Gene Expression In Eukaryotes

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Chromosome Territories

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Regions of the nucleus preferentially occupied by particular chromosomes

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Transcription Factories

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Hotspots for gene transcription where all the machinery for transcription are located (e.g., RNA polymerase)

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Nucleosome

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A basic unit of DNA packaging in eukaryotes, consisting of a segment of DNA wound in sequence around eight histone protein cores

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Interchromosomal Domains

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Channels between chromosomes that contain little or no DNA

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"Closed" Chromatin

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The tight association of DNA with nucleosomes and other chromatin-binding proteins that inhibits access of the DNA to the proteins involved in many functions including transcription

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"Open" Chromatin

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"Open" to transcription regulatory factors and enzymes such as RNA polymerases

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Histone Acetyltransferase

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Enzyme that catalyzes histone acetylation to result in "open" chromatin conformation

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Acetylation

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Decreases the positive charge on histones, resulting in a reduced affinity of the histone for DNA. In turn, this may assist the formation of open chromatin conformations which would allow the binding of transcription regulatory proteins to the DNA

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Histone Deacetylases

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Remove acetyl groups from the N-terminus to result in "closed" chromatin conformation

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Chromatin Remodelling Complexes

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Multi-subunit complexes that use ATP to move and rearrange nucleosomes along the DNA to make regions of the chromosome accessible to transcription regulatory proteins

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CpG Islands

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CpG rich regions of the genome where methylation tends to occur

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Hemimethylated

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New strand is not methylated, old strand is methylated

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Maintenance Methylation

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Process that methylates non-methylated daughter strand as well

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Genetic Imprinting

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- Epigenetic phenomenon by which certain genes are expressed in a parent-of-origin specific manner

- An imprinted allele is said to be "silenced"

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Promoter Elements

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Short nucleotide sequences within promoters that bind specific regulatory factors

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Core Promoter

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Determines the accurate initiation of transcription by RNAP II

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Proximal Promoter Elements

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Those that modulate the efficiency of basal levels of transcription

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Focused Promoter

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- Specifies transcription initiation at a single specific nucleotide (the transcription start site)

- Associated with genes whose transcription levels are highly regulated

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Dispersed Promoters

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- Promoters that direct initiation from a number of weak transcription start sites located over a 50-100 nucleotide region to produce multiple transcripts

- Common in vertebrates

- Associated with genes that are transcribed constitutively

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Enhancer

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- DNA sequence that regulates transcription by increasing transcriptional level by 1000 - 10 000 fold

- Can be located on either side of a gene, at some distance from the gene, or within the gene

- Cis-acting

- Both front and reverse orientation of the enhancer can be understood

- Placing an enhancer in front of a new gene will result in the enhancing of that gene

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Silencer

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- DNA sequence that acts upon eukaryotic genes to repress the level of transcription initiation

- Cis-acting

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Activator

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A transcription factor that increases levels of transcription

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Repressor

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A transcription factor that reduces levels of transcription

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General Transcription Factors

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Transcription factors necessary for basal levels of transcription

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Regulatory Transcription Factors

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Transcription factors that influence the ability of RNA polymerase to transcribe

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DNA-Binding Domain

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- Region of transcription factor that binds to specific DNA sequences present in the cis-acting regulatory site

- Characteristic 3D structures are:

1) helix-turn-helix motif

2) zinc finger motif

3) basic leucine zipper motif

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Helix-Turn-Helix Motif

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- One characteristic 3D structure of a DNA-binding domain of both eukaryotic and prokaryotic transcription factors

- "Turn" of several amino acids

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Zinc-Finger Motif

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- One characteristic 3D structure of a DNA-binding domain of transcription factors

- Recognition helix often has positively charged amino acids that help it bind to negatively charged DNA

- Beta sheets and alpha sheets are connected by zinc

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Basic Leucine Zipper Motif

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- One characteristic 3D structure of a DNA-binding domain of transcription factors

- Contains a region called a leucine zipper that maintains a coil formation

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Alternative Splicing

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Generation of different forms of mRNA from identical pre-mRNA molecules, so that expression of one gene can give rise to a number of proteins, with similar or different functions

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AU - Rich Element

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- Stretch of A and U ribonucleotides located in the 3' untranslated regions of mRNAs that have short, regulated half lives

- Recruit degrading protein complexes

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p53 Protein

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- Important example of post translational regulation

- Essential to protect normal cells from the effects of DNA damage and other stresses

- Transcription factor that increases the transcription of a number of genes whose products are involved in cell-cycle arrest, DNA repair and apoptosis

- Quantity increases when the cell is under stress

- Ubiquine marks p53 for degradation under normal cellular conditions

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Decapping Enzymes

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Enzymes that remove the 7-methylguanosine cap rendering the mRNA unstable

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Nonsense-Mediated Decay

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- Example of endonucleolytic cleavage that determine mRNA stability

- Occurs when translation terminates at premature stop codons

- Endonucleases attack the mRNA near the stop codon, leaving unprotected ends that are degraded by exonucleases

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Small Interfering RNAs (siRNA)

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- Involved in RNA-induced gene silencing

- Short, double-stranded RNA molecules derived from longer RNA molecules that are linear, double-stranded and located in the cell cytoplasm

- In nature, arise as a result of viruses or the expression of transposons (which synthesize double-stranded RNA during their life cycles)

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Dicer

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- Enzyme complex that cleaves RNAs to make siRNA

- Recognizes double-stranded RNA

- Used in the lab

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Micro RNAs (miRNA)

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- Involved in RNA-induced gene silencing

- Short, double-stranded RNA molecules derived from single-stranded RNAs that are transcribed within the nucleus from the cel's own genome and that contain a double-stranded stem-loop structure (stem loop is cleaved and its fragments are exported our of the nucleus)

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RNA-Induced Silencing Complex

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Enzyme complex involved in RNA-induced gene silencing

- Associates with siRNA or miRNA to denature short, double-stranded RNA and degrade the sense strand

- As an RNA-RISC complex, it seeks out mRNA molecules that are complementary to the anti-sense strand to cleave or bind them

- mRNA molecules that are not quite complementary to the anti-sense strand are bound to inhibit translation

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RNA-Induced Transcription Silencing Complex

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- Enzyme complex involved in RNA-induced silencing

- Associates with siRNA or miRNA and targets specific gene promoters or larger regions of chromatin to recruit chromatin modification enzymes

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Antigen

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A molecule, usually a protein, that brings about an immune response

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Immunoglobulin (Antibody)

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- Synthesized by B lymphocytes (B cells) that undergo development and maturation in the bone marrow'

- Molecules consist of 4 polypeptide chains - two identical light chains and two identical heavy chains

- Y-shaped

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Constant Region

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Region at the C-terminus of light and heavy chains of an immunoglobulin molecule

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Variable Region

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- Region at the N-terminus of light and heavy chains of an immunoglobulin molecule

- 4 variable regions form a unique structure that recognizes one specific antigen

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B Cell

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- B lymphocyte

- Type of blood cell that synthesizes immunoglobulins

- Each B cell synthesizes only one type of immunoglobulin