BackgroundAn 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.ResultsHere 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.ConclusionsOur 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.

Randomly seeded Petri dish cultures of embryonic human lung fibroblasts generate, in the course of their growth, highly ordered cellular arrangements . Thick, bilaterally symmetrical ridges with an axial polarity and an orthogonal, multilayered internal organization are observed within stationary cultures . The generation of these structures has been investigated . Ridges result from the spontaneous aggregation of cells in postconfluent cultures brought about by directed cell movements . These movements are promoted by the localized production of extracellular matrix sheets containing collagen, which provide new substrates for cellular colonization . Cells that have colonized one matrix substrate may secrete another above themselves, which will in turn be colonized . By a continuation of this cycle, thick stacks consisting of alternate layers of cells and matrix are produced to yield the observed aggregations . The distribution and shape of ridges in a culture imply that matrix substrates are confined to specific locations . The suggested control hypothesis assumes that all the cells in fibroblast cultures are potential producers of a single species of matrix . The serviceability of this matrix as a substrate for cellular colonization, however, is destroyed if the producer cells are motile . Matrix substrates, therefore, are only made by nonmotile cells . 8We have observed that fetal lung fibroblasts passaged in Petri dish cultures exhibit pronounced multilayering, growing to approximately six confluence equivalents before net growth ceases . This behaviour contrasts with that of lines of fetal gut fibroblasts which attain their maximum cell density only slightly after confluence and show little or no multilayering . This paper considers morphogenetic aspects of multilayering and examines the form and generation of the dense cellular associations observed in stationary cultures of fetal lung fibroblasts . MATERIALS AND METHODS Cell LinesLines of fibroblasts were established from the lungs of human fetuses 10-16 wk after conception, by using primary cultures of chopped fragments or cell suspensions prepared with trypsin (Difco Laboratories, Inc ., Detroit, Mich . ; 1 :300) and collagenase (Worthington C .L .S . ; Worthington Biochemical Corp ., Freehold, N .J .) . To eliminate nonfibroblastic cells, lines were subcultured at least twice before use .Cultures were seeded, after trypsin dispersal of parent cultures, usually in Falcon disposable plastic on

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.