Biology-2

[twang15]

inhibitor activator promoter enhancer motif predict disorder region

[twang15]

Transcription Factor Enrichment Analysis

1. Detecting differential activation of transcription factors (TFs) in response to perturbation provides insight into cellular processes. Transcription Factor Enrichment Analysis (TFEA) is a robust and reliable computational method that detects differential activity of hundreds of TFs given any set of perturbation data. TFEA draws inspiration from GSEA and detects positional motif enrichment within a list of ranked regions of interest (ROIs)

[twang15]

Custom genome, linear or graphical

enhancer-enriched promoter-enriched repressive active policy copy number inhibitor activator promotor enhancer

[twang15]

Gene regulation by Amoeba Sisters

• DNA polymerase, DNA primer
• RNA polymerase, promoter, operator, repressor/inihibitor
• Lactose

Gene regulation-2

• regulatory genes vs structural genes (20400)
• regulatory genes control the transcription of structural genes
• 98% regulatory gene vs 2% structural gene
• regulatory gene (a few thousands of bp away from promoter) -> regulatory protein (repressor)
• regulatory sequence including promoter and operator. promoter is the sequence portion of regulatory sequence where RNA polymerase binds to; operator is a switch (bound state: off or free state: on) to control whether RNA polymerase can move to structural genes
• regulatory protein controls the binding of RNA polymerase to regulatory sequence

• Operon: Group of genes, copied to a single mRNA and then translate by ribosome into different related proteins
• CAP site: a DNA sequence where catabolite activator protein binds, just behind the promoter, CAP increases rate of transcription of LAC genes by making RNA polymerase more efficient

[twang15]

Epigenetics

1. DNA methylation (happened on DNA sequence directly) can prevent transcription: methylate, methylation,
   • • demethylation can remove methyl groups
2. Histone modification
   • Histone methylation also prevents transcription
   • Histone acetylation: loose the wrapping of DNA strands around histones, so to facilitate the transcription
   • Histone deacelyation: remove the acetyl groups so that DNA strands wrap histone more tightly
3. TF binding
4. both internal factor and external (environmental) can affect the transcription

[twang15]

Gene structure and Gene transcription

distal control element (a few thousand bp upstream of structural gene): non-coding sequence

• enhancer: a group of distal control elements, helping the binding of RNA polymerase to structural DNA sequence
• activator: a specific transcription factor

Promoter: 100~1000 bp in length

[twang15]

1. Transcription factors are inactive in the cytoplasm and need to be activated and translocated to the nucleus.
2. Transcription factors bind to specific DNA sequences, therefore different genes bind different combinations of factors.
3. Binding site: within ~1000 bp upstream of promoter region

steps for TF to take effects