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RNA Polymerase I
RNA polymerase 1 (also known as Pol I) is, in higher eukaryotes, the polymerase that only transcribes ribosomal RNA (but not 5S rRNA, which is synthesized by RNA polymerase III), a type of RNA that accounts for over 50% of the total RNA synthesized in a cell. Structure and function Pol I is a 590 kDa enzyme that consists of 14 protein subunits (polypeptides), and its crystal structure in the yeast ''Saccharomyces cerevisiae'' was solved at 2.8Å resolution in 2013. Twelve of its subunits have identical or related counterparts in RNA polymerase II (Pol II) and RNA polymerase III (Pol III). The other two subunits are related to Pol II initiation factors and have structural homologues in Pol III. Ribosomal DNA transcription is confined to the nucleolus, where about 400 copies of the 42.9-kb rDNA gene are present, arranged as tandem repeats in nucleolus organizer regions. Each copy contains a ~13.3 kb sequence encoding the 18S ribosomal RNA, 18S, the 5.8S, and the 28S RNA molecul ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Eukaryotes
Eukaryotes () are organisms whose cells have a nucleus. All animals, plants, fungi, and many unicellular organisms, are Eukaryotes. They belong to the group of organisms Eukaryota or Eukarya, which is one of the three domains of life. Bacteria and Archaea (both prokaryotes) make up the other two domains. The eukaryotes are usually now regarded as having emerged in the Archaea or as a sister of the Asgard archaea. This implies that there are only two domains of life, Bacteria and Archaea, with eukaryotes incorporated among archaea. Eukaryotes represent a small minority of the number of organisms, but, due to their generally much larger size, their collective global biomass is estimated to be about equal to that of prokaryotes. Eukaryotes emerged approximately 2.3–1.8 billion years ago, during the Proterozoic eon, likely as flagellated phagotrophs. Their name comes from the Greek εὖ (''eu'', "well" or "good") and κάρυον (''karyon'', "nut" or "kernel"). Eu ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
28S Ribosomal RNA
28S ribosomal RNA is the structural ribosomal RNA (rRNA) for the large subunit (LSU) of eukaryotic cytoplasmic ribosomes, and thus one of the basic components of all eukaryotic cells. It has a size of 25S in plants and 28S in mammals, hence the alias of 25S–28S rRNA. Combined with 5.8S rRNA to the 5' side, it is the eukaryotic nuclear homologue of the prokaryotic 23S and mitochondrial 16S ribosomal RNAs. Use in phylogeny The genes coding for 28S rRNA are referred to as 28S rDNA. The comparison of the sequences from these genes are sometimes used in molecular analysis to construct phylogenetic trees, for example in protists, fungi, insects, arachnids, tardigrades, and vertebrates. Structure The 28S rRNA is typically 4000–5000 nt long. Some eukaryotes cleave 28S rRNA into two parts before assembling both into the ribosome, a phenomenon termed the "hidden break". Databases Several databases provide alignments and annotations of LSU rRNA sequences for comparati ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Nucleosome
A nucleosome is the basic structural unit of DNA packaging in eukaryotes. The structure of a nucleosome consists of a segment of DNA wound around eight histone proteins and resembles thread wrapped around a spool. The nucleosome is the fundamental subunit of chromatin. Each nucleosome is composed of a little less than two turns of DNA wrapped around a set of eight proteins called histones, which are known as a histone octamer. Each histone octamer is composed of two copies each of the histone proteins H2A, H2B, H3, and H4. DNA must be compacted into nucleosomes to fit within the cell nucleus. In addition to nucleosome wrapping, eukaryotic chromatin is further compacted by being folded into a series of more complex structures, eventually forming a chromosome. Each human cell contains about 30 million nucleosomes. Nucleosomes are thought to carry epigenetically inherited information in the form of covalent modifications of their core histones. Nucleosome positions in the gen ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
RRN3
RNA polymerase I-specific transcription initiation factor RRN3 is an enzyme that in humans is encoded by the ''RRN3'' gene. Interactions RRN3 has been shown to interact with TAF1B TATA box-binding protein-associated factor RNA polymerase I subunit B is an enzyme that in humans is encoded by the ''TAF1B'' gene. Function Initiation of transcription by RNA polymerase I requires the formation of a complex composed of the TAT .... References Further reading * * * * * * * * {{gene-16-stub ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
HMG-box
In molecular biology, the HMG-box (high mobility group box) is a protein domain which is involved in DNA binding. Structure The structure of the HMG-box domain contains three alpha helices separated by loops (see figure to the right). Function HMG-box containing proteins only bind non- B-type DNA conformations (kinked or unwound) with high affinity. HMG-box domains are found in some high mobility group proteins, which are involved in the regulation of DNA-dependent processes such as transcription, replication, and DNA repair, all of which require changing the conformation of chromatin Chromatin is a complex of DNA and protein found in eukaryotic cells. The primary function is to package long DNA molecules into more compact, denser structures. This prevents the strands from becoming tangled and also plays important roles in r .... The single and the double box HMG proteins alter DNA architecture by inducing bends upon binding.D. Murugesapillai ''et al''Single-molecule stud ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
TBP-associated Factor
The TBP-associated factors (TAF) are proteins that associate with the TATA-binding protein in transcription initiation. It is a part of the transcription initiation factor TFIID multimeric protein complex. It also makes up many other factors, including SL1. They mediate the formation of the transcription preinitiation complex, a step preceding transcription of DNA to RNA by RNA polymerase II. TAFs have a signature N-terminal histone-like fold domain (HFD). This domain is implicated in the pairwise interaction among specific TAFs. Function TFIID TFIID plays a central role in mediating promoter responses to various activators and repressors. It binds tightly to TAFII-250 and directly interacts with TAFII-40. TFIID is composed of TATA binding protein (TBP) and a number of TBP-associated factors (TAFS). TAF is part of the TFIID complex, and interacts with the following: * Specific transcriptional activators * Basal transcription factors * Other TAFIIs * Specific DNA sequences, ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
TATA-binding Protein
The TATA-binding protein (TBP) is a general transcription factor that binds specifically to a DNA sequence called the TATA box. This DNA sequence is found about 30 base pairs upstream of the transcription start site in some eukaryotic gene promoters. TBP gene family TBP is a member of a small gene family of TBP-related factors. The first TBP-related factor (TRF/TRF1) was identified in the fruit fly Drosophila, but appears to be fly or insect-specific. Subsequently TBPL1/TRF2 was found in the genomes of many metazoans, whereas vertebrate genomes encode a third vertebrate family member, TBPL2/TRF3. In specific cell types or on specific promoters TBP can be replaced by one of these TBP-related factors, some of which interact with the TATA box similarly to TBP. Role as transcription factor TBP is a subunit of the eukaryotic general transcription factor TFIID. TFIID is the first protein to bind to DNA during the formation of the transcription preinitiation complex of RNA po ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Selective Factor 1
Selective factor 1 (also known as SL1) is a transcription factor that binds to the promoter of genes and recruits a preinitiation complex to which RNA polymerase I will bind to and begin the transcription of ribosomal RNA (rRNA). Discovery SL1 was discovered by Robert Tjian and his colleagues in 1985 when they separated a HeLa cell extract into two functional fractions. One factor has RNA polymerase I activity, but no ability to initiate accurate transcription of a human rRNA template. This transcription factor, SL1, showed species specificity. That is, it could distinguish between the human and mouse rRNA promoter, and added increasing amount of human template at the expense of the mice template. Tijian and coworkers went on to show that by footprinting a partially purified polymerase 1 preparation could bind to the human rRNA promoter. In particular it causes a footprint over a region of the UCE called ''A site''. This binding is not due to polymerase I itself but to a transc ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
UBTF
Nucleolar transcription factor 1 is a protein that in humans is encoded by the ''UBTF'' gene. Function Upstream binding factor (UBF) is a transcription factor required for expression of the 18S, 5.8S, and 28S ribosomal RNAs, along with SL1 (a complex of TBP (MIM 600075) and three TBP-associated factors or 'TAFs'). Two UBF polypeptides, of 94 and 97 kD, exist in the human (Bell et al., 1988). UBF is a nucleolar phosphoprotein with both DNA binding and transactivation domains. Sequence-specific DNA binding to the core and upstream control elements of the human rRNA promoter is mediated through several HMG boxes (Jantzen et al., 1990). upplied by OMIMref name="entrez" /> Interactions UBTF has been shown to interact with: * CSNK2A1, * RB1, * TAF1C, and * TAF1 Transcription initiation factor TFIID subunit 1, also known as transcription initiation factor TFIID 250 kDa subunit (TAFII-250) or TBP-associated factor 250 kDa (p250), is a protein that in humans is encoded by the ' ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
TATA Box
In molecular biology, the TATA box (also called the Goldberg–Hogness box) is a sequence of DNA found in the core promoter region of genes in archaea and eukaryotes. The bacterial homolog of the TATA box is called the Pribnow box which has a shorter consensus sequence. The TATA box is considered a non-coding DNA sequence (also known as a cis-regulatory element). It was termed the "TATA box" as it contains a consensus sequence characterized by repeating T and A base pairs. How the term "box" originated is unclear. In the 1980s, while investigating nucleotide sequences in mouse genome loci, the Hogness box sequence was found and "boxed in" at the -31 position. When consensus nucleotides and alternative ones were compared, homologous regions were "boxed" by the researchers. The boxing in of sequences sheds light on the origin of the term "box". The TATA box was first identified in 1978 as a component of eukaryotic promoters. Transcription is initiated at the TATA box in TAT ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Transcription Factors
In molecular biology, a transcription factor (TF) (or sequence-specific DNA-binding factor) is a protein that controls the rate of transcription of genetic information from DNA to messenger RNA, by binding to a specific DNA sequence. The function of TFs is to regulate—turn on and off—genes in order to make sure that they are expressed in the desired cells at the right time and in the right amount throughout the life of the cell and the organism. Groups of TFs function in a coordinated fashion to direct cell division, cell growth, and cell death throughout life; cell migration and organization (body plan) during embryonic development; and intermittently in response to signals from outside the cell, such as a hormone. There are up to 1600 TFs in the human genome. Transcription factors are members of the proteome as well as regulome. TFs work alone or with other proteins in a complex, by promoting (as an activator), or blocking (as a repressor) the recruitment of RNA po ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Promoter (biology)
In genetics, a promoter is a sequence of DNA to which proteins bind to initiate transcription of a single RNA transcript from the DNA downstream of the promoter. The RNA transcript may encode a protein (mRNA), or can have a function in and of itself, such as tRNA or rRNA. Promoters are located near the transcription start sites of genes, upstream on the DNA (towards the 5' region of the sense strand). Promoters can be about 100–1000 base pairs long, the sequence of which is highly dependent on the gene and product of transcription, type or class of RNA polymerase recruited to the site, and species of organism. Promoters control gene expression in bacteria and eukaryotes. RNA polymerase must attach to DNA near a gene for transcription to occur. Promoter DNA sequences provide an enzyme binding site. The -10 sequence is TATAAT. -35 sequences are conserved on average, but not in most promoters. Artificial promoters with conserved -10 and -35 elements transcribe more slowly. All D ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
