expressed sequence tag

Examples of expressed sequence tag in the following topics:

• Physical Maps and Integration with Genetic Maps

  • Physical maps display the physical distance between genes and can be constructed using cytogenetic, radiation hybrid, or sequence mapping.
  • There are three methods used to create a physical map: cytogenetic mapping, radiation hybrid mapping, and sequence mapping.
  • Sequence mapping resulted from DNA sequencing technology that allowed for the creation of detailed physical maps with distances measured in terms of the number of base pairs.
  • A genetic site used to generate a physical map with sequencing technology (a sequence-tagged site, or STS) is a unique sequence in the genome with a known exact chromosomal location.
  • An expressed sequence tag (EST) and a single sequence length polymorphism (SSLP) are common STSs.

• DNA Sequencing Techniques

  • As each differently-sized fragment exits the capillary column, a laser excites the flourescent tag on its terminal nucleotide.
  • Each sequencing reaction is a modified replication reaction involving flourescently-tagged nucleotides, but no chain-terminating dideoxy nucleotides are needed.
  • Sanger sequence can only produce several hundred nucleotides of sequence per reaction.
  • Most next-generation sequencing techniques generate even smaller blocks of sequence.
  • The smallest fragments were terminated earliest, and they come out of the column first, so the order in which different fluorescent tags exit the column is also the sequence of the strand.

• Epigenetic Control: Regulating Access to Genes within the Chromosome

  • These tags are not permanent, but may be added or removed as needed.
  • The tags do not alter the DNA base sequence, but they do alter how tightly wound the DNA is around the histone proteins .
  • These changes to DNA are inherited from parent to offspring, such that while the DNA sequence is not altered, the pattern of gene expression is passed to the next generation.
  • Transcription factors can bind, allowing gene expression to occur.
  • Modifications affect nucleosome spacing and gene expression.

• Uses of Genome Sequences

  • Genome sequences and expression can be analyzed using DNA microarrays, which can contribute to detection of disease and genetic disorders.
  • DNA microarrays are methods used to detect gene expression by analyzing an array of DNA fragments that are fixed to a glass slide or a silicon chip to identify active genes and identify sequences .
  • Although the study of medical applications of genome sequencing is interesting, this discipline tends to dwell on abnormal gene function.
  • It sounds great to have all the knowledge we can get from whole-genome sequencing; however, humans have a responsibility to use this knowledge wisely.
  • DNA microarrays can be used to analyze gene expression within the genome.

• Regulating Protein Activity and Longevity

  • These changes can alter protein function, epigenetic accessibility, transcription, mRNA stability, or translation; all resulting in changes in expression of various genes.
  • One way to control gene expression is to alter the longevity of the protein: ubiquitination shortens a protein's lifespan.
  • Proteins with ubiquitin tags are marked for degradation within the proteasome.

• The trp Operon: A Repressor Operon

  • However, when tryptophan availability is low, the switch controlling the operon is turned on, transcription is initiated, the genes are expressed, and tryptophan is synthesized.
  • A DNA sequence that codes for proteins is referred to as the coding region.
  • The promoter sequence is upstream of the transcriptional start site.
  • A DNA sequence called the operator sequence is encoded between the promoter region and the first trp-coding gene.
  • Explain the relationship between structure and function of an operon and the ways in which repressors regulate gene expression

• Transcriptional Enhancers and Repressors

  • Enhancer regions are binding sequences, or sites, for transcription factors.
  • Therefore, a nucleotide sequence thousands of nucleotides away can fold over and interact with a specific promoter .
  • A corepressor is a protein that decreases gene expression by binding to a transcription factor that contains a DNA-binding domain.
  • An enhancer is a DNA sequence that promotes transcription.
  • Each enhancer is made up of short DNA sequences called distal control elements.

• mRNA Processing

  • While RNA Polymerase II is still transcribing downstream of the proper end of a gene, the pre-mRNA is cleaved by an endonuclease-containing protein complex between an AAUAAA consensus sequence and a GU-rich sequence.
  • Eukaryotic genes are composed of exons, which correspond to protein-coding sequences (ex-on signifies that they are expressed), and intervening sequences called introns (int-ron denotes their intervening role), which may be involved in gene regulation, but are removed from the pre-mRNA during processing.
  • Intron sequences in mRNA do not encode functional proteins.
  • It is possible that introns slow down gene expression because it takes longer to transcribe pre-mRNAs with lots of introns.
  • This cleavage is done by an endonuclease-containing protein complex that binds to an AAUAAA sequence upstream of the cleavage site and to a GU-rich sequence downstream of the cut site.

• The Process and Purpose of Gene Expression Regulation

  • Whereas each cell shares the same genome and DNA sequence, each cell does not turn on, or express, the same set of genes.
  • Therefore, only a small subset of proteins is expressed in a cell that constitutes its proteome.
  • Specialized proteins that make up the eye (iris, lens, and cornea) are only expressed in the eye, whereas the specialized proteins in the heart (pacemaker cells, heart muscle, and valves) are only expressed in the heart.
  • This complexity ensures the proper expression in the proper cell at the proper time.
  • In this section, you will learn about the various methods of gene regulation and the mechanisms used to control gene expression, such as: epigenetic, transcriptional, post-transcriptional, translational, and post-translational controls in eukaryotic gene expression, and transcriptional control in prokaryotic gene expression.

• The Central Dogma: DNA Encodes RNA and RNA Encodes Protein

  • The stop codon UGA is sometimes used to encode a 21st amino acid called selenocysteine (Sec), but only if the mRNA additionally contains a specific sequence of nucleotides called a selenocysteine insertion sequence (SECIS).
  • It states that genes specify the sequence of mRNA molecules, which in turn specify the sequence of proteins .
  • Transcription is the process of creating a complementary RNA copy of a sequence of DNA.
  • Transcription is the first step in gene expression.
  • Transfer RNA, or tRNA, translates the sequence of codons on the mRNA strand.