Transcripts from both strands of a satellite DNA occur on lampbrush chromosome loops of the newt Notophthalmus

The Genomics of Plant Satellite DNA

The twenty-first century began with a certain indifference to the research of satellite DNA (satDNA). Neither genome sequencing projects were able to accurately encompass the study of satDNA nor classic methodologies were able to go further in undertaking a better comprehensive study of the whole set of satDNA sequences of a genome. Nonetheless, knowledge of satDNA has progressively advanced during this century with the advent of new analytical techniques. The enormous advantages that genome-wide approaches have brought to its analysis have now stimulated a renewed interest in the study of satDNA. At this point, we can look back and try to assess more accurately many of the key questions that were left unsolved in the past about this enigmatic and important component of the genome. I review here the understanding gathered on plant satDNAs over the last few decades with an eye on the near future.

Centromeres Transcription and Transcripts for Better and for Worse

Centromeres are chromosomal regions that are essential for the faithful transmission of genetic material through each cell division. They represent the chromosomal platform on which assembles a protein complex, the kinetochore, which mediates attachment to the mitotic spindle. In most organisms, centromeres assemble on large arrays of tandem satellite repeats, although their DNA sequences and organization are highly divergent among species. It has become evident that centromeres are not defined by underlying DNA sequences, but are instead epigenetically defined by the deposition of the centromere-specific histone H3 variant, CENP-A. In addition, and although long regarded as silent chromosomal loci, centromeres are in fact transcriptionally competent in most species, yet at low levels in normal somatic cells, but where the resulting transcripts participate in centromere architecture, identity, and function. In this chapter, we discuss the various roles proposed for centromere transcription and their transcripts, and the potential molecular mechanisms involved. We also discuss pathological cases in which unscheduled transcription of centromeric repeats or aberrant accumulation of their transcripts are pathological signatures of chromosomal instability diseases. In sum, tight regulation of centromeric satellite repeats transcription is critical for healthy development and tissue homeostasis, and thus prevents the emergence of disease states.

Functional Significance of Satellite DNAs: Insights From Drosophila

Since their discovery more than 60 years ago, satellite repeats are still one of the most enigmatic parts of eukaryotic genomes. Being non-coding DNA, satellites were earlier considered to be non-functional “junk,” but recently this concept has been extensively revised. Satellite DNA contributes to the essential processes of formation of crucial chromosome structures, heterochromatin establishment, dosage compensation, reproductive isolation, genome stability and development. Genomic abundance of satellites is under stabilizing selection owing of their role in the maintenance of vital regions of the genome – centromeres, pericentromeric regions, and telomeres. Many satellites are transcribed with the generation of long or small non-coding RNAs. Misregulation of their expression is found to lead to various defects in the maintenance of genomic architecture, chromosome segregation and gametogenesis. This review summarizes our current knowledge concerning satellite functions, the mechanisms of regulation and evolution of satellites, focusing on recent findings in Drosophila. We discuss here experimental and bioinformatics data obtained in Drosophila in recent years, suggesting relevance of our analysis to a wide range of eukaryotic organisms.

Roles for Non-coding RNAs in Spatial Genome Organization

Genetic loci are non-randomly arranged in the nucleus of the cell. This order, which is important to overall genome expression and stability, is maintained by a growing number of factors including the nuclear envelope, various genetic elements and dedicated protein complexes. Here, we review evidence supporting roles for non-coding RNAs (ncRNAs) in the regulation of spatial genome organization and its impact on gene expression and cell survival. Specifically, we discuss how ncRNAs from single-copy and repetitive DNA loci contribute to spatial genome organization by impacting perinuclear chromosome tethering, major nuclear compartments, chromatin looping, and various chromosomal structures. Overall, our analysis of the literature highlights central functions for ncRNAs and their transcription in the modulation of spatial genome organization with connections to human health and disease.

Satellite DNA: An Evolving Topic

Satellite DNA represents one of the most fascinating parts of the repetitive fraction of the eukaryotic genome. Since the discovery of highly repetitive tandem DNA in the 1960s, a lot of literature has extensively covered various topics related to the structure, organization, function, and evolution of such sequences. Today, with the advent of genomic tools, the study of satellite DNA has regained a great interest. Thus, Next-Generation Sequencing (NGS), together with high-throughput in silico analysis of the information contained in NGS reads, has revolutionized the analysis of the repetitive fraction of the eukaryotic genomes. The whole of the historical and current approaches to the topic gives us a broad view of the function and evolution of satellite DNA and its role in chromosomal evolution. Currently, we have extensive information on the molecular, chromosomal, biological, and population factors that affect the evolutionary fate of satellite DNA, knowledge that gives rise to a series of hypotheses that get on well with each other about the origin, spreading, and evolution of satellite DNA. In this paper, I review these hypotheses from a methodological, conceptual, and historical perspective and frame them in the context of chromosomal organization and evolution.

Chromatin-associated noncoding RNAs in development and inheritance

Noncoding RNAs (ncRNAs) have emerged as crucial players in chromatin regulation. Their diversity allows them to partake in the regulation of numerous cellular processes across species. During development, long and short ncRNAs act in conjunction with each other where long ncRNAs (lncRNAs) are best understood in establishing appropriate gene expression patterns, while short ncRNAs (sRNAs) are known to establish constitutive heterochromatin and suppress mobile elements. Additionally, increasing evidence demonstrates roles of sRNAs in several typically lncRNA-mediated processes such as dosage compensation, indicating a complex regulatory network of noncoding RNAs. Together, various ncRNAs establish many mitotically heritable epigenetic marks during development. Additionally, they participate in mechanisms that regulate maintenance of these epigenetic marks during the lifespan of the organism. Interestingly, some epigenetic traits are transmitted to the next generation(s) via paramutations or transgenerational inheritance mediated by sRNAs. In this review, we give an overview of the various functions and regulations of ncRNAs and the mechanisms they employ in the establishment and maintenance of epigenetic marks and multi-generational transmission of epigenetic traits. WIREs RNA 2017, 8:e1435. doi: 10.1002/wrna.1435 For further resources related to this article, please visit the WIREs website.

Transcription of highly repetitive tandemly organized DNA in amphibians and birds: A historical overview and modern concepts

Tandemly organized highly repetitive DNA sequences are crucial structural and functional elements of eukaryotic genomes. Despite extensive evidence, satellite DNA remains an enigmatic part of the eukaryotic genome, with biological role and significance of tandem repeat transcripts remaining rather obscure. Data on tandem repeats transcription in amphibian and avian model organisms is fragmentary despite their genomes being thoroughly characterized. Review systematically covers historical and modern data on transcription of amphibian and avian satellite DNA in somatic cells and during meiosis when chromosomes acquire special lampbrush form. We highlight how transcription of tandemly repetitive DNA sequences is organized in interphase nucleus and on lampbrush chromosomes. We offer LTR-activation hypotheses of widespread satellite DNA transcription initiation during oogenesis. Recent explanations are provided for the significance of high-yield production of non-coding RNA derived from tandemly organized highly repetitive DNA. In many cases the data on the transcription of satellite DNA can be extrapolated from lampbrush chromosomes to interphase chromosomes. Lampbrush chromosomes with applied novel technical approaches such as superresolution imaging, chromosome microdissection followed by high-throughput sequencing, dynamic observation in life-like conditions provide amazing opportunities for investigation mechanisms of the satellite DNA transcription.

ChromoShake: a chromosome dynamics simulator reveals that chromatin loops stiffen centromeric chromatin

ChromoShake is a three-dimensional simulator designed to find the thermodynamically favored states for given chromosome geometries. The simulator has been applied to a geometric model based on experimentally determined positions and fluctuations of DNA and the distribution of cohesin and condensin in the budding yeast centromere. Simulations of chromatin in differing initial configurations reveal novel principles for understanding the structure and function of a eukaryotic centromere. The entropic position of DNA loops mirrors their experimental position, consistent with their radial displacement from the spindle axis. The barrel-like distribution of cohesin complexes surrounding the central spindle in metaphase is a consequence of the size of the DNA loops within the pericentromere to which cohesin is bound. Linkage between DNA loops of different centromeres is requisite to recapitulate experimentally determined correlations in DNA motion. The consequences of radial loops and cohesin and condensin binding are to stiffen the DNA along the spindle axis, imparting an active function to the centromere in mitosis.

A step to the gigantic genome of the desert locust: chromosome sizes and repeated DNAs

The desert locust (Schistocerca gregaria) has been used as material for numerous cytogenetic studies. Its genome size is estimated to be 8.55 Gb of DNA comprised in 11 autosomes and the X chromosome. Its X0/XX sex chromosome determinism therefore results in females having 24 chromosomes whereas males have 23. Surprisingly, little is known about the DNA content of this locust's huge chromosomes. Here, we use the Feulgen Image Analysis Densitometry and C-banding techniques to respectively estimate the DNA quantity and heterochromatin content of each chromosome. We also identify three satellite DNAs using both restriction endonucleases and next-generation sequencing. We then use fluorescent in situ hybridization to determine the chromosomal location of these satellite DNAs as well as that of six tandem repeat DNA gene families. The combination of the results obtained in this work allows distinguishing between the different chromosomes not only by size, but also by the kind of repetitive DNAs that they contain. The recent publication of the draft genome of the migratory locust (Locusta migratoria), the largest animal genome hitherto sequenced, invites for sequencing even larger genomes. S. gregaria is a pest that causes high economic losses. It is thus among the primary candidates for genome sequencing. But this species genome is about 50 % larger than that of L. migratoria, and although next-generation sequencing currently allows sequencing large genomes, sequencing it would mean a greater challenge. The chromosome sizes and markers provided here should not only help planning the sequencing project and guide the assembly but would also facilitate assigning assembled linkage groups to actual chromosomes.

Molecular characterization and chromosomal distribution of a species-specific transcribed centromeric satellite repeat from the olive fruit fly, Bactrocera oleae

Satellite repetitive sequences that accumulate in the heterochromatin consist a large fraction of a genome and due to their properties are suggested to be implicated in centromere function. Current knowledge of heterochromatic regions of Bactrocera oleae genome, the major pest of the olive tree, is practically nonexistent. In our effort to explore the repetitive DNA portion of B. oleae genome, a novel satellite sequence designated BoR300 was isolated and cloned. The present study describes the genomic organization, abundance and chromosomal distribution of BoR300 which is organized in tandem, forming arrays of 298 bp-long monomers. Sequence analysis showed an AT content of 60.4%, a CENP-B like-motif and a high curvature value based on predictive models. Comparative analysis among randomly selected monomers demonstrated a high degree of sequence homogeneity (88%-97%) of BoR300 repeats, which are present at approximately 3,000 copies per haploid genome accounting for about 0.28% of the total genomic DNA, based on two independent qPCR approaches. In addition, expression of the repeat was also confirmed through RT-PCR, by which BoR300 transcripts were detected in both sexes. Fluorescence in situ hybridization (FISH) of BoR300 on mitotic metaphases and polytene chromosomes revealed signals to the centromeres of two out of the six chromosomes which indicated a chromosome-specific centromeric localization. Moreover, BoR300 is not conserved in the closely related Bactrocera species tested and it is also absent in other dipterans, but it's rather restricted to the B. oleae genome. This feature of species-specificity attributed to BoR300 satellite makes it a good candidate as an identification probe of the insect among its relatives at early development stages.

Noisy silence: non-coding RNA and heterochromatin formation at repetitive elements

A significant fraction of eukaryotic genomes comprises repetitive sequences, including rRNA genes, centromeres, telomeres, and retrotransposons. Repetitive elements are hotspots for recombination and represent a serious challenge for genome integrity. Maintaining these repeated elements in a compact heterochromatic structure suppresses recombination and unwanted mutagenic transposition, and is therefore indispensable for genomic stability. Paradoxically, repetitive elements are not transcriptionally inert, but produce RNA that has important functions in regulating and reinforcing the heterochromatic state. Here, we review the role of non-coding RNA (ncRNA) in recruiting chromatin-modifying enzymes to repetitive genomic loci to establish a repressive chromatin structure that safeguards chromosome integrity and genome stability.

High-resolution mapping and transcriptional activity analysis of chicken centromere sequences on giant lampbrush chromosomes

Exploration into morphofunctional organisation of centromere DNA sequences is important for understanding the mechanisms of kinetochore specification and assembly. In-depth epigenetic analysis of DNA fragments associated with centromeric nucleosome proteins has demonstrated unique features of centromere organisation in chicken karyotype: there are both mature centromeres, which comprise chromosome-specific homogeneous arrays of tandem repeats, and recently evolved primitive centromeres, which consist of non-tandemly organised DNA sequences. In this work, we describe the arrangement and transcriptional activity of chicken centromere repeats for Cen1, Cen2, Cen3, Cen4, Cen7, Cen8, and Cen11 and non-repetitive centromere sequences of chromosomes 5, 27, and Z using highly elongated lampbrush chromosomes, which are characteristic of the diplotene stage of oogenesis. The degree of chromatin packaging and fine spatial organisations of tandemly repetitive and non-tandemly repetitive centromeric sequences significantly differ at the lampbrush stage. Using DNA/RNA FISH, we have demonstrated that during the lampbrush stage, DNA sequences are transcribed within the centromere regions of chromosomes that lack centromere-specific tandem repeats. In contrast, chromosome-specific centromeric repeats Cen1, Cen2, Cen3, Cen4, Cen7, Cen8, and Cen11 do not demonstrate any transcriptional activity during the lampbrush stage. In addition, we found that CNM repeat cluster localises adjacent to non-repetitive centromeric sequences in chicken microchromosome 27 indicating that centromere region in this chromosome is repeat-rich. Cross-species FISH allowed localisation of the sequences homologous to centromeric DNA of chicken chromosomes 5 and 27 in centromere regions of quail orthologous chromosomes.

Cytological maps of lampbrush chromosomes of European water frogs (Pelophylax esculentus complex) from the Eastern Ukraine

Background

Hybridogenesis (hemiclonal inheritance) is a kind of clonal reproduction in which hybrids between parental species are reproduced by crossing with one of the parental species. European water frogs (Pelophylax esculentus complex) represent an appropriate model for studying interspecies hybridization, processes of hemiclonal inheritance and polyploidization. P. esculentus complex consists of two parental species, P. ridibundus (the lake frog) and P. lessonae (the pool frog), and their hybridogenetic hybrid – P. esculentus (the edible frog). Parental and hybrid frogs can reproduce syntopically and form hemiclonal population systems. For studying mechanisms underlying the maintenance of water frog population systems it is required to characterize the karyotypes transmitted in gametes of parental and different hybrid animals of both sexes.

Results

In order to obtain an instrument for characterization of oocyte karyotypes in hybrid female frogs, we constructed cytological maps of lampbrush chromosomes from oocytes of both parental species originating in Eastern Ukraine. We further identified certain molecular components of chromosomal marker structures and mapped coilin-rich spheres and granules, chromosome associated nucleoli and special loops accumulating splicing factors. We recorded the dissimilarities between P. ridibundus and P. lessonae lampbrush chromosomes in the length of orthologous chromosomes, number and location of marker structures and interstitial (TTAGGG)_n-repeat sites as well as activity of nucleolus organizer. Satellite repeat RrS1 was mapped in centromere regions of lampbrush chromosomes of the both species. Additionally, we discovered transcripts of RrS1 repeat in oocytes of P. ridibundus and P. lessonae. Moreover, G-rich transcripts of telomere repeat were revealed in association with terminal regions of P. ridibundus and P. lessonae lampbrush chromosomes.

Conclusions

The constructed cytological maps of lampbrush chromosomes of P. ridibundus and P. lessonae provide basis to define the type of genome transmitted within individual oocytes of P. esculentus females with different ploidy and from various population systems.

Mammalian satellite DNA: a speaking dumb

The tandemly organized highly repetitive satellite DNA is the main DNA component of centromeric/pericentromeric constitutive heterochromatin. For almost a century, it was considered as "junk DNA," only a small portion of which is used for kinetochore formation. The current review summarizes recent data about satellite DNA transcription. The possible functions of the transcripts are discussed.

The role of ncRNA in centromeres: a lesson from marsupials

Though centromeres have been thought to be comprised of repetitive, transcriptionally inactive DNA, new evidence suggests that eukaryotic centromeres produce a variety of transcripts and that RNA is essential for centromere competence. It has been proposed that centromere satellite transcripts play an essential role in centromere function through demarcation of the kinetochore-binding domain. However, the regional limits and regulation of transcription within the mammalian centromere are unknown. Analysis of transcriptional domains within the centromere in mammalian models is impeded by the unbridgeable expanse of satellite monomers throughout the pericentromere. The comparatively small size of the wallaby centromere and the evolutionary role of the centromere in marsupial speciation events position the wallaby centromere as a tractable and valuable mammalian centromere model. We highlight the current understanding of the wallaby centromere and the role of transcription in centromere function.

Genomic organization and transcription analysis of the 195-bp satellite DNA in Trypanosoma cruzi

The 195-bp satellite DNA is the most abundant Trypanosoma cruzi repetitive sequence. Here we show by RNA blotting and RT-PCR that 195 SAT is intensely transcribed. We observed a positive correlation between the level of satellite RNA and the abundance of the satellite copies in the genome of T. cruzi strains and that the satellite expression is not developmentally regulated. By analyzing CL Brener individual reads, we estimated that 195 SAT corresponds to approximately 5% of the CL Brener genome. 195 SAT elements were found in only 37 annotated contigs, indicating that a large number of satellite copies were not incorporated into the assembled data. The assembled satellite units are distributed in non-syntenic regions with Trypanosoma brucei and Leishmania major genomes, enriched with surface proteins, retroelements, RHS and hypothetical proteins. Satellite repeats were not observed in annotated subtelomeric regions. We report that 12 satellite sequences are truncated by the retroelement VIPER.

Tandem 41-bp repeats in chicken and Japanese quail genomes: FISH mapping and transcription analysis on lampbrush chromosomes

The chromosomal distribution of 41-bp repeats, known as CNM and PO41 repeats in the chicken genome and BglII repeats in the Japanese quail, was analyzed precisely using giant lampbrush chromosomes (LBC) from chicken, Japanese quail, and turkey growing oocytes. The PO41 repeat is conserved in all galliform species, whereas the other repeats are species specific. In chicken and quail, the centromere and subtelomere regions share homologous satellite sequences. RNA polymerase II transcribes the 41-bp repeats in both centromere and subtelomere regions. Ongoing transcription of these repeats was demonstrated by incorporation of BrUTP injected into oocytes at the lampbrush stage. RNA complementary to both strands of CNM and PO41 repeats is present on chicken LBC loops, whereas strand-specific G-rich transcripts are characteristic of BglII repeats in the Japanese quail. The RNA from 41-bp repeats does not undergo cotranscriptional U snRNP-dependent splicing. At the same time, the ribonucleoprotein matrix of transcription units with C-rich RNA of CNM and PO41 repeats was enriched with hnRNP protein K. Potential promoters for satellite transcription are discussed.

Novel noncoding RNA from human Y distal heterochromatic block (Yq12) generates testis-specific chimeric CDC2L2

The human Y chromosome, because it is enriched in repetitive DNA, has been very intractable to genetic and molecular analyses. There is no previous evidence for developmental stage- and testis-specific transcription from the male-specific region of the Y (MSY). Here, we present evidence for the first time for a developmental stage- and testis-specific transcription from MSY distal heterochromatic block. We isolated two novel RNAs, which localize to Yq12 in multiple copies, show testis-specific expression, and lack active X-homologs. Experimental evidence shows that one of the above Yq12 noncoding RNAs (ncRNAs) trans-splices with CDC2L2 mRNA from chromosome 1p36.3 locus to generate a testis-specific chimeric beta sv13 isoform. This 67-nt 5'UTR provided by the Yq12 transcript contains within it a Y box protein-binding CCAAT motif, indicating translational regulation of the beta sv13 isoform in testis. This is also the first report of trans-splicing between a Y chromosomal and an autosomal transcript.

Functional elements residing within satellite DNAs

Satellite DNAs represent a fast-evolving portion of the eukaryotic genome whose evolution is proposed to be driven by the stochastic process of molecular drive. Recent results indicate that satellite DNAs are subject to certain structural constraints, which are probably related to their interaction with proteins involved in the establishment of specific chromatin structures. The evolutionary persistence and high sequence conservation of some satellites, as well as the presence of stage- or tissue-specific, differentially expressed transcripts in several species, are consistent with the hypothesis that satellite DNA could have a regulatory role in eukaryotic organisms. Although the role of most transcripts is not known, some act as precursors of small interfering RNAs, which are now recognized as having an important role in chromatin modulation and the control of gene expression. Furthermore, some transcripts are involved in the cellular response to stress.

Structural and functional characterization of noncoding repetitive RNAs transcribed in stressed human cells

Thermal and chemical stresses induce the formation in human cells of novel and transient nuclear structures called nuclear stress bodies (nSBs). These contain heat shock factor 1 (HSF-1) and a specific subset of pre-mRNA processing factors. Nuclear stress bodies are assembled on specific pericentromeric heterochromatic domains containing satellite III (SatIII) DNA. In response to stress, these domains change their epigenetic status from heterochromatin to euchromatin and are transcribed in poly-adenylated RNAs that remain associated with nSBs. In this article, we describe the cloning, sequencing, and functional characterization of these transcripts. They are composed of SatIII repeats and originate from the transcription of multiple sites within the SatIII arrays. Interestingly, the level of SatIII RNAs can be down-regulated both by antisense oligonucleotides and small interfering RNAs (siRNA). Knockdown of SatIII RNA by siRNAs requires the activity of Argonaute 2, a component of the RNA-induced silencing complex. Down-regulation of satellite III RNAs significantly affects the recruitment of RNA processing factors to nSBs without altering the association of HSF-1 with these structures nor the presence of acetylated histones within nSBs. Thus, satellite III RNAs have a major role in the formation of nSBs.

Read-through histone transcripts containing 3' adenylate tails are zygotically expressed in Xenopus embryos and undergo processing to mature transcripts when introduced into oocyte nuclei

Messages encoding replication-dependent histone genes generally terminate with a stem-loop structure and lack polyadenylate tails. Adenylated histone transcripts were identified in Xenopus oocytes, though the role of the adenylate tracts is unknown. We report isolation of cDNAs from Xenopus embryos encoding histone mRNAs with 3' adenylate tracts. They also contain targets for stem-loop binding protein and U7 snRNA, which are required for histone RNA processing. One sequence is a read-through transcript containing a complete version of the downstream gene from the anti-parallel strand, similar to the RNAs from lampbrush loops of Notophthalmus oocytes. We injected read-through transcripts into Xenopus oocyte nuclei and they were processed to mature histone RNAs. Our results suggest that addition of 3' adenylate sequences might be a normal part of histone RNA synthesis. Also, these results shed light on the enigma of the developmental regulation of adenylated histone transcripts in Xenopus oocytes.

A possible meiotic function of the peculiar patterns of gene expression in mammalian spermatogenic cells

This review focuses on the striking differences in the patterns of transcription and translation in somatic and spermatogenic cells in mammals. In early haploid cells, mRNA translation evidently functions to restrict the synthesis of certain proteins, notably protamines, to transcriptionally inert late haploid cells. However, this does not explain why a substantial proportion of virtually all mRNA species are sequestered in translationally inactive free-messenger ribonucleoprotein particles (free-mRNPs) in meiotic cells, since most mRNAs undergo little or no increase in translational activity in transcriptionally active early haploid cells. In addition, most mRNAs in meiotic cells appear to be overexpressed because they are never fully loaded on polysomes and the levels of the corresponding protein are often much lower than the mRNA and are sometimes undetectable. A large number of genes are expressed at grossly higher levels in meiotic and/or early haploid spermatogenic cells than in somatic cells, yet they too are translated inefficiently. Many genes utilize alternative promoters in somatic and spermatogenic cells. Some of the resulting spermatogenic cell-altered transcripts (SCATs) encode proteins with novel functions, while others contain features in their 5'-UTRs, secondary structure or upstream reading frames, that are predicted to inhibit translation. This review proposes that the transcriptional machinery is modified to provide access to specific DNA sequences during meiosis, which leads to mRNA overexpression and creates a need for translational fine-tuning to prevent deleterious consequences of overproducing proteins.

Centromeric tandem repeat from the chaffinch genome: Isolation and molecular characterization

A new family of avian centromeric satellites is described. The highly repeated sequence, designated FCP (Fringilla coelebs PstI element), was cloned from the 500-bp PstI digest fraction of the chaffinch (Fringilla coelebs L.) genomic DNA, sequenced, and characterized. The FCP repeat was found to have 505–506 bp length of monomer, 57% content of GC, to compose about 0.9% of the chaffinch genome, and to be highly methylated. Results of Southern-blot hybridization of cloned FCP element onto genomic DNA digested with different restriction enzymes, and sequencing directly from total genomic DNA using FCP-specific primers and ThermoFidelase enzyme (Fidelity Systems Inc.) were in agreement with a tandem arrangement of this repeat in the chaffinch genome. Five positions of single-nucleotide polymorphism (SNP) were found in the FCP monomers using direct genomic sequencing. Fluorescence in situ hybridization (FISH) with FCP probe and primed in situ labelling (PRINS) with FCP specific primers showed that the FCP elements occupy pericentric regions of all chaffinch chromosomes. On chromosome spreads, the fluorescent signals were also observed in the intercentromeric connectives between nonhomologous chromosomes. The results suggest that the centromeric FCP repeat is responsible for chromosome ordering during mitosis in chaffinch.Key words: satellite DNA, centromeric heterochromatin, Fringilla coelebs.

Variability of DNA methylation pattern in somatic and germ cells in male newt (Amphibia, Urodela) Triturus cristatus carnifex

In a survey of several mammalian genomes, namely humans, rodents and bovines, the differences in the 5-methylcytosine (m5C) content show that repeated DNA sequences from sperm were undermethylated and from various somatic tissues were heavily methylated. This report shows a pattern of methylation in male newt (Amphibia, Urodela) Triturus cristatus carnifex (T. c. c.) unlike that so far described by other authors in mammals. Using methylation sensitive and insensitive enzymes (HpaII and MspI) and successive 3' terminal labelling (fill-in), we found a greater degree of DNA methylation in premeiotic germ and sperm cells compared to somatic tissue such as hepatocytes. Furthermore the degree of total DNA methylation in spermatozoa appears somewhere between premeiotic germ cells and somatic tissue. Blot hybridization shows that two highly conserved repetitive sequences in amphibian T. c. c., pTvm1 and pTvm8, contribute significantly to the degree of DNA methylation, suggesting a function for these sequences, such as a role in transcriptional regulation.

The Y chromosomal fertility factor Threads in Drosophila hydei harbors a functional gene encoding an axonemal dynein beta heavy chain protein

To understand the contradiction between megabase-sized lampbrush loops and putative protein encoding genes both associated with the loci of Y chromosomal fertility genes of Drosophila on the molecular level, we used PCR-mediated cloning to identify and isolate the cDNA sequence of the Y chromosomal Drosophila hydei gene DhDhc7(Y). Alignment of the sequences of the putative protein DhDhc7(Y) and the outer arm dynein beta heavy chain protein DYH2 of Tripneustes gratilla shows homology over the entire length of the protein chains. Therefore the proteins can be assumed to fulfill orthologous functions within the sperm tail axonemes of both species. Functional dynein beta heavy chain molecules, however, are necessary for the assembly and attachment of outer dynein arms within the sperm tail axoneme. Localization of DhDhc7(Y) to the fertility factor Threads, comprising at least 5.1 Mb of transcriptionally active repetitive DNA, results from an infertile Threads- mutant where large clusters of Threads specifically transcribed satellites and parts of DhDhc7(Y) encoding sequences are missing simultaneously. Consequently, the complete lack of the outer dynein arms in Threads- males most probably causes sperm immotility and hence infertility of the fly. Moreover, preliminary sequence analysis and several other features support the hypothesis that DhDhc7(Y) on the lampbrush loops Threads in D. hydei and Dhc-Yh3 on the lampbrush loops kl-5 in Drosophila melanogaster on the heterochromatic Y chromosome of both species might indeed code for orthologous dynein beta heavy chain proteins.

The transcriptional basis of chromosome pairing

Pairing between homologous chromosomes is essential for successful meiosis; generally only paired homologs recombine and segregate correctly into haploid germ cells. Homologs also pair in some somatic cells (e.g. in diploid and polytene cells of Drosophila). How homologs find their partners is a mystery. First, I review some explanations of how they might do so; most involve base-pairing (i.e. DNA-DNA) interactions. Then I discuss the remarkable fact that chromosomes only pair when they are transcriptionally active. Finally, I present a general model for pairing based upon the DNA-protein interactions involved in transcription. Each chromosome in the haploid set has a unique array of transcription units strung along its length. Therefore, each chromatin fibre will be folded into a unique array of loops associated with clusters of polymerases and transcription factors; only homologs share similar arrays. As these loops and clusters, or transcription factories, move continually, they make and break contact with others. Correct pairing would be nucleated when a promoter in a loop tethered to one factory binds to a homologous polymerizing site in another factory, before transcription stabilizes the association. This increases the chances that adjacent promoters will bind to their homologs, so that chromosomes eventually become zipped together with their partners. Pairing is then the inevitable consequence of transcription of partially-condensed chromosomes.

Transcription of lampbrush chromosomes of a centromerically localized highly repeated DNA in pigeon (Columba) relates to sequence arrangement

A highly repetitive, centromerically localized DNA sequence (PR1) has been isolated from the genomic DNA of two species of pigeon (Columba livia and C. palumbus). PR1 is approximately 900 bp long. It includes a sequence that is similar to the CENP-B box of mammals. It represents about 5% of the genome in C. livia and 2% in C. palumbus. In both species, tandem arrays of PR1 form part of larger repeating units. The organization of PR1 repeats and the larger repeating units is strikingly different in the two species. The large repeating units in C. livia include long (at least 14 units) tandem arrays of PR1 interspersed with relatively short intervening sequences. The large repeats of C. palumbus have much shorter (4 units or fewer) PR1 arrays interspersed with longer sections of non-PR1 DNA. PR1 is transcribed on short lampbrush loops in the centromeric regions of all lampbrush bivalents of C. palumbus. In C. livia, it is not transcribed at any of the major pericentromeric sites at which it is known to be present, although it is transcribed at one minor centromeric site on chromosome 2. It is proposed that transcription of the noncoding PR1 sequence on lampbrush chromosomes of pigeons relates to its genomic organization. The proposal is discussed with regard to the 'read-through' hypothesis for transcription on lampbrush loops.

Organisation and origin of a B chromosome centromeric sequence from Brachycome dichromosomatica

Brachycome dichromosomatica is an Australian native daisy that has two pairs of A chromosomes and up to three B chromosomes in some populations. A putative B-specific tandem repeat DNA sequence (Bd49) was isolated previously. Here we describe further characterisation of this sequence and investigate its possible origin. Southern analysis showed that all individual B chromosomes examined have highly methylated tandem repeats of Bd49 but differences in banding pattern for distinct B isolates suggested that the sequence is in a state of flux. Using in situ hybridisation, the sequence was shown to be located at the centromeric region of the B chromosome. Southern analysis of genomic DNA with Bd49 demonstrated that multiple copies of the sequence exist in the genomes of B. eriogona, B. ciliaris, B. segmentosa and B. multifida (none of which have B chromosomes) whereas other species tested (including 0B plants of B. dichromosomatica and 0B and +B B. curvicarpa and B. dentata) have few or no copies. Genomic clones and Bd49-like sequences derived by the polymerase chain reaction (PCR) were obtained from five species but determination of phylogenetic relationships within the genus and inference as to the possible origin of the B chromosome were problematic because of extensive intragenomic heterogeneity of the sequences.

Transcripts from opposite strands of gamma satellite DNA are differentially expressed during mouse development

Using in vitro immuno-selected retinoic acid response elements, we have isolated mouse genomic clones containing major (gamma) satellite DNA repeats that are considered as typical of chromosome centromeres. Several cDNA clones were then isolated from a F9 cell cDNA library and were found to harbor variants of the 234-base pair consensus gamma satellite monomer. In Northern analysis, these satellite DNA sequences hybridized predominantly to an approximately 1.8-kb RNA species in polyadenylated RNA from P19 cells. These transcripts were strongly repressed by retinoic acid, and nuclear run-on assays revealed that this repression was, at least in part, mediated at the transcriptional level. Satellite transcripts were also detected in HeLa cells, where they were similarly down-regulated by retinoids. Heterogeneously sized satellite transcripts were detected in RNA from specific mouse tissues, such as fetuses (but not placenta), adult liver, and testis. In situ hybridization analysis revealed that satellite transcripts are generated from opposite DNA strands and are differentially expressed in cells of the developing central nervous system as well as in adult liver and testis. These data may have implications on retinoic acid-mediated transcriptional regulation and centromere function.

Cytoplasmic localization of transcripts of a complex G+C-rich crab satellite DNA

The primary sequence and higher order structures of a G+C-rich satellite DNA of the Bermuda land crab Gecarcinus lateralis have been described previously. The repeat unit of the satellite is approximately 2.1 kb. In exploring a possible function for this satellite, we asked whether it is transcribed. As a probe for transcripts, we used a segment of DNA amplified from a 368 bp EcoRI fragment from the very highly conserved 3' end of the satellite DNA. During polymerase chain reaction (PCR) amplification, the probe was simultaneously either radiolabeled or biotinylated. Tissue- and stage-specific transcripts were observed when blots of poly(A)+ mRNAs recovered from polysomes isolated from crab tissues [including midgut gland (hepatopancreas), limb bud, and claw muscle] were probed with the satellite DNA fragment. The presence of satellite transcripts in polysomal mRNAs is strong evidence that the transcripts had reached the cytoplasm. To corroborate the presence of transcripts in the cytoplasm, we investigated in situ hybridization of satellite probes with RNAs in tissue sections. Biotinylated satellite DNA probes were applied to sections of midgut gland, limb bud papilla, ovary, or testis of anecdysial crabs. Retention of RNAs in tissue sections was improved by UV-irradiation prior to hybridization. Transcripts were abundant in the cytoplasm of all tissues except testis. Sections of crab midgut gland treated with RNase A prior to hybridization and sections of mouse pancreatic tumor served as controls; neither showed any signals with the probe.

Cloning of a brain-type aldolase cDNA and changes in its mRNA level during oogenesis and early embryogenesis in Xenopus laevis

A full length cDNA clone (cXALD3) for Xenopus laevis aldolase mRNA, which exists abundantly in oocytes, was isolated from Xenopus laevis ovary cDNA library, and its nucleotide sequence was determined. The cDNA was 1.8 kb in length and encoded 363 amino acids. From the deduced amino acid sequence and the Northern blot analysis of the RNAs from several adult tissues, this clone was concluded to be a brain-type aldolase gene. The XALD3 mRNA level per egg or embryo was high during early oogenesis, but was markedly reduced during late oogenesis and was maintained at low level during early embryogenesis until it started to increase at the late neurula stage. The mRNA was also detected in testis. The characteristic change in the temporal pattern of expression and the distribution of XALD3 mRNA among different tissues suggest a possibility that brain type aldolase may play some important roles in gametogenesis and in neurulation.

Characterization of an unusually conserved AluI highly reiterated DNA sequence family from the honeybee, Apis mellifera

An AluI family of highly reiterated nontranscribed sequences has been found in the genome of the honeybee Apis mellifera. This repeated sequence is shown to be present at approximately 23,000 copies per haploid genome constituting about 2% of the total genomic DNA. The nucleotide sequence of 10 monomers was determined. The consensus sequences is 176 nucleotides long and has an A + T content of 58%. There are clusters of both direct and inverted repeats. Internal subrepeating units ranging from 11 to 17 nucleotides are observed, suggesting that it could have evolved from a shorter sequence. DNA sequence data reveal that this repeat class is unusually homogeneous compared to the other class of invertebrate highly reiterated DNA sequences. The average pairwise sequence divergence between the repeats is 2.5%. In spite of this unusual homogeneity, divergence has been found in the repeated sequence hybridization ladder between four different honeybee subspecies. Therefore, the AluI highly reiterated sequences provide a new probe for fingerprinting in A. m. mellifera.

Cloning and characterization of a highly conserved satellite DNA sequence specific for the phytoparasitic nematode Bursaphelenchus xylophilus

The phytoparasitic nematode, Bursaphelenchus xylophilus, contains an unusually abundant satellite DNA which constitutes up to 30% of its genome. It is represented as a tandemly repeated MspI-site-containing sequence with a monomeric unit of 160 bp. Thirteen monomers were cloned and sequenced. The consensus sequence is 62% A+T-rich, with the presence of direct and inverted repeat clusters. Monomers of the sequence are very similar, showing on average 3.9% divergence from the calculated consensus. The results suggest that some homogenizing mechanism is acting to maintain the homogeneity of this satellite DNA despite its abundance and that it is not transcribed.

U7 small nuclear RNA in C snurposomes of the Xenopus germinal vesicle

In the amphibian germinal vesicle small nuclear RNAs (snRNAs) occur in morphologically distinct structures called snurposomes. Three types (A, B, and C) have been distinguished on the basis of cytological appearance and snRNA composition. C snurposomes in Xenopus are spherical bodies ranging in diameter from < 1 microns to about 10 microns. They stain intensely with antibodies against trimethylguanosine and the small nuclear ribonucleoprotein-specific Sm antigen but give weak or negative in situ hybridization reactions for the snRNAs involved in pre-mRNA splicing (U1, U2, U4, U5, and U6). We show here that C snurposomes in the Xenopus germinal vesicle contain U7 snRNA, an snRNA of low abundance involved in processing the 3' end of histone pre-mRNA. Xenopus U7 is 58 nucleotides long and is capped at the 5' end with trimethylguanosine. C snurposomes are often associated with B snurposomes, which contain the splicing snRNAs but not U7; B and C snurposomes together constitute a morphologically complex structure known as a sphere or sphere organelle. Although most spheres and C snurposomes are extrachromosomal, a few are attached at the histone gene loci on chromosomes 8, 9, and 16. Because they contain U7 snRNA and occur at the sites of histone pre-mRNA synthesis, C snurposomes presumably play a role in processing histone transcripts.

A centromeric satellite DNA of the unisexual Bacillus atticus (Insecta: Phasmatodea)

In the parthenogenetic Bacillus atticus atticus, widespread over most of the Mediterranean basin, a highly repeated satellite DNA (BaB300) has been detected and analysed. BgI II, Taq I and Alu I restriction enzymes cut 316 bp long repeating units from the BaB300 family. These are non-coding, AT rich and well conserved in the three isolated populations studied. By in situ hybridization, the satellite has been located in the centromeric heterochromatin of a subset of medium- and small-sized chromosomes, including the Xs. Related sequences have been found in the bisexual B. grandii grandii and in its specific hybrid B. whitei (=B. rossius/grandii grandii), while they are absent from B. rossius redtenbacheri. These data support the genetic affinity relationships within the genus Bacillus inferred from morphological, allozymic and karyological data. They also encourage further comparisons among Bacillus hybrids, in order to trace their parental genomes in the hybrid nuclei, and within the B. atticus complex (i.e. additional samples of B. a. atticus and diploid/triploid cytotypes of B. a. carius) to study repetitive DNA turnover in unisexual organisms.

Independent deposition of heterogeneous nuclear ribonucleoproteins and small nuclear ribonucleoprotein particles at sites of transcription

The major nuclear ribonucleoproteins (RNPs) involved in pre-mRNA processing are classified in broad terms either as small nuclear RNPs (snRNPs), which are major participants in the splicing reaction, or heterogeneous nuclear RNPs (hnRNPs), which traditionally have been thought to function in general pre-mRNA packaging. We obtained antibodies that recognize these two classes of RNP in Drosophila melanogaster. Using a sequential immunostaining technique to compare directly the distribution of these RNPs on Drosophila polytene chromosomes, we found that the two patterns were very similar qualitatively but not quantitatively, arguing for the independent deposition of the two RNP types and supporting a role for hnRNP proteins, but not snRNPs, in general transcript packaging.

Microdissection and cloning of DNA from landmark loops of amphibian lampbrush chromosomes

Microdissection of the "globular" and "granular" landmark loops of Pleurodeles lampbrush chromosomes and subsequent cloning of their DNA yielded several recombinant clones. The 6.6-kb insert of one of them was subcloned and the 600 bp of one subclone was characterized by Southern and slot hybridizations as well as by sequencing. This sequence, designated p130B, was shown to belong to a class of moderately repetitive DNA. RNA expression of this sequence was investigated by in situ hybridization of p130B to the nascent transcripts of lateral loops. Results showed that: (1) the same transcripts were not always found in matrices of landmarks exhibiting the same morphological features; (2) the same transcripts were expressed in loops of different morphological types. Based on these results we suggest that even if there is a morphological similarity of landmark loops, this does not reflect total similarity of their transcripts.

Small nuclear ribonucleoproteins and heterogeneous nuclear ribonucleoproteins in the amphibian germinal vesicle: loops, spheres, and snurposomes

We have examined the distribution of snRNPs in the germinal vesicle (GV) of frogs and salamanders by immunofluorescent staining and in situ nucleic acid hybridization. The major snRNAs involved in pre-mRNA splicing (U1, U2, U4, U5, and U6) occur together in nearly all loops of the lampbrush chromosomes, and in hundreds to thousands of small granules (1-4 microns diameter) suspended in the nucleoplasm. The loops and granules also contain several antigens that are regularly associated with snRNAs or spliceosomes (the Sm antigen, U1- and U2-specific antigens, and the splicing factor SC35). A second type of granule, often distinguishable by morphology, contains only U1 snRNA and associated antigens. We propose the term "snurposome" to describe the granules that contain snRNPs ("snurps"). Those that contain only U1 snRNA are A snurposomes, whereas those that contain all the splicing snRNAs are B snurposomes. GVs contain a third type of snRNP granule, which we call the C snurposome. C snurposomes range in size from less than 1 micron to giant structures greater than 20 microns in diameter. Usually, although not invariably, they have B snurposomes on their surface. They may also contain from one to hundreds of inclusions. Because of their remarkably spherical shape, C snurposomes with their associated B snurposomes have long been referred to as spheres or sphere organelles. Most spheres are free in the nucleoplasm, but a few are attached to chromosomes at specific chromosome loci, the sphere organizers (SOs). The relationship of sphere organelles to other snRNP-containing structures in the GV is obscure. We show by immunofluorescent staining that the lampbrush loops and B snurposomes also react with antibodies against heterogeneous nuclear ribonucleoproteins (hnRNPs). Transcription units on the loops are uniformly stained by anti-hnRNP and anti-snRNP antibodies, suggesting that nascent transcripts are associated with hnRNPs and snRNPs along their entire length, perhaps in the form of a unitary hnRNP/snRNP particle. That B snurposomes contain so many components involved in pre-mRNA packaging and processing suggests that they may serve as sites for assembly and storage of hnRNP/snRNP complexes destined for transport to the nascent transcripts on the lampbrush chromosome loops.

Two dispersed highly repeated DNA families of Triturus vulgaris meridionalis (Amphibia, Urodela) are widely conserved among Salamandridae

Two BamHI families of repeated sequences were characterized from the genome of the Italian smooth newt, Triturus vulgaris meridionalis (Amphibia, Urodela). The first family, which is divided into subfamilies, consists of tandemly arranged arrays whose basic repeat is around 398 bp long; these arrays are dispersed throughout the entire chromosome sets of the various species of Triturus tested. Moreover the family is widely conserved among Salamandridae, being detected by genomic DNA blotting of Notophthalmus viridescens, Taricha granulosa, Salamandrina terdigitata and Euproctus platycephalus. The second BamHI family is represented by a cloned sequence of 419 bp, which is dispersed in the chromosome set of several species of Triturus. The sequence is also conserved in S. terdigitata and in E. platycephalus but is not detectable in N. viridescens or T. granulosa. The cloned sequence is most probably only part of a longer unit interspersed within the Triturus genome.

Characterisation of a short, highly repeated and centromerically localised DNA sequence in crested and marbled newts of the genus Triturus

A 32-33 bp highly repeated DNA sequence, TkS1, has been isolated from genomic DNA of the newt Triturus karelini digested with the restriction endonucleases HaeIII or AluI. TkS1 is known to be localised in the centromeric heterochromatin of all the chromosomes in T. karelini and the related species T. cristatus. TkS1 has been shown to be present in varying amounts in the genomic DNA of a range of species of Triturus, including representatives of the two main subgenera Triturus and Palaeotriton. A programme of sequencing of monomers, dimers and trimers of TkS1 was carried out in order to determine the level of conservation of the sequence within and between species of Triturus. Altogether 204 monomer (32/33 bp) clones were made of TkS1 from three individuals of T. karelini, and one individual each of T. cristatus, T. carnifex, T. dobrogicus and T. marmoratus, all members of the subgenus Triturus and the cristatus species group. A number of dimer (64 bp) and trimer (96 bp) clones were also made from DNA of a single specimen of T. karelini digested with HaeIII or AluI. Three distinct types of TkS1 were identified in all species examined, except for T. marmoratus where only two of the types were found. The types were distinguished on the basis of certain recurring divergent patterns in monomers sequenced from T. karelini. Type 1 is mainly characterised by the presence of an AluI site at positions 24-27 and type 3 mainly by the presence of an additional base (C) at position 14. Type 2 normally lacks the AluI site and the C at position 14, as well as having a number of other distinguishing features. TkS1 and its three types have remained remarkably constant in sequence since before the divergence of T. marmoratus from other species in the cristatus species group, about 10 million years ago. Examination of all 204 monomer clones and comparison with consensus sequences for the three types shows less than 5% divergence at any one position in the sequence. There is good evidence from examination of dimer and trimer clones of TkS1 that the different types are intermingled with each other, and all three types are likely to be present on all chromosomes. Dimeric (64 bp) TkS1 clones constructed from AluI fragments of T. karelini DNA show evidence of a trimeric (96 bp) "supertype" with the pattern type 1-type 3-type 1 that is much more common than would be expected on a random basis.(ABSTRACT TRUNCATED AT 400 WORDS)

Two highly reiterated nucleotide sequences in the low C-value genome of Panagrellus redivivus

Two families of highly reiterated satellite nucleotide (nt) sequences have been found in the genome of the sexually separated nematode Panagrellus redivivus. The repeats are arranged in tandem arrays but the different satellites are not intermingled. Monomeric lengths are of 155 bp for one kind and 167 bp for the other; they were named E155 and E167. The A + T content is elevated in both families (i.e., 59.5%, and 65.3%, respectively). No similarity was found between the two satellites nor to other known highly repetitive elements. Furthermore, nt methylation as well as transcriptional activity were negative. An internal subrepeating unit, about 30 bp long, was observed in E167, implying that it could have evolved from a shorter sequence. Reiteration frequencies are approx. 30,000 and 40,000 copies per haploid genome, for E155 and E167, respectively, constituting together about 17% of the total DNA. This figure is astonishingly high, considering a C-value of 70,000 kb in P. redivivus, which is thought to be the lower limit for metazoans. Hence, the genome complexity is approx. 58,000 kb. In contrast to the nematodes Ascaris lumbricoides and Parascaris equorum, however, P. redivivus does not seem to eliminate large blocks of satellite DNA in the presomatic cells during early development.

Transcription of a satellite DNA on two Y chromosome loops of Drosophila melanogaster

Primary spermatocyte nuclei of Drosophila melanogaster exhibit three giant lampbrush-like loops formed by the kl-5, kl-3 and ks-1 Y chromosome fertility factors. Detailed mapping of satellite DNA sequences along the Y chromosome has recently shown that AA-GAC satellite repeats are a significant component of the kl-5 and ks-1 loop-forming regions. To determine whether these simple repeated sequences are transcribed on the loop structures we performed a series of DNA-RNA in situ hybridization experiments to fixed loop preparations using as a probe cloned AAGAC repeats. These experiments showed that the probe hybridizes with homologous transcripts specifically associated with the kl-5 and ks-1 loops. These transcripts are detected at all stages of development of these two loops, do not appear to migrate to the cytoplasm and are degraded when loops disintegrate during the first meiotic prophase. Moreover, an examination of the testes revealed that the transcription of the AAGAC sequences is restricted to the loops of primary spermatocytes; the other cell types of D. melanogaster spermatogenesis do not exhibit nuclear or cytoplasmic labeling. These experiments were confirmed by RNA blotting analysis which showed that transcription of the AAGAC sequences occurs in wild-type testes but not in X/O testes. The patterns of hybridization to the RNA blots indicated that the transcripts are highly heterogeneous in size, from large (migration at limiting mobility) to less than 1 kb. We discuss the possible function of the AAGAC satellite transcripts, in the light of the available information on the Y chromosome loops of D. melanogaster.

Satellite DNAs contain sequences that induced curvature

The repeating units of mouse, rat, and alpha-monkey satellites have been cloned. All three show properties that are characteristic of curved DNA: (i) their migration in polyacrylamide gels is slower than predicted from their sequences, and (ii) they appear as curved molecules when visualized by electron microscopy. All three satellite repeats contain runs of d(A.T)n greater than or equal to 3 residues that are likely to be responsible for their curvature. From analysis of 20 different satellite DNA sequences, we conclude that, in satellite DNA, adenine residues show a high tendency to cluster in groups of three or more.