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Eukaryotes vs. Prokaryotes
Regulatory sequences make up a small portion of the genome that does not encode for proteins. These regulatory sequences determine the level, location and chronology of gene expression. Regulatory sequences primarily dictate transcriptional regulation, that is, if and when a gene is transcribed. The initiation of transcription of a gene is under the influence of promoters, regulatory elements and proteins known as transcription factors. Promoters are regions of DNA that include a sequence responsible for the proper transcription of a protein-coding sequence of DNA, known as a gene. Regulatory elements are regions of non-coding DNA that regulate the transcription of nearby genes. Transcription factors are proteins that interact with promoters, and other specific DNA sequences within the regulatory regions, to determine the pattern of gene expression. While both eukaryotes and prokaryotes require promoters and transcription factors to regulate transcription, they differ in the type of regulatory machinery used.

Prokaryotes
Prokaryotic organisms are single-celled organisms that do not have a defined nucleus. Therefore, the DNA within prokaryotes is found within the cytoplasm, available for simultaneous transcription and translation. The regulation of transcription is the primary method to control protein expression in a prokaryotic cell. Prokaryotes differ from eukaryotes in that they contain operons; a single unit of DNA that acts to regulate the expression of multiple genes at once. These operons react in response to environmental changes and activate transcription of specific genes in response to such changes. Operons contain promoter DNA sequences as well as operator sequences. In bacteria, the promoter contains two short sequence elements approximately -10 and -35 nucleotides upstream from the transcription start site. The sequence at -10 (the -10 element) has the sequence TATAAT, while the sequence at -35 (the -35 element) has sequence TTGACA. These sequences promote the binding of RNA polymerase, allowing transcription of the gene of interest.

Operator
An operator is a sequence of DNA found near the promoter of an operon that can be recognized by a repressor protein. When a repressor protein binds to the operator site, transcription of the gene, or genes, is blocked.

Repressor
A repressor is a type of transcription factor that binds to a cis-acting element, such as an operator site, and prevents transcription. When an inducer is present, it binds with the repressor, causing the repressor to change shape and release from the operator. When this happens, the RNA polymerase can proceed with transcription, and protein synthesis begins and continues until another repressor binds with the operator.

Eukaryotes
Eukaryotic organisms are multi-cellular and contain organelles which increase their complexity. In eukaryotic cells, the DNA is contained inside of the nucleus where it is transcribed into RNA. The RNA strand is then processed into protein in the cytoplasm outside of the nucleus. Regulation of gene expression can occur at all stages of this process. During transcriptional regulation, promoter sequences determine the site of transcription initiation and direct the binding of RNA polymerase. There are three types of promoter sequences that have been identified in eukaryotic DNA: the TATA box, initiator proteins, and CpG Islands. Eukaryotes also have unique transcriptional factors known as activators, enhancers, and silencers. Activators bind to enhancers, which are discrete DNA units located at point along the chromosome, to form an activator-enhancer complex. The activator-enhancer complex then causes the DNA to bend, so that additional transcription factors have better access to the promoter sequence. These additional transcription factors recruit RNA polymerase to initiate transcription. Silencers are repressor proteins that block transcription through binding to the DNA sequence.

TATA Box
An important promoter sequence found in many genes is the TATA Box. The TATA box is a conserved region rich in adenine and thymine and is slightly upstream (approximately 25 to 30 bp) of the start site of transcription. The TATA box is a regulatory sequence found only in eukaryotes and has an important role in the determining the position of the start of transcription. Instead of a TATA Box, some eukaryotic genes contain another promoter element called an initiator. The initiator sequence has a similar function as the TATA box, in that it recruits RNA polymerase in order for transcription to begin.

CpG Islands
Genes that are expressed ("turned-on") most of the time, in most cells, are known as “house-keeping genes”. These genes contain large amounts of the DNA nucleotides, cytosine and guanine. These parts of the DNA sequences with large amounts of cytosine and guanine are known as CpG islands. These CpG islands are found in the promoters of these genes and serve as binding sites for transcription factors. CpG Islands are also targets for DNA methylation. DNA methylation occurs when a chemical compound, known methyl group, is added to the DNA sequence. When DNA methylation occurs at a gene promoter sequence, the expression of the gene is modified. When a CG-promoter is methylated, gene transcription is inhibited.