Prokaryotic Gene Expression Regulation Quiz 4

Study Notes

Prokaryotic Gene Expression Regulation

Nucleoid shape is influenced by NAPs (nucleoid-associated proteins), non-coding RNAs (ncRNAs), and transcription processes. NAPs have structural and regulatory functions, impacting chromosome shape, interactions with ncRNAs, transcription, and silencing.
DNA methylation primarily occurs at guanine (G) bases.
The Restriction-Modification (R-M) system protects bacterial genomes by using methylases and endonucleases to identify and destroy foreign DNA while preserving the host DNA.
RNA turnover is affected by RNase abundance, location, and interactions with other molecules (including non-coding RNAs). Changes in RNA turnover affect protein availability.
Translation in bacteria can be regulated through ribosome binding sites, codon usage bias, and post-translational modifications.
Riboswitches and attenuation are examples of cis-encoded non-coding RNA (ncRNA) elements that directly affect gene expression.
Cis-encoded ncRNAs are located within the same gene, differing from trans-encoded ncRNAs, which are located elsewhere in the genome. In bacteria, they affect transcription, translation, mRNA stability, and xenogenic silencing.
Activators and repressors play roles in initiating or stopping transcription in bacteria, using methods such as steric hindrance, roadblocks, DNA looping or altering activator function.
Inducible operons are expressed only when a specific substrate is present.
Repressible operons are usually on but can be turned off by a repressor.
The lac operon is influenced by both positive and negative control mechanisms. High lactose, low glucose conditions result in the expression of genes in the lac operon.
The trp operon is both inducible and repressible. Trytophan presence leads to repression.
The two hairpins (2:3 and 3:4) in the trp operon are critical for regulation, with the 2:3 structure acting as an antiterminator, while the 3:4 one acts as an attenuator.

Eukaryotic Gene Expression Regulation

Chromatin structure and the genome affect gene expression. Genes within the active, euchromatic regions are typically unmethylated and toward the interior of the nucleus.
DNA methylation primarily occurs at adenine (A) bases.
In eukaryotes, gene expression is defined by the methylation patterns of the genome, not solely methylated DNA.
Imprinted loci are characterized by differential methylation patterns on the maternal and paternal chromosomes, resulting in different gene expression.
CpG islands and transposable elements are often methylated regions of the genome.
X-inactivation is an epigenetic process during early embryonic development that balances X-linked gene expression.
Transcriptional regulation can involve nucleosome positioning, use of alternative promoters and terminators, enhancers, ncRNAs, and the global epigenetic landscape.
Non-coding RNAs (ncRNAs) can impact transcription in various ways, including anti-sense regulation and influencing DNA methylation patterns.
Alternative splicing is a crucial post-transcriptional gene expression mechanism.
Post-transcriptional gene regulatory mechanisms include modifications and processing to the RNA transcripts (for example: base modifications, RNA turnover, and RNA editing).
In eukaryotes, translation is a target of regulation.