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
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. ...
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 ...
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 ...
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. ...
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 ...
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…
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.
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 ...
Neutrinos, once produced in the nuclear reactions of the solar core, will leave the Sun travelling to Earth in less than 8 minutes. These neutrinos stream freely to Earth, subject only to interactions with baryons in a weak scale with a typical scattering cross section of the order of 10-44 cm2, and hence are natural "messengers" of the physical processes occurring in the Suns deepest layers. In a paper to be published in the scientific journal "Science" [1], Ilidio Lopes (from Évora University and Instituto Superior Técnico) and Joseph Silk (from Oxford University) suggest that the presence of dark matter particles in the Suns interior, depending upon their mass among other properties, can cause a significant drop in its central temperature, leading to a decrease in the neutrino fluxes being produced in the Suns core. The calculations have shown that, in some dark matter scenarios, an isothermal solar core is formed. In another paper published in "The Astrophysical Journal Letters" [2], ...
Astronomers using the Chandra X-ray Observatory and the XMM-Newton have recorded an unusual emission of X-ray light from a remote cluster of galaxies which may turn out to be evidence of dark matter. Astronomers think dark matter constitutes 85% of the matter in the Universe, but does not emit or ab...
The coding capacity of the genome is not controlled solely by DNA sequences, but is rather fine-tuned through epigenetic factors and the nuclear structure. In the Yildirim lab, we study how epigenetic mechanisms, particularly those that are mediated by long noncoding RNAs (ncRNAs), complement gene expression, impact genome stability and define cell fate decisions. Other research in the lab focuses on understanding how chromatin-nuclear envelope interactions mediate gene expression programs in stem cells. We are interested in defining the molecular bases of these interactions and delineating their significance in driving gene expression and genome functions. We approach these two main areas of research by utilizing a variety of genetic, cell biological and genomics tools using mouse stem cells and mouse models. In the long run, a detailed understanding of the genetic, epigenetic, and cellular mechanisms that are mediated by long ncRNAs and nuclear structure will allow us to explore their causal ...
Over the last decade it has become clear that non-coding RNAs are important players in virtually all physiological processes. Deregulation of non-coding RNAs contributes to diseases including cancer.. In our studies we focus on understanding how small and long non-coding RNAs contribute to the pathogenesis of B-cell lymphoma. These include studies on MYC -regulated miRNAs and lncRNAs, miRNA-lncRNA interactions and the role of lncRNAs in epigenetics.. Keywords: B-cell lymphoma, non-coding RNAs, microRNA, lncRNAs ...
Vast majority of transcripts in eukaryotic organisms are non-coding RNAs (ncRNAs). Except for traditional non-coding transcripts ribosomal RNA (rRNA) and transfer RNA (tRNA), both of which play essential roles in protein translation…
Non-coding transcripts play an important role in gene expression regulation in all species, including budding and fission yeast. Such regulatory transcripts include intergenic ncRNA (non-coding RNA), 5 and 3 UTRs, introns and antisense transcripts. In the present review, we discuss advantages and limitations of recently developed sequencing techniques, such as ESTs, DNA microarrays, RNA-Seq (RNA sequencing), DRS (direct RNA sequencing) and TIF-Seq (transcript isoform sequencing). We provide an overview of methods applied in yeast and how each of them has contributed to our knowledge of gene expression regulation and transcription.
TY - JOUR. T1 - Genetic and epigenetic underpinnings of sex differences in the brain and in neurological and psychiatric disease susceptibility. AU - Qureshi, Irfan A.. AU - Mehler, Mark F.. PY - 2010. Y1 - 2010. N2 - There are numerous examples of sex differences in brain and behavior and in susceptibility to a broad range of brain diseases. For example, gene expression is sexually dimorphic during brain development, adult life, and aging. These differences are orchestrated by the interplay between genetic, hormonal, and environmental influences. However, the molecular mechanisms that underpin these differences have not been fully elucidated. Because recent studies have highlighted the key roles played by epigenetic processes in regulating gene expression and mediating brain form and function, this chapter reviews emerging evidence that shows how epigenetic mechanisms including DNA methylation, histone modifications, and chromatin remodeling, and non-coding RNAs (ncRNAs) are responsible for ...
Copy number gain of the 8q24.21 chromosomal region have been a prominent mutation in many human cancers and are associated with poor prognosis. The well-characterized MYC oncogene, which resides in the 8q24.21 region, has been, conventionally, the attractive candidate driving these cancers. However, MYC is often co-gained with an adjacent "gene desert" region. This "gene desert" often encompasses the long non-coding RNA gene PVT1, the CCDC26 gene candidate, and the GSDMC gene. Whether low copy number gain of one or more of these genes drives neoplasia is not known. We used chromosome engineering in mice to develop strains containing an extra copy of 1) Myc, 2) Pvt1, Ccdc26, Gsdmc, and 3) Myc, Pvt1, Ccdc26, Gsdmc. When rat Neu was introduced into these three strains to test for changes in latency and penetrance in mammary tumor development, only the mice with an extra copy of Myc, Pvt1, Ccdc26, Gsdmc, (but not those with an extra copy of Myc or Pvt1,Ccdc26,Gsdmc), developed adenocarcinomas with ...
Epigenetics refers to heritable mechanisms able to modulate gene expression that do not involve alteration of the genomic DNA sequence. Classically, mechanisms such as DNA methylation and histone modifications were part of this classification. Today, this field of study has been expanded and includes also the large class of non-coding RNAs (ncRNAs). Indeed, with the extraordinary possibilities introduced by the next-generation sequencing approaches, our knowledge of the mammalian transcriptome has greatly improved. Today, we have identifying thousands of ncRNAs, and unsurprisingly, a direct association between ncRNA dysregulation and development of cardiovascular pathologies has been identified. This class of gene modulators is further divided into short- and long-ncRNAs. Among the short-ncRNA sub-group, the best-characterized players are represented by highly conserved RNAs named microRNAs (miRNAs). MiRNAs principally inhibit gene expression, and their involvement in cardiovascular diseases has been
Growing insights about a significant, yet poorly understood, part of the genome - the dark matter of DNA-have fundamentally changed the way scientists approach the study of diseases. The human genome contains about 20,000 ...
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A gene is a locatable region of genomic sequence, corresponding to a unit of inheritance, which is associated with regulatory regions, transcribed regions and/or other functional sequence regions.[1][2] The physical development and phenotype of organisms can be thought of as a product of genes interacting with each other and with the environment.[3] A concise definition of a gene, taking into account complex patterns of regulation and transcription, genic conservation and non-coding RNA genes, has been proposed by Gerstein et al.[4] "A gene is a union of genomic sequences encoding a coherent set of potentially overlapping functional products". Colloquially, the term gene is often used to refer to an inheritable trait which is usually accompanied by a phenotype as in ("tall genes" or "bad genes") -- the proper scientific term for this is allele. In cells, genes consist of a long strand of DNA that contains a promoter, which controls the activity of a gene, and coding and non-coding sequence. ...
The inert two-Higgs-doublet model (i2HDM) is a theoretically well-motivated example of a minimal consistent dark matter (DM) model which provides monojet, mono-Z, mono-Higgs, and vector-boson-fusion+ETmiss signatures at the LHC, complemented by signals in direct and indirect DM search experiments. In this paper we have performed a detailed analysis of the constraints in the full five-dimensional parameter space of the i2HDM, coming from perturbativity, unitarity, electroweak precision data, Higgs data from the LHC, DM relic density, direct/indirect DM detection, and LHC monojet analysis, as well as implications of experimental LHC studies on disappearing charged tracks relevant to a high DM mass region. We demonstrate the complementarity of the above constraints and present projections for future LHC data and direct DM detection experiments to probe further i2HDM parameter space. The model is implemented into the CalcHEP and micrOMEGAs packages, which are publicly available at the HEPMDB ...
The idea seems to be that you have an array of single stranded DNA attached to a gold chip. A dark matter particle transfers kinetic energy into a gold nucleus, sending it flying through the DNA array and severing the chemical bonds along its trajectory. The severed DNA is collected, amplified via PCR (a molecular biology technique for rapid DNA replication, for those who havent heard of it), and sequenced. Since each DNA strand in the array has a different sequence, the identity of the severed DNA strands provides a record of the 3-dimensional direction in which the gold nucleus traveled. This is then compared to the time of day to test the hypothesis that the earth travels into the dark matter field while rotating towards Cygnus, and away from it while rotating away from Cygnus ...
Keep scrolling to read the first chapter of Dark Matter I love Thursday nights. They have a feel to them thats outside of time. Its our tradition, just t
even so, my understanding is that your model does not have much fudge room in the form of free parameters. So lets say one takes a well-studied galaxy with 99.9% dark matter and another one with 0% dark matter and in between them 10% 20% etc. and then plots them onto your graph - what will the fit look like? In another words, when you are comparing how well your theory matches the observed regularities, does it fit better within some representative subset of examples that have a certain dark matter ratio according to the competing WIMP models, or does it fit across any such apparent ratio? I am fully aware you model does not have any dark matter - doing away with dark matter completely would be great - but could it be also that some dark matter makes it easier to explain what is seen in the microwave background?. ReplyDelete ...
even so, my understanding is that your model does not have much fudge room in the form of free parameters. So lets say one takes a well-studied galaxy with 99.9% dark matter and another one with 0% dark matter and in between them 10% 20% etc. and then plots them onto your graph - what will the fit look like? In another words, when you are comparing how well your theory matches the observed regularities, does it fit better within some representative subset of examples that have a certain dark matter ratio according to the competing WIMP models, or does it fit across any such apparent ratio? I am fully aware you model does not have any dark matter - doing away with dark matter completely would be great - but could it be also that some dark matter makes it easier to explain what is seen in the microwave background?. ReplyDelete ...
Shadowy hints of dark matters true nature are set to be boosted by a new particle and gamma-ray detector being launched into orbit
Nearly a mile underground in an abandoned gold mine, one of the most important quests in physics has come up empty-handed in the search for the elusive substance known as dark matter, scientists announced Wednesday.
The title of my previous posting was Has dark matter been found?. The answer came in thursday and was Probably not!. Peter Woit told about the outcome of the experiment. There were two events with the estimated background of .8 events and the probability of observing two or more events is 23 per cent. Therefore the result could be argued to be noise. The experiment was however very useful since it poses an upper bound 7.0×10-44 cm2 for a WIMP of mass 70 GeV at the 90 per cent confidence level. The mass of 70 GeV would maximize the cross section if WIMP corresponds to a dark matter particle. Otherwise the lower bound for mass is 2 GeV: not very informative! The cross section estimate is not absolute but relies on standard model dark matter halos of galaxies based on WIMPs allowing to estimate the density of dark matter particles and their flux to the detector. If one assumes that the density is of same order of magnitude as the density of ordinary particles the upper bound on the cross section ...
A new study has deepened the mystery of dark matter, that evasive substance that keeps entire galaxies together. The standard cosmological model may be wrong as a result.
The first tantalising signs of gas within a filament of dark matter have been glimpsed at the site of a cataclysmic collision between galaxy clusters
Since I had a wicked time DJing at Dark Matter 2 on June 9th, 2007, I am very glad to say that the live recording of my set turned out well enough to warrant sharing it! This set features several ...
Complete information for DANT1 gene (RNA Gene), DXZ4 Associated Non-Coding Transcript 1, Proximal, including: function, proteins, disorders, pathways, orthologs, and expression. GeneCards - The Human Gene Compendium
It has been known since the late 1970s that many DNA sequences are transcribed but not translated. Moreover, most protein-coding genes in mammals are fragmented, with only a small fraction of the primary RNA transcript being spliced together to form messenger RNA. For many years it was assumed that untranslated RNA molecules served no useful purpose but, starting in the mid-1990s, a small body of researchers, including the present author (Mattick, 1994), have been arguing that these RNAs transmit regulatory information, possibly associated with the emergence of multicellular organisms. This is supported by the observation that the proportion of noncoding genomic sequences broadly correlates with developmental complexity, reaching over 98% in mammals (Liu et al., 2013), although others have argued that the increase in genome size is due to the inefficiency of selection against non-functional elements as body size goes up and population size goes down (Lynch, 2007 ...
Long non-protein-coding RNA (lncRNA) sequences are often transcribed from the opposite, or antisense, strand of a protein coding gene. In the past few years, research has shown that these lncRNAs play a number of regulatory roles in the cell. For exa. 5 Comments. ...