Announcement Structure Analysis

Transcription

1 Announcement Structure Analysis BSC 4439/BSC 5436: Biomedical Informatics: Structure Analysis Spring 2019, CB117 Monday and Wednesday 12:00 1:15pm Office hour: Monday and Wednesday 1:15 2pm Topics include but not limited to mirna, RNA structure, protein motifs, protein structure, and protein DNA interaction

2 Gene Regulation ABC

3 Genome is fixed Cells are dynamic A genome is static Every cell in our body has a copy of same genome A cell is dynamic Responds to external conditions Most cells follow a cell cycle of division Cells differentiate during development

4 Gene regulation Gene regulation is responsible for the dynamic cell Gene expression varies according to: Cell type Cell cycle External conditions Location

5 Where gene regulation takes place Opening of chromatin Transcription Translation Protein stability Protein modifications

6 Transcriptional Regulation Strongest regulation happens during transcription Best place to regulate: No energy wasted making intermediate products However, slowest response time After a receptor notices a change: 1. Cascade message to nucleus 2. Open chromatin & bind transcription factors 3. Recruit RNA polymerase and transcribe 4. Splice mrna and send to cytoplasm 5. Translate into protein

7 Transcription Factors Binding to DNA Transcription regulation: Certain transcription factors bind DNA Binding recognizes DNA substrings: Regulatory motifs

8 Promoter and Enhancers Promoter necessary to start transcription Enhancers can affect transcription from afar

9 Regulation of Genes Transcription Factor (Protein) RNA polymerase (Protein) DNA Regulatory Element Gene

10 Regulation of Genes Transcription Factor (Protein) RNA polymerase DNA Regulatory Element Gene

11 Regulation of Genes Transcription Factor New protein RNA polymerase DNA Regulatory Element Gene

12 Example: A Human heat shock protein SP CCAAT AP2 HSE CCAAT SP1 TATA AP2 0 GENE promoter of heat shock hsp70 TATA box: positioning transcription start TATA, CCAAT: constitutive transcription GRE: glucocorticoid response MRE: metal response HSE: heat shock element

13 The cis regulatory elements in Endo16 Development 128, (2001)

14 The Cell as a Regulatory Network If C then D A B C Make D gene D If B then NOT D If A and B then D D Genes = wires Motifs = gates D C gene B Make B If D then B

15 Gel mobility shift assay An electrophoretic mobility shift assay (EMSA), also referred as a gel shift assay, gel mobility shift assay, band shift assay, or gel retardation assay, is a common affinity electrophoresis technique used to study protein DNA or protein RNA interactions. This procedure can determine if a protein or mixture of proteins is capable of binding to a given DNA or RNA sequence, and can sometimes indicate if more than one protein molecule is involved in the binding complex.

16 DNase Footprinting assay The cleavage pattern of the DNA in the absence of a DNA binding protein, typically referred to as free DNA, is compared to the cleavage pattern of DNA in the presence of a DNA binding protein. If the protein binds DNA, the binding site is protected from enzymatic cleavage. This protection will result in a clear area on the gel which is referred to as the "footprint".

17 DNase footprinting

18 Average length of non coding sequences with average length of 2 10^4bp, minimal length of 100bp and maximal length of 4 10^6bp

19 Where should we start Measuring gene transcription in a high throughput fashion by microarray

20 What is a microarray

21 Two color array vs. one color array

22 Results of Clustering Gene Expression Human tumor patient and normal cells; various conditions Cluster or Classify genes according to tumors Cluster tumors according to genes

23 4. Analysis of Clustered Data Statistical Significance of Clusters Regulatory motifs responsible for common expression Regulatory Networks Experimental Verification

24 Clusters of regulatory regions at the NGS era