Transcription is the process of copying a segment of DNA into RNA. Some segments of DNA are transcribed into RNA molecules that can encode proteins , called messenger RNA (mRNA). Other segments of DNA are transcribed into RNA molecules called non-coding RNAs (ncRNAs).
84-408: 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 . In virology , the term transcription is used when referring to mRNA synthesis from a viral RNA molecule. The genome of many RNA viruses
168-416: A purine or pyrimidine nucleobase (sometimes termed nitrogenous base or simply base ), a pentose sugar , and a phosphate group which makes the molecule acidic. The substructure consisting of a nucleobase plus sugar is termed a nucleoside . Nucleic acid types differ in the structure of the sugar in their nucleotides–DNA contains 2'- deoxyribose while RNA contains ribose (where the only difference
252-474: A CpG island while only about 6% of enhancer sequences have a CpG island. CpG islands constitute regulatory sequences, since if CpG islands are methylated in the promoter of a gene this can reduce or silence gene transcription. DNA methylation regulates gene transcription through interaction with methyl binding domain (MBD) proteins, such as MeCP2, MBD1 and MBD2. These MBD proteins bind most strongly to highly methylated CpG islands . These MBD proteins have both
336-448: A DNA complement. Only one of the two DNA strands serves as a template for transcription. The antisense strand of DNA is read by RNA polymerase from the 3' end to the 5' end during transcription (3' → 5'). The complementary RNA is created in the opposite direction, in the 5' → 3' direction, matching the sequence of the sense strand except switching uracil for thymine. This directionality is because RNA polymerase can only add nucleotides to
420-412: A human cell) generally bind to specific motifs on an enhancer and a small combination of these enhancer-bound transcription factors, when brought close to a promoter by a DNA loop, govern level of transcription of the target gene. Mediator (a complex usually consisting of about 26 proteins in an interacting structure) communicates regulatory signals from enhancer DNA-bound transcription factors directly to
504-471: A methyl-CpG-binding domain as well as a transcription repression domain. They bind to methylated DNA and guide or direct protein complexes with chromatin remodeling and/or histone modifying activity to methylated CpG islands. MBD proteins generally repress local chromatin such as by catalyzing the introduction of repressive histone marks, or creating an overall repressive chromatin environment through nucleosome remodeling and chromatin reorganization. As noted in
588-540: A promoter. (RNA polymerase is called a holoenzyme when sigma subunit is attached to the core enzyme which is consist of 2 α subunits, 1 β subunit, 1 β' subunit only). Unlike eukaryotes, the initiating nucleotide of nascent bacterial mRNA is not capped with a modified guanine nucleotide. The initiating nucleotide of bacterial transcripts bears a 5′ triphosphate (5′-PPP), which can be used for genome-wide mapping of transcription initiation sites. In archaea and eukaryotes , RNA polymerase contains subunits homologous to each of
672-464: A recent study, it has been shown that, in addition to demarcating TADs , CTCF mediates promoter–enhancer loops, often located in promoter-proximal regions, to facilitate the promoter–enhancer interactions within one TAD. This is in line with the concept that a subpopulation of CTCF associates with the RNA polymerase II (Pol II) protein complex to activate transcription. It is likely that CTCF helps to bridge
756-526: A regular double helix, and can adopt highly complex three-dimensional structures that are based on short stretches of intramolecular base-paired sequences including both Watson-Crick and noncanonical base pairs, and a wide range of complex tertiary interactions. Nucleic acid molecules are usually unbranched and may occur as linear and circular molecules. For example, bacterial chromosomes, plasmids , mitochondrial DNA , and chloroplast DNA are usually circular double-stranded DNA molecules, while chromosomes of
840-620: A single copy of a gene. The characteristic elongation rates in prokaryotes and eukaryotes are about 10–100 nts/sec. In eukaryotes, however, nucleosomes act as major barriers to transcribing polymerases during transcription elongation. In these organisms, the pausing induced by nucleosomes can be regulated by transcription elongation factors such as TFIIS. Elongation also involves a proofreading mechanism that can replace incorrectly incorporated bases. In eukaryotes, this may correspond with short pauses during transcription that allow appropriate RNA editing factors to bind. These pauses may be intrinsic to
924-462: A study of brain cortical neurons, 24,937 loops were found, bringing enhancers to their target promoters. Multiple enhancers, each often at tens or hundred of thousands of nucleotides distant from their target genes, loop to their target gene promoters and can coordinate with each other to control transcription of their common target gene. The schematic illustration in this section shows an enhancer looping around to come into close physical proximity with
SECTION 10
#17328022109641008-414: Is rifampicin , which inhibits bacterial transcription of DNA into mRNA by inhibiting DNA-dependent RNA polymerase by binding its beta-subunit, while 8-hydroxyquinoline is an antifungal transcription inhibitor. The effects of histone methylation may also work to inhibit the action of transcription. Potent, bioactive natural products like triptolide that inhibit mammalian transcription via inhibition of
1092-486: Is a transcription factor that in humans is encoded by the CTCF gene . CTCF is involved in many cellular processes, including transcriptional regulation , insulator activity, V(D)J recombination and regulation of chromatin architecture. CCCTC-Binding factor or CTCF was initially discovered as a negative regulator of the chicken c-myc gene. This protein was found to be binding to three regularly spaced repeats of
1176-407: Is a particular transcription factor that is important for regulation of methylation of CpG islands. An EGR1 transcription factor binding site is frequently located in enhancer or promoter sequences. There are about 12,000 binding sites for EGR1 in the mammalian genome and about half of EGR1 binding sites are located in promoters and half in enhancers. The binding of EGR1 to its target DNA binding site
1260-528: Is a single molecule that contains 247 million base pairs ). In most cases, naturally occurring DNA molecules are double-stranded and RNA molecules are single-stranded. There are numerous exceptions, however—some viruses have genomes made of double-stranded RNA and other viruses have single-stranded DNA genomes, and, in some circumstances, nucleic acid structures with three or four strands can form. Nucleic acids are linear polymers (chains) of nucleotides. Each nucleotide consists of three components:
1344-546: Is also altered in response to signals. The three mammalian DNA methyltransferasess (DNMT1, DNMT3A, and DNMT3B) catalyze the addition of methyl groups to cytosines in DNA. While DNMT1 is a maintenance methyltransferase, DNMT3A and DNMT3B can carry out new methylations. There are also two splice protein isoforms produced from the DNMT3A gene: DNA methyltransferase proteins DNMT3A1 and DNMT3A2. The splice isoform DNMT3A2 behaves like
1428-439: Is composed of negative-sense RNA which acts as a template for positive sense viral messenger RNA - a necessary step in the synthesis of viral proteins needed for viral replication . This process is catalyzed by a viral RNA dependent RNA polymerase . A DNA transcription unit encoding for a protein may contain both a coding sequence , which will be translated into the protein, and regulatory sequences , which direct and regulate
1512-570: Is distinguished from naturally occurring DNA or RNA by changes to the backbone of the molecules. CTCF 1X6H , 2CT1 10664 13018 ENSG00000102974 ENSMUSG00000005698 P49711 Q61164 NM_001191022 NM_006565 NM_001363916 NM_181322 NM_001358924 NP_001177951 NP_006556 NP_001350845 NP_001390655 NP_001390656 NP_001390657 NP_001390658 NP_001390659 NP_001390660 NP_001390661 Transcriptional repressor CTCF also known as 11-zinc finger protein or CCCTC-binding factor
1596-652: Is followed by 3' guanine or CpG sites ). 5-methylcytosine (5-mC) is a methylated form of the DNA base cytosine (see Figure). 5-mC is an epigenetic marker found predominantly within CpG sites. About 28 million CpG dinucleotides occur in the human genome. In most tissues of mammals, on average, 70% to 80% of CpG cytosines are methylated (forming 5-methylCpG or 5-mCpG). However, unmethylated cytosines within 5'cytosine-guanine 3' sequences often occur in groups, called CpG islands , at active promoters. About 60% of promoter sequences have
1680-476: Is insensitive to cytosine methylation in the DNA. While only small amounts of EGR1 transcription factor protein are detectable in cells that are un-stimulated, translation of the EGR1 gene into protein at one hour after stimulation is drastically elevated. Production of EGR1 transcription factor proteins, in various types of cells, can be stimulated by growth factors, neurotransmitters, hormones, stress and injury. In
1764-599: Is not yet known. One strand of the DNA, the template strand (or noncoding strand), is used as a template for RNA synthesis. As transcription proceeds, RNA polymerase traverses the template strand and uses base pairing complementarity with the DNA template to create an RNA copy (which elongates during the traversal). Although RNA polymerase traverses the template strand from 3' → 5', the coding (non-template) strand and newly formed RNA can also be used as reference points, so transcription can be described as occurring 5' → 3'. This produces an RNA molecule from 5' → 3', an exact copy of
SECTION 20
#17328022109641848-411: Is one of four types of molecules called nucleobases (informally, bases). It is the sequence of these four nucleobases along the backbone that encodes genetic information. This information specifies the sequence of the amino acids within proteins according to the genetic code . The code is read by copying stretches of DNA into the related nucleic acid RNA in a process called transcription. Within cells, DNA
1932-453: Is organized into long sequences called chromosomes. During cell division these chromosomes are duplicated in the process of DNA replication, providing each cell its own complete set of chromosomes. Eukaryotic organisms (animals, plants, fungi, and protists) store most of their DNA inside the cell nucleus and some of their DNA in organelles, such as mitochondria or chloroplasts. In contrast, prokaryotes (bacteria and archaea) store their DNA only in
2016-409: Is regulated by many cis-regulatory elements , including core promoter and promoter-proximal elements that are located near the transcription start sites of genes. Core promoters combined with general transcription factors are sufficient to direct transcription initiation, but generally have low basal activity. Other important cis-regulatory modules are localized in DNA regions that are distant from
2100-426: Is synthesized, at which point promoter escape occurs and a transcription elongation complex is formed. Mechanistically, promoter escape occurs through DNA scrunching , providing the energy needed to break interactions between RNA polymerase holoenzyme and the promoter. In bacteria, it was historically thought that the sigma factor is definitely released after promoter clearance occurs. This theory had been known as
2184-561: Is the nucleotide , each of which contains a pentose sugar ( ribose or deoxyribose ), a phosphate group, and a nucleobase . Nucleic acids are also generated within the laboratory, through the use of enzymes (DNA and RNA polymerases) and by solid-phase chemical synthesis . Nucleic acids are generally very large molecules. Indeed, DNA molecules are probably the largest individual molecules known. Well-studied biological nucleic acid molecules range in size from 21 nucleotides ( small interfering RNA ) to large chromosomes ( human chromosome 1
2268-480: Is the presence of a hydroxyl group ). Also, the nucleobases found in the two nucleic acid types are different: adenine , cytosine , and guanine are found in both RNA and DNA, while thymine occurs in DNA and uracil occurs in RNA. The sugars and phosphates in nucleic acids are connected to each other in an alternating chain (sugar-phosphate backbone) through phosphodiester linkages. In conventional nomenclature ,
2352-563: Is unknown if CTCF directly evokes the outcome or if it does so indirectly (in particular through its looping role). The protein CTCF plays a heavy role in repressing the insulin-like growth factor 2 gene, by binding to the H-19 imprinting control region (ICR) along with differentially-methylated region-1 ( DMR1 ) and MAR3 . Binding of targeting sequence elements by CTCF can block the interaction between enhancers and promoters, therefore limiting
2436-462: The Mfd ATPase can remove a RNA polymerase stalled at a lesion by prying open its clamp. It also recruits nucleotide excision repair machinery to repair the lesion. Mfd is proposed to also resolve conflicts between DNA replication and transcription. In eukayrotes, ATPase TTF2 helps to suppress the action of RNAP I and II during mitosis , preventing errors in chromosomal segregation. In archaea,
2520-484: The University of Tübingen , Germany. He discovered a new substance, which he called nuclein and which - depending on how his results are interpreted in detail - can be seen in modern terms either as a nucleid acid- histone complex or as the actual nucleid acid. Phoeber Aaron Theodor Levene, an American biochemist determined the basic structure of nucleic acids. In the early 1880s, Albrecht Kossel further purified
2604-744: The consensus sequence CCGCGNGGNGGCAG (in IUPAC notation ). This sequence is defined by 11 zinc finger motifs in its structure. CTCF's binding is disrupted by CpG methylation of the DNA it binds to. On the other hand, CTCF binding may set boundaries for the spreading of DNA methylation. In recent studies, CTCF binding loss is reported to increase localized CpG methylation, which reflected another epigenetic remodeling role of CTCF in human genome. CTCF binds to an average of about 55,000 DNA sites in 19 diverse cell types (12 normal and 7 immortal) and in total 77,811 distinct binding sites across all 19 cell types. CTCF's ability to bind to multiple sequences through
Transcription (biology) - Misplaced Pages Continue
2688-574: The nucleus , and for the presence of phosphate groups (related to phosphoric acid). Although first discovered within the nucleus of eukaryotic cells, nucleic acids are now known to be found in all life forms including within bacteria , archaea , mitochondria , chloroplasts , and viruses (There is debate as to whether viruses are living or non-living ). All living cells contain both DNA and RNA (except some cells such as mature red blood cells), while viruses contain either DNA or RNA, but usually not both. The basic component of biological nucleic acids
2772-495: The obligate release model. However, later data showed that upon and following promoter clearance, the sigma factor is released according to a stochastic model known as the stochastic release model . In eukaryotes, at an RNA polymerase II-dependent promoter, upon promoter clearance, TFIIH phosphorylates serine 5 on the carboxy terminal domain of RNA polymerase II, leading to the recruitment of capping enzyme (CE). The exact mechanism of how CE induces promoter clearance in eukaryotes
2856-599: The sequence of nucleotides . Nucleotide sequences are of great importance in biology since they carry the ultimate instructions that encode all biological molecules, molecular assemblies, subcellular and cellular structures, organs, and organisms, and directly enable cognition, memory, and behavior. Enormous efforts have gone into the development of experimental methods to determine the nucleotide sequence of biological DNA and RNA molecules, and today hundreds of millions of nucleotides are sequenced daily at genome centers and smaller laboratories worldwide. In addition to maintaining
2940-463: The sugar is ribose , the polymer is RNA; if the sugar is deoxyribose , a variant of ribose, the polymer is DNA. Nucleic acids are chemical compounds that are found in nature. They carry information in cells and make up genetic material. These acids are very common in all living things, where they create, encode, and store information in every living cell of every life-form on Earth. In turn, they send and express that information inside and outside
3024-477: The 3' end of the growing mRNA chain. This use of only the 3' → 5' DNA strand eliminates the need for the Okazaki fragments that are seen in DNA replication. This also removes the need for an RNA primer to initiate RNA synthesis, as is the case in DNA replication. The non -template (sense) strand of DNA is called the coding strand , because its sequence is the same as the newly created RNA transcript (except for
3108-604: The BRCA1 promoter (see Low expression of BRCA1 in breast and ovarian cancers ). Active transcription units are clustered in the nucleus, in discrete sites called transcription factories or euchromatin . Such sites can be visualized by allowing engaged polymerases to extend their transcripts in tagged precursors (Br-UTP or Br-U) and immuno-labeling the tagged nascent RNA. Transcription factories can also be localized using fluorescence in situ hybridization or marked by antibodies directed against polymerases. There are ~10,000 factories in
3192-527: The Eta ATPase is proposed to play a similar role. Genome damage occurs with a high frequency, estimated to range between tens and hundreds of thousands of DNA damages arising in each cell every day. The process of transcription is a major source of DNA damage, due to the formation of single-strand DNA intermediates that are vulnerable to damage. The regulation of transcription by processes using base excision repair and/or topoisomerases to cut and remodel
3276-579: The GenBank nucleic acid sequence database, the National Center for Biotechnology Information (NCBI) provides analysis and retrieval resources for the data in GenBank and other biological data made available through the NCBI web site. Deoxyribonucleic acid (DNA) is a nucleic acid containing the genetic instructions used in the development and functioning of all known living organisms. The chemical DNA
3360-504: The RNA polymerase II (pol II) enzyme bound to the promoter. Enhancers, when active, are generally transcribed from both strands of DNA with RNA polymerases acting in two different directions, producing two enhancer RNAs (eRNAs) as illustrated in the Figure. An inactive enhancer may be bound by an inactive transcription factor. Phosphorylation of the transcription factor may activate it and that activated transcription factor may then activate
3444-399: The RNA polymerase and one or more general transcription factors binding to a DNA promoter sequence to form an RNA polymerase-promoter closed complex. In the closed complex, the promoter DNA is still fully double-stranded. RNA polymerase, assisted by one or more general transcription factors, then unwinds approximately 14 base pairs of DNA to form an RNA polymerase-promoter open complex. In
Transcription (biology) - Misplaced Pages Continue
3528-650: The RNA polymerase or due to chromatin structure. Double-strand breaks in actively transcribed regions of DNA are repaired by homologous recombination during the S and G2 phases of the cell cycle . Since transcription enhances the accessibility of DNA to exogenous chemicals and internal metabolites that can cause recombinogenic lesions, homologous recombination of a particular DNA sequence may be strongly stimulated by transcription. Bacteria use two different strategies for transcription termination – Rho-independent termination and Rho-dependent termination. In Rho-independent transcription termination , RNA transcription stops when
3612-439: The RNA strand, and reverse transcriptase synthesises a complementary strand of DNA to form a double helix DNA structure (cDNA). The cDNA is integrated into the host cell's genome by the enzyme integrase , which causes the host cell to generate viral proteins that reassemble into new viral particles. In HIV, subsequent to this, the host cell undergoes programmed cell death, or apoptosis , of T cells . However, in other retroviruses,
3696-467: The RNA synthesized by these enzymes had properties that suggested the existence of an additional factor needed to terminate transcription correctly. Roger D. Kornberg won the 2006 Nobel Prize in Chemistry "for his studies of the molecular basis of eukaryotic transcription ". Transcription can be measured and detected in a variety of ways: Some viruses (such as HIV , the cause of AIDS ), have
3780-1100: The XPB subunit of the general transcription factor TFIIH has been recently reported as a glucose conjugate for targeting hypoxic cancer cells with increased glucose transporter production. In vertebrates, the majority of gene promoters contain a CpG island with numerous CpG sites . When many of a gene's promoter CpG sites are methylated the gene becomes inhibited (silenced). Colorectal cancers typically have 3 to 6 driver mutations and 33 to 66 hitchhiker or passenger mutations. However, transcriptional inhibition (silencing) may be of more importance than mutation in causing progression to cancer. For example, in colorectal cancers about 600 to 800 genes are transcriptionally inhibited by CpG island methylation (see regulation of transcription in cancer ). Transcriptional repression in cancer can also occur by other epigenetic mechanisms, such as altered production of microRNAs . In breast cancer, transcriptional repression of BRCA1 may occur more frequently by over-produced microRNA-182 than by hypermethylation of
3864-454: The ability to transcribe RNA into DNA. HIV has an RNA genome that is reverse transcribed into DNA. The resulting DNA can be merged with the DNA genome of the host cell. The main enzyme responsible for synthesis of DNA from an RNA template is called reverse transcriptase . In the case of HIV, reverse transcriptase is responsible for synthesizing a complementary DNA strand (cDNA) to the viral RNA genome. The enzyme ribonuclease H then digests
3948-461: The activity of enhancers to certain functional domains. Besides acting as enhancer blocking, CTCF can also act as a chromatin barrier by preventing the spread of heterochromatin structures. CTCF physically binds to itself to form homodimers, which causes the bound DNA to form loops. CTCF also occurs frequently at the boundaries of sections of DNA bound to the nuclear lamina . Using chromatin immuno-precipitation (ChIP) followed by ChIP-seq , it
4032-745: The brain, when neurons are activated, EGR1 proteins are up-regulated and they bind to (recruit) the pre-existing TET1 enzymes that are produced in high amounts in neurons. TET enzymes can catalyse demethylation of 5-methylcytosine. When EGR1 transcription factors bring TET1 enzymes to EGR1 binding sites in promoters, the TET enzymes can demethylate the methylated CpG islands at those promoters. Upon demethylation, these promoters can then initiate transcription of their target genes. Hundreds of genes in neurons are differentially expressed after neuron activation through EGR1 recruitment of TET1 to methylated regulatory sequences in their promoters. The methylation of promoters
4116-520: The carbons to which the phosphate groups attach are the 3'-end and the 5'-end carbons of the sugar. This gives nucleic acids directionality , and the ends of nucleic acid molecules are referred to as 5'-end and 3'-end. The nucleobases are joined to the sugars via an N -glycosidic linkage involving a nucleobase ring nitrogen ( N -1 for pyrimidines and N -9 for purines) and the 1' carbon of the pentose sugar ring. Non-standard nucleosides are also found in both RNA and DNA and usually arise from modification of
4200-446: The cell nucleus. From the inner workings of the cell to the young of a living thing, they contain and provide information via the nucleic acid sequence . This gives the RNA and DNA their unmistakable 'ladder-step' order of nucleotides within their molecules. Both play a crucial role in directing protein synthesis . Strings of nucleotides are bonded to form spiraling backbones and assembled into chains of bases or base-pairs selected from
4284-426: The coding strand (except that thymines are replaced with uracils , and the nucleotides are composed of a ribose (5-carbon) sugar whereas DNA has deoxyribose (one fewer oxygen atom) in its sugar-phosphate backbone). mRNA transcription can involve multiple RNA polymerases on a single DNA template and multiple rounds of transcription (amplification of particular mRNA), so many mRNA molecules can be rapidly produced from
SECTION 50
#17328022109644368-402: The core sequence CCCTC and thus was named CCCTC binding factor. The primary role of CTCF is thought to be in regulating the 3D structure of chromatin. CTCF binds together strands of DNA, thus forming chromatin loops, and anchors DNA to cellular structures like the nuclear lamina . It also defines the boundaries between active and heterochromatic DNA. Since the 3D structure of DNA influences
4452-621: The cytoplasm. Within the chromosomes, chromatin proteins such as histones compact and organize DNA. These compact structures guide the interactions between DNA and other proteins, helping control which parts of the DNA are transcribed. Ribonucleic acid (RNA) functions in converting genetic information from genes into the amino acid sequences of proteins. The three universal types of RNA include transfer RNA (tRNA), messenger RNA (mRNA), and ribosomal RNA (rRNA). Messenger RNA acts to carry genetic sequence information between DNA and ribosomes, directing protein synthesis and carries instructions from DNA in
4536-465: The double-helix structure of DNA . Experimental studies of nucleic acids constitute a major part of modern biological and medical research , and form a foundation for genome and forensic science , and the biotechnology and pharmaceutical industries . The term nucleic acid is the overall name for DNA and RNA, members of a family of biopolymers , and is a type of polynucleotide . Nucleic acids were named for their initial discovery within
4620-415: The enhancer to which it is bound (see small red star representing phosphorylation of transcription factor bound to enhancer in the illustration). An activated enhancer begins transcription of its RNA before activating transcription of messenger RNA from its target gene. Transcription regulation at about 60% of promoters is also controlled by methylation of cytosines within CpG dinucleotides (where 5' cytosine
4704-425: The eukaryotic nucleus are usually linear double-stranded DNA molecules. Most RNA molecules are linear, single-stranded molecules, but both circular and branched molecules can result from RNA splicing reactions. The total amount of pyrimidines in a double-stranded DNA molecule is equal to the total amount of purines. The diameter of the helix is about 20 Å . One DNA or RNA molecule differs from another primarily in
4788-526: The factor. A molecule that allows the genetic material to be realized as a protein was first hypothesized by François Jacob and Jacques Monod . Severo Ochoa won a Nobel Prize in Physiology or Medicine in 1959 for developing a process for synthesizing RNA in vitro with polynucleotide phosphorylase , which was useful for cracking the genetic code . RNA synthesis by RNA polymerase was established in vitro by several laboratories by 1965; however,
4872-632: The five primary, or canonical, nucleobases . RNA usually forms a chain of single bases, whereas DNA forms a chain of base pairs. The bases found in RNA and DNA are: adenine , cytosine , guanine , thymine , and uracil . Thymine occurs only in DNA and uracil only in RNA. Using amino acids and protein synthesis , the specific sequence in DNA of these nucleobase-pairs helps to keep and send coded instructions as genes . In RNA, base-pair sequencing helps to make new proteins that determine most chemical processes of all life forms. Nucleic acid was, partially, first discovered by Friedrich Miescher in 1869 at
4956-534: The five RNA polymerase subunits in bacteria and also contains additional subunits. In archaea and eukaryotes, the functions of the bacterial general transcription factor sigma are performed by multiple general transcription factors that work together. In archaea, there are three general transcription factors: TBP , TFB , and TFE . In eukaryotes, in RNA polymerase II -dependent transcription, there are six general transcription factors: TFIIA , TFIIB (an ortholog of archaeal TFB), TFIID (a multisubunit factor in which
5040-630: The genome also increases the vulnerability of DNA to damage. RNA polymerase plays a very crucial role in all steps including post-transcriptional changes in RNA. As shown in the image in the right it is evident that the CTD (C Terminal Domain) is a tail that changes its shape; this tail will be used as a carrier of splicing, capping and polyadenylation , as shown in the image on the left. Transcription inhibitors can be used as antibiotics against, for example, pathogenic bacteria ( antibacterials ) and fungi ( antifungals ). An example of such an antibacterial
5124-422: The genome that are major gene-regulatory elements. Enhancers control cell-type-specific gene transcription programs, most often by looping through long distances to come in physical proximity with the promoters of their target genes. While there are hundreds of thousands of enhancer DNA regions, for a particular type of tissue only specific enhancers are brought into proximity with the promoters that they regulate. In
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#17328022109645208-416: The host cell remains intact as the virus buds out of the cell. Nucleic acid Nucleic acids are large biomolecules that are crucial in all cells and viruses. They are composed of nucleotides , which are the monomer components: a 5-carbon sugar , a phosphate group and a nitrogenous base . The two main classes of nucleic acids are deoxyribonucleic acid (DNA) and ribonucleic acid (RNA). If
5292-580: The key subunit, TBP , is an ortholog of archaeal TBP), TFIIE (an ortholog of archaeal TFE), TFIIF , and TFIIH . The TFIID is the first component to bind to DNA due to binding of TBP, while TFIIH is the last component to be recruited. In archaea and eukaryotes, the RNA polymerase-promoter closed complex is usually referred to as the " preinitiation complex ". Transcription initiation is regulated by additional proteins, known as activators and repressors , and, in some cases, associated coactivators or corepressors , which modulate formation and function of
5376-538: The mRNA, thus releasing the newly synthesized mRNA from the elongation complex. Transcription termination in eukaryotes is less well understood than in bacteria, but involves cleavage of the new transcript followed by template-independent addition of adenines at its new 3' end, in a process called polyadenylation . Beyond termination by a terminator sequences (which is a part of a gene ), transcription may also need to be terminated when it encounters conditions such as DNA damage or an active replication fork . In bacteria,
5460-463: The newly synthesized RNA molecule forms a G-C-rich hairpin loop followed by a run of Us. When the hairpin forms, the mechanical stress breaks the weak rU-dA bonds, now filling the DNA–RNA hybrid. This pulls the poly-U transcript out of the active site of the RNA polymerase, terminating transcription. In Rho-dependent termination, Rho , a protein factor, destabilizes the interaction between the template and
5544-515: The nucleid acid substance and discovered its highly acidic properties. He later also identified the nucleobases . In 1889 Richard Altmann created the term nucleic acid – at that time DNA and RNA were not differentiated. In 1938 Astbury and Bell published the first X-ray diffraction pattern of DNA. In 1944 the Avery–MacLeod–McCarty experiment showed that DNA is the carrier of genetic information and in 1953 Watson and Crick proposed
5628-413: The nucleoplasm of a HeLa cell , among which are ~8,000 polymerase II factories and ~2,000 polymerase III factories. Each polymerase II factory contains ~8 polymerases. As most active transcription units are associated with only one polymerase, each factory usually contains ~8 different transcription units. These units might be associated through promoters and/or enhancers, with loops forming a "cloud" around
5712-515: The nucleus to ribosome . Ribosomal RNA reads the DNA sequence, and catalyzes peptide bond formation. Transfer RNA serves as the carrier molecule for amino acids to be used in protein synthesis, and is responsible for decoding the mRNA. In addition, many other classes of RNA are now known. Artificial nucleic acid analogues have been designed and synthesized. They include peptide nucleic acid , morpholino - and locked nucleic acid , glycol nucleic acid , and threose nucleic acid . Each of these
5796-412: The open complex, the promoter DNA is partly unwound and single-stranded. The exposed, single-stranded DNA is referred to as the "transcription bubble". RNA polymerase, assisted by one or more general transcription factors, then selects a transcription start site in the transcription bubble, binds to an initiating NTP and an extending NTP (or a short RNA primer and an extending NTP) complementary to
5880-619: The other hand, high-resolution nucleosome mapping studies have demonstrated that the differences of CTCF binding between cell types may be attributed to the differences in nucleosome locations. Methylation loss at CTCF-binding site of some genes has been found to be related to human diseases, including male infertility. CTCF binds to itself to form homodimers . CTCF has also been shown to interact with Y box binding protein 1 . CTCF also co-localizes with cohesin , which extrudes chromatin loops by actively translocating one or two DNA strands through its ring-shaped structure, until it meets CTCF in
5964-647: The previous section, transcription factors are proteins that bind to specific DNA sequences in order to regulate the expression of a gene. The binding sequence for a transcription factor in DNA is usually about 10 or 11 nucleotides long. As summarized in 2009, Vaquerizas et al. indicated there are approximately 1,400 different transcription factors encoded in the human genome by genes that constitute about 6% of all human protein encoding genes. About 94% of transcription factor binding sites (TFBSs) that are associated with signal-responsive genes occur in enhancers while only about 6% of such TFBSs occur in promoters. EGR1 protein
6048-470: The product of a classical immediate-early gene and, for instance, it is robustly and transiently produced after neuronal activation. Where the DNA methyltransferase isoform DNMT3A2 binds and adds methyl groups to cytosines appears to be determined by histone post translational modifications. On the other hand, neural activation causes degradation of DNMT3A1 accompanied by reduced methylation of at least one evaluated targeted promoter. Transcription begins with
6132-417: The promoter of a target gene. The loop is stabilized by a dimer of a connector protein (e.g. dimer of CTCF or YY1 ), with one member of the dimer anchored to its binding motif on the enhancer and the other member anchored to its binding motif on the promoter (represented by the red zigzags in the illustration). Several cell function specific transcription factors (there are about 1,600 transcription factors in
6216-430: The regulation of genes, CTCF's activity influences the expression of genes. CTCF is thought to be a primary part of the activity of insulators , sequences that block the interaction between enhancers and promoters. CTCF binding has also been both shown to promote and repress gene expression. It is unknown whether CTCF affects gene expression solely through its looping activity, or if it has some other, unknown, activity. In
6300-483: The standard nucleosides within the DNA molecule or the primary (initial) RNA transcript. Transfer RNA (tRNA) molecules contain a particularly large number of modified nucleosides. Double-stranded nucleic acids are made up of complementary sequences, in which extensive Watson-Crick base pairing results in a highly repeated and quite uniform nucleic acid double-helical three-dimensional structure. In contrast, single-stranded RNA and DNA molecules are not constrained to
6384-462: The substitution of uracil for thymine). This is the strand that is used by convention when presenting a DNA sequence. Transcription has some proofreading mechanisms, but they are fewer and less effective than the controls for copying DNA. As a result, transcription has a lower copying fidelity than DNA replication. Transcription is divided into initiation , promoter escape , elongation, and termination . Setting up for transcription in mammals
6468-453: The synthesis of that protein. The regulatory sequence before ( upstream from) the coding sequence is called the five prime untranslated regions (5'UTR); the sequence after ( downstream from) the coding sequence is called the three prime untranslated regions (3'UTR). As opposed to DNA replication , transcription results in an RNA complement that includes the nucleotide uracil (U) in all instances where thymine (T) would have occurred in
6552-442: The transcription factor-bound enhancers to transcription start site-proximal regulatory elements and to initiate transcription by interacting with Pol II, thus supporting a role of CTCF in facilitating contacts between transcription regulatory sequences. This model has been demonstrated by the previous work on the beta-globin locus . The binding of CTCF has been shown to have many effects, which are enumerated below. In each case, it
6636-429: The transcription initiation complex. After the first bond is synthesized, the RNA polymerase must escape the promoter. During this time there is a tendency to release the RNA transcript and produce truncated transcripts. This is called abortive initiation , and is common for both eukaryotes and prokaryotes. Abortive initiation continues to occur until an RNA product of a threshold length of approximately 10 nucleotides
6720-455: The transcription start site sequence, and catalyzes bond formation to yield an initial RNA product. In bacteria , RNA polymerase holoenzyme consists of five subunits: 2 α subunits, 1 β subunit, 1 β' subunit, and 1 ω subunit. In bacteria, there is one general RNA transcription factor known as a sigma factor . RNA polymerase core enzyme binds to the bacterial general transcription (sigma) factor to form RNA polymerase holoenzyme and then binds to
6804-510: The transcription start sites. These include enhancers , silencers , insulators and tethering elements. Among this constellation of elements, enhancers and their associated transcription factors have a leading role in the initiation of gene transcription. An enhancer localized in a DNA region distant from the promoter of a gene can have a very large effect on gene transcription, with some genes undergoing up to 100-fold increased transcription due to an activated enhancer. Enhancers are regions of
6888-519: The usage of various combinations of its zinc fingers earned it the status of a “multivalent protein”. More than 30,000 CTCF binding sites have been characterized. The human genome contains anywhere between 15,000 and 40,000 CTCF binding sites depending on cell type, suggesting a widespread role for CTCF in gene regulation. In addition CTCF binding sites act as nucleosome positioning anchors so that, when used to align various genomic signals, multiple flanking nucleosomes can be readily identified. On
6972-672: Was discovered in 1869, but its role in genetic inheritance was not demonstrated until 1943. The DNA segments that carry this genetic information are called genes. Other DNA sequences have structural purposes, or are involved in regulating the use of this genetic information. Along with RNA and proteins, DNA is one of the three major macromolecules that are essential for all known forms of life. DNA consists of two long polymers of monomer units called nucleotides, with backbones made of sugars and phosphate groups joined by ester bonds. These two strands are oriented in opposite directions to each other and are, therefore, antiparallel . Attached to each sugar
7056-453: Was found that CTCF localizes with cohesin genome-wide and affects gene regulatory mechanisms and the higher-order chromatin structure. It is currently believed that the DNA loops are formed by the "loop extrusion" mechanism, whereby the cohesin ring is actively being translocated along the DNA until it meets CTCF. CTCF has to be in a proper orientation to stop cohesin. CTCF binding has been shown to influence mRNA splicing. CTCF binds to
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