Ontogeny of maternal and newly transcribed mRNA analyzed by in situ hybridization during development of Caenorhabditis elegans

Kinetics and specificity of paternal mitochondrial elimination in Caenorhabditis elegans

In most eukaryotes, mitochondria are inherited maternally. The autophagy process is critical for paternal mitochondrial elimination (PME) in Caenorhabditis elegans, but how paternal mitochondria, but not maternal mitochondria, are selectively targeted for degradation is poorly understood. Here we report that mitochondrial dynamics have a profound effect on PME. A defect in fission of paternal mitochondria delays PME, whereas a defect in fusion of paternal mitochondria accelerates PME. Surprisingly, a defect in maternal mitochondrial fusion delays PME, which is reversed by a fission defect in maternal mitochondria or by increasing maternal mitochondrial membrane potential using oligomycin. Electron microscopy and tomography analyses reveal that a proportion of maternal mitochondria are compromised when they fail to fuse normally, leading to their competition for the autophagy machinery with damaged paternal mitochondria and delayed PME. Our study indicates that mitochondrial dynamics play a critical role in regulating both the kinetics and the specificity of PME.

Autophagy mediates the degradation of paternal mitochondria after fertilization in C. elegans to ensure that mitochondria are inherited maternally. Here the authors show that mitochondrial dynamics is critical for the selectivity and kinetics of paternal mitochondrial elimination.

Whole-mount identification of gene transcripts in aphids: protocols and evaluation of probe accessibility

In situ hybridization has become a powerful tool for detecting the temporal and spatial distribution of gene transcripts in prokaryotes and eukaryotes. We report an efficient protocol for whole-mount identification of the expression of mRNAs in the parthenogenetic pea aphid Acyrthosiphon pisum, an emerging model organism with a growing accumulation of genome sequencing data. In addition to steps common for most animal in situ hybridization protocols, we describe processing methods specific to aphids, the accessibility of antisense riboprobes of different lengths in whole-mounted aphids, and signal intensity versus probe lengths. To find substrate combinations that clearly contrast single and double in situ signals in A. pisum, we tested our protocols using riboprobes constructed from two conserved germline markers, Apvasa and Apnanos, and examined colocalized signals in the germaria and developing oocytes. Finally, we propose conditions for stringent permeabilization that may be applied to tissues deep within the aphid embryo.

Expression patterns and transcript processing of ftt-1 and ftt-2, two C. elegans 14-3-3 homologues

A wide diversity of biological functions have been attributed to the highly conserved and ubiquitous 14-3-3 protein family. Yet how much of this diversity is inherent in the basic structure of 14-3-3 and how much is due to isoform specific functions is not yet fully understood. Here, two Caenorhabditis elegans 14-3-3 isoforms whose protein sequences are 90% similar were found to differ significantly in both their genomic structure and expression patterns. The two genes, ftt-1 (IV) (fourteen-three-three) and ftt-2 (X), differ in both the position and sequence of their introns. Since the various intron/exon boundaries respect neither functional nor structural protein motifs, the introns appear to be relatively recent evolutionary additions. ftt-1(IV) encodes three germline enhanced transcripts, two of which are related through the differential use of alternative poly(A) addition sites. RNA in situ hybridization studies reveal high levels of ftt-1 throughout the gonad with particularly high levels in the distal arm. In contrast, ftt-2 (X) encodes a single transcript which is expressed somatically. In embryos, high levels of ftt-1 transcripts appear to be maternally supplied, whereas ftt-2 is expressed as an early zygotic transcript whose expression pattern later localizes to the posterior region of post-proliferative embryos. These expression pattern differences between ftt-1 and ftt-2 suggest that these two 14-3-3 isoforms perform distinct biological roles within the worm.

Early transcription in Caenorhabditis elegans embryos

We have analysed early transcription in devitellinized, cultured embryos of the nematode Caenorhabditis elegans by two methods: measurement of [32P]UTP uptake into TCA-precipitable material and autoradiographic detection of [3H]UTP labelling both in the presence and absence of alpha-amanitin. RNA synthesis was first detected at the 8- to 12-cell stage, and alpha-amanitin sensitivity also appeared at this time, during the cleavages establishing the major founder cell lineages. The requirements for maternally supplied versus embryonically produced gene products in early embryogenesis were examined in the same culture system by observing the effects of alpha-amanitin on cell division and the early stereotyped lineage patterns. In the presence of high levels of alpha-amanitin added at varying times from two cells onward, cell division continued until approximately the 100-cell stage and then stopped during a single round of cell division. The characteristic unequal early cleavages, orientation of cleavage planes and lineage-specific timing of early divisions were unaffected by alpha-amanitin in embryos up to 87 cells. These results indicate that embryonic transcription starts well before gastrulation in C. elegans embryos, but that although embryonic transcripts may have important early functions, maternal products can support at least the mechanics of the first 6 to 7 cell cycles.

Temporal and spatial expression patterns of the small heat shock (hsp16) genes in transgenic Caenorhabditis elegans

The expression of the hsp16 gene family in Caenorhabditis elegans has been examined by introducing hsp16-lacZ fusions into the nematode by transformation. Transcription of the hsp16-lacZ transgenes was totally heat-shock dependent and resulted in the rapid synthesis of detectable levels of beta-galactosidase. Although the two hsp16 gene pairs of C. elegans are highly similar within both their coding and noncoding sequences, quantitative and qualitative differences in the spatial pattern of expression between gene pairs were observed. The hsp16-48 promoter was shown to direct greater expression of beta-galactosidase in muscle and hypodermis, whereas the hsp16-41 promoter was more efficient in intestine and pharyngeal tissue. Transgenes that eliminated one promoter from a gene pair were expressed at reduced levels, particularly in postembryonic stages, suggesting that the heat shock elements in the intergenic region of an hsp16 gene pair may act cooperatively to achieve high levels of expression of both genes. Although the hsp16 gene pairs are never constitutively expressed, their heat inducibility is developmentally restricted; they are not heat inducible during gametogenesis or early embryogenesis. The hsp16 genes represent the first fully inducible system in C. elegans to be characterized in detail at the molecular level, and the promoters of these genes should find wide applicability in studies of tissue- and developmentally regulated genes in this experimental organism.

Quantitative in situ hybridization analysis of glutamic acid decarboxylase messenger RNA in developing rat cerebellum

The appearance and relative amounts of GAD mRNA in rat cerebellar neurons during postnatal development was studied by in situ hybridization. GAD mRNA content within all GABAergic neurons increased during the first month of postnatal development, but the degree and time course of the increase varied among different neuronal types. In newborn rats, GAD mRNA was present only in the prenatally-formed Purkinje and Golgi cells. GAD mRNA in Golgi cells had reached adult levels by postnatal day 14, while GAD mRNA levels in Purkinje cells reached adult levels one week later. Most basket cells expressed GAD mRNA by postnatal day 14, and final levels were attained one week later. Stellate cells in the bottom two-thirds of the molecular layer attained their final GAD mRNA content by postnatal day 21 whereas stellate cells in close proximity to the pial surface were not yet mature at this age. No GAD mRNA was detected within the external granular layer at any time during development. In adult rat, approximately 40% of cerebellar GAD mRNA was contained within the Purkinje cell population, 38% within the stellate cells, 17% within the basket cells, and only 5% within the Golgi cells. Increases in GAD mRNA within GABAergic neurons during cerebellar development correlated with the timing of neuronal maturation and synaptogenesis in these cell populations, suggesting that synaptic activity affects GAD gene expression in developing cerebellum.

A sperm-supplied product essential for initiation of normal embryogenesis in Caenorhabditis elegans is encoded by the paternal-effect embryonic-lethal gene, spe-11

Loss-of-function mutations in the spe-11 gene in Caenorhabditis elegans result in a paternal-effect embryonic-lethal phenotype: fertilization of wild-type oocytes by sperm from homozygous spe-11 mutant males leads to abnormal zygotic development, whereas oocytes from homozygous spe-11 hermaphrodites when fertilized by wild-type sperm develop normally. Embryos fertilized by sperm from homozygous spe-11 worms fail to complete meiosis and show defects in eggshell formation, mitotic spindle orientation, and cytokinesis. Genetic analysis suggests that the spe-11 gene is expressed before the completion of spermatogenesis and that the wild-type locus encodes a product that is present in sperm and participates, directly or indirectly, in initiating the correct program of early events in C. elegans embryos. Such an ontogenetic role of the spe-11+ gene product in early embryogenesis distinguishes spe-11 mutations from the two paternal-effect mutations identified in Drosophila, ms(3)K81 and pal, which primarily affect chromosome behavior. Analysis of spe-11 provides the first step toward genetic dissection of the functions of the sperm in early embryogenesis in C. elegans.

Transcription in nematodes: early Ascaris embryos are transcriptionally active

In this report we analyze early zygotic gene expression in the parasitic nematode Ascaris lumbricoides var. suum. Using synchronous populations of early embryonic stages, nuclei were isolated, and in vitro run-off transcription assays were performed. We find transcriptional activity as early as the 4- to 8-cell stage. The percentage of RNA polymerase II activity, as measured in these assays, is greater than 80% of the total transcription at the 60-cell stage. Furthermore, we show that a specific transcript (actin) can be identified in all early stages tested.

Generation of cell diversity during early embryogenesis in the nematode Caenorhabditis elegans

Caenorhabditis elegans zygotes undergo a series of four differentiative divisions to generate 5 somatic founder cells and a germ-line progenitor cell by the 16- to 24-cell stage of embryogenesis. The pattern of divisions, cell positions, and development of the embryonic cells are invariant from embryo to embryo. Through a combination of embryo manipulation, treatment of embryos with pharmacologic agents, and genetic analysis of maternal-effect embryonic-lethal mutants, researchers in several laboratories have investigated when and how cell differences are generated and cell fates are specified during embryogenesis: 1. Most blastomeres develop in a cell-autonomous manner. They do not need to undergo cell division and they do not require their normal neighbors to express differentiation products characteristic of their lineage. In embryos in which specific cells have been ablated, the fates of neighboring cells do not change to compensate for the missing cells. These observations suggest that most embryonic cells are determined by lineally transmitted internally segregated information. 2. There is at least one clear-cut example of inductive interactions during early development. The anterior daughter of AB gives rise to hypodermis, neurons, pharyngeal muscles, and body wall muscles. Interactions between ABa cells and P1-derived blastomeres are required between the 4- and 28-cell stage for ABa to generate pharyngeal and body wall muscles. ABa appears to be directed to generate hypodermis by internally segregated cues and directed to generate muscle by external cues. 3. Certain of the early internal segregation events require the participation of microfilaments. Disruption of the microfilament array leads to the missegregation of germ granules and of the potential of cells to undergo unequal germ-line-like divisions. Microfilaments may be involved in many other segregation events as well. 4. Several maternal-effect lethal mutants also perturb zygotic segregation events. These par mutants, which divide symmetrically and fail to segregate germ granules, may identify genes whose products interact with microfilaments or otherwise participate in cytoplasmic localization during the early divisions.

DNA synthesis and the control of embryonic gene expression in C. elegans

DNA synthesis in each cell lineage of the early C. elegans embryo was measured using microspectrofluorimetry. Aphidicolin was shown to inhibit DNA synthesis almost instantly and completely. Aphidicolin was then used to investigate how DNA synthesis controls expression of two biochemical markers that appear at different times during gut development: gut granules and a carboxylesterase. We show that marker expression is controlled neither by reaching the normal DNA: cytoplasm ratio, by counting the normal number of rounds of DNA synthesis, nor by a simple lengthening of the cell cycle. Instead, expression of both gut markers requires a short period of DNA synthesis in the first cell cycle after the gut has been clonally established.

Multiple synapsin I messenger RNAs are differentially regulated during neuronal development

Synapsin I is a neuron-specific protein consisting of two isoforms Ia and Ib. It is thought to play a role in the regulation of neurotransmitter release. In this study the structure and expression of two classes of synapsin I mRNA have been examined. The two mRNA classes have molecular sizes of 3.4 and 4.5 kb, respectively. Both classes translate into synapsin I polypeptides and display a high degree of base sequence homology. Utilizing an oligonucleotide-directed RNase H assay we have shown that both mRNA classes have a common start site of transcription and differ from one another toward their 3' ends. The expression of the two synapsin I mRNA classes is differentially regulated during the development of the rat brain and cerebellum. In the cerebellum the 4.5-kb transcript is expressed until postnatal day 7, after which it decreases to an undetectable level. The 3.4-kb mRNA is found throughout cerebellar development and in the adult. This suggests that the 3.4-kb mRNA class consists of messages which can encode both synapsin I polypeptides. Using quantitative Northern blot analysis a peak in the expression of this mRNA was observed at postnatal day 20. The maximum expression of the 3.4-kb class coincides with the period of synaptogenesis in the cerebellum. In addition to the developmental time course of synapsin mRNA expression a description of its spatial distribution throughout the cerebellum was performed using in situ hybridization histochemistry. From postnatal day 15 onwards, with a maximum at postnatal day 20, synapsin mRNA was localized in the internal granule cell layer of the cerebellum. On a cellular level, the granule cells, but not the neighboring Purkinje cells, express high levels of synapsin mRNA. These observations implicate developmentally coordinated differential RNA splicing in the regulation of neuron-specific gene expression and substantiate the correlation of synapsin gene expression with the period of synaptogenic differentiation of neurons.

RNA in the nucleus of a motile plant spermatozoid: characterization by enzyme-gold cytochemistry and in situ hybridization

To investigate the decrease of transcription and to determine the localization of RNA molecules during spermiogenesis in the fern Scolopendrium, we have used the enzyme-gold electron microscope method. During cell differentiation, the labeling decreases over the cytoplasm and increases over the nucleus. In the latter, the nucleolus disappears at the beginning of differentiation and the gold particles that were at first situated over the dispersed chromatin are then located over the condensed chromatin. In mature gametes, gold particles linked to RNA are abundant over the dense and homogeneous nucleus and sparse over the cytoplasm. By using in situ hybridization of RNA-poly(A) tails with radioactive poly(U) probes, we have shown that these RNA molecules are mRNA; they are located in the condensed chromatin of the mature sperm nucleus.

Embryonic expression of a gut-specific esterase in Caenorhabditis elegans

We describe an esterase activity that, by the criterion of histochemical staining, is completely localized to the intestine of the nematode Caenorhabditis elegans. Esterase activity appears in the embryonic gut when the embryo contains 4-8 intestinal precursor cells and 100-150 total cells. Esterase activity is abolished by treating early embryos with alpha-amanitin, indicating that expression depends upon transcription by RNA polymerase II within the developing embryo. In partial embryos produced by lysing one blastomere of a two-cell embryo, esterase expression appears only in descendants of the blastomere that normally produces the gut; esterase expression appears independent of the other non-gut blastomere. In early cleavage-stage embryos in which cytokinesis has been blocked by cytochalasin D, esterase expression appears at the normal time and only in cells in the gut lineage; thus neither normal cell division nor normal embryogenesis is required for lineage-specific expression. However, esterase does not appear in cytochalasin D blocked one-cell embryos. These observations confirm the traditional view that C. elegans development is "mosaic," with each cell following a defined independent program of gene expression.

In situ hybridization--visualization and quantitation of genetic expression in mammalian brain

In situ hybridization techniques have been developed that quantitate the relative levels of specific mRNAs in individual cell types of a heterogeneous tissue, the mammalian brain. Here, we discuss those special procedures and precautions necessary for hybridizing radiolabeled probes to developing and adult brain mRNAs. The probes discussed include double-stranded recombinant DNA, as well as single-stranded DNA, RNA, and polyuridylate. We detail the procedure for determining the relative numbers of hybrids formed and computing the ratio of specific mRNAs to total polyadenylated mRNA and discuss the importance of this ratio for comparison of relative levels of specific mRNAs within and among cell types in an individual brain or between brains.

Detection of mrnas in sea urchin embryos by in situ hybridization using asymmetric RNA probes

Asymmetric RNA probes, which contain only the mRNA coding strand, provide a large increase in hybridization efficiency in situ over that observed with either symmetric (both strands represented) RNA or DNA probes. Asymmetric RNA probes are synthesized in vitro by transcription from recombinants formed between sequences encoding sea urchin mRNAs and the transcription vector R7 delta 7. Using a probe representing early variant histone mRNA sequences we have characterized hybridization to sections of sea urchin embryos with respect to thermal stability of the hybrids formed, optimum temperature, effect of sequence divergence on hybrid thermal stability, and dependence of the hybridization signals on probe concentration and hybridization time. Estimates from the observed signals indicate that a large fraction of target RNAs is both retained in sections and hybridized with probe at saturation. Coupled with measurements of nonspecific background binding of heterologous probes, these data indicate that the method has sufficient sensitivity to detect many moderately abundant mRNAs (20-75 molecules per cell in the 1500-cell pluteus). In situ hybridizations to embryos at different developmental stages show that while histone mRNAs are uniformly distributed in cleaving embryos, different cell lineages of older embryos show large differences in accumulation of these mRNAs.

Developmental changes in poly(A) polymerase activity in Artemia

The levels of poly(A) polymerase activity have been determined during Artemia early development. Poly(A) polymerase activity increases steadily during postgastrular embryonic development reaching a maximum shortly after hatching. The rise of poly(A) polymerase is concomitant with an increase in poly(A) content and with a change in the subcellular distribution of the enzyme activity, the major increase corresponding to the nuclear fraction. Only one isoenzyme of poly(A) polymerase has been identified in Artemia embryos and nauplii despite changes in enzyme levels and subcellular changes during early development. Poly(A) polymerase is not associated with the cytoplasmic poly(A)-containing ribonucleoprotein particles stored in Artemia dormant embryos.

Location of specific messenger RNAs in Caenorhabditis elegans by cytological hybridization

We have developed an autoradiographic technique for detecting specific Caenorhabditis elegans messenger RNA molecules in situ by hybridization of labeled, cloned DNA probes to fixed tissue sections and squashes of embryos and adults. We report analyses with probes of actin and collagen gene sequences from a C. elegans genomic clone library. Hybridization is RNase sensitive and tissue specific. In adults the actin probe, which recognizes cytoplasmic as well as muscle actin mRNA, hybridizes strongly to muscle and distal gonad (ovary), somewhat less strongly to maturing oocytes, and weakly to intestine. The collagen probe hybridizes weakly to distal gonad and intestine and very strongly to subcuticular tissues, in particular to the hypodermal cells and syncytial cytoplasm of the lateral hypodermal ridges, which are the sites of cuticle synthesis. In embryos, hybridization to squashes indicates that actin message is present at fertilization, decreases during early cleavage, and then increases again during morphogenesis. By contrast, collagen message is absent until the 100-cell stage and then increases rapidly during morphogenesis. The number of cells labeled is consistent with the view that the collagen probe hybridizes to hypodermal precursor cells. We estimate that our present methods can detect messages representing about 0.2% or more of the total mRNA population, and increases in this sensitivity should be possible. Therefore, the cytological hybridization technique should be useful for determining temporal and spatial patterns of specific mRNA distributions during development, at least for abundant and moderately abundant messages.

Brain protein and messenger RNA identification in the same cell

We have devised techniques with which to detect specific proteins as well as mRNAs in individual cells of the nervous system. We have localized proteins to specific cells in sections of the neonatal rat cerebellum by immunofluorescence and in the same cells have localized mRNAs by in situ hybridization. The specific protein identified was glial fibrillary acidic protein. The [3H] complementary DNA probes used in the in situ hybridization experiments were synthesized using as templates polyadenylated mRNAs isolated from neonatal rat cerebellum. Such dual detection can be used to assess the cellular sites of synthesis of the many proteins that have been localized in brain and other tissues by immunohistochemistry.