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Epitranscriptomic Sequencing
In epitranscriptomic sequencing, most methods focus on either (1) enrichment and purification of the modified RNA molecules before running on the RNA sequencer, or (2) improving or modifying bioinformatics analysis pipelines to call the modification peaks. Most methods have been adapted and optimized for mRNA molecules, except for modified bisulfite sequencing for profiling 5-methylcytidine which was optimized for tRNAs and rRNAs. There are seven major classes of chemical modifications found in RNA molecules: N6-Methyladenosine, N6-methyladenosine, 2'-O-methylation, 2'-O-methylation, N6,2'-O-dimethyladenosine, 5-Methylcytidine, 5-methylcytidine, 5-Hydroxymethylcytosine, 5-hydroxylmethylcytidine, inosine, and pseudouridine.Li, X, Xiong, X., and Yi, C. (2017)Epitranscriptomic Sequencing Technologies: decoding RNA modifications Nature Methods. doi:10.1038/NMETH_4110 Various sequencing methods have been developed to profile each type of modification. The scale, resolution, sensitivity ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
RNA Sequencer
Ribonucleic acid (RNA) is a polymeric molecule essential in various biological roles in Genetic code, coding, Translation (biology), decoding, Regulatory RNA, regulation and Gene expression, expression of genes. RNA and deoxyribonucleic acid (DNA) are nucleic acids. Along with lipids, proteins, and carbohydrates, nucleic acids constitute one of the four major macromolecules essential for all known forms of life. Like DNA, RNA is assembled as a chain of nucleotides, but unlike DNA, RNA is found in nature as a single strand folded onto itself, rather than a paired double strand. Cellular organisms use messenger RNA (''mRNA'') to convey genetic information (using the nucleobase, nitrogenous bases of guanine, uracil, adenine, and cytosine, denoted by the letters G, U, A, and C) that directs synthesis of specific proteins. Many viruses encode their genetic information using an RNA genome. Some RNA molecules play an active role within cells by catalyzing biological reactions, control ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Uracil
Uracil () (symbol U or Ura) is one of the four nucleobases in the nucleic acid RNA. The others are adenine (A), cytosine (C), and guanine (G). In RNA, uracil binds to adenine via two hydrogen bonds. In DNA, the uracil nucleobase is replaced by thymine (T). Uracil is a demethylated form of thymine. Uracil is a common and naturally occurring pyrimidine derivative. The name "uracil" was coined in 1885 by the German chemist Robert Behrend, who was attempting to synthesize derivatives of uric acid. Originally discovered in 1900 by Alberto Ascoli, it was isolated by hydrolysis of yeast nuclein; it was also found in bovine thymus and spleen, herring sperm, and wheat germ. It is a planar, unsaturated compound that has the ability to absorb light. Based on 12C/13C isotopic ratios of organic compounds found in the Murchison meteorite, it is believed that uracil, xanthine, and related molecules can also be formed extraterrestrially. Data from the Cassini mission, orbitin ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Covalent Bond
A covalent bond is a chemical bond that involves the sharing of electrons to form electron pairs between atoms. These electron pairs are known as shared pairs or bonding pairs. The stable balance of attractive and repulsive forces between atoms, when they share electrons, is known as covalent bonding. For many molecules, the sharing of electrons allows each atom to attain the equivalent of a full valence shell, corresponding to a stable electronic configuration. In organic chemistry, covalent bonding is much more common than ionic bonding. Covalent bonding also includes many kinds of interactions, including σ-bonding, π-bonding, metal-to-metal bonding, agostic interactions, bent bonds, three-center two-electron bonds and three-center four-electron bonds. The term ''covalent bond'' dates from 1939. The prefix ''co-'' means ''jointly, associated in action, partnered to a lesser degree, '' etc.; thus a "co-valent bond", in essence, means that the atoms share "valence" ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Proteinase K
In molecular biology Proteinase K (, ''protease K'', ''endopeptidase K'', ''Tritirachium alkaline proteinase'', ''Tritirachium album serine proteinase'', ''Tritirachium album proteinase K'') is a broad-spectrum serine protease. The enzyme was discovered in 1974 in extracts of the fungus ''Engyodontium album'' (formerly '' Tritirachium album''). Proteinase K is able to digest hair (keratin), hence, the name "Proteinase K". The predominant site of cleavage is the peptide bond adjacent to the carboxyl group of aliphatic and aromatic amino acids with blocked alpha amino groups. It is commonly used for its broad specificity. This enzyme belongs to Peptidase family S8 (subtilisin). The molecular weight of Proteinase K is 28,900 daltons (28.9 kDa). Enzyme activity Activated by calcium, the enzyme digests proteins preferentially after hydrophobic amino acids (aliphatic, aromatic and other hydrophobic amino acids). Although calcium ions do not affect the enzyme activity, they do contr ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Competition Elution
Competition is a rivalry where two or more parties strive for a common goal which cannot be shared: where one's gain is the other's loss (an example of which is a zero-sum game). Competition can arise between entities such as organisms, individuals, economic and social groups, etc. The rivalry can be over attainment of any exclusive goal, including recognition: Competition occurs in nature, between living organisms which co-exist in the same environment. Animals compete over water supplies, food, mates, and other biological resources. Humans usually compete for food and mates, though when these needs are met deep rivalries often arise over the pursuit of wealth, power, prestige, and fame when in a static, repetitive, or unchanging environment. Competition is a major tenet of market economies and business, often associated with business competition as companies are in competition with at least one other firm over the same group of customers. Competition inside a company is usua ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Growth Media
A growth medium or culture medium is a solid, liquid, or semi-solid designed to support the growth of a population of microorganisms or cells via the process of cell proliferation or small plants like the moss '' Physcomitrella patens''. Different types of media are used for growing different types of cells. The two major types of growth media are those used for cell culture, which use specific cell types derived from plants or animals, and those used for microbiological culture, which are used for growing microorganisms such as bacteria or fungi. The most common growth media for microorganisms are nutrient broths and agar plates; specialized media are sometimes required for microorganism and cell culture growth. Some organisms, termed fastidious organisms, require specialized environments due to complex nutritional requirements. Viruses, for example, are obligate intracellular parasites and require a growth medium containing living cells. Types The most common growth ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Cross-linking Immunoprecipitation
Cross-linking immunoprecipitation (CLIP) is a method used in molecular biology that combines UV cross-linking with immunoprecipitation in order to analyse protein interactions with RNA or to precisely locate RNA modifications (e.g. m6A). CLIP-based techniques can be used to map RNA binding protein binding sites or RNA modification sites of interest on a genome-wide scale, thereby increasing the understanding of post-transcriptional regulatory networks. Workflow CLIP begins with the in-vivo cross-linking of RNA-protein complexes using ultraviolet light (UV). Upon UV exposure, covalent bonds are formed between proteins and nucleic acids that are in close proximity. The cross-linked cells are then lysed, and the protein of interest is isolated via immunoprecipitation. In order to allow for sequence specific priming of reverse transcription, RNA adapters are ligated to the 3' ends, while radiolabeled phosphates are transferred to the 5' ends of the RNA fragments. The RNA-protein comple ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
RNA Immunoprecipitation
Immunoprecipitation (IP) is the technique of precipitating a protein antigen out of solution using an antibody that specifically binds to that particular protein. This process can be used to isolate and concentrate a particular protein from a sample containing many thousands of different proteins. Immunoprecipitation requires that the antibody be coupled to a solid substrate at some point in the procedure. Types Individual protein immunoprecipitation (IP) Involves using an antibody that is specific for a known protein to isolate that particular protein out of a solution containing many different proteins. These solutions will often be in the form of a crude lysate of a plant or animal tissue. Other sample types could be body fluids or other samples of biological origin. Protein complex immunoprecipitation (Co-IP) Immunoprecipitation of intact protein complexes (i.e. antigen along with any proteins or ligands that are bound to it) is known as co-immunoprecipitation ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Transcriptome
The transcriptome is the set of all RNA transcripts, including coding and non-coding, in an individual or a population of cells. The term can also sometimes be used to refer to all RNAs, or just mRNA, depending on the particular experiment. The term ''transcriptome'' is a portmanteau of the words ''transcript'' and ''genome''; it is associated with the process of transcript production during the biological process of transcription. The early stages of transcriptome annotations began with cDNA libraries published in the 1980s. Subsequently, the advent of high-throughput technology led to faster and more efficient ways of obtaining data about the transcriptome. Two biological techniques are used to study the transcriptome, namely DNA microarray, a hybridization-based technique and RNA-seq, a sequence-based approach. RNA-seq is the preferred method and has been the dominant transcriptomics technique since the 2010s. Single-cell transcriptomics allows tracking of transcript chang ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
NcRNA
A non-coding RNA (ncRNA) is a functional RNA molecule that is not translated into a protein. The DNA sequence from which a functional non-coding RNA is transcribed is often called an RNA gene. Abundant and functionally important types of non-coding RNAs include transfer RNAs (tRNAs) and ribosomal RNAs (rRNAs), as well as small RNAs such as microRNAs, siRNAs, piRNAs, snoRNAs, snRNAs, exRNAs, scaRNAs and the long ncRNAs such as Xist and HOTAIR. The number of non-coding RNAs within the human genome is unknown; however, recent transcriptomic and bioinformatic studies suggest that there are thousands of non-coding transcripts. Many of the newly identified ncRNAs have not been validated for their function. There is no consensus in the literature on how much of non-coding transcription is functional. Some researchers have argued that many ncRNAs are non-functional (sometimes referred to as "junk RNA"), spurious transcriptions. Others, however, disagree, arguing instead that ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
