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STARR-seq Methodology
STARR-seq (short for self-transcribing active regulatory region sequencing) is a method to assay enhancer activity for millions of candidates from arbitrary sources of DNA. It is used to identify the sequences that act as transcriptional enhancers in a direct, quantitative, and genome-wide manner. In eukaryotes, transcription is regulated by sequence-specific DNA-binding proteins (transcription factors) associated with a gene’s promoter and also by distant control sequences including enhancers. Enhancers are non-coding DNA sequences, containing several binding sites for a variety of transcription factors. They typically recruit transcriptional factors that modulate chromatin structure and directly interact with the transcription machinery placed at the promoter of a gene. Enhancers are able to regulate transcription of target genes in a cell type-specific manner, independent of their location or distance from the promoter of genes. In certain contexts (see Transvection (genetic ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
STARR-seq Methodology
STARR-seq (short for self-transcribing active regulatory region sequencing) is a method to assay enhancer activity for millions of candidates from arbitrary sources of DNA. It is used to identify the sequences that act as transcriptional enhancers in a direct, quantitative, and genome-wide manner. In eukaryotes, transcription is regulated by sequence-specific DNA-binding proteins (transcription factors) associated with a gene’s promoter and also by distant control sequences including enhancers. Enhancers are non-coding DNA sequences, containing several binding sites for a variety of transcription factors. They typically recruit transcriptional factors that modulate chromatin structure and directly interact with the transcription machinery placed at the promoter of a gene. Enhancers are able to regulate transcription of target genes in a cell type-specific manner, independent of their location or distance from the promoter of genes. In certain contexts (see Transvection (genetic ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
RNAs
The Royal Naval Air Service (RNAS) was the air arm of the Royal Navy, under the direction of the Admiralty's Air Department, and existed formally from 1 July 1914 to 1 April 1918, when it was merged with the British Army's Royal Flying Corps to form the Royal Air Force (RAF), the world's first independent air force. It was replaced by the Fleet Air Arm, initially consisting of those RAF units that normally operated from ships, but emerging as a separate unit similar to the original RNAS by the time of World War 2. Background In 1908, the British Government recognised the military potential of aircraft. The Prime Minister, H. H. Asquith, approved the formation of an "Advisory Committee for Aeronautics" and an "Aerial Sub-Committee of the Committee of Imperial Defence". Both committees were composed of politicians, army officers and Royal Navy officers. On 21 July 1908 Captain Reginald Bacon, who was a member of the Aerial Navigation sub-committee, submitted to the First Sea L ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Expression Quantitative Trait Loci
Expression quantitative trait loci (eQTLs) are genomic loci that explain variation in expression levels of mRNAs. Distant and local, trans- and cis-eQTLs, respectively An expression quantitative trait is an amount of an mRNA transcript or a protein. These are usually the product of a single gene with a specific chromosomal location. This distinguishes expression quantitative traits from most complex traits, which are not the product of the expression of a single gene. Chromosomal loci that explain variance in expression traits are called eQTLs. eQTLs located near the gene-of-origin (gene which produces the transcript or protein) are referred to as local eQTLs or cis-eQTLs. By contrast, those located distant from their gene of origin, often on different chromosomes, are referred to as distant eQTLs or trans-eQTLs. The first genome-wide study of gene expression was carried out in yeast and published in 2002. The initial wave of eQTL studies employed microarrays to measure genome ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Ribosomal Protein
A ribosomal protein (r-protein or rProtein) is any of the proteins that, in conjunction with rRNA, make up the ribosomal subunits involved in the cellular process of translation. ''E. coli'', other bacteria and Archaea have a 30S small subunit and a 50S large subunit, whereas humans and yeasts have a 40S small subunit and a 60S large subunit. Equivalent subunits are frequently numbered differently between bacteria, Archaea, yeasts and humans. A large part of the knowledge about these organic molecules has come from the study of '' E. coli'' ribosomes. All ribosomal proteins have been isolated and many specific antibodies have been produced. These, together with electronic microscopy and the use of certain reactives, have allowed for the determination of the topography of the proteins in the ribosome. More recently, a near-complete (near)atomic picture of the ribosomal proteins is emerging from the latest high-resolution cryo-EM data (including ). Conservation Ribosomal prot ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Neuropeptide
Neuropeptides are chemical messengers made up of small chains of amino acids that are synthesized and released by neurons. Neuropeptides typically bind to G protein-coupled receptors (GPCRs) to modulate neural activity and other tissues like the gut, muscles, and heart. There are over 100 known neuropeptides, representing the largest and most diverse class of signaling molecules in the nervous system. Neuropeptides are synthesized from large precursor proteins which are cleaved and post-translationally processed then packaged into dense core vesicles. Neuropeptides are often co-released with other neuropeptides and neurotransmitters in a single neuron, yielding a multitude of effects. Once released, neuropeptides can diffuse widely to affect a broad range of targets. Synthesis Neuropeptides are synthesized from large, inactive precursor proteins called prepropeptides. Prepropeptides contain sequences for a family of distinct peptides and often contain repeated copies of the sa ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Cytoskeleton
The cytoskeleton is a complex, dynamic network of interlinking protein filaments present in the cytoplasm of all cells, including those of bacteria and archaea. In eukaryotes, it extends from the cell nucleus to the cell membrane and is composed of similar proteins in the various organisms. It is composed of three main components, microfilaments, intermediate filaments and microtubules, and these are all capable of rapid growth or disassembly dependent on the cell's requirements. A multitude of functions can be performed by the cytoskeleton. Its primary function is to give the cell its shape and mechanical resistance to deformation, and through association with extracellular connective tissue and other cells it stabilizes entire tissues. The cytoskeleton can also contract, thereby deforming the cell and the cell's environment and allowing cells to migrate. Moreover, it is involved in many cell signaling pathways and in the uptake of extracellular material ( endocytosis), the ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Housekeeping Genes
In molecular biology, housekeeping genes are typically constitutive genes that are required for the maintenance of basic cellular function, and are expressed in all cells of an organism under normal and patho-physiological conditions. Although some housekeeping genes are expressed at relatively constant rates in most non-pathological situations, the expression of other housekeeping genes may vary depending on experimental conditions. The origin of the term "housekeeping gene" remains obscure. Literature from 1976 used the term to describe specifically tRNA and rRNA. For experimental purposes, the expression of one or multiple housekeeping genes is used as a reference point for the analysis of expression levels of other genes. The key criterion for the use of a housekeeping gene in this manner is that the chosen housekeeping gene is uniformly expressed with low variance under both control and experimental conditions. Validation of housekeeping genes should be performed before th ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Transcription Start Site
Transcription is the process of copying a segment of DNA into RNA. The segments of DNA transcribed into RNA molecules that can encode proteins are said to produce messenger RNA (mRNA). Other segments of DNA are copied into RNA molecules called non-coding RNAs (ncRNAs). mRNA comprises only 1–3% of total RNA samples. Less than 2% of the human genome can be transcribed into mRNA ( Human genome#Coding vs. noncoding DNA), while at least 80% of mammalian genomic DNA can be actively transcribed (in one or more types of cells), with the majority of this 80% considered to be ncRNA. Both DNA and RNA are nucleic acids, which use base pairs of nucleotides as a complementary language. During transcription, a DNA sequence is read by an RNA polymerase, which produces a complementary, antiparallel RNA strand called a primary transcript. Transcription proceeds in the following general steps: # RNA polymerase, together with one or more general transcription factors, binds to promoter DNA ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Intergenic Region
An intergenic region is a stretch of DNA sequences located between genes. Intergenic regions may contain functional elements and junk DNA. ''Inter''genic regions should not be confused with ''intra''genic regions (or introns), which are non-coding regions that are found ''within'' genes, especially within the genes of eukaryotic organisms. Properties and functions Intergenic regions may contain a number of functional DNA sequences such as promoters and regulatory elements, enhancers, spacers, and (in eukaryotes) centromeres. They may also contain origins of replication, scaffold attachment regions, and transposons and viruses. Non-functional DNA elements such as pseudogenes and repetitive DNA, both of which are types of junk DNA, can also be found in intergenic regions—although they may also be located within genes in introns. As all scientific knowledge is ultimately tentative—and in principle subject to revision given better evidence—it is possible s ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Introns
An intron is any nucleotide sequence within a gene that is not expressed or operative in the final RNA product. The word ''intron'' is derived from the term ''intragenic region'', i.e. a region inside a gene."The notion of the cistron .e., gene... must be replaced by that of a transcription unit containing regions which will be lost from the mature messenger – which I suggest we call introns (for intragenic regions) – alternating with regions which will be expressed – exons." (Gilbert 1978) The term ''intron'' refers to both the DNA sequence within a gene and the corresponding RNA sequence in RNA transcripts. The non-intron sequences that become joined by this RNA processing to form the mature RNA are called exons. Introns are found in the genes of most organisms and many viruses and they can be located in both protein-coding genes and genes that function as RNA (noncoding genes). There are four main types of introns: tRNA introns, group I introns, group II introns, and s ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Reference Genome
A reference genome (also known as a reference assembly) is a digital nucleic acid sequence database, assembled by scientists as a representative example of the set of genes in one idealized individual organism of a species. As they are assembled from the sequencing of DNA from a number of individual donors, reference genomes do not accurately represent the set of genes of any single individual organism. Instead a reference provides a haploid mosaic of different DNA sequences from each donor. For example, the most recent human reference genome (assembly '' GRCh38/hg38'') is derived from >60 genomic clone libraries. There are reference genomes for multiple species of viruses, bacteria, fungus, plants, and animals. Reference genomes are typically used as a guide on which new genomes are built, enabling them to be assembled much more quickly and cheaply than the initial Human Genome Project. Reference genomes can be accessed online at several locations, using dedicated browsers s ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Paired End Sequencing
In genetics, shotgun sequencing is a method used for sequencing random DNA strands. It is named by analogy with the rapidly expanding, quasi-random shot grouping of a shotgun. The chain-termination method of DNA sequencing ("Sanger sequencing") can only be used for short DNA strands of 100 to 1000 base pairs. Due to this size limit, longer sequences are subdivided into smaller fragments that can be sequenced separately, and these sequences are assembled to give the overall sequence. In shotgun sequencing, DNA is broken up randomly into numerous small segments, which are sequenced using the chain termination method to obtain ''reads''. Multiple overlapping reads for the target DNA are obtained by performing several rounds of this fragmentation and sequencing. Computer programs then use the overlapping ends of different reads to assemble them into a continuous sequence. Shotgun sequencing was one of the precursor technologies that was responsible for enabling whole genome seq ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
