Target sites for SINE integration in Brassica genomes display nuclear matrix binding activity

Short interspersed nuclear elements (SINEs) are ubiquitous components of complex animal and plant genomes. SINEs are believed to be important players in eukaryotic genome evolution. Studies on SINE integration sites have revealed non-random integration without strict nucleotide sequence requirements for the integration target, suggesting that the targeted DNA might assume specific secondary structures or protein associations. Here, we report that S1 SINE elements in the genomes of Brassica show an interesting preference for matrix attachment regions (MARs). Ten cloned genomic regions were tested for their ability to bind the nuclear matrix both before and after a SINE integration event. Eight of the genomic regions targeted by S1 display strong affinity for the nuclear matrix, while two show weaker binding. The SINE S1 did not display any matrix-binding capacity on its own in either non-methylated or methylated forms. In vivo, an integrated S1 is methylated while the surrounding genomic regions may remain undermethylated or undergo methylation. However, tested genomic regions containing methylated S1, with or without methylated flanking genomic sequences, were found to vary in their ability to bind the matrix in vitro. These results suggest a possible molecular basis for a preferential targeting of SINEs to MARs and a possible impact of the integration events upon gene and genome function.

Two Arabidopsis homologs of the animal trithorax genes: a new structural domain is a signature feature of the trithorax gene family

Two Arabidopsis genes have been characterized as first examples of plant genes homologous to the animal trithorax genes. The Arabidopsis genes are highly similar but display different tissue and development expression patterns. One of them was ubiquitously expressed, with highest levels registered in young seedlings. The other gene was less active in all tested tissues, was not expressed in mature leaves but was highly expressed in roots. A new structural motif common to all TRX-related proteins has been identified. This new architectural element was found only in genes of multicellular species and is present in all genes belonging to the trithorax family. Along with the SET domain and the PHD fingers, this new element is a signature feature for the trithorax gene family.

Colinearity and its exceptions in orthologous adh regions of maize and sorghum

Orthologous adh regions of the sorghum and maize genomes were sequenced and analyzed. Nine known or candidate genes, including adh1, were found in a 225-kilobase (kb) maize sequence. In a 78-kb space of sorghum, the nine homologues of the maize genes were identified in a colinear order, plus five additional genes. The major fraction of DNA in maize, occupying 166 kb (74%), is represented by 22 long terminal repeat (LTR) retrotransposons. About 6% of the sequence belongs to 33 miniature inverted-repeat transposable elements (MITEs), remnants of DNA transposons, 4 simple sequence repeats, and low-copy-number DNAs of unknown origin. In contrast, no LTR retroelements were detected in the orthologous sorghum region. The unconserved sorghum DNA is composed of 20 putative MITEs, transposon-like elements, 5 simple sequence repeats, and low-copy-number DNAs of unknown origin. No MITEs were discovered in the 166 kb of DNA occupied by the maize LTR retrotransposons. In both species, MITEs were found in the space between genes and inside introns, indicating specific insertion and/or retention for these elements. Two adjacent sorghum genes, including one gene missing in maize, had colinear homologues on Arabidopsis chromosome IV, suggesting two rearrangements in the sorghum and three in the maize genome in comparison to a four-gene region of Arabidopsis. Hence, multiple small rearrangements may be present even in largely colinear genomic regions. These studies revealed a much higher degree of diversity at a microstructural level than predicted by genetic mapping studies for closely related grass species, as well as for comparisons of monocots and dicots.

Grass genomes

For the most part, studies of grass genome structure have been limited to the generation of whole-genome genetic maps or the fine structure and sequence analysis of single genes or gene clusters. We have investigated large contiguous segments of the genomes of maize, sorghum, and rice, primarily focusing on intergenic spaces. Our data indicate that much (>50%) of the maize genome is composed of interspersed repetitive DNAs, primarily nested retrotransposons that insert between genes. These retroelements are less abundant in smaller genome plants, including rice and sorghum. Although 5- to 200-kb blocks of methylated, presumably heterochromatic, retrotransposons flank most maize genes, rice and sorghum genes are often adjacent. Similar genes are commonly found in the same relative chromosomal locations and orientations in each of these three species, although there are numerous exceptions to this collinearity (i.e., rearrangements) that can be detected at the levels of both the recombinational map and cloned DNA. Evolutionarily conserved sequences are largely confined to genes and their regulatory elements. Our results indicate that a knowledge of grass genome structure will be a useful tool for gene discovery and isolation, but the general rules and biological significance of grass genome organization remain to be determined. Moreover, the nature and frequency of exceptions to the general patterns of grass genome structure and collinearity are still largely unknown and will require extensive further investigation.

Matrix attachment regions and structural colinearity in the genomes of two grass species

In order to gain insights into the relationship between spatial organization of the genome and genome function we have initiated studies of the co-linear Sh2/A1- homologous regions of rice (30 kb) and sorghum (50 kb). We have identified the locations of matrix attachment regions (MARs) in these homologous chromosome segments, which could serve as anchors for individual structural units or loops. Despite the fact that the nucleotide sequences serving as MARs were not detectably conserved, the general organizational patterns of MARs relative to the neighboring genes were preserved. All identified genes were placed in individual loops that were of comparable size for homologous genes. Hence, gene composition, gene orientation, gene order and the placement of genes into structural units has been evolutionarily conserved in this region. Our analysis demonstrated that the occurrence of various 'MAR motifs' is not indicative of MAR location. However, most of the MARs discovered in the two genomic regions were found to co-localize with miniature inverted repeat transposable elements (MITEs), suggesting that MITEs preferentially insert near MARs and/or that they can serve as MARs.

Gene identification in a complex chromosomal continuum by local genomic cross-referencing

Most higher plants have complex genomes containing large quantities of repetitive DNA interspersed with low-copy-number sequences. Many of these repetitive DNAs are mobile and have homology to RNAs in various cell types. This can make it difficult to identify the genes in a long chromosomal continuum. It was decided to use genic sequence conservation and grass genome co-linearity as tools for gene identification. A bacterial artificial chromosome (BAC) clone containing sorghum genomic DNA was selected using a maize Adh1 probe. The 165 kb sorghum BAC was tested for hybridization to a set of clones representing the contiguous 280 kb of DNA flanking maize Adh1. None of the repetitive maize DNAs hybridized, but most of the low-copy-number sequences did. A low-copy-number sequence that did cross-hybridize was found to be a gene, while one that did not was found to be a low-copy-number retrotransposon that was named Reina. Regions of cross-hybridization were co-linear between the two genomes, but closer together in the smaller sorghum genome. These results indicate that local genomic cross-referencing by hybridization of orthologous clones can be an efficient and rapid technique for gene identification and studies of genome organization.

Nested retrotransposons in the intergenic regions of the maize genome

The relative organization of genes and repetitive DNAs in complex eukaryotic genomes is not well understood. Diagnostic sequencing indicated that a 280-kilobase region containing the maize Adh1-F and u22 genes is composed primarily of retrotransposons inserted within each other. Ten retroelement families were discovered, with reiteration frequencies ranging from 10 to 30,000 copies per haploid genome. These retrotransposons accounted for more than 60 percent of the Adh1-F region and at least 50 percent of the nuclear DNA of maize. These elements were largely intact and are dispersed throughout the gene-containing regions of the maize genome.

The Hybaid Lecture. Microcollinearity and segmental duplication in the evolution of grass nuclear genomes

Recent studies have shown that grass genomes have very similar gene compositions and regions of conserved gene order, as exemplified by collinear genetic maps of DNA markers. We have begun the detailed study of sequence organization in large (100-500 kb) segments of the nuclear genomes of maize, sorghum and rice. Our results indicate collinearity of genes in the regions homoeologous to the maize adh1 and sh2-a1 genes. Comparable genes were found to be physically closer to each other in grasses with small genomes (rice and sorghum) than they are in maize. In several instances, we have found evidence of tandem and 'distantly tandem' duplications of segments containing maize and sorghum genes. These duplications complicate characterizations of microcollinearity and could also interfere with some map-based approaches to gene isolation.

Matrix attachment regions and transcribed sequences within a long chromosomal continuum containing maize Adh1

We provide evidence for the location of matrix attachment sites along a contiguous region of 280 kb on maize chromosome 1. We define nine potential loops that vary in length from 6 kb to > 75 kb. The distribution of the different classes of DNA within this continuum with respect to the predicted structural loops reveals an interesting correlation: the long stretches of mixed classes of highly repetitive DNAs are often segregated into topologically sequestered units, whereas low-copy-number DNAs (including the alcohol dehydrogenase1 [adh1] gene) are positioned in separate loops. Contrary to expectations, several classes of highly repeated elements with representatives in this region were found to be transcribed, and some of these exhibited tissue-specific patterns of expression.

Stably DNA-bound chromosomal proteins

DNA accomplishes its biological function in a complex with nuclear proteins. A minor protein fraction has been found in chromatin which could not be dissociated from DNA by reagents abolishing non-covalent type of interactions. The controversy surrounding the nature of the protein moiety and the nature of the bond linking the two components on the one hand, and the fact pointing to its evolutionary conservatism and metabolic stability on the other, make it necessary to critically evaluate the data in view of the possible biological function for such proteins.

DNA sequences tightly bound to proteins in mouse chromatin: identification of murine MER sequences

The finding of stably (tightly) associated DNA-protein complexes in eukaryotic chromatin has provoked many hypotheses and speculations concerning their possible role. While the answer of this question is not envisaged yet, it is clear that elucidation of the nature of the individual components involved in such complexes is a necessary step in this direction. Here, the nature of several mouse DNA sequences in the vicinity of a putative stably attached protein is studied. Eight independently isolated clones containing such sequences were compared to known sequences in GenBank. Two clones were found to belong to different subfamilies of repetitive sequences, organized into a larger family--the L1md family. One clone harbors a sequence that is a member of the Alu-type family. Four of the cloned sequences are preset in low copy numbers, but the computer search found similar sequences in various genomic regions of different rodents. These facts, together with the finding that regions homologous to the above clones often flank other repetitive elements in the genome, suggest that the cloned sequences belong to new, not yet described families of repeats in the murine genome. It is possible that they correspond to the medium reiteration frequency sequences, MER-sequences, discovered recently in the human genome (Jurka, 1990; Kaplan and Duncan, 1990). Particularly intriguing is the homology found at the integration sites of polyoma virus in two transformed cell lines with two of these clones.

Isolation of matrices from maize leaf nuclei: identification of a matrix-binding site adjacent to the Adh1 gene

Nuclear matrices were isolated from maize leaves by the two conventional methods usually employed for the preparation of the corresponding structures of animal origin. It is demonstrated that functionally competent matrices, recognizing and specifically binding the MAR-containing DNA of the mouse kappa-immunoglobulin gene may be prepared by both 2 M NaCl and LIS extractions of maize nuclei. A DNA region with a high affinity for the nuclear matrix was identified at the 5' end of the maize Adh1-S gene, distal to the promoter region. The presence of sites of reported altered chromatin structure in this particular region is discussed. While the proximity and the cohabitation of MARs with different regulatory elements is a common feature of matrix association regions in animal systems, this is the first plant MAR identified in a region of known significance for gene regulation.

Binding of sequences from the 5'- and 3'-nontranscribed spacers of the rat rDNA locus to the nucleolar matrix

Nucleolar matrix structures were obtained under different extraction conditions from highly purified isolated nucleoli. Their ultrastructural appearance, protein composition and capacity to bind rDNA preferentially were studied in a model binding system. A region spanning approximately 25 kb in the rat ribosomal gene locus was screened for DNA sites capable of specifically interacting with the proteins of the nucleolar matrix (MARs). Two such sites were identified: one is located on an EcoRV-KpnI fragment in the 5'-nontranscribed spacer region, between two repetitive elements and close to the transcription initiation site; the other MAR is on a PvuII-BamHI fragment located in the 3'-nontranscribed region, encompassing an element 85% homologous to a B2-sequence. The two MARs are located in regions rich in polypyrimidine/polypurine tracks and contain a few elements homologous to the consensus sequence for topoisomerase II. This indicates that the "attachment sites" for the ribosomal genes belong to the same class of sequences as the MARs attaching the chromosomal DNA to the nuclear matrix.

Interaction of MAR-sequences with nuclear matrix proteins

The recent discovery of DNA sequences responsible for the specific attachment of chromosomal DNA to the nuclear skeleton (MARs/SARs) was an important step towards our understanding of the functional and structural organization of eukaryotic chromatin [Mirkovitch et al.: Cell 44:273-282, 1984; Cockerill and Garrard: Cell 44:273-282, 1986]. A most important question, however, remains the nature of the matrix proteins involved in the specific binding of the MARs. It has been shown that topoisomerase II and histone H1 were capable of a specific interaction with SARs by the formation of precipitable complexes [Adachi et al.: EMBO J8:3997-4006, 1989; Izaurralde et al.: J Mol Biol 210:573-585, 1989]. Here, applying a different approach, we were able to "visualize" some of the skeletal proteins recognizing and specifically binding MAR-sequences. It is shown that the major matrix proteins are practically the same in both salt- and LIS-extracted matrices. However, the relative MAR-binding activity of the individual protein components may be different, depending on the method of matrix preparation. The immunological approach applied here allowed us to identify some of the individual MAR-binding matrix proteins. Histone H1 and nuclear actin are shown to be not only important components of the matrix, but to be involved in a highly efficient interaction with MAR-sequences as well. Evidence is presented that proteins recognized by the anti-HMG antibodies also participate in MAR-interactions.

Matrix attachment sites in the murine alpha-globin gene

DNA sequences with a high affinity for nuclear matrix proteins have been identified and localized in the mouse alpha-globin gene. These matrix association regions (MARs) are adjacent, covering the first intron and part of the 5'-coding sequence. The binding sites are in close proximity to DNase I hypersensitive sites and other important signal sequences. The proteins of the nuclear lamina do not bind the alpha-globin gene MARs in the in vitro binding assay. The finding of MARs in the mouse alpha-globin gene creates an apparent paradox, since works from other authors and our results presented here indicate that this gene is not bound to the nuclear matrix in vivo. This contradiction is difficult to explain at present but different possibilities are accounted for in the text.

An evolutionarily conserved protein fraction stably linked to DNA

Chromatins from four evolutionarily remote species (insect, fish, amphibian and bird) were isolated, high-salt-extracted and extensively deproteinized to remove noncovalently associated proteins. A protein fraction resisting the extraction procedures was found firmly linked to DNA in all four chromatins. Two-dimensional tryptic peptide mapping revealed a remarkable evolutionary conservativeness of this protein component, suggesting an indispensable function for it in the nucleus.

A protein fraction stably linked to DNA in plant chromatin

DNA from the chromatin of roots and shoots of maize seedlings was isolated and extensively deproteinized by repeated high-salt extractions, by subsequent deproteinizations eliminating noncovalently associated proteins and by CsC1 density gradient centrifugation. Nevertheless, a protein component resisting all extraction procedures was found firmly associated to plant nuclear DNA. This component was responsible for the (125)I uptake when a DNA preparation had been labeled by the chloramine-T method.A residual oligodeoxynucleotide-oligopeptide complex was obtained after extensive digestions of the initial DNA-protein complex with proteases and nucleases. The stability of this complex to different chemical treatments suggested a phosphoester type of a linkage. The hydrolysis of this complex by phosphodiesterases indicated that the protein component was linked to plant chromosomal DNA through a phosphodiester bond formed by a hydroxyaminoacid and a 5'-end DNA phosphate. Two-dimensional tryptic peptide mapping of the proteins isolated from the two maize chromatins revealed a high degree of similarity to the corresponding proteins of animal origin. Its conservative structure suggests an important role for this protein component in the functioning of the eukaryotic genome.

Metabolic behaviour of a stable DNA-protein complex

1. A stable DNA-protein complex resisting all treatments dissociating noncovalently associated proteins was isolated from mouse erythroleukemia cells. 2. Two-dimensional tryptic peptide mapping of this DNA-linked protein component revealed a remarkable similarity to the maps of the corresponding proteins from other mammalian chromatins. 3. Labelling experiments showed that the protein component was metabolically stable.

Stable DNA-protein complexes in eukaryotic chromatin

Demembranized sperm and somatic nuclei of mammalian origin were extracted with high salt/urea/2-mercaptoethanol, treated with detergents and purified in CsCl density gradients to isolate DNA. Under these conditions a protein component still remained bound to DNA. This stable DNA-protein complex could be reduced to an oligodeoxynucleotide-peptide complex by extensive sequential digestions with DNase I and Pronase E. Chemical and enzymatic treatments of this complex indicated the presence of a phosphoester bond between DNA and a hydroxyamino acid. Two-dimensional tryptic peptide mapping revealed a remarkable similarity among the covalently linked protein components in all types of chromatin studied. These maps differed from the maps of mammalian topoisomerases I and II.

Tightly bound nonprotamine proteins from ram sperm nuclei studied by one- and two-dimensional peptide mapping

The tightly bound proteins of ram sperm nuclei (TBSP) have been recovered as a fraction co-sedimenting with DNA after high salt-urea deprotamination of the nuclei. TBSP were studied by two-dimensional (2D)-tryptic peptide mapping and by one-dimensional (1D)-partial proteolysis mapping. The 2D maps revealed a strong homology among the proteins, irrespective of substantial differences in their molecular masses. This homology was supported also by the 1D-mapping data. The 2D-tryptic maps of TBSP were compared to those of lamb liver lamins but no apparent similarity was detected. TBSP were found to react positively to a test for the presence of carbohydrate residues, suggesting that these proteins are glycoproteins as established earlier for the lamins. The 2D maps of several proteins of seminal plasma origin, used as a control, displayed completely different peptide profiles.

A study on the heterogeneity of histone H1 from dry maize embryos

Maize dry embryo cells have been chosen as model for the study of H1 histone complement of metabolically inactive plant chromatin. H1 has been fractionated into two distinct bands in acetic acid/urea gels. Analysis of each of these bands in SDS-containing gels has shown that maize embryo H1 is heterogeneous, consisting of at least six proteins. Cross-reactivity of maize H1 species with antibodies against mouse liver total H1 and against its individual variants indicates that they share common immunological determinants but differ substantially from each other when compared by peptide mapping. It is concluded that a couple of the plant H1 subfractions are related to animal H1A histone and that another one is related to H1B histone. The other three maize H1 variants are closely related to each other and they also share common immunological determinants with mouse H1A, and possibly with H1B. All maize H1 species slightly cross-react with antibodies against H1 degree, suggesting that no one of the plant subfractions could be characterized as H1 degree in particular. One of the proteins co-extracted and comigrating with H1 is most probably an embryo storage protein.

An H1-like protein from the sperm chromatin of Mytilus galloprovincialis

We have isolated and purified a sperm-specific protein (S3) from the mussel M. galloprovincialis. Antibodies against S3 were raised in rabbits and used for its immunological comparison to somatic histones. The results showed that S3 did not share common immunological determinants with H2b or any other core histone-contrary to the suggestion that it was an H2b-like protein (Ausio and Subirana, 1982). With H1 there was a crossreaction between S3 and anti-H1 as well as with H1 and anti-S3. Although similar to somatic H1, S3 is not identical with it. This fact makes S3 an interesting example of another protein of the H1-H5 type, present in a completely inactive chromatin.

Biochemical and ultrastructural study of the sperm chromatin from Mytilus galloprovincialis

Protein composition and ultrastructure of the mature spermatozoa of the mussel Mytilus galloprovincialis were studied upon gradual decondensation of the nuclei with increasing NaCl concentration. Three types of protein were found, associated with the sperm DNA: (1) the sperm-specific proteins S1, S2 and S3 (80% of the acid-soluble proteins); (2) the four core histones (20%); (3) three non-histone proteins tightly bound to DNA (about 4 micrograms protein per 100 micrograms DNA). The sperm-specific protein S3 was the first to dissociate at about 0.5 M NaCl and electron micrographs of spread nuclei indicated its participation in the final compaction of the nucleus. Hypotonically treated sperm nuclei revealed the presence of 21-25 nm large granules irregularly scattered along some of the DNA fibers. These granules correspond to the 'superbeads' of histone-containing chromatins. The tightly bound non-histone proteins were represented by a triplet in the range 60-80 kD. They formed 30-60 nm large annular bodies holding DNA fibers and resisting high salt-detergent treatment.

Trout sperm chromatin. II. Ultrastructural aspects after salt dissociation of proteins

The ultrastructural organization of the trout sperm nucleus was studied in ultrathin sections and spread preparations after partial decondensation of the nucleus with increasing NaCl concentrations. The obtained results suggest that the organization of the trout sperm chromatin is much more complex than a pure nucleoprotamine. Three types of complexes were observed. The first one results from the association of DNA with protamines. This complex appears as a fibrous network when partially decondensed nuclei are digested with DNase I indicating that at least a part of DNA remains protected by protamines and favours models accepting a colinear alignment of the latter on the DNA molecules. The second type of structures represent the DNA-protamine fibers compacted into dense clumps which appear as separate compaction units seen upon partial decondensation of the sperm nucleus. A third type are complexes of the ring-shaped granular bodies tightly associated with DNA and resisting high salt-urea and detergent treatment.

Trout sperm chromatin. I. Biochemical and immunological study of the protein composition

Compact sperm chromatin was obtained from mature trout sperm nuclei resistant to sonication and detergent treatments. 0.5 to 2 M NaCl caused a gradual decondensation of this chromatin and the dependence of the percentage of dissociated proteins on the salt concentration indicated cooperativity of the dissociation process. Urea alone was insufficient to decondense the nuclei. The only proteins dissociated from the sperm nuclei by NaCl alone or combined with urea were protamines. Besides protamines, tightly bound nonprotamine proteins resisting high salt-urea extraction were detected in the sperm nucleus. Part of them could be solubilized by 1% sodium dodecyl sulphate (SDS) and displayed the characteristics of the core histones: they were soluble in 0.25 N H2SO4, their electrophoretic mobilities were similar to those of trout liver core histones, and they shared common antigenic determinants with the latter. The rest of the tightly bound proteins resisted 1% SDS treatment and could be obtained after an extensive digestion of DNA with DNase I. These were nonhistone proteins similar in mobility to the protein triplet characteristic of the lamina-pore complex and an additional high molecular weight protein.

Nonprotamine nucleoprotein ultrastructures in mature ram sperm nuclei

Nuclei from mature ram spermatozoa were treated with a solution of 0.25 M 2-mercaptoethanol, 2 M NaCl, 4 to 8 M urea to dissociate protamines and some other proteins from DNA. The material remaining after such a treatment was spread for electron microscopy in the microcentrifugation chamber. Two types of structures were observed determined by proteins of nonprotamine nature. The first type was represented by protein bodies of an irregular ringlike shape to which DNA fibers were anchored to form a network. This structure determines the shape of the sperm head and may correspond to the nuclear skeleton described in somatic cells. The second type of structures were chromatin fibers containing beads of approximately nucleosomal size. These rough fibers were unevenly distributed in the nucleus and were much less frequent than the smooth fibers usually observed. Both types of structures were determined by unusually firmly bound proteins. They were resistant not only to the reduction of disulfide bonds and to high salt and urea concentrations but also to 2% sodium dodecysulfate and to 5 M guanidine chloride. These results show that apart from packing of DNA in a nucleoprotamine complex, two levels of DNA organization can be observed in the ram sperm nucleus: the first level consists of two kinds of DNA fibers (smooth and rough); in the second level of DNA is organized in domains fixed by a proteinous nuclear skeleton.