Gene Regulation and Genomics - GRE

Tandem arrays are used for extremely important genes, like ribosomal RNA genes that are vital for organism function. The arrays serve to allow massive parallelized encoding of these genes, because many copies are required.

The correct answer is rRNA genes and ITS have highly conserved regions and highly divergent regions. Both prokaryotes and eukaryotes have rRNA genes and ITS, making these ideal targets for molecular typing. In order to amplify, then sequence these regions for evolutionary comparisons, universal primers are designed to anneal within the highly conserved regions and amplify through the highly divergent regions. The divergent regions of rRNA genes and ITS allow for specie to specie comparison and identification.

When two sequences have less than 20% identity, it is almost impossible to align them and identify that they are actually orthologs. This is especially the case in huge genome data sets, in which it is impossible to find matching sequences by hand.

The key factors that distinguish pseudogenes are that they are sequences that result from a duplication event in the genome, but have since mutated without selection pressure and have become nonfunctional.

Organisms with large genomes tend to have very high levels of transposons. For instance, this is the case in our own genomes. It is hypothesized that in some organisms, there is a breakdown of systems that control insertion of transposons into the genome, resulting in large expansions.

Genetic linkages are determined by frequencies of recombination. These are measures of how often chromosomal crossovers will take place between two genes. The closer the loci of the two genes are on a chromosome, the less likely a crossover event will separate the two genes. If the recombination frequencies are sufficiently low, the genes are considered to be linked.

Genetic linkage has nothing to do with genes coding for the same mRNA, sharing a promoter, or overlapping one another. Linked genes still code for distinctly separate traits/proteins and have different loci (don't overlap).

Transposable elements are portions of the DNA that are free to move around the genome and are generally considered non-coding DNA. This can be potentially dangerous, however. Transposable elements can insert themselves in the coding regions of genes, thus making them non-functional. This can lead to disease. Both eukaryotic and prokaryotic genomes contain transposable elements.

Class I transposable elements are RNA-mediated elements of a single evolutionary origin, and are found in yeast, which only have class I elements, and in eukaryotes, which have both class I and class II elements. Bacteria only have class II elements, and hence are not included in the correct answer to this question.

Barbara McClintock named the transposons that are defective, and serve as sites of chromosomal breakage where other transposons insert (the associator, Ac) the dissociators. These were likely transposons that lacked the transposase that catalyzes their movement.

Two transposons flanking an antibiotic resistance gene can easily move between bacteria and confer new resistance. A mix of transposons and new genes such as this is called a composite transposon. Recall that bacteria exchange genetic information via conjugation, transduction, and transformation.

LTR stands for Long Terminal Repeats, which are 250-500 base pair repeats located on the ends of a transposon. These repeats encode a series of proteins, most significantly transposase. These are very likely to be early evolutionarily stages of retroviruses.

Non-LTR retrotransposons use an endonuclease that nicks thymine-rich host DNA, which eventually leads to incorporation of the transposon by host DNA repair functions. These other methods are all associated with different specializations of transposon.

The only difference between most LTR retrotransposons and retroviruses are that retroviruses can encode an envelope protein. Phylogenetic analyses have shown that retrotransposons and retroviruses are extremely closely related, and may be direct ancestors of one another.

Movement of transposons is very commonly controlled by RNA interference. The RNAi system cuts up problematic RNAs, and uses these small pieces to target transposons for destruction.

It is hypothesized that transposons can rapidly move through populations and species by horizontal transfer, most likely through viruses.

The correct answer is to promote formation of euchromatin and increase gene expression. Acetylation of histones "relaxes" DNA coiling around histones by reducing the affinity between histones and DNA. This allows transcription factors to bind promoter regions and promote increased gene expression via transcription.

The correct answer is that mediator is a coactivator of transcription and serves to recruit transcription factors and RNA polymerase II. Mediator does not directly initiate transcription; however, by protein-protein interactions, it recruits the necessary proteins to sites of transcription.

Upstream signaling, such as from a toll-like receptor, causes IKK to phosphorylate IkB, signaling for its ubiquitin-mediated degradation. Since NFkB is no longer bound by its inhibitor, IkB, it translocates to the nucleus where it binds specific motifs in the genome to recruit other transcriptional machinery and initiate transcription.

The correct answer is recruiting DNA polymerase. DNA polymerase is involved in DNA replication, not transcription. Pioneer transcription factors can bind specific DNA motifs and promote euchromatin formation, allowing other transcription factors to bind the less organized DNA. Transcription factors can recruit other transcription factors and the RNA polymerase holoenzyme to promoters to promote gene-specific transcription.

Activation of the lac operon is necessary for the transport and metabolism of lactose sugars by E. coli. Lactose sugars actively work to remove a repressor that statically inhibits transcription; however, high concentrations of glucose (and, thus, low concentrations of cAMP) will prevent these genes from being transcribed rigorously. In order for the lac operon to be active at high levels, lactose must be present and glucose must be absent.