• Introduction
• Basic Genetic Mechanisms
• Eukaryotic Gene Regulation
• Test 1
• The Human Genome Projects
• Genome I - Genes
• Genome II – Repetitive DNA
• Genome III - Variation
• Test 2
• Genes and Diseases
• Pharmacogenomics
• Test 3
• Your Presentations
• Your Presentations
• Happy New Year!
Molecular GeneticsThe Human Genome: Biology and Medicine
http://priede.bf.lu.lv/ Studiju materiāli / MolekularasBioloģijas / MolGen / EN
http://priede.bf.lu.lv/ Studiju materiāli / MolekularasBioloģijas / MolGen / EN
Two ways of genome regulation
Genomes, 3rd Edition
Chromatin and gene activity
The types of interphase chromatin
The Positional effect – variability in gene expression that occurs after a new gene has been inserted into eukaryotic
chromosome
1. Euchromatin– the ‘usual ‘ form– contains (potentially) active genes
2. Heterochromatin– more condensed form– additional proteins (HP1)
– constitutive• no genes• feature of all cells• e.g., centromeric, telomeric DNA
– facultative• in some cells some of the time• inactive genes
Molecular Biology of the Cell, 5th Edition
Two ways in which chromatin structure can influence gene expression
Genomes, 3rd Edition , modified
heterochromatin – genes unaccessible
euchromatin - genes accessible
1
2Gene OFF Gene ON
Types of alterations in euchromatin structure
1. Modifications of histones• activating (here)• repressing
2. Nucleosome remodeling• remodeling (here)• histone replacement• histone removal
The major types of histone modifications
Recombinant DNA, 3rd Edition
Modifications of histones convey a specific meaning to chromatin (‘Histone code’)
Gene activity is substantially affected by DNA methylation
CG sequences; leads to silencing; CpG islands - usually in promoters
A model for the link between DNA methylation and gene silencing
Genomes, 3rd Edition (modificēts)
MeCP2protein
methyl-CpG-binding protein (MeCP) components of a histone deacetylase complex (HDAC)
Regulatory sequences and gene activity
Eukaryotes, like you, have many regulatory elements
Molecular Biology of the Gene, 5th Edition
Regulatory sequence – DNA sequence to which a gene regulatory protein binds
Major types of regulatory DNA elements in eukaryotes
S – silencer P – promoter I – insulator E – enhancer
TF – transkrition factor
heterochromatin
2010, 11, 439-446
o Promoters – recognition sequences for binding of RNA polymerase
o Enhancers – increase transcription of a related geneo Silencers – decrease transcription of a related gene
o Insulators or boundary elements – block undesirable influences on genes:1. enhancer blockers – prevent ‘communication’ between enhancers and
unrelated promoters2. barrier sequences – prevent spread of heterochromatin3. combined
o LCR – locus control regions – activate some gene clusters
Composition of regulatory DNA elements is modular
Genomes, 3rd Edition
RNA polymerase II promoter modules (Genomes, 3rd Ed.)
The core promoter moduleso in all promoterso BRE, TATA, Inr, DPEo recognised by general transcription factors
Basal promoter moduleso present in many RNA polymerase II promoterso set the basal level of transcription initiation, without responding to any tissue-specific signalso the CAAT box (recognised by the activators NF1 and NFY), the GC box (SP1)…
Response moduleso found upstream of various geneso enable response to general signals from outside of the cello CRE (the cyclic AMP response element) recognised by the CREB activator; SRE (serume response element), recognised by serume response factor…
Cell-specific moduleso are located in the promoters of genes that are expressed in just 1 type of tissueo the erythroid module, which is binding site for the GATA-1 activator; the myoblast module, recognised by MyoD…
Modules for developmental regulatorso mediate expression of genes that are active at specific developmental stages
Levine M & Tjian R (2003) Nature, 424, 147
This ensures efficient combinatorial control of gene expression
A model for the control region of the human -globin gene
What type of promoter recognition is characteristic to you?
Genomes, 3rd Edition
Transcription initiation in eukaryotes requires General Transcription Factors (TF)
Some genes have alternative promoters, eg, dystrophin gene
Genomes, 3rd Edition
Cilvēka distrofīna gēns
Alternative promoters
C, cortical tissues; M, muscle; Ce, cerebellum; R, retinal tissue (and also
brain and cardiac tissue); CNS, central nervous system (and also kidney);
S, Schwann cells; G, general (most tissues other than muscle).
Eukaryotic transcription initiation also needs activator proteins
Genomes, 3rd Edition
Activators aid the assembly of the transcription initiation complex
Activator
Chromatin remodelling or modifying complexes
Multi-subunit cofactors(mediators)
Levine M & Tjian R (2003) Nature, 424, 147
Activators may act from a large distance
Two models: (i) direct-contact model (here); (ii) tracking model
Writing and reading the histone code during transcription initiation
INSULATORS divide genome into functional domains
gene A enhancer gene B
insulator(enhancer blocker)
insulator(barrier sequence)
Insulators prevent inappropriate activation from enhancers thus maintaining the independence of
a functional domain
Molecular Biology of the Gene, 5th Edition
Models for enhancer-blocking activity
E – enhancerEB - enhancer-blocker proteins
A model for establishment of silencing and barrier activity
2010, 11, 439-446
S – silencer, B – barrier elements, TF – transcription factor, CR – chromatin remodellers, HM – histone-modifying enzymes, R – repressor proteins
Activity of some gene clusters requires LCRs
Composition of chicken -globin LCR
Vol. 7, 703-713
RNA interference
miRNA (micro RNA)• Regulation of gene expression – at least 30% of
human genes• Precursor (pre-miRNA) – single-stranded RNA• Origin – transcripts of cell
siRNA (small interfering RNA)• Defense against viruses and expansion of transposons• Precursor – double-stranded RNA• Origin - various
Phenomenon when very short RNAs (21-22 nts) repress – or silence – expression of genes with
homology to those RNAs
RISC = RNA-induced silencing complex
dsRNA = double-stranded RNA
RISC = RNA-induced silencing complex
dsRNA = double-stranded RNA
Mechanism of RNA interference
Molecular Biology of the Gene, 6th Edition (modified)
miRNA processing and mechanism of action
miRNAs are coded in both coding and noncoding sequences
Molecular Biology of the Gene, 6th Edition (modified)
EPIGENETICS
Waddington, 1942: “[T]he branch of biology which studies the causal interactions between genes and their products, which bring the phenotype into being” (epi[genesis] +genetics).
Literally: epi (Greek: επί- on, over) genetics – something working above DNA.
EPIGENETIC INHERITANCE
Any heritable difference in the phenotype of a cell that does not result from changes in the nucleotide sequence of DNA
Specific epigenetic phenomena: 1. dosage compensation: a) X-chromosome inactivation; b) mono-allelic expression; 2. imprinting (parent-of-origin specific differences in gene activity)
Inheritance of DNA methylation
DNMT1 (DNA methyltransferase 1)
Inheritance of histone modifications
Imprinting
Mechanism of imprinting in the mammalian Igf2 locus
Molecular Biology of the Gene, 5th Edition
X chromosome inactivation
Mechanism of mammalian X chromosome inactivation
XIC : X-inactivation center XIST: X-inactivation specific transcript
Molecular Biology of the Gene, 6th Edition
Identical twins are not identical
Phenotype = Genotype + Epigenotype + Environment
• Introduction
• Basic Genetic Mechanisms
• Eukaryotic Gene Regulation
• Test 1
• The Human Genome Projects
• Genome I - Genes
• Genome II – Repetitive DNA
• Genome III - Variation
• Test 2
• Genes and Diseases
• Pharmacogenomics
• Test 3
• Your Presentations
• Your Presentations
• Happy New Year!
Molecular GeneticsThe Human Genome: Biology and Medicine
http://priede.bf.lu.lv/ Studiju materiāli / MolekularasBioloģijas / MolGen / EN
http://priede.bf.lu.lv/ Studiju materiāli / MolekularasBioloģijas / MolGen / EN
