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Despite comprising up to 5% of the genome, little is known about the functions of the proteins encoded by<jats:italic>pir<\/jats:italic>genes.<jats:italic>P. chabaudi<\/jats:italic>causes chronic infection in mice, which may be due to antigenic variation. In this model,<jats:italic>pir<\/jats:italic>genes are called<jats:italic>cir<\/jats:italic>s and may be involved in this mechanism, allowing evasion of host immune responses. In order to fully understand the role(s) of CIR proteins during<jats:italic>P. chabaudi<\/jats:italic>infection, a detailed characterization of the<jats:italic>cir<\/jats:italic>gene family was required.<\/jats:p><\/jats:sec><jats:sec><jats:title>Results<\/jats:title><jats:p>The<jats:italic>cir<\/jats:italic>repertoire was annotated and a detailed bioinformatic characterization of the encoded CIR proteins was performed. Two major sub-families were identified, which have been named A and B. Members of each sub-family displayed different amino acid motifs, and were thus predicted to have undergone functional divergence. In addition, the expression of the entire<jats:italic>cir<\/jats:italic>repertoire was analyzed via RNA sequencing and microarray. Up to 40% of the<jats:italic>cir<\/jats:italic>gene repertoire was expressed in the parasite population during infection, and dominant<jats:italic>cir<\/jats:italic>transcripts could be identified. In addition, some differences were observed in the pattern of expression between the<jats:italic>cir<\/jats:italic>subgroups at the peak of<jats:italic>P. chabaudi<\/jats:italic>infection. Finally, specific<jats:italic>cir<\/jats:italic>genes were expressed at different time points during asexual blood stages.<\/jats:p><\/jats:sec><jats:sec><jats:title>Conclusions<\/jats:title><jats:p>In conclusion, the large number of<jats:italic>cir<\/jats:italic>genes and their expression throughout the intraerythrocytic cycle of development indicates that CIR proteins are likely to be important for parasite survival. In particular, the detection of dominant<jats:italic>cir<\/jats:italic>transcripts at the peak of<jats:italic>P. chabaudi<\/jats:italic>infection supports the idea that CIR proteins are expressed, and could perform important functions in the biology of this parasite. Further application of the methodologies described here may allow the elucidation of CIR sub-family A and B protein functions, including their contribution to antigenic variation and immune evasion.<\/jats:p><\/jats:sec>","DOI":"10.1186\/1471-2164-13-125","type":"journal-article","created":{"date-parts":[[2012,3,29]],"date-time":"2012-03-29T20:14:12Z","timestamp":1333052052000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":27,"title":["Characterization and gene expression analysis of the cir multi-gene family of plasmodium chabaudi chabaudi (AS)"],"prefix":"10.1186","volume":"13","author":[{"given":"Jennifer","family":"Lawton","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Thibaut","family":"Brugat","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Yam Xue","family":"Yan","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Adam James","family":"Reid","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Ulrike","family":"B\u00f6hme","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Thomas Dan","family":"Otto","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Arnab","family":"Pain","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Andrew","family":"Jackson","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Matthew","family":"Berriman","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Deirdre","family":"Cunningham","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Peter","family":"Preiser","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Jean","family":"Langhorne","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"297","published-online":{"date-parts":[[2012,3,29]]},"reference":[{"issue":"9","key":"4036_CR1","doi-asserted-by":"publisher","first-page":"e1001083","DOI":"10.1371\/journal.ppat.1001083","volume":"6","author":"L Joergensen","year":"2010","unstructured":"Joergensen L, Bengtsson DC, Bengtsson A, Ronander E, Berger SS, Turner L, Dalgaard MB, Cham GK, Victor ME, Lavstsen T: Surface co-expression of two different Pf EMP1 antigens on single plasmodium falciparum-infected erythrocytes facilitates binding to ICAM1 and PECAM1. 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