• The Basics of Microarrays
• 42 min
  1. How to design a successful microarray experiment

  • Dr. Rainer Breitling
• Microarrays in the Understanding of the Biology of the Cell and Whole Organism
• 51 min
  2. Genome-wide mapping of estrogen: receptor binding sites and activity

  • Prof. Jason Carroll
• Microarrays in the Diagnosis, Prognosis and Treatment of Disease
• 35 min
  3. Single nucleotide polymorphism microarrays in the analysis of cancer

  • Dr. Rameen Beroukhim
• Archived Lectures *These may not cover the latest advances in the field
• 23 min
  4. The use of statistics in microarray studies

  • Dr. Ernst Wit
• 42 min
  5. Simultaneous microarray measurement of nuclear and whole cell changes in gene expression reveals overlapping but distinct patterns of transcriptional regulation

  • Dr. Chris Cheadle
• 38 min
  6. Global analysis of gene translation

  • Prof. Philip Tofilon
• 36 min
  7. Microarrays in the study of the basic mechanisms of evolution

  • Dr. Greg Gibson
• 41 min
  8. The use of microarrays to understand the biology and toxicology of low dose arsenic

  • Prof. Joshua Hamilton
• 46 min
  9. The bioinformatics of microarrays

  • Dr. Maureen Sartor
• 44 min
  10. Genome-wide profiling of microRNAs: from scientist benchside to patient bedside

  • Prof. George Calin
• 42 min
  11. Microarrays: their design and use

  • Prof. Craig R. Tomlinson
• 67 min
  12. Cancer systems biology: dissection and analysis of context-specific molecular interaction networks

  • Prof. Andrea Califano
• 35 min
  13. Utilizing microarrays to study posttranscriptional regulatory mechanisms of plants

  • Dr. Brian Gregory

Printable Handouts

PDF

Navigable Slide Index

1. Introduction
2. mRNA structure
3. The cap binding complex
4. Arabidopsis ABH1 is the large subunit of the CBC
5. Phenotypes of abh1-1 mutant plants (1)
6. Phenotypes of abh1-1 mutant plants (2)
7. Altered phyllotaxy in abh1-1 mutant plants
8. SERRATE mutation effect
9. RNA silencing in plants
10. Model for RNA silencing by microRNAs (miRNAs)
11. Arabidopsis whole genome tiling array (WGA)
12. Tiling microarray analysis
13. pri-miRs transcripts accumulate in abh1-1 mutants
14. Confirmation by qPCR analysis
15. Testing abh1-1 effect on levels of mature miRNAs
16. abh1-1 effect on mature miRNAs
17. abh1-1 effect on 21nucleotide sRNAs
18. ABH1 is required for proper mature miRNA levels
19. Validating the sequencing data with northern blot
20. Schematic of 5'-RACE experiments
21. 5'-RACE experiments: results
22. Enhanced defects in ABH1 AGO1 double mutants
23. ABH1 AGO1 double mutants - fused cotyledons
24. ABH1 AGO1 double mutants - a unique defect
25. Part A - conclusions
26. Utilization of microarrays - part B
27. Introduction to part B: RNA degradation
28. RNA degradation pathways
29. The exosome is required for proper development
30. Inducible system for studying exosome function
31. Using inducible system in conjunction with WGA
32. The exosome regulates specific pri-miRNAs (1)
33. The regulated 5' fragments are polyadenylated
34. 5' fragments accumulate upon exosome depletion
35. Exosome is required for turning over 5' miRNA
36. The exosome regulates specific pri-miRNAs (2)
37. Exosome depletion doesn't effect mature miRNAs
38. Exosome specific transcripts (1)
39. Exosome specific transcripts (2)
40. A genome wide atlas of exosome substrates (1)
41. A genome wide atlas of exosome substrates (2)
42. Overall conclusion
43. Acknowledgements

Topics Covered

• mRNA structure
• The cap-binding complex is required for proper mRNP assembly
• Phenotypes of abh1-1 mutant plants
• Altered phyllotaxy in abh1-1 mutant plants
• RNA silencing in plants
• Arabidopsis whole genome tiling array
• High-throughput sequencing of the smRNA-component of the Arabidopsis transcriptome
• ABH1 is required for proper mature miRNA levels
• 5'-RACE experiments
• Loss of ABH1 enhances the developmental defects of a hypomorphic AGO1 allele
• RNA degradation
• Exosome function in Arabidopsis
• Tiling arrays suggest the exosome regulates specific fragments of primary miRNA transcripts
• Many of the new transcription units only seen upon exosome-depletion are associated with smRNAs and repetitive elements
• A genome-wide atlas of exosome substrates in Arabidopsis

Links

Series:

• Microarrays

Categories:

• Cell Biology
• Methods
• Plant & Animal Sciences

Talk Citation

Publication History

• Published on September 10, 2009
• Archived on February 25, 2021

Financial Disclosures

• Dr. Brian Gregory has not informed HSTalks of any commercial/financial relationship that it is appropriate to disclose.