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protein coding genes but also some non coding rnas e g snrnas snornas or long non coding rnas rna polymerase iii transcribes 5s rrna transfer rna trna genes and some small non coding rnas e g 7sk transcription ends when the polymerase encounters a sequence called the terminator mrna processing edit main article post transcriptional modification while transcription of prokaryotic protein coding genes creates messenger rna mrna that is ready for translation into protein transcription of eukaryotic genes leaves a primary transcript of rna pre rna which first has to undergo a series of modifications to become a mature rna types and steps involved in the maturation processes vary between coding and non coding prernas i e even though prerna molecules for both mrna and trna undergo splicing the steps and machinery involved are different 3 the processing of non coding rna is described below non coding rna maturation the processing of pre mrna include 5 capping which is set of enzymatic reactions that add 7 methylguanosine m 7 g to the 5 end of pre mrna and thus protect the rna from degradation by exonucleases 4 the m 7 g cap is then bound by cap binding complex heterodimer cbp20 cbp80 which aids in mrna export to cytoplasm and also protect the rna from decapping 5 another modification is 3 cleavage and polyadenylation 6 they occur if polyadenylation signal sequence 5 aauaaa 3 is present in pre mrna which is usually between protein coding sequence and terminator 7 the pre mrna is first cleaved and then a series of 200 adenines a are added to form poly a tail which protects the rna from degradation 8 the poly a tail is bound by multiple poly a binding proteins pabps necessary for mrna export and translation re initiation 9 in the inverse process of deadenylation poly a tails are shortened by the ccr4 not 3 5 exonuclease which often leads to full transcript decay 10 illustration of exons and introns in pre mrna and the formation of mature mrna by splicing the utrs in green are non coding parts of exons at the ends of the mrna a very important modification of eukaryotic pre mrna is rna splicing the majority of eukaryotic pre mrnas consist of alternating segments called exons and introns 11 during the process of splicing an rna protein catalytical complex known as spliceosome catalyzes two transesterification reactions which remove an intron and release it in form of lariat structure and then splice neighbouring exons together 12 in certain cases some introns or exons can be either removed or retained in mature mrna 13 this so called alternative splicing creates series of different transcripts originating from a single gene because these transcripts can be potentially translated into different proteins splicing extends the complexity of eukaryotic gene expression and the size of a species proteome 14 extensive rna processing may be an evolutionary advantage made possible by the nucleus of eukaryotes in prokaryotes transcription and translation happen together whilst in eukaryotes the nuclear membrane separates the two processes giving time for rna processing to occur 15 non coding rna maturation edit main articles trna maturation rrna maturation and mirna maturation in most organisms non coding genes ncrna are transcribed as precursors that undergo further processing in the case of ribosomal rnas rrna they are often transcribed as a pre rrna that contains one or more rrnas the pre rrna is cleaved and modified 2 o methylation and pseudouridine formation at specific sites by approximately 150 different small nucleolus restricted rna species called snornas snornas associate with proteins forming snornps while snorna part basepair with the target rna and thus position the modification at a precise site the protein part performs the catalytical reaction in eukaryotes in particular a snornp called rnase mrp cleaves the 45s pre rrna into the 28s 5 8s and 18s rrnas the rrna and rna processing factors form large aggregates called the nucleolus 16 in the case of transfer rna trna for example the 5 sequence is removed by rnase p 17 whereas the 3 end is removed by the trnase z enzyme 18 and the non templated 3 cca tail is added by a nucleotidyl transferase 19 in the case of micro rna mirna mirnas are first transcribed as primary transcripts or pri mirna with a cap and poly a tail and processed to short 70 nucleotide stem loop structures known as pre mirna in the cell nucleus by the enzymes drosha and pasha after being exported it is then processed to mature mirnas in the cytoplasm by interaction with the endonuclease dicer which also initiates the formation of the rna induced silencing complex risc composed of the argonaute protein even snrnas and snornas themselves undergo series of modification before they become part of functional rnp complex 20 this is done either in the nucleoplasm or in the specialized compartments called cajal bodies 21 their bases are methylated or pseudouridinilated by a group of small cajal body specific rnas scarnas which are structurally similar to snornas 22 translation edit main article translation biology for some non coding rna the mature rna is the final gene product 23 in the case of messenger rna mrna the rna is an information carrier coding for the synthesis of one or more proteins mrna carrying a single protein sequence common in eukaryotes is monocistronic whilst mrna carrying multiple protein sequences common in prokaryotes is known as polycistronic during the translation trna charged with amino acid enters the ribosome and aligns with the correct mrna triplet ribosome then adds amino acid to growing protein chain every mrna consists of three parts a 5 untranslated region 5 utr a protein coding region or open reading frame orf and a 3 untranslated region 3 utr the coding region carries information for protein synthesis encoded by the genetic code to form triplets each triplet of nucleotides of the coding region is called a codon and corresponds to a binding site complementary to an anticodon triplet in transfer rna transfer rnas with the same anticodon sequence always carry an identical type of amino acid amino acids are then chained together by the ribosome according to the order of triplets in the coding region the ribosome helps transfer rna to bind to messenger rna and takes the amino acid from each transfer rna and makes a structure less protein out of it 24 25 each mrna molecule is translated into many protein molecules on average 2800 in mammals 26 27 in prokaryotes translation generally occurs at the point of transcription co transcriptionally often using a messenger rna that is still in the process of being created in eukaryotes translation can occur in a variety of regions of the cell depending on where the protein being written is supposed to be major locations are the cytoplasm for soluble cytoplasmic proteins and the membrane of the endoplasmic reticulum for proteins that are for export from the cell or insertion into a cell membrane proteins that are supposed to be produced at the endoplasmic reticulum are recognised part way through the translation process this is governed by the signal recognition particle a protein that binds to the ribosome and directs it to the endoplasmic reticulum when it finds a signal peptide on the growing nascent amino acid chain 28 regulation edit main article regulation of gene expression the patchy colours of a tortoiseshell cat are the result of different levels of expression of pigmentation genes in different areas of the skin regulation of gene expression is the control of the amount and timing of appearance of the functional product of a gene control of expression is vital to allow a cell to produce the gene products it needs when it needs them in turn this gives cells the flexibility to adapt to a variable environment external signals damage to the cell and other stimuli more generally gene regulation gives the cell control over all structure and function and is the basis for cellular differentiation morphogenesis and the versatility and adaptability of any organism numerous terms are used to describe types of genes depending on how they are regulated these include a constitutive gene is a gene that is transcribed continually as opposed to a facultative gene which is only transcribed when needed a housekeeping gene is a gene that is required to maintain basic cellular function and so is typically expressed in all cell types of an organism examples include actin gapdh and ubiquitin some housekeeping genes are transcribed at a relatively constant rate and these genes can be used as a reference point in experiments to measure the expression rates of other genes a facultative gene is a gene only transcribed when needed as opposed to a constitutive gene an inducible gene is a gene whose expression is either responsive to environmental change or dependent on the position in the cell cycle any step of gene expression may be modulated from the dna rna transcription step to post translational modification of a protein the stability of the final gene product whether it is rna or protein also contributes to the expression level of the gene an unstable product results in a low expression level in general gene expression is regulated through changes 29 in the number and type of interactions between molecules 30 that collectively influence transcription of dna 31 and translation of rna 32 some simple examples of where gene expression is important are control of insulin expression so it gives a signal for blood glucose regulation x chromosome inactivation in female mammals to prevent an overdose of the genes it contains cyclin expression levels control progression through the eukaryotic cell cycle transcriptional edit main article transcriptional regulation when lactose is present in a prokaryote it acts as an inducer and inactivates the repressor so that the genes for lactose metabolism can be transcribed regulation of transcription can be broken down into three main routes of influence genetic direct interaction of a control factor with the gene modulation interaction of a control factor with the transcription machinery and epigenetic non sequence changes in dna structure that influence transcription 33 34 the lambda repressor transcription factor green binds as a dimer to major groove of dna target red and blue and disables initiation of transcription from pdb 1lmb direct interaction with dna is the simplest and the most direct method by which a protein changes transcription levels 35 genes often have several protein binding sites around the coding region with the specific function of regulating transcription 36 there are many classes of regulatory dna binding sites known as enhancers insulators and silencers 37 the mechanisms for regulating transcription are varied from blocking key binding sites on the dna for rna polymerase to acting as an activator and promoting transcription by assisting rna polymerase binding 38 the activity of transcription factors is further modulated by intracellular signals causing protein post translational modification including phosphorylation acetylation or glycosylation 39 these changes influence a transcription factor s ability to bind directly or indirectly to promoter dna to recruit rna polymerase or to favor elongation of a newly synthesized rna molecule 40 the nuclear membrane in eukaryotes allows further regulation of transcription factors by the duration of their presence in the nucleus which is regulated by reversible changes in their structure and by binding of other proteins 41 environmental stimuli or endocrine signals 42 may cause modification of regulatory proteins 43 eliciting cascades of intracellular signals 44 which result in regulation of gene expression it has become apparent that there is a significant influence of non dna sequence specific effects on transcription 45 these effects are referred to as epigenetic and involve the higher order structure of dna non sequence specific dna binding proteins and chemical modification of dna 46 in general epigenetic effects alter the accessibility of dna to proteins and so modulate transcription 47 in eukaryotes dna is organized in form of nucleosomes note how the dna blue and green is tightly wrapped around the protein core made of histone octamer ribbon coils restricting access to the dna from pdb 1kx5 in eukaryotes the structure of chromatin controlled by the histone code regulates access to dna with significant impacts on the expression of genes in euchromatin and heterochromatin areas 48 enhancers transcription factors mediator complex and dna loops edit regulation of transcription in mammals an active enhancer regulatory region is enabled to interact with the promoter region of its target gene by formation of a chromosome loop this can initiate messenger rna mrna synthesis by rna polymerase ii rnap ii bound to the promoter at the transcription start site of the gene the loop is stabilized by one architectural protein anchored to the enhancer and one anchored to the promoter and these proteins are joined to form a dimer red zigzags specific regulatory transcription factors bind to dna sequence motifs on the enhancer general transcription factors bind to the promoter when a transcription factor is activated by a signal here indicated as phosphorylation shown by a small red star on a transcription factor on the enhancer the enhancer is activated and can now activate its target promoter the active enhancer is transcribed on each strand of dna in opposite directions by bound rnap iis mediator proteins a complex consisting of about 26 proteins in an interacting structure communicate regulatory signals from the enhancer dna bound transcription factors to the promoter gene expression in mammals is regulated by many cis regulatory elements including core promoters and promoter proximal elements that are located near the transcription start sites of genes upstream on the dna towards the 5 region of the sense strand other important cis regulatory modules are localized in dna regions that are distant from the transcription start sites these include enhancers silencers insulators and tethering elements 49 enhancers and their associated transcription factors have a leading role in the regulation of gene expression 50 enhancers are genome regions that regulate genes enhancers control cell type specific gene expression programs most often by looping through long distances to come in physical proximity with the promoters of their target genes 51 multiple enhancers each often tens or hundred of thousands of nucleotides distant from their target genes loop to their target gene promoters and coordinate with each other to control gene expression 51 the illustration shows an enhancer looping around to come into proximity with the promoter of a target gene the loop is stabilized by a dimer of a connector protein e g dimer of ctcf or yy1 one member of the dimer is anchored to its bindin...