Alternative splicing of mRNA from a single genetic locus

Alternative splicing of mRNA from a single genetic locus

Alternative splicing refers to variation in the way that transcripts from a sin- gle genetic locus are processed posttranscriptional. This phenomenon, now widely known in eukaryotic cells, was virtually unheard of 20 years ago. Understanding that higher plant and animal cells can differentially process a particular species of pre-mRNA molecules goes a long way toward explaining how a cell with approximately 20,000 different genes can encode significantly greater numbers of transcripts which, in turn, may be able to encode several hundred thousand (or more) proteins. By joining together various combinations of exons and even changing the functionality of introns, a remarkable diversity of proteins may result from a seeming economy of genomic sequences. Upon completion of the human genome project, the apparent paucity of genes came as a great surprise, given the complexity of the proteome. In the context of alternative transcript processing and posttranslational modification of proteins, the known number of genes in most species is not inconsistent with the biochemical complexity of the cell. The more common strategies used by cells to accomplish alternative splicing are known as exon skipping, intron retention, the manifestation of cryptic introns, and nonsense-mediated mRNA decay. These phenomena can occur within a single cell in response to the environmental stimuli or may occur in a tissue-specific manner in order to support the physiology of the organism. Details pertaining to these fascinating posttranscriptional phenomena were recently reviewed ( Louzada, 2007 ). It is important to understand that alternative processing of transcripts may also involve modulating the addition of the poly(A) tail associated with the transcripts ’ 3 end through the use of alternative polyadenylation sites. Such poly(A) variants may well influence the stability of the transcript in the cell as well as the precise combination of exons which are manifested in the mature mRNA.

mRNA stability, transport, and turnover

mRNA stability, transport, and turnover

A fundamental regulator of gene expression in all cell types and in all subcellu-lar compartments is the stability of translatable transcripts. In general, mRNAs do not have long half-lives, presumably so as to prevent the over-production of a normal protein which could, in turn, disrupt homeostasis and give rise to a disease state. At the same time, mRNAs must remain stable long enough to become recognized and engaged by the translation apparatus, which are the intrinsic functions of the 5 cap. If large quantities of a protein are to be produced in a cell, one may expect that the corresponding gene will be tran-scribed with a greater frequency than other genes with, for example, house-keeping functions. Similarly, the formation of mRNA secondary structures close to the 5 end in both plants animals can severely limit the scanning of the mRNA such that the initiation of translation is all but inhibited ( Pain, 1996 ; Kozak, 1991 ; Dinesh-Kumar and Miller, 1993 ; Futterer and Hohn, 1996 ; for review, see Kozak, 1999 ). At the other end of the molecule, the length of the poly(A) tail itself plays a role in mRNA stability, as shortening of the poly(A) tail results in destabiliza-tion of cytoplasmic transcripts ( Decker and Parker, 1994 ; Beelman and Parker, 1995 ). Early studies demonstrated that the enzymatic removal of the poly(A) tract from globin mRNA results in a rapid loss of translatability in frog oocytes due to rapid degradation ( Huez et al ., 1974 ; Marbaix et al ., 1975 ). More recent studies have demonstrated the role of the 3 AREs; deletion of these sequences greatly reduces the rate of deadenylation, thereby prolonging mRNA in the cytoplasm ( Wilson and Treisman, 1988 ; Shyu et al ., 1991 ; Decker and Parker, 1993 ; Chen and Shyu, 1994 ). Further, an increasing body of evidence is suggesting that both the length and nucleotide composition of the 5 UTR and 3 UTR play a previously unrecognized role in the stability of the tran-script (reviewed by Lewin, 2008 ). Finally, another recently discovered pathway known as nonsense-mediated mRNA decay appears to be at work in eukaryotic cells which rapidly targets for degradation mRNAs.

Messenger RNA

A great many genes are transcribed constitutively by RNA polymerase II 13 , and it is clear that large quantities of heterogeneous nuclear RNA (hnRNA) are turned over in the nucleus.In eukaryotic cells, messenger RNAs (mRNA) are derived from precursor hnRNA through a series of modifying reactions, which include formation of the 5 cap, methylation, splicing, 3 end processing, and frequently, polyadenylation. Only 1 – 3% of the total RNA in the cytoplasm of a typical eukaryotic cell is mature mRNA. RNA is produced at different rates from different loci; therefore, each mRNA species is classified based on its cytoplasmic prevalence or, more properly, its abundance. There are three official such categories, high abundance, medium abundance, and low abundance mRNAs and, in the mind of this Author, the unofficial very low abundance category.
Highly abundant transcripts are present in hundreds of copies per cell. These are most often observed when a cell is producing an enormous quantity of a particular protein or is high specialized or differentiated to perform a unique function. Medium abundance transcripts are best thought of as being present in dozens of copies per cell; many genes with housekeeping 14 functions manifest their mRNAs at this level of prevalence in the cell. Low abundance mRNAs are generally prevalent in 10 or fewer copies per cell and often are difficult to assay
by many of the older classical techniques, such as Northern analysis , without some form of enrichment in order to increase the statistical probability that such rare messages will be detectable. Very low bundance mRNAs are those present in fewer than one copy per cell, a designation which generally is generally associated with heterogeneous tissue samples or, very commonly, in cases where cancer cells growin in culture manifest a variable, heterogeneous karyotype. In the past these types of mRNAs were referred to as the “ hard to clone genes ” , though newer methods.

DNA– Protein Interactions

The first DNA-binding proteins studied by scientists were regu-latory proteins from bacteria, where they act to control perhaps thesimplest genetic systems found in Nature. Many of these bacterialproteins act as ‘repressors’ of gene activity (see the upper part of thepicture) if they bind tightly to a base-sequence of DNAwhich over-laps the ‘promoter’ sequence, where an RNA polymerase enzymecan also bind. They can thereby prevent the binding of RNA poly-merase to a particular promoter, through direct competition for thesame local segment of DNA. In general, such repressor proteinsreduce the rate at which RNAis made from a promoter; and indeedsuch repression of RNA synthesis may be specific to just one or afew genes in an entire organism, if the repressor binds to only oneor a few sites on an entire chromosome.In bacteria, repressor proteins play an important role in reducinglocal rates of transcription; but in plants, animals and other organ-isms whose cells have nuclei – known collectively as eukaryotes1–the chromosome structure itself tends to repress transcription.Indeed, in nucleated organisms it is the activation of genes thatseems to be the more important aspect of gene regulation. Thatprocess is managed by ‘activators’ of transcription that bind specifically to DNAin the general vicinityof a binding site for RNA polymerase. The activator protein maythen increase the rate at which RNA is made, by directly assistingthe RNA polymerase enzyme and its auxiliary proteins to bind at the promoter sequence, through a network of protein-to-protein contacts; or else indirectly by helping to ‘recruit’ enzymes that canchemically modify the chromatin For instance, cer-tain transcription activators may direct histone acetylases to thegeneral region of a specific gene. The resulting modification of his-tones may cause the chromatin to decompact near that promoter,and thereby make it more accessible to RNA polymerase and itsauxiliary proteins.‘DNA looping’ may represent a somewhat more complex exam-ple of how genes are regulated in three dimensions, and not just inone or two, by some linear or planar arrangement of DNA bindingsites. In the latter case, two or more repressor or activator proteinsmay bind to the same piece of DNA, and then join together to cre-ate a small loop or coil, which can affect gene activity very strongly(either positively or negatively) on account of its stable structure.

Purification of polysome-engaged mRNA

Purification of polysome-engaged mRNA

mRNA is an excellent parameter of gene expression but it is not the only one. Thorough assessment of regulation of this aspect of the cellular biochemistry is multifaceted. Standard RNA isolation techniques, even when coupled to PCR, reveal information about the steady-state abundance of certain RNAs in the cell at the moment of cell lysis, yet reveal nothing at all about the translational fate of the transcripts of experimental interest. Recall that the gene expression is also controlled at the translational and posttranslational levels. Clearer definition of the translational aspect of gene expression may be gained by collecting and analyzing the mRNA fraction that has engaged the translational machinery. The polysome fraction of the cell (all mRNAs engaged by ribosomes) is a fairly accurate indicator of the proportion of the mRNA mass that has actually advanced to the translational level along the gene expression pathway. In the cell, some polysomes are associated with the endo- plasmic reticulum (presumably synthesizing secreted proteins, mitochondrial proteins, and proteins embedded in the membrane) while others remain as free polysomes, which are believed to synthesize proteins that will remain in the cytoplasm or move into the nucleus. Thus, the isolation of polysome-engaged mRNA is used to profile gene expression at the translational level and may well be a more accurate indicator of both efficiency of translation initiation as well as the phenotype identity of the cells under investigation.

Trans-splicing: mRNA repair

An overwhelming majority of higher plant and animal (eukaryotic) genes consist of coding regions known as exons that are separated by intervening, non-coding regions known as introns. In the course of gene expression, transcription results in the synthesis of a large, immature pre-mRNA molecules, consisting of both coding (exon) and non-coding (intron) sequences from a specific gene locus. The process of mRNA maturation involves the removal of introns and the joining together (ligation) of exons so that all of the coding information is contiguous. Generically known as splicing, these well-orchestrated events involve the forma- tion of a spliceosome, i.e. an RNA splicing complex, and involves the removal of introns and the ligation of exons from the same RNA molecule. Nearly all of the splicing that occurs in the cell, as described above, is known as cis -splicing because the exons from a single pre-mRNA molecule are ligated together. In contrast, trans -splicing involves the joining of exons from two different RNA molecules, resulting in the formation of a hybrid (chimeric) RNA molecule. Like cis -splicing, trans -splicing is a naturally occurring proc- ess in eukaryotes, albeit at a much, much lower frequency, though it has been reported that as many of 70% of all mRNAs in the nematode C. elegans may be subject to trans- splicing (reviewed by Hastings, 2005 ). Trans - splicing has the potential to be adapted both in vitro and in vivo to produce an astonishing array of designer proteins, not to mention potential to repair defective mRNAs. SMaRT (spliceosome-mediated RNA trans -splicing) technology, a patented spliceosome-mediated trans- splicing process owned by VIRxSYS, attempts to correct cellular damage caused by the formation of aber- rant proteins by fixing or “ reprogramming ” defective pre-mRNA molecules so that only normal proteins are produced, even when a mutation is harbored and persists in the DNA. Naturally occurring transcription produces.

Alternative splicing of mRNA from a single genetic locus

Alternative splicing refers to variation in the way that transcripts from a sin- gle genetic locus are processed posttranscriptionally. This phenomenon, now widely known in eukaryotic cells, was virtually unheard of 20 years ago. Understanding that higher plant and animal cells can differentially process a particular species of pre-mRNA molecules goes a long way toward explaining how a cell with approximately 20,000 different genes can encode significantly greater numbers of transcripts which, in turn, may be able to encode several hundred thousand (or more) proteins. By joining together various combinations of exons and even changing the functionality of introns, a remarkable diversity of proteins may result from a seeming economy of genomic sequences. Upon completion of the human genome project, the apparent paucity of genes came as a great surprise, given the complexity of the proteome. In the context of alternative transcript processing and posttranslational modification of proteins, the known number of genes in most species is not inconsistent with the biochemical complexity of the cell.

Bicistronic mRNAs

Although the one mRNA, one polypeptide relationship is widespread among eukaryotes, bicistronic mRNAs have been identified in certain organisms. A bicistronic mRNA is capable of directing the synthesis of two different pro- teins. One might think of biscistronic mRNAs as the eukaryotic answer to the polycistronic mRNAs that are nearly universally observed among prokaryotes. Taking this a step further, functional tricistronic mRNAs, encoding three dif- ferent polypeptides, are in use in certain in vitro applications. Due to the pecu- liarities associated with translation in eukaryotes, the first (upstream) encoded protein is synthesized in the 5 -cap dependent manner usually associated with translation of monocistronic mRNAs while initiation of the synthesis of the second (downstream) polypeptide is under the control by an internal ribos- ome entry site (IRES) which allows ribosome assembly in a non-cap-dependent manner. This translation strategy is widespread among eukaryotic viruses and, while still considered a rarity in higher animal cells, there are reports of bicistronic mRNAs in plants, including the tomato tomPro1 locus and in Arabidopsis (see Farrell and Bassett, 2007 for a recent review). It is also pos- sible for a single-reading-frame mRNA to produce two or more polypeptides by cleavage of large precursor protein (a zymogen, for example), such as with the animal hormones oxytocin and vasopressin (Richter, 1983). These observa- tions have lead investigators to rethink the entire process of the regulation of gene expression and to analyze gene expression data circumspectly.

Topology of a typical mRNA molecule

A typical human fibroblast cell contains approximately 1 picogram (pg) of mRNA, which is equivalent to about 10 6 molecules transcribed from a particular subset of an estimated 25,000 – 30,000 genes. While this mRNA heterogeneity reflects the diversity of proteins that these mRNAs encode, a typical eukaryotic mRNA molecule shares several topological features with nearly all other mRNA molecules. As will become evident from the descriptions which follow, producing a function mRNA molecule is amazingly complex.

Bioelectronic DNA

Bioelectronic DNA detection involves forming an electronic circuit mediated by nucleic acid hybridization and it serves as the basis for a DNA detection system called eSensor™ .This system uses low-density DNA chips containing electrodes coated with DNA capture probes.Target DNA present in the ample hybridizes specifically both to capture probes and ferrocene labeled signal probes in solution thereby generating an electric current. Currente Sensor DNA chips contain as many as 36 electrodes for simultaneous detection of multiple pathogens from a single sample.
Many pathogens cause both acute and chronic disease at relatively low copy number and may be difficult or impossible to propagate in culture. Thus, most pathogen detection systems rely on nucleic acid amplification by using polymerase chain reaction (PCR). One highly effective amplification strategy targets conserved sequences among the family of organisms of interest. Such broad-range PCR strategies have been used to identify and characterize several known and previously uncharacterized bacteria and viruses. In order to maximize the utility of these effective pathogen nucleic acid amplification systems, amplification needs to be coupled with rapid, sensitive, and specific detection.
Bioelectronic DNA detection by use of the eSensor chip might fulfill this need.

RNA polymerases and the products of transcription

Genes are transcribed by enzymes known as RNA polymerases, thereby pro- ducing the major types of RNA, including ribosomal RNA (rRNA), transfer RNA (tRNA), and mRNA, as well as all of the smaller RNA species. Eukaryotic genes are transcribed by one of four nuclear RNA polymerases; these enzymes are among the largest and most complex proteins in the cell and consist of more subunits than their prokaryotic counterpart. The eukaryotic enzymes are properly known as RNA polymerases I, II, III, and IV, each of which is responsible for transcribing a different class of genes. Prokaryotes, in contrast, exhibit only one type of RNA polymerase, which transcribes all classes of RNA. RNA polymerases are active only in the presence of DNA, and require the nucleotides ATP, CTP, GTP, and UTP as precur- sors, myriad transcription factors. As is the case in the synthesis of all nucleic acid molecules, RNA transcripts are assembled only in the 5 → 3 direction. Transcription involves three distinct phases, namely, initiation, elongation, and termination, all of which have been described in great detail elsewhere and the details of which are beyond the scope of this volume. Briefly, initiation involves the attachment of RNA polymerase to a DNA template promoter, via transcription, activation, and initiation factors, followed by the acquisition of what will be the first ribonu- cleotide in the RNA molecule. Elongation involves the sequential addition of ribonucleotides to the nascent chain, a process also involving accessory protein elongation factors. Termination is the completion of RNA synthesis, whether appropriately or prematurely, and the disengagement of both the newly synthe- sized RNA and the RNA polymerase from the DNA template. Transcription termination, as with initiation and elongation, is sequence-dependent and is influenced by the presence of small proteins (termination factors) as well as the transient formation of RNA 2 ° structures. Mutations notwithstanding, the nucleotide sequence of the resulting RNA molecule is identical to the coding strand of the DNA from which it is derived, the only difference being the sub- stitution of the base uracil for thymine.

Types of RNA

Transcription results in the production of RNA molecules, often generically referred to as transcripts. Traditionally, the transcripts observed within a cell were broadly classified as ribosomal RNA (rRNA), transfer RNA (tRNA), heterogeneous nuclear RNA (hnRNA), or messenger RNA (mRNA), as well as a collection of small RNAs of previously unknown function. Now, however, one must include the extremely diverse population of miRNAs and other RNAs which are of immense interest in the study of the regulation of gene expression . Each category of RNA, which is synthesized by a different type of RNA polymerase, performs a different function in the cell. These highly diverse populations of RNA are not represented in equal amounts in the cell and the relative amount of each is directly related to the physiology of the cell.
rRNA is the most abundant RNA component in the cell. In prokaryotic cells the major rRNA species are the 23S rRNA, 16S rRNA, and 5S rRNA. The eukaryotic counterparts are identified as the 28S rRNA, 18S rRNA, and 5S rRNA, as well as a fourth ribosomal transcript, the 5.8S rRNA. These molecules form the scaffolding of ribosomes, which become translationally competent when decorated with myriad ribosomal proteins. At present there are 55 known prokaryotic ribosomal proteins and 82 known eukaryotic ribosomal proteins. Not all ribosomes are functional at any given time, and the existence of a pool of transiently inactive ribosomes is itself a regulator of gene expression. The super abundance of rRNA is often exploited as both an RNA mass loading control as well as internal molecular weight markers for electrophoresis.

three dimensions, and consider the shape of a DNA helix

Only the first two base-pairs are shown, but then we show all parts of the sugar–phosphate chains. These chains wrap as spirals around an imaginary cylindrical surface of radius 9Å, and each sugar ring is represented by a dot. a side view of the cylinder for just one of the two sugar–phosphate chains. Here the phosphates, P0, P1, P2, etc. – counting from the top – are drawn as open circles, and the same lengths of 6.0Å, 3.3Å, and 5Å that were found for our skew-ladder characterize the path of these phosphates through space. Finally, a top view along the vertical axis of the DNAcylinder. Again, for the sake of sim-plicity, only one chain is shown, and the phosphates along it arelabeled P0, P1,…, P10. Each successive phosphate in this view lies 3.3Å further away from us than the one before. The chain is shown with a break between P10 and P0, because P11 lies directly behind P0 in
this view: it is 11 3.3Å 36Åfurther away from us, when we look down into the plane of the paper.