Differential antisense transcription from the Dictyostelium EB4 gene locus: implications on antisense-mediated regulation of mRNA stability

Abundantly expressed class of noncoding RNAs conserved through the multicellular evolution of dictyostelid social amoebas

Aggregative multicellularity has evolved multiple times in diverse groups of eukaryotes, exemplified by the well-studied development of dictyostelid social amoebas, for example, Dictyostelium discoideum However, it is still poorly understood why multicellularity emerged in these amoebas while the majority of other members of Amoebozoa are unicellular. Previously, a novel type of noncoding RNA, Class I RNAs, was identified in D. discoideum and shown to be important for normal multicellular development. Here, we investigated Class I RNA evolution and its connection to multicellular development. We identified a large number of new Class I RNA genes by constructing a covariance model combined with a scoring system based on conserved upstream sequences. Multiple genes were predicted in representatives of each major group of Dictyostelia and expression analysis confirmed that our search approach identifies expressed Class I RNA genes with high accuracy and sensitivity and that the RNAs are developmentally regulated. Further studies showed that Class I RNAs are ubiquitous in Dictyostelia and share highly conserved structure and sequence motifs. In addition, Class I RNA genes appear to be unique to dictyostelid social amoebas because they could not be identified in outgroup genomes, including their closest known relatives. Our results show that Class I RNA is an ancient class of ncRNAs, likely to have been present in the last common ancestor of Dictyostelia dating back at least 600 million years. Based on previous functional analyses and the presented evolutionary investigation, we hypothesize that Class I RNAs were involved in evolution of multicellularity in Dictyostelia.

Characterization of auxin transporter PIN6 plasma membrane targeting reveals a function for PIN6 in plant bolting

Auxin gradients are sustained by series of influx and efflux carriers whose subcellular localization is sensitive to both exogenous and endogenous factors. Recently the localization of the Arabidopsis thaliana auxin efflux carrier PIN-FORMED (PIN) 6 was reported to be tissue-specific and regulated through unknown mechanisms. Here, we used genetic, molecular and pharmacological approaches to characterize the molecular mechanism(s) controlling the subcellular localization of PIN6. PIN6 localizes to endomembrane domains in tissues with low PIN6 expression levels such as roots, but localizes at the plasma membrane (PM) in tissues with increased PIN6 expression such as the inflorescence stem and nectary glands. We provide evidence that this dual localization is controlled by PIN6 phosphorylation and demonstrate that PIN6 is phosphorylated by mitogen-activated protein kinases (MAPKs) MPK4 and MPK6. The analysis of transgenic plants expressing PIN6 at PM or in endomembrane domains reveals that PIN6 subcellular localization is critical for Arabidopsis inflorescence stem elongation post-flowering (bolting). In line with a role for PIN6 in plant bolting, inflorescence stems elongate faster in pin6 mutant plants than in wild-type plants. We propose that PIN6 subcellular localization is under the control of developmental signals acting on tissue-specific determinants controlling PIN6-expression levels and PIN6 phosphorylation.

The Long Noncoding RNA Transcriptome of Dictyostelium discoideum Development

Dictyostelium discoideum live in the soil as single cells, engulfing bacteria and growing vegetatively. Upon starvation, tens of thousands of amoebae enter a developmental program that includes aggregation, multicellular differentiation, and sporulation. Major shifts across the protein-coding transcriptome accompany these developmental changes. However, no study has presented a global survey of long noncoding RNAs (ncRNAs) in D. discoideum To characterize the antisense and long intergenic noncoding RNA (lncRNA) transcriptome, we analyzed previously published developmental time course samples using an RNA-sequencing (RNA-seq) library preparation method that selectively depletes ribosomal RNAs (rRNAs). We detected the accumulation of transcripts for 9833 protein-coding messenger RNAs (mRNAs), 621 lncRNAs, and 162 putative antisense RNAs (asRNAs). The noncoding RNAs were interspersed throughout the genome, and were distinct in expression level, length, and nucleotide composition. The noncoding transcriptome displayed a temporal profile similar to the coding transcriptome, with stages of gradual change interspersed with larger leaps. The transcription profiles of some noncoding RNAs were strongly correlated with known differentially expressed coding RNAs, hinting at a functional role for these molecules during development. Examining the mitochondrial transcriptome, we modeled two novel antisense transcripts. We applied yet another ribosomal depletion method to a subset of the samples to better retain transfer RNA (tRNA) transcripts. We observed polymorphisms in tRNA anticodons that suggested a post-transcriptional means by which D. discoideum compensates for codons missing in the genomic complement of tRNAs. We concluded that the prevalence and characteristics of long ncRNAs indicate that these molecules are relevant to the progression of molecular and cellular phenotypes during development.

Characteristics of Antisense Transcript Promoters and the Regulation of Their Activity

Recently, an increasing number of studies on natural antisense transcripts have been reported, especially regarding their classification, temporal and spatial expression patterns, regulatory functions and mechanisms. It is well established that natural antisense transcripts are produced from the strand opposite to the strand encoding a protein. Despite the pivotal roles of natural antisense transcripts in regulating the expression of target genes, the transcriptional mechanisms initiated by antisense promoters (ASPs) remain unknown. To date, nearly all of the studies conducted on this topic have focused on the ASP of a single gene of interest, whereas no study has systematically analyzed the locations of ASPs in the genome, ASP activity, or factors influencing this activity. This review focuses on elaborating on and summarizing the characteristics of ASPs to extend our knowledge about the mechanisms of antisense transcript initiation.

Deficiency of X-linked inverted duplicates with male-biased expression and the underlying evolutionary mechanisms in the Drosophila genome

Inverted duplicates (IDs) are pervasive in genomes and have been reported to play functional roles in various biological processes. However, the general underlying evolutionary forces that maintain IDs in genomes remain largely elusive. Through a systematic screening of the Drosophila melanogaster genome, 20,223 IDs were detected in nonrepetitive intergenic regions, far more than expectation under the neutrality model. 3,846 of these IDs were identified to have stable hairpin structure (i.e., the structural IDs). Based on whole-genome transcriptome profiling data, we found 628 unannotated expressed structural IDs, which had significantly different genomic distributions and structural properties from the unexpressed IDs. Among the expressed structural IDs, 130 exhibited higher expression in males than in females (i.e., male-biased expression). Compared with sex-unbiased ones, these male-biased IDs were significantly underrepresented on the X chromosome, similar to previously reported pattern of male-biased protein-coding genes. These analyses suggest that a selection-driven process, rather than a purely neutral mutation-driven mechanism, contributes to the maintenance of IDs in the Drosophila genome.

Pseudogene-derived small interference RNAs regulate gene expression in African Trypanosoma brucei

Pseudogenes have been shown to acquire unique regulatory roles from more and more organisms. We report the observation of a cluster of siRNAs derived from pseudogenes of African Trypanosoma brucei using high through-put analysis. We show that these pseudogene-derived siRNAs suppress gene expression through RNA interference. The discovery that siRNAs may originate from pseudogenes and regulate gene expression in a unicellular eukaryote provides insights into the functional roles of pseudogenes and into the origin of noncoding small RNAs.

Characterization of the Dictyostelium homolog of chromatin binding protein DET1 suggests a conserved pathway regulating cell type specification and developmental plasticity

DET1 (De-etiolated 1) is a chromatin binding protein involved in developmental regulation in both plants and animals. DET1 is largely restricted to multicellular eukaryotes, and here we report the characterization of a DET1 homolog from the social amoeba Dictyostelium discoideum. As in other species, Dictyostelium DET1 is nuclear localized. In contrast to other species, where it is an essential protein, loss of DET1 is nonlethal in Dictyostelium, although viability is significantly reduced. The phenotype of the det1(-) mutant is highly pleiotropic and results in a large degree of heterogeneity in developmental parameters. Loss of DET1 results in delayed and abnormal development with enlarged aggregation territories. Mutant slugs displayed cell type patterning with a bias toward the prestalk pathway. A number of DET1-interacting proteins are conserved in Dictyostelium, and the apparently conserved role of DET1 in regulatory pathways involving the bZIP transcription factors DimB, c-Jun, and HY5 suggests a highly conserved mechanism regulating development in multicellular eukaryotes. While the mechanism by which DET1 functions is unclear, it appears that it has a key role in regulation of developmental plasticity and integration of information on environmental conditions into the developmental program of an organism.

Noncoding RNA in development

Non-protein-coding sequences increasingly dominate the genomes of multicellular organisms as their complexity increases, in contrast to protein-coding genes, which remain relatively static. Most of the mammalian genome and indeed that of all eukaryotes is expressed in a cell- and tissue-specific manner, and there is mounting evidence that much of this transcription is involved in the regulation of differentiation and development. Different classes of small and large noncoding RNAs (ncRNAs) have been shown to regulate almost every level of gene expression, including the activation and repression of homeotic genes and the targeting of chromatin-remodeling complexes. ncRNAs are involved in developmental processes in both simple and complex eukaryotes, and we illustrate this in the latter by focusing on the animal germline, brain, and eye. While most have yet to be systematically studied, the emerging evidence suggests that there is a vast hidden layer of regulatory ncRNAs that constitutes the majority of the genomic programming of multicellular organisms and plays a major role in controlling the epigenetic trajectories that underlie their ontogeny.

Highly expressed genes are associated with inverse antisense transcription in mouse

There is a growing evidence, that antisense transcription might have a key role in a range of human diseases. Although predefined sense-antisense pairs were extensively studied, the antisense expression of the known sense genes is rarely investigated. We retrieved and correlated the expression of sense and antisense sequences of 1182 mouse transcripts to assess the prevalence and to find the characteristic pattern of antisense transcription. We contrasted three Affymetrix MGU74A version 1 mouse genome chips to six MGU74A version 2 chips. For these 1182 transcripts, the version 1 chips contain the antisense sequences of the transcripts presented on the version 2 chips. The original data was taken from the GEO database (GDS431 and GDS432). As the Affymetrix data are semiquantitative, the relative expression levels of antisense partners were analysed. We detected antisense transcription, although the average antisense expression is shifted towards smaller expression values (MGU74A version 1, 516; version 2, 1688). An inverse direct correlation between sense and antisense expression values could be observed at high expression values. At a very high relative expression--above 40,000--the Pearson correlation coefficient is getting closer to -1. Transcripts with high inverse expression ratio may be correlated to the investigated gene (major histocompatibility complex class II trans activator). The ratio of sense to antisense transcripts varied among different chromosomes; on chromosomes 14 and 1 the level of antisense expression was higher than that of sense. We conclude that antisense transcription is a common phenomenon in the mouse genome. The hypothesis of regulatory role of antisense transcripts is supported by the inverse antisense gene expression of highly expressed genes.

Treasure hunt in an amoeba: non-coding RNAs in Dictyostelium discoideum

The traditional view of RNA being merely an intermediate in the transfer of genetic information, as mRNA, spliceosomal RNA, tRNA, and rRNA, has become outdated. The recent discovery of numerous regulatory RNAs with a plethora of functions in biological processes has truly revolutionized our understanding of gene regulation. Tiny RNAs such as microRNAs and small interfering RNAs play vital roles at different levels of gene control. Small nucleolar RNAs are much more abundant than previously recognized, and new functions beyond processing and modification of rRNA have recently emerged. Longer non-coding RNAs (ncRNAs) can also have important regulatory roles in the cell, e.g., antisense RNAs that control their target mRNAs. The majority of these important findings arose from analyses in various model organisms. In this review, we focus on ncRNAs in the social amoeba Dictyostelium discoideum. This important genetically tractable model organism has recently received renewed attention in terms of discovery, regulation and functional studies of ncRNAs. Old and recent findings are discussed and put in context of what we today know about ncRNAs in other organisms.

Evidence that noncoding RNA dutA is a multicopy suppressor of Dictyostelium discoideum STAT protein Dd-STATa

Dd-STATa, a Dictyostelium discoideum homologue of metazoan STAT transcription factors, is necessary for culmination. We created a mutant strain with partial Dd-STATa activity and used it to screen for unlinked suppressor genes. We screened approximately 450,000 clones from a slug-stage cDNA library for their ability to rescue the culmination defect when overexpressed. There were 12 multicopy suppressors of Dd-STATa, of which 4 encoded segments of a known noncoding RNA, dutA. Expression of dutA is specific to the pstA zone, the region where Dd-STATa is activated. In suppressed strains the expression patterns of several putative Dd-STATa target genes become similar to the wild-type strain. In addition, the amount of the tyrosine-phosphorylated form of Dd-STATa is significantly increased in the suppressed strain. These results indicate that partial copies of dutA may act upstream of Dd-STATa to regulate tyrosine phosphorylation by an unknown mechanism.

PSoL: a positive sample only learning algorithm for finding non-coding RNA genes

MOTIVATION

Small non-coding RNA (ncRNA) genes play important regulatory roles in a variety of cellular processes. However, detection of ncRNA genes is a great challenge to both experimental and computational approaches. In this study, we describe a new approach called positive sample only learning (PSoL) to predict ncRNA genes in the Escherichia coli genome. Although PSoL is a machine learning method for classification, it requires no negative training data, which, in general, is hard to define properly and affects the performance of machine learning dramatically. In addition, using the support vector machine (SVM) as the core learning algorithm, PSoL can integrate many different kinds of information to improve the accuracy of prediction. Besides the application of PSoL for predicting ncRNAs, PSoL is applicable to many other bioinformatics problems as well.

RESULTS

The PSoL method is assessed by 5-fold cross-validation experiments which show that PSoL can achieve about 80% accuracy in recovery of known ncRNAs. We compared PSoL predictions with five previously published results. The PSoL method has the highest percentage of predictions overlapping with those from other methods.

Abundant novel transcriptional units and unconventional gene pairs on human chromosome 22

Novel transcriptional units (TUs) are EST-supported transcribed features not corresponding to known genes. Unconventional gene pairs (UGPs) are pairs of genes and/or TUs sharing exon-to-exon cis-antisense overlaps or putative bidirectional promoters. Computational TU and UGP discovery followed by manual curation was performed in the entire published 34.9-Mb human chromosome 22 euchromatic sequence. Novel TUs (n = 517) were as abundant as known genes (n = 492) and typically did not have nonprimate DNA and protein homologies. One hundred seventy-one (33%) of TUs, but only 13 (3%) of genes, both lacked nonprimate conservation and localized to gaps in the human-mouse BLASTZ alignment. Novel TUs were richer in exonic primate-specific interspersed repetitive elements (P = 0.001) and were more likely to rely on splice junctions provided by them, than were known genes: 19% of spliced TUs, versus 5% of spliced genes, had a splice site within a primate-specific repeat. Hence, novel TUs and known genes may represent different portions of the transcriptome. Two hundred nine (21%) of chromosome 22 transcripts participated in 77 cis-antisense and 42 promoter-sharing UGPs. Transcripts involved simultaneously in both UGP types were more common than was expected (P = 0.01). UGPs were nonrandomly distributed along the sequence: 89 (75%) clustered in distinct regions, the sum of which equaled 4.4 Mb (<13% of the chromosome). Eighty (67%) of the UGPs possessed significant locus structure differences between primates and rodents. Since some TUs may be functional noncoding transcripts and since the cis-regulatory potential of UGPs is well recognized, TUs and UGPs specific to the primate lineage may contribute to the genomic basis for primate-specific phenotypes.

Sexuality and parasitism share common regulatory pathways in the fungus Parasitella parasitica

Parasitella parasitica, a facultative mycoparasite of zygomycetous fungi, forms cytoplasmic fusions with its hosts during infection. Thus, the organism is an efficient donor of genetic material in parasexual host-parasite interactions. Recognition between parasite and host is mediated by trisporoids, which are also responsible for sexual communication. The TDH gene for one of the key enzymes of trisporic acid biosynthesis, 4-dihydromethyl-trisporate dehydrogenase, was cloned and its transcription analysed. TDH was cloned on a 6175-bp insert and was found to map in a complex cluster of genes that suggest post-transcriptional antisense regulation. Histochemical TDH analysis in developing parasitic or sexual structures shows high enzymatic activity in Parasitella. TDH is linked to a gene for a putative acyl-CoA thioesterase (ACT). Two ORFs were identified in the 5'-region of the TDH gene, a third one, coding for 176 amino acids overlaps the ACT gene in antisense direction completely. Expression levels of ACT and ORF1 depend on parasitic and sexual interactions.

NONCODE: an integrated knowledge database of non-coding RNAs

NONCODE is an integrated knowledge database dedicated to non-coding RNAs (ncRNAs), that is to say, RNAs that function without being translated into proteins. All ncRNAs in NONCODE were filtered automatically from literature and GenBank, and were later manually curated. The distinctive features of NONCODE are as follows: (i) the ncRNAs in NONCODE include almost all the types of ncRNAs, except transfer RNAs and ribosomal RNAs. (ii) All ncRNA sequences and their related information (e.g. function, cellular role, cellular location, chromosomal information, etc.) in NONCODE have been confirmed manually by consulting relevant literature: more than 80% of the entries are based on experimental data. (iii) Based on the cellular process and function, which a given ncRNA is involved in, we introduced a novel classification system, labeled process function class, to integrate existing classification systems. (iv) In addition, some 1100 ncRNAs have been grouped into nine other classes according to whether they are specific to gender or tissue or associated with tumors and diseases, etc. (v) NONCODE provides a user-friendly interface, a visualization platform and a convenient search option, allowing efficient recovery of sequence, regulatory elements in the flanking sequences, secondary structure, related publications and other information. The first release of NONCODE (v1.0) contains 5339 non-redundant sequences from 861 organisms, including eukaryotes, eubacteria, archaebacteria, virus and viroids. Access is free for all users through a web interface at http://noncode.bioinfo.org.cn.

A database search for double-strand containing RNAs in Dictyostelium discoideum

In eukaryotic cells, double-stranded RNA is degraded to 21mers and triggers RNA interference. Using a pattern description language, we have searched the EMBL database for sequences with the potential to form double strands in cis in Dictyostelium discoideum. No extended inverted repeats were found in mRNAs. However, the antisense direction of some mRNAs encoding regulatory or developmentally regulated proteins showed the ability to form double-stranded regions. In EST archives, we found potential double strands derived from a few genes, but these transcripts are not continuously encoded in the genome. Most likely, they represent hybrid molecules of sense and antisense RNAs.

Regulation of growth and differentiation in Dictyostelium

In general, growth and differentiation are mutually exclusive, but they are cooperatively regulated during the course of development. Thus, the process of a cell's transition from growth to differentiation is of general importance not only for the development of organisms but also for the initiation of malignant transformation, in which this process is reversed. The cellular slime mold Dictyostelium, a wonderful model organism, grows and multiplies as long as nutrients are supplied, and its differentiation is triggered by starvation. A strict checkpoint (growth/differentiation transition or GDT point), from which cells start differentiating in response to starvation, has been specified in the cell cycle of D. discoideum Ax-2 cells. Accordingly, integration of GDT point-specific events with starvation-induced events is needed to understand the mechanism regulating GDTs. A variety of intercellular and intracellular signals are involved positively or negatively in the initiation of differentiation, making a series of cross-talks. As was expected from the presence of GDT points, the cell's positioning in cell masses and subsequent cell-type choices occur depending on the cell's phase in the cell cycle at the onset of starvation. Since novel and somewhat unexpected multiple functions of mitochondria in cell movement, differentiation, and pattern formation have been well realized in Dictyostelium cells, they are reviewed in this article.

Role of endogenous antisense RNA in cardiac gene regulation

Endogenous antisense RNA has been detected for a range of eukaryotic genes and now appears to be a common phenomenon in mammalian cells. Its abundance compared to levels of its complementary sense mRNA indicates that antisense RNA may be involved in posttrancriptional regulation of a gene. In general a downregulating effect on gene expression has been demonstrated or suggested. Due to the heterogeneity in origin and character of different antisense transcripts alternative functions such as stabilizing the corresponding sense transcript and being part of gene recombination must be considered. Regulation by endogenous antisense RNA has been shown for a plethora of genes, including cardiac genes, such as myosin heavy chainMHC, atrial light chain, and troponin I. There is now growing evidence that antisense transcription is involved in human disease, and it is reasonable to consider antisense as a target for intervention procedures. Here we review the progress in our understanding of as well as the controversies arising from investigating the regulatory mechanisms of antisense RNA, with special focus on cardiac genes. Finally, links between antisense transcription and heart disease and the possible use of antisense as a target of cardiac intervention procedures are discussed.

Novel non-coding RNAs in Dictyostelium discoideum and their expression during development

The quest for non-coding RNAs (ncRNAs) in the last few years has revealed a surprisingly large number of small RNAs belonging to previously known as well as entirely novel classes. Computational and experimental approaches have uncovered new ncRNAs in all kingdoms of life. In this work, we used a shotgun cloning approach to construct full-length cDNA libraries of small RNAs from the eukaryotic model organism Dictyostelium discoideum. Interestingly, two entirely novel classes of RNAs were identified of which one is developmentally regulated. The RNAs within each class share conserved 5'- and 3'-termini that can potentially form stem structures. RNAs of both classes show predominantly cytoplasmic localization. In addition, based on conserved structure and/or sequence motifs, several of the identified ncRNAs could be divided into classes known from other organisms, e.g. 18 small nucleolar RNA candidates (17 box C/D, of which a few are developmentally regulated, and one box H/ACA). Two ncRNAs showed a high degree of similarity to the small nuclear U2 RNA and signal recognition particle RNA (SRP RNA), respectively. Furthermore, the majority of the regions upstream of the sequences encoding the isolated RNAs share conserved motifs that may constitute new promoter elements.

The upstream open reading frame mediates constitutive effects on translation of cytochrome p-450c27 from the seventh in-frame AUG codon in rat liver

The 2.3-kb mRNA that codes for cytochrome P-450c27 (CYP27) has an unexpectedly long 5'-untranslated region (UTR) that holds six AUGs, leading to several upstream open reading frames (uORFs). The initiation of translation from the seventh AUG forms a putative 55-kDa precursor, which is processed in mitochondria to form a 52-kDa mature protein. The first three AUGs form fully overlapping uORF1, uORF2, and uORF3 that are in-frame with the seventh AUG and next two form fully overlapping uORF4 and uORF5 that are out-of-frame with the seventh AUG. Although not recognized by the scanning ribosomes under normal conditions, the sixth in-frame AUG forms a putative 57-kDa extension of the main open reading frame. The purpose of this study was to identify the elements in the 5'-UTR that direct CYP27 mRNA translation exclusively from the seventh AUG. Expression of 5' deletion mutants in COS cells reveal that the intact 5'-UTR not only directs the initiation of translation from the seventh AUG but also acts as a negative regulator. A 2-kb deletion mutant that lacks uORF1 initiates translation equally from the sixth and the seventh AUGs, forming both 57- and 55-kDa precursor proteins with a 2-fold increase in rate of translation. However, induction in translation does not affect the levels of the mature 52-kDa form in mitochondria but causes accumulation of the precursor form in cytosol not seen in COS cells transfected with wild-type cDNA. Mutation of the stop codon that terminates uORF1 completely shifts the initiation of translation from the seventh to the first AUG, forming a 67-kDa precursor that is processed into a 52-kDa mature protein in mitochondria. Confirmation of the bicistronic nature of CYP27 mRNA by epitope mapping of uORF1 suggests that translation of CYP27 mRNA from the seventh AUG is directed and regulated by uORF1 expression.

Comparative analysis of spore coat formation, structure, and function in Dictyostelium

Dictyostelium produces spores at the end of its developmental cycle to propagate the lineage. The spore coat is an essential feature of spore biology contributing a semipermeable chemical and physical barrier to protect the enclosed amoeba. The coat is assembled from secreted proteins and a polysaccharide, and from cellulose produced at the cell surface. They are organized into a polarized molecular sandwich with proteins forming layers surrounding the microfibrillar cellulose core. Genetic and biochemical studies are beginning to provide insight into how the deliveries of protein and cellulose to the cell surface are coordinated and how cysteine-rich domains of the proteins interact to form the layers. A multidomain inner layer protein, SP85/PsB, seems to have a central role in regulating coat assembly and contributing to a core structural module that bridges proteins to cellulose. Coat formation and structure have many parallels in walls from plant, algal, yeast, protist, and animal cells.

A survey of small RNA-encoding genes in Escherichia coli

Small RNA (sRNA) molecules have gained much interest lately, as recent genome-wide studies have shown that they are widespread in a variety of organisms. The relatively small family of 10 known sRNA-encoding genes in Escherichia coli has been significantly expanded during the past two years with the discovery of 45 novel genes. Most of these genes are still uncharacterized and their cellular roles are unknown. In this survey we examined the sequence and genomic features of the 55 currently known sRNA-encoding genes in E.coli, attempting to identify their common characteristics. Such characterization is important for both expanding our understanding of this unique gene family and for improving the methods to predict and identify sRNA-encoding genes based on genomic information.

Non-coding ribonucleic acids--a class of their own?

Non-coding ribonucleic acids (RNAs) do not contain a peptide-encoding open reading frame and are therefore not translated into proteins. They are expressed in all phyla, and in eukaryotic cells they are found in the nucleus, cytoplasm, and mitochondria. Non-coding RNAs either can exert structural functions, as do transfer and ribosomal RNAs, or they can regulate gene expression. Non-coding RNAs with regulatory functions differ in size ranging from a few nucleotides to over 100 kb and have diverse cell- or development-specific functions. Some of the non-coding RNAs associate with human diseases. This chapter summarizes the current knowledge about regulatory non-coding RNAs.

Stable expression of antisense RNAs targeted to the 5' non-coding region confers heterotypic inhibition to foot-and-mouth disease virus infection

The antiviral potential of transcripts targeted to the non-coding regions (NCRs) of foot-and-mouth disease virus (FMDV) RNA have been studied during transient and constitutive expression in susceptible BHK-21 cells. Transient expression of antisense transcripts corresponding to the 5' and 3'NCRs, alone or in combination, confers specific inhibition of homologous (serotype C) virus infection in BHK-21 cells. Constitutive expression of antisense 5'NCR transcripts (5'AS) exerted higher levels of inhibition to homologous and heterologous (serotypes O, A, Asia, SAT 1, SAT 2 and SAT 3) FMDV infection, as estimated by a 10-fold reduction in virus titre in the supernatants from infected clones and by a plaque reduction assay. These inhibitions were also observed, albeit to a lesser extent, in clones stably expressing antisense 3'NCR transcripts. The antiviral response was specific for FMDV, as the picornavirus encephalomyocarditis virus was not inhibited in any of the transformed cell lines. In all cases, a correlation was found between the level of transcript expression and the extent of virus inhibition. The potential to efficiently inhibit FMDV, including isolates representing the seven serotypes, by expressing interfering 5'AS transcripts opens the possibility of developing transgenic animals with a reduced susceptibility to FMDV.

An endogenous RNA transcript antisense to CNG(alpha)1 cation channel mRNA

CNG channels are cyclic nucleotide-gated Ca(2+)-permeable channels that are suggested to be involved in the activity-dependent alterations of synaptic strength that are thought to underlie information storage in the CNS. In this study, we isolated an endogenous RNA transcript antisense to CNG(alpha)1 mRNA. This transcript was capable of down-regulating the expression of sense CNG(alpha)1 in the Xenopus oocyte expression system. RT-PCR, Northern blot, and in situ hybridization analyses showed that the transcript was coexpressed with CNG(alpha)1 mRNA in many regions of human brain, notably in those regions that were involved in long-term potentiation and long-term depression, such as hippocampal CA1 and CA3, dentate gyrus, and cerebellar Purkinje layer. Comparison of expression patterns between adult and fetal cerebral cortex revealed that there were concurrent developmental changes in the expression levels of anti-CNG1 and CNG(alpha)1. Treatment of human glioma cell T98 with thyroid hormone T(3) caused a significant increase in anti-CNG1 expression and a parallel decrease in sense CNG(alpha)1 expression. These data suggest that the suppression of CNG(alpha)1 expression by anti-CNG1 may play an important role in neuronal functions, especially in synaptic plasticity and cortical development. Endogenous antisense RNA-mediated regulation may represent a new mechanism through which the activity of ion channels can be regulated in the human CNS.

Natural antisense (rTSalpha) RNA induces site-specific cleavage of thymidylate synthase mRNA

The 3' untranslated region (UTR) of rTSalpha RNA is complementary (i.e., antisense) to human thymidylate synthase (TS) RNA. When HEp2 cells (human epidermoid carcinoma) progressed from late-log to plateau phase growth, ribonuclease protection assay (RPA) revealed an inverse correlation between the levels of rTSalpha RNA and TS mRNA, suggesting a possible effect of rTSalpha RNA on TS mRNA levels. HEp2 cells expressing a Tet-On transactivator were transiently co-transfected with pHook-1 and a construct containing rTSalpha (protein and antisense RNA), rTSalphaDelta3' (rTSalpha protein only), rTSalpha-3' (antisense RNA-luciferase) or luciferase. Transfected cells were selected and evaluated for the effects of induced transgene expression on TS mRNA. Induced expression of transfected rTSalpha or rTSalpha-3', but not rTSalphaDelta3' or luciferase, resulted in decreased TS mRNA levels as measured by RPA. These results demonstrated that the antisense region of rTSalpha RNA is necessary and sufficient for this down-regulation of TS mRNA. RPA for TS mRNA also showed the enhanced appearance of two partial-length protected fragments in rTSalpha or rTSalpha-3' transfected cells. RPA stringency evaluations and primer extension assays indicated that TS mRNA is cleaved in vivo in a site-specific manner. These data demonstrate that rTS gene expression likely plays a role in down-regulating TS through a natural RNA-based antisense mechanism.

Overlapping of MINK and CHRNE gene loci in the course of mammalian evolution

Overlapping of genes, especially in an anti-parallel fashion, is quite rare in eukaryotic genomes. We have found a rare instance of exon overlapping involving CHRNE and MINK gene loci on chromosome 17 in humans. CHRNE codes for the epsilon subunit of the nicotinic acetylcholine receptor (AChRepsilon) whereas MINK encodes a serine/threonine kinase belonging to the GCK family. To elucidate the evolutionary trail of this gene overlapping event, we examined the genomes of a number of primates and found that mutations in the polyadenylation signal of the CHRNE gene in early hominoids led to the overlap. Upon extending this analysis to genomes of other orders of placental mammals, we observed that the overlapping occurred at least three times independently during the course of mammalian evolution. Because CHRNE and MINK are differentially expressed, the potentially hazardous mutations responsible for the exon overlap seem to have escaped evolutionary pressures by differential temporo-spatial expression of the two genes.

Antisense-RNA regulation and RNA interference

For a long time, RNA has been merely regarded as a molecule that can either function as a messenger (mRNA) or as part of the translational machinery (tRNA, rRNA). Meanwhile, it became clear that RNAs are versatile molecules that do not only play key roles in many important biological processes like splicing, editing, protein export and others, but can also--like enzymes--act catalytically. Two important aspects of RNA function--antisense-RNA control and RNA interference (RNAi)--are emphasized in this review. Antisense-RNA control functions in all three kingdoms of life--although the majority of examples are known from bacteria. In contrast, RNAi, gene silencing triggered by double-stranded RNA, the oldest and most ubiquitous antiviral system, is exclusively found in eukaryotes. Our current knowledge about occurrence, biological roles and mechanisms of action of antisense RNAs as well as the recent findings about involved genes/enzymes and the putative mechanism of RNAi are summarized. An interesting intersection between both regulatory mechanisms is briefly discussed.

The KLHL1-antisense transcript ( KLHL1AS) is evolutionarily conserved

Spinocerebellar ataxia type 8 (SCA8) is caused by a CTG expansion in an untranslated, endogenous antisense RNA that overlaps the Kelch-like 1 ( KLHL1) gene. The normal function of this transcript is currently unknown. We have now identified the promoter region for the KLHL1-antisense ( KLHL1AS) RNA and report that a Klhl1as transcript is present in the mouse as well. Human and mouse KLHL1AS are transcribed from homologous promoter regions in the first intron of KLHL1 and extend through the transcription and translation start sites as well as the first splice donor sequence of KLHL1. We found that the mouse Klhl1as RNA is not spliced and terminates in a polyadenylation site in the Klhl1 promoter region, whereas both the present and previous work show that human KLHL1AS is highly variably spliced into processed transcripts that contain up to six exons. Mouse Klhl1as transcript was detected in RNA isolated from the cerebellum and from total adult brain and total fetal tissue, and at a low level in testis and ovary. Similarly, human KLHL1AS is expressed in various brain tissues, including the cerebellum, the tissue most affected by SCA8, and was detected at low levels in testis and kidney. The evolutionary conservation of this antisense/sense transcriptional organization strongly indicates that KLHL1AS transcripts play a significant biological role in both human and mouse, presumably as a regulator of KLHL1 expression.

The abundance of sterile transcripts in Giardia lamblia

The protozoan parasite Giardia lamblia synthesizes a diverse and surprisingly abundant array of sterile transcripts unable to code for proteins. Random sampling of cDNAs from two evolutionarily divergent Giardia strains indicates that approximately 20% of cDNAs in the libraries represent polyadenylated sterile transcripts. RNase protection analysis and northern blot hybridization of three sterile transcript loci demonstrated that both the sterile transcript and a complementary mRNA were made in each case, further categorizing these sterile transcripts as antisense transcripts. Investigation of the genomic loci for these same three sterile antisense transcripts showed typical transcription units for the sense transcripts, but still failed to reveal a usable open reading frame for the sterile antisense transcripts. 5'-RACE mapped the transcription start site for one of the sterile antisense transcripts to an AT-rich region, as is typical for GIARDIA: It is unclear whether these sterile transcripts represent errors in transcription or whether they have regulatory functions within the cell, although preliminary investigations failed to reveal evidence for a role in developmental gene regulation. In either case, the presence of such a large pool of sterile antisense transcripts is dramatic evidence of the unusual molecular machinery of the early diverging protist G.lamblia.

Binding of IRE-BP to its cognate RNA sequence: SFM studies on a universal RNA backbone for the analysis of RNA-protein interaction

We have used an RNA consisting of the potato spindle tuber viroid (PSTVd) and 240 bp of double-stranded RNA derived from the GUS gene as a backbone for scanning force microscope (SFM) studies on RNA binding proteins. The in vitro transcribed RNA forms a rod-like structure of apparent 130 nm in length with a completely base paired central part flanked by the incompletely paired viroid helix with bulges on both sides. The termini of the molecule consist of loops such that no blunt or staggered RNA ends are exposed. Suitable, asymmetrical restriction sites in the construct allow for the insertion of sequences of interest, e. g. protein binding sites. We have inserted the IRE (iron responsive element) sequence into the construct and have used in vitro transcripts to study binding of IRE-BP. Relative binding frequencies show that 70% of the protein binds to the expected site in the molecule while only a slightly enhanced binding is observed at the termini. In the GUS-PSTVd-IRE backbone, the orientation of the molecule is easily determined by IRE-BP binding. It thus provides a versatile tool to study specific as well as preferential interaction of other proteins with sequences or structures inserted into a different part of the molecule.

Novel small RNA-encoding genes in the intergenic regions of Escherichia coli

BACKGROUND

Small, untranslated RNA molecules were identified initially in bacteria, but examples can be found in all kingdoms of life. These RNAs carry out diverse functions, and many of them are regulators of gene expression. Genes encoding small, untranslated RNAs are difficult to detect experimentally or to predict by traditional sequence analysis approaches. Thus, in spite of the rising recognition that such RNAs may play key roles in bacterial physiology, many of the small RNAs known to date were discovered fortuitously.

RESULTS

To search the Escherichia coli genome sequence for genes encoding small RNAs, we developed a computational strategy employing transcription signals and genomic features of the known small RNA-encoding genes. The search, for which we used rather restrictive criteria, has led to the prediction of 24 putative sRNA-encoding genes, of which 23 were tested experimentally. Here we report on the discovery of 14 genes encoding novel small RNAs in E. coli and their expression patterns under a variety of physiological conditions. Most of the newly discovered RNAs are abundant. Interestingly, the expression level of a significant number of these RNAs increases upon entry into stationary phase.

CONCLUSIONS

Based on our results, we conclude that small RNAs are much more widespread than previously imagined and that these versatile molecules may play important roles in the fine-tuning of cell responses to changing environments.

Identification of clathrin-adaptor medium chains in Dictyostelium discoideum: differential expression during development

Clathrin-adaptor complexes (APs) are vesicle coat components that participate in cargo selectivity and transport vesicle formation. Here we cloned and characterized apm1, apm3 and apm4 cDNAs encoding AP medium chains (mu) in D. discoideum. Amino acid comparison suggested that predicted proteins were homologous to known mu1, mu3 and mu4 subunits of mammalian APs as they shared 69, 51, and 26% identity with mouse mu1A, human mu3A and human mu4, respectively. In all chains, amino acid residues predicted to interact with tyrosine based sorting signals were conserved. Southern blot analysis indicated only one copy of each gene in D. discoideum genome. Expression of apm1 and apm3 mRNAs stayed relatively constant during vegetative growth and throughout development. In contrast, apm4 was poorly expressed in amoebae but became well detectable by RT-PCR upon cell differentiation. This regulated expression of coat proteins enlightens the importance of intracellular membrane transport vesicles during development in D. discoideum and strengthens this attractive model organism for studying the function of coat complexes in vivo.

Multiple S gene family members including natural antisense transcripts are differentially expressed during development of maize flowers

Within the large Brassica S gene family, SLG (S locus glycoprotein) and SRK (S locus receptor kinase) participate to the control of pollen-stigma self-incompatibility. In the self-compatible species maize, S gene family members are predominantly expressed in vegetative organs but are also expressed to a lesser extent in the stigma (silk). To determine if the expression of any S gene family members correlates with female receptivity, we analyzed their expression in developing maize silks. We show that a large family of maize S transcripts is expressed in developing silks. Surprisingly, we isolated a cDNA complementary to a large portion of the antisense strand of the maize receptor kinase S domain. Rapid amplification of cDNA ends (RACE)-polymerase chain reaction, RNase protection, and Northern hybridization with single-stranded riboprobes confirmed that natural antisense S transcripts exist in leaves and seedling shoots and in all sexual tissues tested except mature pollen. These natural antisense S transcripts co-exist with several less abundant sense S transcripts. The accumulation of sense and antisense S transcripts is differentially regulated during pollen and silk development. Thus, these results support a role for S gene family members in sexual tissue development and/or compatible pollination and reveal a new level of complexity in the regulation and function of the S gene family in maize.

Cloning and analysis of the mouse Fanconi anemia group A cDNA and an overlapping penta zinc finger cDNA

Despite the cloning of four disease-associated genes for Fanconi anemia (FA), the molecular pathogenesis of FA remains largely unknown. To study FA complementation group A using the mouse as a model system, we cloned and characterized the mouse homolog of the human FANCA cDNA. The mouse cDNA (Fanca) encodes a 161-kDa protein that shares 65% amino acid sequence identity with human FANCA. Fanca is located at the distal region of mouse chromosome 8 and has a ubiquitous pattern of expression in embryonic and adult tissues. Expression of the mouse cDNA in human FA-A cells restores the cellular drug sensitivity to normal levels. Thus, the expression pattern, protein structure, chromosomal location, and function of FANCA are conserved in the mouse. We also isolated a novel zinc finger protein, Zfp276, which has five C(2)H(2) domains. Interestingly, Zfp276 is situated in the Fanca locus, and the 3'UTR of its cDNA overlaps with the last four exons of Fanca in a tail-to-tail manner. Zfp276 is expressed in the same tissues as Fanca, but does not complement the mitomycin C (MMC)-sensitive phenotype of FA-A cells. The overlapping genomic organization between Zfp276 and Fanca may have relevance to the disease phenotype of FA.

Human transaldolase-associated repetitive elements are transcribed by RNA polymerase III

Repetitive elements flanked by exons 2 and 3 of the human transaldolase gene, thus termed transaldolase-associated repetitive elements, TARE, were identified in human DNA. Nonpolyadenylated TARE transcripts were detected by Northern blot analysis and cloned by reverse transcriptase-mediated polymerase chain reaction from human T lymphocytes. A dominant 1085-nucleotide long transcript, TARE-6, contained two adjacent Alu elements, a right monomer and a complete dimer, oriented opposite to the direction of transcription of the transaldolase gene. Reverse transcriptase-polymerase chain reaction and in vitro transcription analyses showed that transcription of TARE-6 proceeded in the orientation of the RNA pol III promoter of the Alu dimer and opposite to the orientation of the TAL-H gene. TAREs lacking RNA polymerase III promoter showed no transcriptional activity. In vitro transcription of TARE-6 was resistant to 1 microg/ml alpha-amanitin but sensitive to 100 microg/ml alpha-amanitin and tagetitoxin, suggesting involvement of RNA polymerase III. TAREs in both the transaldolase and HSAG-1 genomic loci were surrounded by TA target site duplications. Homologies between transaldolase and HSAG-1 break off internally at splice donor and acceptor sites. The results suggest RNA polymerase III-mediated transcription of TARE may be a source of repetitive elements, contributing to distinct genes and thus shaping the human genome.

Applying in vivo expression technology (IVET) to the fungal pathogen Histoplasma capsulatum

Understanding how pathogens survive within the host cell is of paramount importance in the development of vaccines and therapeutic agents. This task has been particularly daunting in the study of fungal pathogens due to the lack of easily manipulated genetic systems. In recent years several molecular genetic reporter systems have been developed to identify genes expressed during the infection process and potential virulence determinants. The development of one method in particular, in vivo expression technology (IVET), has led to the discovery of several genes from various bacterial pathogens necessary for survival during infection. The recent development of molecular genetic tools for Histoplasma capsulatum has enabled us to adapt the IVET technology for this pathogenic fungus utilizing the URA5 gene, which is essential for H. capsulatum survival in mice and in cultured macrophages, as a reporter of in vivo gene expression. We report the first successful application of IVET screening of a fungal pathogen for genes expressed exclusively during infection.

Distinct features of post-transcriptional gene silencing by antisense transgenes in single copy and inverted T-DNA repeat loci

The application of antisense transgenes in plants is a powerful tool to inhibit gene expression. The underlying mechanism of this inhibition is still poorly understood. High levels of antisense RNA (as-RNA) are expected to result in strong silencing but often there is no clear correlation between as-RNA levels and the degree of silencing. To obtain insight into these puzzling observations, we have analyzed several petunia transformants of which the pigmentation gene chalcone synthase (Chs) is post-transcriptionally silenced in corollas by antisense (as) Chs transgenes. The transformants were examined with respect to the steady-state as-RNA level, transcription level of the as-transgenes, the repetitiveness and structure of the integrated T-DNAs, and the methylation status of the transgenes. This revealed that the transformants can be divided in two classes: the first class contains a single copy (S) T-DNA of which the as-Chs gene is transcribed, although several-fold lower than the endogenous Chs genes. As there are not sufficient as-RNAs to degrade every mRNA, we speculate that silencing is induced by double-stranded RNA. The second class contains two T-DNAs which are arranged as inverted repeats (IRs). These IR loci are severely methylated and the as-Chs transgenes transcriptionally barely active. The strongest silencing was observed with IR loci in which the as-Chs transgenes were proximal to the centre of the IR. Similar features have been described for co-suppression by IRs composed of sense Chs transgenes, suggesting that silencing by antisense IRs also occurs by co-suppression, either via ectopic DNA pairing or via dsRNA.

Developmental gene regulation in Giardia lamblia: first evidence for an encystation-specific promoter and differential 5' mRNA processing

Giardia lamblia must encyst to survive in the environment and subsequently infect new hosts. We investigated the expression of glucosamine-6-phosphate isomerase (Gln6PI), the first enzyme required for biosynthesis of N-acetylgalactosamine, for the major cyst wall polysaccharide. We isolated two Gln6PI genes that encode proteins with large areas of identity, but distinctive central and terminal regions. Both recombinant enzymes have comparable kinetics. Interestingly, these genes have distinct patterns of expression. Gln6PI-A has a conventional, short 5' untranslated region (UTR), and is expressed at a low level during vegetative growth and encystation. The Gln6PI-B gene has two transcripts - one is expressed constitutively and the second species is highly upregulated during encystation. The non-regulated Gln6PI-B transcript has the longest 5'-UTR known for Giardia and is 5' capped or blocked. In contrast, the Gln6PI-B upregulated transcript has a short, non-capped 5'-UTR. A small promoter region (< 56 bp upstream from the start codon) is sufficient for the regulated expression of Gln6PI-B. Gln6PI-B also has an antisense overlapping transcript that is expressed constitutively. A shorter antisense transcript is detected during encystation. This is the first report of a developmentally regulated promoter in Giardia, as well as evidence for a potential role of 5' RNA processing and antisense RNA in differential gene regulation.

In vivo structure of two divergent promoters at the human PCNA locus. Synthesis of antisense RNA and S phase-dependent binding of E2F complexes in intron 1

Proliferating cell nuclear antigen (PCNA) synthesis is strictly regulated during the cell cycle. To investigate PCNA transcriptional regulation, we have analyzed protein-DNA interactions at the promoter region and in the first intron in quiescent fibroblasts and following serum stimulation. Twenty putative protein-binding sites, distributed in two divergent promoters at the PCNA locus, were identified in vivo by genomic footprinting. These elements bind transcription factors continuously throughout the cell cycle with the exception of one E2F consensus site, located in the first intron at position +583. This E2F site becomes strongly occupied 18 h after serum stimulation, implying that an E2F activator complex plays a role in activation of the PCNA gene at the onset of S phase. We detected a 500-600-base pair-long antisense transcript by Northern blot analysis. This RNA has no apparent coding capacity and is constitutively transcribed from a promoter located within the first intron. We suggest that silencing of the PCNA gene is accomplished through base pairing between sense pre-mRNA and antisense RNA. The binding of S phase-specific E2F complexes at the +583 element may help to overcome the negative effect of the antisense transcript, which results in up-regulation of PCNA expression in proliferating cells.

Gene identification by shotgun antisense

Shotgun antisense is a technique to make a random set of mutant cells or organisms in such a way that one can select an interesting mutant and then sequence part of the mutated gene within a day. In addition to the fantastic rapidity with which one can identify the mutated gene, there are more advantages of this technique over other mutagenesis techniques: (1) one can identify genes that when completely repressed are lethal; (2) one can select which sets of genes will be mutated; and (3) genes that are expressed from multiple copies can be repressed and thus identified.

A novel intron element operates posttranscriptionally To regulate human N-myc expression

Precisely regulated expression of oncogenes and tumor suppressor genes is essential for normal development, and deregulated expression can lead to cancer. The human N-myc gene normally is expressed in only a subset of fetal epithelial tissues, and its expression is extinguished in all adult tissues except transiently in pre-B lymphocytes. The N-myc gene is overexpressed due to genomic amplification in the childhood tumor neuroblastoma. In previous work to investigate mechanisms of regulation of human N-myc gene expression, we observed that N-myc promoter-chloramphemicol acelyltransferase reporter constructs containing sequences 5' to exon 1 were active in all cell types examined, regardless of whether endogenous N-myc RNA was detected. In contrast, inclusion of the first exon and a portion of the first intron allowed expression only in those cell types with detectable endogenous N-myc transcripts. We investigated further the mechanisms by which this tissue-specific control of N-myc expression is achieved. Using nuclear run-on analyses, we determined that the N-myc gene is actively transcribed in all cell types examined, indicating a posttranscriptional mode of regulation. Using a series of N-myc intron 1 deletion constructs, we localized a 116-bp element (tissue-specific element [TSE]) within the first intron that directs tissue-specific N-myc expression. The TSE can function independently to regulate expression of a heterologous promoter-reporter minigene in a cell-specific pattern that mirrors the expression pattern of the endogenous N-myc gene. Surprisingly, the TSE can function in both sense and antisense orientations to regulate gene expression. Our data indicate that the human N-myc TSE functions through a posttranscriptional mechanism to regulate N-myc expression.

Antisense RNA: function and fate of duplex RNA in cells of higher eukaryotes

There is ample evidence that cells of higher eukaryotes express double-stranded RNA molecules (dsRNAs) either naturally or as the result of viral infection or aberrant, bidirectional transcriptional readthrough. These duplex molecules can exist in either the cytoplasmic or nuclear compartments. Cells have evolved distinct ways of responding to dsRNAs, depending on the nature and location of the duplexes. Since dsRNA molecules are not thought to exist naturally within the cytoplasm, dsRNA in this compartment is most often associated with viral infections. Cells have evolved defensive strategies against such molecules, primarily involving the interferon response pathway. Nuclear dsRNA, however, does not induce interferons and may play an important posttranscriptional regulatory role. Nuclear dsRNA appears to be the substrate for enzymes which deaminate adenosine residues to inosine residues within the polynucleotide structure, resulting in partial or full unwinding. Extensively modified RNAs are either rapidly degraded or retained within the nucleus, whereas transcripts with few modifications may be transported to the cytoplasm, where they serve to produce altered proteins. This review summarizes our current knowledge about the function and fate of dsRNA in cells of higher eukaryotes and its potential manipulation as a research and therapeutic tool.

Mobilization of chromatin-bound Mcm proteins by micrococcal nuclease

Mcm (minichromosome maintenance) proteins are important components of the eukaryotic replication initiation apparatus. We investigate the binding of human Mcm proteins to HeLa cell chromatin using micrococcal nuclease as a tool. In previous work we prepared chromatin under low ionic strength conditions. The use of a low salt buffer was necessary to prevent the dissociation of Mcm proteins. Here we use chromatin prepared at more physiological salt concentrations (100 mM NaCl) following the procedure of Fujita et al. (J. Biol. Chem. 272, 10928-10935; 1997) who had shown that ATP stabilizes the interaction of Mcm proteins with chromatin. We show here that micrococcal nuclease released Mcm proteins early during the digestion process suggesting that Mcm proteins reside on chromatin sites which are more open to nuclease attack than bulk chromatin. Released Mcm proteins sedimented through glycerol gradients as a multiprotein complex comprising several of the six known human Mcm proteins.