• The aim of this mini-review is to discuss emerging epigenetic roles of long non-coding RNAs (lncRNAs) in Acute Myeloid Leukemia (AML). (frontiersin.org)
  • In particular, there are incremental examples of the participation of the distinct class of long non-coding RNAs (lncRNAs) in AML epigenetic regulation, some of which have translational potential. (frontiersin.org)
  • Recent studies have revealed the importance of long noncoding RNAs (lncRNAs) as tissue-specific regulators of gene expression. (nature.com)
  • We determine a comprehensive map of lineage-specific lncRNAs in human dermal lymphatic and blood vascular endothelial cells (LECs and BECs), combining RNA-Seq and CAGE-Seq. (nature.com)
  • In the latest genome annotation, lncRNAs, which are arbitrarily defined as noncoding RNAs longer than 200 nucleotides, constitute ~72% of the transcribed genome 13 , whereas mRNAs comprise only 19%, indicating the need for functional annotation of lncRNAs. (nature.com)
  • Mammalian transcriptomes contain thousands of long noncoding RNAs (lncRNAs). (biomedcentral.com)
  • Some lncRNAs originate from intragenic enhancers which, when active, behave as alternative promoters producing transcripts that are processed using the canonical signals of their host gene. (biomedcentral.com)
  • We have followed up this observation by analyzing intergenic lncRNAs to determine the extent to which they might also originate from intergenic enhancers. (biomedcentral.com)
  • We integrated high-resolution maps of transcriptional initiation and transcription to annotate a conservative set of intergenic lncRNAs expressed in mouse erythroblasts. (biomedcentral.com)
  • We subclassified intergenic lncRNAs according to chromatin status at transcriptional initiation regions, defined by relative levels of histone H3K4 mono- and trimethylation. (biomedcentral.com)
  • We have determined globally the sites of initiation of intergenic lncRNAs in erythroid cells, allowing us to distinguish two similarly abundant classes of transcripts. (biomedcentral.com)
  • Different correlations between the levels of elncRNAs, plncRNAs and expression of neighboring genes suggest that functional lncRNAs from the two classes may play contrasting roles in regulating the transcript abundance of local or distal loci. (biomedcentral.com)
  • At least 50,000 lncRNAs are expressed from intergenic regions of the human genome, more than twice the number of protein-coding genes [ 5 ]. (biomedcentral.com)
  • In this study, for simplicity, we refer to intergenic lncRNAs as those that are transcribed by RNA-polymerase II, 5′ end capped and polyadenylated. (biomedcentral.com)
  • Here we address two important, and incompletely answered, questions concerning the origins (transcriptional initiation regions (TIRs)) and classification of intergenic lncRNAs. (biomedcentral.com)
  • First, what is the relative prevalence of promoter- and enhancer-associated transcripts within sets of transcripts that are annotated simply as being intergenic lncRNAs? (biomedcentral.com)
  • Recent studies have discovered that long noncoding RNAs (lncRNAs) are novel regulatory molecules that play important roles in various biological processes. (biomedcentral.com)
  • We categorized the testis-specific lncRNAs and found that a large portion corresponded to long intergenic ncRNAs (lincRNAs). (biomedcentral.com)
  • LncRNAs are arbitrarily defined as noncoding RNAs longer than 200 nucleotides. (biomedcentral.com)
  • However, although numerous studies have investigated the protein-coding genes that show tissue-specific expression and play important roles during spermatogenesis, no previous study has comprehensively identified and characterized the mouse testis-specific lncRNAs. (biomedcentral.com)
  • Here, we used microarray analysis to profile the previously annotated lncRNAs and mRNAs expressed in various mouse tissues, including testis. (biomedcentral.com)
  • By comparing the lncRNA and mRNA expression profiles among the tissues, we identified lncRNAs and mRNAs that showed differential expression in each tissue. (biomedcentral.com)
  • We found that testis has the largest number of tissue-specific lncRNAs. (biomedcentral.com)
  • By using a precise lncRNA identification pipeline, we identified 1315 putative lncRNAs and 1166 known lncRNAs in spleen tissue. (hvri.ac.cn)
  • Co-expression analysis identified integrated lncRNA-mRNA and gene-gene interaction networks, implying that hub genes or lncRNAs exert critical influence on MD resistance and tumorigenesis. (hvri.ac.cn)
  • Recently, there has been strong interest in exploring the roles of non-coding RNAs, including circular RNAs (circRNAs), long non-coding RNAs (lncRNAs) and microRNAs (miRNAs), in the process of GC [ 2 - 4 ]. (archivesofmedicalscience.com)
  • Long noncoding RNAs (lncRNAs) are important regulators in cancer progression. (oncotarget.com)
  • Previous lncRNAs profile studies have demonstrated aberrant expression of a series of lncRNAs, including taurine upregulated gene 1 (TUG1), in ICC specimens [ 5 ]. (oncotarget.com)
  • Long non-coding RNAs (lncRNAs) have shown promise as biomarkers in other cancer types and in some cases functionally contribute to tumor development and progression. (biomedcentral.com)
  • Long non-coding RNAs (lncRNAs) have moved into the focus of cancer research as good candidates for tumor biomarkers and as regulators of various neoplastic cell properties. (biomedcentral.com)
  • In general, lncRNAs are defined as being longer than 200 nucleotides and lacking a functional open reading frame. (biomedcentral.com)
  • Some lncRNAs (referred to as long intergenic non-coding RNAs, lincRNAs) are transcribed from separate loci, whereas others are transcribed divergently from promoters of protein-coding genes or in antisense direction to these. (biomedcentral.com)
  • Long non-coding RNAs (lncRNAs) participate in regulating biological processes, especially host-pathogen interactions. (biomedcentral.com)
  • A RNA sequencing method (RNA-seq) was used to confirm the differential expression profiles of lncRNAs in Plasmodium yeolii 17XL ( P.y 17XL)-infected BALB/c mice. (biomedcentral.com)
  • GO and KEGG pathway analyses demonstrated that these four differentially expressed lncRNAs were associated with co-localized/co-expressed protein-coding genes that were totally enriched in malaria and with the transforming growth factor beta (TGF-β) signaling pathway. (biomedcentral.com)
  • At present, it is known that lncRNAs participate in transcriptional and post-transcriptional gene regulation. (biomedcentral.com)
  • Long non-coding RNAs (lncRNAs) are non-coding RNAs longer than 200 nucleotides that function as regulatory factors in many human diseases, including cancer. (jcancer.org)
  • Some of them are for non-coding RNA transcripts longer than 200 nucleotides, called long non-coding RNAs (lncRNAs) [ 1 , 2 ]. (jcancer.org)
  • To date, it is well known that lncRNAs participate in chromatin modifications and transcriptional and translational regulation of protein-encoding genes or regulate protein function and activity through specific binding [ 3 - 5 ]. (jcancer.org)
  • In tumor tissues, lncRNAs are markedly deregulated and pervasively involved in development and progression of cancers [ 6 - 8 ]. (jcancer.org)
  • Purpose: GG-H whole transcriptome array analysis suggested involvement of PININ (PNN) in the alternative splicing of multiple long non-coding RNAs (lncRNAs). (molvis.org)
  • Methods: Total RNA was isolated from PNN knockdown human corneal epithelial (HCET) cells or Pnn-deficient mouse corneas, and subjected to real-time-PCR (RT-PCR) assays, and the alternatively spliced lncRNAs were counted. (molvis.org)
  • Alternatively spliced lncRNAs were detected with in situ hybridization with variant-specific RNA probes on human cornea sections. (molvis.org)
  • Long noncoding RNAs (lncRNAs) play crucial roles in tumorigenesis, and lncRNA taurine-upregulated gene 1 ( TUG1 ) has been proven to be associated with several human cancers. (biomedcentral.com)
  • Despite their lack of protein-coding potential, lncRNAs and circRNAs have emerged as key determinants in gene regulation, acting to fine-tune transcriptional and signaling output. (lncrnablog.com)
  • NONCODE is a systematic database that is dedicated to presenting the most complete collection and annotation of non-coding RNAs (ncRNAs), especially long non-coding RNAs (lncRNAs). (lncrnablog.com)
  • Long non-coding RNAs (lncRNAs) are emerging as important regulators in different biological processes through various ways. (lncrnablog.com)
  • Lnc2Meth, an interactive resource to identify regulatory relationships between human long non-coding RNAs (lncRNAs) and DNA methylation, is not only a manually curated collection and annotation of experimentally supported lncRNAs-DNA methylation associations but also a platform that effectively integrates tools for calculating and identifying the differentially methylated lncRNAs and protein-coding genes (PCGs) in diverse human diseases. (lncrnablog.com)
  • Long non-coding RNAs (lncRNAs) play important functional roles in various biological processes. (lncrnablog.com)
  • The subcellular localisation of long noncoding RNAs (lncRNAs) holds valuable clues to their molecular function. (lncrnablog.com)
  • We highlight the role of SE-driven genes, enhancer RNAs (eRNAs), lncRNAs, and miRNAs in the digestive system tumor growth and progression. (ijbs.com)
  • Therefore, diverse cellular compartments orchestrated by multiple environment-driving factors make the mechanisms underlying asthma extraordinary complex and unclear, particularly with respect to long noncoding RNAs (lncRNAs). (researchsquare.com)
  • lncRNAs have been reported to possess multiple functions including regulation of gene expression, transcriptional activation and silencing of genes and thus play critical roles in a diversity of cellular process [ 14 , 15 ]. (researchsquare.com)
  • ncRNAs can be classified into long ncRNAs (lncRNAs) and small ncRNAs (sncRNAs) [ 4 ]. (ijbs.com)
  • Transcriptome analysis has been utilized extensively to identify non-coding RNAs such as miRNAs and long intergenic non-coding (LINC) RNAs. (intechopen.com)
  • Moreover, circRNAs have four major functions, including as competing endogenous RNAs (ceRNAs) to sponge microRNAs (miRNAs), interaction with RNA binding proteins to regulate the cell cycle and proliferation and the management of gene transcription and protein translation [ 8 , 9 ]. (archivesofmedicalscience.com)
  • miRNAs are small, non-coding and single-stranded RNAs (approximately 22 nucleotides) and function as post-transcriptional regulators to modulate gene expression by sequence-specific interaction with their 3′-untranslated regions (3′-UTRs) [ 14 ]. (archivesofmedicalscience.com)
  • SncRNAs are less than 200 nt in length, consisting of microRNAs (miRNAs), Piwi-interacting RNAs (piRNAs), endogenous small interfering RNAs (endo-siRNAs or esiRNAs) and transcription initiation RNAs (tiRNAs) [ 6 ]. (ijbs.com)
  • CRT effects are related to alterations in genes and microRNAs (miRs) expression, which regulate cardiac processes involved in cardiac apoptosis, cardiac fibrosis, cardiac hypertrophy and angiogenesis, and membrane channel ionic currents. (hindawi.com)
  • The most recent equine transcriptome based on RNA-seq from several tissues was a prime opportunity to obtain a concurrent long non-coding RNA (lncRNA) database. (lncrnablog.com)
  • disruption from the genes for these lincRNAs in pluripotent stem cells accompanied by whole-transcriptome evaluation recognizes HPAT5 as an essential component from the pluripotency network. (healthcarecoremeasures.com)
  • Results In the present study, we performed a systematic transcriptome analysis based on the deep RNA sequencing of ten asthmatic children before and after desensitization treatment. (researchsquare.com)
  • Notably, circRNAs display cell-type, tissue-type and developmental-stage specific expression patterns in eukaryotic transcriptome, which reveals their significant regulatory functions in gene expression. (ijbs.com)
  • However, it has been proven that more than 62% of genomic DNA serves as a template for transcription, which indicates that there are abundant non-coding RNAs (ncRNAs) in human transcriptome [ 2 , 3 ]. (ijbs.com)
  • MiR-30a-5p expression and promoter methylation were quantitatively assessed by PCR in a tissue set (Cohort #1) and urine sets (Cohorts #2 and 3) from IPOPorto and Homburg University Hospital. (biomedcentral.com)
  • NcRNAs such as those involved in RNA interference can be independently inherited, and can also direct chromatin modification and DNA methylation see [7, 8] RNA Inheritance of Acquired Characters , and Nucleic Acid Invaders from Food Confirmed , SiS 63). (i-sis.org.uk)
  • Soon after fertilization, the vast majority of methylcytosine in sperm is converted by the Tet3 enzyme to hydroxymethylcytosine that gets lost by dilution during replication, effectively erasing cytosine methylation patterns except for a subset that is maintained, including those of some imprinted genes. (i-sis.org.uk)
  • Small RNAs including short-interfering (si)RNAs and piRNAs, and long RNAs such as long intergenic noncoding (linc)RNAs can direct histone modifications and cytosine methylation. (i-sis.org.uk)
  • Epigenetic control of gene expression lasts through multiple cell divisions without alterations in primary DNA sequence and can occur via mechanisms that include histone modification and DNA methylation. (stanford.edu)
  • Aberrant changes in epigenetic mechanisms regulating DNA methylation, histone methylation and acetylation, expression of noncoding RNAs, and mRNA methylation are associated with the initiation, growth, and progression of digestive system tumors [ 2 , 4 ]. (ijbs.com)
  • Long intergenic noncoding RNAs (lincRNAs) are increasingly recognized as key chromatin regulators, yet few studies have characterized lincRNAs in a single tissue under diverse conditions. (omicsdi.org)
  • Here, we analyzed 45 mouse liver RNA sequencing (RNA-Seq) data sets collected under diverse conditions to systematically characterize 4,961 liver lincRNAs, 59% of them novel, with regard to gene structures, species conservation, chromatin accessibility, transcription factor binding, and epigenetic states. (omicsdi.org)
  • Sex-biased expression characterized 247 liver lincRNAs, with many being nuclear RNA enriched and regulated by growth hormone. (omicsdi.org)
  • Recently, long intergenic non-coding RNAs (lincRNAs) have been shown to regulate the magnitude, duration, and resolution of these responses. (umassmed.edu)
  • Genomic analysis identified 250 protein-coding genes located near (≤ 10 kb) 194 of the loci encoding testis-specific lincRNAs. (biomedcentral.com)
  • The Kim lab is particularly interested in the role of micro-RNAs (miRNA) and long intergenic non-coding RNAs (lincRNAs). (umaine.edu)
  • Long intergenic noncoding RNAs (lincRNAs) derive from a large number of loci in mammalian genomes and so are frequently enriched in transposable elements (TEs). (healthcarecoremeasures.com)
  • A growing body of evidence indicates that epigenetic regulators rely, amongst other factors, on their interaction with untranslated RNA molecules for guidance to particular targets on DNA. (frontiersin.org)
  • However, a growing body of evidence suggests that recruitment, stability, and function of epigenetic factors can be mediated by non-protein-coding RNAs. (frontiersin.org)
  • Deep RNA-DNA, RNA-protein interaction studies, and phenotype rescue analyses reveal that LETR1 is a nuclear trans-acting lncRNA modulating, via key epigenetic factors, the expression of essential target genes, including KLF4 and SEMA3C , governing the growth and migratory ability of LECs. (nature.com)
  • The vast majority of embryonal tumors like neuroblastoma arise from aberrant genetic and epigenetic changes that control the survival, proliferation and differentiation of specific tissues. (prolekarniky.cz)
  • That was the beginning of the epigenetic revolution [1] ( Epigenetic Inheritance - What Genes Remember , SiS 41). (i-sis.org.uk)
  • Noncoding RNA sequences can regulate gene expression via interactions with epigenetic and other control mechanisms. (stanford.edu)
  • The function of histone modifying epigenetic regulators and noncoding RNA as central mediators of epithelial stem cell renewal and differentiation represent major emerging areas of study in the lab. (stanford.edu)
  • The multistep transformation of normal cells into malignant cells involves genetic and epigenetic alterations that promote the aberrant expression of critical oncogenes and tumor suppressor genes [ 1 , 2 ]. (ijbs.com)
  • In the post-genomic era, the cancer research is focused on the dysregulation of transcriptional dysregulation mediated by epigenetic modifications in the enhancer, SE, and gene promoter regions of key tumor suppressor and tumor-promoting genes [ 5 , 6 ]. (ijbs.com)
  • SEs are defined as large clusters of active enhancers in large clusters that are enriched with high levels of transcription factors (TFs), master co-factors, mediator complexes, RNA polymerase II (RNA pol II), and epigenetic modifications [ 5 , 7 ]. (ijbs.com)
  • On the other hand, environmental factors have been reported to modulate epigenetic modifications and thereby affect gene expression and phenotype [ 11 , 12 ]. (researchsquare.com)
  • Bioinformatics analysis revealed that several of the AS events could result in the production of novel tissue-specific proteins. (biomedcentral.com)
  • According to the structural prediction from Alphafold, it mainly consists of a long alpha helical region, which is a relatively rare structure in human proteins. (wikipedia.org)
  • Ribonucleic acid (RNA) codes for proteins and carries genetic information in all living cells. (case.edu)
  • When we explored the mechanisms underlying these effects, we found that TUG1 acts as an endogenous competing RNA (ceRNA) that 'sponges' miR-145, thereby preventing the degradation of Sirt3 mRNA and increasing expression of Sirt3 and GDH proteins. (oncotarget.com)
  • 200 nucleotides in length, and although they do not encode proteins, they can regulate gene expression. (biomedcentral.com)
  • Finally, we discuss clinical significance of the CRISPR-Cas9 gene editing system and inhibitors of SE-related proteins such as BET and CDK7 as potential cancer therapeutics. (ijbs.com)
  • Given that the minor spliceosome is ubiquitously expressed, we hypothesized that these restricted phenotypes might be caused by the tissue-specific regulation of the minor spliceosome targets, i.e. minor intron-containing genes (MIGs). (biomedcentral.com)
  • Hepatic Long Intergenic Noncoding RNAs: High Promoter Conservation and Dynamic, Sex-Dependent Transcriptional Regulation by Growth Hormone. (omicsdi.org)
  • Genome-wide analysis of chromatin states reveals distinct mechanisms of sex-dependent gene regulation in male and female mouse liver. (omicsdi.org)
  • i) Sex-biased DHS, but not sex-biased genes, are frequently characterized by sex-differential chromatin states, indicating distal regulation. (omicsdi.org)
  • Gene ontology (GO) analysis showed that these protein-coding genes were enriched for transcriptional regulation-related terms. (biomedcentral.com)
  • It is a key regulator of the cell cycle and has been shown to play a role in the regulation of cell division, gene expression, and apoptosis. (silexon.ai)
  • In addition to classical gene regulatory networks noted above, we have recently identified a central role for additional biologic mechanisms, namely gene regulation by chromatin regulators and by noncoding RNAs. (stanford.edu)
  • The CRT-induced "reverse molecular remodeling" in responders patients is related to an increase in the expression of genes involved in the regulation of excitation-contraction coupling and a reversal in the isoforms switching of the contractile genes [ 9 ] ultimately leading to remodeling effects and improving of myocardial performance. (hindawi.com)
  • Among these candidate genes, CUGBP and Elav-like family member 1 ( CELF1 ) are potential targets of TUG1 in-trans regulation. (biomedcentral.com)
  • RNA immunoprecipitation was then performed to examine whether TUG1 RNA was bound to PRC2, a TUG1 -involved regulation mechanism reported in previous studies. (biomedcentral.com)
  • Using TUG1 4C sequencing and bioinformatic analysis, we found CELF1 to be a potential target of TUG1 RNA in in-trans regulation. (biomedcentral.com)
  • Researchers from the Centre for Genomic Regulation and the University of Bern have created "LncATLAS", a comprehensive resource of lncRNA localisation in human cells based on RNA-sequencing datasets. (lncrnablog.com)
  • Chromosome aberrations can affect one or more genes in a complex manner, such as by changing the regulation of gene expression, by disrupting exons, and by creating fusion genes. (biomedcentral.com)
  • Non (protein)-coding RNAs are the most abundant transcriptional products of the coding genome, and comprise several different classes of molecules with unique lengths, conformations and targets. (frontiersin.org)
  • The blood and lymphatic vascular systems are essential for the efficient transport of oxygen, nutrients, signaling molecules, and leukocytes to and from peripheral tissues, the removal of waste products, and the preservation of fluid homeostasis. (nature.com)
  • In cancers, these RNA molecules are not only "turned on," but also appear to be activated in cells that are likely to progress to cancer. (case.edu)
  • In their study, the researchers performed the first discovery and characterization of a specialized sub-class of what is known as "long intergenic" non-coding RNA molecules in esophageal malignancy. (case.edu)
  • What they found: A panel of these molecules was also "turned on" in cancer tissues and in pre-malignant tissues (for example, those at a high risk for becoming cancer). (case.edu)
  • And these RNA molecules can be detected in patient biopsy tissues using routine imaging. (case.edu)
  • Those RNA molecules also seem to inhibit the growth of esophageal cancer cells by regulating other genes potentially involved in cancer development, thus providing new opportunities for therapeutic targeting of these cancers, the authors concluded. (case.edu)
  • Our study opens a new area of investigation by implicating these RNA molecules as additional players in esophageal cancer," Guda said. (case.edu)
  • Our goal is to understand how and when these molecules are turned-on during esophageal cancer development, and how they control other genes involved in cancer processes. (case.edu)
  • With this new knowledge, the team hopes to test whether the RNA molecules can be integrated into CWRU's EsoCheck molecular diagnostic panel-licensed to Lucid Diagnostics-for detecting cells at a high risk of becoming cancerous. (case.edu)
  • They also want to test whether blocking the RNA molecules, or blocking the genes controlled by these molecules, might lead to a new treatment strategy for a cancer that is often lethal. (case.edu)
  • CircRNAs are a novel class of endogenous noncoding RNA and are characterized by single-stranded, covalently closed circular molecules without 5′ to 3′ polarity and a polyadenylated tail [ 5 , 6 ]. (archivesofmedicalscience.com)
  • The term "oncotarget" encompasses all molecules, pathways, cellular functions, cell types, and even tissues that can be viewed as targets relevant to cancer as well as other diseases. (oncotarget.com)
  • Conclusions Our study successfully discovered many key noncoding RNA molecules related to pathogenesis of asthma and relevant treatment, which may provide novel biomarkers and therapeutic targets for asthmatic diagnose and therapy. (researchsquare.com)
  • Using an integrative annotation pipeline, we assembled tissue-specific RNA-Seq libraries from 113 datasets and constructed 48 359 transcript models of protein-coding genes in eleven tissues. (jcvi.org)
  • In addition, we annotated various classes of non-coding RNA including microRNA, long intergenic RNA, small nucleolar RNA, natural antisense transcript, small nuclear RNA, and small RNA using published datasets and in-house analytic results. (jcvi.org)
  • C6orf163 has been observed to be near-ubiquitously expressed at low levels in RNA-seq datasets. (wikipedia.org)
  • Search the gene expression profiles from curated DataSets in the Gene Expression Omnibus (GEO) repository. (cancerindex.org)
  • A comprehensive annotation of its genome paves the way for understanding the functions and activities of all types of transcripts, including mRNA, the various classes of non-coding RNA, and small RNA. (jcvi.org)
  • Integrated analysis of lncRNA and mRNA repertoires in Marek's disease infected spleens identifies genes relevant to resistance. (hvri.ac.cn)
  • An anticodon is a trinucleotide sequence located at one end of a transfer RNA (tRNA) molecule, which is complementary to a corresponding codon in a messenger RNA (mRNA) sequence. (genome.gov)
  • In a cell, antisense DNA serves as the template for producing messenger RNA (mRNA), which directs the synthesis of a protein. (genome.gov)
  • However, circRNAs were initially regarded as viral genomes or byproducts of pre-mRNA alternative splicing, and thus they did not gain much attention for a long time [ 15 ]. (ijbs.com)
  • Therefore, this complex regulatory network requires precise control of gene expression patterns at both transcriptional and post-transcriptional levels in order to ensure proper maturation, differentiation, and formation of blood and lymphatic vessels. (nature.com)
  • Most plastid genes are presumably transcribed as polycistronic mRNAs which then undergo various post-transcriptional modifications [ 3 ]. (biomedcentral.com)
  • Circular RNAs (circRNAs), a novel type of non-coding RNAs (ncRNAs), are ubiquitously expressed in eukaryotic cells during post-transcriptional processes. (ijbs.com)
  • ncRNAs play important roles in controlling gene expression at both transcriptional and post-transcriptional levels. (ijbs.com)
  • Altogether, we identified 635 novel protein-coding genes, 508 novel transcribed regions, 5178 non-coding RNAs, and 35 846 small RNA loci that were formerly unannotated. (jcvi.org)
  • Genome-wide methylome and RNA sequencing data from a set of ccRCC and normal tissue samples from The Cancer Genome Atlas (TCGA) database were integrated to identify candidate CpG loci involved in cancer onset. (biomedcentral.com)
  • ii) Trimethylation of histone H3 at K27 (H3K27me3) is a major sex-biased repressive mark at highly female-biased but not at highly male-biased genes. (omicsdi.org)
  • We then sought to address specificity of MIG expression, minor intron retention, and alternative splicing (AS) across mouse and human tissues. (biomedcentral.com)
  • We then analyzed the RNAseq data from eleven different mouse tissues, which revealed tissue-specific MIG expression and minor intron retention. (biomedcentral.com)
  • Splicing of introns is required for the expression of most eukaryotic genes. (biomedcentral.com)
  • Analysis of the splicing events and RNA-Seq based expression profiles revealed the landscapes of gene structures, untranslated regions, and splicing activities to be more intricate than previously appreciated. (jcvi.org)
  • Over the last two decades, several laboratories have used a wide range of techniques encompassing expressed sequence tag (EST) analysis, serial analysis of gene expression (SAGE), microarray and next-generation sequencing (NGS) technologies for analysing the chickpea transcriptomes. (intechopen.com)
  • Gene expression analyses using NGS platforms were carried out in the vegetative and reproductive tissues such as shoot, root, mature leaf, flower bud, young pod, seed and nodule by various groups which resulted in identification of several tissue-specific transcripts. (intechopen.com)
  • In this study, our main goal was to determine these signatures, by evaluating the gene expression of paired colorectal adenoma and adenocarcinoma samples to identify novel genetic markers in association to the adenoma-adenocarcinoma stage transition. (bvsalud.org)
  • METHODS: Ten paired adenoma and adenocarcinoma colorectal samples were subjected to microarray gene expression analysis. (bvsalud.org)
  • In particular, the FANTOM (Functional Annotation of the Mammalian Genome) consortium pioneered the discovery of the noncoding RNA world by providing, through Cap Analysis of Gene Expression (CAGE-Seq), the first evidence that large portions of our genome are transcribed, producing a multitude of sense and antisense transcripts 12 . (nature.com)
  • Chromatin state maps were developed to elucidate sex differences in chromatin structure and their impact on sex-differential chromatin accessibility and sex-biased gene expression in mouse liver. (omicsdi.org)
  • Results were integrated with genome-wide binding data for five transcription factors implicated in growth hormone-regulated, sex-biased liver gene expression, leading to the following findings. (omicsdi.org)
  • Chromatin states are thus a major determinant of sex-biased chromatin accessibility and gene expression, with FOXA pioneer factors proposed to confer sex-dependent chromatin opening and STAT5, but not BCL6, regulating sex-biased genes by binding to sites in a sex-biased chromatin state. (omicsdi.org)
  • Sex differences in the incidence and progression of many liver diseases, including liver fibrosis and hepatocellular carcinoma, are associated with sex-biased hepatic expression of hundreds of genes. (omicsdi.org)
  • An inducible gene expression program is a hallmark of the host inflammatory response. (umassmed.edu)
  • Among these is lincRNA-Cox2, a dynamically regulated gene that broadly controls immune gene expression. (umassmed.edu)
  • LincRNA-Cox2-deficient macrophages and murine tissues had altered expression of inflammatory genes. (umassmed.edu)
  • Transcriptomic studies from various tissues revealed that deletion of the lincRNA-Cox2 locus also strongly impaired the basal and inducible expression of the neighboring gene prostaglandin-endoperoxide synthase (Ptgs2), encoding cyclooxygenase-2, a key enzyme in the prostaglandin biosynthesis pathway. (umassmed.edu)
  • Of considerable interest, we found that expression of elncRNAs, but not plncRNAs, is associated with enhanced expression of neighboring protein-coding genes during erythropoiesis. (biomedcentral.com)
  • Altered expression of this gene has been observed in multiple human cancers. (cancerindex.org)
  • Consequently, little is known about how gene expression changes in response to genomic rearrangements in plastids. (biomedcentral.com)
  • We demonstrate that the expression of plastid coding genes is strongly functionally dependent among conifer species. (biomedcentral.com)
  • This finding indicates that plastomic rearrangement influences gene expression. (biomedcentral.com)
  • We also compared plastid gene expression levels among conifers and demonstrated a strong association between gene expression and plastomic rearrangements. (biomedcentral.com)
  • The AAV non-coding RNA expression vector is a highly efficient vehicle for in vitro and in vivo delivery of non-coding RNAs of interest. (vectorbuilder.kr)
  • The AAV non-coding RNA expression vector uses an RNA polymerase II promoter to drive the expression of the user-selected non-coding RNA gene. (vectorbuilder.kr)
  • The AAV non-coding RNA expression vector is first constructed as a plasmid in E. coli. (vectorbuilder.kr)
  • some of these genes were also found to be the hub genes in the co-expression network analyzed by WGCNA. (hvri.ac.cn)
  • Circular RNAs (circRNAs) have been identified as competing endogenous RNAs (ceRNAs) to mediate gene expression participating in the progression of multiple cancers, including gastric carcinoma (GC). (archivesofmedicalscience.com)
  • In addition, gene expression and protein levels in GC tissues and cell lines were measured using RT-qPCR and western blotting, respectively. (archivesofmedicalscience.com)
  • Our results demonstrated that the hsa_circ_0017728 expression level was up-regulated in GC tissues and cell lines and closely associated with poor overall survival and pathological differentiation, higher TNM stage and lymph node metastasis. (archivesofmedicalscience.com)
  • CASC9 expression discriminated tumors from normal tissues with even higher specificity than HOTAIR, a lncRNA previously suggested as an HNSCC biomarker. (biomedcentral.com)
  • This process is mediated by 2 mutually exclusive programs of gene expression: 1) an undifferentiated program supporting proliferation by stem cells within the basal layer and 2) a differentiation program instructing growth arrest and differentiation-associated programmed cell death in suprabasal layers. (stanford.edu)
  • Circulating long non-coding RNAs NKILA, NEAT1, MALAT1, and MIAT expression and their association in type 2 diabetes mellitus. (informaticsstudies.org)
  • thus, Pnn may affect crucial alternative splicing (AS) decisions and, in turn, impact cell-type specific gene expression. (molvis.org)
  • This gene has no protein-coding homolog in any other genome but its presence is supported by evidence from expression and hybridization data. (ubc.ca)
  • Long non-coding RNA LINC00926 regulates WNT10B signaling pathway thereby altering inflammatory gene expression in PTSD. (nih.gov)
  • This is largely a result of the complex effects of breakpoints on gene structure, function and expression. (biomedcentral.com)
  • Finally, we summarize the possible molecular consequences of chromosome aberrations for gene expression and function, and we discuss approaches for identification and unraveling the molecular determinants of congenital disease phenotypes. (biomedcentral.com)
  • More importantly, circRNAs serve as microRNA (miRNA) sponges and crucial regulators of gene expression. (ijbs.com)
  • Our understanding of plastid transcriptomes is limited to a few model plants whose plastid genomes (plastomes) have a highly conserved gene order. (biomedcentral.com)
  • Plastid genomes (plastomes) of land plants are highly conserved in their gene content and order. (biomedcentral.com)
  • Hence, one way to decipher the tumorigenic contribution of germline changes in highly conserved genes such as PHOX2B is to understand how they perturb normal development. (prolekarniky.cz)
  • LINC00930 is a highly conserved non-coding RNA molecule that is expressed in various tissues and cells throughout the body. (silexon.ai)
  • Sex-biased genes were clustered by chromatin environments and mapped to DNase-hypersensitive sites (DHS) classified by sex bias in chromatin accessibility and enhancer modifications. (omicsdi.org)
  • By utilizing different genetic manipulations in vitro and in vivo, we found that lincRNA-Cox2 functions through an enhancer RNA mechanism to regulate Ptgs2. (umassmed.edu)
  • The results demonstrated that TUG1 RNA was bound to enhancer of zeste protein 2/embryonic ectoderm development (EZH2/EED), which is essential for PRC2. (biomedcentral.com)
  • Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analyses were performed to elucidate the potential functions of Plasmodium -induced genes. (biomedcentral.com)
  • In our study, hsa_circ_0017728 as a potential oncogene competing endogenous RNA (ceRNA) was investigated in the progression and development of gastric carcinogenesis. (archivesofmedicalscience.com)
  • As a result, the transcript generated from this vector does not correspond precisely to the selected non-coding RNA gene, but contains some additional sequences both upstream and downstream. (vectorbuilder.kr)
  • In the current report, a systematic approach is implemented to catalogue regulatory elements within HERVs, as a roadmap to potential functions of HERV sequences in gene networks. (mdpi.com)
  • Efforts to resolve the transcribed sequences in the equine genome have focused on protein-coding RNA. (lncrnablog.com)
  • For RNA polymerase II-mediated transcription, the start site is typically in the 3' region of the promoter while the termination site is within the polyA signal sequence. (vectorbuilder.kr)
  • For instance, H19 is the first lncRNA transcribed by RNA polymerase II and is expressed mainly in human embryonic cells. (jcancer.org)
  • C6orf163 is a human protein encoded by the C6orf163 gene. (wikipedia.org)
  • C6orf163 is predicted to be part of a readthrough locus with its neighboring genes on the plus strand, SMIM8 (small integral membrane protein 8, also known as C6orf162), LINC01590 (long intergenic non-coding RNA 1590), and CFAP206 (cilia and flagella associated protein 206). (wikipedia.org)
  • The human C6orf163 protein is 329 amino acids long and has a molecular weight of 38 kDa. (wikipedia.org)
  • Strikingly, we found that liver-specific lincRNA gene promoters are more highly species conserved and have a significantly higher frequency of proximal binding by liver transcription factors than liver-specific protein-coding gene promoters. (omicsdi.org)
  • The protein encoded by this gene is a member of the CMGC family of serine/threonine protein kinases. (cancerindex.org)
  • What does this gene/protein do? (cancerindex.org)
  • What pathways are this gene/protein implicaed in? (cancerindex.org)
  • We present evidence for the de novo origin of the Wookiee wookiee protein-coding gene GLABR since their divergence from humans. (ubc.ca)
  • To begin, we hypothesize that distinct morphological features, in other words, hairiness are a result of Wookiee specific protein-coding gene(s). (ubc.ca)
  • For example, the current Ensembl version proposes a Chiss ortholog of BLU31 (gene responsible for their characteristic blue skin), but further investigation concluded that the "gene" lacks possible introns and thus cannot produce any resemblance of a protein in wookiee. (ubc.ca)
  • Cell-permeable peptides (CPPs) have been widely studied as an attractive drug delivery system to deliver therapeutic macromolecules such as DNA RNA and protein into cells. (healthcarecoremeasures.com)
  • They underlie genetic disease in roughly 15% of patients with multiple congenital abnormalities and/or mental retardation (MCA/MR). In genetic diagnostics, the pathogenicity of chromosomal aberrations in these patients is typically assessed based on criteria such as phenotypic similarity to other patients with the same or overlapping aberration, absence in healthy individuals, de novo occurrence, and protein coding gene content. (biomedcentral.com)
  • A protein consists of one or more chains of amino acids (called polypeptides) whose sequence is encoded in a gene. (genome.gov)
  • Studies of human genome demonstrate that protein-coding genes only occupy less than 2% of the entire genome [ 1 ]. (ijbs.com)
  • We are currently pursuing studies of the dominant signaling and gene regulatory networks that control this process, including the Ras/MAPK cascade, which is required for stem cell-mediated self-renewal and the p53 transcription factor family member, p63, which is required for epidermal differentiation. (stanford.edu)
  • The sex-biased lincRNA genes are enriched for nearby and correspondingly sex-biased accessible chromatin regions, as well as sex-biased binding sites for growth hormone-regulated transcriptional activators (STAT5, hepatocyte nuclear factor 6 [HNF6], FOXA1, and FOXA2) and transcriptional repressors (CUX2 and BCL6). (omicsdi.org)
  • Genes in active, inactive, and poised chromatin states exhibited differential responsiveness to ligand-activated nuclear receptors and distinct enrichments for functional gene categories. (omicsdi.org)
  • iv) Sex-biased STAT5 binding is enriched at sex-biased DHS marked as active enhancers and preferentially targets sex-biased genes with sex-differences in local chromatin marks. (omicsdi.org)
  • v) The male-biased repressor BCL6 preferentially targets female-biased genes and regulatory sites in a sex-independent chromatin state. (omicsdi.org)
  • Second, do differences in the chromatin status at intergenic lncRNA TIRs reflect their potential function? (biomedcentral.com)
  • Future studies should investigate gene-by-environment interactions and employ functional imaging to understand how salience network structure translates to psychiatric disorder risk. (nature.com)
  • These new models, which we term Multi-Functional Human Tissue Genetics, allow up to 10 alleles or more to be altered simultaneously, permitting genetic experiments with an unprecedented degree of rapidity and complexity. (stanford.edu)
  • To address this and to also study the oncogenic potential of unregulated function of dominant regulators of epithelial homeostasis noted above, we developed Multi-Functional Human Tissue Genetics noted above which, when combined with skin tissue regeneration on immune deficient mice, has permitted the molecular reconstruction of events sufficient to trigger human cancer. (stanford.edu)
  • Deregulation of the lncRNA taurine upregulated gene 1 (TUG1) predicts poor prognosis and is implicated in the development of several cancers. (oncotarget.com)
  • The lncRNA taurine-upregulated gene 1 ( TUG1 ) is a nonprotein-coding gene located on chromosome 22q12.2 that transcribes to a 6.7-kilobase-long, spliced, and polyadenylated RNA. (biomedcentral.com)
  • These two classes of 5′ capped and polyadenylated RNA transcripts are indistinguishable with regard to their length, number of exons or transcriptional orientation relative to their closest neighboring gene. (biomedcentral.com)
  • CircRNAs are predominantly generated in eukaryotes via four cyclized models: back-spliced exons, circular intronic RNAs, exon-intron circRNAs and intergenic circRNAs [ 7 , 8 ]. (archivesofmedicalscience.com)
  • Mutations in the APC, DCC, KRAS and TP53 genes have been associated with the progression of sporadic CRC, occurring at defined pathological stages of the tumor progression and consequently modulating several genes in the corresponding signaling pathways. (bvsalud.org)
  • Therefore, the identification of gene signatures that occur at each stage during the CRC progression is critical and can present an impact on the diagnosis and prognosis of the patient. (bvsalud.org)
  • Gene regulatory network perturbations contribute to the development and progression of cancer, however, molecular determinants that mediate transcriptional perturbations remain a fundamental. (lncrnablog.com)
  • Accumulating evidence suggests that diverse non-coding RNAs (ncRNAs) are involved in the progression of a wide variety of diseases. (lncrnablog.com)
  • High-throughput sequencing was used to determine differentially expressed circRNAs in GC tissues and corresponding non-cancerous tissues. (archivesofmedicalscience.com)
  • These differentially expressed immune-related genes were deemed to have a role in the process of Plasmodium infection in the host via dendritic/T regulatory cells and the TGF-β/Smad 2/3 signaling pathway. (biomedcentral.com)
  • This allows the use of tissue-specific, inducible, or variable-strength promoters, enabling a variety of experimental applications. (vectorbuilder.kr)
  • Diversification of transcriptional modulation: large-scale identification and characterization of putative alternative promoters of human genes. (nih.gov)
  • 100.000 cCREs in total), dispersed within the genome and present in cis-regulatory regions of ~81% of human genes, as calculated following gene enrichment analysis. (mdpi.com)
  • The core transcription regulatory loop of the digestive system tumors is complex and a high density of transcription regulatory complexes in the SEs and the crosstalk between SEs and the noncoding RNAs. (ijbs.com)
  • H19 gene is reactivated and up-regulated during tissue regeneration or tumorigenesis [ 11 , 12 ]. (jcancer.org)
  • Gene pathway analysis using the 689 DEG identified important cancer pathways such as remodeling of the extracellular matrix and epithelial-mesenchymal transition. (bvsalud.org)
  • Long noncoding RNA NALT1-induced gastric cancer invasion and metastasis via NOTCH signaling pathway. (nih.gov)
  • Emerging evidence indicates a putative role of long noncoding RNAs in regulating mitochondrial functions and metabolism. (informaticsstudies.org)
  • Strand-specific RNAseq data show a nearly full transcription of both plastomic strands and detect C-to-U RNA-editing sites at both sense and antisense transcripts. (biomedcentral.com)
  • Strand-specific RNA libraries have the advantage of allowing for the discrimination of sense and antisense transcripts [ 17 ]. (biomedcentral.com)
  • We took advantage of this to (1) investigate the full transcription capability of both plastomic strands, (2) estimate the relative number of plastid coding and antisense transcripts, and (3) identify plastid C-to-U RNA-editing sites separately at sense and antisense transcripts in conifers. (biomedcentral.com)
  • Furthermore, bioinformatics approaches are employed to provide in silico evidences for the link between long noncoding RNAs and mitochondrial gene interaction in obesity. (informaticsstudies.org)
  • According to the bioinformatic analysis result of TUG1 4C sequencing data, 83 candidate genes and their interaction regions were identified. (biomedcentral.com)
  • Long noncoding RNA (lncRNA) is strongly associated with various cancers and many other diseases. (hvri.ac.cn)
  • Skin malignancies, including epidermal squamous cell carcinoma (SCC), alone account for nearly as many cancers as all other tissues combined. (stanford.edu)
  • C6orf163 is a 20.6 kb gene encoded on the plus strand of chromosome 6 (6q15). (wikipedia.org)
  • This SNP mapped to a locus on chromosome 5q35.2 harboring genes involved in neuronal development and regeneration. (nature.com)
  • 0: an updated resource of RNA-associated diseases, providing RNA-disease analysis, enrichment and prediction. (informaticsstudies.org)
  • Our results show that the GLABR gene is responsible for robust hair growth in Wookiees, and that inactivation of this gene results in reduced androgenic hair growth or hairless phenotype. (ubc.ca)
  • Our experimental focus is on the mammalian setting using multiomics, informatics, mouse genetics, human genetics, single cell studies, and new human tissue platforms. (stanford.edu)
  • This updated Arabidopsis genome annotation with a substantially increased resolution of gene models will not only further our understanding of the biological processes of this plant model but also of other species. (jcvi.org)
  • Network analysis depicted both intergenic correlation and correlation between genes and MD traits. (hvri.ac.cn)
  • The Kim lab recently completed RNA sequencing analysis to measure the dysregulation of genes in response to these factors in zebrafish embryos. (umaine.edu)
  • Module analysis disclosed 17 genes associated to asthma at distinct level. (researchsquare.com)
  • Loss of Malat1 does not modify age-or diet-induced adipose tissue accretion and insulin resistance in mice. (informaticsstudies.org)
  • To understand how the immune system is being modulated by these factors the role of non-coding RNAs (ncRNA) were investigated. (umaine.edu)
  • Furthermore, other near-human species such as Zeltron, Chiss , and Sullustan share the human ortholog of this locus, which supports the inference that the ancestral sequence was noncoding, and that the GLABR has de novo origins in the Wookiee. (ubc.ca)