ENCODE Pseudogenes and Transcription

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ENCODE Pseudogenes and Transcription

• Deyou Zheng
• Yale University
• 7-05-05, ENCODE-GT

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Pseudogenes in ENCODE Regions

• 211 pseudogenes were identified using an updated
  computational pipeline (Zhang et al. 2003) and
  manual curation.
• Compare Yale pseudogenes with pseudogenes from
  VEGA group and the ENSEMBL group.

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Break Down of Yale Pseudogenes
r20.31

• More pseudogenes in the manually picked
  regions.
• 211 Pseudogenes can be separated into 104
  processed, 19 duplicated and 88 others.
  Others those cant be clearly binned to
  processed or duplicated, e.g., fragments.
• Numbers of genes and pseudogenes are weakly
  correlated in ENCODE regions.

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Intersection of Pseudogenes with Transcription
Data
Pseudogenes
GIS-PET
CAGE
Transcription factors binding sites from ChIP-Chip
Sequence conservation in rat, mouse and chimp
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Example of a Pseudogene with Various
Transcription Evidence
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Intersection of Pseudogenes with Transcription
Data
Yale Pseudogenes Yale Pseudogenes Yale Pseudogenes Vega Pseudogenes Vega Pseudogenes Vega Pseudogenes
ENm ENr Total ENm ENr Total
Pseudogenes 136 75 211 112 66 178
Yale-TARS 54-61 33-39 87-98 47-57 36-47 83-103
Affy-TARs 28-48 26-36 54-84 27-43 35-43 62-85
GIS-PET 1 2 3 2 3 5
CAGE 5 10 15 5 7 12
EST 10 5 15 9 6 15

• By random chance, 20-30 Yale pseudogenes will
  intersect with TARs.
• 40 ENCODE pseudogenes intersect with TARs. So
  high percentage?

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Intersection of TARs with Pseudogenes
Affy-Unique-TAR
Yale-Unique-TAR
No. of TARs Overlapping a Pseudogene
Yale-not-Unique-TAR
Affy-not-Unique-TAR
No. of TARs

• Not-unique TAR one with a sequence of 60 bp
  (3 probes) mapping to gt 1 genomic
  locations ( 95 identity).

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Summary

• 211 Pseudogenes (253, Yale Vega) in ENCODE
  regions.
• Some pseudogenes (lt 7) might be transcribed
  based on GIS-PET, CAGE or EST data.
• About one half of pseudogenes overlap with TARs.
• Non-unique TARs intersect with pseudogenes 5
  times more often than unique TARs, probably due
  to cross-hybridization.
• Comparison with previous analysis
• A more detailed survey found that 12-16 of chr22
  pseudogenes intersected with TARs from tiling
  microarray (Zheng et al., 2005).
• Both a chr22 and a whole genome analysis showed
  that 5 human pseudogenes are likely transcribed
  (Zheng et al., 2005 Harrison et al., 2005).
• Cheng et al. (2005) also reported that
  pseudogene-overlapping TARs are usually not
  unique. We repeat their analysis using ENCODE
  pseudogenes and find the same.
• Refs
• Cheng et al., 2005, Transcriptional maps of 10
  human chromosomes at 5-nucleotide resolution.
  Science. 308(5725) 1149-54.
• Harrison et al., 2005, Transcribed processed
  pseudogenes in the human genome an intermediate
  form of expressed retrosequence lacking
  protein-coding ability. Nucleic Acids Res. 33(8)
  2374-83.
• Zheng et al., 2005, Integrated pseudogene
  annotation for human chromosome 22 evidence for
  transcription. J Mol Biol. 349(1)27-45.

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