Regulation of Transcription and Translation

1. Regulation of Transcription and Translation Lily Chen Mariam Khan Kuldeep Mahal Cecilia Tuma

2. Differential Gene Expression • all organisms regulate which genes are expressed at any time • must turn genes on + off  • in response to signals from external/internal environments • cell differentiation = specialization in form + function of cells (occurs during development of multi-cellular organisms) • almost all cells in an organism contain an identical genome • but genes expressed in the cells of each type is unique, letting cells carry their specific function

3. Differential Gene Expression • differential gene expression = expression of diff genes by cells w/ same genome • so: differences between cell types not due to diff genes present • transcription proteins of a cell must locate the right genes at the right time • if gene expression is awry = serious imbalance i.e. cancer 

4. There is a potential control point where gene expression can be turned on/off, accelerated/slowed down. Chromatin modification with DNA unpacking involving histone acetylation must occur first before genes are available for transcription.

5. Regulation of Chromatin Structure • structural organization of chromatin (packing cell's DNA into compact form that fits in nucleus) = important step in regulating gene expression • chromatin wraps around histones (proteins) to form nucleosomes • genes w/ heterochromatin (highly condensed) = not expressed usually • location of gene's promoter also affects its transcription • certain chemical modifications to histones + DNA of chromatin influence chromatin structure + gene expression

6. Histone Modifications • chemical modifications to histones = direct role in regulation of gene transcription • some histone molecules in a nucleosome protrude outward • so histone tails = accessible to diff modifying enzymes • enzymes = catalyze addition/removal of specific chemical group • histone acetylation = acetyl groups (-COCH3) attached to positively charged lysines in histone tails • acetylated histone tails of a nucleosome no longer binds to neighboring nucleosomes due to neutralized positive charge • (binding promotes the folding of chromatin into more compact structure) • no binding means chromatin has looser structure • result: transcription proteins = easier access to genes in acetylated region

7. a) Histone tails protrude outward from a nucleosomeb) acetylation of histone tails = loose chromatin structure = allows transcription

8. Histone Modifications Cont'd • deacetylation = removal of acetyl groups • other chemical groups can be reversibly attached to amino acids in histone tails • methylation = addition of methyl groups (-CH3) to histone tails • leads to condensation of chromatin • histone code hypothesis: specific combinations of modifications help determine chromatin configuration --> influencing transcription  • not the overall level of histone acetylation

9. DNA Methylation -          addition of methyl groups to bases in DNA after DNA is synthesized -          inactive DNA is more methylated than actively transcribed DNA -          genes are more heavily methylated in cells in which they are not expressed o       removal of extra methyl groups à turn on these genes -          certain proteins that bind to methylated DNA recruit histone deacetylation enzymes o       dual mechanism can repress transcription -          essential for long-term inactivation of genes during cell differentiation (in embryo)

10. -          genes stay methylated through cell division -          methylation enzymes correctly methylate daughter strand à DNA sites where one strand is already methylated o       methylation patterns are passed on -          genomic imprintingà methylation permanently regulates expression of maternal/paternal allele of certain genes at start of development

11. - epigenetic inheritanceà inheritance of traits transmitted by mechanisms not directly involving the nucleotide sequence - enzymes that modify chromatin structure à important part for regulating transcription -          chromatin-modifying enzymes provide initial control o       makes DNA more/less able to bind transcription machinery -          initiation of transcription à most important step in which gene expression is regulated Epigenetic Inheritance Regulation of Transcription Initiation

12. Organization of a Typical Eukaryotic Gene -          transcription initiation complex assembles on promoter sequence at end of gene -          RNA polymerase III transcribes gene and creates pre-mRNA o       RNA processing turns it into mature mRNA -          Control elementsà segments of noncoding DNA that help regulate transcription by binding certain proteins -          Control elements and proteins are critical to precise regulation

13. The Roles of Transcription Factors -          transcription factorsà proteins that assist eukaryotic RNA polymerase -          protein-protein interactions -          once complete initiation complex has assembled à polymerase can produce a complementary strand of RNA -          interaction of transcription factors and RNA polymerase II à low rate of initiation and production of few RNA transcriptions -          In eukaryotes: o       High levels depend on reaction of control elements with other proteins

14. Enhancers and Specific Transcription Factors -          proximal control elementsà control elements that are close to the promoter -          distant control elements à groups are called enhancers o       nucleotides of a gene or within an intron o       gene may have multiple enhancers -          activatorà protein that binds to an enhancer and stimulate transcription of a gene -          protein-mediated bending of DNA brings about mediator proteins o       mediator proteinsà interact with proteins at promoter

15. -          multiple protein-protein interactions assemble and position initiation complex on promoter -          two common structural elements in a large number of activator proteins: • DNA-binding domain (part of protein’s 3D structure) • one or more activation domains (bind other proteins à allow sequence of protein-protein interactions)

16. Enhancers and Specific Transcription Factors Continued… - Some specific transcription factors work as receptors = inhibit expression of a particular molecule o   Some can block the binding of activators while others bind directly to their own control elements in an enhancer and act to turn off transcription -  Some activators and repressors act indirectly by influencing chromatin structure – recruitment of chromatin modifying proteins = most common repression mechanism in eukaryotes

17. Combinatorial Control of Gene Activation -  In eukaryotes – precise control of transcription depends a lot on binding of activators to DNA control elements -  On average, each enhancer =composed of about 10 control elements, each can only bind to 1 or 2 specific transcription factors o   Particular combination of control elements in enhancer associated with a gene = more important than one unique control element in regulating transcription -  Particular combination of control elements  = able to activate transcription only when certain proteins present

18. Coordinately Controlled Genes - in prokaryotes, coordinately controlled genes often clustered together in an operon which is regulated by single promoter and transcribed into single mRNA molecule – genes expressed together - some co-expressed genes = clustered near one another on same chromosome o each eukaryotic gene in these clusters has its own promoter and is individually transcribed – regulation of these clustered genes may involve changes in chromatin structure that make group of genes available or unavailable for transcription

19. - co-expressed eukaryotic genes commonly scattered over different chromosomes – then, coordinate gene expression depends on  association of specific control element or combination of elements with every gene of a dispersed group - coordinate control of dispersed genes occurs in response to external chemical signals - many signal molecules bind to receptors on a cell’s surface and never enter cell  - can control gene expression indirectly by triggering signal transduction pathways that lead to activation of particular transcription activators/receptors - genes with same control elements are activated by same chemical signals

20. Cell Type - Specific Transcription

21. Post Transcriptional Regulation-Gene expression after transcription Gene expression at RNA Processing level Alternative RNA splicing regulation where different mRNA molecules are produced from the same primary transcript mRNA Degradation prokaryotic mRNA molecules degrade within a few minutes after synthesis eukaryotic mRNA can survive for hours, days, sometimes weeks ex: hemoglobin polypeptide mRNA are very stable and therefore long-lived shortening of poly-A tail can help start degrading mRNA  removes the 5' cap which is regulated by specific nucleotide sequences when cap is removed, the enzymes eat up the mRNA

22. the nucleotide sequence that regulates the length of mRNA is often in the untranslated 3' region MicroRNAs(miRNAs) blocks gene expression small single-stranded RNA molecules that form a double-stranded structure which an enzyme (Dicer) then cuts it into two strands-> one degrades, the other binds to complementary mRNA molecules->miRNA then either degrades the target mRNA or blocks it from translation RNA interference technique that silences gene expression-> small interfering RNAs (siRNAs) that have similar functions as miRNAs So What? RNAi pathways can lead to destruction of RNA-> believed to have originated from a natural defense against RNA viruses

23. Regulation of gene expression by miRNAs

24. Initiation of Translation(IT) regulation of gene expression occurring at initiation stage IT can be blocked by regulatory proteins binging to sequences or structures in the untranslated region -> prevents ribosome attachment Global Control!(muhahah) activation or inactivation of protein factors required to begin IT translation of egg cell mRNA triggered by IT factors->response: synthesis of encoded and stored proteins Protein Processing and Degradation last chance for gene expression controlling: after translation chemical modifications of proteins to become functional, protein activity regulated by reversible additions of phosphate groups or sugars, transportation Selective Degradation regulates the lifetime of protein functions to mark a protein for destruction->cell attaches to small proteins (ubiquitin) to the target protein->protein complexes (proteasomes) recognize the marked protein and degrade them

25. Degradation of a protein by a proteasome