ENCODE Project

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ENCODE Project

• Identification and analysis of functional
  elements in 1 of the human genome by the ENCODE
  pilot project
• Nature, V 447, June 14, 2007

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Overview

• Hope to gain insights on transcription,
  chromatin remodeling, messenger RNA splicing, DNA
  replication, and other genomic processes
• What does ENCODE stand for?
• How much DNA was examined?
• How many genes/transcripts?

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Experimental Techniques
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Identify Transcripts

• hybridization of RNA to tiling arrays (TxFrags)
• tag sequencing of cap-selected RNA
• DNA and EST sequencing, annotation, integrated
  annotation, and bioinformatics analysis (GENCODE)

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Transcript Connectivity

• protein-coding loci are more transcriptionally
  complex than previously thought
• 19 of pseudogenes transcribed

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Transcripts

• What of bases were represented in a primary
  transcript?
• How many transcription start sites (TSS's) were
  found?

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Aggregate Signals from ChIP-chip/Chromatin
Structure Assays Showing Chromatin Accessibility
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Not Covered

• DNA replication coordination
• Chromatin Architecture
• Evolutionary constraint

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Summaries

• Majority of bases are associated with at least 1
  primary transcript and many transcripts link
  distal regions
• Found many novel non-protein-coding transcripts
  (with many overlapping protein-coding loci)
• Numerous transcription start sites were
  identified
• Regulatory sequences surround transcription start
  sites -- and are symmetrically distributed

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End