HOX Pro: a specialized database for clusters and networks of homeobox genes

It is now clear that the homeobox motif is well conserved across metazoan phyla. It has been established experimentally that a subset of genes containing this motif plays key roles in the orchestration of gene expression during development. Auto- and cross-regulatory functional interactions join homeobox genes into genetic networks. We have developed a specialized database HOX-Pro in order to arrange all available data on structure, function, phylogeny and evolution of Hox genes, Hox clusters and Hox networks. Its primary location is http://www.iephb.nw.ru/hoxpro. The database is also mirrored at http://www.mssm.edu/molbio/hoxpro. The HOX-Pro database is aimed at: (i) analysis and classification of regulatory and coding regions in diverse homeobox and related genes; (ii) comparative analysis of organization of 'Hox-based' genetic networks in the sea urchin Strongylocentrotus purpuratus, the fruit fly Drosophila melanogaster and the mouse Mus musculus; and (iii) analysis of phylogeny and evolution of homeobox genes and clusters.     

HOX genes in embryo- and phylogenesis

This review is concerned with the structure and function of the protein products and homeobox genes of the HOX complex. We also trace a relationship between morphological evolution and the evolution of the homeotic complex.     

Homology in coding and non-coding DNA sequences: a parsimony perspective

Putative synapomorphy assessment (primary homology assessment) is distinct for DNA strings having a codon structure (hereafter, coding DNA) versus those lacking it (hereafter, non-coding DNA). The first requires the identification of a reading frame and of usually few in-frame insertions and deletions. In non-coding DNA, where length variation is much more common, putative synapomorphy assessment is considerably less straightforward and highly depends on the alignment method. Appreciating the existence of evolutionary constraints, alignments that consider patterns associated with specific putative evolutionary events are favored. Once the sequences have been aligned, the postulated putative evolutionary events need to be coded as an additional step. In order for the alignments and the alignment coding to be falsifiable, they should be carried out using justified and explicitly formulated criteria. Alternative coding methods for the most common patterns present in alignments of non-coding DNA are discussed here. Simpler putative synapomorphy assessment will not always correlate to more reliable phylogenetic information because simplicity does not necessarily correlate to the degree of homoplasy. The use of non-coding DNA can result in more laborious coding, but at the same time in more corroborated hypotheses, mirroring their accuracy for phylogenetic inference.     

Sex determining genes and sexual differentiation in a marsupial.

The role of genes in the differentiation of the testis and ovary has been extensively studied in the human and the mouse. Despite over a decade of investigations, the precise roles of genes and their interactions in the pathway of sex determination are still unclear. We have chosen to take a comparative look at sex determination and differentiation to gain insights into the evolution and the conserved functions of these genes. To achieve this, we have examined a wide variety of eutherian sex determining genes in a marsupial, the tammar wallaby, to determine which genes have a conserved and fundamental mammalian sex determining role. These investigations have provided many unique insights. Here, we review the recent molecular and endocrine investigations into sexual development in marsupials, and highlight how these studies have shed light on the roles of genes and hormones in mammalian sex determination and differentiation.     

piRNA-like RNAs in the marsupial Monodelphis domestica identify transcription clusters and likely marsupial transposon targets

PIWI-interacting RNAs (piRNAs) are a recently discovered class of small noncoding RNAs that have been detected in human, mouse, rat, zebrafish, and Drosophila genomes. We have utilized a size-directed small-RNA cloning procedure to clone and map more than 300 candidate piRNA-like small RNAs in the genome of the marsupial species Monodelphis domestica. Our results are consistent with those from other species in that the piRNA-like candidate sequences range in size from 28 to 31 nucleotides, show a pronounced preference for uridine at the 5′ end, are transcribed from a few large clusters, appear to target transposons, and display virtually no sequence conservation.     

Correlations between the coding and non-coding regions in DNA.

In this paper various aspects of codon usage and k-tuple correlations in the DNA are compared. It is shown that the correlation structures of the coding and the non-coding regions are very similar and that codon usage is reasonably specific for large groups of organisms. These results suggest that the origin of codon usage is related to the origin and structure of the DNA.     

Evolution of the shell coat and yolk in amniotes: a marsupial perspective

Two characters distinguish oogenesis and early development in marsupials and monotremes: (1) the shell coat that persists from the zygote to somite stages in marsupials or until hatching in monotremes; and (2) the numerous, apparently almost empty vesicles that appear in primary oocytes, increase during oogenesis in marsupials and monotremes before being shed into the cleavage cavity and are preferentially distributed to the trophoblast lineage in marsupials, but comprise the latebra in monotremes. Analysis of these unusual characters used Southern analysis of genomic DNA dot blots and histology and electron microscopy. The evidence suggests that the marsupial shell coat protein, CP4, was probably characteristic of the egg of the mammalian ancestor. Further, the vesicles, present in marsupials during oogensis and cleavage and in eutherian mammals during blastocyst formation are the residual elements of white yolk present in the larger yolky eggs of monotemes and sauropsids. By comparison with the function of the vesicle components in marsupials, it is suggested that one role for the white yolk in monotremes and the sauropsids is to provide extracellular matrix (ECM), especially hyaluronan containing stabilizing proteins, for epithelial construction. Thus, as oviparity was replaced by viviparity, egg size was reduced, the germinal cytoplasm was retained, and yellow yolk was markedly reduced or lost in marsupials and eutherians. The white yolk was retained in monotremes and marsupials where blastocyst epithelial construction requires ECM support, and its appearance is heterochronously shifted to after compaction, when blastocyst formation and expansion occurs, in eutherian mammals.     

Distributions of dimeric tandem repeats in non-coding and coding DNA sequences

We study the length distribution functions for the 16 possible distinct dimeric tandem repeats in DNA sequences of diverse taxonomic partitions of GenBank (known human and mouse genomes, and complete genomes of Caenorhabditis elegans and yeast). For coding DNA, we find that all 16 distribution functions are exponential. For non-coding DNA, the distribution functions for most of the dimeric repeats have surprisingly long tails, that fit a power-law function. We hypothesize that: (i) the exponential distributions of dimeric repeats in protein coding sequences indicate strong evolutionary pressure against tandem repeat expansion in coding DNA sequences; and (ii) long tails in the distributions of dimers in non-coding DNA may be a result of various mutational mechanisms. These long, non-exponential tails in the distribution of dimeric repeats in non-coding DNA are hypothesized to be due to the higher tolerance of non-coding DNA to mutations. By comparing genomes of various phylogenetic types of organisms, we find that the shapes of the distributions are not universal, but rather depend on the specific class of species and the type of a dimer.     

Isolation and characterization of marsupial IL5 genes

The genomic nucleotide sequence and chromosomal position of the interleukin 5 (IL5) gene has been described for the model marsupial Macropus eugenii (tammar wallaby). A 272 base pair genomic IL5 polymerase chain reaction (PCR) product spanning exon 3, intron 3, and exon 4 was generated using stripe-faced dunnart (Sminthopsis macroura) DNA. This PCR product was used to isolate a genomic lambda clone containing the complete IL5 gene from a tammar wallaby EMBL3 lambda library. Sequencing revealed that the tammar wallaby IL5 gene consists of four exons separated by three introns. Comparison of the marsupial coding sequence with coding sequences from eutherian species revealed 61 to 69% identity at the nucleotide level and 48 to 63% identity at the amino acid (aa) level. A polymorphic complex compound microsatellite was identified within intron 2 of the tammar wallaby IL5 gene. This microsatellite was also found in other marsupials including the swamp wallaby, tree kangaroo, stripe-faced dunnart, South American opossum, brushtail possum, and koala. Fluorescence in situ hybridization using DNA from the IL5 clone on tammar wallaby chromosomes indicated that the IL5 gene is located on Chromosome 1.     

The non-coding genome: a universe in expansion for fine-tuning the coding world

A report on the EMBO/EMBL Symposium on The Non-Coding Genome, held in Heidelberg, Germany, 9-12 October, 2013.We share 98% coding genome similarity with mouse and have about the same number of protein coding genes as worms, yet the differences in complexity are obvious. Where is this complexity encoded? A huge change in our understanding of genome evolution and regulation of gene expression arrived with the development of high-throughput sequencing technologies. It turns out that most of our genome is transcribed, but only a small percentage has coding information imbedded. The rest of the genome, the non-coding genome, mistakenly labeled as ‘junk DNA’, is where evolutionary complexity resides. In The Non-Coding Genome meeting, several research studies delved deeper into the importance of the non-coding genome, identifying novel classes of non-coding RNAs (ncRNAs) and novel regulatory functions, and expanding our knowledge about this new world, opening more exciting questions to study and answer.     

A rapid method for illustrating features in both coding and non-coding regions of a genome

A bitmap display of the Fourier spectra has been developed which allows convenient whole chromosome scanning for genes and other features. Use of a limited sliding window gives rapid visualization and localization of coding regions in the chromosomes, as well as non-coding features such as repetitive DNA. The method works particularly well on organisms with a skewed base composition, to provide an overview of genomic features.     

Identification of coding and non-coding sequences using local Holder exponent formalism

MOTIVATION: Accurate prediction of genes in genomes has always been a challenging task for bioinformaticians and computational biologists. The discovery of existence of distinct scaling relations in coding and non-coding sequences has led to new perspectives in the understanding of the DNA sequences. This has motivated us to exploit the differences in the local singularity distributions for characterization and classification of coding and non-coding sequences. RESULTS: The local singularity density distribution in the coding and non-coding sequences of four genomes was first estimated using the wavelet transform modulus maxima methodology. Support vector machines classifier was then trained with the extracted features. The trained classifier is able to provide an average test accuracy of 97.7%. The local singularity features in a DNA sequence can be exploited for successful identification of coding and non-coding sequences. CONTACT: Available on request from bd.kulkarni@ncl.res.in.