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Lecture

Module 8(1-2) - March15-19 - BIO 2C03.docx

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Department
Biology
Course Code
BIOLOGY 2C03
Professor
Joe Kim

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BIO 2C03 2013 Module 8Lecture 1The Dark Genome March 15 The Genome Before 2005Complexity in higher eukaryotes is explained by o Higher frequency of alternative splicing o Frequent use of alternative promoters termination sites etc o More extensive use of posttranslational modifications phosphorylation acetylation methylation SUMOylation Ubiquitinylation etcThe mouse genome has a predicted 22000 genes but only 16700 transcripts have been clonedA few percent of the genome 310 is transcribed into RNAYeast has 6000 the fly has 12000 the nematode has 19000 genesMuch of the gene discovery effort is evidencebased and relies extensively on the characterization of EST librariesTherefore the genome is a desert composed mainly of junk DNAMore complete analysis of transcripts expressed in mammalian genomes Driven by posthuman genome projects as early as 2003Dependent on large research consortia such as FATOM or ENCOMDEBased on novel technologies eg Tiling Arrays Deep Sequencing Analysis and genomicbioinformatics toolsGlobal Genome TranscriptionA New View of the TranscriptomeAccording to the FANTOM Consortium circa 2005 o The mouse genome may infact contain as many as 181047 distinct TU transcriptional units o Most 625 of the mouse and human genome appear to be transcribed o Therefore the genome is organized as Transcription Forests covering most of the genome and interspersed with some Transcriptional DesertsMost recent data obtained with tiling arrays and deepsequencing suggest that circa 93 of the mammalian genome is actually transcribedMost of the RNA is nonprotein codingFANTOMFunctional ANnotation Of the Mammalian Genomeinternational research consortium for functional annotation of full length cDNAs funded by RIKEN JapanENCODEENCylopedia Of DNAElementsinternational consortium of researchers interested in genome structure regulatory elements noncoding RNAs etc funded by the National Human Genome Research Institute USATiling Arrays Complexity of transcription around a hypothetical game 1
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