Week 9 Readings

17.2 Transcription and RNA Processing in Eukaryotes (M/T)

  • Additional levels of gene regulation

    • mRNA processing

    • DNA packaging

    • separation of space of transcription and translation


Transcription is a key control point in gene expression

  • we need a group of coordination actions of proteins to regulate gene expression

  • Regulatory Transcription Factors

    • has two binding sites

      • one will bind with a DNA sequence (enhancer)

      • other binding site will recruit general transcription factors and will attract RNA polymerase complex (will make an RNA transcript complementary to the template)


  • Binding with silencers will repress transcription

  • All protein coding genes will use the same RNA polymerase complex

  • Combinatorial Control: transcription of a gene with multiple silencers and enhancers depends on the presence of a particular combination of regulatory transcription factors


RNA Processing is also important in gene regulation

  • Transcription in the nucleus

  • Translation will happen in the cytoplasm

    • the separation of these processes will allow for evolution and modifications

      • the addition of the 5’ cap and a string of 250 adenosine nucleotides to the 3’ end (poly (A) tail)

  • The poly a tail will help determine the length of the RNA

  • The length of the primary transcript is longer than the actual mRNA

    • since it will contain exons (expressed regions) and introns (removed)

    • exons are joined together through RNA splicing and the removal of the introns → spliceosome


  • Alternative splicing: regulating gene expression since the primary transcript can be spliced in different ways to yield different proteins

    • spliceosome recognizes an exon as an intro

    • generate different processed mRNAs and different proteins


  • RNA Editing: RNA molecules can become a substrate for enzymes that modify particular bases in the RNA

    • not all transcripts are edited and some copies may be edited more than others

      • transcripts from the same genes can produce multiple types of proteins



17.3 Messenger RNA to Phenotype in Eukaryotes (M/T)

  • mRNA travels through nuclear pores and can be modifies in the cytoplasm


Small Regulatory RNAs promote mRNA degradation or inhibit translation

  • Small Regulatory RNAs: regulatory RNA molecules

    • siRNA (small interferring RNA)

    • miRNA (microRNA)


Translation regulation control the rate,timing, and location of protein synthesis

  • Almost all mRNA contain

    • 5’ cap

    • 5’ untranslated region

    • open reading fream

    • 3’ untranslated region

    • poly (a) tail

  • regions will cause for mRNA to be translated in certain places in the cell

  • Cap structure is one of the main recognition signals for the translation initiation

  • 3’ UTR and the poly (a) tail will create a loop in the mRNA to bring the 3’ end to the start site for translation

  • the secondary folded structure of the 5’ UTRR, the distance from the 5’ cap to the AUG initiation codon, the sequences flanking the AUG initiation codon will make the mRNA molecules accessible to translation



Protein structure and chemical modification modulate protein effects on phenotype

  • Posttranslation Modification: protein are modified after translation to regulate their structure and their function

    • ex. having some protein be activated at some points

  • Chaperones: will help portein fold properlly

  • Modifications helps with protein activity



17.4 Chromatin Remodeling and Epigenetics (M/T)

  • Chromatin: DNA is packaged in this form

    • when coiled then the DNA is not accessible for transcription

  • Chromatin remodeling: nucleosome are repositioned to expose different stretches of DNA


Gene expression can be influence by chemical modification of DNA or histones

  • Histone Tail: strings of amino acids that protrude from the histone proteins in the nucleosome

    • histone modification occurs to ensure that the proper genes are turned on or off


  • Methylation: repression of genes

    • occurs in CpG islands


  • Epigenetic: changes to the way the DNA is packaged → the modification of cytosine bases, posttranslation modification of histone tails, alteration in chromatin structure

    • affects gene expression


  • Imprinting: preprogrammed epigentic changes

    • occurs forever in somatic cells


Gene Expression can be regulated at the level of an entire chromosome

  • Each copy of the gene is regulated independently of other copies

    • dosage compensation: the differential regulation of x chromosomal genes in females and in males

      • repressing the expression of an x chromosome in females

  • Gene expression can be regulated at different levels


    • chromatin

    • transcription

    • RNA processing

    • mRNA stability

    • translation

    • posttranslation


Groups

Your lifestyle choices can affect gene expression in your own genome

  • most of the regulation steps are determined by physiological state of cells which is determined by the environment

  • there will be feedback with gene expression and the environment since if the individaul is intaking the protein through food then the body will not express that protein


Genome Browser Video:

  • how to set up the window:

    • reset the settings

    • use the gene code v48

    • look at comparative genomics


Exploring the reference Human Genome:

  • conservation of the genome shows the importance of the gene


Isoforms: splice variants of a gene


how to idenitfy promoter region, start end of transcription, nucleotides in mRNA

  • promoter you would look at the start of the transcript

  • click on the gene to see the length of it in base pairs

  • will also show the length of the coding region


how to determine start and end of translation?

  • translation with start at the broad region of the first exon

  • zoom in to see the stop codon, 5’ UGA 3’

  • open reading frame: codes for a protein and starts with a start codon

  • mRNA will first be processed to remove the introns and translation will begin

  • UTRs are not include in translation

  • zooming in will tell you the amount of amino acids or zooming in at the end of the 3’ region


How to distinguish between the forward and reverse strands

forward: 5’ to 3’

reverse: 3’ to 5’ but will got 5’ to 3

  • Reverse strand represents an identical copy to the mRNA sequence but the t’s will be u’s

  • protein coding DNA will contian the instruction need to make proteins

    • contains exons and introns


how to read acetylation data associated with genic and intergenic regions?

how to distringuish between conserved and not conserved regions

  • genic: contains introns and exons

  • intergenic: spaces between genic regions


  • acetylation in the layered region


12.2 Recombinant DNA and DNA Editing (W/R)