Determination of dosage compensation of the mammalian X chromosome by RNA-seq is dependent on analytical approach.

BACKGROUND: An enduring question surrounding sex chromosome evolution is whether effective hemizygosity in the heterogametic sex leads inevitably to dosage compensation of sex-linked genes, and whether this compensation has been observed in a variety of organisms. Incongruence in the conclusions reached in some recent reports has been attributed to different high-throughput approaches to transcriptome analysis. However, recent reports each utilizing RNA-seq to gauge X-linked gene expression relative to autosomal gene expression also arrived at diametrically opposed conclusions regarding X chromosome dosage compensation in mammals. RESULTS: Here we analyze RNA-seq data from X-monosomic female human and mouse tissues, which are uncomplicated by genes that escape X-inactivation, as well as published RNA-seq data to describe relative X expression (RXE). We find that the determination of RXE is highly dependent upon a variety of computational, statistical and biological assumptions underlying RNA-seq analysis. Parameters implemented in short-read mapping programs, choice of reference genome annotation, expression data distribution, tissue source for RNA and RNA-seq library construction method have profound effects on comparing expression levels across chromosomes. CONCLUSIONS: Our analysis shows that the high number of paralogous gene families on the mammalian X chromosome relative to autosomes contributes to the ambiguity in RXE calculations, RNA-seq analysis that takes into account that single- and multi-copy genes are compensated differently supports the conclusion that, in many somatic tissues, the mammalian X is up-regulated compared to the autosomes.

Tissue-Specific Transcriptome for Poeciliopsis prolifica Reveals Evidence for Genetic Adaptation Related to the Evolution of a Placental Fish.

The evolution of the placenta is an excellent model to examine the evolutionary processes underlying adaptive complexity due to the recent, independent derivation of placentation in divergent animal lineages. In fishes, the family Poeciliidae offers the opportunity to study placental evolution with respect to variation in degree of post-fertilization maternal provisioning among closely related sister species. In this study, we present a detailed examination of a new reference transcriptome sequence for the live-bearing, matrotrophic fish, Poeciliopsis prolifica, from multiple-tissue RNA-seq data. We describe the genetic components active in liver, brain, late-stage embryo, and the maternal placental/ovarian complex, as well as associated patterns of positive selection in a suite of orthologous genes found in fishes. Results indicate the expression of many signaling transcripts, "non-coding" sequences and repetitive elements in the maternal placental/ovarian complex. Moreover, patterns of positive selection in protein sequence evolution were found associated with live-bearing fishes, generally, and the placental P. prolifica, specifically, that appear independent of the general live-bearer lifestyle. Much of the observed patterns of gene expression and positive selection are congruent with the evolution of placentation in fish functionally converging with mammalian placental evolution and with the patterns of rapid evolution facilitated by the teleost-specific whole genome duplication event.

Factors that predict conversion in patients undergoing laparoscopic surgery for Crohn's disease.

BACKGROUND: To identify factors that would predict conversion in patients undergoing laparoscopic surgery for Crohn's disease. METHODS: Data were collected retrospectively. All procedures were performed by an experienced laparoscopic surgeon. RESULTS: Forty-eight patients underwent 57 laparoscopic procedures. Twenty-six of these procedures were for recurrent disease. The conversion rate was 42.3% (11 of 26) for recurrent disease and 13% (4 of 31) for primary disease. On univariate analysis age (P = 0.02), surgery for recurrence (P = 0.02), time from diagnosis (P = 0.03), and the presence of a clinical mass (P = 0.03) were factors that predicted conversion. On multivariate analysis these factors except time from diagnosis still remained significant. Patients who did not undergo a conversion had significantly better post operative outcomes. There was no difference in the incidence of major or minor complications or the number of resections in both groups. CONCLUSIONS: The conversion rate for the whole group was 28%. The rate is higher in patients who are over 40 years of age who are undergoing procedures for recurrence.