1. ENCODE Pseudogenes and Transcription
Deyou Zheng
Yale University
, ENCODE-GT

2. 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.
113
VEGA 40
Yale 75 23
ENSEMBL 2 9
211 Yale pseudogenes, 178 Vega pseudogenes, are common. 2

3. Break Down of Yale Pseudogenes
Manually Picked (ENm*)
Randomly Picked (ENr*)
No. of Genes
No. of Pseudogenes
r2=0.31
In 44 encode regions: 104 processed, 19 duplicated, 88 others, total up to 211
More pseudogenes in the manually picked regions.
211 Pseudogenes can be separated into 104 processed, 19 duplicated and 88 others Others – those can’t be clearly binned to processed or duplicated, e.g., fragments.
Numbers of genes and pseudogenes are weakly correlated in ENCODE regions. 3

4. Intersection of Pseudogenes with Transcription Data
ENm004
Yale TARs using Oligo-microarray
Affymetrix TARs using Oligo-microarray
GIS-PET
CAGE
Interesting aspect of pseudogenes – transcription
EST
Transcription factors binding sites from ChIP-Chip
Sequence conservation in rat, mouse and chimp 4

5. Example of a Pseudogene with Various Transcription Evidence
Yale_Pgene_58 5

6. Intersection of Pseudogenes with Transcription Data
Yale Pseudogenes
Vega Pseudogenes
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 5
CAGE 10 15 7 12
EST 9 6
By random chance, Yale pseudogenes will intersect with TARs.
~40% ENCODE pseudogenes intersect with TARs. So high percentage? 6

7. Intersection of TARs with Pseudogenes
Affy-Unique-TAR
Yale-Unique-TAR
No. of TARs Overlapping a Pseudogene
Affy-not-Unique-TAR
Yale-not-Unique-TAR
No. of TARs
Not-”unique” TAR: one with a sequence of 60 bp (~3 probes) mapping to > 1 genomic locations (≥ 95% identity). 7 7

8. Summary 8 211 Pseudogenes (253, Yale + Vega) in ENCODE regions.
Some pseudogenes (< 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):
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):
Zheng et al., 2005, Integrated pseudogene annotation for human chromosome 22: evidence for transcription. J Mol Biol. 349(1):27-45. 8