This article is part of the series on: Gene expression a Molecular biology topic (portal)

Introduction to Genetics

General flow: DNA > RNA > Protein

special transfers (RNA > RNA, RNA > DNA, Protein > Protein)

Genetic code

Transcription

Transcription (Transcription factors, RNA Polymerase,promoter)

post-transcriptional modification (hnRNA,Splicing)

Translation

Translation (Ribosome,tRNA)

post-translational modification (functional groups, peptides, structural changes)

gene regulation

epigenetic regulation (Hox genes, Genomic imprinting)

transcriptional regulation

post-transcriptional regulation (sequestration, alternative splicing,miRNA)

post-translational regulation (reversible,irrevesible)

Transcription is the synthesis of RNA under the direction of DNA. Both nucleic acid sequences use the same language, and the information is simply transcribed, or copied, from one molecule to the other. DNA sequence is enzymatically copied by RNA polymerase to produce a complementary nucleotide RNA strand, called messenger RNA (mRNA), because it carries a genetic message from the DNA to the protein-synthesizing machinery of the cell. Deoxyribonucleic acid ( DNA) is a Nucleic acid that contains the genetic instructions used in the development and functioning of all known Enzymes are Biomolecules that catalyze ( ie increase the rates of Chemical reactions Almost all enzymes are Proteins RNA polymerase ( RNAP or RNApol) is an Enzyme that produces RNA. Ribonucleic acid ( RNA) is a Nucleic acid that consists of a long chain of Nucleotide units One significant difference between RNA and DNA sequence is the presence of U, or uracil in RNA instead of the T, or thymine of DNA. Uracil is a common and naturally occurring Pyrimidine derivative Thymine is one of the four bases in the Nucleic acid of DNA that make up the letters ATGC In the case of protein-encoding DNA, transcription is the first step that usually leads to the expression of the genes, by the production of the mRNA intermediate, which is a faithful transcript of the gene's protein-building instruction. Gene expression is the process by which inheritable information from a Gene, such as the DNA sequence, is made into a functional Gene product, such Messenger ribonucleic acid ( mRNA) is a molecule of RNA encoding a chemical "blueprint" for a Protein product The stretch of DNA that is transcribed into an RNA molecule is called a transcription unit. A transcription unit that is translated into protein contains sequences that direct and regulate protein synthesis in addition to coding the sequence that is translated into protein. The regulatory sequence that is before, or 5', of the coding sequence is called 5' untranslated region (5'UTR), and sequence found following, or 3', of the coding sequence is called 3' untranslated region (3'UTR). The five prime untranslated region ( 5' UTR) also known as the leader sequence, is a particular section of Messenger RNA (mRNA and the DNA that codes for The three prime untranslated region (3' UTR is a particular section of Messenger RNA (mRNA Transcription has some proofreading mechanisms, but they are fewer and less effective than the controls for copying DNA; therefore, transcription has a lower copying fidelity than DNA replication. DNA replication is the process of copying a double-stranded DNA molecule to form two double-stranded molecules ^[1]

As in DNA replication, RNA is synthesized in the 5' → 3' direction (from the point of view of the growing RNA transcript). DNA replication is the process of copying a double-stranded DNA molecule to form two double-stranded molecules Only one of the two DNA strands is transcribed. This strand is called the template strand, because it provides the template for ordering the sequence of nucleotides in an RNA transcript. The other strand is called the coding strand, because its sequence is the same as the newly created RNA transcript (except for thymine being substituted for uracil). Thymine is one of the four bases in the Nucleic acid of DNA that make up the letters ATGC Uracil is a common and naturally occurring Pyrimidine derivative The DNA template strand is read 3' → 5' by RNA polymerase and the new RNA strand is synthesized in the 5'→ 3' direction. RNA polymerase binds to the 3' end of a gene (promoter) on the DNA template strand and travels toward the 5' end. In Biology, a promoter is a region of DNA that facilitates the transcription of a particular Gene.

Transcription is divided into 5 stages: pre-initiation, initiation, promoter clearance, elongation and termination.

Prokaryotic vs. eukaryotic transcription

A micrograph of ongoing gene transcription of ribosomal RNA illustrating the growing primary transcripts. Ribosomal RNA ( rRNA) is the central component of the Ribosome, the protein manufacturing machinery of all living cells. A primary transcript is an RNA molecule that has not yet undergone any modification after its synthesis. "Begin" indicates the 3' end of the DNA template strand, where new RNA synthesis begins; "end" indicates the 5' end, where the primary transcripts are almost complete. Directionality, in Molecular biology, refers to the end-to-end chemical orientation of a single strand of Nucleic acid. Directionality, in Molecular biology, refers to the end-to-end chemical orientation of a single strand of Nucleic acid.

• Prokaryotic transcription occurs in the cytoplasm alongside translation. Prokaryotic transcription is the process in which Messenger RNA transcripts of genetic material in Prokaryotes are produced to be translated for the production of The cytoplasm is the contents of a cell that is enclosed within the Plasma membrane. Translation is the first stage of Protein biosynthesis (part of the overall process of Gene expression)
• Eukaryotic transcription is primarily localized to the nucleus, where it is separated from the cytoplasm by the nuclear membrane. Eukaryotic transcription is more complex than Prokaryotic transcription. In Cell biology, the nucleus (pl nuclei; from Latin la ''nucleus'' or la ''nuculeus'' "little nut" or kernel is a membrane-enclosed The cytoplasm is the contents of a cell that is enclosed within the Plasma membrane. The transcript is then transported into the cytoplasm where translation occurs.
• Another important difference is that eukaryotic DNA is wound around histones to form nucleosomes and packaged as chromatin. In Biology, histones are the chief Protein components of Chromatin. Nucleosomes form the fundamental repeating units of eukaryotic Chromatin, which is used to pack the large eukaryotic genomes into the nucleus while still ensuring Chromatin is the complex basis of DNA and protein that makes up Chromosomes It is found inside the nuclei of eukaryotic cells, and within the Chromatin has a strong influence on the accessibility of the DNA to transcription factors and the transcriptional machinery including RNA polymerase. In the field of Molecular biology, a transcription factor (sometimes called a sequence-specific DNA binding factor is a Protein that binds to specific sequences RNA polymerase ( RNAP or RNApol) is an Enzyme that produces RNA.
• In prokaryotes, mRNA is not modified. Eukaryotic mRNA is modified through RNA splicing, 5' end capping, and the addition of a polyA tail. In Molecular biology, splicing is a modification of an RNA after transcription, in which Introns are removed and Exons are joined ^[2]

Pre-Initiation

Unlike DNA replication, transcription does not need a primer to start. DNA replication is the process of copying a double-stranded DNA molecule to form two double-stranded molecules A primer is a strand of Nucleic acid that serves as a starting point for DNA replication. RNA polymerase simply binds to the DNA and, along with other cofactors, unwinds the DNA to create an initiation bubble so that the RNA polymerase has access to the single-stranded DNA template. However, RNA Polymerase does require a promoter like sequence.

Proximal (core) Promoters: TATA promoters are found around -30 bp to the start site of transcription. Not all genes have TATA box promoters and there exists TATA-less promoters as well. The TATA promoter consensus sequence is TATA(A/T)A(A/T).

The following are the steps involved in TATA Promoter Complex formation: 1. General transcription factors bind 2. TFIID, TFIIA, TFIIB, TFIIF (w/RNA Polymerase), TFIIH/E The complex is called the closed pre-initiation complex and is closed. Once the structure is opened by TFIIH initiation starts.

Initiation

Simple diagram of transcription initiation. RNAP = RNA polymerase

In bacteria, transcription begins with the binding of RNA polymerase to the promoter in DNA. The Bacteria ( singular: bacterium) are a large group of unicellular Microorganisms Typically a few Micrometres in length bacteria have RNA polymerase ( RNAP or RNApol) is an Enzyme that produces RNA. In Biology, a promoter is a region of DNA that facilitates the transcription of a particular Gene. The RNA polymerase is a core enzyme consisting of five subunits: 2 α subunits, 1 β subunit, 1 β' subunit, and 1 ω subunit. A core enzyme is a RNA Polymerase Enzyme without the Sigma factor (σ At the start of initiation, the core enzyme is associated with a sigma factor (number 70) that aids in finding the appropriate -35 and -10 basepairs downstream of promoter sequences.

Transcription initiation is far more complex in eukaryotes and archaea,^[3] the main difference being that eukaryotic polymerases do not recognize directly their core promoter sequences. Animals Plants fungi, and Protists are eukaryotes (juːˈkærɪɒt or -oʊt Organisms whose cells are organized into complex In eukaryotes, a collection of proteins called transcription factors mediate the binding of RNA polymerase and the initiation of transcription. Only after certain transcription factors are attached to the promoter does the RNA polymerase bind to it. The completed assembly of transcription factors and RNA polymerase bind to the promoter, called transcription initiation complex.

Once the complex has been opened, Initiation starts and the first phosphodiester bond is formed. This is the end of Initiation.

Promoter Clearance

After the first bond is synthesized the RNA polymerase must clear 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 Prokaroytes. Once the transcript reaches approximately 23 nucleotides it no longer slips and Elongation can occur. This is an ATP dependent process.

Promoter clearance also coincides with Phosphorylation of serine 5 on the carboxy terminal domain which is phosphorylated by TFIIH.

Elongation

Simple diagram of transcription elongation

One strand of DNA, the template strand (or non-coding 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. Although RNA polymerase traverses the template strand from 3' → 5', the coding (non-template) strand is usually used as the reference point, so transcription is said to go from 5' → 3'. This produces an RNA molecule from 5' → 3', an exact copy of the coding strand (except that thymines are replaced with uracils, and the nucleotides are composed of a ribose (5-carbon) sugar where DNA has deoxyribose (one less oxygen atom) in its sugar-phosphate backbone). Thymine is one of the four bases in the Nucleic acid of DNA that make up the letters ATGC Uracil is a common and naturally occurring Pyrimidine derivative

Unlike DNA replication, 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 produced from a single copy of a gene. This step also involves a proofreading mechanism that can replace incorrectly incorporated bases.

Prokaryotic elongation starts with the "abortive initiation cycle". During this cycle RNA Polymerase will synthesize mRNA fragments 2-12 nucleotides long. This continues to occur until the σ factor rearranges, which results in the transcription elongation complex (which gives a 35 bp moving footprint). The σ factor is released before 80 nucleotides of mRNA are synthesized.

In Eukaryotic transcription the polymerase can experience pauses. These pauses may be intrinsic to the RNA polymerase or due to chromatin structure. Often the polymerase pauses to allow appropriate RNA editing factors to bind.

Termination

Simple diagram of transcription termination

Bacteria use two different strategies for transcription termination: in Rho-independent transcription termination, RNA transcription stops when the newly synthesized RNA molecule forms a G-C rich hairpin loop, followed by a run of U's, which makes it detach from the DNA template. Intrinsic termination (also called Rho-independent termination) is a mechanism in both Eukaryotes and Prokaryotes that causes MRNA transcription Stem-loop intramolecular Base pairing is a pattern that can occur in single-stranded DNA or more commonly in RNA. In the "Rho-dependent" type of termination, a protein factor called "Rho" destabilizes the interaction between the template and the mRNA, thus releasing the newly synthesized mRNA from the elongation complex. Transcription termination in eukaryotes is less well understood. It involves cleavage of the new transcript, followed by template-independent addition of As at its new 3' end, in a process called polyadenylation. Polyadenylation is the synthesis of a poly(A tail a stretch of RNA where all the bases are Adenines at the end of an RNA molecule

Measuring and detecting transcription

Transcription can be measured and detected in a variety of ways:

• Nuclear Run-on assay, measures the relative abundnace of newly formed transcripts
• RNase protection assay and ChIP-Chip of RNAP, detect active transcription sites
• RT-PCR, measures the absolute abundance of total or nuclear RNA levels, which may however differ from transcription rates
• DNA microarrays measures the relative abundance of the global total or nuclear RNA levels, which may however differ from transcription rates
• In situ hybridization, detects the presence of a transcript

Transcription factories

Active transcription units are clustered in the nucleus, in discrete sites called ‘transcription factories’. A nuclear run-on assay is conducted to identify the Genes that are being transcribed at a certain time Nuclease protection assay is a laboratory technique used in Biochemistry and Genetics to identify individual RNA molecules in a heterogeneous RNA sample ChIP-on-chip (also known as ChIP-chip) is a technique that combines Chromatin immunoprecipitation ( "ChIP") with microarray technology RNA polymerase ( RNAP or RNApol) is an Enzyme that produces RNA. In Molecular biology, reverse transcription polymerase chain reaction (RT-PCR is a Laboratory technique for amplifying a defined piece of a Ribonucleic For terminology see glossary below A DNA microarray is a High-throughput technology used in Molecular biology and in In situ hybridization (ISH is a type of hybridization that uses a labeled Complementary DNA or RNA strand (i Such sites could be visualized after 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 the nucleoplasm of a HeLa cell, among which are ~8,000 polymerase II factories and ~2,000 polymerase III factories. A HeLa cell (also Hela or hela cell) is an immortal cell line used in medical research Each polymerase II factory contains ~8 polymerases. As most active transcription units are associated with only one polymerase, each factory will be associated with ~8 different transcription units. These units might be associated through promoters and/or enhancers, with loops forming a ‘cloud’ around the factory.

History

A molecule which allows the genetic material to be realized as a protein was first hypothesized by Jacob and Monod. François Jacob (born 17 June 1920 in Nancy France) is a French Biologist who together with Jacques Monod, originated See also Jacques-Louis Monod, French-born composer and cousin of Jacques Monod RNA synthesis by RNA polymerase was established in vitro by several laboratories by 1965; however, the RNA synthesized by these enzymes had properties that suggested the existence of an additional factor needed to terminate transcription correctly. RNA polymerase ( RNAP or RNApol) is an Enzyme that produces RNA. In vitro ( Latin: within the glass refers to the technique of performing a given experiment in a controlled environment outside of a living Organism

In 1972, Walter Fiers became the first person to actually prove the existence of the terminating enzyme.

Roger D. Kornberg won the 2006 Nobel Prize in Chemistry "for his studies of the molecular basis of eukaryotic transcription". Roger David Kornberg (born) is an American Biochemist and Professor of Structural biology at Stanford University School of Medicine The Nobel Prize in Chemistry (Nobelpriset i kemi is awarded annually by the Royal Swedish Academy of Sciences to scientists in the various fields of Chemistry. ^[4]

Reverse transcription

Scheme of reverse transcription

Some viruses (such as HIV, the cause of AIDS), have the ability to transcribe RNA into DNA. Human immunodeficiency virus ( HIV) is a Lentivirus (a member of the Retrovirus family that can lead to acquired immunodeficiency syndrome HIV has an RNA genome that is duplicated 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 Biochemistry, a reverse transcriptase, also known as RNA-dependent DNA polymerase, is a DNA polymerase Enzyme that transcribes In the case of HIV, reverse transcriptase is responsible for synthesizing a complementary DNA strand (cDNA) to the viral RNA genome. In Genetics, complementary DNA ( cDNA) is DNA synthesized from a mature MRNA template in a reaction catalyzed by the enzyme Reverse An associated enzyme, ribonuclease H, digests the RNA strand, and reverse transcriptase synthesises a complementary strand of DNA to form a double helix DNA structure. This cDNA is integrated into the host cell's genome via another enzyme (integrase) causing the host cell to generate viral proteins which reassemble into new viral particles. Integrase is an enzyme produced by a Retrovirus (including HIV) that enables its genetic material to be integrated into the DNA of the infected cell Subsequently, the host cell undergoes programmed cell death (apoptosis).

Some eukaryotic cells contain an enzyme with reverse transcription activity called telomerase. Telomerase is an Enzyme that adds specific DNA sequence repeats ("TTAGGG" in all vertebrates to the 3' ("three prime" end of DNA strands in the Telomerase is a reverse transcriptase that lengthens the ends of linear chromosomes. In Biochemistry, a reverse transcriptase, also known as RNA-dependent DNA polymerase, is a DNA polymerase Enzyme that transcribes A chromosome is an organized structure of DNA and Protein that is found in cells. Telomerase carries an RNA template from which it synthesizes DNA repeating sequence, or "junk" DNA. Ribonucleic acid ( RNA) is a Nucleic acid that consists of a long chain of Nucleotide units This repeated sequence of "junk" DNA is important because every time a linear chromosome is duplicated, it is shortened in length. With "junk" DNA at the ends of chromosomes, the shortening eliminates some repeated, or junk sequence, rather than the protein-encoding DNA sequence that is further away from the chromosome ends. Telomerase is often activated in cancer cells to enable cancer cells to duplicate their genomes without losing important protein-coding DNA sequence. Activation of telomerase can be part of the process that allows cancer cells to become immortal.

References

1. ^ Berg J, Tymoczko JL, Stryer L (2006). Biochemistry, 6th ed. , San Francisco: W. H. Freeman. ISBN 0716787245.  
2. ^ Robert J. Brooker Genetics: analysis and principles. 2nd edition. (New York: McGraw-Hill 2005) Chapter 12 "Gene transcription and RNA modification" pp. 318-325.
3. ^ Mohamed Ouhammouch, Robert E. Dewhurst, Winfried Hausner, Michael Thomm, and E. Peter Geiduschek (2003). "Activation of archaeal transcription by recruitment of the TATA-binding protein". Proceedings of the National Academy of Sciences of the United States of America 100 (9): 5097. doi:10.1073/pnas.0837150100. A digital object identifier ( DOI) is a permanent identifier given to an Electronic document.  
4. ^ Chemistry 2006. Nobel Foundation. Retrieved on 2007-03-29. Year 2007 ( MMVII) was a Common year starting on Monday of the Gregorian calendar in the 21st century. Events 1461 - Wars of the Roses: Battle of Towton - Edward of York defeats Queen Margaret to become King

See also

• Genetics
• Molecular biology
• Translation - process of decoding RNA to form polypeptides. Genetics (from Ancient Greek grc-Latn genetikos, “genitive” and that from grc-Latn genesis, “origin” a discipline of Biology, is Molecular biology is the study of Biology at a molecular level Translation is the first stage of Protein biosynthesis (part of the overall process of Gene expression) Peptides (from the Greek πεπτίδια, "small digestibles" are short Polymers formed from the linking in a defined order of α- Amino
• Splicing - process of removing introns from precursor messenger RNA (pre-mRNA) to make form messenger RNA (mRNA). In Molecular biology, splicing is a modification of an RNA after transcription, in which Introns are removed and Exons are joined Introns, derived from the term "intragenic regions" and also called intervening sequence (IVS are DNA regions in a Gene that are not translated into Precursor mRNA ( pre-mRNA) also termed heterogeneous nuclear RNA ( hnRNA) is an immature single strand of messenger ribonucleic acid ( MRNA Messenger ribonucleic acid ( mRNA) is a molecule of RNA encoding a chemical "blueprint" for a Protein product
• Reverse transcription - process viruses use to make DNA from RNA
• Crick's central dogma - DNA is transcribed to RNA which is translated to polypeptides, never the other way around. Reverse transcription is the process of making a double stranded DNA (deoxyribonucleic acid molecule from a single stranded RNA (ribonucleic acid template A virus (from the Latin virus meaning Toxin or Poison) is a sub-microscopic infectious agent that is unable The central dogma of molecular biology was first enunciated by Francis Crick in 1958 and re-stated in a Nature paper published in 1970

Further reading

• Lehninger Principles of Biochemistry, 4th edition, David L. Nelson & Michael M. Cox
• Principles of Nuclear Structure and Function, Peter R. Cook
• Essential Genetics, Peter J. Russell

External links

• Interactive Java simulation of transcription initiation. From Center for Models of Life at the Niels Bohr Institute.
• Interactive Java simulation of transcription interference--a game of promoter dominance in bacterial virus. From Center for Models of Life at the Niels Bohr Institute.