title: Analysis of the transcriptome of the protozoan Theileria parva using MPSS reveals that the majority of genes are transcriptionally active in the schizont stage.
abstract: Massively parallel signature sequencing (MPSS) was used to analyze the transcriptome of the intracellular protozoan Theileria parva. In total 1,095,000, 20 bp sequences representing 4371 different signatures were generated from T.parva schizonts. Reproducible signatures were identified within 73% of potentially detectable predicted genes and 83% had signatures in at least one MPSS cycle. A predicted leader peptide was detected on 405 expressed genes. The quantitative range of signatures was 4-52,256 transcripts per million (t.p.m.). Rare transcripts (<50 t.p.m.) were detected from 36% of genes. Sequence signatures approximated a lognormal distribution, as in microarray. Transcripts were widely distributed throughout the genome, although only 47% of 138 telomere-associated open reading frames exhibited signatures. Antisense signatures comprised 13.8% of the total, comparable with Plasmodium. Eighty five predicted genes with antisense signatures lacked a sense signature. Antisense transcripts were independently amplified from schizont cDNA and verified by sequencing. The MPSS transcripts per million for seven genes encoding schizont antigens recognized by bovine CD8 T cells varied 1000-fold. There was concordance between transcription and protein expression for heat shock proteins that were very highly expressed according to MPSS and proteomics. The data suggests a low level of baseline transcription from the majority of protein-coding genes.
authors.affiliation: The International Livestock Research Institute (ILRI), PO Box 30709, Nairobi, Kenya. r.bishop@cgiar.org
authors.forename: Richard
authors.initials: R
authors.lastname: Bishop
authors.forename: Trushar
authors.initials: T
authors.lastname: Shah
authors.forename: Roger
authors.initials: R
authors.lastname: Pelle
authors.forename: David
authors.initials: D
authors.lastname: Hoyle
authors.forename: Terry
authors.initials: T
authors.lastname: Pearson
authors.forename: Lee
authors.initials: L
authors.lastname: Haines
authors.forename: Andrew
authors.initials: A
authors.lastname: Brass
authors.forename: Helen
authors.initials: H
authors.lastname: Hulme
authors.forename: Simon P
authors.initials: SP
authors.lastname: Graham
authors.forename: Evans L N
authors.initials: EL
authors.lastname: Taracha
authors.forename: Simon
authors.initials: S
authors.lastname: Kanga
authors.forename: Charles
authors.initials: C
authors.lastname: Lu
authors.forename: Brian
authors.initials: B
authors.lastname: Hass
authors.forename: Jennifer
authors.initials: J
authors.lastname: Wortman
authors.forename: Owen
authors.initials: O
authors.lastname: White
authors.forename: Malcolm J
authors.initials: MJ
authors.lastname: Gardner
authors.forename: Vishvanath
authors.initials: V
authors.lastname: Nene
authors.forename: Etienne P
authors.initials: EP
authors.lastname: de Villiers
mesh_terms: D000818:Animals; D018503:Genome, Protozoan; D023281:Genomics / Q000379:methods*; D016366:Open Reading Frames; D015800:Protozoan Proteins / Q000096:biosynthesis / Q000235:genetics; D016372:RNA, Antisense / Q000096:biosynthesis / Q000737:chemistry; D016053:RNA, Protozoan / Q000032:analysis / Q000096:biosynthesis* / Q000737:chemistry; D017423:Sequence Analysis, RNA; D016615:Telomere / Q000737:chemistry; D016797:Theileria parva / Q000235:genetics* / Q000254:growth & development / Q000378:metabolism; D015533:Transcriptional Activation
chemical_list: D015800:Protozoan Proteins; D016372:RNA, Antisense; D016053:RNA, Protozoan