Genome organization ,gene expression sand regulation

gene expression and its ragulation, genomic organization,

1. GENOME ORGANIZATION The hereditary material i.e. DNA( deoxyribonuclic acid) of an organism is composed of an array of arrangementof four nucleotides in a specific pattern. These nucleotides present an inherent information as a function of their order. The genome of all organisms (except some viruses and prions ) is composed of one to multiple number of these DNA molecule

2. Organisms have a vast array of ways in which their respective genomes are organized. A comparison of the genomic organization of six major model organisms shows size expansion with the increase of complexity of the organism. There is a more than 300-fold difference between the genome sizes of yeast and mammals, but only a modest 4- to 5-fold increase in overall gene number . However, the ratio of coding to non-coding and repetitive sequences is indicative of the complexity of the genome: The largely "open" genomes of unicellular fungi have relatively little non-coding DNA compared with the highly heterochromatic genomes of  multicellular  organisms.

3. GENE EXPRESSION It is the process by which information from a gene is used in the synthesis of a functional gene product. These products are often proteins, but in non-protein coding genes such as transfer RNA ( tRNA ) or small nuclear RNA ( snRNA ) genes, the product is a functional RNA. The process of gene expression is used by all known lifes —eukaryotes(including  multicellular organisms), prokaryotes (bacteria and  archaea ), and utilized by viruses—to generate the macromolecular machinery for life.

4. MECHANISM TRANSCRIPTION NON-CODING RNA MATURATION RNA EXPORT TRANSLATION FOLDING TRANSLOCATION PROTEIN TRANSPORT

5. MECHANISM 1) TRANSCRIPTION  Gene is a stretch of DNA that encodes information. Genomic DNA consists of two antiparallel and reverse complementary strands. Each having 5' and 3‘ ends. With respect to a gene, the two strands may be labeled the "template strand," which serves as a blueprint for the production of an RNA transcript, and the "coding strand," which includes the DNA version of the transcript sequence.

6. 2)Non-coding RNA maturation In most organisms non-coding genes ( ncRNA ) are 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. 

7. 3)RNA export In eukaryotes most mature RNA must be exported to the cytoplasm from the nucleus. While some RNAs function in the nucleus, many RNAs are transported through the nuclear pores and into the  cytosol . Notably this includes all RNA types involved in protein synthesis. In some cases RNAs are additionally transported to a specific part of the cytoplasm, such as a synapse they are then towed by motor proteins that bind through linker proteins to specific sequences (called " zipcodes ") on the RNA.

8. 4 ) TRANSLATION For some RNA (non-coding RNA) the mature RNA is the final gene product. 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 .

9. 5)FOLDING  polypeptide folds into its characteristic and functional three-dimensional structure from a random coil.  Each protein exists as an unfolded polypeptide or random coil when translated from a sequence of mRNA into a linear chain of amino acids. This polypeptide lacks any developed three-dimensional structure . Amino acids interact with each other to produce a well-defined three-dimensional structure, the folded protein known as the native state. The resulting three-dimensional structure is determined by the amino acid sequence .

10. 6)Translocation Secretory proteins of eukaryotes or prokaryotes must be translocated to enter the secretory pathway. Newly synthesized proteins are directed to the eukaryotic Sec61 or prokaryotic SecYEG translocation channel by signal peptides. The efficiency of protein secretion in eukaryotes is very dependent on the signal peptide which has been used.

11. 7) Protein transport Many proteins are destined for other parts of the cell than the cytosol and a wide range of signalling sequences or (signal peptides) are used to direct proteins to where they are supposed to be. In prokaryotes this is normally a simple process due to limited compartmentalisation of the cell. However, in eukaryotes there is a great variety of different targeting processes to ensure the protein arrives at the correct organelle. Not all proteins remain within the cell and many are exported, for example, digestive enzymes, hormones and extracellular matrix proteins. In eukaryotes the export pathway is well developed and the main mechanism for the export of these proteins is translocation to the endoplasmic reticulum, followed by transport via the Golgi apparatus.

12. REGULATION OF GENE Regulation of gene expression refers to 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.

13. 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 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.

14. TRANSCRIPTIONAL REGULATION 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). The lambda repressor transcription factor (green) binds as a dimer to major groove of DNA target (red and blue) and disables initiation of transcription. Direct interaction with DNA is the simplest and the most direct method by which a protein changes transcription levels. Genes often have several protein binding sites around the coding region with the specific function of regulating transcription. There are many classes of regulatory DNA binding sites known as enhancers, insulators and silencers. The mechanisms for regulating transcription are very 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.

15. TRANSLATIONAL REGULATION Direct regulation of translation is less prevalent than control of transcription or mRNA stability but is occasionally used. Inhibition of protein translation is a major target for toxins and antibiotics, so they can kill a cell by overriding its normal gene expression control. Protein synthesis inhibitors include the antibiotic neomycin and the toxin  ricin . Protein degradation Once protein synthesis is complete, the level of expression of that protein can be reduced by protein degradation. There are major protein degradation pathways in all prokaryotes and eukaryotes, of which the  proteasome  is a common component. An unneeded or damaged protein is often labeled for degradation by addition of ubiquitin .

16. MEASUREMENTS Measuring gene expression is an important part of many life sciences, as the ability to quantify the level at which a particular gene is expressed within a cell, tissue or organism can provide a lot of valuable information. For example, measuring gene expression can: Identify viral infection of a cell (viral protein expression). Determine an individual's susceptibility to cancer ( oncogene  expression). Find if a bacterium is resistant to penicillin (beta- lactamase  expression

17. SMALL INTERFERING RNA Small interfering RNA ( siRNA ), sometimes known as short interfering RNA or silencing RNA, is a class of double-stranded RNA molecules, 20-25 base pairs in length, similar to  miRNA , and operating within the RNA interference ( RNAi ) pathway . . It interferes with the expression of specific genes with complementary nucleotide sequences by degrading mRNA after transcription preventing translation.

18. MECHANISM Long dsRNA (which can come from hairpin, complementary RNAs, and RNA-dependent RNA polymerases) is cleaved by an endo-ribonuclease called Dicer. Dicer cuts the long dsRNA to form short interfering RNA or siRNA ; this is what enables the molecules to form the RNA-Induced Silencing Complex (RISC). Once siRNA enters the cell it gets incorporated into other proteins to form the RISC. Once the siRNA is part of the RISC complex, the siRNA is unwound to form single stranded siRNA . The strand that is thermodynamically less stable due to its base pairing at the 5´end is chosen to remain part of the RISC-complex The single stranded siRNA which is part of the RISC complex now can scan and find a complementary mRNA Once the single stranded siRNA (part of the RISC complex) binds to its target mRNA, it induces mRNA cleavage.

19. Importance One of the biggest challenges to siRNA and RNAi based therapeutics is intracellular delivery.  Delivery of siRNA via  nanoparticles  has shown promise.siRNA   oligos  in vivo are vulnerable to degradation by plasma and tissue nucleases and have shown only mild effectiveness in localized delivery sites, such as the human eye.Delivering pure DNA to target organisms is challenging because its large size and structure prevents it from diffusing readily across membranes .  siRNA oligos circumvent this problem due to their small size of 21-23 oligos.This allows delivery via nano -scale delivery vehicles called nanovectors .

20. Micro RNA A microRNA (  miRNA ) is a small non-coding RNA molecule (containing about 22 nucleotides) found in plants, animals and some viruses, that functions in RNA silencing and post-transcriptional regulation of gene expression.  Encoded by nuclear DNA in plants and animals and by viral DNA in certain viruses whose genome is based on DNA, miRNAs function via base-pairing with complementary sequences within mRNA molecules. As a result, these mRNA molecules are silenced, by one or more of the following processes: (1) Cleavage of the mRNA strand into two pieces, (2) Destabilization of the mRNA through shortening of its poly(A) tail, (3) Less efficient translation of the mRNA into proteins by  ribosomes

21. IMPORTANCE It is useful in Biogenesis and molecular mechanisms Cancer and inflammation Cardiovascular development and Pathogenesis of endocrine treatment

22. Gene mapping Gene mapping describes the methods used to identify the locus of a gene and the distances between genes. The essence of all genome mapping is to place a collection of molecular markers onto their respective positions on the genome.  Molecular markers come in all forms. Genes can be viewed as one special type of genetic markers in the construction of genome maps, and mapped the same way as any other markers. There are two distinctive types of "Maps" used : Genetic maps Physical maps.

23. While both maps are a collection of genetic markers and gene loci, genetic maps' distances are based on the genetic linkage information . while physical maps use actual physical distances usually measured in number of base pairs. While the physical map could be a more " accurate" representation of the genome, genetic maps often offer insights into the nature of different regions of the chromosome, e.g. the genetic distance to physical distance ratio varies greatly at different genomic regions which reflects different recombination rates, and such rate is often indicative of euchromatic (usually gene-rich) vs heterochromatic (usually gene poor) regions of the genome.

24. Gene sequencing Gene sequencing is sometimes mistakenly referred to as "genome mapping" by non-biologists. The process of "shotgun sequencing" resembles the process of physical mapping: it shatters the genome into small fragments, characterizes each fragment, then puts them back together (more recent sequencing technologies are drastically different). While the scope, purpose and process are totally different, a genome assembly can be viewed as the "ultimate" form of physical map, in that it provides in a much better way all the information that a traditional physical map can offer.

25. Use Identification of genes is usually the first step in understanding a genome of a species; mapping of the gene is usually the first step of identification of the gene. Gene mapping is usually the starting point of many important downstream studies. Disease association [ The process to identify a genetic element that is responsible for a disease is also referred to as "mapping". If the locus in which the search is performed is already considerably constrained, the search is called the fine mapping of a gene. This information is derived from the investigation of disease manifestations in large families (genetic linkage) or from populations-based genetic association studies.