TY - JOUR. T1 - The long intergenic noncoding RNA landscape of human lymphocytes highlights the regulation of T cell differentiation by linc-MAF-4. AU - Ranzani, Valeria. AU - Rossetti, Grazisa. AU - Panzeri, Ilaria. AU - Arrigoni, Alberto. AU - Bonnal, Raoul J P. AU - Curti, Serena. AU - Gruarin, Paola. AU - Provasi, Elena. AU - Sugliano, Elisa. AU - Marconi, Maurizio. AU - De Francesco, Raffaele. AU - Geginat, Jens. AU - Bodega, Beatrice. AU - Abrignani, Sergio. AU - Pagani, Massimiliano. PY - 2015/2/17. Y1 - 2015/2/17. N2 - Long noncoding RNAs are emerging as important regulators of cellular functions, but little is known of their role in the human immune system. Here we investigated long intergenic noncoding RNAs (lincRNAs) in 13 subsets of T lymphocytes and B lymphocytes by next-generation sequencing-based RNA sequencing (RNA-seq analysis) and de novo transcriptome reconstruction. We identified over 500 previously unknown lincRNAs and described lincRNA signatures. Expression of linc-MAF-4, ...
Long intergenic noncoding RNAs (lincRNAs) play important roles in disease, but the vast majority of these transcripts remain uncharacterized. A team led by researchers from Duke University defined a set of 54,944 human lincRNAs by drawing on four publicly available lincRNA datasets, and annotated ~2.5 million single-nucleotide polymorphisms from each of 15 cardiometabolic genome-wide association study datasets into these lincRNAs. They identified hundreds of lincRNAs with at least one trait-associated SNP: 898 SNPs in 343 unique lincRNAs at 5% false discovery rate, and 469 SNPs in 146 unique lincRNAs meeting Bonferroni-corrected P ,0.05. An additional 64 trait-associated lincRNAs were identified using a class-level testing strategy at Bonferroni-corrected P ,0.05. To better understand the genomic context and prioritize trait-associated lincRNAs, the team examined the pattern of linkage disequilibrium between SNPs in the lincRNAs and SNPs that met genome-wide-significance in the region (±500 kb ...
Noncoding RNAs have been extensively described in plant and animal transcriptomes by using high-throughput sequencing technology. Of these non-coding RNAs, a growing number of long intergenic noncoding RNAs (lincRNAs) have been described in multicellular organisms, however the origins and functions of many lincRNAs remain to be explored. In many eukaryotic genomes, transposable elements (TEs) are widely distributed and often account for large fractions of plant and animal genomes yet the contribution of TEs to lincRNAs is largely unknown. By using strand-specific RNA sequencing, researchers from the Shanghai Center for Plant Stress Biology profiled the expression patterns of lincRNAs in Arabidopsis, rice and maize, and identified 47, 611 and 398 TE-associated lincRNAs (TE-lincRNAs), respectively. TE-lincRNAs were more often derived from retrotransposons than DNA transposons and as retrotransposon copy number in both rice and maize genomes so did TE-lincRNAs. The researchers validated the ...
Whole transcriptome analyses have revealed a large number of novel transcripts including long and short noncoding RNAs (ncRNAs). Currently, there is great interest in characterizing the functions of the different classes of ncRNAs and their relevance to cellular processes. In particular, nuclear long ncRNAs may be involved in controlling various aspects of biological regulation, such as stress responses. By a combination of bioinformatic and experimental approaches, we identified 25 novel nuclear long ncRNAs from 6,088,565 full-length human cDNA sequences. Some nuclear long ncRNAs were conserved among vertebrates, whereas others were found only among primates. Expression profiling of the nuclear long ncRNAs in human tissues revealed that most were expressed ubiquitously. A subset of the identified nuclear long ncRNAs was induced by the genotoxic agents mitomycin C or doxorubicin, in HeLa Tet-off cells. There were no commonly altered nuclear long ncRNAs between mitomycin C- and doxorubicin-treated cells.
BACKGROUND: Long considered to be the building block of life, it is now apparent that protein is only one of many functional products generated by the eukaryotic genome. Indeed, more of the human genome is transcribed into noncoding sequence than into protein-coding sequence. Nevertheless, whilst we have developed a deep understanding of the relationships between evolutionary constraint and function for protein-coding sequence, little is known about these relationships for non-coding transcribed sequence. This dearth of information is partially attributable to a lack of established non-protein-coding RNA (ncRNA) orthologs among birds and mammals within sequence and expression databases. RESULTS: Here, we performed a multi-disciplinary study of four highly conserved and brain-expressed transcripts selected from a list of mouse long intergenic noncoding RNA (lncRNA) loci that generally show pronounced evolutionary constraint within their putative promoter regions and across exon-intron boundaries. We
Long non-coding RNAs (long ncRNAs, lncRNA) are defined as transcripts longer than 200 nucleotides that are not translated into protein. This somewhat arbitrary limit distinguishes long ncRNAs from small non-coding RNAs such as microRNAs (miRNAs), short interfering RNAs (siRNAs), Piwi-interacting RNAs (piRNAs), small nucleolar RNAs (snoRNAs), and other short RNAs. However, very recent research has shown that some lncRNAs have been misannotated and do in fact encode proteins. A recent study found only one-fifth of transcription across the human genome is associated with protein-coding genes, indicating at least four times more long non-coding than coding RNA sequences. However, it is large-scale complementary DNA (cDNA) sequencing projects such as FANTOM (Functional Annotation of Mammalian cDNA) that reveal the complexity of this transcription. The FANTOM3 project identified ~35,000 non-coding transcripts from ~10,000 distinct loci that bear many signatures of mRNAs, including 5 capping, ...
Whilst only approximately 1.06% of the human genome appears to encode protein [1, 2] at least four times this amount is transcribed into stable non-protein-coding RNA (ncRNA) transcripts [3-5]. Unfortunately, the biological relevance of the vast majority of this extensive and interleaving network of coding RNAs and ncRNAs remains far from clear. One possibility is that many ncRNAs result simply from transcriptional noise. If so, their sequence and transcription might be expected not to be conserved outside of restricted phyletic lineages. Indeed, the finding that only 14% of the well-defined mouse long intergenic ncRNAs (lncRNAs) identified in the FANTOM projects [6, 7] have a transcribed ortholog in human (based on analyses of known EST and cDNA data sets) [2] argues against their functionality. Similarly, known human intergenic lncRNA loci are generally not conserved in sequence at statistically significant levels in the mouse genome [3, 8, 9], and there is little evidence for conserved ...
Non-protein-coding RNAs (ncRNAs) are increasingly being recognized as having important regulatory roles. Although much recent attention has focused on tiny 22- to 25-nucleotide microRNAs, several functional ncRNAs are orders of magnitude larger in size. Examples of such macro ncRNAs include Xist and Air, which in mouse are 18 and 108 kilobases (Kb), respectively. We surveyed the 102,801 FANTOM3 mouse cDNA clones and found that Air and Xist were present not as single, full-length transcripts but as a cluster of multiple, shorter cDNAs, which were unspliced, had little coding potential, and were most likely primed from internal adenine-rich regions within longer parental transcripts. We therefore conducted a genome-wide search for regional clusters of such cDNAs to find novel macro ncRNA candidates. Sixty-six regions were identified, each of which mapped outside known protein-coding loci and which had a mean length of 92 Kb. We detected several known long ncRNAs within these regions, supporting the basic
So-called long noncoding RNAs (ncRNAs) are transcripts that are larger than small regulatory RNAs, such as microRNAs (miRNAs) and small nucleolar RNAs (snoRNAs), that have traditionally been thought not to encode proteins because they contain only short open reading frames (sORFs). Recent studies, however, have indicated that some sORFs of long ncRNAs are translated. One such translated long ncRNA is that transcribed from the polished rice (pri) locus in the fruit fly Drosophila melanogaster, which encodes four peptides 11 to 32 amino acids in length. Loss-of-function mutations in pri phenocopy loss of shavenbaby (svb), which encodes a transcription factor required for formation of hairs called trichomes on the dorsal epidermis of the fly embryo. Kondo et al. report that, in pri mutants, expression of svb was normal, but expression of genes and reporters activated by Svb was reduced. The svb locus encodes three transcription factor isoforms that share the same DNA binding and transcriptional ...
The majority of the human genome is transcribed into non-protein-coding RNA. Hence, RNA is also the primary product of the cancer genome. We have defined the ncRNA expression landscape of lung, breast and liver cancer providing a comprehensive expression map of over 17000 long ncRNAs and discovering new lncRNAs associated with cancer whose molecular and cellular functions we are currently elucidating exploiting our custom siRNA library targeting 638 tumor-associated lncRNAs. The nuclear lncRNA MALAT1 was one of the first lncRNAs associated with cancer: it is associated with metastasis development in lung cancer. However, its high abundance and nuclear localization have hampered its functional analysis. To uncover its functional importance, we developed a MALAT1 knockout model in human lung tumor cells by genomically integrating RNA destabilizing elements site-specifically into the MALAT1 locus. This approach yielded a 1000-fold silencing of MALAT1 providing a unique loss-of-function model. ...
TY - JOUR. T1 - The non-coding transcripts of hsr-omega gene in Drosophila. T2 - Do they regulate trafficking and availability of nuclear RNA-processing factors?. AU - Lakhotia, S. C.. AU - Ray, Pritha. AU - Rajendra, T. K.. AU - Prasanth, K. V.. PY - 1999/8/25. Y1 - 1999/8/25. N2 - The 93D or hsr-omega (hsrω) is an unusual non-protein-coding gene with multiple transcription products which are dynamically expressed in most cell types of Drosophila melanogaster and this gene, besides being a member of the heat shock gene family, is uniquely induced in polytene cells by a variety of amides. The various aspects of this genes organization, regulation and inducible properties are briefly reviewed. Recent data in our laboratory show that absence of the hsr-omega transcripts because of nullosomy or over-expression of the these transcripts in specific cell types due to mutation in the promoter region of this gene results in specific phenotypes. It is known from several earlier and our recent studies ...
2:30-3:30 PM. Guest Speaker: Chiara Arina (Insitut dAstrophysique de Paris and Université Pierre et Marie Curie (Paris 6)). Talk Title: A WIMP view of particle dark matter: from data analysis to theoretical models. Abstract: The astroparticle experiments have reached unprecedented sensitivities, releasing constantly suggestive hints and stringent constraints that seem to chase each other. Considering as an example the direct dark matter detection data, I will show how uncertainties affect the theoretical interpretation of these bounds/hints. These results serve as guidelines for dark matter model building. I will discuss how inference of the properties WIMPs can be enhanced by the complementarity of dark matter searches and LHC and what are the consequences for theoretical motivated dark matter models. A particular focus will be on supersymmetric models in which the sneutrino can be the dark matter candidate. I will close on predictions and expectations for detection in a relatively close ...
The ALICE collaboration has presented new results on the production rates of antideuterons based on data collected at the highest collision energy delivered so far at the Large Hadron Collider. The antideuteron is composed of an antiproton and an antineutron. The new measurements are important because the presence of antideuterons in space is a promising indirect signature of dark matter candidates. The results mark a step forward in the search for dark matter.. Recent astrophysical and cosmological results point towards dark matter being the dominant form of matter in the universe, accounting for approximately 85% of all matter. The nature of dark matter remains a great mystery, and cracking its secrets would open a new door for physics.. Detecting antideuterons in space could be an indirect signature of dark matter, since they could be produced during the annihilation or decay of neutralinos or sneutrinos, which are hypothetical dark matter particles.. Various experiments are on the hunt for ...
Significance: Levels of platelet noncoding RNAs (ncRNAs) are altered by disease, and ncRNAs may exert functions inside and outside of platelets. Their role in physiologic hemostasis and pathologic thrombosis remains to be explored. Recent Advances: The number of RNA classes identified in platelets has been growing since the past decade. Apart from coding messenger RNAs, the RNA landscape in platelets comprises ncRNAs such as microRNAs, circular RNAs, long ncRNAs, YRNAs, and potentially environmentally derived exogenous ncRNAs. Recent research has focused on the function of platelet RNAs beyond platelets, mediated through protective RNA shuttles or even cellular uptake of entire platelets. Multiple studies have also explored the potential of platelet RNAs as novel biomarkers. Critical Issues: Platelet preparations can contain contaminating leukocytes. Even few leukocytes may contribute a substantial amount of RNA. As biomarkers, platelet RNAs have shown associations with platelet activation, but ...
Invitrogen). Normal meningeal RNA samples were purchased from BioChain and Analytical Biological Services, or extracted from normal…Normal meningeal genomic DNA samples were either purchased fromBioChain and Analytical Biological Services or extracted from normal ...
Imprinted genes play essential roles in development, and their allelic expression is mediated by imprinting control regions (ICRs). The Dlk1-Dio3 locus is among the few imprinted domains controlled by a paternally methylated ICR. The unmethylated maternal copy activates imprinted expression early in development through an unknown mechanism. We find that in mouse embryonic stem cells (ESCs) and in blastocysts, this function is linked to maternal, bidirectional expression of noncoding RNAs (ncRNAs) from the ICR. Disruption of ICR ncRNA expression in ESCs affected gene expression in cis, led to acquisition of aberrant histone and DNA methylation, delayed replication timing along the domain on the maternal chromosome, and changed its subnuclear localization. The epigenetic alterations persisted during differentiation and affected the neurogenic potential of the stem cells. Our data indicate that monoallelic expression at an ICR of enhancer RNA-like ncRNAs controls imprinted gene expression, ...
It is amazing that the team has managed to achieve such precision from only the first year of their survey, said National Science Foundation Program Director Nigel Sharp. Now that their analysis techniques are developed and tested, we look forward with eager anticipation to breakthrough results as the survey continues.. DES scientists used two methods to measure dark matter. First, they created maps of galaxy positions as tracers, and second, they precisely measured the shapes of 26 million galaxies to directly map the patterns of dark matter over billions of light-years, using a technique called gravitational lensing.. To make these ultraprecise measurements, the DES team developed new ways to detect the tiny lensing distortions of galaxy images, an effect not even visible to the eye, enabling revolutionary advances in understanding these cosmic signals. In the process, they created the largest guide to spotting dark matter in the cosmos ever drawn (see image). The new dark matter map is 10 ...
Numerical simulation showing the distribution of dark matter in a large volume of the universe. The box shown spans a distance of about 1 billion light-years. The structures are displayed so that the brighter regions have a higher density (that is, more dark matter) than the darker regions. The dark matter is concentrated into a web-like distribution of filaments that intersect at dense nodes where great clusters of galaxies are expected to form and become visible. At the rear of the cube (to the left), three blue disks represent three distant galaxies. The yellow lines that cross the box represent light rays from those galaxies propagating through the universe. In the absence of intervening matter, the light would travel on straight lines but in the presence of matter, the paths of the rays are evidently deflected by the gravitational effects of the clumpy matter (the breaks in the yellow lines illustrate the light passing behind a clump of dark matter). The light from a distant galaxy rarely ...
I know what dark matter is. Dark matter is the pit around a sandcastle. Yes, when you build a sandcastle in a flat beach, there is always a pit formed around it. That means, the density of a vacuum in that gravitational pit is lower than expected. On average, the density of matter in the space between the stars of the Milky Way is 0.1 neutral hydrogen atoms per cubic centimetre. In a gravitational pit around a galaxy (or a cluster of galaxies) the density of matter is drastically lower than that value, so there we have what we call dark matter. The rapidly formed clusters of matter in outer space produce deeper gravitational pits around them. If the formation of clusters of matter is slow, their gravitational pits are shallow. That explains the reason why some galaxies, or cluster of galaxies, dont exhibit great amounts of that alleged dark matter, but others do. So, a gravitational pit is a gravitational anti-well, If, by definition, we put the value of the gravitational potential of a flat ...
I know what dark matter is. Dark matter is the pit around a sandcastle. Yes, when you build a sandcastle in a flat beach, there is always a pit formed around it. That means, the density of a vacuum in that gravitational pit is lower than expected. On average, the density of matter in the space between the stars of the Milky Way is 0.1 neutral hydrogen atoms per cubic centimetre. In a gravitational pit around a galaxy (or a cluster of galaxies) the density of matter is drastically lower than that value, so there we have what we call dark matter. The rapidly formed clusters of matter in outer space produce deeper gravitational pits around them. If the formation of clusters of matter is slow, their gravitational pits are shallow. That explains the reason why some galaxies, or cluster of galaxies, dont exhibit great amounts of that alleged dark matter, but others do. So, a gravitational pit is a gravitational anti-well, If, by definition, we put the value of the gravitational potential of a flat ...
Show moreNon-protein-coding RNAs (ncRNAs) are RNA molecules that function directly at the level of RNA without translating into protein. They play important biological functions in all three domains of life, i.e. Eukarya, Bacteria and Archaea. To understand the working mechanisms and the functions of ncRNAs in various species, a fundamental step is to identify both known and novel ncRNAs from large-scale biological data.Large-scale genomic data includes both genomic sequence data and NGS sequencing data. Both types of genomic data provide great opportunity for identifying ncRNAs. For genomic sequence data, a lot of ncRNA identification tools that use comparative sequence analysis have been developed. These methods work well for ncRNAs that have strong sequence similarity. However, they are not well-suited for detecting ncRNAs that are remotely homologous. Next generation sequencing (NGS), while it opens a new horizon for annotating and understanding known and novel ncRNAs, also introduces many ...
Show moreNon-protein-coding RNAs (ncRNAs) are RNA molecules that function directly at the level of RNA without translating into protein. They play important biological functions in all three domains of life, i.e. Eukarya, Bacteria and Archaea. To understand the working mechanisms and the functions of ncRNAs in various species, a fundamental step is to identify both known and novel ncRNAs from large-scale biological data.Large-scale genomic data includes both genomic sequence data and NGS sequencing data. Both types of genomic data provide great opportunity for identifying ncRNAs. For genomic sequence data, a lot of ncRNA identification tools that use comparative sequence analysis have been developed. These methods work well for ncRNAs that have strong sequence similarity. However, they are not well-suited for detecting ncRNAs that are remotely homologous. Next generation sequencing (NGS), while it opens a new horizon for annotating and understanding known and novel ncRNAs, also introduces many ...
New discoveries and accelerating progresses in the field of noncoding RNAs (ncRNAs) continuously challenges our deep-rooted doctrines in biology and sometimes our imagination. A growing body of evidence indicates that ncRNAs are important players in oncogenesis. While a stunning list of ncRNAs has been discovered, only a small portion of them has been examined for their biological activities and very few have been characterized for the molecular mechanisms of their action. To date, ncRNAs have been shown to regulate a wide range of biological processes, including chromatin remodeling, gene transcription, mRNA translation and protein function. Dysregulation of ncRNAs contributes to the pathogenesis of a variety of cancers and aberrant ncRNA expression has a high potential to be prognostic in some cancers. Thus, a new cancer research era has begun to identify novel key players of ncRNAs in oncogenesis. In this review, we will first discuss the function and regulation of miRNAs, especially focusing on the
It is becoming increasingly evident that noncoding RNA (ncRNA) constitutes an important component of chromatin and that ncRNA has a critical role in organizing the chromatin architecture and epigenetic memory by acting as an interface with the chromatin modifying machinery. Xist is the only RNA that has been shown to regulate gene expression by modulating chromatin structure using a multilayered silencing pathway. Recent emerging evidence indicates that long ncRNAs such as Kcnq1ot1 and Air which map to the Kcnq1 and Igf2r imprinted gene clusters, respectively, mediate the transcriptional silencing of multiple genes by interacting with chromatin and recruiting the chromatin modifying machinery. Though there are some parallels in the mechanistic actions of Kcnq1ot1 and Air, they seem to differ greatly in the way they achieve the silencing of overlapping and nonoverlapping genes. By reviewing the latest available evidence, we propose that Kcnq1ot1 RNA itself seems to play a critical role in the ...
The interesting thing about nematodes is that their genomic organization of both snoRNAs and other ncRNAs is quite different from other animals, says Chen. In contrast to the genomes of other metazoans, where most snoRNAs are found in introns and are under the control of independent promoters, nematode snoRNA loci are both intergenic and intronic (with and without promoters). Interestingly, plant snoRNAs are primarily located in intergenic regions. Other ncRNA genes (i.e., non-snoRNA genes) are mainly located in intergenic regions in both plants and animals. But in nematodes, Chen s team found that many of these other ncRNA genes are located in the introns of host protein-coding genes and are under the control of independent promoter elements ...
The profiling approaches used in this study have led to several novel discoveries in rat genomics, VSMC and Ang II-mediated gene regulation. Because rats are a widely used model organism for research related to CVDs, diabetes mellitus, and other pathologies, it is imperative to analyze their transcriptome in-depth. Our annotation of novel transcripts significantly expands the existing number of known transcripts expressed in the rat genome, which, compared with the human and mouse genomes, remains less well annotated. We found that, similar to mouse and human, the rat genome contains lncRNAs that are less abundantly expressed than previously annotated rat transcripts.22 Notably, our studies revealed that the identified lncRNAs may function as host transcripts for small RNAs, such as miRNAs. Our analysis of the transcriptome and epigenome associated with H3K4me3 and H3K36me3 uncovered that Lnc-Ang362 is proximal to miR-221 and miR-222. Based on the enrichment of H3K4me3, which is at the TSS of ...
Hardy, Rowan S., Doig, Craig L., Hussain, Zahrah, OLeary, Mary, Morgan, Stuart A., Pearson, Mark J., Naylor, Amy, Jones, Simon W., Filer, Andrew, Stewart, Paul M., Buckley, Christopher D., Lavery, Gareth G., Cooper, Mark S. and Raza, Karim (2016). 11β-Hydroxysteroid dehydrogenase type 1 within muscle protects against the adverse effects of local inflammation. Journal of Pathology, 240 (4), pp. 472-483. Pearson, Mark J. and Jones, Simon W. (2016). Review:Long Noncoding RNAs in the Regulation of Inflammatory Pathways in Rheumatoid Arthritis and Osteoarthritis. Arthritis and Rheumatology, 68 (11), pp. 2575-2583. Pearson, Mark J., Philp, Ashleigh M., Heward, James A., Roux, Benoit T., Walsh, David A., Davis, Edward T., Lindsay, Mark A. and Jones, Simon W. (2016). Long Intergenic Noncoding RNAs Mediate the Human Chondrocyte Inflammatory Response and Are Differentially Expressed in Osteoarthritis Cartilage. Arthritis and Rheumatology, 68 (4), pp. 845-856. ...
Theres more of the universe that we dont understand than we do understand. Ordinary matter-the stuff that scientists have spent decades studying-makes up around five percent of the universe. The remainder is thought to be comprised of dark energy (around 70 percent) and dark matter (around 25 percent). What is all this dark stuff and how do we know its there if we cant even see it directly? We know that dark matter exists because it acts on the cosmos in a number of ways. In the 1930s, an astrophysicist named Fritz Zwicky realized that, in order to act the way they do, galaxy clusters must contain a lot more mass than was actually visible. If the galaxies also contained unseen dark matter, everything made a lot more sense. Then, in the 1970s, astronomer Vera Rubin discovered that stars at the edge of a galaxy move just as quickly as stars near the center. This observation makes sense if the visible stars were surrounded by a halo of something invisible: dark matter. Since then, a number of other
The trouble is that while it isnt that hard to devise a dark matter model or modified gravity model that is consistent with a lot of observations made by astronomers, devising one that is consistent with all of the observations turns out to be devilishly hard. Some of the early, very simple version of each model, such as a model with a single kind of dark matter particle with a particular mass in the 100s of GeV (100 times the mass of a proton more or less), or an early toy model with a very simple modification of gravity, dont fit the data. The former generates the wrong shaped dark matter halos and has other problems at the galactic scale, even though it does a great job at the cosmological scale of the entire universes structure. The latter works fine at galactic scales, but fails in galactic clusters where it predicts effects that are too small (among other things ...
Matt Strassler [April 18, 2012] Its not easy to see dark matter, which makes up most of the matter in the universe. Its dark. And yet, there is one way that dark matter might, in a sense, shine. How? If dark matter is made from particles that are their own anti-particles (as is true for…
Scientists from MIPT, the Institute for Nuclear Research (INR) of the Russian Academy of Sciences, and Novosibirsk State University (NSU) have discovered that the proportion of unstable particles in the composition of dark matter in the days immediately after the Big Bang was no more than 2%-5%. Their study has been published in Physical Review D. The discrepancy between the cosmological parameters in the modern Universe and the Universe shortly after the Big Bang can be explained by the fact that the proportion of dark matter has decreased. We have now, for the first time, been able to calculate how much dark matter could have been lost and what the corresponding size of the unstable component would be, says a co-author of the study academician Igor Tkachev, Head of the Department of Experimental Physics at INR and a lecturer at MIPTs Department of Fundamental Interactions and Cosmology. Astronomers first suspected that there was a large proportion of hidden mass in the Universe back in ...
Cells display a set of RNA molecules at one time point, reflecting thus the cellular transcriptional steady state, configuring therefore its transcriptome. It is basically composed of two different classes of RNA molecules; protein-coding RNAs (cRNAs) and protein non-coding RNAs (ncRNAs). Sequencing of the human genome and subsequently the ENCODE project identified that more than 80% of the genome is transcribed in some type of RNA. Importantly, only 3% of these transcripts correspond to protein-coding RNAs, pointing that ncRNAs are as important or even more as cRNAs. ncRNAs have pivotal roles in development, differentiation and disease. Non-coding RNAs can be classified into two distinct classes according to their length; i.e., small (<200 nt="" and="" long="">200 nt) noncoding RNAs. The structure, biogenesis and functional roles of small non-coding RNA have been widely studied, particularly for microRNAs (miRNAs). In contrast to microRNAs, our current understanding
Continual discoveries on non-coding RNA (ncRNA) have changed the landscape of human genetics and molecular biology. Over the past ten years it has become clear that ncRNAs are involved in many physiological cellular processes and contribute to molecular alterations in pathological conditions. Several classes of ncRNAs, such as small interfering RNAs, microRNAs, PIWI-associated RNAs, small nucleolar RNAs and transcribed ultra-conserved regions, are implicated in cancer, heart diseases, immune disorders, and neurodegenerative and metabolic diseases. ncRNAs have a fundamental role in gene regulation and, given their molecular nature, they are thus both emerging therapeutic targets and innovative intervention tools. Next-generation sequencing technologies (for example SOLiD or Genome Analyzer) are having a substantial role in the high-throughput detection of ncRNAs. Tools for non-invasive diagnostics now include monitoring body fluid concentrations of ncRNAs, and new clinical opportunities include silencing
Having just returned from an EMBO organised conference on non-coding RNA (ncRNA), I am bursting with facts about non-coding RNA which may be of interest (or not) to some of you. ncRNAs are RNAs that have been transcribed from the genome but do not get translated into protein. There is a burgeoning interest in them mainly…
Recent studies have unveiled the numerous roles of non-coding RNAs (ncRNAs) highlighting the biological significance of these previously overlooked RNA species. NcRNAs and especially microRNAs (miRNAs) and, more recently, long ncRNAs (lncRNAs) are currently in the center of biological research; involved in a plethora of biological processes affecting cell homeostasis. miRNAs are considered post-transcriptional gene regulators enabling translational repression, mRNA degradation and gene silencing thus playing a major role in gene expression. They bind on their target usually by partial or complete base pairing on specific miRNA recognition elements (MREs) on mRNA as well as other non-coding RNA sequences such as lncRNAs. Recent findings have also revealed some of the cellular mechanisms involving lncRNAs. For instance, lncRNAs have been shown to be associated to chromatin remodeling; structural scaffolding of nuclear protein substructures; cell cycle regulation; binding to Polycomb repressive ...
Oral cancer is a multifactorial pathology and is characterized by the lack of efficient treatment and accurate diagnostic tools. This is mainly due the late diagnosis; therefore, reliable biomarkers for the timely detection of the disease and patient stratification are required. Non-coding RNAs (ncRNAs) are key elements in the physiological and pathological processes of various cancers, which is also reflected in oral cancer development and progression. A better understanding of their role could give a more thorough perspective on the future treatment options for this cancer type. This review offers a glimpse into the ncRNA involvement in oral cancer, which can help the medical community tap into the world of ncRNAs and lay the ground for more powerful diagnostic, prognostic and treatment tools for oral cancer that will ultimately help build a brighter future for these patients.
The steroid receptor RNA activator is a functional RNA suspected to participate in the mechanisms underlying breast tumor progression. This RNA is also able to encode for a protein, Steroid Receptor RNA Activator Protein (SRAP), whose exact function remains to be determined. Our aim was to assess, in a large breast cancer cohort, whether levels of this protein could be associated with outcome or established clinical parameters. Following antibody validation, SRAP expression was assessed by tissue-microarray (TMA) analysis of 372 breast tumors. Clinical follow-up and parameters such as steroid receptor and node status were available for all the corresponding cases. Immunohistochemical scores were independently determined by three investigators and averaged. Statistical analyses were performed using standard univariate and multivariate tests. SRAP levels were significantly (Mann-Whitney rank sum test, P | 0.05) higher in estrogen receptor-alpha positive (ER+, n = 271), in progesterone receptor positive
Two new studies report that x-rays emanating from the hearts of nearby galaxies and galaxy clusters could be signs of particles of dark matter decaying in space.. X-rays of a specific wavelength emanating from the hearts of nearby galaxies and galaxy clusters could be signs of particles of dark matter decaying in space, two independent teams of astronomers report. If that interpretation is correct, then dark matter could consist of strange particles called sterile neutrinos that weigh about 1/100 as much as an electron. However, some other researches are skeptical.. For decades, astronomers and astrophysicists have thought that some sort of mysterious dark matter must provide the gravity that keeps individual galaxies from falling apart. In fact, the current standard model of cosmology indicates that a typical galaxy forms within a vast clump, or halo, of dark matter whose gravity keeps the stars from flying out into space. However, scientists do not know what dark matter is, as they have never ...
LncRNAs are among the least well-understood of non-protein-coding RNAs. They were previously considered merely transcriptional noise [11] but have increasingly garnered attention in recent years. Newer studies have shown that lncRNAs are involved in EMT. For example, several lncRNAs can be involved in the regulation or activation of the WNT signaling pathway in the Twist-induced EMT process [20]. H19 can promote pancreatic cancer metastasis by derepressing let-7s suppression on its target HMGA2-mediated EMT [21]. However, to our knowledge, no previous study has focused on the microarray expression profile of lncRNAs in LECs during EMT. Thus, we conducted the current study to assess the role of lncRNAs in the development and progression of EMT in LECs from the perspective of lncRNA.. In this study, we chose the HLE B-3 cell line. It is a primary cell line of LECs that is immortalized via infection with an adenovirus 12-SV40 virus, and can be used to investigate HLE physiology and cataracts ...
TY - JOUR. T1 - Long noncoding RNA complementarity and target transcripts abundance. AU - Zealy, Richard W.. AU - Fomin, Mikhail. AU - Davila, Sylvia. AU - Makowsky, Daniel. AU - Thigpen, Haley. AU - McDowell, Catherine H.. AU - Cummings, James C.. AU - Lee, Edward S.. AU - Kwon, Sang Ho. AU - Min, Kyung Won. AU - Yoon, Je Hyun. PY - 2018/3. Y1 - 2018/3. N2 - Eukaryotic mRNA metabolism regulates its stability, localization, and translation using complementarity with counter-part RNAs. To modulate their stability, small and long noncoding RNAs can establish complementarity with their target mRNAs. Although complementarity of small interfering RNAs and microRNAs with target mRNAs has been studied thoroughly, partial complementarity of long noncoding RNAs (lncRNAs) with their target mRNAs has not been investigated clearly. To address that research gap, our lab investigated whether the sequence complementarity of two lncRNAs, lincRNA-p21 and OIP5-AS1, influenced the quantity of target RNA ...
The long noncoding RNA, TINCR, functions as a competing endogenous RNA to regulate PDK1 expression by sponging miR-375 in gastric cancer Zhaoliang Chen,1 Hong Liu,1 Huili Yang,1 Yukai Gao,1 Gongwen Zhang,1 Jiaojiao Hu2 1Department of Oncology, Binzhou Central Hospital, Binzhou, Shandong, 2Department of Hematology, Zhongda Hospital, Southeast University, Nanjing, China Background: Accumulating evidence indicates that the long noncoding RNA, TINCR, plays a critical role in cancer progression and metastasis. However, the overall biological role and mechanisms of TINCR that were involved in human gastric cancer (GC) progression remain largely unknown.Methods: TINCR expression was measured in 56 paired tumor and adjacent nontumor tissue samples by real-time polymerase chain reaction (PCR). Insights of the mechanism of competitive endogenous RNAs (ceRNAs) were gained from bioinformatic analysis, luciferase assays. The effects of TINCR and miR-375 on GC cell apoptosis and proliferation were studied by RNA
The noncoding form of the steroid receptor RNA activator (SRA, AF092038, http://annolnc.cbi.pku.edu.cn/cases/SRA) has been reported to function as a noncoding RNA by Lanz et al. [41] and is the first lncRNA that has experimentally derived secondary structure, which was derived by Novikova et al. [42]. In the interactive secondary structure plot with vertebrate phyloP score as color overlay, it is easy to identify two conserved regions. One is a hairpin region from base 30 to 72 (Fig. 3a). With approximately 75% of bases colored red, this conserved sub-structure is clearly distinguishable from others. In fact, this region corresponds to the most conserved H2 sub-structure highlighted by Novikova et al. [42]. Site-directed mutagenesis of this region reduced the co-activation performance of SRA by 40% [43], suggesting the importance of lncRNA secondary structure on its function [44]. The other distinct region is a three-way junction hairpin sub-structure from base 506 to 555 with 78% colored red ...
The steroid receptor RNA activator gene (SRA1) generates two distinct entities. SRA RNA coactivates several NRs whereas SRA protein (SRAP) is suspected to regulate the activity of several transcription factors, including estrogen receptors (ER). Splicing of SRA intron-1 is the major event defining SRAP coding frame. Fully spliced, coding SRA and intron-1 retained, non-coding SRA coexist in breast cancer cells. The relative proportion between the two types of SRA RNA maintains a balance between two genetically linked entities, SRA and SRAP. In this study, a minigene model was used to demonstrate that the primary sequence of SRA exon-1-intron-1-exon-2 is sufficient for alternative splicing of SRA intron-1. In addition, a modified oligoribonucleotidic construct promotes SRA intron-1 retention in breast cancer cells. This oligoribonucleotide differentially alters estradiol-induced transcription of ER regulated genes. Together, results presented herein demonstrate that the SRA-SRAP balance, which can ...
Long non-coding RNAs (lncRNAs), representing a large proportion of non-coding transcripts across the human genome, are evolutionally conserved and biologically functional. At least one-third of the phenotype-related loci identified by genome-wide association studies (GWAS) are mapped to non-coding intervals. However, the relationships between phenotype-related loci and lncRNAs are largely unknown. Utilizing the 1000 Genomes data, we compared single-nucleotide polymorphisms (SNPs) within the sequences of lncRNA and protein-coding genes as defined in the Ensembl database. We further annotated the phenotype-related SNPs reported by GWAS at lncRNA intervals. Because prostate cancer (PCa) risk-related loci were enriched in lncRNAs, we then performed meta-analysis of two existing GWAS for discovery and an additional sample set for replication, revealing PCa risk-related loci at lncRNA regions. The SNP density in regions of lncRNA was similar to that in protein-coding regions, but they were less ...
Long noncoding RNA NEAT1 promotes cell proliferation and invasion by regulating hnRNP A2 expression in hepatocellular carcinoma cells Yuanyi Mang, Li Li, Jianghua Ran, Shengning Zhang, Jing Liu, Laibang Li, Yiming Chen, Jian Liu, Yang Gao, Gang Ren Department of Hepato-Biliary-Pancreatic Surgery, The Calmette Affiliated Hospital of Kunming Medical University, The First Hospital of Kunming, Kunming, Yunnan, People’s Republic of China Abstract: Growing evidence demonstrates that long noncoding RNAs (lncRNAs) are involved in the progression of various cancers, including hepatocellular carcinoma (HCC). The role of nuclear-enriched abundant transcript 1 (NEAT1), an essential lncRNA for the formation of nuclear body paraspeckles, has not been fully explored in HCC. We aimed to determine the expression, roles and functional mechanisms of NEAT1 in the proliferation and invasion of HCC. Based on real-time polymerase chain reaction data, we suggest that NEAT1 is upregulated in HCC tissues compared with
Brett Smith for redOrbit.com - Your Universe Online. According to astrophysicists, dark matter is the key to understanding the universe as it comprises 85 percent of all mass found in it and is suspected to have caused the growth of galaxies.. In a new study to be presented at the Royal Astronomical Societys National Astronomy Meeting, scientists from that countrys Durham University have found a possible explanation for why some dark matter didnt form galaxies in the early Universe - gas that would have created galaxy was sterilized by the heat from the first stars that formed in the Universe.. Ive been losing sleep over this for the last 30 years, said Carlos Frenk, Director of Durham Universitys Institute for Computational Cosmology. Dark matter is the key to everything we know about galaxies, but we still dont know its exact nature. Understanding how galaxies formed holds the key to the dark matter mystery.. According to theory, dark matter in the early Universe trapped interstellar ...
Delimiting distinct chromatin domains is essential for temporal and spatial regulation of gene expression. Within the X-inactivation centre region (Xic), the Xist locus, which triggers X-inactivation, is juxtaposed to a large domain of H3K27 trimethylation (H3K27me3). We describe here that developmentally regulated transcription of Tsix, a crucial non-coding antisense to Xist, is required to block the spreading of the H3K27me3 domain to the adjacent H3K4me2-rich Xist region. Analyses of a series of distinct Tsix mutations suggest that the underlying mechanism involves the RNA Polymerase II accumulating at the Tsix 3-end. Furthermore, we report additional unexpected long-range effects of Tsix on the distal sub-region of the Xic, involved in Xic-Xic trans-interactions. These data point toward a role for transcription of non-coding RNAs as a developmental strategy for the establishment of functionally distinct domains within the mammalian genome.
Transcriptomic analyses have identified tens of thousands of intergenic, intronic, and cis-antisense long noncoding RNAs (lncRNAs) that are expressed from mammalian genomes. Despite progress in functional characterization, little is known about the post-transcriptional regulation of lncRNAs and their half-lives. Although many are easily detectable by a variety of techniques, it has been assumed that lncRNAs are generally unstable, but this has not been examined genome-wide. Utilizing a custom noncoding RNA array, we determined the half-lives of ∼800 lncRNAs and ∼12,000 mRNAs in the mouse Neuro-2a cell line. We find only a minority of lncRNAs are unstable. LncRNA half-lives vary over a wide range, comparable to, although on average less than, that of mRNAs, suggestive of complex metabolism and widespread functionality. Combining half-lives with comprehensive lncRNA annotations identified hundreds of unstable (half-life | 2 h) intergenic, cis-antisense, and intronic lncRNAs, as well as lncRNAs showing
Full Text - Long noncoding RNAs (lncRNAs) are known to exert their effects to tumor progression. In this study, the role of the lncRNA GAS5 (growth arrest specific 5) was confirmed in reducing non-small cell lung cancer (NSCLC) cisplatin (DDP) resistance. In NSCLC tissue samples, GAS5 expression decreased significantly. Low GAS5 levels were positively correlated with NSCLC characteristics including TNM, tumor size and lymphatic metastasis. Functionally, GAS5 significantly reduced NSCLC/DDP cell migration, invasion and epithelial-mesenchymal transition (EMT) progression in vitro. In vivo, GAS5 upregulation inhibited remarkably NSCLC/DDP cell tumor growth. Mechanism analysis suggested that GAS5 was a molecular sponge of miR-217, inhibiting the expression of phospholysine phosphohistidine inorganic pyrophosphate phosphatase (LHPP). In conclusion, this study reveals that the GAS5/miR-217/LHPP pathway reduces NSCLC cisplatin resistance and that LHPP may serve as a potential therapeutic target
TY - JOUR. T1 - Long non-coding RNA (lncRNA) transcriptional landscape in breast cancer identifies LINC01614 as non-favorable prognostic biomarker regulated by TGFβ and focal adhesion kinase (FAK) signaling. AU - Vishnubalaji, Radhakrishnan. AU - Shaath, Hibah. AU - Elkord, Eyad. AU - Alajez, Nehad M.. PY - 2019/12/1. Y1 - 2019/12/1. N2 - Long non-coding RNAs (lncRNAs) represent a class of epigenetic regulators implicated in a number of physiological and pathological conditions. Herein, we characterized the lncRNA expression portrait from 837 patients with invasive breast cancer and 105 normals from the cancer genome atlas (TCGA), which revealed eighteen upregulated and forty-six downregulated lncRNAs. Clustering analysis revealed distinct lncRNA profile for the triple negative breast cancer (TNBC) and normal breast tissue, while less separation was observed among the HER2+HR+, HER2+HR−, HER2−HR+ molecular subtypes. LINC01614, and LINC01235 correlated with worse disease-free survival (DFS), ...
Most large elliptical galaxies are found in groups and clusters of galaxies, and are likely the product of the merger of two spiral galaxies. In such an environment, the dark matter halos can be stripped away by gravitational tidal force and added to other galaxies or the group as a whole. Therefore, it is difficult to determine how much dark matter the original galaxies had, and how much they have lost to the group as a whole through interactions with their environment.. The importance of the issue of the intrinsic amount of dark matter associated with an elliptical galaxy has recently increased owing to a report by an international team of astronomers led by Aaron Romanowsky of the University of Nottingham, United Kingdom. This team found little, if any evidence of dark matter in three relatively nearby elliptical galaxies. Two of these were in loose galaxy groups, and one was isolated. Their result, based on optical data from the 4.2 meter William Herschel Telescope on the Spanish island of ...
TY - JOUR. T1 - Spatiotemporal expression and transcriptional perturbations by long noncoding RNAs in the mouse brain. AU - Goff, Loyal A.. AU - Groff, Abigail F.. AU - Sauvageau, Martin. AU - Trayes-Gibson, Zachary. AU - Sanchez-Gomez, Diana B.. AU - Morse, Michael. AU - Martin, Ryan D.. AU - Elcavage, Lara E.. AU - Liapis, Stephen C.. AU - Gonzalez-Celeiro, Meryem. AU - Plana, Olivia. AU - Li, Eric. AU - Gerhardinger, Chiara. AU - Tomassy, Giulio S.. AU - Arlotta, Paola. AU - Rinn, John L.. PY - 2015/6/2. Y1 - 2015/6/2. N2 - Long noncoding RNAs (lncRNAs) have been implicated in numerous cellular processes including brain development. However, the in vivo expression dynamics and molecular pathways regulated by these loci are not well understood. Here, we leveraged a cohort of 13 lncRNA-null mutant mouse models to investigate the spatiotemporal expression of lncRNAs in the developing and adult brain and the transcriptome alterations resulting from the loss of these lncRNA loci. We show that ...
Hepatocellular carcinoma (HCC) is a common malignant tumor with high fatality rate. Recent studies reported that up-regulation of long non-coding RNA antisense non-coding RNA in the INK4 locus (lncRNA ANRIL) was found in HCC tissues, and which could affect HCC cells biological processes. However, the potential molecular mechanism of ANRIL in HCC is still unclear. The study aimed to uncover the effect of ANRIL on HepG2 cells growth, migration and invasion. The knockdown expression vectors of ANRIL were transfected into HepG2 cells, and qRT-PCR, CCK-8, flow cytometry, Transwell and western blot assays were performed to analyze the effect of ANRIL on cell proliferation, apoptosis, migration and invasion. The relative expression of miR-191 was then examined in ANRIL knockdown vector transfected cells. These experiments were repeated again for exploring the effect of miR-191 on HepG2 cells. NF-κB and Wnt/β-catenin signaling pathways were examined by using western blot assay. Knockdown of ANRIL inhibited
Researchers have found a set of long non-coding RNAs (lncRNAs) - RNA molecules with no protein-coding capacity - that participate in the metastatic process of ovarian cancer cells.. Inhibiting one of these molecules, called DNM3OS, reduced migration and invasion, suggesting that targeting lncRNAs might be a viable approach for treating ovarian cancer.. The study, Decoding critical long non-coding RNA in ovarian cancer epithelial-to-mesenchymal transition, was published in the journal Nature Communications.. Metastasis, which refers to the spread of cancer cells, is a common occurrence in patients with ovarian cancer and occurs in as many as 80 percent of patients. Metastasis is dependent on the ability of cancer cells to undergo a process called epithelial-to-mesenchymal transition (EMT), which allows cells to detach from other cancer cells and enter circulation.. Recent studies have suggested that lncRNAs are involved in the metastatic process. These molecules are known to regulate gene ...
Zhang, Liu, Gao, Zhang, Zhang (2019) Long noncoding RNA XIST acts as a competing endogenous RNA to promote malignant melanoma growth and metastasis by sponging miR-217 Panminerva medica ...
Long Noncoding RNA (lncRNA) FOXD2-AS1 Promotes Cell Proliferation and Metastasis in Hepatocellular Carcinoma by Regulating MiR-185/AKT Axis - Related articles #918230
Spermatogenesis, which is the complex and highly regulated process of producing haploid spermatozoa, involves testis-specific transcripts. Recent studies have discovered that long noncoding RNAs (lncRNAs) are novel regulatory molecules that play important roles in various biological processes. However, there has been no report on the comprehensive identification of testis-specific lncRNAs in mice. We performed microarray analysis of transcripts from mouse brain, heart, kidney, liver and testis. We found that testis harbored the highest proportion of tissue-specific lncRNAs (11%; 1607 of 14,256). Testis also harbored the largest number of tissue-specific mRNAs among the examined tissues, but the proportion was lower than that of lncRNAs (7%; 1090 of 16,587). We categorized the testis-specific lncRNAs and found that a large portion corresponded to long intergenic ncRNAs (lincRNAs). Genomic analysis identified 250 protein-coding genes located near (≤ 10 kb) 194 of the loci encoding testis-specific
title: The long noncoding RNA LUCAT1 promotes tumorigenesis by controlling ubiquitination and stability of DNA methyltransferase 1 in esophageal squamous cell carcinoma, doi: 10.1016/j.canlet.2017.12.016, category: Article
Long Noncoding RNA HOTTIP Promotes Nasopharyngeal Cancer Cell Proliferation, Migration, and Invasion by Inhibiting miR-4301 - Order reprints #912728
Circulating Long Noncoding RNA as a Potential Target for Prostate Cancer. . Biblioteca virtual para leer y descargar libros, documentos, trabajos y tesis universitarias en PDF. Material universiario, documentación y tareas realizadas por universitarios en nuestra biblioteca. Para descargar gratis y para leer online.
Keywords: lengthy non-coding RNA (lncRNA) immunoprecipitation MS2 coat-binding proteins ribonucleoprotein complicated (RNP) RT-PCR biochemistry 1 Intro Recently it is becoming clear RGS12 a significant part of the transcriptome encodes gene items that tend unable to WP1130 become translated into protein. Such transcripts higher than ~200-nt in length are termed long non-coding RNAs (lncRNAs) and they may either lie in intergenic regions (lincRNAs) or overlap with protein-coding genes. That the number of lncRNAs encoded by the human genome likely far outstrips the number of protein-coding mRNAs [1] indicates that lncRNAs generally are the products of an impressive level of faulty transcription or alternatively serve yet-to-be-discovered cellular functions. Differentiating between these two possibilities requires the careful application of biochemical techniques. For those few lncRNAs that have an ascribed function [2] a combination of genetic and biochemical experiments has moved the field ...
XCI can occur randomly or by imprinting, this is where the paternal X chromosome is silenced in the preimplantation embryo and extraembryonic tissue. Random XCI occurs in the epiblast and can inactivate either the maternally or paternally inherited X chromosome, resulting is an active and inactive chromosome, which is transmitted to descendant cells. Some studies have analysed the random XCI in KS patients, and found that there is a skewed inactivation of one allele and this has been detected in a variety of cases. Many other studies have been conducted and this has led to skewed XCI ranges from around 10-40% of cases in KS patients[24]. The X-inactivation centre which initiates XCI contains the X (inactive) specific transcript (XIST). XIST encodes an untranslated RNA which can coat and silence the X chromosome. In addition to non-coding transcripts, XCI involves chromatin modifiers and factors of nuclear organisation. Together these lead to a changed chromatin structure and spatial ...
Additionally, the high complexity of transcriptional regulation can be derived from the involvement of non-coding RNAs (ncRNAs). Indeed, research over the last two decades has revealed new classes of ncRNAs, including microRNAs (miRNAs), small nucleolar RNAs (snoRNAs), long ncRNAs (lncRNAs), round RNAs (circRNAs), and enhancer RNAs (eRNAs), each with different regulatory features and altogether owned by a more substantial RNA conversation network ultimately managing the creation of the ultimate protein [4]. Latest advances in omics and computational biology possess provided novel tools that enable someone to integrate different layers of information from biophysical, biochemical, and molecular cell biology research. Subsequently, these book strategies supplied a fuller knowledge of how DNA series information, epigenetic adjustments, and transcription equipment cooperate to modify gene appearance. Of note, a lot of the brand-new molecular biomarkers and healing targets for many human pathologies ...
Year after year, researches keep it up their impossible mission-like struggle (without Tom Cruise, of course) to find the totally hypothetical substance (or whatever it may be) called dark matter! What would it be? In astronomy and cosmology, dark matter is a type of matter hypothesized to account for a large part of the total mass in the universe. Dark matter cannot be seen directly…
BACKGROUND:The long non-coding RNA (lncRNA) metastasis-associated lung adenocarcinoma transcript 1 (MALAT1) is expressed highly in various types of tumors. Moreover, the tumor-initiating role of MALAT1 has been probed in the context of breast cancer. This study was set to investigate the regulatory role of MALAT1 on the chemosensitivity of breast cancer cells to taxanes (Tax) and adriamycin (Adr). MATERIAL AND METHODS:Following the measurement of MALAT1 expression in patients with breast cancer by means of qRT-PCR, the connection between the MALAT1 expression pattern and the prognosis of breast cancer patients as well as the molecular typing of breast cancer patients was analyzed using Kaplan-Meier survival analysis and receiver operating characteristic (ROC) curves. Next, the analysis between the expression of MALAT1 and the clinical symptoms of breast cancer patients was carried out. Subsequently, we generated taxane-resistant MCF-7 cells (MCF-7/Tax) and purchased Adr-resistant MCF-7 cells (MCF-7/Adr)
Scientists in the USA have found a novel noncoding gene that alters proliferation in cancer cells to help tumour development.. The team, at the University of Michigan in Ann Arbor, identified THOR (Testis-associated Highly-conserved Oncogenic long noncoding RNA) while investigating an unexplored area of the genome harbouring a class of genes called long non-coding RNAs (ribonucleic acid) (lncRNAs). These genes do not contain information to make proteins, therefore they have long been regarded as junk DNA. More recently, non-coding regions of the genome have proved to have diverse functions in health and disease.. The study, published in Cell, demonstrates that the newly discovered non-coding gene is highly conserved in different species, including humans, mice and zebrafish. Genes that are evolutionarily conserved are likely important for biological processes. The fact that we found THOR to be a highly conserved IncRNA was exciting, said Dr Arul Chinnaiyan, who led the team.. When the ...
Despite increasing evidence to indicate that long non-coding RNAs (lncRNAs) are novel regulators of immunity, there has been no systematic attempt to identify and characterise the lncRNAs whose expression are changed following the induction of the innate immune response. To address this issue, we have employed next generation sequencing data to determine the changes in the lncRNA profile in 4 human (monocytes, macrophages, epithelium and chondrocytes) and 4 mouse cells types (RAW 264.7 macrophages, bone marrow derived macrophages, peritoneal macrophages and splenic dendritic cells) following exposure to the pro-inflammatory mediators, lipopolysaccharide (LPS) or interleukin-1. We show differential expression of 204 human and 210 mouse lncRNAs, with positional analysis demonstrating correlation with immune related genes. These lncRNAs are predominantly cell-type specific, composed of large regions of repeat sequences and show poor evolutionary conservation. Comparison within the human and mouse
To evaluate the relevance of our chicken lncRNA set, we analyzed the gene expression profiles of the three classes putative lncRNA transcripts, new mRNAs and ambiguous RNAs and also compared the structural features of our lncRNAs with those of the mouse and human lncRNAs. As expected, the 2193 putative lncRNA genes are on average tenfold less expressed than the known or new protein-coding genes, and the ambiguous RNAs have an intermediate expression (Fig. 1b). This is in accordance with previous findings in mammals that showed that lncRNAs are far less expressed than protein-coding genes [6, 29-31]. Then, we characterized the structural features of these chicken putative lncRNA transcripts in comparison to the human and mouse lncRNAs available in Ensembl and compared them with the protein-coding RNAs available in Ensembl for these three species. Overall, the features observed for the chicken lncRNAs are consistent with those observed in mammals in the human and mouse ENCODE projects [6] ...
Long noncoding RNAs (lncRNAs) are key regulators of chromatin state, yet the nature and sites of RNA-chromatin interaction are mostly unknown. Here we introduce Chromatin Isolation by RNA Purification (ChIRP), where tiling oligonucleotides retrieve specific lncRNAs with bound protein and DNA sequenc …
Non-coding RNAs constitute almost 98% of the human genome. Long non-coding RNA (lnc RNA) is a large class of this family where the RNA sequences are more than 200 nucleotides long and do not encode for proteins.
Heart development is a dynamic process that involves transcriptome expression changes and cis (enhancer and promoter activities) and trans (transcription factor binding) regulation. Much previous work has established the regulatory mechanisms in this process.1-3 As the importance of noncoding RNAs in regulating expression and epigenetic modifications is gaining recognition in heart development, researchers have discovered long noncoding RNA (lncRNA) that directly regulate heart development and disease.4,5 For example, the lncRNA Fendrr binds to the PRC2 and TrxG/MLL complex and acts as a modulator of chromatin signatures to regulate gene activity in mouse heart.6 The lncRNA Braveheart also interacts with a component of the PRC2 complex during cardiac commitment.7 Interestingly, lncRNAs have been implicated in common cardiac congenital abnormalities, such as ventricular septal defects.8 They have also been implicated in aberrant chromatin conformations in the region of enhancer, silencer, and ...
Purpose : The role of long noncoding RNAs (lncRNAs) in ocular angiogenesis is largely unknown. The purpose of the project is to identify human endothelial cell (EC)-specific lncRNAs and test their involvement in ocular angiogenesis. Methods : lncRNA profiling using ocular EC lines and non EC lines was performed to identify EC-specific lncRNAs. Quantitative RT-PCR and and bioinformatics analysis were used to confirm the microarray results, and test their involvement in angiogenesis. Various angiogenesis assays, including Matrigel assays and EC-fibroblast co-culture assays were used to study the candidate lncRNAs in angiogenesis. Results : We identified ~500 lncRNAs that are enriched more than 2 folds in primary endothelial cells (ECs) compared to non-EC cells. A list of the lncRNAs show a correlated expression profile with nearby coding mRNAs that are implicated in vascular development by functional enrichment analysis. For many of them, the EC-specific expression is more robust than their ...