Comparative transcriptomic analysis and structure prediction of novel Newt proteins

Notophthalmus viridescens (Red-spotted Newt) possess amazing capabilities to regenerate their organs and other tissues. Previously, using a de novo assembly of the newt transcriptome combined with proteomic validation, our group identified a novel family of five protein members expressed in adult tissues during regeneration in Notophthalmus viridescens. The presence of a putative signal peptide suggests that all these proteins are secretory in nature. Here we employed iterative threading assembly refinement (I-TASSER) server to generate three-dimensional structure of these novel Newt proteins and predicted their function. Our data suggests that these proteins could act as ion transporters, and be involved in redox reaction(s). Due to absence of transgenic approaches in N. viridescens, and conservation of genetic machinery across species, we generated transgenic Drosophila melanogaster to misexpress these genes. Expression of 2775 transcripts were compared between these five newly identified Newt genes. We found that genes involved in the developmental process, cell cycle, apoptosis, and immune response are among those that are highly enriched. To validate the RNA Seq. data, expression of six highly regulated genes were verified using real time Quantitative Polymerase Chain Reaction (RT-qPCR). These graded gene expression patterns provide insight into the function of novel protein family identified in Newt, and layout a map for future studies in the field.

Dependence of the structure and mechanics of metaphase chromosomes on oxidized cysteines

We have found that reagents that reduce oxidized cysteines lead to destabilization of metaphase chromosome folding, suggesting that chemically linked cysteine residues may play a structural role in mitotic chromosome organization, in accord with classical studies by Dounce et al. (J Theor Biol 42:275-285, 1973) and Sumner (J Cell Sci 70:177-188, 1984a). Human chromosomes isolated into buffer unfold when exposed to dithiothreitol (DTT) or tris(2-carboxyethyl)phosphine (TCEP). In micromanipulation experiments which allow us to examine the mechanics of individual metaphase chromosomes, we have found that the gel-like elastic stiffness of native metaphase chromosomes is dramatically suppressed by DTT and TCEP, even before the chromosomes become appreciably unfolded. We also report protein labeling experiments on human metaphase chromosomes which allow us to tag oxidized and reduction-sensitive cysteine residues. PAGE analysis using fluorescent labels shows a small number of labeled bands. Mass spectrometry analysis of similarly labeled proteins provides a list of candidates for proteins with oxidized cysteines involved in chromosome organization, notably including components of condensin I, cohesin, the nucleosome-interacting proteins RCC1 and RCC2, as well as the RNA/DNA-binding protein NONO/p54NRB.

MARCKS-like protein is an initiating molecule in axolotl appendage regeneration

Identifying key molecules that launch regeneration has been a long-sought goal. Multiple regenerative animals show an initial wound-associated proliferative response that transits into sustained proliferation if a considerable portion of the body part has been removed. In the axolotl, appendage amputation initiates a round of wound-associated cell cycle induction followed by continued proliferation that is dependent on nerve-derived signals. A wound-associated molecule that triggers the initial proliferative response to launch regeneration has remained obscure. Here, using an expression cloning strategy followed by in vivo gain- and loss-of-function assays, we identified axolotl MARCKS-like protein (MLP) as an extracellularly released factor that induces the initial cell cycle response during axolotl appendage regeneration. The identification of a regeneration-initiating molecule opens the possibility of understanding how to elicit regeneration in other animals.

Transcriptome analysis of newt lens regeneration reveals distinct gradients in gene expression patterns

Regeneration of the lens in newts is quite a unique process. The lens is removed in its entirety and regeneration ensues from the pigment epithelial cells of the dorsal iris via transdifferentiation. The same type of cells from the ventral iris are not capable of regenerating a lens. It is, thus, expected that differences between dorsal and ventral iris during the process of regeneration might provide important clues pertaining to the mechanism of regeneration. In this paper, we employed next generation RNA-seq to determine gene expression patterns during lens regeneration in Notophthalmus viridescens. The expression of more than 38,000 transcripts was compared between dorsal and ventral iris. Although very few genes were found to be dorsal- or ventral-specific, certain groups of genes were up-regulated specifically in the dorsal iris. These genes are involved in cell cycle, gene regulation, cytoskeleton and immune response. In addition, the expression of six highly regulated genes, TBX5, FGF10, UNC5B, VAX2, NR2F5, and NTN1, was verified using qRT-PCR. These graded gene expression patterns provide insight into the mechanism of lens regeneration, the markers that are specific to dorsal or ventral iris, and layout a map for future studies in the field.

Newt opportunities for understanding the dedifferentiation process

Urodele amphibians, such as the newt Notophthalmus viridescens, have the unique ability to regenerate limbs, spinal cord, eye structures, and many vital organs through a process called epimorphic regeneration. Although the cellular basis of regeneration has been studied in detail, we know relatively little about the molecular controls of the process. This review provides an overview of forelimb regeneration in the newt, addressing what we know about cellular and molecular aspects. Particular focus is placed on the dedifferentiation process, which yields a population of embryonic-like pluripotent cells that will eventually reform the lost structure. This cellular plasticity seems to be the key to regenerative ability. We discuss the dedifferentiation process in newt forelimb regeneration and outline the various studies that have revealed that mammalian cells also have the ability to dedifferentiate if given the appropriate triggers.

Expression profiles of elastase1 (NvElastaseI) and secretory leukocyte protease inhibitor (NvSLPI) during forelimb regeneration in adult Notophthalmus viridescens suggest a role in epithelial remodeling and delamination

Extracellular proteases and their inhibitors may regulate a number of important processes involved in forelimb regeneration in the adult newt, including epithelial remodeling, breakdown of extracellular matrix, and dedifferentiation. We have identified a newt homologue of human ElastaseI (NvElastaseI) and its potential inhibitor, SLPI (NvSLPI), and evaluated their spatial and temporal expression during limb regeneration. NvElastaseI is upregulated early in regeneration and is associated with subdermal and wound epithelial cells, suggesting an involvement in wound healing and the generation of the wound epithelium. Up until 15 days post-amputation, NvElastaseI is also scattered throughout the developing blastema and may have a role in the dedifferentiation of stump tissues. NvSLPI is found at the interface between the intact skin and the wound epithelium, and may limit NvElastaseI activity. NvSLPI is also expressed in dermal glands, and is likely involved in anti-microbial activity or function. Quite apart from regeneration, complementary patterns of expression of NvElastaseI and NvSLPI are associated with newt epithelial sloughing.

Proteolysis of mitotic chromosomes induces gradual and anisotropic decondensation correlated with a reduction of elastic modulus and structural sensitivity to rarely cutting restriction enzymes

The effect of nonspecific proteolysis on the structure of single isolated mitotic newt chromosomes was studied using chromosome elastic response as an assay. Exposure to either trypsin or proteinase K gradually decondensed and softened chromosomes but without entirely eliminating their elastic response. Analysis of chromosome morphology revealed anisotropic decondensation upon digestion, with length increasing more than width. Prolonged protease treatment resulted only in further swelling of the chromosome without complete dissolution. Mild trypsinization induced sensitivity of chromosome elasticity to five- and six-base-specific restriction enzymes. These results, combined with previous studies of effects of nucleases on mitotic chromosome structure, indicate that mild proteolysis gradually reduces the density of chromatin-constraining elements in the mitotic chromosome, providing evidence consistent with an anisotropically folded "chromatin network" model of mitotic chromosome architecture.

Nvbeta-actin and NvGAPDH as normalization factors for gene expression analysis in limb regenerates and cultured blastema cells of the adult newt, Notophthalmus viridescens

The red-spotted newt has the ability to fully regenerate complex structures by creating a pool of dedifferentiated cells that arise in response to tissue injury. An understanding of the mechanisms involved in the regenerative ability of the newt is limited by a lack of characterized assays. This deficiency includes the cloning and validation of housekeeping genes for normalizing gene expression data. We describe the cloning, characterization and real-time quantitative PCR evaluation of the normalization potential of the newt homologues of cytoplasmic beta-actin and GAPDH during newt limb regeneration and within the blastemal B1H1 cell line. Nvbeta-actin demonstrates a heterogeneous expression during limb regeneration and may be associated with differentiation state. The level of Nvbeta-actin expression in B1H1 cultures under conditions of myogenesis and serum resupplementation varies with the treatment. NvGAPDH is ubiquitously expressed during limb regeneration and within B1H1 cultures and does not demonstrate overall variations in expression levels. Thus, NvGAPDH is a more appropriate normalization factor in gene expression analyses during limb regeneration and treatments of B1H1 cultures.

Identification of cDNAs associated with late dedifferentiation in adult newt forelimb regeneration

Epimorphic limb regeneration in the adult newt involves the dedifferentiation of differentiated cells to yield a pluripotent blastemal cell. These mesenchymal-like cells proliferate and subsequently respond to patterning and differentiation cues to form a new limb. Understanding the dedifferentiation process requires the selective identification of dedifferentiating cells within the heterogeneous population of cells in the regenerate. In this study, representational differences analysis was used to produce an enriched population of dedifferentiation-associated cDNA fragments. Fifty-nine unique cDNA fragments were identified, sequenced, and analyzed using bioinformatics tools and databases. Some of these clones demonstrate significant similarity to known genes in other species. Other clones can be linked by homology to pathways previously implicated in the dedifferentiation process. These data will form the basis for further analyses to elucidate the role of candidate genes in the dedifferentiation process during newt forelimb regeneration.

Distinctive expression of Myf5 in relation to differentiation and plasticity of newt muscle cells

Regeneration in urodele amphibians such as the newt reflects the local plasticity of differentiated cells. Newt myotubes and myofibres undergo S phase re-entry and cellularisation in the limb blastema, and we have analysed the regulation of Myf5 in relation to these events. Surprisingly, Myf5 was expressed after fusion in cultured newt myotubes and in myofibers of the adult limb, in contrast to its familiar expression in myoblasts in other vertebrates. Its expression was markedly down regulated in cultured newt myotubes after S phase re-entry induced by serum stimulation, as well as by exposure to the trisubstituted purine called myoseverin which induces cellularisation. We have attempted to relate this striking difference from other vertebrates to the requirement for multinucleate urodele muscle cells to contribute to the regeneration blastema.

Unique expression patterns of the retinoblastoma (Rb) gene in intact and lens regeneration-undergoing newt eyes

Based on the role of retinoblastoma (Rb) in lens development and in the cell cycle reentry of muscle cells during limb regeneration, we have analyzed expression or Rb patterns in intact and lens regeneration-undergoing newt eyes. We find that in intact newt eye Rb is expressed in the retina as a gradient with higher levels in the photoreceptor layer and virtually no expression in the ganglion layer. In addition, a second gradient was detected within the photoreceptor layer with expression diminishing at the dorsal and ventral regions. In the intact lens, Rb is expressed in the lens epithelium and in the differentiating lens fibers at the bow region. During lens regeneration, Rb is expressed very strongly in the differentiating lens fibers, but not in the lens epithelium. Using an antibody specific to the hyperphosphorylated form of Rb, we detected the inactive protein only in the pigment epithelial cells of the iris. These distinct patterns might be related to the regenerative potential of the lens in the newt.

Different regulation of T-box genes Tbx4 and Tbx5 during limb development and limb regeneration

The T-domain transcription factors Tbx4 and Tbx5 have been implicated, by virtue of their limb-type specific expression, in controlling the identity of vertebrate legs and arms, respectively. To study the roles of these genes in developing and regenerating limbs, we cloned Tbx4 and Tbx5 cDNAs from the newt, and generated antisera that recognize Tbx4 or Tbx5 proteins. We show here that, in two urodele amphibians, newts and axolotls, the regulation of Tbx4 and Tbx5 differs from higher vertebrates. At the mRNA and protein level, both Tbx4 and Tbx5 are expressed in developing hindlimbs as well as in developing forelimbs. The coexpression of these genes argues that additional factors are involved in the control of limb type-specific patterns. In addition, newt and axolotl Tbx4 and Tbx5 expression is regulated differently during embryogenesis and regenerative morphogenesis. During regeneration, Tbx5 is exclusively upregulated in the forelimbs, whereas Tbx4 is exclusively upregulated in the hindlimbs. This indicates that, on a molecular level, different regulatory mechanisms control the shaping of identical limb structures and that regeneration is not simply a reiteration of developmental gene programs.

Hox C6 expression during development and regeneration of forelimbs in larval Notophthalmus viridescens

A central theme concerning the epimorphic regenerative potential of urodele amphibian appendages is that limb regeneration in the adult parallels larval limb development. Results of previous research have led to the suggestion that homeobox containing genes are "re-expressed" during the epimorphic regeneration of forelimbs of adult Notophthalmus viridescens in patterns which retrace larval limb development. However, to date no literature exists concerning expression patterns of any homeobox containing genes during larval development of this species. The lack of such information has been a hindrance in exploring the similarities as well as differences which exist between limb regeneration in adults and limb development in larvae. Here we report the first such results of the localization of Hox C6 (formerly, NvHBox-1) in developing and regenerating forelimbs of N. viridescens larvae as demonstrated by whole-mount in situ hybridization. Inasmuch as the pattern of Hox C6 expression is similar in developing forelimb buds of larvae and epimorphically regenerating forelimb blastemata of both adults and larvae, our results support the paradigm that epimorphic regeneration in adult newts parallels larval forelimb development. However, in contrast with observations which document the presence of Hox C6 in both intact, as well as regenerating hindlimbs and tails of adult newts, our results reveal no such Hox C6 expression during larval development of hindlimbs or the tail. As such, our findings indicate that critical differences in larval hindlimb and tail development versus adult expression patterns of this gene in these two appendages may be due primarily to differences in gene regulation as opposed to gene function. Thus, the apparent ability of urodeles to regulate genes in such a highly co-ordinated fashion so as to replace lost, differentiated, appendicular structures in adult animals may assist, at least in part, in better elucidating the phenomenon of epimorphic regeneration.

Molecular cloning of the Notophthalmus viridescens radical fringe cDNA and characterization of its expression during forelimb development and adult forelimb regeneration

Larval and adult newts provide important experimental models to study limb development and regeneration. These animals have exceptional ability to regenerate their appendages, as well as other vital structures. Our research examines the role of the fringe gene (fng) in the developing and regenerating adult newt forelimb. Fringe codes for a secretory protein. It was first discovered in Drosophila, and later homologues were isolated in Xenopus laevis, chick and mouse. This gene has been highly conserved throughout evolution, indicating its crucial role in vertebrate and invertebrate development. We have isolated, cloned, and sequenced the full length of the Notophthalmus viridescens radical fringe cDNA (nrFng) by screening a newt forelimb blastema cDNA library with a 500-bp fragment of the Xenopus lunatic fringe cDNA. The newt fringe cDNA codes for a 396 amino acid protein with a predicted N-terminal signal sequence. Newt fringe shows high homology with radical fringe homologues of many species. Whole mount mRNA in situ hybridization on several stages of newt limb development reveals that nrFng is first expressed in the limb field, with intense expression as the limb bud develops. However, gene expression diminishes with more advanced digit development. A significant role in adult forelimb regeneration is also evident, as we isolated the cDNA from a regeneration-specific library and found it highly expressed during the regenerative phases of active cell division and then down regulated at sites undergoing differentiation and morphogenesis.

Identification of newt connective tissue growth factor as a target of retinoid regulation in limb blastemal cells

In order to analyse target genes regulated by retinoic acid in urodele limb regeneration, we have used pseudotyped retroviruses to obtain stably transfected newt limb blastemal (progenitor) cells in culture which express chimeric retinoic acid/thyroid hormone receptors delta1 or delta2. After treatment with thyroid hormone to activate the chimeric receptors, we used a polymerase chain reaction (PCR)-based subtraction method to identify target genes which are retinoid regulated. Newt connective tissue growth factor, a secreted protein recognised in several vertebrates, has been identified in this way and found to be expressed in the limb blastema and regulated by retinoic acid. This approach should permit a systematic analysis of retinoid target genes in limb regeneration.

Novel requirements in peripheral structures of the extended satellite 2 hammerhead

A number of RNAs that infect plants self-cleave using a domain called the hammerhead. The consensus plant hammerhead has three base paired stem structures. Stems I and III flank the cleaved phosphodiester and are connected to stem II by two unpaired and highly conserved sequences. We demonstrated previously that satellite 2 transcripts from the newt, Notophthalmus viridescens, use a modified hammerhead structure for self-cleavage. Here we show that hammerheads with similar modifications occur in satellite 2 from species representing two additional families of salamanders (Ambystoma talpoideum and Amphiuma tridactylum). The distinctive features of the modified satellite 2 hammerheads include unusually short stem III regions and internally looped extensions to stem I that are required for cleavage. However, despite the strict nucleotide requirement in the internal stem I loop of the newt hammerhead, the details of the stem I extensions differ in the three salamanders. An analysis of chimeric transcripts indicated that, in order for a specific stem I extension to be functional, it must be compatible with other regions of the modified satellite 2 hammerhead. One such region is stem II, and a mutational analysis has confirmed that there are specific sequence and/or structural requirements in stem II.

Re-programming of expression of the KGFR and bek variants of fibroblast growth factor receptor 2 during limb regeneration in newts (Notophthalmus viridescens)

We have previously shown, by in situ hybridization, that fibroblast growth factor receptor 2 (FGFR2) is present in the basal layer of wound epithelium during limb regeneration in newts (Notophthalmus viridescens). In contrast, FGFR1 expression is observed throughout the blastema mesenchyme but is distinctly absent from the wound epithelium (Poulin et al. [1993] Development 119:353-361). Sequence analysis revealed that we have isolated both the KGFR and bek variants of FGFR2. These two variants differ only in the second half of the last of their three (or two) Ig-like domains. In this report, we show the expression patterns of FGFR2 variants during limb regeneration by in situ hybridization. During the pre-blastema stages of regeneration, FGFR2 expression was observed in the basal layer of the wound epithelium and in the cells of the periosteum. The wound epithelial hybridization was observed when the KGFR-specific probe was used while the bek-specific probe hybridized to mRNA in the cells of the periosteum. As regeneration progresses to the blastema stages, KGFR expression continued to be observed in the basal layer of the wound epithelium with additional hybridization seen in the blastema mesenchyme closely associated with the bisected bones. The bek-specific hybridization pattern observed at this stage corresponds specifically to the mesenchymal hybridization. In the differentiation stages of regeneration, the mesenchymal expression of FGFR2 becomes restricted to the cells of the condensing cartilage and later to the perichondrium. Interestingly, there appears to be a dorsoventral gradient of the expression of both KGFR and bek variants of FGFR2, which are opposite each other at the later stages of regeneration. Thus, re-programming of expression of the two FGFR2 variants is required during the initial wound closure of limb regeneration. Remarkably, the expression patterns of KGFR and bek mimic those observed in the mouse limb bud during early embryonic development (Orr-Urtreger et al. [1993] Dev. Biol. 18:475-486). Moreover, our results suggest that the two FGFR2 variants have distinct roles in limb regeneration. Further investigation regarding the potential sources of the FGF ligands will help establish the roles that FGFs and FGFRs play in limb regeneration.

Expression and activity of the newt Msx-1 gene in relation to limb regeneration

The Msx-1 homeobox gene is expressed in various contexts during vertebrate development, including the progress zone of the avian and mouse limb bud. Expression of mouse Msx-1 in a cultured myogenic cell line conferred a transformed phenotype and inhibited fusion into myotubes. It has been proposed that Msx-1 expression is required to maintain certain cells in a proliferating and undifferentiated state and may be associated with the ability to regenerate limbs. Urodele amphibians such as the newt regenerate their limbs by formation of a growth zone or blastema, and we have isolated and sequenced newt Msx-1 (NvMsx-1) from a limb blastemal cDNA library. NvMsx-1 expression was detectable in RNA preparations from both limb and tail and their regeneration blastemas, although cultured cells established from limb blastemal mesenchyme gave negative results. When either COS cells or cultured newt blastemal cells were cotransfected with an expression vector for NvMsx-1 and reporter plasmids containing multiple homeobox protein binding sites, NvMsx-1 repressed reporter expression. If NvMsx-1 was expressed together with a marker enzyme in cultured newt blastemal cells, no significant difference in DNA synthesis was observed relative to control transfectants. When myogenic mononucleate cells were transfected with NvMsx-1 and subsequently exposed to low serum to promote fusion, the fraction of Msx-1 positive cells in myotubes was comparable to a control transfected population analysed in the same culture. These results indicate that although Msx-1 expression could be important for limb regeneration, it does not exert a cell-autonomous effect on proliferation or myogenic differentiation of cultured blastemal cells.

Transcription of satellite 2 DNA from the newt is driven by a snRNA type of promoter

The transcriptional promoter of satellite 2 from the eastern newt, Notophthalmus viridescens, was analyzed by assaying the activity of deleted or mutated satellite 2 clones in Xenopus laevis oocytes. Two elements in the promoter were found to be important for transcription. These elements have sequences that are similar to the sequences of the octamer and the proximal sequence element of vertebrate snRNA genes transcribed by RNA polymerase II. Furthermore, the organization of these elements and their respective roles in transcription are the same as their organization and roles in the snRNA genes. To further investigate the relationship between the satellite 2 and snRNA gene promoters, the ability of the satellite 2 promoter to drive transcription of a true snRNA gene was tested. The satellite 2 promoter initiated transcription of the Xenopus U1b2 snRNA gene as efficiently as the native U1b2 promoter, and the 3' ends of the resulting U1b2 transcripts were accurately formed. This latter result confirms that the satellite 2 promoter is a functional analog of the snRNA promoter, since 3'-end formation of snRNA genes transcribed by RNA polymerase II requires that transcription be initiated from a compatible promoter. The structural and functional similarities between the satellite 2 and the snRNA gene promoters suggest that these elements are evolutionarily related. These findings were used to extend a previously proposed model concerning the nature and derivation of satellite 2.

Lampbrush chromosomes. Asymmetric loops

Although the study of lampbrush chromosomes has proved highly informative over the years, some aspects of their structure remain strangely enigmatic.

Conserved sequence and functional domains in satellite 2 from three families of salamanders

Thirteen satellite 2 elements from Ambystoma talpoideum and 16 from Amphiuma tridactylum were cloned, sequenced, and compared with the satellite 2 consensus from Notophthalmus viridescens. These elements have maintained a high degree of similarity during the 65-200 Myr that the salamander families, represented by the three species, have been separated. The DNA sequences of the consensus elements from A. talpoideum and A. tridactylum are 81% similar, and both are approximately 65% similar to the N. viridescens consensus. In addition to its DNA sequence, the functional properties of satellite 2 have also been conserved. By selecting and analyzing clones that closely mimicked the consensus of each species, we were able to demonstrate that satellite 2 from each species was capable of promoting transcription after injection into Xenopus laevis oocytes and that synthetic transcripts of satellite 2 from each species were capable of catalyzing their own site-specific cleavage. These properties may be related to the process of retroposition, which was previously proposed to be responsible for the genomic proliferation of satellite 2. Each of these functional properties also has general biological interest.

Delta retinoic acid receptor isoform delta 1 is distinguished by its exceptional N-terminal sequence and abundance in the limb regeneration blastema

In amphibian limb regeneration memory for position in the proximal-distal axis can be respecified by retinoic acid. The favoured candidates to mediate this effect are the retinoic acid receptors (RARs) and of the RARs identified in the regeneration blastema, the delta receptor is the most abundant. The presence in blastemal mesenchyme of at least two delta receptor isoforms, delta 1 and delta 2, alternatively spliced at the A-B junction, was demonstrated in expression studies and by PCR cloning. The delta 1 receptor is abundant in regenerative structures such as the limb and tail, whereas the delta 2 and alpha receptors show a more uniform pattern of expression across adult newt tissues. Full-length cloning of the delta 1 receptor established the presence of an unusually long open reading frame and N-terminal sequence that appears unique among vertebrate retinoic acid receptors. Transient transfection of expression constructs into COS cells followed by Western blotting confirmed the existence of at least three potential initiation sites for delta 1 translation. The possibility that delta 1 RAR expression may specify positional memory directly was tested in RNase protection experiments. delta 1 receptor message is increased on amputation, but does not exhibit a pronounced differential distribution along the proximal-distal axis in normal and regenerating limbs, nor does it show a persistent alteration in expression levels following a dose of retinoic acid sufficient to respecify position. The possibility that the morphogenetic effects of RA may be mediated through receptor interactions is raised by the finding that single mesenchymal blastemal cells in culture can express multiple RAR subtypes (delta 1 and alpha) and isoforms (delta 1 and delta 2).

Transcription of the histone loci on lampbrush chromosomes of the newt Notophthalmus viridescens

We have investigated transcription of the histone gene cluster on lampbrush chromosomes of the newt Notophthalmus viridescens. Clusters of the five histone genes are separated by long tracts of a DNA repeat called satellite 1. Previous in situ hybridization results demonstrated the presence of histone gene coding regions, intergene spacers, and flanking satellite repeats in giant transcription units on lampbrush chromosomes. These results suggested a model in which transcription initiates at histone gene promoters and continues through the rest of the gene cluster into satellite repeats. The readthrough transcription model predicts that spacer regions upstream of the first promoter in the gene cluster should be absent from nascent transcripts on chromosome loops. We have used such upstream spacer probes for in situ hybridization to lampbrush chromosomes. Contrary to our expectation, the results show that upstream spacer regions are transcribed, and indicate that transcription often initiates upstream of the first histone gene promoter. The relationship of giant transcription units in oocyte nuclei to cytoplasmic histone mRNA is discussed.

Self-cleaving transcripts of satellite DNA from the newt

Satellite 2 of the newt, Notophthalmus viridescens, is a 330 bp tandemly repeated sequence scattered throughout the genome. Cytoplasmic transcripts homologous to satellite 2 are found in a variety of tissues. Most of the transcripts correspond precisely in length to the DNA repeat unit or to whole multiples of that repeat. We show here that dimer-sized satellite 2 transcripts, synthesized with SP6 RNA polymerase from a plasmid clone, undergo site-specific, self-catalyzed cleavage in vitro. The reaction proceeds at neutral pH and requires Mg++ but no other cofactor or energy source. The cleavage products have 5'-hydroxyl and 3'-phosphate groups, at least some of which are in the form of 2',3'-cyclic phosphates. In this respect the reaction resembles the self-cleavage of certain small, infectious RNAs found in plants. Furthermore, the in vitro cleavage of satellite 2 transcripts occurs within a sequence that is homologous to the conserved cleavage site of the infectious RNAs. The existence of monomer and multimer transcripts in the cell suggests that the monomer may arise by site-specific cleavage of long primary transcripts. However, the 5' end of the cellular monomer is 46 or 47 bases upstream of the in vitro cleavage site, suggesting that factors in the cell may modify the cleavage reaction.