Gene expression and regulation

• Genome


  The complete set of genes or genetic material present in a cell or organism
• Transcriptome


  The set of all RNA molecules from protein coding (mRNA) to noncoding RNA, including rRNA, tRNA, lncRNA, pri-miRNA, and others
• Proteome


  The entire complement of proteins that is or can be expressed by a cell, tissue, or organism
• All cells in the organism share the same genome; its activation by different instructions will cause the cell to differentiate
• The transcriptome represents the genetic instructions that have been actively transcribed into RNA molecules
• The transcriptome includes all rRNA, tRNA and mRNA sequences (including all variants produced via alternative splicing)
• The proteome is all proteins expressed within a cell/tissue/organism at a particular time
• The amount of proteome is bigger, because proteins can be modified by different processes, to promote further variations
• Genes of different genes in different cells will leads to different patterns of development in these cells (there fore different characteristics)
• Epigenetics


  The study of how chemical and environmental triggers influence gene expression patterns
• Epigenesis


  The specific development of an organism from an undifferentiated egg cell into a complex multicellular organism via differential gene expression
• Unlike genetic changes (mutations), epigenetic modifications do not alter the DNA sequence and are potentially reversible
• Epigenetics is the study about how environment influence gene expression; epigenesis is differentiation of cells via differential gene expression
• Gene expression


  The process by which genetic information is used to produce RNA and proteins
• Gene expression allows cell differentiation to occur
• Proteins that regulate gene expression

  • Transcription factors
  • Regulatory proteins
• Transcription factors


  A group of proteins that impact gene expression; control the process of binding RNA polymerase to DNA
• Activator proteins


  Part of transcriptional factors that bind to enhancers and help RNA polymerase bind to promoters
• Promoters


  The first section of DNA, a non-coding region to which RNA polymerase binds to initiate transcription
• Enhancers


  Non-coding regions of DNA that regulate gene expression and transcription of that gene; determine which genes should or should not be transcribed
• Transcriptional factors influence activator proteins, which then attach to promoters to initiate transcription; enhancers control how much and which genes should be transcribed
• RNA degradation is the breaking down of RNA to avoid viruses
• mRNA persistence is the continuation of using the same mRNA in translation
• Lactose is milk sugar
• RNA does modification after it is used in transcription, to regulate how many times it will be used
• If mRNA can be used multiple times, more proteins can be produced (this is how mRNA is regulated during translation)
• All somatic cells are genetically identical; differences in the expression of genes lead to phenotypic differences between cells
• Epigenesis


  The specific development of an organism from an undifferentiated egg cell into a complex multicellular organism via differential gene expression
• Nucleosome


  One DNA that is wrapped around histone
• Nucleosomes


  • They play a fundamental role in regulating chromatin structure and accessibility to transcriptional machinery
  • When DNA is supercoiled (wrapped tightly) around histone proteins, it forms a condensed structure called heterochromatin, which reduces transcription
  • When DNA is loosely packed around histone proteins, it is called euchromatin, which is more accessible to RNA polymerase and other transcription machinery, resulting in increased transcription and enhanced gene expression
• DNA methylation


  The addition of a methyl group to a molecule, which represses transcription by preventing transcription factors from binding
• Acetylation


  The addition of an acetyl group to amino acids in a histone tail, which decreases the overall charge of the histone protein and reduces the electrostatic attraction between the histone and DNA, making the DNA more accessible to transcription machinery and usually resulting in increased gene expression
• Methylation


  The addition of a methyl group to amino acids in histone tails, which can impact gene expression by causing nucleosomes to pack tightly together, preventing transcription factors from binding the DNA and resulting in reduced gene expression
• The environment has a big influence on gene expression
• Environmental factors affecting gene expression

  • Sun exposure (or UV radiation) stimulating melanocytes to produce more melanin
  • Temperature changes activating or repressing genes involved in plant development stages
  • Exposure to air pollution affecting DNA methylation patterns
  • Nutrients in diet directly acting as ligands for transcription factors or being metabolized to affect gene expression
• Epigenetic inheritance refers to the inheritance of non-genetic information that can influence gene expression and phenotypic traits
• For epigenetic inheritance to occur during sexual reproduction, epigenetic changes must occur in germline cells and be maintained during meiosis and passed on to the offspring
• Somatic cells have the same genome but different gene expression and transcriptomes due to environmental differences and epigenetic changes, resulting in unique proteomes
• After fertilization, almost all epigenetic tags are removed to reset the epigenetic environment, but some tags (about 1%) are retained as imprinted genes
• Differences between tigons and ligers


  • Ligers tend to be larger in size than tigers or lions because they inherit an imprinted gene for large size from the male lion
  • Tigons tend to be the same size or smaller than tigers or lions because they do not inherit the imprinted gene for large size