dev gen CH 3

• Differential Gene Expression is the process by which cells become different from one another based on the unique combination of genes that are active or expressed.
• how the cells become different?

  Cells contain the same DNA, but DNA is active or inactive in each. So, their physical and morphological features are different.
• beginning of central dogma

  1. Transcription: In nucleus, RNA polymerase II, transcribes a complementary copy of a region of the genomic DNA (gene) into a single-stranded pre-mRNA molecule. 
  2. Processing: pre-mRNA transcript undergoes processing (poly tail A attached)  to make a finalized messenger RNA strand.
  3. Transport out of nucleus: Finalized messenger RNA strand gets out of the nucleus.

  
• ending of central dogma

  4. Translation: The mRNA complexes with a ribosome, and its information is translated into an ordered polymer of amino acids. 

  5. Protein folding and modification: The polypeptide adopts secondary and tertiary structures through proper folding and potential modifications

  6. The protein is now said to be “expressed” and can carry out its specific function (e.g., as a transmembrane receptor).

  
• across organisms, some of the gene functions are conserved
• Steps in the production of β-globin (beta global) and hemoglobin proves the second postulate of differential gene expression, that only a small percentage of the genome is expressed in each cell. 


  The DNA is very long, put only parts of it are functioning. Intron Is non coding, exon is coding
• What are major transcription factors and why transcription factors and its regulation is so important?

  Homeodomian, Basic helix loop helix (bHLH), basic leucine zipper (bZip), Zinc finger, Sry Sox, and MADS box

  Transcription factors are important because they control the expression of genes, which is crucial for cell function, development, and response to environmental cues. Their regulation ensures proper gene expression and cellular homeostasis.
• The bridge between enhancer and promoter can be made by transcription factors

  • Transcription factors assemble on the enhancer, but the promoter is not used until the GATA1 transcription factor binds to the promoter. 
  • GATA1 can recruit several other transcription factors, including Ldb1, which forms a link uniting the enhancer-bound factors to the promoter-bound factors.
  • In this way, the chromatin loops brings the enhancer to the promoter. The example shown here is the mouse β-globin gene.

  
• Enhancer 


  A DNA sequence that controls the efficiency and rate of transcription from a specific promoter. Enhancers bind specific transcription factors that activate the gene by (1) recruiting enzymes (such as histone acetyltransferases) that break up the nucleosomes in the area or (2) stabilizing the transcription initiation complex.

  A) enhancers

  B) promoter

  C) transcription factors

  D) gene

  
• enhancer region modularity

  In developing brain cells, brain specific transcription factors bind to the brain-specific enhancer, causing it 

  • to bind to the Mediator
  • stabilize RNA polymerase II (RNA Pol II) at the promoter
  • mRNA is expressed in the brain

  The gene is transcribed in the brain cells only; the limb enhancer does not function. 

  
• Promoter 


  Region of a gene containing the DNA sequence to which RNA polymerase II binds to initiate transcription.
• Silencer 


  A DNA regulatory element that binds transcription factors that actively repress the transcription of a particular gene.
• Some major transcription factor families and subfamilies - Homeodomian 


  Hox - axis formation

  POU - pituitary development; neural fate

  Lim - head development

  Pax - neural specification; eye and muscle development
• Some major transcription factor families and subfamilies

  • Basic helix loop helix (bHLH) - muscle and nerve specification, drosophila sex determination; pigmentation
  • Basic leucine zipper (bZip) - liver differentiation; fat cell specification
• Some major transcription factor families and subfamilies - Zinc finger

  • standard - Drosophila segmentation
  • Nuclear hormone receptors - secondary sex determination
• Some major transcription factor families and subfamilies

  • Sry sox - mammalian primary sex determination
  • MADS box - floral organ identity
• Epigenetics 


  The study of mechanisms that act on the phenotype without changing the nucleotide sequence of the DNA. Specifically, these changes work “outside the gene” by altering gene expression rather than by altering the gene sequence as mutation does. 
• Methylation condense nucleosomes more tightly, preventing access to promoter sites and thus preventing gene transcription.


  Acetylation loosens nucleosome packing, exposing the DNA to RNA polymerase II and transcription factors that will activate the genes.
• label the following

  A) acetylation

  B) methylation

  
• Epigenetic regulation can be accomplished by histone modification


  Histone: Positively charged proteins that are the major protein component of chromatin
• nucleosomes can be modified through methylated DNA

  • Nucleosome: The basic unit of chromatin structure, composed of an octamer of histone proteins (two molecules each of histones H2A, H2B, H3, and H4) wrapped with two loops containing approximately 147 base pairs of DNA.
  • Histone methylation: The addition of methyl groups to histones. Can either activate or further repress transcription, depending on the amino acid that is methylated and the presence of other methyl or acetyl groups in the vicinity.
• Some examples of alternative pre-mRNA splicing 

  1. cassette exon
  2. mutually exclusive exons
  3. alternative 5' splice site section
  4. alternative 3" splice site section
• The Dscam gene of Drosophila can produce 38,016 different types of proteins by alternative pre-mRNA splicing
• Mechanisms of differential gene expression during mRNA translation

  • Differential mRNA longevity

  • The longer the mRNA persists, the more proteins can be translated from it. 
  • The stability of a message often depends on the length of its poly A tail. The length, in turn, depends largely on 3’ un translated region. 
• Mechanisms of differential gene expression during mRNA translation •Stored oocyte mRNAs results selective inhibition of mRNA translation

  • oocyte is still in the ovary, the oocytes makes and stores mRNAs that will be used only after fertilization. 
  • messages stay in a dormant state until fertilization (maternal mRNAs use a strategy not to make a complete mRNA until baby needs it)
  • Some of stored mRNAs encode proteins needed during cleavage when the embryo is making enormous amounts of chromatin, cell membrane and cytoskeleton
  • The stored mRNAs and proteins are called maternal contributions
• RNA interference (RNAi)

  Process by which miRNAs inhibit expression of specific genes by degrading their mRNAs.
• Mechanisms of differential gene expression during mRNA translation •Control of mRNA expression by cytoplasmic localization

  • Not only is the timing of mRNA translation regulated, but so is the place of RNA expression. A majority of mRNAs (about 70% in Drosophila embryos) are localized to specific places in the cell 
  • ex: diffusion and local anchoring
  • where the mRNA is located, anterior or posterior, determines if it gets translated because the mRNA is anchored

  
• Mechanisms of differential gene expression during Post translational Protein Modification

  • Post-translational modification (PTM) refers to the covalent and generally enzymatic modification of proteins following protein synthesis. 
  • genome: The complete DNA sequence of an individual organism.
  • transcriptome: Total messenger RNAs (mRNAs) expressed by genes in an organism or a specific type of tissue or cell.
  • proteome: The number and type of proteins encoded by the genome.