Exercises: Gene regulation and genomes

All the cells in your body possess the same DNA, yet a neuron and a muscle cell are very different. Explain what causes this difference with reference to gene expression.

What is a constitutive gene and what is a regulated gene? Give an example of each type and explain why it is advantageous for the cell to regulate some of its genes.

Name two general differences between the genome of a prokaryotic cell and that of a eukaryotic cell (location, DNA shape, presence of introns).

Define intron and exon, and state what happens to each of them during the maturation of the mRNA in eukaryotic cells.

What is a transcription factor? Explain briefly what role it plays in the regulation of gene expression and to which regions of the DNA it binds.

What does it mean that a gene is silenced in a cell? Explain one way in which the cell can prevent a given gene from being transcribed.

The human genome contains about $20000$ protein-coding genes, but these occupy only a small part of the total DNA. State what other types of sequences the genome contains and what functions are attributed to some of the non-coding regions.

What is a promoter and what role does it play in the regulation of transcription? Explain what may happen if a mutation disables the promoter of a gene.

In eukaryotic cells, DNA is packaged bound to histones forming chromatin. Explain how the degree of chromatin compaction influences gene expression.

In eukaryotic cells there are regulatory sequences called enhancers that can be located thousands of base pairs away from the gene they regulate. Explain how they can act over such a distance, referring to the folding of chromatin and to transcription factors.

MicroRNAs are small RNAs that do not encode proteins but regulate gene expression. Explain how they act on the target mRNAs, whether their effect is activating or inhibitory, and why they are considered a post-transcriptional level of regulation.

Compare the regulation of gene expression in prokaryotes and in eukaryotes (number of control levels, speed of response to the environment, organization of the genes) and explain why more possible points of regulation exist in eukaryotic cells.

Only about $1.5\ \%$ of the human genome corresponds to protein-coding sequences. Calculate how many base pairs that percentage is equivalent to in a genome of $3 \times 10^9$ base pairs and explain what is known today about the rest of the genome (regulatory sequences, introns, mobile elements, repeats).

In a colorectal carcinoma biopsy, it is detected that the tumor suppressor gene MLH1 is completely silenced, which prevents DNA mismatch repair. When sequencing the gene in the tumor, its nucleotide sequence is identical to that of healthy tissue; however, molecular analysis reveals dense hypermethylation of cytosines in CpG islands of its promoter region. When the tumor cells are cultured with 5-azacytidine (a DNA methyltransferase inhibitor), MLH1 expression resumes.

1. a) Based on these data, justify why the silencing of MLH1 in this tumor constitutes an epigenetic event and not a genetic mutation.
2. b) Explain the physical-molecular mechanism by which the presence of methyl groups on promoter cytosines prevents gene transcription, referring to the binding of transcription factors and chromatin remodeling.
3. c) When these 5-azacytidine-treated tumor cells divide in a drug-free medium, new cell generations can inherit the methylation pattern and silence the gene again. Justify how DNA methylation is maintained and transmitted during cell replication by maintenance methyltransferases.

Analyze the following table with genomic data from three representative organisms:

1. a) A student claims that, since Paris japonica has a genome nearly 50 times larger than the human genome, it must possess a proportionally higher biological and anatomical complexity. Refute their claim using the data and explain what the C-value paradox consists of.
2. b) In light of the data in the table, explain which types of sequences make up the vast majority of non-coding DNA in eukaryotes and why a bacterium cannot tolerate such a high proportion of non-coding DNA.

At the end of the 19th century, August Weismann proposed that cell differentiation during embryonic development occurred through a selective and progressive loss of genes: each cell lineage would retain only the DNA necessary to perform its specialized function.

1. a) Describe the basis of a historic experiment (such as Gurdon's nuclear transfer in amphibians or the cloning of Dolly the sheep) and explain how its results definitively refuted Weismann's hypothesis.
2. b) If a neuron and a hepatocyte from the same adult human individual possess exactly the same genome, justify which molecular mechanisms (specific transcription factors and epigenetic modifications such as DNA methylation and histone acetylation) allow each to express a largely different set of proteins and stably maintain its identity.

In Drosophila melanogaster, the dominant gain-of-function mutation Antennapedia (Antp) causes the Antp gene, whose normal expression is restricted to the second thoracic segment to induce leg development, to be erroneously transcribed in the imaginal discs of the head. As a consequence, the flies develop fully formed legs instead of antennae.

1. a) Based on this case, deduce what molecular function the proteins encoded by homeotic (Hox) genes perform, and explain how the activation of a single gene is capable of triggering the coordinated morphogenesis of an entire appendage.
2. b) A student puts forward the hypothesis that, if a fly with a homozygous null deletion mutation of Antp (total loss of function) is isolated, the embryo will be born without a head. Refute this hypothesis and predict, with reasoning, what anatomical alteration you would expect to observe in the thorax of said individual.