• Although epigenetically silenced, endogenous retroviral (ERV) genes become activated in tumors and function to ignite immune responses. (frontiersin.org)
  • PacBio Iso-Seq data were generated for five distinct tissues to improve the functional annotation of 34,587 protein-coding genes and 42,329 transcripts. (nature.com)
  • Viral infection of sperm or egg cells can result in viral genes being permanently incorporated into the host genome, and the genetic remnants of ancient viruses - known as human endogenous retroviruses (HERV) - make up about 8% of the human genome. (scienceblog.com)
  • Although no longer infectious, some HERVs still contain intact genes, and the production of HERV RNA transcripts in human cells has been linked to some cancers. (scienceblog.com)
  • In exploring the basis for this unexpected outcome, Rich and his wife Carolyn Napoli discovered the process of co-suppression, through which introduction of an additional copy of a host gene resulted in the loss of transcripts, from both the endogenous and introduced genes. (aspb.org)
  • Both genes showed an increase in transcript levels until 36 h after explant inoculation, and a subsequent down-regulation, before the initiation of exponential growth. (frontiersin.org)
  • DcAOX genes' were further explored in a plant pot experiment in response to chilling, which confirmed the early AOX transcript increase prior to the induction of a specific anti-freezing gene. (frontiersin.org)
  • With the exception of late blight resistance, the other novel traits (i.e. reduced asparagine levels, lower levels of reducing sugars, and reduced black spot bruising) are achieved through the transcription of inverted repeat sequences containing small fragments of DNA from five different endogenous genes (i.e. (canada.ca)
  • Asn1 , Ppo5 , PhL , R1 , and VInv ), which results in the reduced level of mRNA transcripts (and subsequently expressed proteins) for those same genes using the RNA interference (RNAi) pathway. (canada.ca)
  • This is the first saRNA drug to enter clinical trials, and we have been investigating whether this technology could be extended to activate endogenous immune stimulatory genes for utilization in cancer immunotherapy. (aacrjournals.org)
  • We use these engineered Cas9 activation complexes to investigate sgRNA targeting rules for effective transcriptional activation, demonstrate multiplexed activation of 10 genes simultaneously, and upregulate long intergenic non-coding RNA (lincRNA) transcripts. (cdc.gov)
  • These dCas9-activator fusions targeted to the promoter region of endogenous genes can then modulate gene expression 7 - 11 . (cdc.gov)
  • lncRNA HOX transcript antisense RNA (HOTAIR) represses gene expression through recruitment of chromatin modifiers. (biomedcentral.com)
  • The expression of HOX transcript antisense RNA lncRNA is increased in GBM and is significantly associated with high grade brain tumors ( 13 ). (spandidos-publications.com)
  • this we presumed would be some form of the Chs transcript, perhaps the antisense form. (aspb.org)
  • mRNA transcripts for osteopontin were determined using RT- -PCR with specific primers. (bvsalud.org)
  • mRNA transcripts were detected in all culture conditions since the first day of culture. (bvsalud.org)
  • Translation is required for miRNA-dependent decay of endogenous transcripts. (nih.gov)
  • A recently discovered dimension of post-transcriptional gene regulation involves co-regulatory crosstalk between RNA transcripts, which compete for common pools of microRNA (miRNA) molecules. (biomedcentral.com)
  • Based on the competing endogenous RNA hypothesis, DElncRNA‑micro RNA (miRNA)‑DEmRNA interactions were obtained by target gene prediction. (spandidos-publications.com)
  • In this current study, we utilized an endogenous microRNA (miRNA) cluster as a platform to express multiple anti-HIV small RNAs. (ca.gov)
  • MicroRNAs (miRNAs) are small regulatory non-coding RNAs, resulting from the cleavage of long primary transcripts (pri-miRNAs) in the nucleus by the Microprocessor complex generating precursors (pre-miRNAs) that are then exported to the cytoplasm and processed into mature miRNAs. (mdpi.com)
  • Additionally, as competitive endogenous RNAs (ceRNAs), lncRNAs and messenger RNAs (mRNAs) can regulate one other by competing for the shared microRNAs (miRNAs/miRs) ( 14 , 15 ). (spandidos-publications.com)
  • Endogenous MCM7 MicroRNA Cluster as a Novel Platform to Multiplex Small Interfering and Nucleolar RNAs for Combinational HIV-1 Gene Therapy. (ca.gov)
  • Although the current generation of dCas9-based transcription activators is able to achieve up-regulation of some endogenous loci, the magnitude of transcriptional up-regulation achieved by individual single-guide RNAs (sgRNAs) 12 typically ranges from low to ineffective 8 - 11 . (cdc.gov)
  • Selective transcription of homologous genomic sequences of N- and X-tropic endogenous retroviruses in BALB/C mouse tissues. (microbiologyresearch.org)
  • We describe structure-guided engineering of a CRISPR-Cas9 complex to mediate efficient transcriptional activation at endogenous genomic loci. (cdc.gov)
  • Minigene splicing outcomes were similar in HEK293 cells and the human retinoblastoma cell line WERI-Rb1, the latter retaining a cone photoreceptor expression profile including endogenous OPN1LW and OPN1MW gene expression. (nih.gov)
  • Programmable DNA binding proteins have emerged as an exciting platform for engineering synthetic transcription factors for modulating endogenous gene expression 5 - 11 . (cdc.gov)
  • For example, lncRNA nuclear paraspeckle assembly transcript 1 (NEAT1) is highly expressed in GBM tissues and perturbed expression of NEAT1 suppresses cell proliferation and invasion ( 10 ). (spandidos-publications.com)
  • Alternative splicing of this gene results in several transcript variants, some of which have been characterized by the presence or absence of an ALU cassette insert and a short or long C-terminal region. (cancerindex.org)
  • In this study, we used an enrichment of scRNA-seq mitochondrial reads and a robust computational method to identify clonally relevant mitochondrial variants as endogenous genetic barcodes for clonal tracking of early embryonic hematopoiesis from hPSC. (biorxiv.org)
  • Our study highlights the power of mitochondrial variants as an endogenous marker for clonal tracking in modeling human development from stem cells. (biorxiv.org)
  • Transcription of endogenous C-type virus in resting and proliferating tissues of BALB/Mo mice. (microbiologyresearch.org)
  • Changes in transcription of endogenous type-C virus genome during mouse liver regeneration. (microbiologyresearch.org)
  • Nonetheless, present approaches for measuring transcript half-lives (e.g. transcription shutoff) are usually poisonous or technically advanced. (computablegenomix.com)
  • This protocol allows us to monitor endogenous mitophagy complexes in human tissues such as beta cells, facilitating mitophagy research in pivotal translationally-relevant tissues. (jove.com)
  • Supplementary_files_format_and_content: 4sU_TPM_table.txt contains the expression levels of transcript exons and introns (Transcripts Per Million, TPM). (nih.gov)
  • To address this knowledge gap, researchers used RNA sequence data from the Genotype Tissue and Expression project to investigate the presence of transcripts belonging to a recent HERV subgroup, HML-2, in non-diseased tissues. (scienceblog.com)
  • A bacterial lacZ gene and neomycin resistance cassette was inserted to replace a 52 bp segment within the coding portion of exon 1 such that the endogenous gene promoter drives expression of beta-galactosidase. (jax.org)
  • While RT-PCR analysis detects high levels of RNA transcripts in the kidney and very low levels in the brain, beta-galactosidase expression from this allele is detectable in brain and kidney. (jax.org)
  • therefore, the conditions that alter the expression of this gene (and consequently synthesis of the BDNF protein) affect endogenous BDNF production to a similar extent in both neurons and megakaryocytes. (zrtlab.com)
  • We showed that these effects were recapitulated in vitro by increasing endogenous UCP2 expression using saRNA. (aacrjournals.org)
  • However, it is difficult to capture the complexity of transcript isoform variance using these libraries, and large cDNA sequences are often difficult to clone into size-limited viral expression vectors. (cdc.gov)
  • Variations in hybridization of RNA from different mouse tissues and embryos to endogenous C-type virus DNA transcripts. (microbiologyresearch.org)
  • The authors detected HML-2 transcripts in all tissue types, with elevated levels in cerebellum, pituitary, testis, and thyroid tissues. (scienceblog.com)
  • John Coffin, the senior author, adds, "We have found that nearly all normal human tissues express, in their RNA, one or another of about three dozen endogenous proviruses, remnants of widespread retrovirus infection of our distant ancestors. (scienceblog.com)
  • We explored the use of naturally occurring somatic mutations in mitochondrial transcripts detected in single-cell RNA-seq as genetic lineage barcodes in HPSC. (biorxiv.org)
  • Endogenous uncertainty was more prevalent during discussions on situation assessment and plan formulation. (lancs.ac.uk)
  • Trem2 T66M homozygous and heterozygous mice express Trem2 transcripts at endogenous levels. (alzforum.org)
  • To survive stress, eukaryotes selectively translate stress-related transcripts while inhibiting growth-associated protein production. (biorxiv.org)
  • These results suggested that the endogenous neurogenic capacity of retinal Mller glial cells could be improved by this little molecular agonist from the SHH signaling pathway. (exposed-skin-care.net)
  • To identify common features shared by transcripts with stress-upregulated translation efficiency (TE-up), we first performed high-resolution ribosome-sequencing in Arabidopsis during pattern-triggered immunity and found that TE-up transcripts are enriched with upstream open reading frames (uORFs). (biorxiv.org)
  • Using in planta nucleotide-resolution mRNA structurome probing, we discovered that this stress-induced switch in translation is mediated by highly structured regions detected downstream of uAUGs in TE-up transcripts. (biorxiv.org)
  • Are there common features in transcripts that are responsible for stress-induced translation? (biorxiv.org)
  • Dealing with endogenous uncertainties would entail targeting decision making specific to the problem incident (e.g., introduce training or policy to reduce redundant fixation on rote-repetitive superordinate goals and focus on more short-term actionable goals during situation assessments). (lancs.ac.uk)
  • Endogenous virus-specific RNA in uninfected BALB/c cell line JLS-V9. (microbiologyresearch.org)
  • Changes in the frequency of specific transcripts during development of the pancreas. (microbiologyresearch.org)
  • HML-2 ORF Transcripts in the Human Body: This map of the human body (adapted from the GTEx consortium website with permission) displays the possible expressed Human endogenous proviral HML-2 ORFs in each tissue sampled. (scienceblog.com)
  • Stably introduced into cancer cell lines, the system reports on elevated endogenous ADAR1 editing activity induced by interferon as well as knockdown of ADAR1 and ADAR2. (cancerindex.org)
  • We designed saRNA to target the IL-23A, IL-36g, OX40L, and UCP2 transcripts using our proprietary algorithm that bind to long noncoding RNA at position +2000 to -2000 nucleotides relative to the transcriptional start site. (aacrjournals.org)
  • This report is not a verbatim transcript of the meeting proceedings, nor does it embellish, interpret, or expand upon matters or agenda topics that were incomplete, unclear, or not addressed. (cdc.gov)
  • 2. Onco-exaptation of an endogenous retroviral LTR drives IRF5 expression in Hodgkin lymphoma. (nih.gov)
  • 4. A clear link between endogenous retroviral LTR activity and Hodgkin's lymphoma. (nih.gov)
  • We work largely with mice and the various host range subgroups of the mouse leukemia viruses (MLVs), which are members of the gammaretrovirus genus, although we have expanded our interests to investigate other endogenous retroviral genera in mice as well as in humans and frogs, and we are examining restriction factors active against retroviruses other than MLVs. (nih.gov)
  • Insertion of the retroviral vector into an expressed gene leads to the splicing of the endogenous upstream exons into this cassette to generate a fusion transcript. (taconic.com)
  • However, for some transcripts, particularly a family of retroviral enveloppes (K family), there are huge gaps sometimes. (biostars.org)
  • 7. Existence of Two Distinct Infectious Endogenous Retroviruses in Domestic Cats and Their Different Strategies for Adaptation to Transcriptional Regulation. (nih.gov)
  • 20. Utility of next-generation RNA-sequencing in identifying chimeric transcription involving human endogenous retroviruses. (nih.gov)
  • A second series of projects deals with endogenous retroviruses (ERVs) of mice and other vertebrates. (nih.gov)
  • I have been using Salmon to quantify RNA-seq of tumoral tissues using a quasi index of 161 transcripts, part of them being endogenous retroviruses sequences. (biostars.org)
  • After its degradation, IκBα is rapidly resynthesized to act as an endogenous inhibitory signal for NF-κB, and monitoring IκBα mRNA expression is a powerful tool to investigate the activity of the transcription factor within the CNS during immune stimuli. (jneurosci.org)
  • ADARx Pharmaceuticals is a genetic medicine company focused on the base editing of messenger Ribonucleic Acid (mRNA) transcripts. (cbinsights.com)
  • ADARx Pharmaceuticals discovers and develops therapeutics that utilize a family of endogenous enzymes called adenosine deaminase acting on RNA to target and correct single-point mutations on an mRNA, allowing the production of desired and functional proteins to be restored. (cbinsights.com)
  • Total RNA (including mRNA and miRNA) was extracted from the collected tissues, and the expression value data of RNA were processed into the Transcripts Per Million (TPM) and presented in log2 form. (biomedcentral.com)
  • Two mutant alleles were isolated for a subunit of the NTC/Prp19 complexes, which specifically impaired pre-mRNA splicing of early zygotic but not maternally encoded transcripts. (sdbonline.org)
  • A time-course using anti-p53 shRNA-directed knockdown of the endogenous p53 mRNA transcript demonstrates how the QuantiMir Kit can be used to measure both p53 siRNA (orange bars) and p53 mRNA (blue line) via qPCR. (systembio.com)
  • We hypothesize that MDI-exposure induces endogenous circRNA(s) to regulate hsa-miR-206-3p in MØs. (cdc.gov)
  • This approach allows us to distinguish Notch-dependent nascent transcripts in the nucleus from mature mRNAs in the cytoplasm. (elifesciences.org)
  • Our findings offer a new window into the Notch transcriptional response and demonstrate the importance of assaying nascent transcripts at active transcription sites as a readout for canonical signaling. (elifesciences.org)
  • Yet virtually no studies of any canonical signaling pathway have tackled the question of how they modulate nuclear transcription (i.e. generation of nascent transcripts at active transcription sites) during animal development. (elifesciences.org)
  • Or does it tune the probability of transcriptional firing and number of nascent transcripts produced? (elifesciences.org)
  • but no analyses have been done at the resolution of nascent transcripts at active transcription sites in the nucleus. (elifesciences.org)
  • Previously, we could show that Xenopus ADAR1 is associated with nascent transcripts on transcriptionally active lampbrush chromosomes, indicating that initial substrate binding and possibly editing itself occurs cotranscriptionally. (rupress.org)
  • Multiple alternatively spliced transcript variants that encode the same protein have been described for this gene. (cancerindex.org)
  • Both transcripts are predicted to encode the same protein. (sdbonline.org)
  • Previously, our laboratory revealed that MDI exposure downregulates endogenous microRNA(miR)-206-3p, activating miR-206-3p-regulated signaling, including PPP3CA/calcineurin/NFAT signaling activation in MØs, to increase chemokine production and promote chemotaxis activities of immune cells. (cdc.gov)
  • Early publications that demonstrated CRISPR gene editing in mammalian cells combined the crRNA and tracrRNA sequences to form one long transcript called asingle-guide RNA (sgRNA). (genengnews.com)
  • Splicing from this signal to the exons downstream of the insertion gives rise to a fusion transcript that can be used to generate a sequence tag of the trapped gene. (taconic.com)
  • The BTK gene also contains termination codons in all reading frames to prevent translation of downstream fusion transcripts. (taconic.com)
  • Pseudogene transcripts can provide a novel tier of gene regulation through generation of endogenous siRNAs or miRNA-binding sites. (nih.gov)
  • PGE2 may mediate fever generation in response to both endogenous and exogenous pyrogens by acting at the EP3 receptor. (multispaninc.com)
  • Conventional RNA in situ hybridization to endogenous Notch targets has also been used as a readout of Notch signaling, for example during segmentation of the zebrafish embryo ( Hoyle and Ish-Horowicz, 2013 ), but this method cannot resolve individual chromosomal loci and typically cannot resolve individual cells. (elifesciences.org)
  • The hybridization signal for these transcripts was localized to the edge of the ventricles and the site of infusion. (jneurosci.org)
  • Several endogenous circRNAs have been reported to regulate endogenous hsa-miR-206-3p levels through potential ceRNA mechanisms. (cdc.gov)
  • In recent years, the discovery of the competitive endogenous RNA (ceRNA) mechanism has since attracted the attention of many researchers and has stimulated many relevant studies since Salmena et al. (biomedcentral.com)
  • First specific aims was to develop mouse two photon opthalmoscope to diagnose and to perform functional images in live animals through endogenous fluorophore that are related to retinoid cycle because retinoids, particularly retinol and retinyl ester, are flourescent and we can utilize those property for diagnostic purpose of functional responses to light in live animals. (nih.gov)
  • 19. Integrated epigenomic profiling reveals endogenous retrovirus reactivation in renal cell carcinoma. (nih.gov)
  • Influence of intramammary estrogen levels and BCRF on estrogen receptor (ESR) activation, ESR-related proliferation (indicated by levels of marker transcripts), oxidative stress (indicated by levels of GCLC transcript and oxidative derivatives of cholesterol), and levels of transcripts encoding enzymes involved in estrogen biotransformation was identified by multiple linear regression models. (springer.com)
  • How repeat transcripts get exported from the nucleus is unknown. (nature.com)
  • We further demonstrate that either depleting SRSF1 or preventing its interaction with NXF1 specifically inhibits the nuclear export of pathological C9ORF72 transcripts, the production of dipeptide-repeat proteins and alleviates neurotoxicity in Drosophila , patient-derived neurons and neuronal cell models. (nature.com)
  • Con la implementación del sistema GAL4>UAS en una línea resistente de Drosophila melanogaster, que carecía de la subunidad α6 endógena, demostramos que la expresión ectópica de isoformas silvestres de Ccα6 restablecen la susceptibilidad, mientras que la expresión del alelo truncado Ccα63aQ68* (que porta la mutación 3aQ68*) no lo hace. (upm.es)
  • Taken together, we show that repeat RNA-sequestration of SRSF1 triggers the NXF1-dependent nuclear export of C9ORF72 transcripts retaining expanded hexanucleotide repeats and reveal a novel promising therapeutic target for neuroprotection. (nature.com)
  • 9. Endogenous retrovirus long terminal repeats as ready-to-use mobile promoters: the case of primate beta3GAL-T5. (nih.gov)
  • 15. The solitary long terminal repeats of ERV-9 endogenous retrovirus are conserved during primate evolution and possess enhancer activities in embryonic and hematopoietic cells. (nih.gov)
  • The cccDNA is the template for HBV transcripts, including the pre-genome (pg) RNA and messenger RNA for viral proteins. (nih.gov)
  • The LEAPER 2.0 technology utilizes the endogenous ADAR proteins present in cells to achieve proficient and precise RNA editing. (biomedcentral.com)
  • As a result, measurement of C-Peptide can be used as a substitute marker for monitoring endogenous insulin production, which is particularly important in diabetes research. (aacc.org)
  • If so, that means that the same number of sequenced fragments could be explained without these transcripts, and so the assignment of a near-0 abundance to them may be reasonable. (biostars.org)
  • Correspondingly, the endogenous levels of IRF4 and -7 are correlated with that of the BIC transcript in Epstein-Barr virus (EBV)-transformed cells. (nih.gov)
  • Basically, having transcripts with many mapping reads but large gaps in coverage be assigned abundance close to 0, especially when there are other transcripts _without_ gaps in coverage explaining the same reads, is exactly what you would expect. (biostars.org)
  • Another quick thing you could try is to find these transcripts that get assigned 0 or near-0 abundance, and remove them from the reference. (biostars.org)
  • In 1982, Ruda was able to demonstrate that the endogenous, or internally produced, opioid enkephalin made direct synaptic contact with the spinal cord neurons projecting to the thalamus , implying that these projection pathways were a major site of this peptide's modulation of sensory input about pain. (nih.gov)
  • Furthermore, a small early zygotic transcript with multiple introns was poorly spliced in wild-type embryos. (sdbonline.org)
  • Conclusions: These results suggest MDI-exposure may downregulate endogenous hsa-miR-206-3p through induction of hsa_circ_0008726/DNAJB6 thus contributing to the upregulation of hsa-miR-206-3p-mediated regulations in MØs. (cdc.gov)
  • The endogenous system uses two RNA elements, CRISPR RNA (crRNA) and trans-activating RNA (tracrRNA), which come together and guide the Cas9 nuclease to the target DNA. (genengnews.com)
  • These scientists have a system that mimics the endogenous system through a synthetic two-component approach that preserves individual crRNA and tracrRNA. (genengnews.com)