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Preliminary radiation hybrid map for river buffalo chromosome 6 and comparison to bovine chromosome 3

Stafuzza, N. B.; Ianella, P.; Miziara, M. N.; Agarwala, R.; Schaffer, A. A.; Riggs, P. K.; Womack, J. E.; Amaral, M. E. J.
Fonte: Blackwell Publishing Publicador: Blackwell Publishing
Tipo: Artigo de Revista Científica Formato: 406-409
ENG
Relevância na Pesquisa
65.9%
We present the first radiation hybrid (RH) map of river buffalo (Bubalus bubalis) chromosome 6 (BBU6) developed with a recently constructed river buffalo whole-genome RH panel (BBURH5000). The preliminary map contains 33 cattle-derived markers, including 12 microsatellites, 19 coding genes and two ESTs, distributed across two linkage groups. Retention frequencies for markers ranged from 14.4% to 40.0%. Most of the marker orders within the linkage groups on BBU6 were consistent with the cattle genome sequence and RH maps. This preliminary RH map is the starting point for comparing gene order between river buffalo and cattle, presenting an opportunity for the examination of micro-rearrangements of these chromosomes. Also, resources for positional candidate cloning in river buffalo are enhanced.

Senescence of immortal human fibroblasts by the introduction of normal human chromosome 6.

Sandhu, A K; Hubbard, K; Kaur, G P; Jha, K K; Ozer, H L; Athwal, R S
Fonte: PubMed Publicador: PubMed
Tipo: Artigo de Revista Científica
Publicado em 07/06/1994 EN
Relevância na Pesquisa
46.08%
In these studies we show that introduction of a normal human chromosome 6 or 6q can suppress the immortal phenotype of simian virus 40-transformed human fibroblasts (SV/HF). Normal human fibroblasts have a limited life span in culture. Immortal clones of SV/HF displayed nonrandom rearrangements in chromosome 6. Single human chromosomes present in mouse/human monochromosomal hybrids were introduced into SV/HF via microcell fusion and maintained by selection for a dominant selectable marker gpt, previously integrated into the human chromosome. Clones of SV/HF cells bearing chromosome 6 displayed limited potential for cell division and morphological characteristics of senescent cells. The loss of chromosome 6 from the suppressed clones correlated with the reappearance of immortal clones. Introduced chromosome 6 in the senescing cells was distinguished from those of parental cells by the analysis for DNA sequences specific for the donor chromosome. Our results further show that suppression of immortal phenotype in SV/HF is specific to chromosome 6. Introduction of individual human chromosomes 2, 8, or 19 did not impart cellular senescence in SV/HF. In addition, introduction of chromosome 6 into human glioblastoma cells did not lead to senescence. Based upon these results we propose that at least one of the genes (SEN6) for cellular senescence in human fibroblasts is present on the long arm of chromosome 6.

A High-Resolution HAPPY Map of Dictyostelium discoideum Chromosome 6

Konfortov, Bernard A.; Cohen, Helen M.; Bankier, Alan T.; Dear, Paul H.
Fonte: Cold Spring Harbor Laboratory Press Publicador: Cold Spring Harbor Laboratory Press
Tipo: Artigo de Revista Científica
Publicado em /11/2000 EN
Relevância na Pesquisa
46.03%
We have made a high-resolution HAPPY map of chromosome 6 of Dictyostelium discoideum consisting of 300 sequence-tagged sites with an average spacing of 14 kb along the ∼4-Mb chromosome. The majority of the marker sequences were derived from randomly chosen clones from four different chromosome 6–enriched plasmid libraries or from subclones of YACs previously mapped to chromosome 6. The map appears to span the entire chromosome, although marker density is greater in some regions than in others and is lowest within the telomeric region. Our map largely supports previous gene-based maps of this chromosome but reveals a number of errors in the physical map. In addition, we find that a high proportion of the plasmid sequences derived from gel-enriched chromosome 6 (and that form the basis of a chromosome-specific sequencing project) originates from other chromosomes.

Construction of a map of the short arm of human chromosome 6.

Leach, R; DeMars, R; Hasstedt, S; White, R
Fonte: PubMed Publicador: PubMed
Tipo: Artigo de Revista Científica
Publicado em /06/1986 EN
Relevância na Pesquisa
45.97%
Four DNA sequences that reveal restriction fragment length polymorphisms (RFLPs) on the short arm of human chromosome 6 have been identified. Two of these sequences were isolated from recombinant DNA libraries enriched for DNA from human chromosome 6, one was isolated as a subclone from a human DNA segment having homology to an HLA class I sequence, and one was isolated by virtue of its homology to part of the insulin gene. Genetic linkage was determined among these four polymorphic sequences and several genes known to be on chromosome 6: glyoxylase I (GLO1), HLA-DR alpha, HLA-DQ alpha, and HLA-B. Additionally, two of the four RFLPs were regionally localized by using 53 deletion cell lines that had been typed for HLA-A, -B, and -DR, and for glyoxylase I. A genetic map of the short arm of chromosome 6 has been constructed on the basis of linkage studies with the eight markers. The map spans a minimum of 60 recombinational units and will be useful in the study of HLA-associated diseases.

Two nonallelic tRNAiMet genes are located in the p23 leads to q12 region of human chromosome 6.

Naylor, S L; Sakaguchi, A Y; Shows, T B; Grzeschik, K H; Holmes, M; Zasloff, M
Fonte: PubMed Publicador: PubMed
Tipo: Artigo de Revista Científica
Publicado em /08/1983 EN
Relevância na Pesquisa
45.97%
Two nonallelic human tRNAiMet genes were assigned to chromosome 6 by filter hybridization of DNA from human-rodent somatic cell hybrids by using probes containing unique sequences from the regions flanking each tRNAiMet gene. These unique sequence probes thus allowed each tRNAiMet gene to be analyzed individually in cell hybrids. Both tRNAiMet genes segregated in the hybrid cells with the chromosome 6 enzyme markers, soluble malic enzyme and the mitochondrial form of superoxide dismutase, and also with a karyotypically normal chromosome 6. By using hybrid clones containing translocations that divide chromosome 6 into five segments, both tRNAiMet genes were assigned to the p23 leads to q12 region. These results raise the possibility that other tRNAiMet genes may be syntenic with the two described in this study and illustrate the utility of using unique flanking sequences to identify members of a multigene family.

Location of the genes for human heavy chain immunoglobulin to chromosome 6

Smith, Moyra; Hirschhorn, Kurt
Fonte: PubMed Publicador: PubMed
Tipo: Artigo de Revista Científica
Publicado em /07/1978 EN
Relevância na Pesquisa
45.97%
Immunoglobulin synthesis was examined in 31 man-mouse hybrid clones produced by fusing RAG mouse cells with human lymphoid cells. Cells were grown in serum-free medium containing [14C]leucine and a 14C-labeled amino acid mixture. Spent medium was dialyzed, concentrated, and subjected to radioimmunoelectrophoresis. Eighteen clones were found to produce material that gave a radiolabeled precipitin line with anti-human IgG (γ-chain specific). Production of material which was indistinguishable on radioimmunoelectrophoresis from human Ig γ heavy chain, was dependent on the presence in hybrid clones of human chromosome 6. The material was found to have the ion-exchange elution characteristics of human IgG. When radiolabeled spent medium from human lymphoid lines and from chromosome 6-positive hybrid clones was exposed to protein A-Sepharose and bound material eluted with 8 M urea was subjected to sodium dodecyl sulfate polyacrylamide gel electrophoresis, three radiolabeled peaks occurred with molecular weights of approximately 55,000 (coinciding with that of Ig γ heavy chain), 40,000 and 25,000 (coinciding with that of Ig light chains). No similar peaks were detected in experiments where spent medium from RAG cells was treated identically. These studies lead us to conclude that certain RAG-human lymphoid hybrid clones produce human IgG and that the structural genes for γ heavy chains are located on human chromosome 6. These results also imply that the locus coding for human α...

A gene on human chromosome 6 functions in assembly of tissue-specific adenosine deaminase isozymes

Koch, George; Shows, Thomas B.
Fonte: PubMed Publicador: PubMed
Tipo: Artigo de Revista Científica
Publicado em /08/1978 EN
Relevância na Pesquisa
46.05%
In human tissues, adenosine deaminase (ADA) (adenosine aminohydrolase; EC 3.5.4.4) activity can be separated by gel electrophoresis into several isozymes. A structural gene (ADA) on chromosome 20 codes for the “erythrocyte” isozyme, ADA-1, which is also expressed in some nonerythroid tissues. Nonerythroid cells also differentially express five ADA “tissue isozymes” of a greater molecular weight than ADA-1. Each ADA tissue isozyme has a characteristic electrophoretic mobility and tissue distribution. It has been suggested that these ADA tissue isozymes are composed of ADA-1 and other components. We report that the expression of one of these tissue isozymes, ADA-d, is dependent upon ADA on chromosome 20 and another gene on chromosome 6 which functions in the assembly of the ADA tissue isozymes. In human-mouse hybrids segregating human chromosomes, chromosome 6+,20+ hybrids express both ADA-1 and ADA-d; chromosome 6-,20+ hybrids express only ADA-1; while 6+,20- hybrids have no human ADA activity. ADA-d formation also occurs in vitro by self-assembly when an extract of human erythrocytes or chromosome 6-,20+ hybrids is mixed with a homogenate of chromosome 6+,20- hybrids. The gene on chromosome 6, designated ADCP, codes for an adenosine deaminase complexing protein. The product of ADCP presumably combines with ADA-1 to form the ADA tissue isozymes. The data are consistent with the hypothesis that the distribution of enzymatic activity between ADA-1 and the tissue isozymes depends on the expression of the gene for ADA complexing protein...

Mapping of the genes encoding the HLA-DR alpha chain and the HLA-related antigens to a chromosome 6 deletion by using genomic blotting.

Erlich, H A; Stetler, D; Saiki, R; Gladstone, P; Pious, D
Fonte: PubMed Publicador: PubMed
Tipo: Artigo de Revista Científica
Publicado em /04/1983 EN
Relevância na Pesquisa
46.02%
We have used genomic blotting with DNA from a human cell line that has a small deletion on chromosome 6 (6.3.6) and from its parent cell line (T5-1) to map DNA fragments complementary to cloned DNA sequences encoding the HLA-B7 antigen (class I) and the alpha chain of the HLA-DR antigen (class II). The 6.3.6 variant fails to express the HLA-A, -B, -C, and -DR and MB specificities associated with one of the parental T5-1 haplotypes and has a visible deletion in the short arm of one chromosome 6 (1). The gene locus assignment was based on the expectation that, if the chromosomal location of the DNA sequences used as a hybridization probe were within the deletion, then the relative amount or size (or both) of genomic restriction fragments that hybridize to the probe in T5-1 and in 6.3.6 DNAs should differ predictably. By comparing the genomic blot patterns from T5-1 and 6.3.6 DNAs, we have shown directly that the loss of haplotype expression was due to deletion of the structural genes and have mapped the structural gene for the HLA-DR alpha chain to the chromosomal location (6p2105-6p23) defined by the 6.3.6 deletion. A cDNA clone encoding the alpha chain of the HLA-DR antigen hybridized to two genomic fragments, 4.2 and 3.8 kilobases long...

Assignment of the major histocompatibility complex to a region of the short arm of human chromosome 6.

Francke, U; Pellegrino, M A
Fonte: PubMed Publicador: PubMed
Tipo: Artigo de Revista Científica
Publicado em /03/1977 EN
Relevância na Pesquisa
46.07%
Interspecific cell hybrids containing defined parts of human chromosome 6 were used for regional mapping of gene loci previously assigned to chromosome 6: the human leukocyte antigens (HLA) region, phosphoglucomutase-3 (PGM3; alpha-D-glucose-1,6-bisphosphate:alpha-D-glucose-1-phosphate phosphotransferase, EC 2.7.5.1) and malic enzyme-1 [malic dehydrogenase(decarboxylating) (NADP+), L-malate:NADP+ oxidoreductase (oxaloacetate-decarboxylating), EC 1.1.1.40]. Human fibroblasts containing a balanced reciprocal translocation between the short arms of chromosome 1 and chromosome 6--designated t(1;6) (p3200;p2100)--were fused with an established line of Chinese hamster cells. Hybrid clones with segregating human chromosomes were studied for the presence of the translocation chromosomes 1T and 6T and their normal homologues 1 and 6. Six clones that had retained 1T, three clones with 6T, and three clones with 6 and 6T as controls, were analyzed by a microabsorption test for expression of the allelic antigens HLA-A2 and HLA-A3, both of which were present on the human parental cells. HLA-A2 segregated with the 1T translocation chromosome and HLA-A3 with the normal chromosome 6. Hybrid clones with 6T did not possess an HLA-A gene. In contrast...

Partial Paternal Uniparental Disomy of Chromosome 6 in an Infant with Neonatal Diabetes, Macroglossia, and Craniofacial Abnormalities

Das, S.; Lese, C. M.; Song, M.; Jensen, J. L.; Wells, L. A.; Barnoski, B. L.; Roseberry, J. A.; Camacho, J. M.; Ledbetter, D. H.; Schnur, R. E.
Fonte: The American Society of Human Genetics Publicador: The American Society of Human Genetics
Tipo: Artigo de Revista Científica
EN
Relevância na Pesquisa
46%
Neonatal diabetes, which can be transient or permanent, is defined as hyperglycemia that presents within the first month of life and requires insulin therapy. Transient neonatal diabetes mellitus has been associated with abnormalities of the paternally inherited copy of chromosome 6, including duplications of a portion of the long arm of chromosome 6 and uniparental disomy, implicating overexpression of an imprinted gene in this disorder. To date, all patients with transient neonatal diabetes mellitus and uniparental disomy have had complete paternal isodisomy. We describe a patient with neonatal diabetes, macroglossia, and craniofacial abnormalities, with partial paternal uniparental disomy of chromosome 6 involving the distal portion of 6q, from 6q24-qter. This observation demonstrates that mitotic recombination of chromosome 6 can also give rise to uniparental disomy and neonatal diabetes, a situation similar to that observed in Beckwith-Wiedemann syndrome, another imprinted disorder. This finding has clinical implications, since somatic mosaicism for uniparental disomy of chromosome 6 should also be considered in patients with transient neonatal diabetes mellitus.

Molecular cytogenetic evidence for amplification of chromosome-specific alphoid sequences at enlarged C-bands on chromosome 6.

Jabs, E W; Carpenter, N
Fonte: PubMed Publicador: PubMed
Tipo: Artigo de Revista Científica
Publicado em /07/1988 EN
Relevância na Pesquisa
45.97%
We have characterized variant centromeric regions of chromosome 6 segregating in two families. The heteromorphism, 6ph+, stains negatively with G- and Q-banding and darkly with C-banding. The variant C-band regions measure two to three times the length of their homologues. The centromeric regions of the variant chromosome 6 and its homologue are not significantly elongated by adding 5-azacytidine to culture. We determined that the amount of the alphoid centromeric repeat 308 (DZ61), which is chromosome 6 specific, is amplified two- to threefold in the genomes of individuals with the 6ph+ variants. In situ hybridization localized the increase in 308 repeats to the 6ph+ region. These results suggest an association between amplification of chromosome-specific alphoid sequences and enlargement of specific C-band regions.

Chromatin Structure and Physical Mapping of Chromosome 6 of Potato and Comparative Analyses With Tomato

Iovene, Marina; Wielgus, Susan M.; Simon, Philipp W.; Buell, C. Robin; Jiang, Jiming
Fonte: Genetics Society of America Publicador: Genetics Society of America
Tipo: Artigo de Revista Científica
Publicado em /11/2008 EN
Relevância na Pesquisa
45.99%
Potato (Solanum tuberosum) has the densest genetic linkage map and one of the earliest established cytogenetic maps among all plant species. However, there has been limited effort to integrate these maps. Here, we report fluorescence in situ hybridization (FISH) mapping of 30 genetic marker-anchored bacterial artificial chromosome (BAC) clones on the pachytene chromosome 6 of potato. The FISH mapping results allowed us to define the genetic positions of the centromere and the pericentromeric heterochromatin and to relate chromatin structure to the distribution of recombination along the chromosome. A drastic reduction of recombination was associated with the pericentromeric heterochromatin that accounts for ∼28% of the physical length of the pachytene chromosome. The pachytene chromosomes 6 of potato and tomato (S. lycopersicum) share a similar morphology. However, distinct differences of heterochromatin distribution were observed between the two chromosomes. FISH mapping of several potato BACs on tomato pachytene chromosome 6 revealed an overall colinearity between the two chromosomes. A chromosome inversion was observed in the euchromatic region of the short arms. These results show that the potato and tomato genomes contain more chromosomal rearrangements than those reported previously on the basis of comparative genetic linkage mapping.

Small regions of overlapping deletions on 6q26 in human astrocytic tumours identified using chromosome 6 tile path array CGH

Ichimura, Koichi; Mungall, Andrew J; Fiegler, Heike; Pearson, Danita M.; Dunham, Ian; Carter, Nigel P; Collins, V. Peter
Fonte: PubMed Publicador: PubMed
Tipo: Artigo de Revista Científica
Publicado em 23/02/2006 EN
Relevância na Pesquisa
46%
Deletions of chromosome 6 are a common abnormality in diverse human malignancies including astrocytic tumours, suggesting the presence of tumour suppressor genes (TSG). In order to help identify candidate TSGs, we have constructed a chromosome 6 tile path microarray. The array contains 1780 clones (778 PACs and 1002 BACs) that cover 98.3% of the published chromosome 6 sequences. A total of 104 adult astrocytic tumours (10 diffuse astrocytomas, 30 anaplastic astrocytomas (AA), 64 glioblastomas (GB)) were analysed using this array. Single copy number change was successfully detected and the result was in general concordant with a microsatellite analysis. The pattern of copy number change was complex with multiple interstitial deletions/gains. However, a predominance of telomeric 6q deletions was seen. Two small common and overlapping regions of deletion at 6q26 were identified. One was 1002 kb in size and contained PACRG and QKI, while the second was 199 kb and harbours a single gene, ARID1B. The data show that the chromosome 6 tile path array is useful in mapping copy number changes with high resolution and accuracy. We confirmed the high frequency of chromosome 6 deletions in AA and GB, and identified two novel commonly deleted regions that may harbour TSGs.

Mosaic Ring Chromosome 6 in an Infant with Significant Patent Ductus Arteriosus and Multiple Congenital Anomalies

Lee, Seung Jae; Han, Dong Kyun; Cho, Hwa Jin; Cho, Young Kuk; Ma, Jae Sook
Fonte: The Korean Academy of Medical Sciences Publicador: The Korean Academy of Medical Sciences
Tipo: Artigo de Revista Científica
EN
Relevância na Pesquisa
46%
The clinical features of ring chromosome 6 include central nervous system anomalies, growth retardation, facial dysmorphism and other congenital anomalies. Ring chromosome 6 occurs rarely and manifests as various phenotypes. We report the case of mosaic ring chromosome 6 by conventional karyotyping in a 7-day-old male infant diagnosed with a large patent ductus arteriosus (PDA) with hypoplasia of aortic valve and aortic arch. These have not been previously reported with ring chromosome 6. He recovered from heart failure symptoms after ligation of the PDA. He showed infantile failure to thrive and delayed milestone in a follow-up evaluation. To the best of our knowledge, this is the first report of a Korean individual with ring chromosome 6 and hemodynamically significant PDA.

Periventricular heterotopia and white matter abnormalities in a girl with mosaic ring chromosome 6

Nishigaki, Satsuki; Hamazaki, Takashi; Saito, Mika; Yamamoto, Toshiyuki; Seto, Toshiyuki; Shintaku, Haruo
Fonte: BioMed Central Publicador: BioMed Central
Tipo: Artigo de Revista Científica
Publicado em 26/07/2015 EN
Relevância na Pesquisa
46%
Ring chromosome 6 is a rare chromosome abnormality that arises typically de novo. The phenotypes can be highly variable, ranging from almost normal to severe malformations and neurological defects. We report a case of a 3-year-old girl with mosaic ring chromosome 6 who presented with being small for gestational age and intellectual disability, and whose brain MRI later revealed periventricular heterotopia and white matter abnormalities. Mosaicism was identified in peripheral blood cells examined by standard G-bands, mos 46,XX,r(6)(p25q27)[67]/45,XX,-6[25]/46,XX,dic r(6:6)(p25q27:p25q27)[6]/47,XX,r(6)(p25q27) × 2[2]. Using array-comparative genomic hybridization, we identified terminal deletion of 6q27 (1.5 Mb) and no deletion on 6p. To our knowledge, this is the first report of periventricular heterotopia and white matter abnormalities manifested in a patient with ring chromosome 6. These central nervous system malformations are further discussed in relation to molecular genetics.

Fortuitous detection of uniparental isodisomy of chromosome 6.

Bittencourt, M C; Morris, M A; Chabod, J; Gos, A; Lamy, B; Fellmann, F; Antonarakis, S E; Plouvier, E; Herve, P; Tiberghien, P
Fonte: PubMed Publicador: PubMed
Tipo: Artigo de Revista Científica
Publicado em /01/1997 EN
Relevância na Pesquisa
45.99%
Uniparental isodisomy is defined as the inheritance of two copies of the same parental chromosome and can result in defects when it produces homozygosity for a recessive mutation or in the presence of imprinting. We describe the detection of a chromosome 6 uniparental isodisomy in a 9 year old girl, discovered during a search for an HLA identical sib. HLA typing, erythrocyte phenotyping, and genotypes of microsatellite polymorphisms were compatible with a paternal isodisomy of chromosome 6, with normal biparental origin of the other chromosomes. Paternal cells were not responsive to the patient's cells in mixed lymphocyte cultures. This fortuitous detection of a chromosome 6 isodisomy suggests that cases of chromosome 6 UPD may not be deleterious and may therefore go undetected.

Evolutionary descent of a human chromosome 6 neocentromere: A jump back to 17 million years ago

Capozzi, Oronzo; Purgato, Stefania; D'Addabbo, Pietro; Archidiacono, Nicoletta; Battaglia, Paola; Baroncini, Anna; Capucci, Antonella; Stanyon, Roscoe; Della Valle, Giuliano; Rocchi, Mariano
Fonte: Cold Spring Harbor Laboratory Press Publicador: Cold Spring Harbor Laboratory Press
Tipo: Artigo de Revista Científica
Publicado em /05/2009 EN
Relevância na Pesquisa
45.97%
Molecular cytogenetics provides a visual, pictorial record of the tree of life, and in this respect the fusion origin of human chromosome 2 is a well-known paradigmatic example. Here we report on a variant chromosome 6 in which the centromere jumped to 6p22.1. ChIP-chip experiments with antibodies against the centromeric proteins CENP-A and CENP-C exactly defined the neocentromere as lying at chr6:26,407–26,491 kb. We investigated in detail the evolutionary history of chromosome 6 in primates and found that the primate ancestor had a homologous chromosome with the same marker order, but with the centromere located at 6p22.1. Sometime between 17 and 23 million years ago (Mya), in the common ancestor of humans and apes, the centromere of chromosome 6 moved from 6p22.1 to its current location. The neocentromere we discovered, consequently, has jumped back to the ancestral position, where a latent centromere-forming potentiality persisted for at least 17 Myr. Because all living organisms form a tree of life, as first conceived by Darwin, evolutionary perspectives can provide compelling underlying explicative grounds for contemporary genomic phenomena.

Evolution of mammalian sex chromosomes and sex determination genes: insights from monotremes.

Toledo-Flores, Deborah Fernanda
Fonte: Universidade de Adelaide Publicador: Universidade de Adelaide
Tipo: Tese de Doutorado
Publicado em //2015
Relevância na Pesquisa
46.02%
Genetic sex determination systems are generally based on the presence of differentiated sex chromosomes. Birds have a ZZ/ZW sex chromosome system in which males are ZZ and females ZW, whereas mammals have an XX/XY system with males being XY and females XX. Monotremes have an extraordinary sex chromosome system that consists of multiple sex chromosomes: 5X5Y in platypus and 5X4Y in echidna. Intriguingly, the monotreme sex chromosomes show extensive homology to the bird ZW and not to the therian XY. However, sex determination in monotremes is still a mystery; the Y-specific Sry gene that triggers male sex determination in therian mammals is absent and so far very few genes have been identified on Y chromosomes in monotremes. To gain more insights into the gene content of Y-chromosomes and to identify potential sex determination genes in the platypus a collaborative large scale transcriptomic approach led to the identification of new male specific genes including the anti-Muellerian hormone AMH that I mapped to Y₅, this makes Amhy an exciting new candidate for sex determination in monotremes. Platypus chromosome 6 is largely homologous to the therian X and therefore it represents the therian proto sex chromosome. In addition, this autosome features a large heteromorphic nucleolus organizer region (NOR) and associates with the sex chromosomes during male meiosis (Casey and Daish personal communication). I investigated chromosome 6 heteromorphism in both sexes and found a number of sex-specific characteristics related to the extent of the NOR heteromorphism...

In silico analysis for the presence of HARDY an Arabidopsis drought tolerance DNA binding transcription factor product in chromosome 6 of Sorghum bicolor genome

Arun K. Shanker; M Maheswari; S K. Yadav; B Ventateswarlu
Fonte: Nature Preceedings Publicador: Nature Preceedings
Tipo: Manuscript
Relevância na Pesquisa
45.97%
Expression of the Arabidopsis HARDY (hrd) DNA binding transcription factor (555 bp present on chromosome 2) has been shown to increase WUE in rice by Karaba et al 2007 (PNAS, 104:15270–15275). We conducted a detail analysis of the complete sorghum genome for the similarity/presence of either DNA, mRNA or protein product of the Arabidopsis HARDY (hrd) DNA binding transcription factor (555 bp present on chromosome 2). Chromosome 6 showed a sequence match of 61.5 percent positive between 61 and 255 mRNA residues of the query region. Further confirmation was obtained by TBLASTN which showed that chromosome 6 of the sorghum genome has a region between 54948120 and 54948668 which has 80 amino acid similarities out of the 185 residues. A homology model was constructed and verified using Anolea, Gromos and Verify3D. Scanning the motif for possible activation sites revealed that there was a protein kinase C phosphorylation site between 15th and 20th residue. The study indicates the possibility of the presence of a DNA binding transcription factor in chromosome 6 of Sorghum bicolor with 60 percent similarity to that of Arabidopsis hrd DNA binding transcription factor.

In silico analysis for the presence of HARDY an Arabidopsis drought tolerance DNA binding transcription factor product in chromosome 6 of Sorghum bicolor genome

Arun K. Shanker; M Maheswari; S K. Yadav; B Ventateswarlu
Fonte: Nature Preceedings Publicador: Nature Preceedings
Tipo: Manuscript
Relevância na Pesquisa
45.97%
Expression of the Arabidopsis HARDY (hrd) DNA binding transcription factor (555 bp present on chromosome 2) has been shown to increase WUE in rice by Karaba et al 2007 (PNAS, 104:15270–15275). We conducted a detail analysis of the complete sorghum genome for the similarity/presence of either DNA, mRNA or protein product of the Arabidopsis HARDY (hrd) DNA binding transcription factor (555 bp present on chromosome 2). Chromosome 6 showed a sequence match of 61.5 percent positive between 61 and 255 mRNA residues of the query region. Further confirmation was obtained by TBLASTN which showed that chromosome 6 of the sorghum genome has a region between 54948120 and 54948668 which has 80 amino acid similarities out of the 185 residues. A homology model was constructed and verified using Anolea, Gromos and Verify3D. Scanning the motif for possible activation sites revealed that there was a protein kinase C phosphorylation site between 15th and 20th residue. The study indicates the possibility of the presence of a DNA binding transcription factor in chromosome 6 of Sorghum bicolor with 60 percent similarity to that of Arabidopsis hrd DNA binding transcription factor.