Lecture 10: Genomes & DNA Technologies

The Human Genome

• Only 1.5% of the genome codes for proteins (primarily exons)

  • 44% codes for repetitive DNA (transposable elements and related sequences)

  • 15% codes for repetitive DNA unrelated to transposable elements

  • 15% codes for an unknown function or no function at all (telomeres and centromeres that serve structural purposes)

  • 24% codes for introns and regulatory sequences

• Genome = entire DNA composition of your cells

• Pseudogenes…inactivated, nonfunctional copies of genes that are not expressed as proteins.

  • may have no promoter or are out of frame, etc.

  • some act as microRNAs meant for RNA interference

• Approx. 15% of the genome has no known function at all!

Arrangement of Genes

• ~400 genes per chromosome

• Genes are sparsely distributed

• Introns make up the majority of the sequence

• Human genes are very sparsely distributed and not as dense as other genomes

NOTE: Telomeres replace what is lost in transcription (?)

Identifying Genes

• Reverse transcriptase can be used to identify genes…synthesizing DNA from an mRNA template (property of viruses and telomerase)

  • Primers can be used to amplify anything with a poly-A tail!

  • Can cause errors such as genes being missed upon analysis. This is caused by not all genes being expressed and certain introns and exons being spliced out.

• Open Reading Frames…use reading frames that analyze genes in their codons (three at a time) to understand function.

• Transcriptional Noise…term from RNAs that appear to not code for anything viable (noncoding RNA or ncRNA)

  • may be useful RNAs that can be isolated to analyze functions

Origins of Genetic Variation

• Variety in the gene pool for a species is crucial (think evolution and survival)!

• Genes and genomes can be altered by several mechanisms:

  • mutations, duplications, rearrangements, and the infusion of exogenous DNA (foreign genetic material) all contribute to genome evolution

• Gene Duplication…misalignment of homologous chromosomes which leads to crossovers between short, repeated DNA sequences in these adjacent homologous chromosomes.

  • gives rise to families of related genes…allows for subtypes of different genes

  • e.g., the globin family (hemoglobin, etc.)

• Whole Genome Duplication…allows for selective breeding which is specifically useful to farmers for growing crops that are larger, more flavorful, and bear more seeds for reproduction.

  • Not tolerated well in animals, but are common in plants

  • e.g., apples and potatoes

• Exon Shuffling…generates proteins with new combinations of protein domains (“secret superpower” of introns).

  • new domains allow the recipient genes new abilities or modes of allosteric regulation.

  • NOT THE SAME AS mRNA SPLICING: Splicing specifically effects RNA while exon shuffling occurs in the DNA sequence itself!

  • would not have the portions necessary to splice out specific regions.

  • like horizontal transfer…transfer from one gene to another.

• Transposition…moving a portion of the genome into a different portion of the genome (aka. portion of one chromosome breaks off and meshes with another chromosome).

  • places genes under one regulatory source under another regulatory source.

  • causes dramatic alterations in the body plan of an organism.

  • the mutation may not benefit the species and, thus, will not propagate.

• Conserved Sequences…functional important genome regions or “islands” that appear in conserved DNA sequences.

  • high conservation of exon regions.

  • additional sequences that are lost may be useless for certain species or may code for different species.

  • Looking at how regions of sequences, including introns, play a significant role over time and across species.

Horizontal Gene Transfer

• Vertical Gene Transfer…represents the typical mode of inheritance from parent to offspring.

• Horizontal Gene Transfer…movement of genetic information between two organisms in a lateral sense (from one cell to another).

  • organisms are of the same species but unrelated

  • exchange is commonly unidirectional

  • Often in “bits” of genetic information

• Transformation…bacterial cells that are “competent” take up exogenous DNA, which means it may become included in DNA sequence.

  • competent bacteria result from alterations in the cell walls and cytoplasm often coming from stressful environmental conditions.

• Plasmids…commonly the vectors for horizontal transfer of genes between bacteria.

  • short, circular pieces of DNA that independently replicates within bacteria

  • Do not contain genes necessary for basic processes of life but may contain useful genes that aid in survival (growth/reproduction), but will be lost of found to be unnecessary

  • much smaller than bacterial chromosomes

  • used in the lab for gene delivery, making them a genetic vector

• Transduction…bacteriophages mediate the transfer of DNA; phages may be viral vectors.

  • Generalized Transduction…phage carries random DNA segment from donor to recipient as a result of accidental incorporation of bacterial DNA into the phage when it formed.

  • Specialized Transduction…only certain DNA segments are transferred

• Conjugation…mediated by sex-pilus protruding from the donor cell targeting the recipient cell.

  • occurs between same species or closely related ones.

  • transferred plasmids contain genes for sex-pilus and possibly useful genes

  • only non-lethal method for donor cells

Mobile Genetic Elements

• Plasmids…exchanged by prokaryotes; can also be hosted in some eukaryotes

• Transposons…transposable elements that can migrate or copy themselves into new locations.

  • segments of DNA that move from one location to another in the same or different DNA molecule

  • known as a “jumping gene”

  • can be found in the genomes of organisms ranging from simple bacteria to humans

  • contain inverted

• Viral Genomes…by their very nature mobile in that viruses are eventually genetic material delivery mechanisms.

• Group I & II Introns…self-splicing introns that may have other ribozyme activities (not discussed here)