Linear Order Of Genes Research Articles

Complete plastomes of 17 species of maples (Sapindaceae: Acer): comparative analyses and phylogenomic implications

The genus Acer, commonly known as maple, is a large plant lineage that comprises many economically and ecologically important species. However, because of low interspecific morphological variations and scarcity of molecular data, it is challenging to estimate the enigmatic phylogeny of Acer, limiting further utilization and conservation of maples. In this study, we generated complete plastomes of 17 species of maples representing 10 major sections of Acer and conducted comprehensively comparative genomic and phylogenomic analyses in Acer. The 17 plastomes are perfectly conserved in linear gene order and range narrowly in length of 155–157 kb with four constituent parts (LSC, SSC, IRa and IRb), whereas three IR types (amplum-, flabellatum- and yangbiense-like) are observed and the IR borders variation resulted in remarkable gene content divergence (132–134). In addition, there are apparently heterogeneous sequence divergences across the cp genome and 20 noncoding loci with fast evolutionary rates are further identified as potential molecular markers for subsequent studies on Acer. Furthermore, whole plastome sequences obtained the highest phylogenetic resolution and provided strong support for most backbone nodes of Acer among the seven analyzed data sets (LSC, SSC, IRs, coding, noncoding, 20-markers and whole-cp-genome), highlighting the significance of increasing informative sites in resolving intractable phylogenetic relationships of Acer. The section Negundo diverged firstly in Acer and close relationships among sects. Arguta, Ginnala, Macrantha, Oblonga, Pentaphylla, Platanoidea and Trifoliata were uncovered. Interspecific relationships within species-rich sects. Macrantha, Palmata and Platanoidea are also clearly resolved by plastid phylogenomics.

Abstract 4189: Cancer drugs on the fly: whole-animal chemical screening in Drosophila identifies unexpected role for EGFR in RAF intestinal stem cell tumors

Abstract A major challenge in cancer therapeutics is to identify drugs that target cancer stem cells. This presents a problem for traditional cell-based screening approaches because the complex cellular interactions underlying stem cell biology are difficult to recapitulate in vitro. Conversely, mice, which are arguably among the best animal models for cancer—are not amenable to high-throughput screening. However, many aspects of stem cell initiated tumorigenesis can be modeled in the fruit fly Drosophila melanogaster, which due to its small size is well suited for large-scale screens. The Drosophila intestine, in particular, presents a compelling model to study stem-cell derived intestinal tumors because Drosophila intestinal stem cells share many features with their mammalian counterparts including a propensity to form tumors in response to mutations in WNT, NOTCH, or EGFR signaling. We therefore developed an in vivo screening pipeline using adult Drosophila, to identify compounds that can suppress the growth of stem cell initiated tumors. In previous work we showed that ectopically expressing a constitutively active human c-RAF transgene, RAF(gof) in Drosophila intestinal stem cells results in fast growing tumors that are sensitive to several FDA approved chemotherapeutics. These results establish the clinical relevance of using Drosophila to model stem cell cancers. Here we present results from a screen of known bioactives, that reveal an unexpected role of the EGF receptor, EGFR, in RAF(gof) intestinal stem cell tumors. Based on the linear order of genes in the canonical RAF pathway—EGFR→RAS→RAF→MEK→ERK—we expected that drugs that inhibit genes acting downstream of RAF would score as hits in the screen, whereas genes that act upstream of RAF would not. Indeed, that same logic is applied when assessing whether to give human patients certain pathway specific drugs: patients with activating mutations in RAS or RAF are typically not given drugs that target the upstream EGFR. Consistent with our expectation, we found that drugs that inhibit genes downstream of RAF, effectively stopped Raf(gof) tumor growth. However, to our surprise, we also found that inhibitors of EGFR blocked the growth of RAF(gof) tumors. Using RNAi against EGFR, we genetically validated the chemical results. Our preliminary evidence suggests that EGFR is required in a parallel pathway, upstream of AKT. These findings are significant because they suggest that in some cases, human patients with RAF activated tumors may benefit from drug therapies that target EGFR. Importantly, our results demonstrate that taking an unbiased approach in assessing which drug therapies to apply to a given cancer, may yield unexpectedly good results. Citation Format: Michele Markstein, Hannah Dayton, Samantha Dettorre. Cancer drugs on the fly: whole-animal chemical screening in Drosophila identifies unexpected role for EGFR in RAF intestinal stem cell tumors. [abstract]. In: Proceedings of the 107th Annual Meeting of the American Association for Cancer Research; 2016 Apr 16-20; New Orleans, LA. Philadelphia (PA): AACR; Cancer Res 2016;76(14 Suppl):Abstract nr 4189.

Topologically associated domains enriched for lineage-specific genes reveal expression-dependent nuclear topologies during myogenesis

The linear distribution of genes across chromosomes and the spatial localization of genes within the nucleus are related to their transcriptional regulation. The mechanistic consequences of linear gene order, and how it may relate to the functional output of genome organization, remain to be fully resolved, however. Here we tested the relationship between linear and 3D organization of gene regulation during myogenesis. Our analysis has identified a subset of topologically associated domains (TADs) that are significantly enriched for muscle-specific genes. These lineage-enriched TADs demonstrate an expression-dependent pattern of nuclear organization that influences the positioning of adjacent nonenriched TADs. Therefore, lineage-enriched TADs inform cell-specific genome organization during myogenesis. The reduction of allelic spatial distance of one of these domains, which contains Myogenin, correlates with reduced transcriptional variability, identifying a potential role for lineage-specific nuclear topology. Using a fusion-based strategy to decouple mitosis and myotube formation, we demonstrate that the cell-specific topology of syncytial nuclei is dependent on cell division. We propose that the effects of linear and spatial organization of gene loci on gene regulation are linked through TAD architecture, and that mitosis is critical for establishing nuclear topologies during cellular differentiation.

A synteny-based draft genome sequence of the forage grass Lolium perenne.

Here we report the draft genome sequence of perennial ryegrass (Lolium perenne), an economically important forage and turf grass species that is widely cultivated in temperate regions worldwide. It is classified along with wheat, barley, oats and Brachypodium distachyon in the Pooideae sub-family of the grass family (Poaceae). Transcriptome data was used to identify 28,455 gene models, and we utilized macro-co-linearity between perennial ryegrass and barley, and synteny within the grass family, to establish a synteny-based linear gene order. The gametophytic self-incompatibility mechanism enables the pistil of a plant to reject self-pollen and therefore promote out-crossing. We have used the sequence assembly to characterize transcriptional changes in the stigma during pollination with both compatible and incompatible pollen. Characterization of the pollen transcriptome identified homologs to pollen allergens from a range of species, many of which were expressed to very high levels in mature pollen grains, and are potentially involved in the self-incompatibility mechanism. The genome sequence provides a valuable resource for future breeding efforts based on genomic prediction, and will accelerate the development of new varieties for more productive grasslands.

Reticulate Evolution of the Rye Genome

Rye (Secale cereale) is closely related to wheat (Triticum aestivum) and barley (Hordeum vulgare). Due to its large genome (~8 Gb) and its regional importance, genome analysis of rye has lagged behind other cereals. Here, we established a virtual linear gene order model (genome zipper) comprising 22,426 or 72% of the detected set of 31,008 rye genes. This was achieved by high-throughput transcript mapping, chromosome survey sequencing, and integration of conserved synteny information of three sequenced model grass genomes (Brachypodium distachyon, rice [Oryza sativa], and sorghum [Sorghum bicolor]). This enabled a genome-wide high-density comparative analysis of rye/barley/model grass genome synteny. Seventeen conserved syntenic linkage blocks making up the rye and barley genomes were defined in comparison to model grass genomes. Six major translocations shaped the modern rye genome in comparison to a putative Triticeae ancestral genome. Strikingly dissimilar conserved syntenic gene content, gene sequence diversity signatures, and phylogenetic networks were found for individual rye syntenic blocks. This indicates that introgressive hybridizations (diploid or polyploidy hybrid speciation) and/or a series of whole-genome or chromosome duplications played a role in rye speciation and genome evolution.

Comparative linkage mapping of the Grey coat colour gene in horses1

Grey horses are born coloured, turn progressively grey and often develop melanomas late in life. Grey shows an autosomal dominant inheritance and the locus has previously been mapped to horse chromosome 25 (ECA25), around the TXN gene. We have now developed eight new single nucleotide polymorphisms (SNPs) associated with genes on ECA25 using information on the linear order of genes on human chromosome 9q, as well as the human and mouse coding sequences. These SNPs were mapped in relation to the Grey locus using more than 300 progeny from matings between two Swedish Warmblood grey stallions and non-grey mares. Grey was firmly assigned to an interval with flanking markers NANS and ABCA1. This corresponds to a region of approximately 6.9 Mb on human chromosome 9q. Furthermore, no recombination was observed between Grey, TGFBR1 and TMEFF1, the last two being 1.4 Mb apart in human. There are no obvious candidate genes in this region and none of the genes has been associated with pigmentation disorders or melanoma development, suggesting that the grey phenotype is caused by a mutation in a novel gene.

Spatial arrangement and macrodomain organization of bacterial chromosomes

Recent developments in fluorescence microscopy have shown that bacterial chromosomes have a defined spatial arrangement that preserves the linear order of genes on the genetic map. These approaches also revealed that large portions of the chromosome in Escherichia coli or Bacillus subtilis are concentrated in the same cellular space, suggesting an organization as large regions defined as macrodomains. In E. coli, two macrodomains of 1 Mb containing the replication origin (Ori) and the replication terminus (Ter) have been shown to relocalize at specific steps of the cell cycle. A genetic analysis of the collision probability between distant DNA sites in E. coli has confirmed the presence of macrodomains by revealing the existence of large regions that do not collide with each other. Two macrodomains defined by the genetic approach coincide with the Ori and Ter macrodomains, and two new macrodomains flanking the Ter macrodomain have been identified. Altogether, these results indicate that the E. coli chromosome has a ring organization with four structured and two less-structured regions. Implications for chromosome dynamics during the cell cycle and future prospects for the characterization and understanding of macrodomain organization are discussed.

Retention of Latent Centromeres in the Mammalian Genome

The centromere is a cytologically defined entity that possesses a conserved and restricted function in the cell: it is the site of kinetochore assembly and spindle attachment. Despite its conserved function, the centromere is a highly mutable portion of the chromosome, carrying little sequence conservation across taxa. This divergence has made studying the movement of a centromere, either within a single karyotype or between species, a challenging endeavor. Several hypotheses have been proposed to explain the permutability of centromere location within a chromosome. This permutability is termed "centromere repositioning" when described in an evolutionary context and "neocentromerization" when abnormalities within an individual karyotype are considered. Both are characterized by a shift in location of the functional centromere within a chromosome without a concomitant change in linear gene order. Evolutionary studies across lineages clearly indicate that centromere repositioning is not a rare event in karyotypic evolution and must be considered when examining the evolution of chromosome structure and syntenic order. This paper examines the theories proposed to explain centromere repositioning in mammals. These theories are interpreted in light of evidence gained in human studies and in our presented data from the marsupial model species Macropus eugenii, the tammar wallaby.

Separation of parental genomes in human blood and bone marrow cells and its implications

The linear order of genes is apparently interrupted at chromosomal ends. Our observations on human blood and bone marrow cells indicate that the chromosomes of each of the two parental sets maintain coherence, perhaps in tandem, forming a ring. Two such rings in a diploid cell join building a larger ring, which folds up to form the interphase nucleus. The linear order of genes thus extends beyond the chromosomal ends. These observations become especially significant when seen in the light of cell biologic findings on interaction of chromosomes or chromatin and centrioles in different cell cycle phases, in polymorphonuclear cells and during the zygotic developments. They may explain how the genomic order and the sequential continuity of the genes are maintained and why such order remains often cryptic.

Chromosome arrangement within a bacterium.

The contour length of the circular chromosome of bacteria is greater than a millimeter but must be accommodated within a cell that is only a few micrometers in length. Bacteria do not have nucleosomes and little is known about the arrangement of the chromosome inside a prokaryotic cell. We have investigated the arrangement of chromosomal DNA within the bacterium Bacillus subtilis by using fluorescence microscopy to visualize two sites on the chromosome simultaneously in the same cell. Indirect immunofluorescence with antibodies against the chromosome partition protein Spo0J were used to visualize the replication origin region of the chromosome. Green fluorescent protein fused to the lactose operon repressor Lacl was used to decorate tandem copies of the lactose operon operator lacO. A cassette of tandem operators was separately inserted into the chromosome near the origin (359 degrees), near the replication terminus (181 degrees), or at two points in between (90 degrees and 270 degrees). The results show that the layout of the chromosome is dynamic but is principally arranged with the origin and terminus maximally apart and the quarter points of the chromosome in between. The use of cytological methods to visualize two chromosomal sites in the same cell has provided a glimpse of the arrangement of a bacterial chromosome. We conclude that, to a first approximation, the folding of the bacterial chromosome is consistent with, and may preserve, the linear order of genes on the DNA.

Heterochromatic trans-inactivation of Drosophila white transgenes.

Position effect variegation of most Drosophila melanogaster genes, including the white eye pigment gene is recessive. We find that this is not always the case for white transgenes. Three examples are described in which a lesion causing variegation is capable of silencing the white transgene on the paired homologue (trans-inactivation). These examples include two different transgene constructs inserted at three distinct genomic locations. The lesions that cause variegation of white minimally disrupt the linear order of genes on the chromosomes, permitting close homologous pairing. At one of these sites, trans-inactivation has also been extended to include a vital gene in the vicinity of the white transgene insertion. These findings suggest that many Drosophila genes, in many positions in the genome, can sense the heterochromatic state of a paired homologue.

A genetic map of bovine chromosome 7 with an interspecific hybrid backcross panel.

A genetic linkage map of bovine Chromosome (Chr) 7 was generated with a Bos taurus x Bos gaurus interspecific hybrid backcross panel. This study included six previously mapped microsatellites and five unmapped expressed genes that were identified by PCR-based restriction fragment length variants (RFLVs). The gene order (from centromere to telomere) and the map distances (in centimorgans) are as follows: cen-BM2607-11.2-LDLR-3.6-AMH,CSF2-11. 2-BP41-19-BM6117-19-SPARC-14.4-FGFA-15.5-BM18 53-11.2-RASA-18. 8-ILSTS006. Previous comparative synteny mapping demonstrated that bovine Chr 7 shares homologous regions with both HSA5q and HSA19p. A break or fusion between AMH and CSF2 in an ancestral chromosome is suggested to account for the current arrangement of these homologous segments in the human and bovine genomes. In this study, we demonstrate that a short proximal portion of BTA7 is homologous with HSA19p, while a larger distal portion of BTA7 is homologous with human Chr 5q. The orientation of these conserved human segments on BTA7 is also demonstrated. Our data show that the linear order of genes has not been conserved within the homologous region of HSA5 and BTA7, and one chromosomal translocation or inversion is proposed to account for this difference.

Chromosomal evolution from the perspective of the bovine gene map

Abstract The bovine genome map has grown from a simple synteny map in 1990 to a chromosomal anchored synteny and linkage map today. The current map is a prototypic artiodactyl map which serves as a useful tool for the study of chromosomal evolution. Syntenic conservation is more pronounced in the cattle and human maps than in either of these relative to mouse . The recent development of the bovine linkage map, however, suggests that linear order of genes within conserved syntenic groups is often disparate. The cattle, human, and mouse maps can be used to delineate pathways of chromosomal evolution from a common mammalian ancestor. Conservation of gene order cannot be assumed from conservation of synteny, however, and the establishment of order of comparative anchor loci is essential for future development of cattle and other mammalian maps used for comparative purposes.

Homeogenes in mammalian development and the evolution of the cranium and central nervous system

Homeobox-containing genes, the homeogenes, are transcriptional regulators conserved in numerous animal groups. In the fruit fly they specify the identity of certain spatial units of development. We present a somewhat subjective summary of the advance triggered in vertebrate developmental biology by the discovery of the homeobox. Emphasis is placed on one group, the Antp (Antennapedia)-like homeogenes. Antp-like homoeogenes are expressed in overlapping longitudinal areas of the neuroectoderm and mesoderm. The genomic organization of these genes is most uniquely connected with their expression. They are organized into unlinked clusters of 8-10 loci. The linear order of genes within the clusters is highly conserved both among clusters within a species and among clusters of distant species. Expression of these genes along the longitudinal body axis uniformly follows a 5'-posterior-3'-anterior rule. Their anterior border of expression stops abruptly at the hindbrain. A hypothesis is proposed, which suggests that much of the mid- and hindbrain, as well as the craniofacial structures, are newly acquired in the evolution of vertebrates, and do not utilize the more ancient Antp-like homeogenes. We assume that these organs have a different group or groups of spatially specific transcriptional regulators.

Anterior boundaries of Hox gene expression in mesoderm-derived structures correlate with the linear gene order along the chromosome

Abstract The developmental expression patterns of four genes, Hox 1.1., Hox 1.2, Hox 1.3 and Hox 3.1, were examined by in situ hybridization to serial embryonic sections. The three genes of the Hox 1 cluster, used in this study, map to adjacent positions along chromosome 6, whereas the Hox 3.1 gene maps to the Hox 3 cluster on chromosome 15. The anterior expression limits in segmented mesoderm varied among the four genes examined. Interestingly, a linear correlation exists between the position of the gene along the chromosome and the extent of anterior expression. Genes that are expressed more posterior are also more restricted in their expression in other mesoderm-derived tissues. The order of expression anterior to posterior was determined as: Hox 1.3, Hox 1.2, Hox 1.1 and Hox 3.1. Similarly, genes of the Drosophila Antennapedia and Bithorax complex specifying segment identity also exhibit anterior expression boundaries that correlate with gene position. The data suggest that Hox genes may specify positional information along the anterior-posterior axis during the formation of the body plan.

Gene organization of murine homeobox-containing gene clusters

A chromosomal walk which links a previously described and a new homeobox to the Hox-2 murine homeobox gene cluster is described, and the nucleotide sequence of the new homeobox is presented. With these new data the Hox-2 gene cluster contains seven loci on an approximately 100-kb-long physical map. Homology comparisons reveal that a significant number of vertebrate homeoboxes are in fact analogous. We also find that the linear order of homologous homeoboxes is similar in the two murine gene complexes, Hox-1 and Hox-2, and among the human homeobox loci on chromosome 17. Conservation of the homeo-domain and the linear gene order of homeobox-containing genes in vertebrates is discussed in light of the interactions and the anteroposterior linear order of homeotic loci in insects.

A physical map of the viral genome for infectious pancreatic necrosis virus Sp: analysis of cell-free translation products derived from viral cDNA clones.

The two segments of double-stranded RNA from infectious pancreatic necrosis virus Sp were cloned into the plasmid vector pUC8. Two sets of overlapping clones were identified by restriction enzyme and Southern blot analyses. Each of these sets was shown by Northern blot analysis to be exclusively related to either segment A or B of the genomic RNA. The entire lengths of the cloned segments were estimated to be 2.9 and 2.6 kilobases, respectively. Sequences from the two segments of viral cDNA were subcloned into the bacteriophage T7 RNA polymerase vectors pT71 and pT72. The activity of the single-stranded RNAs transcribed from these subclones in a rabbit reticulocyte lysate translation system provided information on the polarity of and the protein products coded for by each subclone. The four proteins encoded by the genome of infectious pancreatic necrosis virus were identified among the translation products of the individual cloned segments by immunoprecipitation and sodium dodecyl sulfate-polyacrylamide gel electrophoresis. By constructing plasmids containing deletions in the sequences from either the 5' or 3' end of segment A, we were able to construct a physical map for the larger segment of double-stranded RNA. The proteins derived from these plasmids indicated that the linear gene order for viral proteins encoded in segment A is beta, gamma 2, and gamma 1.

A cluster of five genes specifying the aerobactin iron uptake system of plasmid ColV-K30.

The genetic determinants for the aerobactin iron uptake system of plasmid ColV-K30, cloned as recombinant plasmid pABN1, were mapped by insertional inactivation using Tn1000 (gamma delta). Sites of insertion resulting in loss of aerobactin biosynthesis spanned ca. 5.5 kilobase pairs of cloned ColV-K30 DNA contiguous with a 2-kilobase-pair region in which transposon insertion resulted in loss of the outer membrane ferric-aerobactin receptor protein. Translation products of plasmid pABN1, and of subclones specifying siderophore biosynthesis alone or receptor activity alone, were analyzed by using the maxicell and minicell expression system. Four polypeptides (Mr = 62,000, 35,000, 45,000, and 50,000) are required for biosynthesis of aerobactin. A fifth product (Mr = 74,000) of plasmid pABN1 represents the outer membrane receptor protein. The linear order of genes for these polypeptides was determined by comparing translation products of a series of smaller derivative plasmids and of a number of mutant plasmids carrying Tn1000 at known locations.

Fine structure of chromosomes.

Fine structure of chromosomes.

The Human Body

The Human Body Charles A. Kofoid CopyRight https://doi.org/10.2105/AJPH.18.4.529 Published Online: August 29, 2011