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Genome Regulation and Comparative Genomics
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Genome Regulation and Comparative Genomics
Chapter 2 Study Genome Regulation and Comparative Genomics
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1
Question
What is the main idea behind gene regulation’s complexity?
Answer
Many factors determine when and how genes are expressed.
2
Question
Which molecules connect transcription and translation in gene expression?
Answer
mRNA carries information; ribosome translates it; tRNA delivers amino acids.
3
Question
What is the role of noncoding RNAs (ncRNAs) in the cell?
Answer
They regulate translation, RNA processing, and gene expression beyond coding proteins.
4
Question
What are microRNAs (miRNAs)?
Answer
Small ~22 nt RNAs that regulate gene expression by mRNA silencing.
5
Question
What percentage of the genome is protein-coding?
Answer
Approximately 2%.
6
Question
What is the transcriptome?
Answer
The full set of RNA transcripts produced from the genome.
7
Question
How can comparative genomics help identify functionally important human sequences?
Answer
By comparing human sequences to orthologs in other species to find conserved regions.
8
Question
What is an ortholog?
Answer
A gene in another species that evolved from a common ancestral gene and retains function.
9
Question
Why are ultraconserved elements notable in vertebrate genomes?
Answer
They are perfectly conserved across distant species, suggesting essential regulatory roles.
10
Question
What does purifying selection imply about a sequence?
Answer
Deleterious mutations are removed, conserving the sequence.
11
Question
What type of sequence conservation signals functional importance in genomics?
Answer
Regions that change slowly across species show functional importance.
12
Question
What are L1 elements and Alu elements?
Answer
Both are common dispersed repetitive elements in the genome (LINES and SINES).
13
Question
What does the acronym LINES stand for?
Answer
Long interspersed nuclear elements.
14
Question
What does the acronym SINES stand for?
Answer
Short interspersed nuclear elements.
15
Question
Approximately what fraction of the genome is composed of dispersed repeats?
Answer
About 45%.
16
Question
What is copy-number variation (CNV)?
Answer
Differences in the number of copies of a gene across individuals.
17
Question
In the context of genome evolution, what are segmental duplications?
Answer
Large duplicated segments of chromosomes that contribute to gene copies.
18
Question
What is a gene duplication event?
Answer
Replicates a gene or genomic region, creating extra copies.
19
Question
What is meant by single-copy versus multi-copy genes?
Answer
Some genes exist in one copy; others have multiple copies in the genome.
20
Question
What do comparative genomics studies use to identify conserved regulatory elements?
Answer
Cross-species sequence conservation and functional assays.
21
Question
What is the main idea behind the gene ontology?
Answer
A system classifying gene products by cellular component, molecular function, and biological process.
22
Question
What are two primary roles of RNA in protein synthesis?
Answer
mRNA as messenger; tRNA and rRNA in translation machinery.
23
Question
What is the average length of a microRNA?
Answer
About 22 nucleotides.
24
Question
Why might many ncRNAs be transcribed despite unknown functions?
Answer
They may have regulatory roles or represent transcriptional noise.
25
Question
What is the significance of conserved sequences between human and chimpanzee?
Answer
Indicates strong functional constraint and importance.
26
Question
How does natural selection influence conserved genomic regions?
Answer
It removes deleterious mutations, maintaining functional sequences.
27
Question
What does ultraconserved element uc.223 illustrate?
Answer
Extreme conservation across species implies essential regulatory function.
28
Question
What is the functional implication of enhancer activity observed in ultraconserved elements?
Answer
They can regulate gene expression in vivo.
29
Question
How does repetitive DNA impact genome size and structure?
Answer
It expands genome size and contributes to regulatory and structural roles.
30
Question
What is meant by protein-centric view of gene regulation?
Answer
Emphasizing proteins as primary regulators while RNAs also play roles.