Roles for the Yb body components Armitage and Yb in primary piRNA biogenesis in Drosophila.

PIWI-interacting RNAs (piRNAs) protect genome integrity from transposons. In Drosophila ovarian somas, primary piRNAs are produced and loaded onto Piwi. Here, we describe roles for the cytoplasmic Yb body components Armitage and Yb in somatic primary piRNA biogenesis. Armitage binds to Piwi and is required for localizing Piwi into Yb bodies. Without Armitage or Yb, Piwi is freed from the piRNAs and does not enter the nucleus. Thus, piRNA loading is required for Piwi nuclear entry. We propose that a functional Piwi-piRNA complex is formed and inspected in Yb bodies before its nuclear entry to exert transposon silencing.

A regulatory circuit for piwi by the large Maf gene traffic jam in Drosophila.

PIWI-interacting RNAs (piRNAs) silence retrotransposons in Drosophila germ lines by associating with the PIWI proteins Argonaute 3 (AGO3), Aubergine (Aub) and Piwi. piRNAs in Drosophila are produced from intergenic repetitive genes and piRNA clusters by two systems: the primary processing pathway and the amplification loop. The amplification loop occurs in a Dicer-independent, PIWI-Slicer-dependent manner. However, primary piRNA processing remains elusive. Here we analysed piRNA processing in a Drosophila ovarian somatic cell line where Piwi, but not Aub or AGO3, is expressed; thus, only the primary piRNAs exist. In addition to flamenco, a Piwi-specific piRNA cluster, traffic jam (tj), a large Maf gene, was determined as a new piRNA cluster. piRNAs arising from tj correspond to the untranslated regions of tj messenger RNA and are sense-oriented. piRNA loading on to Piwi may occur in the cytoplasm. zucchini, a gene encoding a putative cytoplasmic nuclease, is required for tj-derived piRNA production. In tj and piwi mutant ovaries, somatic cells fail to intermingle with germ cells and Fasciclin III is overexpressed. Loss of tj abolishes Piwi expression in gonadal somatic cells. Thus, in gonadal somatic cells, tj gives rise simultaneously to two different molecules: the TJ protein, which activates Piwi expression, and piRNAs, which define the Piwi targets for silencing.

Drosophila endogenous small RNAs bind to Argonaute 2 in somatic cells.

RNA silencing is a conserved mechanism in which small RNAs trigger various forms of sequence-specific gene silencing by guiding Argonaute complexes to target RNAs by means of base pairing. RNA silencing is thought to have evolved as a form of nucleic-acid-based immunity to inactivate viruses and transposable elements. Although the activity of transposable elements in animals has been thought largely to be restricted to the germ line, recent studies have shown that they may also actively transpose in somatic cells, creating somatic mosaicism in animals. In the Drosophila germ line, Piwi-interacting RNAs arise from repetitive intergenic elements including retrotransposons by a Dicer-independent pathway and function through the Piwi subfamily of Argonautes to ensure silencing of retrotransposons. Here we show that, in cultured Drosophila S2 cells, Argonaute 2 (AGO2), an AGO subfamily member of Argonautes, associates with endogenous small RNAs of 20-22 nucleotides in length, which we have collectively named endogenous short interfering RNAs (esiRNAs). esiRNAs can be divided into two groups: one that mainly corresponds to a subset of retrotransposons, and the other that arises from stem-loop structures. esiRNAs are produced in a Dicer-2-dependent manner from distinctive genomic loci, are modified at their 3' ends and can direct AGO2 to cleave target RNAs. Mutations in Dicer-2 caused an increase in retrotransposon transcripts. Together, our findings indicate that different types of small RNAs and Argonautes are used to repress retrotransposons in germline and somatic cells in Drosophila.

Functional involvement of Tudor and dPRMT5 in the piRNA processing pathway in Drosophila germlines.

In Drosophila, the PIWI proteins, Aubergine (Aub), AGO3, and Piwi are expressed in germlines and function in silencing transposons by associating with PIWI-interacting RNAs (piRNAs). Recent studies show that PIWI proteins contain symmetric dimethyl-arginines (sDMAs) and that dPRMT5/Capsuleen/DART5 is the modifying enzyme. Here, we show that Tudor (Tud), one of Tud domain-containing proteins, associates with Aub and AGO3, specifically through their sDMA modifications and that these three proteins form heteromeric complexes. piRNA precursor-like molecules are detected in these complexes. The expression levels of Aub and AGO3, along with their degree of sDMA modification, were not changed by tud mutations. However, the population of transposon-derived piRNAs associated with Aub and AGO3 was altered by tud mutations, whereas the total amounts of small RNAs on Aub and AGO3 was increased. Loss of dprmt5 did not change the stability of Aub, but impaired its association with Tud and lowered piRNA association with Aub. Thus, in germline cells, piRNAs are quality-controlled by dPRMT5 that modifies PIWI proteins, in tight association with Tud.

Whole Mount In Situ Hybridization and Morphometric Analysis in Rabbit Embryos.

Rabbits are valuable experimental animals used to evaluate the teratogenicity of chemical entities. If teratogenicity is recognized, it is very important to investigate the pathogenesis to assess the potential risk in humans. For this investigation, whole-mount in situ hybridization (WISH) is highly useful for visualizing spatial and temporal changes in the expression patterns of the targeted genes and or proteins. In this chapter, the WISH method in rabbit embryos, using a digoxigenin-labeled RNA probe, and the morphometric analysis of the expression pattern is described.

Measurements of density and sticking probability of CN(X(2)Sigma(+)) radicals by laser-induced fluorescence spectroscopy.

CN(X(2)Sigma(+)) radicals were produced by the decomposition of BrCN with the microwave discharge flow of Ar under the conditions of Ar pressure in the range of 0.40-0.70 Torr. The laser-induced fluorescence (LIF) spectra of the CN(A(2)Pi(i)-X(2)Sigma(+)), 4-0, 5-1, and 7-2 bands were observed, and their intensities were calibrated against Rayleigh-scattering intensity by Ar atoms, from which the CN(X(2)Sigma(+)) radical density (n(CN(X))) was determined as (0.67+/-0.25) x 10(18) to (4.42+/-0.83) x 10(18) m(-3). Hydrogenated amorphous carbon nitride (a-CN(x):H) films were formed by depositing the CN(X(2)Sigma(+)) radicals on Si substrates in the same reaction system as LIF. The sticking probability (s) of the CN(X(2)Sigma(+)) radicals onto the a-CN(x):H films was determined by using n(CN(X)), the flow speed, and the weight (w) of a-CN(x):H. The s value was determined as (6.4+/-6.4) x 10(-2) to (2.5+/-1.2) x 10(-2), where the errors are predominantly determined by those in n(CN(X)) and w. The procedure described in the present study will provide a methodology to determine the sticking probability of the precursor radicals of the film formation based on the gas-phase LIF spectroscopy.

Trans-octadecenoic Acid Positional Isomers Have Different Accumulation and Catabolism Properties in Mice.

Trans fatty acids (TFA) are considered risk factors for cardiovascular disease (CVD), while the details of distribution and metabolism of the individual isomers are not clear. Here we investigated the accumulation and catabolic rate of TFA positional isomers of octadecenoic acid (18:1) in mice. ICR mice were fed deuterium- and [1-(13)C] stable isotope-labeled trans-9-18:1 (9t-18:1*), trans-10-18:1 (10t-18:1*), or trans-11-18:1 (11t-18:1*) for 2 or 4 weeks, or a TFA mixture (9t-18:1*, 10t-18:1*, and 11t-18:1*) for 3 weeks. Analysis of whole-body tissues by gas chromatography-chemical ionization mass spectrometry revealed the highest 9t-18:1* levels in the heart. Significant differences in the accumulation of the respective trans-18:1 were observed in the heart and erythrocytes, where 9t- > 11t- > 10t-18:1*, but no significant difference was observed in the liver or white adipose tissue (WAT). Mice fed on 11t-18:1 demonstrated accumulation of endogenously synthesized conjugated linoleic acid in the liver, WAT, and heart, but any other metabolites were not found in other groups. Furthermore, we analyzed catabolic rates of single-dose-administered trans-18:1* isomers into [(13)C]-labeled CO2 using isotope-ratio mass spectrometry, and the 10t-18:1*catabolic rate was significantly higher than those of 9t- and 11t-18:1*. We found that the accumulation and catabolism of trans-18:1 positional isomers varied in these mice. Differential accumulation in tissues suggests that individual TFA positional isomers may play different roles in human health.

Regiospecific Distribution of trans-Octadecenoic Acid Positional Isomers in Triacylglycerols of Partially Hydrogenated Vegetable Oil and Ruminant Fat.

It is revealed that binding position of fatty acid in triacylglycerol (TAG) deeply relates to the expression of its function. Therefore, we investigated the binding positions of individual trans-octadecenoic acid (trans-C18:1) positional isomers, known as unhealthy fatty acids, on TAG in partially hydrogenated canola oil (PHCO), milk fat (MF), and beef tallow (BT). The analysis was carried out by the sn-1(3)-selective transesterification of Candida antarctica Lipase B and by using a highly polar ionic liquid capillary column for gas chromatography-flame ionization detection. Trans-9-C18:1, the major trans-C18:1 positional isomer, was selectively located at the sn-2 position of TAG in PHCO, although considerable amounts of trans-9-C18:1 were also esterified at the sn-1(3) position. Meanwhile, trans-11-C18:1, the major isomer in MF and BT, was preferentially located at the sn-1(3) position. These results revealed that the binding position of trans-C18:1 positional isomer varies between various fats and oils.

Common nature in the effects of thalidomide on embryo-fetal development in Kbl:JW and Kbl:NZW rabbits.

The effects of thalidomide on the embryo-fetal development (EFD) of rabbit fetuses and the sensitive periods (SP) for the various malformations were compared between Kbl:JW and Kbl:NZW rabbits to investigate possible strain differences. The post-implantation loss rate and number of placental remnants were increased and the number of live fetuses was decreased in both of the strains in the EFD study and in Kbl:NZW at 300 mg/kg dosed on GD 7-8 in the SP study. In the external and skeletal examinations, head, limb and tail malformations were observed in both the strains in the EFD and SP studies at the same dose levels in the same dosing period. In the visceral examination, hydrocephaly, cardiovascular malformations, absent pulmonary intermedial lobe, diaphragmatic hernia and/or abnormal liver lobation were also observed in both of the strains in the EFD and SP studies at the same dose levels and in the same dosing period. Plasma concentrations of thalidomide were equivalent between the two strains in the SP study. There were strain differences in some parameters, such as the post-implantation loss rate and the frequencies of malformations in forelimb and hindlimb and pulmonary intermedial lobe, but similar types of malformations or variations were induced at the same dose levels on the same dosing period in both strains. Therefore, it is concluded that there were no essential differences in sensitivity of the fetuses to thalidomide between Kbl:JW and NZW rabbits and both of the strains are useful to evaluate the teratogenic effects of thalidomide.

Effects of thalidomide on Fgf8, Bmp4 and Hoxa11 expression in the limb bud in Kbl:JW rabbit embryos.

Thalidomide (TM) induces limb defects in humans and some animal species including rabbits. Although the mechanism of TM-induced limb defects has been investigated for a long period, the limb development-related genes expressions have not been vigorously characterized in rabbits. In this study, we investigated the Fgf8, Bmp4 and Hoxa11 expressions in TM-treated JW rabbit embryos on gestation days (GDs) 10, 11 and 12 by whole mount in situ hybridization. On GDs 10 and 11, growth retardation of the embryo was induced by TM treatment. The Fgf8 expression lengths on GDs 10 and 11 in the forelimb bud were significantly or tended to be decreased in the TM-treated embryos, which was correlated to the growth retardation and was not considered to be directly relevant to the teratogenic effect of TM in the forelimb. The TM-induced characteristic changes in the expression pattern of Hoxa11 and Bmp4 on GDs 10 and/or 11 were not noted. On GD 12, TM-induced growth retardation was not noted and the Fgf8 and Bmp4 expressions were not changed. On the contrary, Hoxa11 expression was narrowed at the anterior region, which was located on the radial side, and was not changed at the middle and posterior regions in the forelimb bud and in all regions in the hindlimb bud. Because the radius malformations were induced by TM treatment, we concluded the decrease in the Hoxa11 expression was related to the TM-induced limb defects and can be a good marker for early prediction of the teratogenic effect of TM.

Stability of the reproductive variables and fetal malformations from control animals and animals treated with thalidomide in Kbl:JW rabbits over two decades.

We retrospectively analyzed the reproductive variables and the spontaneous malformations in the historical control data from the embryo-fetal development studies conducted in our laboratories with Kbl:JW rabbits over two decades (1990-2010) and fetal malformations induced by thalidomide in 1988, 1995 and 2007. These analyses in the control animals revealed that the reproductive variables in dams, total frequencies and profile of external, visceral and skeletal abnormalities and/or variations in the fetuses were stable over two decades. In addition, the characteristics of the malformations induced by thalidomide were reproducible at the three time points. Therefore, it is concluded that Kbl:JW rabbit is one of the useful rabbit strains to evaluate the effects of test substances on embryo-fetal development, especially in view of the chronological stability of spontaneous or drug-induced malformations in the fetuses.

A slicer-mediated mechanism for repeat-associated siRNA 5' end formation in Drosophila.

In Drosophila, repeat-associated small interfering RNAs (rasiRNAs) are produced in the germ line by a Dicer-independent pathway and function through the PIWI subfamily of Argonautes to ensure silencing of retrotransposons. We sequenced small RNAs associated with the PIWI subfamily member AGO3. Although other members of PIWI, Aubergine (Aub) and Piwi, associated with rasiRNAs derived mainly from the antisense strand of retrotransposons, AGO3-associated rasiRNAs arose mainly from the sense strand. Aub- and Piwi-associated rasiRNAs showed a strong preference for uracil at their 5' ends, and AGO3-associated rasiRNAs showed a strong preference for adenine at nucleotide 10. Comparisons between AGO3- and Aub-associated rasiRNAs revealed pairs of rasiRNAs showing complementarities in their first 10 nucleotides. Aub and AGO3 exhibited Slicer activity in vitro. These data support a model in which formation of a 5' terminus within rasiRNA precursors is guided by rasiRNAs originating from transcripts of the other strand in concert with the Slicer activity of PIWI.

Gene silencing mechanisms mediated by Aubergine piRNA complexes in Drosophila male gonad.

Genetic studies have shown that Aubergine (Aub), one of the Piwi subfamily of Argonautes in Drosophila, is essential for germ cell formation and maintaining fertility. aub mutations lead to the accumulation of retrotransposons in ovaries and testes, and Stellate transcripts in testes. Aub in ovaries associates with a variety of Piwi-interacting RNAs (piRNAs) derived from repetitive intergenic elements including retrotransposons. Here we found that Aub in testes also associates with various kinds of piRNAs. Although in ovaries Aub-associated piRNA populations are quite diverse, piRNAs with Aub in testes show a strong bias. The most abundant piRNAs were those corresponding to antisense transcripts of Suppressor of Stellate [Su(Ste)] genes known to be involved in Stellate gene silencing. The second most abundant class was made up of those from chromosome X and showed strong complementarity to vasa transcripts. Immunopurified Aub-piRNA complexes from testes displayed activity in cleaving target RNA containing sequences complementary to Stellate and vasa transcripts. These results provide the first biochemical insights into gene silencing mechanisms mediated by Aub and piRNAs in fly testes.

Specific association of Piwi with rasiRNAs derived from retrotransposon and heterochromatic regions in the Drosophila genome.

In Drosophila, Piwi (P-element-induced wimpy testis), which encodes a protein of the Argonaute family, is essential for germ stem cell self-renewal. Piwi has recently been shown to be a nuclear protein involved in gene silencing of retrotransposons and controlling their mobilization in the male germline. However, little is known about the molecular mechanisms of Piwi-dependent gene silencing. Here we show that endogenous Piwi immunopurified from ovary specifically associates with small RNAs of 25-29 nucleotides in length. Piwi-associated small RNAs were identified by cloning and sequencing as repeat-associated small interfering RNAs (rasiRNAs) derived from repetitive regions, such as retrotransposon and heterochromatic regions, in the Drosophila genome. Northern blot analyses revealed that in vivo Piwi does not associate with microRNAs (miRNAs) and that guide siRNA was not loaded onto Piwi when siRNA duplex was added to ovary lysate. In vitro, recombinant Piwi exhibits target RNA cleavage activity. These data together imply that Piwi functions in nuclear RNA silencing as Slicer by associating specifically with rasiRNAs originating from repetitive targets.