Interactomics and functional associations

Question 1

What are “omics” disciplines?

Answer 1

• contribute to produce lots of “big data”
  
  • Proteomics
  • Interactomics
• data integration is a problem

Question 2

Why omics disciplines?

Answer 2

• function of many genes is still unknown
• biological processes are the product of complex interactions
  
  • their combination leads to emerging properties

Question 3

emergent properties

Answer 3

• biological components can assemble and interact in different ways
  
  • understand the properties of the single biological components
• something new is generated
  
  • study the emerging properties

Question 4

Big data and omics

Answer 4

• big data sets that may be useful to understand physical and functional interactions of genes and proteins
  
  • help clarify processes and functions
• two genes or proteins interact -> likely participate in the same biological process
  
  • physical or behavioural
• associate genes to functions -> finding genes that share similar behavior -> infer gene functions

Question 5

Proteomics

Answer 5

• analyze and identify thousands of proteins in a single experiment
  
  • based on Mass Spectrometry (M/S)
  • evaluate the mass of molecules accurately
• protein mixture is digested -> “trypsin”
  
  • cleave proteins exactly at the K (lysine) and R (arginine) residues
  • cut in 10 amino acids long peptides
• potential protein can be searched by matching molecular weight of expected peptides
  
  • most of large ones can be univocally associated

Question 6

Interactomics

Answer 6

• study of protein interactions
• yeast two hybrids method
  
  • genetic manipulations of transcription factors of yeast, can activate gene expression (activation [activate gene] and binding domain [recognize])
  • reporter gene makes visualization of the cells where the gene has been activated easy
• mass spectrometry
  
  • construct recombinant “bait” proteins
  • flow through iproteic extract that could contains proteins able to interact with bait
  • binded, rinse an purify -> analyze with mass spectrometry
• everal interactomic databases, different organisms

Question 7

Promoters analysis

Answer 7

• promoters are the regulatory regions that turn on and off genes
• understanding gene regulation is important
  
  • interpret genes
  • associate them according to logic that regulates them
• at the moment full prediction of how gene are regulated is not possible

Question 8

Phylogenetic profiling

Answer 8

• infer functional association of genes
  
  • homologous genes tend to be either present or absent
  • by looking at many organism we are able to mak phylogenetic profiles
• generally done on bacteria

Question 9

microRNA (miRNA)

Answer 9

• small pieces of RNA, regulate the stability of mRNAs

- encoded by the cells

Question 10

Gene regulation in bacteria

Answer 10

• Lac repressor on operon
  
  • lactose makes it detach
  • RNA polymerase can then bind

Question 11

How much regulatory protein is needed to control genes?

Answer 11

• one per gene is not enough, many copies needed
• not only binding sites but also random positions
  
  • one site against several million random positions

Question 12

Gene regulation in Eukaryots

Answer 12

• transcription regulated by several factors
• overall context of elements produces a specific promotor
• binding sites are called
  
  • Regulatory Elements (RE)
  • Transcription Factor Binding Sites (TFBS)
• RE must be at a suitable distance and orientation
  
  • to allow transcription factors to interact

Question 13

Eukaryotic promoter

Answer 13

• proximal promoter and distal promoter (enhancer)
  
  • start of trancription
• some factors always involved with initiation process (TBP)

Question 14

Why analysis of pomoter region is interesting?

Answer 14

• may help in the functional characterization of genes
• identification and analysis not easy
  
  • DNA sequences recognized by transcription factors are small