1. Transcription regulation
BS222 – Genome Science Lecture 4
Transcription regulation
Dr. Vladimir Teif

2. Module structure
Genomes, sequencing projects and genomic databases (VT) (Oct 9, 2018)
Sequencing technologies (VT) (Oct 11, 2018)
Genome architecture I: protein coding genes (VT) (Oct 16, 2018)
Genome architecture II: transcription regulation (VT) (Oct 18, 2018)
Genome architecture III: 3D chromatin organisation (VT) (Oct 23, 2018)
Epigenetics overview (PVW) (Oct 25, 2018)
DNA methylation and other DNA modifications (VT) (Oct 30, 2018)
NGS applications I: Experiments and basic analysis (VT) (Nov 1, 2018)
NGS applications II: Data integration (VT) (Nov 8, 2018).
Comparative genomics (JP, guest lecture) (Nov 13, 2018)
SNPs, CNVs, population genomics (LS, guest lecture) (Nov 15, 2018)
Histone modifications (PVW) (Nov 20, 2018)
Non-coding RNAs (PVW) (Nov 22, 2018)
Genome Stability (PVW) ) (Nov 27, 2018)
Transcriptomics (PVW) (Nov 29, 2018)
Year's best paper (PVW) (Dec 6, 2018)
Revision lecture (all lecturers; spring term)

3. What is oversimplified in this video?
Watch this video:
What is oversimplified in this video?

4. Gene regulation involves many steps
Signal transduction from the cell membrane to the cytoplasm to the nucleus (next year, BS327)
Chromatin organization defines accessibility of regulatory regions (next lecture)
Transcription regulation:
Transcription initiation (this lecture)
Transcription elongation
Transcription termination
Processing of RNA (BS221, next week)
Translation (mRNA, microRNAs)
Post-translational regulation (later, this module)

5. Example of cell signalling

6. Signal molecules enter the nucleus, then the signal has to reach the DNA

7. TF-centric view of gene regulation
Transcription factor (TF) concentrations
Protein assembly at regulatory regions
Transcription start site
Proteins produced (including TFs)
Teif et al. (2013), Methods. 62, 26-38

8. TF-centric view of gene regulation
Transcription factor (TF) concentrations
Enhancer
RNA polymerase: enzyme which makes RNA
Promoter
Proteins produced (including TFs)
Teif et al. (2013), Methods. 62, 26-38

9. Prokaryotic vs. eukaryotic transcription

10. TF-DNA binding in gene regulation

11. Protein-DNA binding is very complex
Repair protein cradles
broken DNA
(Goldberg et al. 2001)
Lac repressor-DNA
complex (Lu et al. 1987)
CAP-DNA complex
(Steitz et al. 1984)

12. Stud-and-tube coupling
…Let’s make it simpler
Stud-and-tube coupling ?

13. …And even simpler! h n j m(g)
But this simple system of short DNA composed of 15 base pairs (bp) (blue) and proteins which cover 3 bp upon binding to DNA (yellow), can still be in
415 = 1,073,741,824 states! h
protein
DNA n
m(g) j
Strength of binding of
this protein to this site
Binding probability
Sum of probabilities of all
possible configurations
of bound proteins to this
DNA sequence

14. Transcription factor binding sites
Any TF can bind to any location on the DNA (if it is free), but different TFs bind different DNA sequence motifs with different affinities (different energies).
Why can they bind everywhere?
What does it mean “free”?
Why all locations have different affinities?
Most TFs can be characterised by a single motif that they “like”. It is called the consensus motif.
Genomic locations which contain sequences similar to the consensus motifs form TF binding sites

15. Learning TF-binding motifs in vitro
Geertz and Merkl (2010) Brief. Func. Genom., 9,

16. Combinatorial TF binding
Sequence
logo
DNA
Proteins
TF binding site
Gene
DNA
Regulatory region
Adapted from [Bejerano Fall09/10]

17. TF-DNA binding concepts
Sequence-specificity
Different protein types
Competitive binding
Nucleosome positioning

18. TF-DNA binding concepts
Cooperative binding
Multilayer assembly
Protein-induced DNA loops

19. Example: Bacteriophage  switch
Infection
Phage 
Lysis
Lysogeny UV

20. Ptaschne M. (2011) Nature Chemical Biology 7, 484–487

21. Bacterial promoters
Source:

22. CI
Cro
(RNAP)
Teif V.B. (2010) Biophys J., 98,

24. For this relatively simple bacterial system one can measure all binding energies in a test tube (in vitro)
Teif V.B. (2010) Biophys J., 98,

25. For each set of TF concentrations we can calculate TF binding maps
…calculate binding maps
For each set of TF concentrations we can calculate TF binding maps
Teif V.B. (2010) Biophys J., 98,

26. For any concentrations of proteins CI and Cro we can predict the activity of genes PR and PRM
Wild-type phage 
Phage  mutant
Teif V.B. (2010) Biophys J., 98,

27. Thus, gene activity is a function of TF concentrations. Which function?
Figure from Mayo et al., 2006
Teif V.B. (2010) Biophys J., 98,

28. Can we “digitise” gene regulation functions for all genes?

29. Gene networks
Blais and Dynlacht (2005) Genes Dev., 19,

31. Eukaryotic transcription factors
General transcription factors are involved in the formation of a transcription pre-initiation complex. Examples: TFIIA, TFIIB, TFIID, TFIIE, TFIIF, and TFIIH.
Specific transcription factors bind at promoters, enhancers and other regulatory regions. They can be distinguished by structure.
Pioneering transcription factors are able to bind to packed chromatin and clear the way for other
weaker transcription factors.

32. Eukaryotic promoters do not have a fixed structure (unlike prokaryotes). They may have different modules:

33. Example: herpes virus promoter

34. Eukaryotic promoter classification
TATA-containing (~24%) - usually with many additional elements.
TATA-less – many of them are “housekeeping” genes which are always expressed
INR-containing (~46%)
CpG island containing (~72%) – these are regulated by DNA methylation
Bidirectional (~10%) – transcription of overlapping genes in both direction

35. Gene enhancers
Enhancer is a DNA region that can be bound by transcription factors to increase the likelihood that transcription of a particular gene will occur.
Chromatin conformation loops and long-range gene regulation. (a) Linear representation of a gene (green box) regulatory landscape showing the position of the gene promoter (brown oval), the immediately proximal regulatory elements (light blue box), and the distal regulatory enhancer (dark blue box), which may be located hundreds or thousands of kilobases from the gene promoter. (b–d) Models of chromatin conformation that may underlie enhancer-promoter communication. In panel b, factors (transcription factors, coactivators, and chromatin remodeling complexes) bound to the enhancer and promoter reorganize the intervening chromatin into a loop that juxtaposes the distal enhancer and gene promoter. In panel c, enhancer-promoter interactions occur by the formation of chromatin miniloops; this model may be particularly applicable to complex regulatory landscapes composed of multiple dispersed enhancer elements. In panel d, the regulatory elements are in a chromatin conformation that keeps them relatively close to the gene promoter but does not necessitate direct enhancer-promoter contact. Factors can diffuse locally from the enhancer to the promoter.

36. Enhanceosome: higher-order protein complex assembled at the enhancer
ß-interferon
enhancer

37. Enhanceosome: higher-order protein complex assembled at the enhancer
ß-interferon enhancer

38. Promoters & enhancers have common features
Kim and Shiekhattar (2015), Cell, 162,

39. How enhancers help promoters regulating gene expression?
Li et al. (2016) Nature Reviews Genetics, 17,

40. How enhancers help promoters regulating gene expression?
Li et al. (2016) Nature Reviews Genetics, 17,

41. How enhancers help promoters regulating gene expression?
Li et al. (2016) Nature Reviews Genetics, 17,

42. How enhancers help promoters regulating gene expression?
Li et al. (2016) Nature Reviews Genetics, 17,

43. Insulators can disrupt promoter/enhancer interactions
Eeckhoute et al., J Cell Science (2009) 122,

44. Levels of cis-regulation:
1) Protein-binding DNA sequence motifs:
TATA box, etc
TF binding sites (TFBS)
2) Cis-regulatory modules composed of several motifs:
Promoters
Enhancers
Insulators
3) Integration over several cis-regulatory modules:
Gene regulatory networks (GRN)
Chromatin domains (will discuss in next lectures)

45. Take home message Cooperative, combinatorial TF binding
TF binding determines when and where to start transcription by RNA polymerase
MUST KNOW:
PROMOTER, ENHANCER, INSULATOR
CIS-REGULATORY REGION, TRANSCRIPTION FACTOR (TF),
Cooperative, combinatorial TF binding
RNA POLYMERASE (RNAP, Pol II)
PROMOTER-ENHANCER INTERACTION
Transcription initiation in prokaryotes vs. eukaryotes
TF binding site (TFBS), consensus motif