From genes to func.on Gene regula.on and transcrip.on

Transcription

1 From genes to func.on Gene regula.on and transcrip.on Systems biology for system engineers Part 2 Sofia Pe(ersson Informa.on Coding Dept. of Electrical Engineering Linköping University

2 The eukaryo.c cell For this seminar we will focus on Ribosomes Cell nucleus Nuclear envelope

3 The genome and its subunits Nucleo7de = Building blocks of DNA and RNA (A, C, G, T and U) wikipedia.org/dna

4 The genome and its subunits Nucleo7de = Building blocks of DNA and RNA (A, C, G, T and U) DNA = double- stranded chain of nucleo.des wikipedia.org/dna

5 The genome and its subunits Nucleo7de = Building blocks of DNA and RNA (A, C, G, T and U) DNA = double- stranded chain of nucleo.des Basepair = two opposing nucleo.des (C G, A T/U) wikipedia.org/dna

6 The genome and its subunits Nucleo7de = Building blocks of DNA and RNA (A, C, G, T and U) DNA = double- stranded chain of nucleo.des Basepair = two opposing nucleo.des (C G, A T/U) Codon = three sequen.al nucleo.des encoding a specific amino acid wikipedia.org/genetic Code

7 The genome and its subunits Nucleo7de = Building blocks of DNA and RNA (A, C, G, T and U) DNA = double- stranded chain of nucleo.des Basepair = two opposing nucleo.des (C G, A T/U) Codon = three sequen.al nucleo.des encoding a specific amino acid Gene = specific part of the genome encoding a protein or RNA molecule DNA Figure 7-10 Essential Cell Biology ( Garland Science 2010)

8 The genome and its subunits Nucleo7de = Building blocks of DNA and RNA (A, C, G, T and U) DNA = double- stranded chain of nucleo.des Basepair = two opposing nucleo.des (C G, A T/U) Codon = three sequen.al nucleo.des encoding a specific amino acid Gene = specific part of the genome encoding a protein or RNA molecule Genome = the en.re DNA code

9 DNA organiza.on in the cell The DNA- helix is wrapped around histone proteins together forming the nucleosome and chroma.n subunits that are condensed into the chromosomes

10 DNA organiza.on in the cell

11 From genes to func.on Gene ac7va7on End product What happens when a gene is ac.vated and how is the end product assembled?

12 From genes to func.on Gene ac7va7on End product Ac.va.on Capping, splicing and export Transport Transcrip.on Transla.on

13 From genes to func.on Ac.va.on Capping, splicing and export Transport Transcrip.on Transla.on

14 Transcrip.on factors A transcrip.on factor is a protein that binds to specific parts of the genome and ac.vates a specific gene howardhughes.trinity.duke.edu

15 Promoter binding Each gene has a promoter region containing a specific binding site that is recognized by the transcrip.on factor. The promoter region lies upstream from the start- of- transcrip.on site. The gene is transcribed from the 3 end of the template strand. Figure 7-10 Essential Cell Biology ( Garland Science 2010)

16 Transcrip.on complex Transcrip.on factor binding is required to form the transcrip.on complexes. This complex includes histone- and chroma.n- modifying molecules as well as RNA polymerase. bea.ki.se

17 From genes to func.on Ac.va.on Capping, splicing and export Transport Transcrip.on Transla.on Ac7va7on Output Loca.on Key players Ac.ve transcrip.on complex at correct site of genome Nucleus Transcrip.on factors, DNA unraveling proteins, RNA polymerase

18 From genes to func.on Ac.va.on Capping, splicing and export Transport Transcrip.on Transla.on

19 Transcrip.on complex Transcrip.on factor binding is required to form the transcrip.on complexes. This complex includes histone- and chroma.n- modifying molecules as well as RNA polymerase. Figure 8-12 Essential Cell Biology ( Garland Science 2010)

20 RNA polymerase RNA polymerase moves along the gene, unwinds the DNA double helix and makes a complementary single- stranded copy of the DNA RNA. Figure 7-7 Essential Cell Biology ( Garland Science 2010)

21 RNA There are several types of RNA that carry out different func.ons. Table 7-1 Essential Cell Biology ( Garland Science 2010)

22 RNA polymerase There are three types of RNA polymerases. For protein- coding genes, RNA polymerase II is ac.ve. Table 7-2 Essential Cell Biology ( Garland Science 2010)

23 Transcrip.on Alberts et al., Essential Cell Biology 2, Garland Science (2004)

24 From genes to func.on Ac.va.on Capping, splicing and export Transport Transcrip.on Transla.on Transcrip7on Output Loca.on Key players RNA strand Nucleus RNA polymerase

25 From genes to func.on Ac.va.on Capping, splicing and export Transport Transcrip.on Transla.on

26 Capping The mrna is modified, or capped, at both ends. The 5 end is quickly capped with a CH 3 - cap, while the 3 end gets a poly- A tail at the end of transcrip.on Figure 7-16a Essential Cell Biology ( Garland Science 2010)

27 Capping The mrna is modified, or capped, at both ends. The 5 end is quickly capped with a CH 3 - cap, while the 3 end gets a poly- A tail at the end of transcrip.on Capping serves two purposes: i) To protect the mrna molecule from degrada.on ii) To enable recogni.on during transla.on Figure 7-16a Essential Cell Biology ( Garland Science 2010)

28 Splicing During splicing the non- coding sec.ons of the mrna, i.e. introns, are removed by a complex of small nuclear ribonucleoproteins (snrnps) called spliceosomes. The intron segments are excluded from the RNA and degraded. Intron loop forma7on Spliceosome forma7on Intron excision and degrada7on Mature mrna forma7on

29 Export The mrna needs to be transported from the nucleus to the ribosomes in the cytoplasm. Export is delayed un.l splicing is complete. Export is accomplished by an ac.ve transport by ribonucleoproteins up un.l the nuclear envelope (membrane), with a protein exchange taking place aaer the membrane is crossed. Figure 7-22 Essential Cell Biology ( Garland Science 2010)

30 From genes to func.on Ac.va.on Capping, splicing and export Transport Transcrip.on Transla.on Capping, slicing and export Output Loca.on Key players Protected and mature mrna molecule exi.ng nucleus Nucleus/cytoplasm Spliceosome, RNPs etc.

31 From genes to func.on Ac.va.on Capping, splicing and export Transport Transcrip.on Transla.on

32 The dic.onary Transla.ng the codon sequences of the gene, or rather the mrna copy, to corresponding amino acids. Figure 7-24 Essential Cell Biology ( Garland Science 2010)

33 The trna molecule The trna acts as a mediator or translator between the codon and the corresponding amino acid Phe: UUC Figure 7-28 Essential Cell Biology ( Garland Science 2010)

34 The ribosome Assembling the amino acids in the correct order and forming pep.de bonds between them. Three trna sites Two subunits containing proteins and RNA (rrna) molecules Figure 7-31 Essential Cell Biology ( Garland Science 2010) Figure 7-32 Essential Cell Biology ( Garland Science 2010)

35 Transla.on Figure 7-33 and 7-35 Essential Cell Biology ( Garland Science 2010)

36 Transla.on Figure 7-33 and 7-35 Essential Cell Biology ( Garland Science 2010)

37 Transla.on Alberts et al., Essential Cell Biology 2, Garland Science (2004)

38 Protein folding Aaer synthesis, the protein folds into a unique shape, given by its lowest energy state. The shape of the protein defines its biological func.on. An altered shape, by misfolding or interac.on with another molecule, alters the biological func.on. Primary structure Secondary structure Ter7ary structure Quaternary structure psu.edu

39 From genes to func.on Ac.va.on Capping, splicing and export Transport Transcrip.on Transla.on Transla7on Output Loca.on Key players Protein that has folded into its correct structure Cytoplasm Ribosomes, trna (amino acids)

40 From genes to func.on Ac.va.on Capping, splicing and export Transport Transcrip.on Transla.on Transport Output Loca.on Key players Ac.ve protein at site of ac.on Cytoplasm/nucleus/extracellular space Miscellaneous

41 From genes to func.on Ac.va.on Capping, splicing and export Transport Transcrip.on Transla.on The en.re chain, from gene ac.va.on to final transport of the synthesized protein, depends on intricate interplays between molecules. Several complexes needs to form, and there are many ways in which things can simply go wrong, either by chance or by design.

42 Control mechanisms There are ways to inac.vate the output func.on of a gene without shudng the gene off. Figure 8-3 Essential Cell Biology ( Garland Science 2010)

43 Control mechanisms Degrada7on Enzyma.c degrada.on or altera.on of the molecule Figure 8-3 Essential Cell Biology ( Garland Science 2010)

44 Control mechanisms Degrada7on Enzyma.c degrada.on or altera.on of the molecule Blocking Steric (physical) hindrance of a molecule or its binding site Figure 8-3 Essential Cell Biology ( Garland Science 2010)

45 Control mechanisms Degrada7on Enzyma.c degrada.on or altera.on of the molecule Blocking Steric (physical) hindrance of a molecule or its binding site Compe77on Simultaneous produc.on of compe.ng, superior protein Figure 8-3 Essential Cell Biology ( Garland Science 2010)

46 Control mechanisms In terms of modeling What is the raw data we are using ( input signal )? A posi.ve detec.on of mrna is not necessarily conclusive evidence that the protein is ac.ve Figure 8-3 Essential Cell Biology ( Garland Science 2010)

47 Transcrip.on control GENE OFF GENE ON Figure 8-17 Essential Cell Biology ( Garland Science 2010)

48 Transla.on control Figure 8-25a Essential Cell Biology ( Garland Science 2010)

49 Gene regulatory proteins What if the end product of a transcrip.on event is a protein that in turn regulates transcrip.on of another gene (or itself)? DNA - > RNA transcrip.on Gene ac.va.on Protein produc.on regulatory proteins transcrip.on factors all other proteins Signaling cascade or signaling pathway A series of sequen.al ac.va.ons of genes A à B à C

50 Ac.vators and repressors Ac7vator A protein that ini.ates or enhances ac.va.on of a transcrip.on factor and/or pathway TF- A > TF- B Repressor A protein that inhibits or diminishes ac.va.on of a transcrip.on factor and/or pathway TF- A TF- B

51 Signaling regula.ons There are several paherns for these types of regula.ons. Kim et al., ICSB 2011

52 Gene regulatory networks The regula.on paherns for a specific subset of genes can be summarized in gene regulatory networks. They can look like this Larsson et al., J of Theor Biol (2011)

53 Gene regulatory networks The regula.on paherns for a specific subset of genes can be summarized in gene regulatory networks. They can also look like this pnas.org

54 Gene regula.on in development All cells in a mul.cellular organism stem from one cell Through asymmetry breaking events (more on that next week), different signaling pathways are ac.vated in the embryonic cells. Figure 8-19 Essential Cell Biology ( Garland Science 2010)

55 Gene regula.on in development These signaling pathways work to guide the cells to their final cell fate In biology this is called differen.a.on Context and sequence mahers! Maduro et al., Biochim Biophys Acta (2009)

56 Concept and philosophy The genome is the archive that contains all the informa.on the organism is (ever) likely to need. RNA is a transcript from the archive, a work order for an end product (either the RNA- molecule or a protein). The mrna work order is processed and transported to the ribosome, where the end product is assembled and shipped off to its designated point of func.on. Who has the master plan?

57 The master plan? Genomics thought they would have the answer. Proteomics did too. So what s next? REGULOMICS A GRN does not contain informa.on on cri.cal concentra.ons and does not describe dynamic behavior.

58 Systems biology at work Regulomics Next genera.on gene regulatory models

59 Systems biology at work Regulomics Next genera.on gene regulatory models Cell lineage and cell fate specifica.on Developmental biology Cancer Regenera.ve medicine

60 Systems biology at work Regulomics Next genera.on gene regulatory models Cell lineage and cell fate specifica.on Developmental biology Cancer Regenera.ve medicine Specific pathways (such as a receptor- ligand systems) New drug therapies Personalized medicine

61 Systems biology at work Regulomics Next genera.on gene regulatory models Cell lineage and cell fate specifica.on Developmental biology Cancer Regenera.ve medicine Specific pathways (such as a receptor- ligand systems) New drug therapies Personalized medicine Enabling cost- effec.ve research Tools that will help researchers find the needle in the hay stack

62 The seminar series ü ü 1. Introduc7on (Robert Forchheimer, March 28) The biological cell, the gene.c code, cell lineages. Terminology 2. From genes to func7ons (Sofia Pehersson, April 4) Gene regula.on and transcrip.on 3. Cell biology (Sofia Pehersson, April 11) Cellular processes 4. Synthe7c biology (invited speaker Erik Gullberg, Uppsala University, April 18) IGEM- 2011/Team Uppsala 5. Models for cell and organism development (Jan- Åke Larsson, April 25) ODE- and PDE- models. Boolean models 6. Case study (Invited speaker Thomas Bürglin, Karolinska Ins.tute, Huddinge, May 16) C. elegans 7. Organism morphology and 3D- modeling (Lena Klasén, May 23) 3D- modeling of cells and cell popula.ons

63 Cell biology Cellular processes Systems biology for system engineers (Part 3) Cell structure Cell cycle and division Cell lineages and cell fates Asymmetry breaking in lineages Cell shape and mo7on (morphology and migra7on) Cell cell and cell substrate contacts Cell mechanics Mechanotransduc7on (conver7ng mechanical signals to biochemical events)