Coordinated posttranscriptional control of gene expression by modular elements including Alu-like repetitive sequences

Comparative Genomics Reveals the High Copy Number Variation of a Retro Transposon in Different Magnaporthe Isolates

Magnaporthe oryzae is one of the fungal pathogens of rice which results in heavy yield losses worldwide. Understanding the genomic structure of M. oryzae is essential for appropriate deployment of the blast resistance in rice crop improvement programs. In this study we sequenced two M. oryzae isolates, RML-29 (avirulent) and RP-2421 (highly virulent) and performed comparative study along with three publically available genomes of 70-15, P131, and Y34. We identified several candidate effectors (>600) and isolate specific sequences from RML-29 and RP-2421, while a core set of 10013 single copy orthologs were found among the isolates. Pan-genome analysis showed extensive presence and absence variations (PAVs). We identified isolate-specific genes across 12 isolates using the pan-genome information. Repeat analysis was separately performed for each of the 15 isolates. This analysis revealed ∼25 times higher copy number of short interspersed nuclear elements (SINE) in virulent than avirulent isolate. We conclude that the extensive PAVs and occurrence of SINE throughout the genome could be one of the major mechanisms by which pathogenic variability is emerging in M. oryzae isolates. The knowledge gained in this comparative genome study can provide understandings about the fungal genome variations in different hosts and environmental conditions, and it will provide resources to effectively manage this important disease of rice.

■ REVIEW : Gene Expression in Nerve Regeneration

Injury of peripheral nerve in mammals leads to a complex but stereotypical pattern of histological events that comprise a highly reproducible sequence of degenerative reactions (Wallerian degeneration) succeeded by regenerative responses. These reactions are based on a corresponding sequence of cellular and mo lecular interactions that, in turn, reflect the differential expression of specific genes with functions in nerve degeneration and repair. We report on more than 60 genes and their products that show a specific pattern of regulation following peripheral nerve lesion. The group of regulated genes encoding, e.g., transcription factors, growth factors and their receptors, cytokines, neuropeptides, myelin proteins and lipid carriers, and cytoskeletal proteins as well as extracellular matrix and cell adhesion molecules. We describe and compare the distinct time-courses and cellular origin of expression and further discuss established or putative mo lecular interrelationships and functions with respect to the contribution of these genes/gene products to the molecular regeneration program of the PNS. NEUROSCIENTIST 3:112-122, 1997

A gene expression restriction network mediated by sense and antisense Alu sequences located on protein-coding messenger RNAs

Background

Alus are primate-specific retrotransposons which account for 10.6% of the human genome. A large number of protein-coding mRNAs are encoded with sense or antisense Alus in the un-translated regions.

Results

We postulated that mRNAs carrying Alus in the two opposite directions can generate double stranded RNAs, capable of regulating the levels of other Alu-carrying mRNAs post-transcriptionally. A gene expression profiling assay showed that the levels of antisense and sense Alus-carrying mRNAs were suppressed in a reversible manner by over-expression of exogenous sense and antisense Alus derived from mRNAs (Family-wise error rate P= 0.0483 and P < 0.0001 respectively). Screening through human mRNAs on the NCBI-RefSeq database, it was found that sense and antisense Alu-carrying transcripts were enriched in distinct cellular functions. Antisense Alu-carrying genes were particularly enriched in neurological and developmental processes, while sense Alu-carrying genes were enriched in immunological functions.

Conclusions

Taken together, we proposed a novel Alu-mediated regulation network capable of stabilizing Alu-carrying mRNA levels in different cell types and restricting the activated expression levels of protein-coding, Alu-carrying mRNAs.

Misfolded human tRNA isodecoder binds and neutralizes a 3' UTR-embedded Alu element

Several classes of small noncoding RNAs are key players in cellular metabolism including mRNA decoding, RNA processing, and mRNA stability. Here we show that a tRNA(Asp) isodecoder, corresponding to a human tRNA-derived sequence, binds to an embedded Alu RNA element contained in the 3' UTR of the human aspartyl-tRNA synthetase mRNA. This interaction between two well-known classes of RNA molecules, tRNA and Alu RNA, is driven by an unexpected structural motif and induces a global rearrangement of the 3' UTR. Besides, this 3' UTR contains two functional polyadenylation signals. We propose a model where the tRNA/Alu interaction would modulate the accessibility of the two alternative polyadenylation sites and regulate the stability of the mRNA. This unique regulation mechanism would link gene expression to RNA polymerase III transcription and may have implications in a primate-specific signal pathway.

Reading TE leaves: new approaches to the identification of transposable element insertions

Transposable elements (TEs) are a tremendous source of genome instability and genetic variation. Of particular interest to investigators of human biology and human evolution are retrotransposon insertions that are recent and/or polymorphic in the human population. As a consequence, the ability to assay large numbers of polymorphic TEs in a given genome is valuable. Five recent manuscripts each propose methods to scan whole human genomes to identify, map, and, in some cases, genotype polymorphic retrotransposon insertions in multiple human genomes simultaneously. These technologies promise to revolutionize our ability to analyze human genomes for TE-based variation important to studies of human variability and human disease. Furthermore, the approaches hold promise for researchers interested in nonhuman genomic variability. Herein, we explore the methods reported in the manuscripts and discuss their applications to aspects of human biology and the biology of other organisms.

Alu and b1 repeats have been selectively retained in the upstream and intronic regions of genes of specific functional classes

Alu and B1 repeats are mobile elements that originated in an initial duplication of the 7SL RNA gene prior to the primate-rodent split about 80 million years ago and currently account for a substantial fraction of the human and mouse genome, respectively. Following the primate-rodent split, Alu and B1 elements spread independently in each of the two genomes in a seemingly random manner, and, according to the prevailing hypothesis, negative selection shaped their final distribution in each genome by forcing the selective loss of certain Alu and B1 copies. In this paper, contrary to the prevailing hypothesis, we present evidence that Alu and B1 elements have been selectively retained in the upstream and intronic regions of genes belonging to specific functional classes. At the same time, we found no evidence for selective loss of these elements in any functional class. A subset of the functional links we discovered corresponds to functions where Alu involvement has actually been experimentally validated, whereas the majority of the functional links we report are novel. Finally, the unexpected finding that Alu and B1 elements show similar biases in their distribution across functional classes, despite having spread independently in their respective genomes, further supports our claim that the extant instances of Alu and B1 elements are the result of positive selection.

Despite their fundamental role in cell regulation, genes account for less than 1% of the human genome. Recent studies have shown that non-genic regions of our DNA may also play an important functional role in human cells. In this paper, we study Alu and B elements, a specific class of such non-genic elements that account for ∼10% of the human genome and ∼7% of the mouse genome respectively. We show that, contrary to the prevailing hypothesis, Alu and B elements have been preferentially retained in the proximity of genes that perform specific functions in the cell. In contrast, we found no evidence for selective loss of these elements in any functional class. Several of the functional classes that we have linked to Alu and B elements are central to the proper working of the cell, and their disruption has previously been shown to lead to the onset of disease. Interestingly, the DNA sequences of Alu and B elements differ substantially between human and mouse, thus hinting at the existence of a potentially large number of non-conserved regulatory elements.

AtCopeg1, the unique gene originated from AtCopia95 retrotransposon family, is sensitive to external hormones and abiotic stresses

Retrotransposons, the important component of eukaryotic genome, are seeds of evolution and play great role in creating new genes. The compact Arabidopsis genome harbors over 200 Copia-like retrotransposons, but mostly silent. Here we isolated an expressed gene AtCopeg1 (Copia evolved gene 1), which shows higher than 90% identity to AtCopia95_I, the consensus sequence encoding AtCopia95 polyprotein. AtCopeg1 is the unique gene evolved from AtCopia95 family. It is an intron-containing gene with two alternative 3' ends. The transcript accumulation of AtCopeg1 is tissue-specific, also significantly affected by external hormones and abiotic stresses. The presence of regulatory elements in its promoter region (originating from AtCopia95_I and AtCopia95 long terminal repeat), is adequate for conferring its essential expression feature. Thus, AtCopeg1 is a versatile functional gene involved in many developmental and adaptive processes probably including the signaling crosstalk of hormone and nutrient stress. Our work highlighted the role of transposable elements in creating new functional genes, and will incite the enthusiasm for isolation and functional characterization of plant genes evolved from those previously considered as selfish and junk DNA.

Mobile DNA elements in primate and human evolution

Roughly 50% of the primate genome consists of mobile, repetitive DNA sequences such as Alu and LINE1 elements. The causes and evolutionary consequences of mobile element insertion, which have received considerable attention during the past decade, are reviewed in this article. Because of their unique mutational mechanisms, these elements are highly useful for answering phylogenetic questions. We demonstrate how they have been used to help resolve a number of questions in primate phylogeny, including the human-chimpanzee-gorilla trichotomy and New World primate phylogeny. Alu and LINE1 element insertion polymorphisms have also been analyzed in human populations to test hypotheses about human evolution and population affinities and to address forensic issues. Finally, these elements have had impacts on the genome itself. We review how they have influenced fundamental ongoing processes like nonhomologous recombination, genomic deletion, and X chromosome inactivation.

Mobile element-based forensic genomics

Mobile elements are commonly referred to as selfish repetitive DNA sequences. However, mobile elements represent a unique and underutilized group of molecular markers. Several of their characteristics make them ideally suited for use as tools in forensic genomic applications. These include their nature as essentially homoplasy-free characters, they are identical by descent, the ancestral state of any insertion is known to be the absence of the element, and many mobile element insertions are lineage specific. In this review, we provide an overview of mobile element biology and describe the application of certain mobile elements, especially the SINEs and other retrotransposons, to forensic genomics. These tools include quantitative species-specific DNA detection, analysis of complex biomaterials, and the inference of geographic origin of human DNA samples.

SINEs of progress: Mobile element applications to molecular ecology

Mobile elements represent a unique and under-utilized set of tools for molecular ecologists. They are essentially homoplasy-free characters with the ability to be genotyped in a simple and efficient manner. Interpretation of the data generated using mobile elements can be simple compared to other genetic markers. They exist in a wide variety of taxa and are useful over a wide selection of temporal ranges within those taxa. Furthermore, their mode of evolution instills them with another advantage over other types of multilocus genotype data: the ability to determine loci applicable to a range of time spans in the history of a taxon. In this review, I discuss the application of mobile element markers, especially short interspersed elements (SINEs), to phylogenetic and population data, with an emphasis on potential applications to molecular ecology.

Novel molecular targets of smokeless tobacco (khaini) in cell culture from oral hyperplasia

Knowledge of molecular mechanism(s) implicated in smokeless tobacco (ST) associated oral carcinogenesis is meager. In an attempt to identify genes that are modulated by ST, we recently reported establishment of an oral epithelial cell culture, AMOL III from oral hyperplasia with hyperkeratosis of a khaini consumer. Herein we aimed to identify novel molecular targets of ST (khaini) in AMOL III cells using differential display. Fourteen novel differentially expressed genes (12 upregulated and 2 downregulated) were identified. These differentially expressed cDNAs were amplified, cloned, sequenced and confirmed by reverse northern blotting. Mainly these genes are components of transcriptional machinery, cell-cell adhesion, signaling, growth and transformation processes. The important novel molecular targets identified included activated leucocyte cell adhesion molecule (ALCAM), CDP-diacylglycerol-inositol 3-phosphatidyl transferase (phosphatidylinositol synthase), CDIPT, an important enzyme in phosphatidyl inositol biosynthesis, ribosomal protein (RPS23), KIAA0121 and growth and transformation factor, E2IG5. Semi-quantitative RT-PCR analysis of these five genes confirmed over-expression of these genes in oral pre-malignant lesions (OPLs) and oral squamous cell carcinomas (OSCCs) of ST consumers underscoring their biological relevance in ST-associated oral tumorigenesis. In depth studies are warranted to determine the functional significance of ALCAM and CDIPT in oral carcinogenesis.

Blockade of murine erythroleukemia cell differentiation by hypomethylating agents causes accumulation of discrete small poly(A)- RNAs hybridized to 3'-end flanking sequences of beta(major) globin gene

Induction of murine erythroleukemia (MEL) cell differentiation is accompanied by transcriptional activation of globin genes and biosynthesis of hemoglobin. In this study, we observed cytoplasmic accumulation of relatively small RNAs of different size (150-600 nt) hybridized to alpha1 and beta(major) globin DNA probes in MEL cells blocked to differentiate by hypomethylating agents (neplanocin A, 3-deazaneplanocin A and cycloleucine). These RNAs lack poly(A) tail and appear to be quite stable. Search within the 3'-end flanking sequences of beta(major) globin gene revealed the presence of a B1 repeat element, several ATG initiation codons, a GATA-1 consensus sequence and sequences recognized by AP-1/NF-E2 and erythroid Krüppel-like factor (EKLF) transcription factors. These data taken together indicate that exposure of MEL cells to hypomethylating agents promotes accumulation of relatively small discrete RNA transcripts lacking poly(A) tail regardless of the presence or absence of inducer dimethylsulfoxide (DMSO). However, the relative steady-state level of small RNAs was comparatively higher in cells co-exposed to inducer and each one of the hypomethylating agents. Although the orientation of these RNAs has not been established as yet, the possibility these small poly(A)- RNAs which are induced by hypomethylating agents may be involved in the blockade of MEL cell differentiation program is discussed.

Increased level of polymerase III transcribed Alu RNA in hepatocellular carcinoma tissue

There have been extensive observations that RNA containing repetitive elements accumulates in transformed cells and tumor tissues. In the present study, we first obtained result consistent with previous observations by in situ hybridization. Then we used primer extension analysis to determine the level of polymerase III directed Alu RNA and found an increased expression of Alu RNA in hepatocellular carcinoma.

Rat adrenoleukodystrophy-related (ALDR) gene: full-length cDNA sequence and new insight in expression

X-linked adrenoleukodystrophy (X-ALD) is an inherited demyelinating disorder due to mutations in the ALD gene, which encodes a peroxisomal ABC half-transporter (ALDP). It has been suggested that ALDP assembles with ALDRP (adrenoleukodystrophy-related protein), a close homologous half-transporter, to form a functional heterodimer. For the first time full-length ALDRP cDNA (5.5 kb) was cloned, and 5' and 3' RACE analysis revealed that alternative usage of polyadenylation sites generates the two transcripts of 3.0 and 5.5 kb observed in the rat in Northern blot analysis. Southern blotting and chromosomal mapping demonstrated one ALDR locus in the rat genome. Characterisation of the 3' flanking region suggested that an ID sequence might be responsible for high expression of the 5.5 kb ALDRP transcript in rat brain. ALDR gene expression was found to be high in the liver of rats before weaning and very low in adult rats; the reverse developmental regulation was observed in the brain. Fenofibrate, which is a potent inducer of the ALDR gene in the liver of adult rats, could not induce the ALDR gene in suckling rats. The exact significance of this result with regard to development of an efficient pharmacological gene therapy for X-ALD is discussed.

Structure and genetic polymorphism of the mouse KCC1 gene

The KCC1 K-Cl cotransporter is a major regulator of erythroid and non-erythroid cell volume, and the KCC1 gene is a candidate modifier gene for sickle cell disease and other hemoglobinopathies. We have cloned and sequenced the mouse KCC1 (mKCC1) gene, defined its intron-exon junctions, and analyzed (AC)/(TG) intragenic polymorphisms. A highly polymorphic (AC) repeat of mKCC1 intron 1 was characterized in musculus strains, and used to prove lack of linkage between the mKCC1 gene and the rol (resistant to osmotic lysis) locus. The intron 1 (AC) repeat in CAST/Ei and SPRET/Ei was not only more divergent in length but also underwent additional sequence variation. A dimorphic (TG) repeat in intron 2 distinguished CAST/Ei from other strains, and an intron 17 B1 Alu-like SINE present in all musculus strains was found to be absent from intron 17 in SPRET/Ei. These and additional described strain-specific polymorphisms will be useful mapping and genetic tools in the study of mouse models of sickle cell disease.

Differential expression of B1-containing transcripts in Leishmania-exposed macrophages

When the parasitic protozoan Leishmania infect host macrophage cells, establishment of the infection requires alteration in the expression of genes in both the parasite and the host cells. In the early phase of infection of macrophages in vitro, Leishmania exposure affects the expression of a group of mouse macrophage genes containing the repetitive transposable element designated B1 sequence. In Leishmania-exposed macrophages compared with unexposed macrophages, small (approximately 0.5 kilobase) B1-containing RNAs (small B1-RNAs) are down-regulated, and large (1-4 kilobases) B1-containing RNAs (large B1-RNA) are up-regulated. The down-regulation of small B1-RNAs precedes the up-regulation of large B1-RNAs in Leishmania-exposed macrophages. These differential B1-containing gene expressions in Leishmania-exposed macrophages were verified using individual small-B1-RNA and large B1-RNA. The differential expressions of the B1-containing RNAs at the early phase of Leishmania-macrophage interaction may associate the establishment of the leishmanial infection.

Impact of transposable elements on the human genome

Presence of transposable elements (TEs) in the human genome has profound effects on genome function, structure and evolution. TE mobility and inter-TE recombination are the origin of a large spectrum of mutations and genome reorganization leading to diseases. From the data provided by the Human Genome Project and from information on the detection and dynamics of TEs within and between species acquired during the last two decades, we now know that these elements are not only involved in mutagenesis but can also participate in many cellular functions including recombination, gene regulation, protein-coding RNA messages and, possibly, cellular stress response and centromere function. TEs also promote a general genome shuffling process that has been important for the evolution of several gene families and for the development of new regulatory pathways.

RNAs from all categories generate retrosequences that may be exapted as novel genes or regulatory elements

While the significance of middle repetitive elements had been neglected for a long time, there are again tendencies to ascribe most members of a given middle repetitive sequence family a functional role--as if the discussion of SINE (short interspersed repetitive elements) function only can occupy extreme positions. In this article, I argue that differences between the various classes of retrosequences concern mainly their copy numbers. Consequently, the function of SINEs should be viewed as pragmatic such as, for example, mRNA-derived retrosequences, without underestimating the impact of retroposition for generation of novel protein coding genes or parts thereof (exon shuffling by retroposition) and in particular of SINEs (and retroelements) in modulating genes and their expression. Rapid genomic change by accumulating retrosequences may even facilitate speciation [McDonald, J.F., 1995. Transposable elements: possible catalysts of organismic evolution. Trends Ecol. Evol. 10, 123-126.] In addition to providing mobile regulatory elements, small RNA-derived retrosequences including SINEs can, in analogy to mRNA-derived retrosequences, also give rise to novel small RNA genes. Perhaps not representative for all SINE/master gene relationships, we gained significant knowledge by studying the small neuronal non-messenger RNAs, namely BC1 RNA in rodents and BC200 RNA in primates. BC1 is the first identified master gene generating a subclass of ID repetitive elements, and BC200 is the only known Alu element (monomeric) that was exapted as a novel small RNA encoding gene.

Translational control of specific genes during differentiation of HL-60 cells

Eukaryotic gene expression can be regulated through selective translation of specific mRNA species. Nevertheless, the limited number of known examples hampers the identification of common mechanisms that regulate translation of specific groups of genes in mammalian cells. We developed a method to identify translationally regulated genes. This method was used to examine the regulation of protein synthesis in HL-60 cells undergoing monocytic differentiation. A partial screening of cellular mRNAs identified five mRNAs whose translation was specifically inhibited and five others that were activated as was indicated by their mobilization onto polysomes. The specifically inhibited mRNAs encoded ribosomal proteins, identified as members of the 5'-terminal oligopyrimidine tract mRNA family. Most of the activated transcripts represented uncharacterized genes. The most actively mobilized transcript (termed TA-40) was an untranslated 1.3-kilobase polyadenylated RNA with unusual structural features, including two Alu-like elements. Following differentiation, a significant change in the cytoplasmic distribution of Alu-containing mRNAs was observed, namely, the enhancement of Alu-containing mRNAs in the polysomes. Our findings support the notion that protein synthesis is regulated during differentiation of HL-60 cells by both global and gene-specific mechanisms and that Alu-like sequences within cytoplasmic mRNAs are involved in such specific regulation.

Control of genes by mammalian retroposons

Available data on possible genetic impacts of mammalian retroposons are reviewed. Most important is the growing number of established examples showing the involvement of retroposons in modulation of expression of protein-coding genes transcribed by RNA polymerase II (Pol II). Retroposons contain conserved blocks of nucleotide sequence for binding of some important Pol II transcription factors as well as sequences involved in regulation of stability of mRNA. Moreover, these mobile genes provide short regions of sequence homology for illegitimate recombinations, leading to diverse genome rearrangements during evolution. Therefore, mammalian retroposons representing a significant fraction of noncoding DNA cannot be considered at present as junk DNA but as important genetic symbionts driving the evolution of regulatory networks controlling gene expression.

Repetitive elements and their genetic applications in zebrafish

Repetitive elements provide important clues about chromosome dynamics, evolutionary forces, and mechanisms for exchange of genetic information between organisms. Repetitive sequences, especially the mobile elements, have many potential applications in genetic research. DNA transposons and retroposons are routinely used for insertional mutagenesis, gene mapping, gene tagging, and gene transfer in several model systems. Once they are developed for the zebrafish, they will greatly facilitate the identification, mapping, and isolation of genes involved in development as well as the investigation of the evolutionary processes that have been shaping eukaryotic genomes. In this review repetitive elements are characterized in terms of their lengths and other physical properties, copy numbers, modes of amplification, and mobilities within a single genome and between genomes. Examples of how they can be used to screen genomes for species and individual strain differences are presented. This review does not cover repetitive gene families that encode well-studied products such as rRNAs, tRNAs, and the like.

A novel family of repeat sequences in the mouse genome responsive to retinoic acid

Repetitive DNA sequences form a substantial portion of eukaryotic genomes and exist as members of families that differ in copy number, length, and sequence. Various functions, including chromosomal integrity, gene regulation, and gene rearrangement have been ascribed to repetitive DNA. Although there is evidence that some repetitive sequences may participate in gene regulation, little is known about how their own expression may be regulated. During the course of gene trapping experiments with embryonic stem (ES) cells, we identified a novel class of expressed repetitive sequences in the mouse, using 5' rapid amplification of cDNA ends-polymerase chain reaction (5' RACE-PCR) to clone fusion transcripts from these lines. The expression of these repeats was induced by retinoic acid (RA) in cultured ES cells examined by Northern blot analyses. In vivo, their expression was spatially restricted in embryos and in the adult brain as determined by RNA in situ hybridization. We designated this family of sequences as Dr (developmentally regulated) repeats. The members of the Dr family, identified by cDNA cloning and through database search, are highly similar in sequence and show peculiar structural features. Our results suggest the expression of Dr-containing transcripts may be part of an ES cell differentiation program triggered by RA.

Molecular basis of the soluble and membrane-bound forms of the murine leukemia inhibitory factor receptor alpha-chain. Expression in normal, gestating, and leukemia inhibitory factor nullizygous mice

The murine leukemia inhibitory factor receptor alpha-chain (mLIFR) exists in a membrane-bound and a soluble form. The two major classes of mRNA transcript correspond to either the soluble or membrane-bound form of the mLIFR. In this study we have identified a complex and heterogeneous pattern of expression of mRNA transcripts for this receptor in normal mouse tissues and cell lines. In order to understand the molecular basis of these transcripts, genomic clones encompassing the region of divergence from the soluble to the membrane-bound form of the receptor were isolated. cDNAs encoding the membrane-bound form of the mLIFR were generated by an alternative splicing event where an exon that is specific to the soluble mLIFR was skipped. The membrane-bound form of the mLIFR was heterogeneously polyadenylated with at least five different sites of polyadenylation. The mRNA transcript encoding the soluble form of the mLIFR contained a region highly homologous to a murine B2 repetitive element, thus providing a possible explanation for the genesis of this transcript. The different forms of the mLIFR were analyzed in a wide range of mouse tissues in pseudopregnant mice and in mice at various stages of pregnancy. Only liver, placenta, and uterus showed an increase in the levels of mLIFR mRNA expression during pregnancy, indicating an important role for the LIFR in this process. However, somewhat surprisingly, there was no detectable difference in mLIFR mRNA levels or levels of soluble protein in leukemia inhibitory factor nullizygous mice when compared with normal mice.

Mg-SINE: a short interspersed nuclear element from the rice blast fungus, Magnaporthe grisea

A short interspersed nuclear element, Mg-SINE, was isolated and characterized from the genome of the rice blast fungus, Magnaporthe grisea. Mg-SINE was isolated as an insertion element within Pot2, an inverted-repeat transposon from M. grisea and shows typical features of a mammalian SINE. Mg-SINE is present as a 0.47-kb interspersed sequence at approximately 100 copies per haploid genome in both rice and non-rice isolates of M. grisea, indicating a common evolutionary origin. Secondary structure analysis of Mg-SINE revealed a tRNA-related region at the 5' end which folds into a cloverleaf structure. Genomic fusions resulting in chimeric Mg-SINEs (Ch-SINEs) composed of a sequence homologous to Mg-SINE at the 3' end and an unrelated sequence at its 5' end were also isolated, indicating that this and other DNA rearrangements mediated by these elements may have a major effect on the genomic architecture of this fungus.

Differentially expressed genes after peripheral nerve injury

In an attempt to identify genes associated with Wallerian degeneration and peripheral nerve regeneration we have performed differential hybridization screening of a cDNA library from crushed rat sciatic nerve (7 days postlesion) using radioactively labeled cDNA prepared from poly(A)+ RNA of normal vs. crushed nerve. Screening of 5,000 randomly selected colonies yielded 24 distinct clones that were regulated following nerve injury. Fifteen of the differentially expressed sequences could be classified as induced, whereas 9 sequences appeared to be repressed at 1 week postcrush. Sequencing and computer-assisted sequence comparison revealed 3 classes of regulated cDNA clones representing 1) novel gene sequences (8 clones) including 3 transcripts containing a repetitive "brain identifier" (ID) element; 2) identified genes (7 clones) with previously undetected expression in the peripheral nervous system (PNS), such as apolipoprotein D, peripheral myelin protein 22kD (PMP22), SPARC (secreted protein, acidic and rich in cysteine), sulfated glycoprotein SGP-1, apoferritin, decorin, and X16/SRp20; and 3) identified genes (9 clones) with known expression in the PNS including, e.g., the myelin protein P0, gamma-actin, vimentin, alpha-tubulin, chargerin II, and cytochrome c-oxidase subunit I. Northern blot and polymerase chain reaction analyses with RNA from crushed and transected nerve demonstrated that sequences with related function, like the group of myelin genes, cytoskeleton genes, genes involved in RNA processing and translation, in lipid transport or energy metabolism showed closely related temporal patterns of expression during nerve degeneration and regeneration. Finally, we compared the differentially expressed genes identified at 7 days after crush injury (this investigation) with the regulated sequences isolated previously by De Leon et al. (J Neurosci Res 29:437-488, 1991) from a 3 day postcrush sciatic nerve cDNA library.

Human signal recognition particle (SRP) Alu-associated protein also binds Alu interspersed repeat sequence RNAs. Characterization of human SRP9

Nearly 1 million interspersed Alu elements reside in the human genome. Alu retrotransposition is presumably mediated by full-length Alu transcripts synthesized by RNA polymerase III, while some polymerase III-synthesized Alu transcripts undergo 3'-processing and accumulate as small cytoplasmic (sc) RNAs of unknown function. Interspersed Alu sequences also reside in the untranslated regions of some mRNAs. The Alu sequence is related to a portion of the 7SL RNA component of signal recognition particle (SRP). This region of 7SL RNA together with 9- and 14-kDa polypeptides (SRP9/14) regulates translational elongation of ribosomes engaged by SRP. Here we characterize human (h) SRP9 and show that it, together with hSRP14 (SRP9/14), forms the activity previously identified as Alu RNA-binding protein (RBP). The primate-specific C-terminal tail of hSRP14 does not appreciably affect binding to scAlu RNA. Kd values for three Alu-homologous scRNAs were determined using Alu RBP (SRP9/14) purified from HeLa cells. The Alu region of 7SL, scAlu, and scB1 RNAs exhibited Kd values of 203 pM, 318 pM, and 1.8 nM, respectively. Finally, Alu RBP can bind with high affinity to synthetic mRNAs that contain interspersed Alus in their untranslated regions.

The inductive effect of a human DNA sequence (HALF1) on the differentiation of a variant rat hepatoma cell (C2) is restricted to episomal forms of the molecule

HALF1, a 4.3 kb human DNA sequence, was originally identified as a double-stranded, closed-circular DNA molecule in revertants from a dedifferentiated rat hepatoma cell (C2) transfected with human liver DNA. Here we report its specific properties in inducing the transition to the hepatic phenotype. (i) In vitro recircularized HALF1 induces reversion after a minimum time lag of 7 days post-transfection. (ii) After induction, the presence of HALF1 is not required for maintaining the induced hepatic state. (iii) HALF1 is detected as a sequence integrated in high molecular mass DNA of human liver. (iv) HALF1 monomer or dimer plasmid constructs do not induce reversion when integrated into the genome of transfectants. (v) Short ubiquitous RNA transcripts (approximately 400 bases) are detected with specific HALF1 probes. These results indicate that the reversion process is linked to the presence of HALF1 extrachromosomal molecules.

Ubiquitous mammalian-wide interspersed repeats (MIRs) are molecular fossils from the mesozoic era

Short interspersed elements (SINEs) are ubiquitous in mammalian genomes. Remarkable variety of these repeats among placental orders indicates that most of them amplified in each lineage independently, following mammalian radiation. Here, we present an ancient family of repeats, whose sequence divergence and common occurrence among placental mammals, marsupials and monotremes indicate their amplification during the Mesozoic era. They are called MIRs for abundant Mammalian-wide Interspersed Repeats. With approximately 120,000 copies still detectable in the human genome (0.2-0.3% DNA), MIRs represent a 'fossilized' record of a major genetic event preceding the radiation of placental orders.

Evolutionary selection against change in many Alu repeat sequences interspersed through primate genomes

Mutations have been examined in the 1500 interspersed Alu repeats of human DNA that have been sequenced and are nearly full length. There is a set of particular changes at certain positions that rarely occur (termed suppressed changes) compared to the average of identical changes of identical nucleotides in the rest of the sequence. The suppressed changes occur in positions that are clustered together in what appear to be sites for protein binding. There is a good correlation of the suppression in different positions, and therefore the joint probability of absence of mutation at many pairs of such positions is significantly higher than that expected at random. The suppression of mutation appears to result from selection that is not due to requirements for Alu sequence replication. The implication is that hundreds of thousands of Alu sequences have sequence-dependent functions in the genome that are selectively important for primates. In a few known cases Alu inserts have been adapted to function in the regulation of gene transcription.

Different domains regulate the human erythropoietin receptor gene transcription

To analyse the 5'-flanking sequences required for the tissue specific transcription of the human erythropoietin receptor (hEpo-R) gene, a DNA region spanning nucleotides -1050 to +135 relative to the transcription initiation site (+1) was explored. Our studies indicate that a minimum promoter (-76/+33) containing GATA and SP1 binding sites at positions -45 and -20 is not sufficient to confer erythroid specific expression to a reporter gene. Erythroid specificity of the promoter was observed either with the (-1050/+33 construct) which contains a cluster of Alu repetitive elements or with the addition of the 135 bp down to the transcription initiation site (-76/+135 construct) which exert a negative control on the promoter activity with a major effect in non erythroid tissues. The latter region can be subdivided on two distinct domains: the +1/+78 region that exerts a positive effect and the +79/+135 region that has a negative effect on the Epo-R promoter activity measured by CAT assays. The first region contains three CANNTG motifs, whereas the second contains an SP1/CACCC motif at position +85. These findings reveal a complex regulation of the hEpo-R gene and provide a working model useful to explain how the minimal promoter, containing GATA/SP1, can be positively and negatively regulated during erythroid differentiation.

BC200 RNA: a neural RNA polymerase III product encoded by a monomeric Alu element

We demonstrate that the BC200 RNA gene, which encodes a neural small cytoplasmic RNA, is a member of the most prodigious family of interspersed repetitive DNA and that its product represents an example of a primate tissue-specific RNA polymerase III transcript. The BC200 RNA gene is an early monomeric member and one of the few postulated transcriptionally active Alu sequences in this family of nearly half a million retropositionally amplified elements dispersed throughout the human genome. Furthermore, the isolation of two pseudogenes, BC200 beta and BC200 gamma, demonstrates the gene's transpositional ability. Interestingly, the BC200 beta pseudogene may have been generated by a conversion-like event after the human/chimpanzee divergence, resulting in an exchange of the left arm of a dimeric Alu element with the BC200 RNA coding sequence. Our data on conserved features of the active BC200 alpha gene suggest that its RNA product has been "exapted" into a function of the primate brain and provides a selective advantage to the species.

Identification and characterization of new human medium reiteration frequency repeats

We report nine new families of human medium reiteration frequency interspersed repetitive elements (MER elements). They were identified by computer-assisted analyses. Six of them were independently confirmed as repetitive families by DNA-DNA hybridization, and the number of elements for each of these families was estimated by plaque hybridization assay. The involvement of some of the reported MER elements in genetic rearrangements is demonstrated.