A general function of noncoding polynucleotide sequences. Mass binding of transconformational proteins

The Landscape of long noncoding RNA classification

Advances in the depth and quality of transcriptome sequencing have revealed many new classes of long noncoding RNAs (lncRNAs). lncRNA classification has mushroomed to accommodate these new findings, even though the real dimensions and complexity of the noncoding transcriptome remain unknown. Although evidence of functionality of specific lncRNAs continues to accumulate, conflicting, confusing, and overlapping terminology has fostered ambiguity and lack of clarity in the field in general. The lack of fundamental conceptual unambiguous classification framework results in a number of challenges in the annotation and interpretation of noncoding transcriptome data. It also might undermine integration of the new genomic methods and datasets in an effort to unravel the function of lncRNA. Here, we review existing lncRNA classifications, nomenclature, and terminology. Then, we describe the conceptual guidelines that have emerged for their classification and functional annotation based on expanding and more comprehensive use of large systems biology-based datasets.

Introns form compositional clusters in parallel with the compositional clusters of the coding sequences to which they pertain

This report deals with the study of compositional properties of human gene sequences evaluating similarities and differences among functionally distinct sectors of the gene independently of the reading frame. To retrieve the compositional information of DNA, we present a neighbor base dependent coding system in which the alphabet of 64 letters (DNA triplets) is compressed to an alphabet of 14 letters here termed triplet composons. The triplets containing the same set of distinct bases in whatever order and number form a triplet composon. The reading of the DNA sequence is performed starting at any letter of the initial triplet and then moving, triplet-to-triplet, until the end of the sequence. The readings were made in an overlapping way along the length of the sequences. The analysis of the compositional content in terms of the composon usage frequencies of the gene sequences shows that: (i) the compositional content of the sequences is far from that of random sequences, even in the case of non-protein coding sequences; (ii) coding sequences can be classified as components of compositional clusters; and (iii) intron sequences in a cluster have the same composon usage frequencies, even as their base composition differs notably from that of their home coding sequences. A comparison of the composon usage frequencies between human and mouse homologous genes indicated that two clusters found in humans do not have their counterpart in mouse whereas the others clusters are stable in both species with respect to their composon usage frequencies in both coding and noncoding sequences.

Combinatorial epigenetics, “junk DNA”, and the evolution of complex organisms

At certain evolutionary junctures, two or more mutations participating in the build-up of a new complex function may be required to become available simultaneously in the same individuals. How could this happen in higher organisms whose populations are small compared to those of microbes, and in which chances of combined nearly simultaneous highly specific favorable mutations are correspondingly low? The question can in principle be answered for regulatory evolution, one of the basic processes of evolutionary change. A combined resetting of transcription rates in several genes could occur in the same individual. It is proposed that, in eukaryotes, changes in epigenetic trends and epigenetically transforming encounters between alternative chromatin structures could arise frequently enough so as to render probable particular conjunctions of changed transcription rates. Such conjunctions could involve mutational changes with low specificity requirements in gene-associated regions of non-protein-coding sequences. The effects of such mutations, notably when they determine the use of histone variants and covalent modifications of histones, can be among those that migrate along chromatin. Changes in chromatin structure are often cellularly inheritable over at least a limited number of generations of cells, and of individuals when the germ line is involved. SINEs and LINEs, which have been considered "junk DNA", are among the repeat sequences that would appear liable to have teleregulatory effects on the function of a nearby promoter, through changes in their numbers and distribution. There may also be present preexisting unstably inheritable epigenetic trends leading to cellular variegation, trends endemic in a cell population based on DNA sequences previously established in the neighborhood. Either way, epigenetically conditioned teleregulatory trends may display only limited penetrance. The imposition at a distance of new chromatin structures with regulatory impact can occur in cis as well as in trans, and is examined as intrachromosomally spreading teleregulation and interchromosomal "gene kissing". The chances for two or more particular epigenetically determined regulatory trends to occur together in a cell are increased thanks to the proposed low specificity requirements for most of the pertinent sequence changes in intergenic and intronic DNA or in the distribution of middle repetitive sequences that have teleregulatory impact. Inheritable epigenetic changes ("epimutations") with effects at a distance would then perdure over the number of generations required for "assimilation" of the several regulatory novelties through the occurrence and selection, gene by gene, of specific classical mutations. These mutations would have effects similar to the epigenetic effects, yet would provide stability and penetrance. The described epigenetic/genetic partnership may well at times have opened the way toward certain complex new functions. Thus, the presence of "junk DNA", through co-determining the (higher or lower) order and the variants of chromatin structure with regulatory effects at a distance, might make an important contribution to the evolution of complex organisms.

Isolation and characterization of Mytilus edulis metallothionein genes

Metallothioneins (MTs) are crucial proteins in all organisms for the regulation of essential metals and the detoxification of heavy metals. Many studies have estimated MT levels in mussel tissues to detect marine metal pollution. In this study, we investigated the MT gene structures of the forms present in Mytilus edulis (blue mussel). One MT-10 (2413 bp) gene and one MT-20 (1906 bp) gene were obtained. These MT genes contain three exons and two long introns. The splicing signals for MT-10 and MT-20 were GTA(T/A)GT-(C/T)AG. The structural organization (length of intron, splicing signals, AT content) of MT-10 and MT-20 is compared with other MT genes.

Noncoding DNA, isochores and gene expression: nucleosome formation potential

The nucleosome formation potential of introns, intergenic spacers and exons of human genes is shown here to negatively correlate with among-tissues breadth of gene expression. The nucleosome formation potential is also found to negatively correlate with the GC content of genomic sequences; the slope of regression line is steeper in exons compared with noncoding DNA (introns and intergenic spacers). The correlation with GC content is independent of sequence length; in turn, the nucleosome formation potential of introns and intergenic spacers positively (albeit weakly) correlates with sequence length independently of GC content. These findings help explain the functional significance of the isochores (regions differing in GC content) in the human genome as a result of optimization of genomic structure for epigenetic complexity and support the notion that noncoding DNA is important for orderly chromatin condensation and chromatin-mediated suppression of tissue-specific genes.

Bendable genes of warm-blooded vertebrates

It is shown that in the genomes of warm-blooded vertebrates the elevation of genic GC-content is associated with an increase in the bendability of the DNA helix, which is both absolute and relative as compared with random sequences. This trend takes place both in exons and introns, being more pronounced in the latter. At the same time, the free energy of melting (delta G) of exons and introns increases only absolutely with elevation of GC-content, whereas it decreases as compared with random sequences (again, this trend is stronger in the introns). In genes of cold-blooded animals, plants, and unicellular organisms, these regularities are weaker and often not consistent. Generally, there is a negative correlation between bendability and melting energy at any fixed GC-content value. This effect is stronger in the introns. These findings suggest that GC-enrichment of genes in the homeotherm vertebrates can be caused by selection for increased bendability of DNA.

Within-intron correlation with base composition of adjacent exons in different genomes

Within-intron difference of correlation with base composition of the adjacent exons was studied in the genomes of 34 species. For this purpose, GC-percent was determined for segments of 50 bp in length taken at both intron margins and in the internal part of the intron. It was found that in certain genomes the coefficient of correlation with GC-percent of the adjacent exon was significantly higher for the intron margin than for the internal part of the intron (homeotherms, cereals). Only part of this difference can be explained by unequal probability of insertion of transposable elements. Those multicellular organisms which have a low or no within-intron difference in correlation with the adjacent exons (anamniotes, invertebrates, dicots) show a higher local compositional heterogeneity (a greater exon/intron contrast in the GC-content). These results are evidence against the mutational bias being a possible explanation for the compositional genome heterogeneity. Thus, in the genomes with a high global heterogeneity there seems to be a selective force for compliance of intron base composition with the adjacent exons. This force is stronger in those parts of the intron that are closer to exons. In addition, the previously found positive general correlation between the genome size and average intron length was confirmed with a much larger dataset. However, within separate phylogenetic groups this rule can be broken, as it occurs in the cereals (family Poaceae), where a negative correlation was found.

Protective nucleosome centering at splice sites as suggested by sequence-directed mapping of the nucleosomes

The characteristic AA(TT) sequence pattern of the nucleosome DNA derived earlier is used for prediction of nucleosome positions around splice junctions of eukaryotic genes. Two large datasets (2000 sequences each) were collected consisting of DNA segments with the exon/intron and intron/exon splice junctions, from various eukaryotic species. Positions of predicted nucleosomes near the junction sites were calculated. Those junctions which are found to belong to the nucleosomes, are located preferentially within a few base pairs from the midpoint of the nucleosome DNA. That is, obligatory GT- and AG-ends of the introns are more frequently located near the nucleosome dyad axis, within the best protected middle 10-15 base pairs of the nucleosome DNA. In addition, a tendency is observed for the strongest nucleosomes to form more often in the introns, in accordance with the hypothesis on the chromatin-organizing role of introns.

Junk DNA and sectorial gene repression

Transcriptional repression in eukaryotes often involves tens or hundreds of kilobase pairs, two to three orders of magnitude more than the bacterial operator/repressor model does. Classical repression, represented by this model, was maintained over the whole span of evolution under different guises, and consists of repressor factors interacting primarily with promoters and, in later evolution, also with enhancers. The use of much larger amounts of DNA in the other mode of repression, here called the sectorial mode ('superrepression'), results in the conceptual transfer of so-called junk DNA to the domain of functional DNA. This contribution to the solution of the c-value paradox involves perhaps 15% of genomic 'junk,' and encompasses the bulk of the introns, thought to fill a stabilizing role in sectorially repressed chromatin structures. In the case of developmental genes, such structures appear to be heterochromatoid in character. However, solid clues regarding general structural features of superrepressed terminal differentiation genes remain elusive. The competition among superrepressible DNA sectors for sectorially binding factors offers, in principle, a molecular mechanism for developmental switches. Position effect variegation may be considered an abnormal manifestation of normal processes that underly development and involve heterochromatoid sectorial repression, which is apparently required for local elimination or modulation of morphological features (morpholysis). Sectorial repression of genes participating either in development or in terminal differentiation is considered instrumental in establishing stable cell types, and provides a basis for the distinction between determination and cell type specification. The gamut of possible stable cell types may have been broadened by the appearance in evolution of heavy isochores. Additional types of relatively frequent GC-rich cis-acting DNA motifs may offer reiterated binding sites to factors endowed with a selective (though not individually strong) affinity for these motifs. The majority of sequence motifs thought to be used in superrepression need not be individually maintained by natural selection. It is re-emphasized that the dispensability of sequences is not an indicator of their nonfunctionality and that in many cases, along noncoding sequences, nucleotides tend to fill functions collectively, rather than individually.

Linguistic complexity of protein sequences as compared to texts of human languages

A notion and a measure of linguistic complexity introduced earlier (Trifonov, 1990) were originally used for analysis of nucleotide sequences. This measure was shown to reflect multiplicity of codes (messages) of different natures superimposed in the sequences. Unlike human language texts, genetic texts are 'read' by cellular mechanisms in several different ways, each time using a different selection of the characters of the same text while skipping others (Trifonov, 1989). Human texts are read in one way only, sequentially and involving all characters (one code). The conceptual significance and essence of the idea on the multiplicity of overlapping codes in genetic sequences, as opposed to human languages, is discussed. The linguistic complexity technique allows a calculation to be made of the structural complexity of any linear sequence of characters irrespective of whether the text is cognized or presently undeciphered. The texts (sequences) are compared exclusively from the point of view of their structural complexity with no reference to the meaning of the texts which is beyond the scope of this article. Results of such a comparison of protein sequences with various texts, written in English, Italian and Welsh are presented. The human texts are found to be structurally simpler than genetic (protein) texts, reflecting, apparently, a difference in the reading modes: single code versus many codes.

Tracking heterochromatin

The Second International Workshop on Drosophila Heterochromatin, held in Honolulu from January 4-7, 1995, brought together about 70 scientists from the US, Canada, Germany, Italy, Russia, and the Netherlands. After the first of these international meetings, five years ago, Mary Lou Pardue and Wolfgang Hennig, in these columns, commented on its proceedings, and on heterochromatin in general. Although the questions that they raised cannot yet be answered exhaustively, important and sometimes surprising new observations have been made, some previously tentative answers have been firmed up, and some theoretical views underwent significant shifts. We wish to reflect here a few of the data presented at the second workshop, and express some thoughts suggested to us by these recent findings.

Statistical analysis of vertebrate sequences reveals that long genes are scarce in GC-rich isochores

We compared the exon/intron organization of vertebrate genes belonging to different isochore classes, as predicted by their GC content at third codon position. Two main features have emerged from the analysis of sequences published in GenBank: (1) genes coding for long proteins (i.e., > or = 500 aa) are almost two times more frequent in GC-poor than in GC-rich isochores; (2) intervening sequences (= sum of introns) are on average three times longer in GC-poor than in GC-rich isochores. These patterns are observed among human, mouse, rat, cow, and even chicken genes and are therefore likely to be common to all warm-blooded vertebrates. Analysis of Xenopus sequences suggests that the same patterns exist in cold-blooded vertebrates. It could be argued that such results do not reflect the reality because sequence databases are not representative of entire genomes. However, analysis of biases in GenBank revealed that the observed discrepancies between GC-rich and GC-poor isochores are not artifactual, and are probably largely underestimated. We investigated the distribution of microsatellites and interspersed repeats in introns of human and mouse genes from different isochores. This analysis confirmed previous studies showing that L1 repeats are almost absent from GC-rich isochores. Microsatellites and SINES (Alu, B1, B2) are found at roughly equal frequencies in introns from all isochore classes. Globally, the presence of repeated sequences does not account for the increased intron length in GC-poor isochores. The relationships between gene structure and global genome organization and evolution are discussed.

Revisiting junk DNA

The distribution of functions within genomes of higher organisms relative to processes that lead to the spread of mutations in populations is examined in its general outlines. A number of points are enumerated that collectively put in question the concept of junk DNA: the plausible compatibility of DNA function with rapid substitution rates; the likelihood of superimposed functions along much of eukaryotic DNA; the potential for a merely conditional functionality in sequence repeats; the apparent adoption of macromolecular waste as a strategy for maintaining a function without selective grooming of individual sequence repeats that carry out the function; the likely requirement that any DNA sequence must be "polite" vis-'a-vis (compatible with) functional sequences in its genomic environment; the existence in germ-cell lineages of selective constraints that are not apparent in populations of individuals; and the fact that DNA techtonics - the appearance and disappearance of genomic DNA - are not incompatible with function. It is pointed out that the inverse correlation between functional constraints and rates of substitution cannot be claimed to be pillar of the neutral theory, because it is also predicted from a selectionist viewpoint. The dispensability of functional structures is brought into relation with the concept of reproductive sufficiency the survivability of genotypes in the absence of fitter alleles.

Splice junctions follow a 205-base ladder

Of all aspects of mRNA maturation the accuracy of intervening sequence excision and exon ligation is, perhaps, the most enigmatic. Attempts to identify the essential elements involved in this process have thus far not yielded any satisfactory answer as to what structural (sequence) features are prerequisite for the vital precision of this process. In our search for underlying structural orders we asked whether exons and introns had any positional preferences within a gene. This analysis led to the unexpected discovery that the DNA length is synchronized between successive 3' splicing sites as well as between successive 5' splicing sites, with a frame of approximately 205 base pairs. This observation reveals additional organization of genes in eukaryotes and, perhaps, links gene splicing with chromatin structure.

Polyploidy in differentiation and evolution

Somatic and generative (germ-line) polyploidy are more widely spread phenomena among living organisms than generally thought. The occurrence of polyploidization and related events in normal and pathological differentiation, their recognized main functions, as well as the structural specificities of polyploid nuclei are reviewed, and the relationship between ontogenetic and phylogenetic events is discussed. The mechanisms leading to the polyploid state, as well as other processes resulting in a genomic condition different from the diploid one (such as DNA under-replication, gene amplification, and chromatin elimination), are briefly sketched. The various changes in chromosomal DNA described are, in conclusion, seen as evidence supporting the paradigm of a "fluid" or dynamic organization of the eukaryotic genome, as being part of a cybernetic feedback regulation system of gene expression. A model is proposed that unifies the aspects of DNA variation, chromatin structure, and diversification in ontogenesis and phylogenesis.

A domain model for eukaryotic DNA organization: a molecular basis for cell differentiation and chromosome evolution

A model for eukaryotic chromatin organization is presented in which the basic structural and functional unit is the DNA domain. This simple model predicts that both chromosome replication and cell type-specific control of gene expression depend on a combination of stable and dynamic DNA-nuclear matrix interactions. The model suggests that in eukaryotes, DNA regulatory processes are controlled mainly by the intranuclear compartmentalization of the specific DNA sequences, and that control of gene expression involves multiple steps of specific DNA-nuclear matrix interactions. Predictions of the model are tested using available biochemical, molecular and cell biological data. In addition, the domain model is discussed as a simple molecular mechanism to explain cell differentiation in multi-cellular organisms and to explain the evolution of eukaryotic genomes consisting mainly of repetitive sequences and "junk" DNA.

Polite DNA: functional density and functional compatibility in genomes

Certain as yet poorly defined functions of DNA appear to involve collectively domain-sized sequences. It is proposed that most sequence segments within a domain may be either functionally superfluous or instrumental, depending on how many related sequences are present in the domain. When redundant and functionally dispensable, such DNA segments presumably still have to conform to compositional or sequence-motif patterns that characterize the domain. In its relations with neighboring sequences, such DNA is required to be "polite." Polite DNA is DNA that, without being crucially involved in function, is subject to constraints of conformity and, through its base composition, respects a function for which it is not required. This concept is developed by contrasting the distribution of specific and general functions over DNA with this distribution as found in proteins and by distinguishing functional compatibility from pivotal functionality. The sequence constraints to which heterochromatin as well as, apparently, long interspersed repetitive sequences are known to be subject seem to imply that DNA, even when it does not carry out a pivotal function, is indeed, at the very least, required to be polite.