Antisense sequence analysis rna. Medical search. Frequent questions

Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation. (nature.com)
The availability of multiple PAS in the same 3' regulatory region enables the inclusion or exclusion of 3' untranslated region (3'UTR) sequences, resulting in transcripts that may differ in particularities involving post-transcriptional processes such as stability, transport and translation ( Mayr, 2016 ), and even protein localization ( Berkovits and Mayr, 2015 ). (frontiersin.org)
Sgt2 and Sgt1 have similar wound-induced expression of RNA in tubers with transcripts accumulating to a maximum within the first 16 hours after wounding and then rapidly declining. (usda.gov)
We describe a method for validation of fusion transcripts detected by RNA-Seq in matched whole-genome sequencing (WGS) data. (biomedcentral.com)
Gene fusions are commonly detected in RNA sequencing (RNA-Seq) data in the form of chimeric fusion transcripts. (biomedcentral.com)
We also discovered evidences for circularization of a few RNA transcripts, both in our own data sets and publicly available data.Designing the tags used in tagRNA-seq led us to the problem of words absent from a text. (dissertations.se)
In the process of exploring the pathogenesis and prognostic factors of tumors by NGS and bioinformatics analysis, long non-coding RNAs (lncRNAs), defined as transcripts longer than 200 bp, have been discovered to play important roles. (researchsquare.com)
Further, the cDNA library analyses identified non-coding RNAs (ncRNAs) and natural antisense transcripts (NATs). (trentu.ca)
Analysis of exon composition in the transcripts of DHRS4 gene cluster revealed that exon 1 was absent in all the transcripts initiated from exon a1 of DHRS4L2 and exon a2 of DHRS4L1 . (biomedcentral.com)
Based on the analysis of gene transcripts and bioinformatic prediction, we propose here that antisense transcription may be involved in the transcriptional initiation regulation of DHRS4 and in the posttranscriptional splicing of DHRS4L2 and DRHS4L1 for the homologous identity of DHRS4 gene cluster. (biomedcentral.com)
Beside the alternative transcriptional start sites, the antisense RNA is novel possible factor serving to remove exon 1 from the transcripts initiated from exon a1 and exon a2 . (biomedcentral.com)
However, a number of snoRNA-like transcripts do not have guide sequences that are complementary to rRNA or snRNA, so they have unknown functions and are called "orphan snoRNAs" [ 8 , 9 ]. (hindawi.com)
Still, analysis of rare cells with random hexamer priming - to allow analysis of a broader range of transcripts - remains challenging. (biomedcentral.com)
Principally, RNAseq is achieved by reverse transcribing RNA into cDNA, introducing sequencing adapters and applying next-generation sequencing to determine the presence of transcripts. (biomedcentral.com)
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)

Therapeutic tiny or short modified antisense oligonucleotides (Tiny ASOs) can block gene expression or modulate splice-switching! (biosyn.com)
Incorporating Locked Nucleic Acid into oligonucleotides increases thermal duplex stability 2 and improves the specificity of oligonucleotide hybridization to target sequences. (sigmaaldrich.com)
Specifically, Locked Nucleic Acid oligonucleotides can be designed to address traditionally problematic target sequences, such as AT- or GC-rich regions. (sigmaaldrich.com)
The antisense oligonucleotides, or ASOs, work by binding to their matching genetic sequence in messenger RNA (mRNA). (longevity.technology)
Oligonucleotides are short DNA or RNA molecules. (biologyonline.com)
Aptamers (from the Latin aptus ("- fit") and Greek meros ("-part") that are oligonucleotides (since other aptamers can be peptide molecules) are created usually from a large random sequence pool and used mainly for research and clinical applications (e.g. as macromolecular drugs). (biologyonline.com)
Antisense oligonucleotides are DNA or RNA strands that are used in antisense therapy. (biologyonline.com)
RNA-like oligonucleotides that are complementary to a portion of a target mRNA molecule. (genomicglossaries.com)
More specifically, antisense oligonucleotides that are useful as reagents for target validation , or as drugs, are engineered molecules that differ from natural RNA but that have a base sequence that is recognized as being complementary to a very specific mRNA sequence. (genomicglossaries.com)
Pharmaceutical biology antisense, antisense DNA, antisense oligonucleotides. (genomicglossaries.com)
Inhibition of Xfoxi1a activities by injection of antisense oligonucleotides leads to suppression of non-CNS ectodermal markers (e.g. keratin ) and expansion of the anterior expression domain of the CNS marker Sox2 . (biologists.com)

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)
To further investigate PNN's role in regulating the alternative splicing of lncRNAs in a corneal epithelial context, we performed detailed analyses for detecting and identifying alternatively spliced 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)
Results: Our analysis uncovered PNN's impact on the transcript levels of several lncRNAs including Linc00085 and HAS2-AS1. (molvis.org)
The sequence analyses and quantification of splice variants of candidate lncRNAs, including RP11-295B20.2, RP11-18I14.1, and RP11-322M19.1, demonstrated complex configuration of their splicing changes, with a significant impact of PNN on the process. (molvis.org)
Long non-coding RNAs (lncRNAs ) are widely involved in the pathogenesis of cancers. (biomedcentral.com)
The current study aimed to evaluate the expression pattern of lncRNAs and messenger RNAs (mRNAs). (biomedcentral.com)
Pearson correlation analysis was applied to evaluate the relationships between selected lncRNAs and mRNAs. (biomedcentral.com)
In conclusion, these results of the RNA-seq and bioinformatic analysis strongly suggested that the dysregulation of lncRNA is involved in the complicated process of CRC development, and providing important insight regarding the lncRNAs involved in CRC. (biomedcentral.com)
The aim of this study was to identify prognostic long non-coding RNAs (lncRNAs) and develop a multi-lncRNA signature for suvival prediction in esophageal squamous cell carcinoma (ESCC). (researchsquare.com)
Here, we study a collection of 75 CLIP-Seq experiments mapping the RNA binding sites for a diverse set of 51 human proteins to explore the role of TEs in post-transcriptional regulation of human mRNAs and lncRNAs via RNA-protein interactions. (biomedcentral.com)
In total, 240 and 1,280 differentially expressed (DE) protein-coding genes and long noncoding RNAs (lncRNAs), respectively, were identified in fish families exhibiting contrasting phenotypes. (mtsu.edu)
Three DE antisense lncRNAs were co-expressed with sense genes known to impact muscle quality traits. (mtsu.edu)
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)
Subsequent antisense oligonucleotide-knockdown transcriptomic profiling of two LEC- and two BEC-specific lncRNAs identifies LETR1 as a critical gatekeeper of the global LEC transcriptome. (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)
Long non-coding RNAs (lncRNAs) are characterized as untranslated RNAs greater than 200 nt in length[ 10 ]. (biomedcentral.com)

Total RNA was extracted from tissues with TRIzol as per the manufacturer's protocol (Invitrogen, USA). (biomedcentral.com)
The use of random hexamer priming allows for analyzing a broader range of RNA species, but comes with the drawback that ribosomal RNA (rRNA) - that can constitute up to 90% of total RNA - is reverse transcribed together with the RNA of interest. (biomedcentral.com)
The kit provided a straightforward procedure for generating random hexamer primed stranded RNAseq libraries from 1-5 ng of total RNA, although an effective solution for reducing the rRNA contribution to the library was lacking. (biomedcentral.com)
RNA Extractions and RT-qPCR Total RNA was extracted using a TRIzol reagent (TaKaRa, Otsu, Japan). (palomid529.com)
Total RNA and protein were extracted 48 h post-treatment. (biomedcentral.com)

Ab initio construction of a eukaryotic transcriptome by massively parallel mRNA sequencing. (nature.com)
A global view of gene activity and alternative splicing by deep sequencing of the human transcriptome. (nature.com)
Evidence of binding and conservation of these motifs in the nonrepetitive transcriptome suggests that TEs have generally appropriated existing sequence preferences of the RBPs. (biomedcentral.com)
RNA-Seq was used to sequence the muscle transcriptome of different families exhibiting divergent phenotypes for each trait. (mtsu.edu)
Recently, deep sequencing of the transcriptome using high-throughput RNA sequencing (RNAseq) increased this estimate showing that more that 60% of intron-containing genes in Arabidopsis are alternatively spliced [ 12 ]. (biomedcentral.com)

Briefly, tagRNA-seq makes it possible to identify the 5' ends of RNAs in bacteria and directly probe for their type, primary or processed, by ligating short RNA sequences, the tags, to the beginnings of RNA molecules. (dissertations.se)
It was also used to study polyadenylation in E. coli, where the ability to identify processed RNA molecules proved to be useful to separate direct and indirect regulatory effects of this mechanism. (dissertations.se)
NATs are endogenous RNA molecules with regions complementary to a protein-coding transcript. (trentu.ca)
Over the last decades, a variety of RNA methods have been developed for the study of RNA-DNA, RNA-RNA, and RNA-protein interactions including RNA complexes with ligand molecules. (biosyn.com)
RNA molecules are functionally diverse and involved in many cellular processes such as catalysis, ligand binding, and protein recognition. (biosyn.com)
RNA molecules are structural flexible and can adopt different structures. (biosyn.com)
RNAs are single-stranded molecules and the unlinked monomer building blocks are known as nucleotides. (biosyn.com)
RNA molecules are generally folded into compact and defined tertiary structures. (biosyn.com)
RNA molecules in solution may adopt secondary structures that are only partially determined by thermodynamics since RNA molecules can undergo conformational changes during interaction with other RNAs, RNA binding proteins or RNA binding peptides. (biosyn.com)
Noteworthily, this allows for sequencing of all tagmented molecules, in contrast to standard tagmentation where only half the library fragments acquire the i5-i7 combination needed for sequencing. (biomedcentral.com)
Because alternative RNA splicing allows different types of mRNA molecules to be created from a single gene, it generates the diversity of protein function and structure that is essential to complex organisms. (genomicglossaries.com)
RNA molecules which hybridize to complementary sequences in either RNA or DNA altering the function of the latter. (genomicglossaries.com)

1. Global Oligonucleotide Synthesis Market analysis and forecast, in terms of value. (maximizemarketresearch.com)
Here, we investigated the therapeutic capability of an antisense oligonucleotide (ASO) targeting mouse Atxn1 in Atxn1154Q/2Q-knockin mice that manifest motor deficits and premature lethality. (jci.org)
T m of duplex between an oligonucleotide and its complementary sequence. (sigmaaldrich.com)
In molecular genetics, they refer to a short sequence synthesised to match a regionwhere a mutation is known to occur, and then used as a probe (oligonucleotide probes). (biologyonline.com)
87(5): 1663-1667] Specifically, the investigators started by priming whole cerebellar RNA with a synthetic oligonucleotide containing a T7 RNA polymerase promoter sequence. (genomicglossaries.com)

Strand-specific, massively parallel cDNA sequencing (RNA-seq) is a powerful tool for transcript discovery, genome annotation and expression profiling. (nature.com)
The research presented here improved U. maydis genome annotation through the analysis of cDNA library sequences and comparative genomics. (trentu.ca)
Over 200 U. maydis NATs were annotated by analyzing full-length cDNA sequences. (trentu.ca)
It involves crosslinking cells to lock RNA-protein interactions, immunoprecipitating the complexes using an antibody specifically targeted to the RBP, sequencing cDNA reverse transcribed from the captured RNA, and statistically analyzing the aligned sequencing reads [ 26 ]. (biomedcentral.com)
Early RNAseq libraries were generated by ligation of sequencing adapters to double stranded (ds) cDNA in a multi-step process. (biomedcentral.com)
Researchers at Stanford University used such a method to produce amplified heterogeneous populations of RNA from limited quantities of cDNA. (genomicglossaries.com)
Amplified RNA synthesized from limited quantities of heterogeneous cDNA. (genomicglossaries.com)
After second- strand cDNA synthesis, T7 RNA polymerase was used to generate aRNA. (genomicglossaries.com)
They also found that the amplicons were similar in size distribution to the parent cDNA and showed sequence heterogeneity. (genomicglossaries.com)

RNA sequencing (RNA-Seq) in CRC tissues and adjacent normal tissues from 6 CRC patients was performed and functional lncRNA-mRNA co-expression network was constructed afterwards. (biomedcentral.com)
We adapted nanopore direct RNA sequencing to examine RNA from a wild-type accession of the model plant Arabidopsis thaliana and a mutant defective in mRNA methylation (m6A). (dundee.ac.uk)
We conclude that nanopore direct RNA sequencing can reveal the complexity of mRNA processing and modification in full-length single molecule reads. (dundee.ac.uk)
Polyadenylation is essential for the stability of the transcript, preventing the mRNA from being the target of posttranscriptional gene silencing (PTGS) via RNA-dependent RNA polymerase 6 (RDR6) in plants ( Luo and Chen, 2007 ). (frontiersin.org)
To expand understanding of the role of snoRNAs in control of gene expression, in this study we tested the ability of artificial box C/D RNAs to affect the maturation of target pre-mRNA. (hindawi.com)
The artificial box C/D RNA directed to the branch point adenosine of the second intron, as well as the analogue directed to the last nucleotide of the second exon of the HSPA8 pre-mRNA caused the most prominent influence on the level of HSPA8 mRNAs. (hindawi.com)
Inasmuch as artificial box C/D RNAs decreased viability of transfected human cells, we propose that natural snoRNAs as well as their artificial analogues can influence the maturation of complementary pre-mRNA and can be effective regulators of vital cellular processes. (hindawi.com)
Uppercase letters in the target pre-mRNA sequences correspond to exons, and small letters indicate the intron sequences. (hindawi.com)
MBII-52 box C/D snoRNA containing a guide sequence complementary to the serotonin receptor 2C pre-mRNA was reported to take part in controlling the posttranscriptional modification of the target pre-mRNA (conversion A to I) [ 11 ]. (hindawi.com)
Using such an approach, it was shown that introducing sequences complementary to a selected pre-mRNA into box C/D RNA structures allowed knockdown of the target mRNA [ 13 ]. (hindawi.com)
A complementary RNA sequence that binds to a naturally occurring (sense) mRNA molecule, thus blocking its translation. (genomicglossaries.com)
Highly specific and effective gene silencing of any disease can be achieved by an accurate knowledge of the target mRNA sequence and rational design of its complementary antisense agents for the downregulation of its protein message. (genomicglossaries.com)
Further analysis revealed that celastrol inhibited HIF-1α protein synthesis, without affecting the expression level of HIF-1α mRNA or degradation of HIF-1α protein. (spandidos-publications.com)

Gene enrichment analysis revealed that these lncRNA-related mRNAs are associated with cell adhesion, collagen adhesion, cell differentiation, and mainly enriched in ECM-receptor interaction and PI3K-Akt signaling pathways. (biomedcentral.com)
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 long non-coding RNA (lncRNA) taurine up-regulated gene1 (Tug1) plays a well-defined role in inflammatory diseases. (biomedcentral.com)

CircRNAs exert their biological effects by 4 different mechanisms: serving as sponges of microRNAs (miRNAs), serving as sponges of RNA binding proteins (RBPs), modulating parental gene transcription, and encoding functional proteins. (techscience.com)
In addition, after transcription, a wide array of RNA-binding proteins interacts with cis -acting elements located mainly in the 3' untranslated region, determining the fate of mRNAs in eukaryotic cells. (frontiersin.org)
Bioinformatic algorithms allowing predicting of biomolecular folding for proteins, peptides, and RNAs, even though sometimes successful, have all their limitations. (biosyn.com)
Since RNA-binding proteins (RBPs) are key players in the post-transcriptional regulation of gene expression precise knowledge of their binding sites is critical for determining their molecular function and for understanding their roles in cell development and disease. (biosyn.com)
We uncovered the functions of ABCE proteins Rli1/ABCE1 and Arb1 in PIC assembly and ribosome biogenesis, and identified the tRNA methyltransferase Gcd10/Gcd14, which contributed to the discovery of the TRAMP-mediated RNA surveillance pathway. (nih.gov)
We detect widespread interactions between RNA binding proteins (RBPs) and many families of TE-derived sequence in the CLIP-Seq data. (biomedcentral.com)
Box C/D RNAs are associated with four snoRNP core proteins: NOP56, NOP58, fibrillarin, and 15.5 kDa [ 5 - 7 ]. (hindawi.com)
Box C/D RNAs contain the following functional elements: boxes C and D, which are essential for snoRNA interaction with specific proteins, and a guide sequence that determines the nucleotide to be modified (Figure 1(a) ). (hindawi.com)
We show that ALS heritability is enriched in splicing variants and in binding sites of 6 RNA-binding proteins including TDP-43 and FUS. (cdc.gov)
The overall aim within the group is to predict recurrences by monitoring breast cancer specific proteins in tumors and patient blood, primarily using a combination of the DNA sequence and mass spectrometric analysis and to translate these findings into clinical routine work. (lu.se)

Whole-genome sequencing (WGS) has the advantage of being able to detect structural variants at a genomic scale, but it is challenging to assess whether a fusion event found purely at the DNA level has the potential to be processed into a functional transcript. (biomedcentral.com)
His team has pioneered novel approaches, including copy number variation (CNV) and structural variation (SV) discovery, as well as whole-genome sequencing, and the development of informatics tools, to delineate loci and genes involved in these conditions. (sfari.org)
Genomic architecture of autism from comprehensive whole-genome sequence annotation. (sfari.org)

In each of the 3 individual isolates, several mismatched nucleotides at the binding site of the antisense primer S80 ( 6 ) were observed. (cdc.gov)
The nucleotides to be complementary to target nucleotides are shown as C . RNA7D* and RNA8D* were constructed by changing the CUGA sequence in both box D and D′ to AAAA. (hindawi.com)
The ribose sugar is the sugar component of the nucleotides that make up RNA. (biologyonline.com)

Ribosomal RNA was removed and the sequencing library was generated using Hieff NGS® MaxUp rRNA Depletion Kit (Yeasen, China) following manufacturer's recommendations. (biomedcentral.com)
Specific tertiary structure types are observed for transfer RNA (tRNA), ribosomal RNA (rRNA), small nuclear RNA (snRNA), certain introns, and ribozymes. (biosyn.com)
Small nucleolar RNAs (snoRNA) are commonly known to be involved in the processing of precursor ribosomal RNA (pre-rRNA) and small nuclear RNAs (snRNAs). (hindawi.com)

MicroRNAs (miRNAs/miRs) are a class of non-coding single-stranded small-molecule RNAs that degrade target gene expression via binding to the 3′-untranslated region. (spandidos-publications.com)
The characterization of RNA and RNA interactions is closely related to transcription, for example, gene expression levels are investigated within a biological context. (biosyn.com)
Recent research has revisited the topic of TE impact on gene expression, noting that the dissemination of highly similar sequence accomplished by TEs is a powerful way to link many diverse genomic regions into a regulatory network [ 7 ]. (biomedcentral.com)
RNA sequencing has become the mainstay for studies of gene expression. (biomedcentral.com)
Endogenous antisense RNAs function as regulators of gene expression by a variety of mechanisms. (genomicglossaries.com)
presents an opportunity to manipulate gene expression within the cells to treat various diseases, and acts as a powerful tool for studying gene function utilizing antisense agents to manage the diseases by regulating the expression of the specific factor that actually causes the particular disease. (genomicglossaries.com)

It was discovered by deep sequencing and its transcription was confirmed by Northern blot and RACE analysis. (wikipedia.org)
Understanding genome organization and gene regulation requires insight into RNA transcription, processing and modification. (dundee.ac.uk)
qRT-PCR of Atf3, Sprr1a, Ddit3 (Chop), and Gfap from retinal RNA four days after optic nerve crush (ONC) compared to uninjured contralateral control (CTL): upregulation of regeneration-associated genes Atf3 and Sprr1a, pro-apoptotic transcription factor Ddit3 (Chop), and reactive astrocyte marker Gfap demonstrates a robust response to injury following ONC. (pharmoptima.com)
By cloning the full length of RNA variants through 5'RACE and 3'RACE, we identified two transcription start sites, within exon a2 and exon 1, of this newly named gene DHRS4L1 using neuroblastoma cell line BE(2)-M17. (biomedcentral.com)
To investigate the transcription of DHRS4L1 and the transcriptional regulation of DHRS4 gene cluster, we cloned the full length RNA variants of DHRS4L1 in this study, and found that DHRS4L1 initiated its transcription from two TSS, exon a2 and exon 1. (biomedcentral.com)
RNA-extraction kits and reverse transcription (RT) kits were obtained from AbGene (Guildford, Surrey, UK) and Sigma-Aldrich (Dorset, England, UK). (iiarjournals.org)
RNA invert transcription PCR was completed using invert transcription kits (TaKaRa). (palomid529.com)

Loss of m6A from 3' untranslated regions is associated with decreased relative transcript abundance and defective RNA 3' end formation. (dundee.ac.uk)
Expressed fusions can be identified in RNA sequencing (RNA-Seq) data, but fusion prediction software often has a high fraction of false positive fusion transcript predictions. (biomedcentral.com)

Alternatively spliced RNA variants are prevalent in the human DHRS4 gene cluster. (biomedcentral.com)
Three generation families: Analysis of de novo variants in autism. (sfari.org)

We here describe a tagmentation-based, rRNA blocked, random hexamer primed RNAseq approach (T-RHEX-RNAseq) for generating stranded RNAseq libraries from very low numbers of FACS sorted cells without RNA purification steps. (biomedcentral.com)
This makes a reduction of rRNA representation in the library an attractive strategy for limiting the need for extensive sequencing. (biomedcentral.com)

Twelve samples (harboring 6 CRC tissues and 6 paired adjacent normal tissues) used in RNA-Sequencing (RNA-Seq) were collected from six Chinese patients who were diagnosed with stage II b or IIIb CRC. (biomedcentral.com)
The raw sequencing data is secondary analyzed, and the 6 pairs of CRC tissues were divided into two groups (group 1 and group 2, corresponding to clinical stage II and III, Table S 1 ) based on their clinical stages. (biomedcentral.com)
Libraries from CRC tissue and adjacent normal tissues were analyzed on a single Genome Analyzer IIx lane (Illumina, USA) using 115 bp sequencing. (biomedcentral.com)
A total of 98 paired ESCC tumor and normal tissues were detected by RNA sequencing and used as test set. (researchsquare.com)
To clarify the function of miR-106a in porcine tissues, we extracted RNA from several tissue of 3C7 time old Guanzhong dark pigs and assessed the appearance of miR-106a by RT-qPCR. (palomid529.com)
Here we describe a detailed survey of alternative splicing in grape based on 124 SOLiD RNAseq analyses from different tissues, stress conditions and genotypes. (biomedcentral.com)

Analysis of genomic DNA shows a simple pattern for Sgt2 indicative of low copy number. (usda.gov)
In cancer, genomic rearrangements can create fusion genes that either combine protein-coding sequences from two different partner genes or place one gene under the control of the promoter of another gene. (biomedcentral.com)
Exon a1 matches with a special intergene sequence, approximate 19 kb upstream of the first exon of DHRS4L2 and 559 bp downstream of the last exon of DHRS4 in the genomic DNA. (biomedcentral.com)
In a number of cases, extant TE sequences have integrated with established genomic functions and been co-opted by the genome for critical roles [ 7 ],[ 8 ]. (biomedcentral.com)
The Streptococcus pyogenes Cas9 (SpCas9) nuclease can be efficiently targeted to genomic loci by means of singleguide RNAs (sgRNAs) to enable genome editing 1 - 10 . (cdc.gov)
Following crRNA and tracrRNA hybridization, SpCas9 is targeted to genomic loci matching a 20-nt guide sequence within the crRNA, immediately upstream of a required 5′-NGG protospacer adjacent motif (PAM) 11 . (cdc.gov)

This model proposed NATs facilitate the maintenance of stored mRNAs through the formation of double-stranded RNA. (trentu.ca)
Bioinformatics analysis revealed that some of these orphan RNAs were complementary to pre-mRNAs or mature mRNAs [ 10 ]. (hindawi.com)

There are multiple published methods for strand-specific RNA-seq, but no consensus exists as to how to choose between them. (nature.com)
Weighing each method's performance and ease, we identified the dUTP second-strand marking and the Illumina RNA ligation methods as the leading protocols, with the former benefitting from the current availability of paired-end sequencing. (nature.com)
Figure 1: Methods for strand-specific RNA-seq. (nature.com)
The drawback is that the amount of data generated in the process is large and extracting useful information from it requires new methods to process and analyze it.The main contribution of this thesis is the development of a novel experimental method coined tagRNA-seq, combining 5'tagRACE, a previously developed technique, with RNA-sequencing technology. (dissertations.se)
The combination of different biochemical methods with computational modelling allows scientists to gain insight into molecular processes in which RNA is involved. (biosyn.com)
The mapping of RNA-protein or RNA-RNA interactions by protein pull-down or affinity pull-down methods allow studying RNA structures, as well as RNA-protein, and RNA-RNA interactions. (biosyn.com)
The field of transcriptomics has during the last two decades evolved from analysis of select genes with PCR-based methods, to broad analysis using microarrays and finally, to the now standard use of RNA sequencing (RNAseq) to characterize full transcriptomes [ 1 ]. (biomedcentral.com)

Based on the results of bioinformatics analysis, we propose a possible mechanism for the transcriptional regulation of the human DHRS4 gene cluster. (biomedcentral.com)

Oligomers are produced synthetically through solid-phase chemical synthesis for use in PCR (polymerase chain reaction, where the oligosaccharide used is referred to as the primer ), DNA sequencing, DNA microarrays, Southern blots, ASO analysis, FISH (florescent in situ hybridization), molecular probing, and library construction. (biologyonline.com)

Finally, in situ hybridization analyses revealed the presence of RP11-295G20.2 in the nuclei of corneal epithelial cells, but not in the stromal cells of the human cornea, while RP11-322M19.1 was present in epithelial and non-epithelial cells. (molvis.org)

More recently, another group of researchers reported that they had developed a process for optimizing low- abundance RNA, by combining aRNA amplification with template- switching. (genomicglossaries.com)

The sequencing of full length polyadenylated RNA - using oligo-dT priming - has been the mainstay for RNAseq. (biomedcentral.com)
We used the RNAseq data to update the existing grape gene prediction with 2,258 new coding genes and 3,336 putative long non-coding RNAs. (biomedcentral.com)

We describe the first report of RNA sequencing of 5' capped (Pol II) RNAs isolated from acutely hepatitis C virus (HCV) infected Huh 7.5 cells that provides a general approach to identifying differentially expressed annotated and unannotated genes that participate in viral-host interactions. (mdpi.com)
b) Base-pairing interactions between an artificial box C/D RNA and target RNAs. (hindawi.com)
Native or wild-type quaternary protein structure is usually born from a single translated protein sequence with one ordered conformation with downstream protein interactions. (medscape.com)
[ 3 ] It is also important to understand that the same polypeptide sequence can produce many different patterns of interresidue or intraresidue interactions. (medscape.com)

RNA which contains an intron sequence that has an enzyme- like catalytic activity. (genomicglossaries.com)
A quantitative analysis of the isoforms indicated that most of the spliced genes have one major isoform and tend to simultaneously co-express a low number of isoforms, typically two, with intron retention being the most frequent alternative splicing event. (biomedcentral.com)

Promoter methylation of p16 INK4A , c-myc and hMSH2 genes was assayed by methylation-specific PCR (MSP) and sequencing (mapping). (wjgnet.com)
rRNAs and snRNAs are the main natural targets of 2′-O-methylation that is mediated by box C/D RNAs. (hindawi.com)
COBRA and bisulphite sequencing revealed RASSF6 and RASSF10 were the only RASSF members with a high frequency of leukaemia-specific methylation. (biomedcentral.com)

RNA is a long, polymer of ribonucleoside monophosphate molecular units or building blocks joined together by phosphodiester linkages. (biosyn.com)

In that case, snoRNAs hold two potential guide sequences [ 2 , 4 ]. (hindawi.com)
Although an sgRNA design consisting of a truncated crRNA and tracrRNA had been previously shown to mediate efficient cleavage in vitro 12 , it failed to achieve detectable cleavage at several loci that were efficiently modified by crRNA-tracrRNA duplexes bearing identical guide sequences 1 . (cdc.gov)

Thus, FLI1 drives tumor metastasis not only through the canonical oncoprotein pathway, but also by using epigenetic mechanisms mediated by its exonic circular RNA. (biomedcentral.com)
The data supported a common role for NATs in smut teliospore development, independent of the RNA interference pathway. (trentu.ca)

Using this CasIP assay, we identified FECR1, a FLI1 exonic circular RNA that binds to the FLI1 promoter and epigenetically activates FLI1 in breast cancer cells. (biomedcentral.com)

Our data suggest that this XRE concatemer site concurrently regulates the expression of both Tiparp gene and its cis anti-sense non-coding RNA following ligand or suspension induced AhR activation. (aspetjournals.org)

Post-transcriptional regulation of human genes by TE-derived sequences has been observed in specific contexts, but has yet to be systematically and comprehensively investigated. (biomedcentral.com)

RNA-sequencing analysis of genes with expression restored to WT levels in ASO-treated Atxn1154Q/2Q mice was used to demonstrate molecular differences between SCA1 pathogenesis in the cerebellum and disease in the medulla. (jci.org)

The use of transposase (Tn5) to fragment ds DNA and integrate sequencing adapters in a single step - so called tagmentation - was first described by Adey et al. (biomedcentral.com)

Protein expression of ER stress and apoptosis factors was analyzed using Western Blot analysis. (karger.com)
We performed northern blot analyses for the guide RNA truncations and found increased levels of expression for the longer tracrRNA sequences, suggesting that improved target cleavage was at least partially due to higher sgRNA expression or stability ( Fig. 1c ). (cdc.gov)

They can bind to the desired complementary sequence, thereby, can target specific RNAs. (biologyonline.com)

The primer sequences employed for real-time qPCR (RT-qPCR) analyses are shown in Desk 1. (palomid529.com)

Desk 1 Primer sequences. (palomid529.com)

Together, these findings support the efficacy and therapeutic importance of directly targeting ATXN1 RNA expression as a strategy for treating both motor deficits and lethality in SCA1. (jci.org)
Our study describes the sequence characteristics of 5' non-coding region of Sema4D, enhances our understanding of the regulatory mechanism of Sema4D and benefits the development of a possible anti-angiogenesis therapeutic strategy for malignancies. (jcancer.org)
Synthetic antisense RNAs are used to effect the functioning of specific genes for investigative or therapeutic purposes. (genomicglossaries.com)

In study by Ono and coworkers, such an antisense element was placed into HBII-180C box C/D RNA instead of the structural element referred to as the M box [ 13 ]. (hindawi.com)

Subsequent differentiation allows for rear- analysis of a set of mouse B lineage cell lines rep- rangements of the Ig light-chain (IgL) genes that replace the resenting defined stages of B cell development us- surrogate light-chain genes on the surface of the B cell [8]. (lu.se)

the CRISPR-associated nuclease Cas9 (SpCas9), a specificity-determining CRISPR RNA (crRNA), and an auxiliary trans-activating crRNA (tracrRNA) 11 . (cdc.gov)

Furthermore, sequence analysis coupled with ChIP assays and reporter gene analysis identified a functional XRE (xenobiotic response element) in the intron1 of mouse Tiparp gene, which was also bound by HIF-1α during hypoxia, and features a concatemer of 4 XRE cores (GCGTG). (aspetjournals.org)
Integrated DNA Technologies acquires Archer™ next generation sequencing research assays to advance actionable scientific discoveries. (idtdna.com)

The Sgt2 nucleic acid sequence is 68% identical to Sgt1 a UDP-galactose:solanidine galactosyl transferase. (usda.gov)
The bold letters in the sequences denote Locked Nucleic Acid bases. (sigmaaldrich.com)
Pink) mutant DNA analysis with Locked Nucleic Acid mutant probe (16mer with 3 Locked Nucleic Acid bases). (sigmaaldrich.com)

An amino terminal fragment of Sgt2 was used to create an antisense transgene under control the Gbss6 promoter and the Ubi3 polyadenylation signal. (usda.gov)
However, better understanding of RNA biology has come with increased interest in studying other RNA species or incompletely processed RNA lacking polyadenylation [ 1 ]. (biomedcentral.com)

These data suggest that FECR1 circular RNA acts as an upstream regulator to control breast cancer tumor growth by coordinating the regulation of DNA methylating and demethylating enzymes. (biomedcentral.com)

Anatomy7

Organisms9

Chemicals and Drugs88

Analytical, Diagnostic and Therapeutic Techniques and Equipment27

Phenomena and Processes84

Disciplines and Occupations1

Information Science4

Health Care3

Transcripts15

Oligonucleotides11

LncRNAs19

Total RNA5

Transcriptome5

Molecules12

Oligonucleotide5

CDNA9

MRNA13

LncRNA3

Proteins10

Whole-genome3

Nucleotides3

Ribosomal3

Gene Expression6

Transcription7

Transcript2

Variants2

RRNA2

Tissues6

Genomic6

MRNAs2

Methods7

Bioinformatics1

Synthesis1

Hybridization1

Abundance1

RNAseq2

Interactions4

Intron2

Methylation3

Long1

Guide sequences2

Pathway2

Binds1

Ligand1

Transcriptional1

Molecular1

Adapters1

Blot2

Complementary sequence1

QPCR1

Primer1

Therapeutic3

Structural1

Subsequent1

Specificity1

Assays2

Nucleic acid3

Polyadenylation2

Upstream1