转录组学transcrip行tomicswxj.ppt

Transcriptomics 转录组学 Transcriptome: An evolving definition (The population of) mRNAs expressed by a genome at any given time (Abbott, 1999) The complete collection of transcribed elements of the genome. (Affymetrix, 2004) Transcribed elements mRNAs: 35, 913 transcripts (including alternative spliced variants) Non-coding RNAs tRNAs (497 genes) rRNAs (243 genes) snmRNAs (small non-messenger RNAs) microRNAs and siRNAs (small interferring RNAs) snoRNAs (small nucleolar RNAs) snRNAs (small nuclear RNAs) Pseudogenes (~ 2,000) Transcriptomics Definition The study of characteristics and regulation of the functional RNA transcript population of a cell/s or organism at a specific time. Scope the population of functional RNA transcripts. the mechanisms that regulate the production of RNA transcripts dynamics of the trancriptome (time, cell type, genotype, external stimuli) Observing the transcriptome Experimental overview: Affymetrix: Gene Expression Arrays Transcripts/Genes Arabidopsis Genome 24,000 C. elegans Genome 22,500 Drosophila Genome 18, 500 E. coli Genome 20, 366 Human Genome U133 Plus 47,000 Mouse Genome 39, 000 Yeast Genome 5, 841 (S. cerevisiae) 5, 031 (S. pombe) Rat Genome 30, 000 Zebrafish 14, 900 Plasmodium/Anopheles 4,300 (P. falciparum) 14,900 (A. gambiae) Barley (25,500), Soybean (37,500 + 23,300 pathogen), Grape (15,700) Canine (21,700), Bovine (23,000) B.subtilis (5,000), S. aureus (3,300 ORFS), Xenopus (14, 400) Microarray and GeneChip Approaches Advantages: Rapid Method and data analysis well described and supported Robust Convenient for directed and focussed studies Disadvantages: Closed system approach Difficult to correlate with absolute transcript number Sensitive to alternative splicing ambiguities Anchoring Enzyme NlaIII, recognition site: The 3’ terminus of adaptor A and Bare both TCCRACTAG, where a recognition site of Tagging Enzyme MmeI flanked with  NlaIII Tagging Enzyme MmeI re