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Summary Fundamentals of Genetics-GEN11806
- Instelling
- Wageningen University (WUR)
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Chapter 12: Regulation of transcription12.1
There are two sets of regulatory proteins: ones that bind directly to DNA and ones that do not. The
first set of regulatory proteins binds to enhancers. Enhancers located closely to core promotors are
part of proximal promotors and are called proximal enhancers. Enhancers located further away are
called distal enhancers. General transcription factors (GTF) binds directly to DNA within core
promotors.
Coregulators (coactivators and corepressors) control the access and recruitment of transcription
factors to DNA and RNA polymerase 2.
Transcription factors can also bind other proteins. The C/EBP binds to the CCAAT box and enhancers.
Some transcription factors have a ligand-binding-domain (binds hormones, vitamins etc.)
All transcription factors contain a DNA binding site and activation/repressor site, some contain a
ligand-binding site and/or dimerization site.
An upstream activation sequence (UAS) has it’s enhancers located upstream of the genes they
regulate (at the 5’ end). Transcription factors coordinately regulate the transcription of multiple
genes involved in the same biological process by binding enhancers common to the genes.
Eukaryotes generally have common transcription regulatory machineries and mechanisms.
Modular means that aspects function independently of one another. Eukaryotic transcription factors
are modular.
Environmental signals alter the activity of eukaryotic transcription by controlling their interactions
with other proteins.
12.2
Core histones and linker histone are canonical histones, involved in packaging. Core histones form a
core complex around which DNA is wrapped to form nucleosomes. Linker histones bind to DNA that
links adjacent nucleosomes. Variant histones are incorporated into nucleosomes.
Core histones have three structural domains: histone folds ( located in the central region of histone
proteins, form alpha helices with hydrophobic interaction), histone-fold extensions and flexible tails
(at the ends of histone proteins, involved in interactions with other non-histone proteins).
Nucleosomes wrap around a histone octamer.
In eukaryotes, DNA is packaged with histone in chromatin. Nucleosomes, the units of chromatin,
each contain two of the copies of each of the core histones, around which is wrapped 146 base pairs
of DNA.
Regions of the genome with few genes, such as centromeres and telomeres are compacted in
heterochromatin throughout the cell cycle (constitutive heterochromatin). Regions that are gene-
rich vary in their level of chromatin (facultative heterochromatin).
Transcription start sites often located in a nucleosome free region (NFR)
Smaller regions of chromatin are organized into topologically associating domains (TADs) whose
DNA sequences preferentially contact one another
Insulators prevent enhancers and their associated transcription factors from activating the
transcription of genes outside of a TAD.
12. 3
Chromatin modification: enzymes alter the chemical structure of amino acids in histones or
nucleotides in DNA to affect recruitment of transcription factors, coregulators and GTF to chromatin.
,Chromatin remodeling: the energy of ATP hydrolysis is used by enzymes to reposition, remove or
replace histone octamers (canonical vs. variant) along the DNA.
Acetylation of histones is a post-translational modification. Acetyl neutralizes the positive charge of
the amino acid lysine, which makes it less drawn to the phosphate backbone of DNA. The DNA is thus
less compacted and more accessible for transcription.
Acetylation of lysines in histones by histone acetyltransferases (HATs) loosens interactions between
nucleosomes and creates a binding site for bromodomains, found in some transcription coregulators.
Transcription is regulated by chemical modifications of amino acids in histones and nucleotides in
DNA. Modifications are added by writer enzymes, removed by eraser enzymes and bound by reader
proteins.
The histone code hypothesis posits that different combinations of histone modifications create
unique binding sites that can be read by transcription coregulators, thereby conferring a variety of
transcriptional outcomes.
Methylation of cytosine in CpG islands at gene promotors is correlated with the repression of
transcription. Like modification of histone proteins, CpG methylation of DNA represses transcription
by altering the affinity of transcription factors, coregulators and GTF for chromatin.
Chromatin is dynamic, nucleosomes are not necessarily in fixed positions on the chromosome.
Chromatin remodeling complexes change nucleosome density, position and subunit composition to
control access of the transcription machinery to DNA.
12.4
There are four types of epigenetic control of transcription, cellular memory, position effect
variegation, genomic imprinting and X-chromosome inactivation.
Polycomb and Trithorax group proteins work in opposition to maintain the repressed and active
transcription states of parent cells in daughter cells.
Position effect variegation: the level of heterochromatin correlates with the level of transcription of
the gene.
Proteins involved in the spread of heterochromatin include writers, readers and erasers of histone
modification.
Paternal imprinting-> father’s copy is silenced
Maternal imprinting-> mom’s copy is silenced
For most diploid organisms, both alleles of a gene are expressed independently, but a few genes in
mammals undergo genomic imprinting.
In X-inactivation, epigenetic mechanisms enacted early in embryonic development silence an entire
chromosome. This to make up for the transcription difference between males and females, since
females have two X chromosomes.
, Chapter 2 Single-gene inheritance
2.1
Most common form of any trait is called the wild type, other phenotypes are called mutants.
The use of mutants to study a trait can be called genetic dissection, because the trait is picked apart
to reveal it’s underlying genetic program.
The genetic approach to understanding a trait is to discover the genes that control it. One approach
to gene discovery is to isolate mutants and check each one for single-gene inheritance patterns.
Pure lines-> all offspring produced by crossing in a pure line results in equal phenotypes for the pure
line trait.
At meiosis, the members of a gene pair segregate equally into the product cells. This is known as
Mendel’s law of equal segregation. Equal segregation is only observable in heterozygotes, making
them critical tools for genetic analysis.
All 1:1 , 3:1 and 1:2:1 genetic ratios are diagnostic of single-gene inheritance and are based on equal
segregation in a heterozygote.
Y/y x Y/y is also called a monohybrid cross.
2.2
Somatic cells undergo mitosis, meiocytes to produce sex cells undergo meiosis. Haploids can
undergo mitosis but not meiosis. The two members of a chromosome pair in diploid organisms are
called homologous chromosomes. The physical separation of chromosome pairs during anaphase 1
of meiosis is the basis for Mendel’s law of equal segregation.
Mitotic division results in the original chromosome number in the product cells. Meiotic division
results in half the original chromosome number in four product cells.
Haploids do not have true sexes, but mating types.
2.3
Mendelian inheritance is shown by any segment of DNA on a chromosome: by genes and their alleles
and by molecular markers not necessarily associated with any biological function.
Most mutations that alter the phenotype alter the amino acid sequence of the gene’s protein
product, resulting in reduced or absent function.
Null alleles: proteins encoding by these mutant alleles completely lack function.
Silent mutations: no impact, functionally wildtype
Leaky mutations: some wildtypes leak into mutant phenotype.
Haplosufficient means that one gene copy has enough function to produce a wildtype phenotype, in
this case, the null-mutant allele will be recessive. When genes are haploinsufficient, the null-mutant
allele will be dominant.
2.4
A dominant mutation in the heterozygous state will be expressed. A cross between heterozygous
dominant and wild type will result in a 1:1 phenotypic ratio in the progeny.
The cross of an individual with unknown heterozygosity with a known homozygous recessive is called
a testcross.
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