncoding RNAs (ncRNAs) that fine-tune the expression of specific genes. The vast majority of known bacterial ncRNAs are encoded from within intergenic regions, where their expression is controlled by promoter and terminator elements, similarly to protein-coding genes. In addition, recent studies have shown that functional ncRNAs can also be derived from gene 3′ untranslated regions (3′UTRs) via an alternative biogenesis pathway, in which the ncRNA segment is separated from the mRNA via RNase cleavage. Here, we report the detection of a large set of decay-generated noncoding RNAs (decRNAs), many of which are completely embedded within protein-coding mRNA regions rather than in the UTRs. We show that these decRNAs are “carved out” of the mRNA through the action of RNase E and that they are predicted to fold into highly stable RNA structures, similar to those of known ncRNAs. A subset of these decRNAs is predicted to interact with Hfq or ProQ or both, which act as ncRNA chaperones, and some decRNAs display evolutionarily conserved sequences and conserved expression patterns between different species. These results suggest that mRNA protein-coding regions may harbor a large set of potentially functional small RNAs. IMPORTANCE Bacteria and archaea utilize regulatory small noncoding RNAs (ncRNAs) to control the expression of specific genetic programs. These ncRNAs are almost exclusively encoded within intergenic regions and are independently transcribed. Here, we report on a large set ncRNAs that are “carved out” from within the protein-coding regions of Escherichia coli mRNAs by cellular RNases. These protected mRNA fragments fold into energetically stable RNA structures, reminiscent of those of intergenic regulatory ncRNAs. In addition, a subset of these ncRNAs coprecipitate with the major ncRNA chaperones Hfq and ProQ and display evolutionarily conserved sequences and conserved expression patterns between different bacterial species. Our data suggest that protein-coding genes can potentially act as a reservoir of regulatory ncRNAs.

scholarly journals MiRNA expression profiling and zeatin dynamic changes in a new model system of in vivo indirect regeneration of tomato

2020 ◽  
Author(s):  
Huiying Cao ◽  
Xinyue Zhang ◽  
Yanye Ruan ◽  
Lijun Zhang ◽  
Zhenhai Cui ◽  
...  
Keyword(s):  
Mirna Expression ◽  
Target Genes ◽  
Higher Plants ◽  
Callus Formation ◽  
Expression Patterns ◽  
Adventitious Shoot ◽  
Model System ◽  
Indirect Regeneration ◽  
Mirna Expression Profiling

AbstractCallus formation and adventitious shoot differentiation could be observed on the cut surface of completely decapitated tomato plants. We propose that this process can be used as a model system to investigate the mechanisms that regulate indirect regeneration of higher plants without the addition of exogenous hormones. This study analyzed the patterns of trans-zeatin and miRNA expression during in vivo regeneration of tomato. Analysis of trans-zeatin revealed that the hormone cytokinin played an important role in in vivo regeneration of tomato. Among 183 miRNAs and 1168 predicted target genes sequences identified, 93 miRNAs and 505 potential targets were selected based on differential expression levels for further characterization. Expression patterns of six miRNAs, including sly-miR166, sly-miR167, sly-miR396, sly-miR397, novel 156, and novel 128, were further validated by qRT-PCR. We speculate that sly-miR156, sly-miR160, sly-miR166, and sly-miR397 play major roles in callus formation of tomato during in vivo regeneration by regulating cytokinin, IAA, and laccase levels. Overall, our microRNA sequence and target analyses of callus formation during in vivo regeneration of tomato provide novel insights into the regulation of regeneration in higher plants.

scholarly journals Genome-wide mRNA and miRNA expression profiling reveal multiple regulatory networks in colorectal cancer

2015 ◽  
Vol 6 (1) ◽  
pp. e1614-e1614 ◽  
Author(s):  
R Vishnubalaji ◽  
R Hamam ◽  
M-H Abdulla ◽  
M A V Mohammed ◽  
M Kassem ◽  
...  
Keyword(s):  
Colorectal Cancer ◽  
Mirna Expression ◽  
Expression Profiling ◽  
Regulatory Networks ◽  
Genome Wide ◽  
Mirna Expression Profiling

scholarly journals MicroRNA Microarray Expression Profiling in Human Myocardial Infarction

2009 ◽  
Vol 27 (6) ◽  
pp. 255-268 ◽  
Author(s):  
Emanuela Boštjančič ◽  
Nina Zidar ◽  
Damjan Glavač
Keyword(s):  
Myocardial Infarction ◽  
Cardiovascular Disease ◽  
Cardiovascular Diseases ◽  
Expression Pattern ◽  
Mirna Expression ◽  
Expression Patterns ◽  
Bioinformatic Analysis ◽  
Pcr Analysis ◽  
Rna Molecules ◽  
Mirna Expression Pattern

MicroRNAs (miRNAs), small non-coding RNA molecules, are negative regulators of gene expression. Recent studies have indicated their role in various forms of cardiovascular disease. In spite of the number of miRNA microarray analyses performed, little is known about the genome-wide miRNA expression pattern in human myocardial infarction (MI). Using miRNA microarrays and bioinformatic analysis, miRNA expression was analyzed on human MI and foetal hearts compared to healthy adult hearts, to determine whether there is any similar expression pattern between MI and foetal hearts, and to identified miRNAs that have not previously been described as dysregulated in cardiovascular diseases. Of 719 miRNAs analyzed, ∼ 50% were expressed in human hearts, 77 miRNAs were absent from all tested tissues and 57 were confidently dysregulated in at least one tested group. Some expression patterns appeared to be similar in MI and foetal hearts. Bioinformatic analysis revealed 10 miRNAs as dysregulated in MI not yet related to cardiovascular disease, and 5 miRNAs previously described only in animal models of cardiovascular diseases. Finally, qRT-PCR analysis confirmed dysregulation of 7 miRNAs,miR-150, miR-186, miR-210, miR-451, and muscle-specific, miR-1 and miR-133a/b; all of these are believed to be involved in various physiological and pathological processes.

scholarly journals Distinct miRNA Signatures and Networks Discern Fetal from Adult Erythroid Differentiation and Primary from Immortalized Erythroid Cells

2021 ◽  
Vol 22 (7) ◽  
pp. 3626
Author(s):  
Panayiota L. Papasavva ◽  
Nikoletta Y. Papaioannou ◽  
Petros Patsali ◽  
Ryo Kurita ◽  
Yukio Nakamura ◽  
...  
Keyword(s):  
Mirna Expression ◽  
Regulatory Networks ◽  
Target Genes ◽  
Human Peripheral Blood ◽  
Expression Patterns ◽  
Erythroid Differentiation ◽  
Erythroid Cell ◽  
Small Rna Sequencing ◽  
Erythroid Cells ◽  
Mirna Regulation

MicroRNAs (miRNAs) are small non-coding RNAs crucial for post-transcriptional and translational regulation of cellular and developmental pathways. The study of miRNAs in erythropoiesis elucidates underlying regulatory mechanisms and facilitates related diagnostic and therapy development. Here, we used DNA Nanoball (DNB) small RNA sequencing to comprehensively characterize miRNAs in human erythroid cell cultures. Based on primary human peripheral-blood-derived CD34+ (hCD34+) cells and two influential erythroid cell lines with adult and fetal hemoglobin expression patterns, HUDEP-2 and HUDEP-1, respectively, our study links differential miRNA expression to erythroid differentiation, cell type, and hemoglobin expression profile. Sequencing results validated by reverse-transcription quantitative PCR (RT-qPCR) of selected miRNAs indicate shared differentiation signatures in primary and immortalized cells, characterized by reduced overall miRNA expression and reciprocal expression increases for individual lineage-specific miRNAs in late-stage erythropoiesis. Despite the high similarity of same-stage hCD34+ and HUDEP-2 cells, differential expression of several miRNAs highlighted informative discrepancies between both cell types. Moreover, a comparison between HUDEP-2 and HUDEP-1 cells displayed changes in miRNAs, transcription factors (TFs), target genes, and pathways associated with globin switching. In resulting TF-miRNA co-regulatory networks, major therapeutically relevant regulators of globin expression were targeted by many co-expressed miRNAs, outlining intricate combinatorial miRNA regulation of globin expression in erythroid cells.

scholarly journals NOVOMIR: De Novo Prediction of MicroRNA-Coding Regions in a Single Plant-Genome

2010 ◽  
Vol 2010 ◽  
pp. 1-10 ◽  
Author(s):  
Jan-Hendrik Teune ◽  
Gerhard Steger
Keyword(s):  
Noncoding Rna ◽  
De Novo ◽  
Plant Genome ◽  
Messenger Rnas ◽  
Protein Coding ◽  
Rna Molecules ◽  
Coding Regions ◽  
Mirna Genes ◽  
Genomic Scale ◽  
Eukaryotic Genomes

MicroRNAs (miRNA) are small regulatory, noncoding RNA molecules that are transcribed as primary miRNAs (pri-miRNA) from eukaryotic genomes. At least in plants, their regulatory activity is mediated through base-pairing with protein-coding messenger RNAs (mRNA) followed by mRNA degradation or translation repression. We describeNOVOMIR, a program for the identification of miRNA genes in plant genomes. It uses a series of filter steps and a statistical model to discriminate a pre-miRNA from other RNAs and does rely neither on prior knowledge of a miRNA target nor on comparative genomics. The sensitivity and specificity ofNOVOMIR for detection of premiRNAs fromArabidopsis thalianais ~0.83 and ~0.99, respectively. Plant pre-miRNAs are more heterogeneous with respect to size and structure than animal pre-miRNAs. Despite these difficulties,NOVOMIR is well suited to perform searches for pre-miRNAs on a genomic scale.NOVOMIR is written in Perl and relies on two additional, free programs for prediction of RNA secondary structure (RNALFOLD, RNASHAPES).

scholarly journals PLncDB V2.0: a comprehensive encyclopedia of plant long noncoding RNAs

2020 ◽  
Vol 49 (D1) ◽  
pp. D1489-D1495 ◽  
Author(s):  
Jingjing Jin ◽  
Peng Lu ◽  
Yalong Xu ◽  
Zefeng Li ◽  
Shizhou Yu ◽  
...  
Keyword(s):  
Noncoding Rna ◽  
Regulatory Networks ◽  
Expression Patterns ◽  
Noncoding Rnas ◽  
Long Noncoding Rnas ◽  
Data Driven ◽  
Rna Seq ◽  
Protein Coding ◽  
User Friendly ◽  
Coding Potential

Abstract Long noncoding RNAs (lncRNAs) are transcripts longer than 200 nucleotides with little or no protein coding potential. The expanding list of lncRNAs and accumulating evidence of their functions in plants have necessitated the creation of a comprehensive database for lncRNA research. However, currently available plant lncRNA databases have some deficiencies, including the lack of lncRNA data from some model plants, uneven annotation standards, a lack of visualization for expression patterns, and the absence of epigenetic information. To overcome these problems, we upgraded our Plant Long noncoding RNA Database (PLncDB, http://plncdb.tobaccodb.org/), which was based on a uniform annotation pipeline. PLncDB V2.0 currently contains 1 246 372 lncRNAs for 80 plant species based on 13 834 RNA-Seq datasets, integrating lncRNA information from four other resources including EVLncRNAs, RNAcentral and etc. Expression patterns and epigenetic signals can be visualized using multiple tools (JBrowse, eFP Browser and EPexplorer). Targets and regulatory networks for lncRNAs are also provided for function exploration. In addition, PLncDB V2.0 is hierarchical and user-friendly and has five built-in search engines. We believe PLncDB V2.0 is useful for the plant lncRNA community and data mining studies and provides a comprehensive resource for data-driven lncRNA research in plants.

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