CBG L09: Control of Gene Information

Comprehensive vocabulary flashcards covering the transcriptional, post-transcriptional, translational, chromatin, and epigenetic levels of gene regulation from the CBG L09 lecture.

Genome

The complete set of genetic information in a cell.

Transcriptome

The collection of RNA transcripts expressed in a cell at a particular time.

Proteome

The collection of proteins expressed in a cell at a particular time.

Phenotype

The observable characteristics and functional properties of a cell or organism.

Constitutive expression

A pattern of gene expression where a gene is expressed relatively consistently because its product is required for basic cellular functions.

Differential expression

A pattern of gene expression where a gene is expressed at different levels, or not expressed at all, depending on the cell type or physiological conditions.

Promoter

A DNA region near the transcription start site that provides binding sites for general transcription factors, helps recruit and position RNA polymerase II, and establishes where transcription begins.

TATA box

A promoter-associated DNA sequence recognised by the TATA-binding protein (TBP), which forms part of the transcription-initiation machinery.

Enhancers

Regulatory DNA sequences that bind sequence-specific transcription factors to increase transcription of target genes, operating with distance and orientation independence.

Transcription factors

Proteins that bind specific DNA sequences to influence transcription by activating or repressing gene expression and recruiting co-activators or regulatory complexes.

Enhancer modularity

The property of gene regulation wherein different enhancers independently direct expression in different tissues, developmental stages, or physiological conditions.

AP-1

A dimeric transcription factor composed of Fos and Jun family proteins that contains a leucine zipper and basic residues, which can be activated downstream of the MAP kinase pathway.

even-skipped (eve)

A fruit-fly developmental gene expressed in $7$ stripes along the embryo, regulated by multiple modular enhancers that each drive expression in specific stripes.

Alpha-thalassaemia

A disorder characterised by reduced alpha-globin production and impaired haemoglobin formation, which can be caused by a mutation in a transcription-factor binding site within an enhancer.

Exons

Sequences retained in mature RNA after splicing that often contain protein-coding information or untranslated regions.

Introns

Non-coding sequences removed from pre-mRNA during RNA splicing.

Alternative splicing

A regulatory mechanism that allows a single gene to generate different mature mRNA transcripts and protein isoforms by including or excluding particular exons.

Beta-thalassaemia

A condition caused by impaired haemoglobin production, which can result from a splice-site mutation that disrupts the inclusion of exon $2$ in mature beta-globin mRNA.

RNA localisation

The transport of selected mRNAs to specific cellular locations prior to translation, often directed by sequences in the $3'$ untranslated region ($3'\text{ UTR}$).

Ferritin

A cellular protein that safely stores iron to prevent the generation of harmful reactive oxygen species, including hydroxyl radicals, via the Fenton reaction.

Iron-responsive element (IRE)

A stem-loop regulatory sequence in the $5'$ UTR of ferritin mRNA that binds iron regulatory proteins when iron is low to inhibit translation initiation.

MicroRNAs (miRNAs)

Short non-coding RNAs that bind complementary sequences in target mRNAs to promote RNA destabilisation, degradation, or translational repression via the RNA-induced silencing complex (RISC).

Ubiquitin

A small regulatory protein attached to target proteins as a signal marking them for degradation by the proteasome.

Proteasome

A cellular protein complex that recognises appropriately ubiquitinated proteins and degrades them into smaller peptides.

Nucleosome

The basic structural unit of chromatin, composed of approximately $147\text{ base pairs}$ of DNA wrapped around an octamer core of two copies each of histones H2A, H2B, H3, and H4.

Epigenetic regulation

Mechanisms that produce changes in gene activity and expression patterns without altering the underlying DNA base sequence.

Writers, erasers, and readers

The tripartite machinery of the histone code, where writers add chemical modifications, erasers remove them, and readers interpret modifications to recruit regulatory complexes.

H3K4 methylation

A histone modification commonly associated with active promoters and gene activation.

H3K9 methylation

A histone modification commonly associated with transcriptional repression and heterochromatin.

H3K27 methylation

A histone modification commonly associated with gene repression, including stable developmental silencing mediated by Polycomb complexes.

H3K27M

A lysine-to-methionine mutation at residue $27$ of histone H3 that disrupts normal methylation regulation in paediatric diffuse midline gliomas.

CpG site

A DNA dinucleotide sequence where cytosine is followed by guanine on the same strand, serving as the primary site for DNA methylation in mammalian cells.

Barr body

The dense, highly compacted inactive X chromosome visible in the nuclei of female mammalian somatic cells.

Mosaicism

The presence of distinct cell populations with different active alleles in a single individual, exemplified by orange and black coat-colour patches in female calico cats resulting from random X-chromosome inactivation.