Genes and Genomes Exam Prep

Cards for Gene Expression

What is gene expression?

The process by which information in DNA is transcribed into RNA and translated into protein; its level (mRNA abundance) reflects gene activity.

Define the transcriptome

The complete set of RNA transcripts present in a cell or tissue at a given time, including mRNAs, ncRNAs and isoforms.

What are the three main regulatory layers that generate expression variation?

Transcriptional control (promoters, enhancers); 2) Chromatin context (histone PTMs, DNA methylation); 3) Post-transcriptional control (alternative splicing, miRNAs). Ultimately determine the amount and timing of gene expression.

How does a promoter differ from an enhancer?

The promoter is a proximal region (~100 bp) at the TSS recruiting Pol II and basal TFs; an enhancer is a distal element (50–1,500 bp) that binds TFs to loop and boost or silence transcription.

What effect does histone acetylation have on chromatin?

HATs add acetyl groups to H3/H4 lysines, neutralizing positive charges, loosening nucleosome–DNA interaction and promoting transcription; HDACs reverse this

Where does DNA methylation occur and how does it silence genes?

CpG islands in promoters (5′–3′ CG dinucleotides). DNMT3A/B lay down 5-mC de novo; DNMT1 maintains it. Methylation blocks TF binding and recruits methyl-CpG binding repressors to condense chromatin.

One key strength and one limitation of qPCR, microarrays and RNA-seq?

• qPCR: + Ultra‐sensitive quantification; – Low throughput, needs prior target design.

• Microarray: + Simultaneous profiling of ~10⁴ genes; – Cross-hybridization, limited dynamic range, no novel transcripts.

• RNA-seq: + Base-pair resolution & discovery of novel isoforms; – Bioinformatics-intensive, batch effects, higher cost.

Name three common pitfalls when interpreting RNA-seq data.

Batch effects (library prep/sequencer differences), 2) Alignment biases (repetitive regions, reference-genome gaps), 3) Normalization choices (RPKM vs. TPM vs. raw counts) can skew differential-expression calls.