Transcriptional Changes in the Ovaries of Perch from Chernobyl.

Fish have been highly exposed to radiation in freshwater systems after the Chernobyl Nuclear Power Plant (NPP) accident in 1986 and in freshwater and marine systems after the more recent Fukushima NPP accident in 2011. In the years after the accident, the radioactivity levels rapidly declined due to radioactive decay and environmental processes, but chronic lower dose exposures persisted. To gain insights into the long-term effects of environmental low dose radiation on fish ovaries development, a high-throughput transcriptomic approach including a de novo assembly was applied to different gonad phenotypes of female perch: developed gonads from reference lakes, developed/irradiated from medium contaminated lake, and both developed/irradiated and undeveloped from more highly contaminated lakes. This is the most comprehensive analysis to date of the gene responses in wildlife reproductive system to radiation. Some gene responses that were modulated in irradiated gonads were found to be involved in biological processes including cell differentiation and proliferation (ggnb2, mod5, rergl), cytoskeleton organization (k1C18, mtpn), gonad development (nell2, tcp4), lipid metabolism (ldah, at11b, nltp), reproduction (cyb5, cyp17A, ovos), DNA damage repair (wdhd1, rad51, hus1), and epigenetic mechanisms (dmap1). Identification of these genes provides a better understanding of the underlying molecular mechanisms underpinning the development of the gonad phenotypes of wild perch and how fish may respond to chronic exposure to radiation in their natural environment, though causal attribution of gene responses remains unclear in the undeveloped gonads.

Subtle effects of radiation on embryo development of the 3-spined stickleback.

The Chernobyl and Fukushima nuclear power plant (NPP) accidents that occurred in 1986 and 2011 respectively have led to many years of chronic radiation exposure of wildlife. However, controversies remain on the dose threshold above which an impact on animal health occurs. Fish have been highly exposed immediately after both accidents in freshwater systems around Chernobyl and in freshwater and marine systems around Fukushima. The dose levels decreased during the years after the accidents, however, little is known about the effects of environmental low doses of radiation on fish health. The present laboratory study assesses the effects of an environmentally relevant dose range of radiation (0.1, 1 and 10 mGy/day) on early life stages of the 3-spined stickleback, Gasterosteus aculeatus. The cardiac physiology and developmental features (head width, diameter, area) of high exposed embryos (10 mGy/day) showed no significant change when compared to controls. Embryos exposed to the medium and high dose were slower to hatch than the controls (between 166 and 195 h post-fertilization). After 10 days of exposure (at 240 h post-fertilization), larvae exposed to the high dose displayed comparable growth to controls. High-throughput sequence analysis of transcriptional changes at this time point revealed no significant changes in gene regulation compared to controls regardless of exposure conditions. Our results suggest that exposure of fish embryos to environmental radiation elicits subtle delays in hatching times, but does not impair the overall growth and physiology, nor the gene expression patterns in the recently hatched larvae.

Relating protein functional diversity to cell type number identifies genes that determine dynamic aspects of chromatin organisation as potential contributors to organismal complexity.

Organismal complexity broadly relates to the number of different cell types within an organism and generally increases across a phylogeny. Whilst gene expression will underpin organismal complexity, it has long been clear that a simple count of gene number is not a sufficient explanation. In this paper, we use open-access information from the Ensembl databases to quantify the functional diversity of human genes that are broadly involved in transcription. Functional diversity is described in terms of the numbers of paralogues, protein isoforms and structural domains for each gene. The change in functional diversity is then calculated for up to nine orthologues from the nematode worm to human and correlated to the change in cell-type number. Those with the highest correlation are subject to gene ontology term enrichment and interaction analyses. We found that a range of genes that encode proteins associated with dynamic changes to chromatin are good candidates to contribute to organismal complexity.

Short linear motif acquisition, exon formation and alternative splicing determine a pathway to diversity for NCoR-family co-repressors.

Vertebrate NCoR-family co-repressors play central roles in the timing of embryo and stem cell differentiation by repressing the activity of a range of transcription factors. They interact with nuclear receptors using short linear motifs (SLiMs) termed co-repressor for nuclear receptor (CoRNR) boxes. Here, we identify the pathway leading to increasing co-repressor diversity across the deuterostomes. The final complement of CoRNR boxes arose in an ancestral cephalochordate, and was encoded in one large exon; the urochordates and vertebrates then split this region between 10 and 12 exons. In Xenopus, alternative splicing is prevalent in NCoR2, but absent in NCoR1. We show for one NCoR1 exon that alternative splicing can be recovered by a single point mutation, suggesting NCoR1 lost the capacity for alternative splicing. Analyses in Xenopus and zebrafish identify that cellular context, rather than gene sequence, predominantly determines species differences in alternative splicing. We identify a pathway to diversity for the NCoR family beginning with the addition of a SLiM, followed by gene duplication, the generation of alternatively spliced isoforms and their differential deployment.

The emergence of Pax7-expressing muscle stem cells during vertebrate head muscle development.

Pax7 expressing muscle stem cells accompany all skeletal muscles in the body and in healthy individuals, efficiently repair muscle after injury. Currently, the in vitro manipulation and culture of these cells is still in its infancy, yet muscle stem cells may be the most promising route toward the therapy of muscle diseases such as muscular dystrophies. It is often overlooked that muscular dystrophies affect head and body skeletal muscle differently. Moreover, these muscles develop differently. Specifically, head muscle and its stem cells develop from the non-somitic head mesoderm which also has cardiac competence. To which extent head muscle stem cells retain properties of the early head mesoderm and might even be able to switch between a skeletal muscle and cardiac fate is not known. This is due to the fact that the timing and mechanisms underlying head muscle stem cell development are still obscure. Consequently, it is not clear at which time point one should compare the properties of head mesodermal cells and head muscle stem cells. To shed light on this, we traced the emergence of head muscle stem cells in the key vertebrate models for myogenesis, chicken, mouse, frog and zebrafish, using Pax7 as key marker. Our study reveals a common theme of head muscle stem cell development that is quite different from the trunk. Unlike trunk muscle stem cells, head muscle stem cells do not have a previous history of Pax7 expression, instead Pax7 expression emerges de-novo. The cells develop late, and well after the head mesoderm has committed to myogenesis. We propose that this unique mechanism of muscle stem cell development is a legacy of the evolutionary history of the chordate head mesoderm.

Evolutionarily conserved morphogenetic movements at the vertebrate head-trunk interface coordinate the transport and assembly of hypopharyngeal structures.

The vertebrate head-trunk interface (occipital region) has been heavily remodelled during evolution, and its development is still poorly understood. In extant jawed vertebrates, this region provides muscle precursors for the throat and tongue (hypopharyngeal/hypobranchial/hypoglossal muscle precursors, HMP) that take a stereotype path rostrally along the pharynx and are thought to reach their target sites via active migration. Yet, this projection pattern emerged in jawless vertebrates before the evolution of migratory muscle precursors. This suggests that a so far elusive, more basic transport mechanism must have existed and may still be traceable today. Here we show for the first time that all occipital tissues participate in well-conserved cell movements. These cell movements are spearheaded by the occipital lateral mesoderm and ectoderm that split into two streams. The rostrally directed stream projects along the floor of the pharynx and reaches as far rostrally as the floor of the mandibular arch and outflow tract of the heart. Notably, this stream leads and engulfs the later emerging HMP, neural crest cells and hypoglossal nerve. When we (i) attempted to redirect hypobranchial/hypoglossal muscle precursors towards various attractants, (ii) placed non-migratory muscle precursors into the occipital environment or (iii) molecularly or (iv) genetically rendered muscle precursors non-migratory, they still followed the trajectory set by the occipital lateral mesoderm and ectoderm. Thus, we have discovered evolutionarily conserved morphogenetic movements, driven by the occipital lateral mesoderm and ectoderm, that ensure cell transport and organ assembly at the head-trunk interface.

Use of non-steroidal anti-inflammatory drugs and prostate cancer risk: a population-based nested case-control study.

BACKGROUND: Despite strong laboratory evidence that non-steroidal anti-inflammatory drugs (NSAIDs) could prevent prostate cancer, epidemiological studies have so far reported conflicting results. Most studies were limited by lack of information on dosage and duration of use of the different classes of NSAIDs. METHODS: We conducted a nested case-control study using data from Saskatchewan Prescription Drug Plan (SPDP) and Cancer Registry to examine the effects of dose and duration of use of five classes of NSAIDs on prostate cancer risk. Cases (N = 9,007) were men aged ≥40 years diagnosed with prostatic carcinoma between 1985 and 2000, and were matched to four controls on age and duration of SPDP membership. Detailed histories of exposure to prescription NSAIDs and other drugs were obtained from the SPDP. RESULTS: Any use of propionates (e.g., ibuprofen, naproxen) was associated with a modest reduction in prostate cancer risk (Odds ratio = 0.90; 95%CI 0.84-0.95), whereas use of other NSAIDs was not. In particular, we did not observe the hypothesized inverse association with aspirin use (1.01; 0.95-1.07). There was no clear evidence of dose-response or duration-response relationships for any of the examined NSAID classes. CONCLUSIONS: Our findings suggest modest benefits of at least some NSAIDs in reducing prostate cancer risk.

Alternative splicing determines the interaction of SMRT isoforms with nuclear receptor-DNA complexes.

Signalling by small molecules, such as retinoic acid, is mediated by heterodimers comprising a class II nuclear receptor and an RXR (retinoid X receptor) subunit. The receptors bind to DNA response elements and act as ligand-dependent transcription factors, but, in the absence of signal, the receptors bind the co-repressors SMRT [silencing mediator for RAR (retinoic acid receptor) and TR (thyroid hormone receptor)] and NCoR (nuclear receptor co-repressor) and repress gene expression. Alternative splicing of the SMRT transcript in mammals generates six isoforms containing 1, 2 or 3 CoRNR (co-repressor for nuclear receptor) box motifs which are responsible for the interactions with nuclear receptors. We show that human cell lines express all six SMRT isoforms and then determine the binding affinity of mouse SMRT isoforms for RAR/RXR and three additional class II nuclear receptor-DNA complexes. This approach demonstrates the importance of the full complement of CoRNR boxes within each SMRT protein, rather than the identity of individual CoRNR boxes, in directing the interaction of SMRT with nuclear receptors. Each class of SMRT isoform displays a distinct feature, as the 1-box isoform discriminates between DNA response elements, the 2-box isoforms promote high-affinity binding to TR complexes and the 3-box isoforms show differential binding to nuclear receptors. Consequently, the differential deployment of SMRT isoforms observed in vivo could significantly expand the regulatory capacity of nuclear receptor signalling.

Xenopus embryos lacking specific isoforms of the corepressor SMRT develop abnormal heads.

The corepressor SMRT acts on a range of transcription factors, including the retinoid and thyroid hormone nuclear receptors. The carboxy-terminal region of SMRT contains CoRNR box motifs that mediate these interactions. We have shown, in Xenopus, that SMRT can exist as isoforms containing either two or three CoRNR boxes depending on the alternative splicing of exon 37b. The number of SMRT transcript isoforms expressed increases during development until all sixteen possible isoforms are identified in the swimming tadpole. To eliminate specific SMRT isoforms, we have developed a process that uses an antisense morpholino oligonucleotide in Xenopus to dictate the outcome of alternative splicing at a defined exon and used this to inhibit the formation of transcripts containing exon 37b. These embryos are therefore limited to the expression of SMRT isoforms that contain two rather than three CoRNR boxes. Analysis of responsive genes in these embryos shows that targets of thyroid hormone, but not retinoid signaling are affected by the elimination of exon 37b. Morpholino-injected embryos have swimming abnormalities and develop altered head morphology, an expanded olfactory epithelium and disorganized peripheral axons. These experiments indicate a critical role for the alternative splicing of SMRT in development.

Developmental and tissue expression of Xenopus laevis RPGR.

PURPOSE: The present study examined the developmental and tissue expression of the retinitis pigmentosa GTPase regulator (RPGR) gene in Xenopus laevis. METHODS: The cDNA for X. laevis RPGR (XRPGR) was isolated from adult eye mRNA by reverse transcription-polymerase chain reaction (RT-PCR) and rapid amplification of cDNA ends. The deduced peptide sequence was aligned with RPGR orthologues. Gene expression was examined by whole-mount in situ hybridization and RT-PCR. The localization of XRPGR in X. laevis photoreceptor cells and XTC-2 cells was determined by immunostaining. RESULTS: The XRPGR(ex1-19) isoform encodes a protein of 727 amino acids containing an RCC1 domain and a C-terminal isoprenylation anchorage motif. It shares 33% to 41% amino acid identity with human, mouse, and dog RPGR. The C-terminal exon of the alternatively spliced RPGR(ORF15) isoform is also conserved across species. XRPGR is expressed at the earliest stages of X. laevis development and persists into adulthood, where expression is highest in the eye. XRPGR is expressed in presumptive eye fields (stages 18 to 22), becoming largely restricted to the central retina (stages 28 to 40). XRPGR protein colocalizes with beta-tubulin at the X. laevis ciliary axoneme and with gamma-tubulin at centrosomes in XTC-2 cells. CONCLUSIONS: XRPGR is widely expressed throughout development but shows highest expression after the appearance of the eye primordium and persists in the eye into adulthood. The data are consistent with XRPGR expression in a single microtubular organelle-the centriole or basal body and associated ciliary transitional zone found in modified sensory cilia of photoreceptors and motile cilia.

The expression and alternative splicing of alpha-neurexins during Xenopus development.

The neurexins are involved in the formation and function of synapses. Each of three genes encodes alpha- and beta-neurexins. Additional diversity (particularly of alpha-neurexins) arises from alternative splicing, resulting in a large number of protein isoforms, the significance of which is currently unclear. We have analysed alpha neurexin expression and alternative splicing during development of the frog Xenopus laevis. Surprisingly, each alpha-neurexin gene is expressed in immature oocytes. During embryonic development, each Xenopus neurexin (nrxn) gene has a distinct temporal expression pattern, with expression being almost exclusively within the neuroepithelium. The spatial expression of nrxnIalpha and nrxnIIalpha is similar in the developing CNS, with staining being observed in the optic cup and in dorsolateral regions of anterior neural tube, but not adjacent to the ventral midline. The pattern of nrxnIIIalpha expression is more restricted, in several domains of the anterior neural tube. In the forebrain, expression was confined to an area in the ventrolateral neural tube; nrxnIIIalpha was also expressed in the hindbrain and spinal cord. By stage 32, a period when synaptogenesis occurs, nrxnIIIalpha is expressed midway along the neural tube's dorso-ventral axis in the hindbrain and anterior spinal cord, at the site of the primary interneuron column. Because of the striking diversity of neurexin isoforms, we analysed alternative splicing of Xenopus transcripts during development and found examples of alternative splice variants of each neurexin. The data demonstrate differential regulation of the alpha neurexins with respect to the gene temporal and spatial expression and alternative splicing.

SMRT has tissue-specific isoform profiles that include a form containing one CoRNR box.

SMRT acts as a corepressor for a range of transcription factors. The amino-terminal part of the protein includes domains that mainly mediate transcriptional repression whilst the carboxy-terminal part includes domains that interact with nuclear receptors using up to three motifs called CoRNR boxes. The region of the SMRT primary transcript encoding the interaction domains is subject to alternative splicing that varies the inclusion of the third CoRNR box. The profile in mice includes an abundant, novel SMRT isoform that possesses just one CoRNR box. Mouse tissues therefore express SMRT isoforms containing one, two or three CoRNR boxes. In frogs, the SMRT isoform profile is tissue-specific. The mouse also shows distinct profiles generated by differential expression levels of the SMRT transcript isoforms. The formation of multiple SMRT isoforms and their tissue-specific regulation indicates a mechanism, whereby cells can define the repertoire of transcription factors regulated by SMRT.

Alternative splicing generates multiple SMRT transcripts encoding conserved repressor domains linked to variable transcription factor interaction domains.

Silencing mediator for retinoid and thyroid hormone receptor (SMRT) and nuclear receptor corepressor protein (NCoR) are corepressors that interact with a range of transcription factors. They both consist of N-terminal repressor domains that associate with histone deacetylases and C-terminal interaction domains (IDs) that contain CoRNR box motifs. These motifs mediate the interaction between corepressors and nuclear receptors (NRs), such as the retinoid and thyroid hormone receptors. However, whilst NCoR produces a single transcript during Xenopus development, xSMRT is subject to alternative splicing at four sites in the 3' part of the transcript, the region encoding the C-terminal IDs. Although this provides the potential to produce 16 different transcripts, only five isoforms are found in early embryos. The sites of alternative splicing predict that the resultant isoforms will differ in their ability to interact with NRs, as one site varies the number of CoRNR boxes, the second site changes the sequence flanking CoRNR box-1 and the other sites delete amino acid residues between CoRNR boxes 1 and 2 and so alter the critical spacing between these motifs. SMRT and NCoR therefore represent paralogues in which one form, SMRT, has evolved the ability to generate multiple isoforms whereas the other, NCoR, is invariant in Xenopus development.

The effects of smoking on the risk of colorectal cancer.

PURPOSE: The aim of this study was to assess the effects of smoking on the risk of colorectal cancer according to anatomic subsite. METHODS: Between 1979 and 1985 a population-based case-control study of cancer at multiple sites was performed in Montréal, which accrued over 4,000 males in total, including cases of colorectal cancer, other cancers, and population controls. The present analysis was restricted to the 585 cases with histologically proven adenocarcinoma of the large bowel, aged 35 to 70 years, who underwent face-to-face interviews and provided adequate smoking histories. Of these, 176 had cancer in the proximal colon, 179 had cancer in the distal colon, and 230 had rectal cancer. Our control group consisted of 405 cancer controls, whose tumor types were considered unrelated to smoking, and 500 population controls. RESULTS: We observed a positive association between cigar smoking and cancer of the rectum. We also found some suggestion of a weak positive association between cigarette smoking and cancer of the proximal colon, an inverse association with cancer of the distal colon, although neither was statistically significant, and no association with rectal cancer. CONCLUSIONS: Cigar smoking seems to be associated with the development of rectal cancer. If the positive association between cigarette smoking and cancer of the proximal colon is real, it might partially explain the proximal shift in the anatomic distribution of colorectal cancer that has been observed, because of the increasing prevalence of cigarette smoking during the middle of the 20th century.

Effects of alcohol consumption on the risk of colorectal cancer among men by anatomical subsite (Canada).

OBJECTIVE: To estimate the effects of alcohol consumption on the risk of colorectal cancer according to anatomical subsite. METHODS: Between 1979 and 1985 a population-based case-control study of cancer at multiple sites was carried out in Montreal. This analysis was restricted to the 585 cases with adenocarcinoma of the large bowel, aged 35-70 years, who underwent face-to-face interviews. Controls (n = 500) were selected either from electoral lists or by random-digit dialing and were frequency-matched to the cases on age. Polytomous logistic regression was used to estimate the risk of cancer of the proximal colon, distal colon, and rectum in relation to the consumption of alcoholic beverages. RESULTS: Daily consumption of alcohol of any type was associated with increased risks of cancer of the distal colon [odds ratio (OR)= 2.3; 95% confidence interval (CI) 1.4-3.7] and the rectum (OR = 1.6; 95% Cl 1.0-2.6), but not with an increased risk of cancer of the proximal colon (OR = 1.0; 95% CI: 0.6-1.7). When type of beverage was considered, beer showed strong associations with cancer at all three subsites (ORs among the heaviest drinkers ranging from 1.8 to 2.4), spirits showed weaker associations with cancer at all three subsites (ORs ranging from 1.4 to 1.6), and wine showed null associations. CONCLUSIONS: The results are consistent with the hypothesis that consumption of alcoholic beverages increases the risk of colorectal cancer. The evidence is strongest for effects on the distal colon and rectum, and, among the three types of beverage, it most strongly implicates beer.