RNA Isoforms
Protein Isoforms
RNA
RNA, Small Interfering
RNA Splicing
RNA Editing
RNA, Ribosomal
RNA, Messenger
RNA, Bacterial
RNA Interference
DNA-Directed RNA Polymerases
Molecular Sequence Data
RNA, Double-Stranded
Isoenzymes
Base Sequence
RNA, Catalytic
Alternative Splicing
Amino Acid Sequence
RNA Polymerase II
RNA, Fungal
RNA Stability
RNA, Antisense
RNA Processing, Post-Transcriptional
RNA, Transfer
RNA, Small Nuclear
From snoRNA to miRNA: Dual function regulatory non-coding RNAs. (1/101)
(+info)Comparative analysis of mRNA isoform expression in cardiac hypertrophy and development reveals multiple post-transcriptional regulatory modules. (2/101)
(+info)Bayesian prediction of tissue-regulated splicing using RNA sequence and cellular context. (3/101)
(+info)L-Ilf3 and L-NF90 traffic to the nucleolus granular component: alternatively-spliced exon 3 encodes a nucleolar localization motif. (4/101)
(+info)Truncated IRAG variants modulate cGMP-mediated inhibition of human colonic smooth muscle cell contraction. (5/101)
(+info)Skipping of an alternative intron in the srsf1 3' untranslated region increases transcript stability. (6/101)
The srsf1 gene encodes serine/arginine-rich splicing factor 1 (SRSF1) that participates in both constitutive and alternative splicing reactions. This gene possesses two ultraconserved elements in the 3' untranslated region (UTR). Skipping of an alternative intron between the two elements has no effect on the protein-coding sequence, but it generates a premature stop codon (PTC)-containing mRNA isoform, whose degradation is considered to depend on nonsense-mediated mRNA decay (NMD). However, several cell lines (HCT116, RKO, HeLa, and WI38 cells) constitutively expressed significant amounts of the srsf1 PTC variant. HCT116 cells expressed the PTC variant nearly equivalent to the major isoform that includes the alternative intron in the 3' UTR. Inhibition of NMD by silencing a key effecter UPF1 or by treatment with cycloheximide failed to increase amounts of the PTC variant in HCT116 cells, and the PTC variant was rather more stable than the major isoform in the presence of actinomycin D. Our results suggest that the original stop codon may escape from the NMD surveillance even in skipping of the alternative intron. The srsf1 gene may produce an alternative splice variant having truncated 3' UTR to relief the microRNA- and/or RNA-binding protein-mediated control of translation or degradation. (+info)Gene expression during normal and FSHD myogenesis. (7/101)
(+info)Transcriptional activity regulates alternative cleavage and polyadenylation. (8/101)
(+info)RNA isoforms, also known as alternative splicing isoforms or splice variants, refer to different forms of RNA (ribonucleic acid) molecules that are generated from a single gene through the process of RNA splicing. During this process, introns (non-coding sequences) are removed and exons (coding sequences) are joined together in various combinations to form mature RNA molecules.
In eukaryotic cells, many genes undergo alternative splicing, which results in the production of multiple RNA isoforms with distinct exon compositions from a single gene. These RNA isoforms can then be translated into different protein products or perform regulatory functions, contributing to proteome diversity and functional complexity in biological systems.
The existence of RNA isoforms has significant implications for genetics, molecular biology, and biomedical research, as they can influence phenotypic traits, disease susceptibility, and therapeutic responses. Identifying and characterizing RNA isoforms are essential for understanding gene function and regulation, as well as for developing novel diagnostic and therapeutic strategies.
Protein isoforms are different forms or variants of a protein that are produced from a single gene through the process of alternative splicing, where different exons (or parts of exons) are included in the mature mRNA molecule. This results in the production of multiple, slightly different proteins that share a common core structure but have distinct sequences and functions. Protein isoforms can also arise from genetic variations such as single nucleotide polymorphisms or mutations that alter the protein-coding sequence of a gene. These differences in protein sequence can affect the stability, localization, activity, or interaction partners of the protein isoform, leading to functional diversity and specialization within cells and organisms.
RNA (Ribonucleic Acid) is a single-stranded, linear polymer of ribonucleotides. It is a nucleic acid present in the cells of all living organisms and some viruses. RNAs play crucial roles in various biological processes such as protein synthesis, gene regulation, and cellular signaling. There are several types of RNA including messenger RNA (mRNA), ribosomal RNA (rRNA), transfer RNA (tRNA), small nuclear RNA (snRNA), microRNA (miRNA), and long non-coding RNA (lncRNA). These RNAs differ in their structure, function, and location within the cell.
Small interfering RNA (siRNA) is a type of short, double-stranded RNA molecule that plays a role in the RNA interference (RNAi) pathway. The RNAi pathway is a natural cellular process that regulates gene expression by targeting and destroying specific messenger RNA (mRNA) molecules, thereby preventing the translation of those mRNAs into proteins.
SiRNAs are typically 20-25 base pairs in length and are generated from longer double-stranded RNA precursors called hairpin RNAs or dsRNAs by an enzyme called Dicer. Once generated, siRNAs associate with a protein complex called the RNA-induced silencing complex (RISC), which uses one strand of the siRNA (the guide strand) to recognize and bind to complementary sequences in the target mRNA. The RISC then cleaves the target mRNA, leading to its degradation and the inhibition of protein synthesis.
SiRNAs have emerged as a powerful tool for studying gene function and have shown promise as therapeutic agents for a variety of diseases, including viral infections, cancer, and genetic disorders. However, their use as therapeutics is still in the early stages of development, and there are challenges associated with delivering siRNAs to specific cells and tissues in the body.
A viral RNA (ribonucleic acid) is the genetic material found in certain types of viruses, as opposed to viruses that contain DNA (deoxyribonucleic acid). These viruses are known as RNA viruses. The RNA can be single-stranded or double-stranded and can exist as several different forms, such as positive-sense, negative-sense, or ambisense RNA. Upon infecting a host cell, the viral RNA uses the host's cellular machinery to translate the genetic information into proteins, leading to the production of new virus particles and the continuation of the viral life cycle. Examples of human diseases caused by RNA viruses include influenza, COVID-19 (SARS-CoV-2), hepatitis C, and polio.
RNA splicing is a post-transcriptional modification process in which the non-coding sequences (introns) are removed and the coding sequences (exons) are joined together in a messenger RNA (mRNA) molecule. This results in a continuous mRNA sequence that can be translated into a single protein. Alternative splicing, where different combinations of exons are included or excluded, allows for the creation of multiple proteins from a single gene.
RNA editing is a process that alters the sequence of a transcribed RNA molecule after it has been synthesized from DNA, but before it is translated into protein. This can result in changes to the amino acid sequence of the resulting protein or to the regulation of gene expression. The most common type of RNA editing in mammals is the hydrolytic deamination of adenosine (A) to inosine (I), catalyzed by a family of enzymes called adenosine deaminases acting on RNA (ADARs). Inosine is recognized as guanosine (G) by the translation machinery, leading to A-to-G changes in the RNA sequence. Other types of RNA editing include cytidine (C) to uridine (U) deamination and insertion/deletion of nucleotides. RNA editing is a crucial mechanism for generating diversity in gene expression and has been implicated in various biological processes, including development, differentiation, and disease.
Ribosomal RNA (rRNA) is a type of RNA molecule that is a key component of ribosomes, which are the cellular structures where protein synthesis occurs in cells. In ribosomes, rRNA plays a crucial role in the process of translation, where genetic information from messenger RNA (mRNA) is translated into proteins.
Ribosomal RNA is synthesized in the nucleus and then transported to the cytoplasm, where it assembles with ribosomal proteins to form ribosomes. Within the ribosome, rRNA provides a structural framework for the assembly of the ribosome and also plays an active role in catalyzing the formation of peptide bonds between amino acids during protein synthesis.
There are several different types of rRNA molecules, including 5S, 5.8S, 18S, and 28S rRNA, which vary in size and function. These rRNA molecules are highly conserved across different species, indicating their essential role in protein synthesis and cellular function.
Messenger RNA (mRNA) is a type of RNA (ribonucleic acid) that carries genetic information copied from DNA in the form of a series of three-base code "words," each of which specifies a particular amino acid. This information is used by the cell's machinery to construct proteins, a process known as translation. After being transcribed from DNA, mRNA travels out of the nucleus to the ribosomes in the cytoplasm where protein synthesis occurs. Once the protein has been synthesized, the mRNA may be degraded and recycled. Post-transcriptional modifications can also occur to mRNA, such as alternative splicing and addition of a 5' cap and a poly(A) tail, which can affect its stability, localization, and translation efficiency.
Bacterial RNA refers to the genetic material present in bacteria that is composed of ribonucleic acid (RNA). Unlike higher organisms, bacteria contain a single circular chromosome made up of DNA, along with smaller circular pieces of DNA called plasmids. These bacterial genetic materials contain the information necessary for the growth and reproduction of the organism.
Bacterial RNA can be divided into three main categories: messenger RNA (mRNA), ribosomal RNA (rRNA), and transfer RNA (tRNA). mRNA carries genetic information copied from DNA, which is then translated into proteins by the rRNA and tRNA molecules. rRNA is a structural component of the ribosome, where protein synthesis occurs, while tRNA acts as an adapter that brings amino acids to the ribosome during protein synthesis.
Bacterial RNA plays a crucial role in various cellular processes, including gene expression, protein synthesis, and regulation of metabolic pathways. Understanding the structure and function of bacterial RNA is essential for developing new antibiotics and other therapeutic strategies to combat bacterial infections.
RNA interference (RNAi) is a biological process in which RNA molecules inhibit the expression of specific genes. This process is mediated by small RNA molecules, including microRNAs (miRNAs) and small interfering RNAs (siRNAs), that bind to complementary sequences on messenger RNA (mRNA) molecules, leading to their degradation or translation inhibition.
RNAi plays a crucial role in regulating gene expression and defending against foreign genetic elements, such as viruses and transposons. It has also emerged as an important tool for studying gene function and developing therapeutic strategies for various diseases, including cancer and viral infections.
DNA-directed RNA polymerases are enzymes that synthesize RNA molecules using a DNA template in a process called transcription. These enzymes read the sequence of nucleotides in a DNA molecule and use it as a blueprint to construct a complementary RNA strand.
The RNA polymerase moves along the DNA template, adding ribonucleotides one by one to the growing RNA chain. The synthesis is directional, starting at the promoter region of the DNA and moving towards the terminator region.
In bacteria, there is a single type of RNA polymerase that is responsible for transcribing all types of RNA (mRNA, tRNA, and rRNA). In eukaryotic cells, however, there are three different types of RNA polymerases: RNA polymerase I, II, and III. Each type is responsible for transcribing specific types of RNA.
RNA polymerases play a crucial role in gene expression, as they link the genetic information encoded in DNA to the production of functional proteins. Inhibition or mutation of these enzymes can have significant consequences for cellular function and survival.
RNA viruses are a type of virus that contain ribonucleic acid (RNA) as their genetic material, as opposed to deoxyribonucleic acid (DNA). RNA viruses replicate by using an enzyme called RNA-dependent RNA polymerase to transcribe and replicate their RNA genome.
There are several different groups of RNA viruses, including:
1. Negative-sense single-stranded RNA viruses: These viruses have a genome that is complementary to the mRNA and must undergo transcription to produce mRNA before translation can occur. Examples include influenza virus, measles virus, and rabies virus.
2. Positive-sense single-stranded RNA viruses: These viruses have a genome that can serve as mRNA and can be directly translated into protein after entry into the host cell. Examples include poliovirus, rhinoviruses, and coronaviruses.
3. Double-stranded RNA viruses: These viruses have a genome consisting of double-stranded RNA and use a complex replication strategy involving both transcription and reverse transcription. Examples include rotaviruses and reoviruses.
RNA viruses are known to cause a wide range of human diseases, ranging from the common cold to more severe illnesses such as hepatitis C, polio, and COVID-19. Due to their high mutation rates and ability to adapt quickly to new environments, RNA viruses can be difficult to control and treat with antiviral drugs or vaccines.
Molecular sequence data refers to the specific arrangement of molecules, most commonly nucleotides in DNA or RNA, or amino acids in proteins, that make up a biological macromolecule. This data is generated through laboratory techniques such as sequencing, and provides information about the exact order of the constituent molecules. This data is crucial in various fields of biology, including genetics, evolution, and molecular biology, allowing for comparisons between different organisms, identification of genetic variations, and studies of gene function and regulation.
I'm happy to help! However, it seems there might be a slight misunderstanding in your question. RNA, or ribonucleic acid, is typically single-stranded. Unlike DNA, which is double-stranded and forms a double helix, RNA usually exists as a single strand of nucleotides.
There are exceptions to this rule, such as certain types of RNA molecules that can form double-stranded structures in specific contexts. For example:
1. Double-Stranded RNA (dsRNA) viruses: These viruses have genomes made entirely of RNA, which is double-stranded throughout or partially double-stranded. The dsRNA viruses include important pathogens such as rotaviruses and reoviruses.
2. Hairpin loops in RNA structures: Some single-stranded RNA molecules can fold back on themselves to form short double-stranded regions, called hairpin loops, within their overall structure. These are often found in ribosomal RNA (rRNA), transfer RNA (tRNA), and messenger RNA (mRNA) molecules.
So, while 'double-stranded RNA' is not a standard medical definition for RNA itself, there are specific instances where RNA can form double-stranded structures as described above.
Isoenzymes, also known as isoforms, are multiple forms of an enzyme that catalyze the same chemical reaction but differ in their amino acid sequence, structure, and/or kinetic properties. They are encoded by different genes or alternative splicing of the same gene. Isoenzymes can be found in various tissues and organs, and they play a crucial role in biological processes such as metabolism, detoxification, and cell signaling. Measurement of isoenzyme levels in body fluids (such as blood) can provide valuable diagnostic information for certain medical conditions, including tissue damage, inflammation, and various diseases.
A base sequence in the context of molecular biology refers to the specific order of nucleotides in a DNA or RNA molecule. In DNA, these nucleotides are adenine (A), guanine (G), cytosine (C), and thymine (T). In RNA, uracil (U) takes the place of thymine. The base sequence contains genetic information that is transcribed into RNA and ultimately translated into proteins. It is the exact order of these bases that determines the genetic code and thus the function of the DNA or RNA molecule.
A catalytic RNA, often referred to as a ribozyme, is a type of RNA molecule that has the ability to act as an enzyme and catalyze chemical reactions. These RNA molecules contain specific sequences and structures that allow them to bind to other molecules and accelerate chemical reactions without being consumed in the process.
Ribozymes play important roles in various biological processes, such as RNA splicing, translation regulation, and gene expression. One of the most well-known ribozymes is the self-splicing intron found in certain RNA molecules, which can excise itself from the host RNA and then ligase the flanking exons together.
The discovery of catalytic RNAs challenged the central dogma of molecular biology, which held that proteins were solely responsible for carrying out biological catalysis. The finding that RNA could also function as an enzyme opened up new avenues of research and expanded our understanding of the complexity and versatility of biological systems.
Alternative splicing is a process in molecular biology that occurs during the post-transcriptional modification of pre-messenger RNA (pre-mRNA) molecules. It involves the removal of non-coding sequences, known as introns, and the joining together of coding sequences, or exons, to form a mature messenger RNA (mRNA) molecule that can be translated into a protein.
In alternative splicing, different combinations of exons are selected and joined together to create multiple distinct mRNA transcripts from a single pre-mRNA template. This process increases the diversity of proteins that can be produced from a limited number of genes, allowing for greater functional complexity in organisms.
Alternative splicing is regulated by various cis-acting elements and trans-acting factors that bind to specific sequences in the pre-mRNA molecule and influence which exons are included or excluded during splicing. Abnormal alternative splicing has been implicated in several human diseases, including cancer, neurological disorders, and cardiovascular disease.
RNA folding, also known as RNA structure formation or RNA tertiary structure prediction, refers to the process by which an RNA molecule folds into a specific three-dimensional shape based on its primary sequence. This shape is determined by intramolecular interactions between nucleotides within the RNA chain, including base pairing (through hydrogen bonding) and stacking interactions. The folded structure of RNA plays a crucial role in its function, as it can create specific binding sites for proteins or other molecules, facilitate or inhibit enzymatic activity, or influence the stability and localization of the RNA within the cell.
RNA folding is a complex process that can be influenced by various factors such as temperature, ionic conditions, and molecular crowding. The folded structure of an RNA molecule can be predicted using computational methods, such as thermodynamic modeling and machine learning algorithms, which take into account the primary sequence and known patterns of base pairing and stacking interactions to generate a model of the three-dimensional structure. However, experimental techniques, such as chemical probing and crystallography, are often necessary to validate and refine these predictions.
An amino acid sequence is the specific order of amino acids in a protein or peptide molecule, formed by the linking of the amino group (-NH2) of one amino acid to the carboxyl group (-COOH) of another amino acid through a peptide bond. The sequence is determined by the genetic code and is unique to each type of protein or peptide. It plays a crucial role in determining the three-dimensional structure and function of proteins.
RNA Polymerase II is a type of enzyme responsible for transcribing DNA into RNA in eukaryotic cells. It plays a crucial role in the process of gene expression, where the information stored in DNA is used to create proteins. Specifically, RNA Polymerase II transcribes protein-coding genes to produce precursor messenger RNA (pre-mRNA), which is then processed into mature mRNA. This mature mRNA serves as a template for protein synthesis during translation.
RNA Polymerase II has a complex structure, consisting of multiple subunits, and it requires the assistance of various transcription factors and coactivators to initiate and regulate transcription. The enzyme recognizes specific promoter sequences in DNA, unwinds the double-stranded DNA, and synthesizes a complementary RNA strand using one of the unwound DNA strands as a template. This process results in the formation of a nascent RNA molecule that is further processed into mature mRNA for protein synthesis or other functional RNAs involved in gene regulation.
Ribonucleic acid (RNA) is a type of nucleic acid that plays a crucial role in the process of gene expression. There are several types of RNA molecules, including messenger RNA (mRNA), ribosomal RNA (rRNA), and transfer RNA (tRNA). These RNA molecules help to transcribe DNA into mRNA, which is then translated into proteins by the ribosomes.
Fungi are a group of eukaryotic organisms that include microorganisms such as yeasts and molds, as well as larger organisms like mushrooms. Like other eukaryotes, fungi contain DNA and RNA as part of their genetic material. The RNA in fungi is similar to the RNA found in other organisms, including humans, and plays a role in gene expression and protein synthesis.
A specific medical definition of "RNA, fungal" does not exist, as RNA is a fundamental component of all living organisms, including fungi. However, RNA can be used as a target for antifungal drugs, as certain enzymes involved in RNA synthesis and processing are unique to fungi and can be inhibited by these drugs. For example, the antifungal drug flucytosine is converted into a toxic metabolite that inhibits fungal RNA and DNA synthesis.
RNA stability refers to the duration that a ribonucleic acid (RNA) molecule remains intact and functional within a cell before it is degraded or broken down into its component nucleotides. Various factors can influence RNA stability, including:
1. Primary sequence: Certain sequences in the RNA molecule may be more susceptible to degradation by ribonucleases (RNases), enzymes that break down RNA.
2. Secondary structure: The formation of stable secondary structures, such as hairpins or stem-loop structures, can protect RNA from degradation.
3. Presence of RNA-binding proteins: Proteins that bind to RNA can either stabilize or destabilize the RNA molecule, depending on the type and location of the protein-RNA interaction.
4. Chemical modifications: Modifications to the RNA nucleotides, such as methylation, can increase RNA stability by preventing degradation.
5. Subcellular localization: The subcellular location of an RNA molecule can affect its stability, with some locations providing more protection from ribonucleases than others.
6. Cellular conditions: Changes in cellular conditions, such as pH or temperature, can also impact RNA stability.
Understanding RNA stability is important for understanding gene regulation and the function of non-coding RNAs, as well as for developing RNA-based therapeutic strategies.
Antisense RNA is a type of RNA molecule that is complementary to another RNA called sense RNA. In the context of gene expression, sense RNA is the RNA transcribed from a protein-coding gene, which serves as a template for translation into a protein. Antisense RNA, on the other hand, is transcribed from the opposite strand of the DNA and is complementary to the sense RNA.
Antisense RNA can bind to its complementary sense RNA through base-pairing, forming a double-stranded RNA structure. This interaction can prevent the sense RNA from being translated into protein or can target it for degradation by cellular machinery, thereby reducing the amount of protein produced from the gene. Antisense RNA can be used as a tool in molecular biology to study gene function or as a therapeutic strategy to silence disease-causing genes.
Post-transcriptional RNA processing refers to the modifications and regulations that occur on RNA molecules after the transcription of DNA into RNA. This process includes several steps:
1. 5' capping: The addition of a cap structure, usually a methylated guanosine triphosphate (GTP), to the 5' end of the RNA molecule. This helps protect the RNA from degradation and plays a role in its transport, stability, and translation.
2. 3' polyadenylation: The addition of a string of adenosine residues (poly(A) tail) to the 3' end of the RNA molecule. This process is important for mRNA stability, export from the nucleus, and translation initiation.
3. Intron removal and exon ligation: Eukaryotic pre-messenger RNAs (pre-mRNAs) contain intronic sequences that do not code for proteins. These introns are removed by a process called splicing, where the flanking exons are joined together to form a continuous mRNA sequence. Alternative splicing can lead to different mature mRNAs from a single pre-mRNA, increasing transcriptomic and proteomic diversity.
4. RNA editing: Specific nucleotide changes in RNA molecules that alter the coding potential or regulatory functions of RNA. This process is catalyzed by enzymes like ADAR (Adenosine Deaminases Acting on RNA) and APOBEC (Apolipoprotein B mRNA Editing Catalytic Polypeptide-like).
5. Chemical modifications: Various chemical modifications can occur on RNA nucleotides, such as methylation, pseudouridination, and isomerization. These modifications can influence RNA stability, localization, and interaction with proteins or other RNAs.
6. Transport and localization: Mature mRNAs are transported from the nucleus to the cytoplasm for translation. In some cases, specific mRNAs are localized to particular cellular compartments to ensure local protein synthesis.
7. Degradation: RNA molecules have finite lifetimes and undergo degradation by various ribonucleases (RNases). The rate of degradation can be influenced by factors such as RNA structure, modifications, or interactions with proteins.
RNA helicases are a class of enzymes that are capable of unwinding RNA secondary structures using the energy derived from ATP hydrolysis. They play crucial roles in various cellular processes involving RNA, such as transcription, splicing, translation, ribosome biogenesis, and RNA degradation. RNA helicases can be divided into several superfamilies based on their sequence and structural similarities, with the two largest being superfamily 1 (SF1) and superfamily 2 (SF2). These enzymes typically contain conserved motifs that are involved in ATP binding and hydrolysis, as well as RNA binding. By unwinding RNA structures, RNA helicases facilitate the access of other proteins to their target RNAs, thereby enabling the coordinated regulation of RNA metabolism.
Transfer RNA (tRNA) is a type of RNA molecule that plays a crucial role in protein synthesis, the process by which cells create proteins. In protein synthesis, tRNAs serve as adaptors, translating the genetic code present in messenger RNA (mRNA) into the corresponding amino acids required to build a protein.
Each tRNA molecule has a distinct structure, consisting of approximately 70-90 nucleotides arranged in a cloverleaf shape with several loops and stems. The most important feature of a tRNA is its anticodon, a sequence of three nucleotides located in one of the loops. This anticodon base-pairs with a complementary codon on the mRNA during translation, ensuring that the correct amino acid is added to the growing polypeptide chain.
Before tRNAs can participate in protein synthesis, they must be charged with their specific amino acids through an enzymatic process involving aminoacyl-tRNA synthetases. These enzymes recognize and bind to both the tRNA and its corresponding amino acid, forming a covalent bond between them. Once charged, the aminoacyl-tRNA complex is ready to engage in translation and contribute to protein formation.
In summary, transfer RNA (tRNA) is a small RNA molecule that facilitates protein synthesis by translating genetic information from messenger RNA into specific amino acids, ultimately leading to the creation of functional proteins within cells.
Small nuclear RNA (snRNA) are a type of RNA molecules that are typically around 100-300 nucleotides in length. They are found within the nucleus of eukaryotic cells and are components of small nuclear ribonucleoproteins (snRNPs), which play important roles in various aspects of RNA processing, including splicing of pre-messenger RNA (pre-mRNA) and regulation of transcription.
There are several classes of snRNAs, each with a distinct function. The most well-studied class is the spliceosomal snRNAs, which include U1, U2, U4, U5, and U6 snRNAs. These snRNAs form complexes with proteins to form small nuclear ribonucleoprotein particles (snRNPs) that recognize specific sequences in pre-mRNA and catalyze the removal of introns during splicing.
Other classes of snRNAs include signal recognition particle (SRP) RNA, which is involved in targeting proteins to the endoplasmic reticulum, and Ro60 RNA, which is associated with autoimmune diseases such as systemic lupus erythematosus.
Overall, small nuclear RNAs are essential components of the cellular machinery that regulates gene expression and protein synthesis in eukaryotic cells.
Gene isoform
Protein isoform
List of RNA-Seq bioinformatics tools
PELP-1
CXorf38 Isoform 1
Transcriptome in vivo analysis tag
HNRNPLL
C8orf58
DAZ2
NKG2D
RHCE (gene)
YIF1A
TMEM171
GHRLOS
C16orf82
Protein function prediction
MEG3
U2 small nuclear RNA auxiliary factor 1
CCDC47
RNA timestamp
Glutamate receptor-interacting protein
EHMT1
RNA splicing
Multiple instance learning
Alternative splicing
RBM23
U1 spliceosomal RNA
40S ribosomal protein S4, Y isoform 1
40S ribosomal protein S4, X isoform
Humanin
Single-cell analysis
ITPA
GRIK2
High-throughput RNA isoform sequencing using programmed cDNA concatenation | Nature Biotechnology
Video: Laurent Jacob, "Efficient RNA isoform identification and quantification from RNA-Seq data with network flows"
Refubium - A conserved structural element in the RNA helicase UPF1 regulates its catalytic activity in an isoform-specific...
Clonal distribution of BCR-ABL1 mutations and splice isoforms by single-molecule long-read RNA sequencing | BMC Cancer | Full...
Gene isoform - Wikipedia
EXPRESSION OF DEVELOPMENTALLY SPECIFIC ISOFORMS ON NON-NMDA MESSENGER-RNAS IN THE HIPPOCAMPUS OF SCHIZOPHRENICS - Wellcome...
Isoform expression quanification from rna seq: flood of tools -
SEQanswers
NEAT1 isoform expression in breast cancer - Edwards - Non-coding RNA Investigation
Revealing missing human protein isoforms based on Ab initio prediction, RNA-seq and proteomics. - PacBio
TGFbeta2 in corneal morphogenesis during mouse embryonic development
Determination of isoform-specific RNA structure with nanopore long reads - Oligonucleotide Therapeutics Society
Human Obesity and Type 2 Diabetes Are Associated With Alterations in SREBP1 Isoform Expression That Are Reproduced Ex Vivo by...
Conserved regulation of RNA processing in somatic cell reprogramming
EXPRESSION OF DEVELOPMENTALLY SPECIFIC ISOFORMS ON NON-NMDA MESSENGER-RNAS IN THE HIPPOCAMPUS OF SCHIZOPHRENICS - Oxford...
ncRNA | Special Issue : CRISPR/Cas Technology Applied to the Study of Non-coding RNAs in Human Disease
MSIQ -joint modeling of multiple RNA-seq samples for accurate isoform quantification | RNA-Seq Blog
An isoform of Dicer protects mammalian stem cells against multiple RNA viruses - Gen Cell Dis
single-cell analysis Genetics & Genomics News | GenomeWeb
Isoform-Specific Regulation of Cytochromes P450 Expression by Estradiol and Progesterone | Drug Metabolism & Disposition
Isoform-specific 3'-untranslated sequences sort alpha-cardiac and beta-cytoplasmic actin messenger RNAs to different...
Lyssavirus P Protein Isoforms Diverge Significantly in Subcellular Interactions Underlying Mechanisms of Interferon Antagonism ...
Analysis of intronic and exonic reads in RNA-seq data characterizes transcriptional and post-transcriptional regulation |...
Assessment of orthologous splicing isoforms in human and mouse orthologous genes | BMC Genomics | Full Text
Two-Tailed RT-qPCR for the Quantification of A-to-I-Edited microRNA Isoforms | Lund University Publications
Publication : USDA ARS
ALG9 protein expression summary - The Human Protein Atlas
![ELAVL3 ELAV like RNA binding protein 3 [Homo sapiens (human)] - Gene - NCBI](data:image/png;base64,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)
ELAVL3 ELAV like RNA binding protein 3 [Homo sapiens (human)] - Gene - NCBI
Transcripts8
- Using biochemical and transcriptome-wide approaches, we find that UPF1 LL can circumvent the protective RNA binding proteins PTBP1 and hnRNP L to preferentially bind and down-regulate transcripts with long 3'UTRs normally shielded from NMD. (nih.gov)
- Such epigenetic changes, including alterations in transcriptome and DNA methylome, have been revealed by genome-wide RNA transcripts and CpG site methylation tests ( 1 - 3 ). (frontiersin.org)
- RNA-Seq analysis provided a comprehensive view of the relative abundance and differential expression of protein-coding and non-coding transcripts from lens epithelial cells and lens fiber cells. (molvis.org)
- 10. Comprehensive analysis of translation from overexpressed circular RNAs reveals pervasive translation from linear transcripts. (nih.gov)
- The poly(A) tail is a homopolymeric stretch of adenosine at the 3′-end of mature RNA transcripts and its length plays an important role in nuclear export, stability, and translational regulation of mRNA. (researchgate.net)
- Library prep methods included cDNA, direct RNA, Rolling Circle Amplification to Concatemeric Consensus (R2C2) to improve the accuracy for nanopore sequencing, as well as CapTrap , a cDNA library preparation method designed to detect 5'-capped, full-length transcripts. (genomeweb.com)
- the HGNC does not routinely name isoforms (i.e. alternate transcripts or splice variants). (bioscience.org)
- This means no separate symbols for protein-coding or non-coding RNA isoforms of a protein-coding locus or alternative transcripts from a non-coding RNA locus. (bioscience.org)
Genes16
- Most genes in mammals generate several transcript isoforms that differ in stability and translational efficiency through alternative splicing. (biomedcentral.com)
- When applied to actual mouse RNA-Seq datasets from six tissues, IUTA identified 2,073 significant genes with clear patterns of differential isoform usage between a pair of tissues. (biomedcentral.com)
- Of these novel RNA isoforms, nearly half impact protein coding exons and are predicted to alter protein localization and function, including the products of breast cancer associated genes ESR1 and ERBB2. (pacb.com)
- Recently some progress has been made to characterize known isoforms of regeneration associated genes (RAGs) using RNA-Seq, which is important in understanding the isoform diversity in the CNS. (wikipedia.org)
- From serving as a protein template to regulating genes, the complex processes involving RNA make it a focal point of study for many scientists. (seqanswers.com)
- These non-coding RNA may be regulatory sequences of the genome, eventually modulating the expression of other genes, and may be a biological signature of specific cell population. (medscape.com)
- The EBSeqHMM package provides functions to identify genes and isoforms that have non-constant expression profile over the time points/positions, and cluster them into expression paths. (rdrr.io)
- The RNA polymerase II enzyme initiates transcription, which is a key step in using the information carried by genes to direct the production (synthesis) of proteins. (medlineplus.gov)
- We found that RNA-Seq identified more differentially expressed genes and correlated with RT-qPCR quantification better than previously published microarray data. (molvis.org)
- In collaboration with Cyril Dominguez and Glenn Burley (Strathclyde), we are interested in the mechanisms by which four-stranded internal structures in the RNA (G4s) affect splicing and, in particular, switch splicing to produce pro-apoptotic isoforms of the genes Bcl-X and Mclk-1. (le.ac.uk)
- These genes were enriched in RNA processing pathways and encoded ~100 SFs, e.g. hnRNPA1. (iscb.org)
- Most human genes have multiple promoters that control the expression of distinct isoforms. (bioconductor.org)
- We name non-coding RNA (ncRNA) genes according to their RNA type, please see our recent review ( https://www.embopress.org/doi/full/10.15252/embj.2019103777 ) for a full description. (bioscience.org)
- A total of 15 , 697 Differentially Expressed Genes (DEGs) with pathway annotation were discovered in RNA-Seq of the faba bean seeds. (scirp.org)
- Hence, we applied RNA-Seq (Quantification) technology to further study Differentially Expressed Genes (DEGs) to discover the KEGG pathway enrichment information within faba bean seeds, both pathways within all seeds in common and the pathways enrichment related to the typical seed traits of Hydration Capacity and Pea seed-borne mosaic virus (PSbMV). (scirp.org)
- Sequence features of genes and their flanking regulatory regions are determinants of RNA transcript isoform expression and have been used as context-independent, plug-and-play modules in synthetic biology. (stanford.edu)
Full-length RNA isoforms2
- The incredible length and unmatched accuracy of HiFi reads have allowed the Anczukow lab to capture many thousands of complete, full-length RNA isoforms in human breast tumors, 66% of which are new to science. (pacb.com)
- We developed a method that starts with bulk tissue and identifies single-cell types and their full-length RNA isoforms without fluorescence-activated cell sorting. (cornell.edu)
High-throughput5
- However, elucidation of RNA editing events at transcriptome-wide level requires increasingly complex computational tools, in turn resulting in a steep entrance barrier for labs who are interested in high-throughput variant calling applications on a large scale but lack the manpower and/or computational expertise. (biomedcentral.com)
- One of the widely used workflows available for high-throughput RNA-seq analyses is Galaxy, which is a reproducible and collaborative analytic platform that offers developers a framework for integrating and sharing their tools and workflows [ 11 , 12 ]. (biomedcentral.com)
- Maša Ivin, Ph.D., Scientific Writer at Lexogen, and Yvonne Goepel Ph.D., Product Manager at Lexogen, remarked that "The high-throughput nature of RNA-seq allows for rapid profiling and deep exploration of the transcriptome. (seqanswers.com)
- To understand the transcriptional changes that take place during the differentiation process, high-throughput RNA-Seq of newborn mouse lens epithelial cells and lens fiber cells was conducted to comprehensively compare the transcriptomes of these two cell types. (molvis.org)
- PROJECT SUMMARY The overall goal of this proposal is to systematically characterize the role of transcription factor isoforms by leveraging high-throughput experimental genomics approaches. (hhs.gov)
Variants5
- Alternatively spliced transcript variants encoding different isoforms have been found for this gene. (nih.gov)
- This tool provides a compilation of and comparison between the patterns of a drugs activity, and both a gene's DNA variants and RNA isoforms, and gives an assessment of whether there are statistically significant relationships between the drug and gene. (nih.gov)
- Two transcript variants encoding distinct isoforms have been identified for this gene. (sigmaaldrich.com)
- The samples were cultured as biological triplicates and spiked with 5'-capped RNA variants produced by Lexogen as controls. (genomeweb.com)
- RNA sequencing enables measurement of single nucleotide variants (SNVs), insertions and deletions, detection of different transcript isoforms, splice variants, and chimeric gene fusions. (selectbiosciences.com)
Quantification3
- We describe a new pipeline for the quantification of individual transcript coding sequences from ribosome profiling using both RNA-seq and Ribo-seq. (iscb.org)
- Modeled after the RNA-Seq Genome Annotation Assessment Project (RGASP) , a previous large-scale benchmarking effort for short-read RNA sequencing, LRGASP proposed three main challenges for the research community to tackle: transcript isoform detection for a well-curated eukaryotic genome, transcript isoform quantification, and de novo transcript isoform identification without a high-quality annotated genome in non-model organisms. (genomeweb.com)
- The seeds of five faba bean varieties (Farah, Nura, PBA Rana, PBA Warda, and PBA Zahra) and one breeding line (AF06125) were used for the RNA-Seq (Quantification) technology analysis, with three biological samples per genotype. (scirp.org)
Proteins10
- Isoforms harboring changes in the CDS have been the most thoroughly characterized because they commonly give rise to proteins with different functional properties. (wikipedia.org)
- One of these splicing factors, NOVA, has a predilection for regulating the splicing of RNAs that encode proteins acting at the neuronal synapse. (nih.gov)
- Similar proteins in other species function as RNA-binding proteins and play central roles in posttranscriptional gene regulation. (sigmaaldrich.com)
- We have made important contributions to identifying the roles of transcription, RNA folding and splice site sequences and the effects of regulatory proteins on the binding of core splicing components. (le.ac.uk)
- However, we realised that the outcome of each event is the result of binding by numerous proteins, often in competition, and that the RNA-protein complexes being studied in extracts were likely to be very heterogeneous assemblages. (le.ac.uk)
- To overcome this, we pioneered (in collaboration with Clive Bagshaw, Dmitry Cherny and Andrew Hudson) the use of single molecule methods in crude extracts, and we have used these to look at the numbers of molecules of particular proteins bound to each molecule of RNA and establish how this affects activation or repression. (le.ac.uk)
- Our offering includes DNA sequencing, as well as RNA and gene expression analysis and future technology for analysing proteins. (nanoporetech.com)
- In addition, the ADAR1 protein controls the function of certain chemical messengers called neurotransmitters at particular sites in the body by modifying the RNA blueprint for receptor proteins that interact with the neurotransmitters. (nih.gov)
- Though a handful of alternative TF isoforms are known to play functionally important (and distinct) roles in the cell, the overwhelming majority-thousands of proteins-remain entirely uncharacterized, and new TF isoforms continue to be discovered. (hhs.gov)
- Both proteins are candidate effectors of apoptotic cell death and consist of three N-terminal RNA-recognition motifs (RRM) and a C-terminal protein-interaction domain (PID). (bdbiosciences.com)
Splicing13
- In gene expression research, the regulation of RNA splicing in cancer cells is of particular interest as alternative splicing events can have a profound influence on essential protein functions, and cancers show high levels of dysregulation in this regard. (pacb.com)
- Many available tools facilitate analyses of one of the two major mechanisms of transcriptome diversity, namely, differential expression of isoforms due to alternative splicing, while the second major mechanism-RNA editing due to post-transcriptional changes of individual nucleotides-remains under-appreciated. (biomedcentral.com)
- To confirm that alternative splicing of the insulin-like growth factor 1 gene occurs in muscle in response to physical activity, oligonucleotide primers were made which specifically amplify the cDNAs of two isoforms (insulin-like growth factors 1Ea and Eb) in the human as well as the rabbit. (nih.gov)
- Although mutations in DNA are the best-studied source of neoantigens that determine response to immune checkpoint blockade, alterations in RNA splicing within cancer cells could similarly result in neoepitope production. (nih.gov)
- Gene transcription into pre-messenger RNA followed by its splicing and maturation into messenger RNA and lastly translation into a protein. (medscape.com)
- Pre-mRNA maturation into mature messenger RNA (mRNA) involves splicing, in which the spliceosome enzymatic complex removes introns. (medscape.com)
- Alternative splicing leads to different protein isoforms. (medscape.com)
- Dr. Darnell will speak about how brain-specific splicing factors interacting with splicing silencer and enhancer elements lead to RNA isoforms in the brain that are different from the corresponding isoforms in other organs. (nih.gov)
- Following this I went to Yale for 2 years (1982-3) on an SERC-NATO fellowship to work with Professor Joan Steitz on RNA splicing. (le.ac.uk)
- Qualitative control, the identity of what is expressed, is achieved by RNA splicing. (le.ac.uk)
- The differential production of transcript isoforms through the mechanism of alternative splicing is crucial in multiple biological processes as well as pathologies, including cancer. (iscb.org)
- Additionally, we performed differential splicing analysis between glia and glioma samples from human and mouse and found consistent changes occurring in both RNA-seq and Ribo-seq for the majority of cases, indicating that changes in the relative abundance of transcript isoforms lead to changes in the production of protein isoforms in the same direction. (iscb.org)
- In this study we describe two previously unknown HDGF isoforms, HDGF-B and HDGF-C, generated via alternative splicing with structurally unrelated N-terminal regions of their hath region, which is clearly different from the well described isoform, HDGF-A. In silico modeling revealed striking differences near the PHWP motif, an essential part of the binding site for glycosaminoglycans and DNA/RNA. (degruyter.com)
Double-stranded RN1
- The encoded protein is a double-stranded RNA binding protein that functions as the non-catalytic subunit of the microprocessor complex. (nih.gov)
MRNA isoforms1
- Single-cell short-read 3' sequencing enables the identification of cellular subtypes, but full-length mRNA isoforms for these cell types cannot be profiled. (cornell.edu)
MRNAs3
- Gene isoforms are mRNAs that are produced from the same locus but are different in their transcription start sites (TSSs), protein coding DNA sequences (CDSs) and/or untranslated regions (UTRs), potentially altering gene function. (wikipedia.org)
- A Comprehensive Map of mRNAs and Their Isoforms across All 14 Renal Tubule Segments of Mouse. (nih.gov)
- however, most of these ~1600 TFs are expressed as a series of protein isoforms encoded by alternatively spliced mRNAs arising from the same locus. (hhs.gov)
Tissues5
- Thus, detecting differential isoform usage for a gene between tissues or cell lines/types (differences in the fraction of total expression of a gene represented by the expression of each of its isoforms) is potentially important for cell and developmental biology. (biomedcentral.com)
- We believe that our analysis of RNA-seq data from six mouse tissues represents the first comprehensive characterization of isoform usage in these tissues. (biomedcentral.com)
- Isoform 1 is strongly predominant in all tissues except in utero where isoform 2 is the main form. (ucsc.edu)
- 14 B23.1, the prevalent isoform in all tissues, 15 contains 294 amino acids, 16 whereas B23.2, a truncated protein, lacks the last 35 C-terminal amino acids of B23.1 and is expressed at very low levels. (haematologica.org)
- The cause of death may also affect the quality of the collected tissues and RNA levels. (nih.gov)
Long intergenic1
- To our knowledge, this is the first study identifying the expression of 254 long intergenic non-coding RNAs (lincRNAs) in the lens, of which 86 lincRNAs displayed differential expression between the two cell types. (molvis.org)
MiRNA1
- We became interested in this problem through the study of miRNA isoforms (isomiRs). (cancer.gov)
20221
- Coming fall 2022, stay on the cutting-edge of cancer research with PacBio's new single-cell RNA sequencing protocol. (pacb.com)
CDNA2
- Using RT-PCR a single insulin-like growth factor 1 isoform cDNA (IGF-1Ea) could be cloned from the normal resting muscles. (nih.gov)
- Here we develop Nanopore 3′ end-capture sequencing (Nano3P-seq), a method that relies on nanopore cDNA sequencing to simultaneously quantify RNA. (researchgate.net)
Genomics1
- Soper recently founded a second company, Sunflower Genomics, which is seeking to market a new DNA/RNA single-molecule sequencing platform. (selectbiosciences.com)
Transcription5
- Pten J2 has a truncated CDS, an alternative transcription start site and a longer 3' UTR compared to the conventional Pten isoform expressed within neurons. (wikipedia.org)
- The DNA sequence of a gene contains a promoter region that is the starting point for the transcription of an antisense DNA strand into pre-messenger RNA (pre-mRNA) by RNA polymerase (Figure 1). (medscape.com)
- This study discovered a putative enhancer RNA for EGFR gene and the reliance of ESCC on AP-1 transcription factor. (frontiersin.org)
- Although NGS has been useful for unraveling RNA structure and function, several technical difficulties remain including the need for reverse transcription and PCR amplification, which can mask epitranscriptomic modifications. (selectbiosciences.com)
- Profiling 120 million full-length transcript molecules across 612 genomic perturbations, we observed sequence-independent alterations to gene expression levels and transcript isoform boundaries that were influenced by neighboring transcription. (stanford.edu)
Roles7
- some of these choices are tightly regulated and the encoded protein isoforms play essential roles in cell growth, development, circadian rhythms, memory etc. (le.ac.uk)
- 4. Translation and functional roles of circular RNAs in human cancer. (nih.gov)
- This observation prompted the hypothesis that these isoforms would have distinct interaction patterns with correspondingly diverse roles on cellular processes. (degruyter.com)
- Thus, decoding the roles of TF isoforms is key to a systems-level understanding of gene regulation. (hhs.gov)
- I will use breast cancer as a model system, as cellular phenotypes such as cell growth are highly biologically relevant to cancer, and a handful of alternative TF isoforms have been shown to play important roles in breast cancer. (hhs.gov)
- I will perform a Cas13d-based pooled screen to identify TF isoforms-both annotated and unannotated-that play biologically important roles in breast cancer cell growth. (hhs.gov)
- 2017. Divergent roles of p120-catenin isoforms linked to altered cell viability, proliferation, and invasiveness in carcinogen-induced rat skin tumors. . (oregonstate.edu)
Molecules2
- Ribonucleic acid (RNA) represents a range of diverse molecules that play a crucial role in many cellular processes. (seqanswers.com)
- RNA molecules can form secondary and tertiary structures that can regulate their localization and function. (researchgate.net)
Neurons1
- Using single-cell isoform RNA-Seq (ScISOr-Seq), we identified RNA isoforms in neurons, astrocytes, microglia, and cell subtypes such as Purkinje and Granule cells, and cell-type-specific combination patterns of distant splice sites. (cornell.edu)
Datasets3
- As the number of RNA-seq datasets that become available to explore transcriptome diversity increases, so does the need for easy-to-use comprehensive computational workflows. (biomedcentral.com)
- 77 LSVs were confirmed using two large independent B-ALL RNA-seq datasets. (iscb.org)
- Using multiple datasets, we find evidence of translation for 50-70% of the isoforms quantified with RNA-seq. (iscb.org)
Regulation2
- This insulin-like growth factor 1 mRNA probably encodes the precursor insulin-like growth factor 1 isoform that is responsible for local muscle growth regulation in response to mechanical stimulation. (nih.gov)
- The use of these alternative promoters enables the regulation of isoform expression pre-transcriptionally. (bioconductor.org)
Genome4
- We present a new method IUTA that is designed to test each gene in the genome for differential isoform usage between two groups of samples. (biomedcentral.com)
- Led by an international coalition of RNA researchers, the benchmarking initiative, dubbed Long-read RNA-Seq Genome Annotation Assessment Project (LRGASP) Consortium, generated over 427 million long-read sequences using both the Pacific Biosciences and Oxford Nanopore Technologies platforms. (genomeweb.com)
- For challenge three, which involved de novo isoform identification, the researchers used a single pooled whole-blood sample from the manatee, the genome of which is not well characterized yet. (genomeweb.com)
- I will employ Cas13d to knock down thousands of TF isoforms in a single experiment, linking, for the first time, cellular phenotypes to TF isoforms, genome-wide. (hhs.gov)
Nuclear2
- Polyadenylation at the 3'-end is a major regulator of messenger RNA and its length is known to affect nuclear export, stability, and translation, among others. (researchgate.net)
- T43199 probable nuclear RNA helicase (DEAD family) - fission yeast (Schizosaccharomyces pombe) (fra. (cornell.edu)
Detection1
- 7. Overexpression-based detection of translatable circular RNAs is vulnerable to coexistent linear RNA byproducts. (nih.gov)
Expression10
- Traditionally, the expression level of individual isoforms is quantified one isoform at a time using a specific primer. (biomedcentral.com)
- Although RNA-Seq conveniently provides a global view of the transcriptome at the gene level, deconvolution of the overall expression of a gene into the expression of its individual isoforms from sequence reads is not trivial because similar isoforms can generate identical sequence reads. (biomedcentral.com)
- In this paper, we focus on detecting differential isoform usage: "differential" meaning differences between two groups of samples and "isoform usage" denoting the set of relative abundances (proportions of total gene expression) of all isoforms of a gene. (biomedcentral.com)
- Experiments carried out by reverse transcriptase-polymerase chain reaction show that the levels of expression of these five galectin-8 isoforms are variable during the culture time in SK-MES-1, a human lung squamous carcinoma cell line. (nih.gov)
- Selective deficiency of NRF1 by lentiviral short-hairpin RNAs in HaCaT cells [ NRF1 -knockdown (KD)] led to decreased expression of γ-glutamate cysteine ligase catalytic subunit (GCLC) and regulatory subunit (GCLM) and a reduced level of intracellular glutathione. (nih.gov)
- The isoform patterns are as defined at CellMiner \ NCI-60 Analysis Tools \ RNA-seq gene expression values. (nih.gov)
- namely learned helplessness, RNA-seq, Gene Ontology and co-expression network analyses to profile the expression pattern of lncRNA and mRNA in the hippocampus of mice. (frontiersin.org)
- The quality of RNA is a key factor used to measure gene expression (whether a gene is turned on or off). (nih.gov)
- Therefore, gene expression measured in post-mortem tissue samples can be affected both by biological responses to death, as well as the loss of RNA that occurs because of cell death. (nih.gov)
- However, genetic context, including the adjacent transcriptional environment, also influences transcript isoform expression levels and boundaries. (stanford.edu)
Quantitative1
- However, there is no quantitative pathways analysis reported for faba bean seeds or RNA-seq with associated related seed traits. (scirp.org)
Transcriptional1
- Here, we present the first application of RNA-Seq to understand the transcriptional changes underlying the differentiation of epithelial cells into fiber cells in the newborn mouse lens. (molvis.org)
Polymerase2
- This protein helps regulate the activity of an enzyme called RNA polymerase II. (medlineplus.gov)
- Majello B, Napolitano G. Control of RNA polymerase II activity by dedicated CTD kinases and phosphatases. (medlineplus.gov)
Patterns2
- Among unique features of AIDD are its ability to infer RNA editing patterns, including ADAR editing, and inclusion of Guttman scale patterns for time series analysis of such editing landscapes. (biomedcentral.com)
- correlations between the isoform and drug activity patterns, and indication of their significance. (nih.gov)
Adenosine3
- The ADAR gene provides instructions for making a protein called RNA-specific adenosine deaminase 1 (ADAR1). (nih.gov)
- Specifically, it attaches (binds) to RNA and changes an RNA building block (nucleotide) called adenosine to another nucleotide called inosine. (nih.gov)
- The adenosine-to-inosine editing performed by ADAR1 is thought to change certain areas of the body's own RNA that the immune system might interpret as belonging to a virus that should be attacked. (nih.gov)
Regulatory2
- So it's hypothesized that Pten J2 works as regulatory RNA to inhibit the activity of Pten. (wikipedia.org)
- Previous studies indicate that the extension of a conserved regulatory loop in the UPF1 LL helicase core confers a decreased propensity to dissociate from RNA upon ATP hydrolysis relative to UPF1 SL , the major UPF1 isoform. (nih.gov)
Sheds Light1
- NEW YORK - A new long-read RNA sequencing benchmarking study sheds light on the strengths and weaknesses of different transcriptome analysis workflows involving various library preparation protocols, sequencing platforms, and analysis tools. (genomeweb.com)
Enrichment1
- The protocol explains the steps needed for RNA sample preparation based on TRIzol extraction and Poly(A)Purist Mag kit enrichment prior to Direct RNA library preparation protocol. (researchgate.net)
Ribonucleic1
- This protein is involved in making changes to (editing) ribonucleic acid (RNA), a chemical cousin of DNA. (nih.gov)
Enhancer1
- Among them, one appeared to act as an enhancer RNA responsible for EGFR overexpression. (frontiersin.org)
ADAR2
- AIDD-based results show importance of diversity of ADAR isoforms, key RNA editing enzymes linked with the innate immune system and viral infections. (biomedcentral.com)
- Effects of Aicardi-Goutieres syndrome mutations predicted from ADAR-RNA structures. (nih.gov)
Maturation1
- RNA polyadenylation plays a central role in RNA maturation, fate, and stability. (researchgate.net)
Sequences1
- Complete and correct isoform sequences make it easier to not only predict gene products and functions, but they can also make correlation studies seeking to appropriately link such information to higher-level phenotypes, such as mortality or survival, more productive. (pacb.com)
Subtypes1
- This article will spotlight various methods scientists have developed to investigate different RNA subtypes and the broader transcriptome. (seqanswers.com)
Characterize1
- Full-length RNA sequencing (RNA-Seq) has been applied to bulk tissue, cell lines and sorted cells to characterize transcriptomes, but applying this technology to single cells has proven to be difficult, with less than ten single-cell transcriptomes having been analyzed thus far. (cornell.edu)
Nanopore1
- This protocol provides a detailed explanation of of the steps necessary for successful Direct RNA Library preparation for Oxford Nanopore Sequencing. (researchgate.net)
Specificity1
- Here, we show that an alternative mammalian-specific isoform of the core NMD factor UPF1, termed UPF1 LL , enables condition-dependent remodeling of NMD specificity. (nih.gov)
Tissue1
- Post-mortem interval (PMI), which is the time between death and sample collection can alter normal RNA levels in post-mortem tissue. (nih.gov)
Motifs1
- This gene encodes a protein containing two conserved tandem RNA recognition motifs. (sigmaaldrich.com)
Quantify1
- proActiv uses RNA-Seq data to quantify promoter activity. (bioconductor.org)
Bioinformatics1
- Many people want to use long-read RNA-seq, but they don't know the best practices," said Kin Fai Au, a professor of computational medicine and bioinformatics at the University of Michigan and one of the organizers of the LRGASP Consortium. (genomeweb.com)
Functional1
- The genetic link between the age-associated changes in these isoforms, as well as the functional consequences, is an exciting field of study and is currently being investigated. (pacb.com)
Interference1
- Many other organisms rely instead on RNA interference (RNAi) mediated by a specialized Dicer protein that cleaves viral double-stranded RNA. (nih.gov)
Analysis5
- The EBSeqHMM package implements an auto-regressive hidden Markov model for statistical analysis in ordered RNA-seq experiments (e.g. time course or spatial course data). (rdrr.io)
- Multi-omics analysis and digital-droplet PCR results demonstrated that several non-coding RNAs in EGFR upstream were upregulated in ESCC cells. (frontiersin.org)
- Experience with RNA research and/or deep sequencing data analysis is a strong plus. (cancer.gov)
- proActiv is a method that enables the analysis of promoters from RNA-Seq data. (bioconductor.org)
- The results of the consortium's analysis, which aims to establish best practices for long-read RNA-seq studies, appeared as a preprint in BioRxiv this summer. (genomeweb.com)
Enzyme1
- Cas13d has recently emerged as a precise, programmatic, and efficient enzyme to use for systematic knockdown of RNA-overcoming many of the limitations exhibited by existing approaches to perturb isoforms en masse. (hhs.gov)
Mammalian1
- A comparison of mammalian transcriptome databases revealed that MALT1 is expressed in two alternative splice isoforms ( Fig. 1a ). (nature.com)
Regulator1
- To ascertain if IGF-1 is a regulator of local muscle growth, total RNA was extracted from rabbit muscle induced to undergo rapid hypertrophy using active stretch and from control muscles. (nih.gov)
Insights1
- Olga Anczukow ( @OlgaAnczukow ), PhD, a leading expert on breast cancer at the Jackson Laboratory, recently presented on how HiFi sequencing (PacBio's highly accurate long-read sequencing technology) with the Iso-Seq method is driving promising new insights into the RNA isoform landscape of cancer . (pacb.com)
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