ENCODE Pseudogenes and Transcription Deyou Zheng Yale University 7-05-05, ENCODE-GT

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, 135-136 are common. 2

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

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

Example of a Pseudogene with Various Transcription Evidence Yale_Pgene_58 5

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, 20-30 Yale pseudogenes will intersect with TARs. ~40% ENCODE pseudogenes intersect with TARs. So high percentage? 6

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

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): 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. 8