Genomes and Genes
Summary: Any of the DNA in between gene-coding DNA, including untranslated regions, 5' and 3' flanking regions, INTRONS, non-functional pseudogenes, and non-functional repetitive sequences. This DNA may or may not encode regulatory functions.
- Davidson S, Starkey A, Mackenzie A. Evidence of uneven selective pressure on different subsets of the conserved human genome; implications for the significance of intronic and intergenic DNA. BMC Genomics. 2009;10:614 pubmed publisher..In addition, the identification of increased plasticity within the conserved intergenic subset suggests an important role for this subset in the adaptation and diversification of the human population. ..
- Sha T, Xu J, Palanichamy M, Zhang H, Li T, Zhao Z, et al. Genetic diversity of the endemic gourmet mushroom Thelephora ganbajun from south-western China. Microbiology. 2008;154:3460-8 pubmed publisher..Our study revealed significant genetic divergence within Th. ganbajun and limited but detectable gene flow among geographical populations of this endemic ectomycorrhizal gourmet mushroom. ..
- Krom N, Ramakrishna W. Comparative analysis of divergent and convergent gene pairs and their expression patterns in rice, Arabidopsis, and populus. Plant Physiol. 2008;147:1763-73 pubmed publisher..Our results suggest that shared as well as unique mechanisms operate in shaping the organization and function of divergent and convergent gene pairs in different plant species. ..
- Sultan M, Schulz M, Richard H, Magen A, Klingenhoff A, Scherf M, et al. A global view of gene activity and alternative splicing by deep sequencing of the human transcriptome. Science. 2008;321:956-60 pubmed publisher..A global survey of messenger RNA splicing events identified 94,241 splice junctions (4096 of which were previously unidentified) and showed that exon skipping is the most prevalent form of alternative splicing. ..
- Mitra A, Han J, Zhang Z, Mitra A. The intergenic region of Arabidopsis thaliana cab1 and cab2 divergent genes functions as a bidirectional promoter. Planta. 2009;229:1015-22 pubmed publisher..Hence, use of bidirectional promoters in heterologous background provides a means to express multiple genes in transgenic plants and aids genetic engineering-based crop improvement. ..
- Colinas J, Schmidler S, Bohrer G, Iordanov B, Benfey P. Intergenic and genic sequence lengths have opposite relationships with respect to gene expression. PLoS ONE. 2008;3:e3670 pubmed publisher..These findings could shed light on the role and influence of noncoding sequences on gene expression. ..
- Wierzbicki A, Haag J, Pikaard C. Noncoding transcription by RNA polymerase Pol IVb/Pol V mediates transcriptional silencing of overlapping and adjacent genes. Cell. 2008;135:635-48 pubmed publisher..Pol IVb/Pol V function provides a solution to a paradox of epigenetic control: the need for transcription in order to transcriptionally silence the same region. ..
- Cox M, Woerner A, Wall J, Hammer M. Intergenic DNA sequences from the human X chromosome reveal high rates of global gene flow. BMC Genet. 2008;9:76 pubmed publisher..g., global mean Nm = 2.4). We conclude that gene flow has played an important role in structuring global human populations and that migration rates should be incorporated as critical parameters in models of human demography. ..
- Ebisuya M, Yamamoto T, Nakajima M, Nishida E. Ripples from neighbouring transcription. Nat Cell Biol. 2008;10:1106-13 pubmed publisher..These results suggest that transcriptional activation has a ripple effect, which may be advantageous for coordinated expression. ..
- Andersson A, Banfield J. Virus population dynamics and acquired virus resistance in natural microbial communities. Science. 2008;320:1047-50 pubmed publisher..Only the most recently acquired spacers match coexisting viruses, which suggests that community stability is achieved by rapid but compensatory shifts in host resistance levels and virus population structure...
- Nagalakshmi U, Wang Z, Waern K, Shou C, Raha D, Gerstein M, et al. The transcriptional landscape of the yeast genome defined by RNA sequencing. Science. 2008;320:1344-9 pubmed publisher..We also found unexpected 3'-end heterogeneity and the presence of many overlapping genes. These results indicate that the yeast transcriptome is more complex than previously appreciated. ..
- González N, Heeb S, Valverde C, Kay E, Reimmann C, Junier T, et al. Genome-wide search reveals a novel GacA-regulated small RNA in Pseudomonas species. BMC Genomics. 2008;9:167 pubmed publisher..Our results also confirm that several GGA motifs are required in an sRNA for sequestration of the RsmA protein. ..
- Kouvelis V, Sialakouma A, Typas M. Mitochondrial gene sequences alone or combined with ITS region sequences provide firm molecular criteria for the classification of Lecanicillium species. Mycol Res. 2008;112:829-44 pubmed publisher..Thus, the usefulness of mt gene sequences as a convenient molecular tool in phylogenetic studies of entomopathogenic fungi was demonstrated. ..
- Deveau H, Barrangou R, Garneau J, Labonté J, Fremaux C, Boyaval P, et al. Phage response to CRISPR-encoded resistance in Streptococcus thermophilus. J Bacteriol. 2008;190:1390-400 pubmed..Finally, we show through the analyses of 20 mutant phages that virulent phages are rapidly evolving through single nucleotide mutations as well as deletions, in response to CRISPR1...
- Gonzalez Escalona N, Jaykus L, DePaola A. Typing of Vibrio vulnificus strains by variability in their 16S-23S rRNA intergenic spacer regions. Foodborne Pathog Dis. 2007;4:327-37 pubmed..These results demonstrate the feasibility of the ISR1 technique for V. vulnificus subtyping and suggest that ISR1 patterns appear to be linked to rrs sequence types and perhaps with virulence. ..
- Pennisi E. Taxonomy. Wanted: a barcode for plants. Science. 2007;318:190-1 pubmed
- Imamura H, Persampieri J, Chuang J. Sequences conserved by selection across mouse and human malaria species. BMC Genomics. 2007;8:372 pubmed..We have built a public database containing all sequence alignments and functional predictions, and we expect this to be a valuable resource to the malaria research community. ..
- Stephen S, Pheasant M, Makunin I, Mattick J. Large-scale appearance of ultraconserved elements in tetrapod genomes and slowdown of the molecular clock. Mol Biol Evol. 2008;25:402-8 pubmed..These elements are different from other conserved noncoding elements and appear to be important regulatory innovations that became fixed following the emergence of vertebrates from the sea to the land. ..
- Horvath P, Romero D, Coûté Monvoisin A, Richards M, Deveau H, Moineau S, et al. Diversity, activity, and evolution of CRISPR loci in Streptococcus thermophilus. J Bacteriol. 2008;190:1401-12 pubmed..Also, CRISPRs provide critical insights into the relationships between prokaryotes and their environments, notably the coevolution of host and viral genomes. ..
- Bagshaw A, Pitt J, Gemmell N. High frequency of microsatellites in S. cerevisiae meiotic recombination hotspots. BMC Genomics. 2008;9:49 pubmed publisher..Some previous evidence has cast doubt on both of these possibilities, and as a result they have not been explored on a large scale, but the strength of the association we report suggests that they deserve further experimental testing. ..
- Greiner S, Wang X, Rauwolf U, Silber M, Mayer K, Meurer J, et al. The complete nucleotide sequences of the five genetically distinct plastid genomes of Oenothera, subsection Oenothera: I. sequence evaluation and plastome evolution. Nucleic Acids Res. 2008;36:2366-78 pubmed publisher..Phylogenetic relationships suggest plastomes I-III in one clade, while plastome IV appears to be closest to the common ancestor...
- Sorek R, Kunin V, Hugenholtz P. CRISPR--a widespread system that provides acquired resistance against phages in bacteria and archaea. Nat Rev Microbiol. 2008;6:181-6 pubmed..CRISPR arrays, together with a group of associated proteins, confer resistance to phages, possibly by an RNA-interference-like mechanism. This Progress discusses the structure and function of this newly recognized antiviral mechanism. ..
- Cromie G, Hyppa R, Cam H, Farah J, Grewal S, Smith G. A discrete class of intergenic DNA dictates meiotic DNA break hotspots in fission yeast. PLoS Genet. 2007;3:e141 pubmed
- Del Val C, Rivas E, Torres Quesada O, Toro N, Jiménez Zurdo J. Identification of differentially expressed small non-coding RNAs in the legume endosymbiont Sinorhizobium meliloti by comparative genomics. Mol Microbiol. 2007;66:1080-91 pubmed..These findings suggest novel regulatory functions for sRNAs related to the interactions of alpha-proteobacteria with their eukaryotic hosts. ..
- Kouvelis V, Ghikas D, Edgington S, Typas M, Moore D. Molecular characterization of isolates of Beauveria bassiana obtained from overwintering and summer populations of Sunn Pest (Eurygaster integriceps). Lett Appl Microbiol. 2008;46:414-20 pubmed publisher..No clear associations with summer Sunn Pest populations were observed. Studies on the genetic variability of biocontrol agents like B. bassiana are indispensable for the development of molecular tools for their future monitoring. ..
- Akhtar P, Singh S, Bifani P, Kaur S, Srivastava B, Srivastava R. Variable-number tandem repeat 3690 polymorphism in Indian clinical isolates of Mycobacterium tuberculosis and its influence on transcription. J Med Microbiol. 2009;58:798-805 pubmed publisher..5-fold upregulation of GFP expression was found with a flanking region containing four VNTR 3690 repeats, indicating that there is a good correlation between VNTR copy number and transcription of lpdA. ..
- Yang Y, Gupta V, Ho L, Zhou B, Fan Q, Zhu Z, et al. Both upstream and downstream intergenic regions are critical for the mob as tumor suppressor gene activity in Drosophila. FEBS Lett. 2008;582:1766-70 pubmed publisher..Consistent with a model that the downstream intergenic region is critical for mats activity, this sequence contains evolutionarily conserved elements and has enhancer activities. ..
- van den Hof K, van den Berg R, Gravendeel B. Chalcone synthase gene lineage diversification confirms allopolyploid evolutionary relationships of European rostrate violets. Mol Biol Evol. 2008;25:2099-108 pubmed publisher..Comparison of the CHS gene lineage tree and the plastid species phylogeny of Viola reconstructed in this study indicates that the different CHS copies present in Viola are the products of both recent and more ancient duplications...
- Ohtomo T, Miyatake S, Kajiyama Y, Umezu Goto M, Kobayashi N, Kaminuma O, et al. Airway eosinophilic inflammation is attenuated in conserved noncoding sequence-1-deficient mice. Int Arch Allergy Immunol. 2008;146 Suppl 1:2-6 pubmed publisher..When mice were sensitized with OVA/aluminum twice, induction of eosinophilia and OVA-specific IgE Ab was not significantly different between CNS-1-/- and CNS-1+/+ mice. CNS-1 locus regulates eosinophilic inflammation in vivo. ..
- Svoboda P. Cloning and sequencing an inverted repeat. Cold Spring Harb Protoc. 2009;2009:pdb.ip64 pubmed publisher..Although we have successfully sequenced IRs using both strategies, we suggest using the latter to sequence transgenic constructs. ..
- Anderson D, von Messling V. Region between the canine distemper virus M and F genes modulates virulence by controlling fusion protein expression. J Virol. 2008;82:10510-8 pubmed publisher..Taken together, our results provide evidence that the region between the morbillivirus M and F genes modulates virulence through transcriptional control of the F gene expression...
- Leonard A, Grimwade J. Initiating chromosome replication in E. coli: it makes sense to recycle. Genes Dev. 2009;23:1145-50 pubmed publisher..Fujimitsu and colleagues propose these sites are necessary to attain the DnaA-ATP threshold during normal growth and are important regulators of initiation timing in bacteria. ..
- Egervärn M, Roos S, Lindmark H. Identification and characterization of antibiotic resistance genes in Lactobacillus reuteri and Lactobacillus plantarum. J Appl Microbiol. 2009;107:1658-68 pubmed publisher..These data provide some of the knowledge required for assessing the possible risk of using Lact. reuteri and Lact. plantarum strains carrying antibiotic resistance genes as starter cultures and probiotics. ..
- Xin G, Glawe D, Doty S. Characterization of three endophytic, indole-3-acetic acid-producing yeasts occurring in Populus trees. Mycol Res. 2009;113:973-80 pubmed publisher..To our knowledge, the yeast strains presented in this study were the first endophytic yeast strains isolated from species of Populus. ..
- Chen J, Xiong X, Wang T, Lu J, Chen S, Wang H. Rapid construction of a plant RNA interference expression vector for hairpin RNA-mediated targeting using a PCR-based method. DNA Cell Biol. 2009;28:605-13 pubmed publisher..Overexpression of hpRNA constructed by a Medicago truncatula xyloglucan endotransglycosylase gene retarded the growth of transgenic M. truncatula roots. ..
- Jones K, McHugh G, Glickstein L, Steere A. Analysis of Borrelia burgdorferi genotypes in patients with Lyme arthritis: High frequency of ribosomal RNA intergenic spacer type 1 strains in antibiotic-refractory arthritis. Arthritis Rheum. 2009;60:2174-82 pubmed publisher..However, RST1 strains were most frequent in patients with antibiotic-refractory arthritis. Our results help to further the understanding of the differential pathogenicity of strains of B burgdorferi. ..
- Ma W, Wang F, Yu L, Xue Y, Wang Y, Wei J, et al. Identification of an intergenic region that is not essential for replication of goatpox virus. Arch Virol. 2010;155:1337-41 pubmed publisher..A comparative growth assay demonstrated the stability of the recombinant virus at the replication level. These results suggest that the intergenic region is not essential for replication of goatpox virus. ..
- Kasowski M, Grubert F, Heffelfinger C, Hariharan M, Asabere A, Waszak S, et al. Variation in transcription factor binding among humans. Science. 2010;328:232-5 pubmed publisher..Our results indicate that many differences in individuals and species occur at the level of TF binding, and they provide insight into the genetic events responsible for these differences. ..
- Chen Y, Solter L, Chien T, Jiang M, Lin H, Fan H, et al. Characterization of a new insect cell line (NTU-YB) derived from the common grass yellow butterfly, Eurema hecabe (Linnaeus) (Pieridae: Lepidoptera) and its susceptibility to microsporidia. J Invertebr Pathol. 2009;102:256-62 pubmed publisher..blanda Nosema isolate, and developing stages were observed in the host cell nuclei as observed in the natural host, E. blanda. The NTU-YB cell line is also susceptible to Nosema bombycis. ..
- Spillings B, Brooke B, Koekemoer L, Chiphwanya J, Coetzee M, Hunt R. A new species concealed by Anopheles funestus Giles, a major malaria vector in Africa. Am J Trop Med Hyg. 2009;81:510-5 pubmed..These molecular and cytogenetic observations support the conclusion that this Malawi population is a new species and it has provisionally been named An. funestus-like. ..
- Takahashi N, Kobayashi R, Kono T. Restoration of Dlk1 and Rtl1 is necessary but insufficient to rescue lethality in intergenic differentially methylated region (IG-DMR)-deficient mice. J Biol Chem. 2010;285:26121-5 pubmed publisher..Thus, we inferred that paternally expressed genes are necessary for perinatal survivability and that maternally expressed ncRNAs are involved in postnatal lethality. ..
- Sakuraba Y, Kimura T, Masuya H, Noguchi H, Sezutsu H, Takahasi K, et al. Identification and characterization of new long conserved noncoding sequences in vertebrates. Mamm Genome. 2008;19:703-12 pubmed publisher..Taken together, these results suggest that mutations occur with equal frequency in LCNS but are eliminated by natural selection during the course of evolution. ..
- Kruger M, Stockinger H, Kruger C, Schüssler A. DNA-based species level detection of Glomeromycota: one PCR primer set for all arbuscular mycorrhizal fungi. New Phytol. 2009;183:212-23 pubmed publisher..Their application will improve the base for deep sequencing approaches; moreover, they can be efficiently used as DNA barcoding primers. ..
- Dieguez Gonzalez R, Calaza M, Perez Pampin E, Balsa A, Blanco F, Canete J, et al. Analysis of TNFAIP3, a feedback inhibitor of nuclear factor-kappaB and the neighbor intergenic 6q23 region in rheumatoid arthritis susceptibility. Arthritis Res Ther. 2009;11:R42 pubmed publisher..Our data are consistent with the hypothesis that several RA genetic factors exist in the 6q23 region, including polymorphisms in the TNFAIP3 gene, like that previously described for systemic lupus erythematosus. ..
- Small H, Sturve J, Bignell J, Longshaw M, Lyons B, Hicks R, et al. Laser-assisted microdissection: a new tool for aquatic molecular parasitology. Dis Aquat Organ. 2008;82:151-6 pubmed publisher..The amplification products were sequenced to confirm the identity of the targeted regions. The techniques, applications, and limitations of LMD to address questions in aquatic molecular pathology and parasitology are discussed. ..
- Cutler S, Bonilla E, Singh R. Population structure of East African relapsing fever Borrelia spp. Emerg Infect Dis. 2010;16:1076-80 pubmed publisher..duttonii and represents an ecotype rather than a species. These observations have disease control implications and suggest LBRF Borrelia spp. could reemerge from its tick-borne reservoirs where vectors coexist...
- Brown H, Modaresi S, Cook J, Latimer K, Peterson D. Genetic variability of archived Cytauxzoon felis histologic specimens from domestic cats in Georgia, 1995-2007. J Vet Diagn Invest. 2009;21:493-8 pubmed..The findings of the current study document the existence of genetically distinct C. felis populations in historical samples and, together with data from contemporary samples, demonstrate a diverse population structure for C. felis...
- Collery M, Smyth D, Tumilty J, Twohig J, Smyth C. Associations between enterotoxin gene cluster types egc1, egc2 and egc3, agr types, enterotoxin and enterotoxin-like gene profiles, and molecular typing characteristics of human nasal carriage and animal isolates of Staphylococcus aureus. J Med Microbiol. 2009;58:13-25 pubmed publisher..One canine and three porcine isolates possessed pseudogenes psient1 and psient2. One porcine and one canine isolate each had the selu(v) gene. Putative relationships between disease-causing propensity and egc type need (re-)evaluation. ..