http://www.biomedcentral.com/bmcgenomics/ The latest research articles published by BMC Genomics 2012-06-01T00:00:00Z Background: Genotyping assays often require substantial amounts of DNA. To overcome the problem of limiting amounts of available DNA, Whole Genome Amplification (WGA) methods have been developed. The multiple displacement amplification (MDA) method using Phi29 polymerase has become the preferred choice due to its high processivity and low error rate. However, the uniformity and fidelity of the amplification process across the genome has not been extensively characterized. Results: To assess amplification uniformity, we used array-based comparative genomic hybridization (aCGH) to evaluate DNA copy number variations (CNVs) in DNAs amplified by two MDA kits: GenomiPhi and REPLI-g. The Agilent Human CGH array containing nearly one million probes was used in this study together with DNAs from a normal subject and 2 cystic fibrosis (CF) patients. Each DNA sample was amplified 4 independent times and compared to its native unamplified DNA. Komogorov distances and Phi correlations showed a high consistency within each sample group. Less than 2% of the probes showed more than 2-fold CNV introduced by the amplification process. The two amplification kits, REPLI-g and GenomiPhi, generate very similar amplified DNA samples despite the differences between the unamplified and amplified DNA samples. The results from aCGH analysis indicated that there were no obvious CNVs in the CFTR gene region due to WGA when compared to unamplified DNA. This was confirmed by quantitative real-time PCR copy number assays at 10 locations within the CFTR gene. DNA sequencing analysis of a 2-kb region within the CFTR gene showed no mutations introduced by WGA. Conclusion: The relatively high uniformity and consistency of the WGA process, coupled with the low replication error rate, suggests that WGA DNA may be suitable for accurate genotyping. Regions of the genome that were consistently under-amplified were found to contain higher than average GC content. Because of the consistent differences between the WGA DNA and the native unamplified DNA, characterization of the genomic region of interest, as described here, will be necessary to ensure the reliability of genotyping results from WGA DNA http://www.biomedcentral.com/1471-2164/13/217 Tao Han Ching-Wei Chang Joshua Kwekel Ying Chen Yun Ge Francisco Martinez-Murillo Donna Roscoe Živana Težak Reena Philip Karen Bijwaard James Fuscoe BMC Genomics 2012, null:217 2012-06-01T00:00:00Z doi:10.1186/1471-2164-13-217 /content/figures/1471-2164-13-217-toc.gif BMC Genomics 1471-2164 ${item.volume} 217 2012-06-01T00:00:00Z PDF Background: The TERT gene encodes the catalytic subunit of the telomerase complex and is responsible for maintaining telomere length. Vertebrate telomerase has been studied in placental mammals, fish, and the chicken, but less attention has been paid to other vertebrates. The platypus occupies an important evolutionary position, providing unique insight into the evolution of mammalian genes. We report the cloning of a platypus TERT (pTERT) ortholog, and provide a comparison with genes of other vertebrates. Results: The pTERT encodes a protein with the high homology to marsupial TERT and avian TERT. Like the TERT of sauropsids and marsupials, as well as that of sharks and echinoderms, pTERT contains extended variable linkers in the N-terminal region suggesting that they were present already in basal vertebrates and lost independently in placental mammals and ray-finned fish. Several alternatively spliced pTERT variants structurally similar to avian TERT variants were identified. Telomerase activity is expressed in all platypus tissues similarly to cold-blooded animals and murine rodents. pTERT was localized on pseudoautosomal regions of sex chromosomes X3/Y2, expanding the homology between human chromosome 5 and platypus sex chromosomes. The synteny analysis suggests that TERT co-localized with sex-linked genes in the last common mammalian ancestor. Interestingly, female platypuses express higher levels of telomerase in heart and liver tissues than do males. Conclusions: pTERT shares many features with TERT of the reptilian outgroup, suggesting that pTERT represents the ancestral mammalian TERT. Features specific to TERT of eutherian mammals have, therefore, evolved more recently after the divergence of monotremes. http://www.biomedcentral.com/1471-2164/13/216 Radmila Hrdličková Jiří Nehyba Shu Lim Frank Grützner Henry Bose BMC Genomics 2012, null:216 2012-06-01T00:00:00Z doi:10.1186/1471-2164-13-216 /content/figures/1471-2164-13-216-toc.gif BMC Genomics 1471-2164 ${item.volume} 216 2012-06-01T00:00:00Z PDF Background: The cellular proteome and metabolome are underlying dynamic regulation allowing rapid adaptation to changes in the environment. System-wide analysis of these dynamics will provide novel insights into mechanisms of stress adaptation for higher photosynthetic organisms. We applied pulsed-SILAC labeling to a photosynthetic organism for the first time and we established a method to study proteome dynamics in the green alga chlamydomonas reinhardtii, an emerging model system for plant biology. In addition, we combined the analysis of protein synthesis with metabolic profiling to study the dynamic changes of metabolism and proteome turnover under salt stress conditions. Results: To study de novo protein synthesis an arginine auxotroph Chlamydomonas strain was cultivated in presence of stable isotope-labeled arginine for 24 hours. From the time course experiment in 3 salt concentrations we could identify more than 2500 proteins and their H/L ratio in at least one experimental condition; for 998 proteins at least 3 ratio counts were detected in the 24 h time point (0 mM NaCl). After fractionation we could identify 3115 proteins and for 1765 of them we determined their de novo synthesis rate. Consistently with previous findings we showed that RuBisCO is among the most prominent proteins in the cell; and similar abundance and turnover for the small and large RuBisCO subunit could be calculated. The D1 protein was identified among proteins with a high synthesis rates. A global median half-life of 45 h was calculated for Chlamydomonas proteins under the chosen conditions. Conclusion: To investigate the temporal co-regulation of the proteome and metabolome, we applied salt stress to chlamydomonas and studied the time dependent regulation of protein expression and changes in the metabolome. The main metabolic response to salt stress was observed within the amino acid metabolism. In particular, proline was up-regulated manifold and according to that an increased carbon flow within the proline biosynthetic pathway could be measured. In parallel the analysis of abundance and de novo synthesis of the corresponding enzymes revealed that metabolic rearrangements precede adjustments of protein abundance. http://www.biomedcentral.com/1471-2164/13/215 Guido Mastrobuoni Susann Irgang Matthias Pietzke Markus Wenzel Heike Assmus Waltraud Schulze Stefan Kempa BMC Genomics 2012, null:215 2012-05-31T00:00:00Z doi:10.1186/1471-2164-13-215 /content/figures/1471-2164-13-215-toc.gif BMC Genomics 1471-2164 ${item.volume} 215 2012-05-31T00:00:00Z PDF Background: Post-transcriptional control of gene expression is mostly conducted by specic elements in untranslated regions (UTRs) of mRNAs, in collaboration with specic binding proteins and RNAs. In several well characterized cases, these RNA elements are known to form stable secondary structures. RNA secondary structures also may have major functional implications for long noncoding RNAs (lncRNAs). Recent transcriptional data has indicated the importance of lncRNAs in brain development and function. However, no methodical efforts to investigate this have been undertaken. Here, we aim to systematically analyze the potential for RNA structure in brain-expressed transcripts. Results: By comprehensive spatial expression analysis of the adult mouse in situ hybridization data of the Allen Mouse Brain Atlas, we show that transcripts (coding as well as non-coding) associated with in silico predicted structured probes are highly and signicantly enriched in almost all analyzed brain regions. Functional implications of these RNA structures and their role in the brain are discussed in detail along with specic examples. We observe that mRNAs with a structure prediction in their UTRs are enriched for binding, transport and localization gene ontology categories. In addition, after manual examination we observe agreement between RNA binding protein interaction sites near the 3' UTR structures and correlated expression patterns. Conclusions: Our results show a potential use for RNA structures in expressed coding as well as noncoding transcripts in the adult mouse brain, and describe the role of structured RNAs in the context of intracellular signaling pathways and regulatory networks. Based on this data we hypothesize that RNA structure is widely involved 1in transcriptional and translational regulatory mechanisms in the brain and ultimately plays a role in brain function. http://www.biomedcentral.com/1471-2164/13/214 Stefan Seemann Susan Sunkin Michael Hawrylycz Walter Ruzzo Jan Gorodkin BMC Genomics 2012, null:214 2012-05-31T00:00:00Z doi:10.1186/1471-2164-13-214 /content/figures/1471-2164-13-214-toc.gif BMC Genomics 1471-2164 ${item.volume} 214 2012-05-31T00:00:00Z PDF Background: Intramuscular fat (IMF) is one of the important factors influencing meat quality, however, for chickens, the molecular regulatory mechanisms underlying this trait have not yet been determined. In this study, a systematic identification of candidate genes and new pathways related to IMF deposition in chicken breast tissue has been made using gene expression profiles of two distinct breeds: Beijing-you (BJY), a slow-growing Chinese breed possessing high meat quality and Arbor Acres (AA), a commercial fast-growing broiler line. Results: Agilent cDNA microarray analyses were conducted to determine gene expression profiles of breast muscle sampled at different developmental stages of BJY and AA chickens. Relative to d 1 when there is no detectable IMF, breast muscle at d 21, d 42, d 90 and d 120 (only for BJY) contained 1310 differentially expressed genes (DEGs) in BJY and 1080 DEGs in AA. Of these, 34-70 DEGs related to lipid metabolism or muscle development processes were examined further in each breed based on Gene Ontology (GO) analysis. The expression of several DEGs was correlated, positively or negatively, with the changing patterns of lipid content or breast weight across the ages sampled, indicating that those genes may play key roles in these developmental processes. In addition, based on KEGG pathway analysis of DEGs in both BJY and AA chickens, it was found that in addition to pathways affecting lipid metabolism (pathways for MAPK & PPAR signaling), cell junction-related pathways (tight junction, ECM-receptor interaction, focal adhesion, regulation of actin cytoskeleton), which play a prominent role in maintaining the integrity of tissues, could contribute to the IMF deposition. Conclusion: The results of this study identified potential candidate genes associated with chicken IMF deposition and imply that IMF deposition in chicken breast muscle is regulated and mediated not only by genes and pathways related to lipid metabolism and muscle development, but also by others involved in cell junctions. These findings establish the groundwork and provide new clues for deciphering the molecular mechanisms underlying IMF deposition in poultry. Further studies at the translational and posttranslational level are now required tovalidate the genes and pathways identified here. http://www.biomedcentral.com/1471-2164/13/213 Huanxian Cui Ranran Liu Guiping Zhao Maiqing Zheng Jilan Chen Jie Wen BMC Genomics 2012, null:213 2012-05-30T00:00:00Z doi:10.1186/1471-2164-13-213 /content/figures/1471-2164-13-213-toc.gif BMC Genomics 1471-2164 ${item.volume} 213 2012-05-30T00:00:00Z PDF Background: The contribution of a gene to the fitness of a bacterium can be assayed by whether and to what degree the bacterium tolerates transposon insertions in that gene. We use this fact to compare the fitness of syntenic homologous genes among related Salmonella strains to reveal differences not apparent at the gene sequence level. Results: A transposon Tn5 derivative was used to construct mutants in Salmonella Typhimurium ATCC14028 (STM1) and Salmonella Typhi Ty2 (STY1), which were then grown in rich media. The locations of 234,152 and 53,556 integration sites, respectively, were mapped by sequencing. These data were compared to similar data available for a different Ty2 strain (STY2) and essential genes identified in E. coli K-12 (ECO). Of 277 genes considered essential in ECO, all had syntenic homologs in STM1, STY1, and STY2, and all but nine genes were either devoid of Tn insertions or had very few. For three of these nine genes, part of the annotated gene lacked Tn integrations (yejM, ftsN and murB). At least one of the other six genes, trpS, had a potentially functionally redundant gene encoded elsewhere in Salmonella but not in ECO. An additional 165 genes were almost entirely devoid of transposon integrations in all three Salmonella strains examined, including many genes associated with protein and DNA synthesis. Four of these genes (STM14_1498.L, STM14_2872, STM14_3360.RJ, and STM14_5442) are not found in E. coli. Notable differences in the extent of gene selection were also observed among the three different Salmonella isolates. Mutations in hns, for example, were selected against in STM1 but not in the two STY strains, which have a defect in rpoS rendering hns nonessential. Conclusions: Comparisons among transposon integration profiles from different members of a species and among related species, all grown in similar conditions, identify differences in gene fitness among syntenic homologous genes. Further differences in fitness profiles among shared genes can be expected in other selective environments, with potential relevance for comparative systems biology. http://www.biomedcentral.com/1471-2164/13/212 Rocio Canals Xiao-Qin Xia Catrina Fronick Sandra Clifton Brian Ahmer Helene Andrews-Polymenis Steffen Porwollik Michael McClelland BMC Genomics 2012, null:212 2012-05-30T00:00:00Z doi:10.1186/1471-2164-13-212 /content/figures/1471-2164-13-212-toc.gif BMC Genomics 1471-2164 ${item.volume} 212 2012-05-30T00:00:00Z PDF Insects detect environmental chemicals via a large and rapidly evolving family of chemosensory receptor proteins. Although our understanding of the molecular genetic basis for Drosophila chemoreception has increased enormously in the last decade, similar understanding in other insects remains limited. The tobacco hornworm, Manduca sexta, has long been an important model for insect chemosensation, particularly from ecological, behavioral, and physiological standpoints. It is also a major agricultural pest on solanaceous crops. However, little sequence information and lack of genetic tools has prevented molecular genetic analysis in this species. The ability to connect molecular genetic mechanisms, including potential lineage-specific genetic changes in chemosensory genes, to previously described behaviors and ecological specializations in this species would be greatly beneficial. Here, we have sequenced transcriptomes from adult and larval chemosensory tissues and we report the identification of new chemosensory receptor genes including 17 novel odorant receptors and one novel gustatory receptor from M. sexta. Further, we demonstrate that systemic RNAi can be used in larval olfactory neurons to reduce expression of chemosensory receptor transcripts. Together, our results further the development of M. sexta as a model for functional analysis of insect chemosensation. http://www.biomedcentral.com/1471-2164/13/211 Natalie Howlett Katherine Dauber Aditi Shukla Brian Morton John Glendinning Elyssa Brent Caroline Gleason Fahmida Islam Denisse Izquierdo Sweta Sanghavi Anika Afroz Aanam Aslam Marissa Barbaro Rebekah Blutstein Margarita Borovka Brianna Desire Ayala Elikhis Qing Fan Katherine Hoffman Amy Huang Dominique Keefe Sarah Lopatin Samara Miller Priyata Patel Danielle Rizzini Alyssa Robinson Karimah Rokins Aneta Turlik Jennifer Mansfield BMC Genomics 2012, null:211 2012-05-30T00:00:00Z doi:10.1186/1471-2164-13-211 /content/figures/1471-2164-13-211-toc.gif BMC Genomics 1471-2164 ${item.volume} 211 2012-05-30T00:00:00Z PDF Background: Microbial degradation of plant cell walls and its conversion to sugars and other byproducts is a key step in the carbon cycle on Earth. In order to process heterogeneous plant-derived biomass, specialized anaerobic bacteria use an elaborate multi-enzyme cellulosome complex to synergistically deconstruct cellulosic substrates. The cellulosome was first discovered in the cellulolytic thermophile, Clostridium thermocellum, and much of our knowledge of this intriguing type of protein composite is based on the cellulosome of this environmentally and biotechnologically important bacterium. The recently sequenced genome of the cellulolytic mesophile, Acetivibrio cellulolyticus, allows detailed comparison of the cellulosomes of these two select cellulosome-producing bacteria. Results: Comprehensive analysis of the A. cellulolyticus draft genome sequence revealed a very sophisticated cellulosome system. Compared to C. thermocellum, the cellulosomal architecture of A. cellulolyticus is much more extensive, whereby the genome encodes for twice the number of cohesin- and dockerin-containing proteins. The A. cellulolyticus genome has thus evolved an inflated number of 143 dockerin-containing genes, coding for multimodular proteins with distinctive catalytic and carbohydrate-binding modules that play critical roles in biomass degradation. Additionally, 41 putative cohesin modules distributed in 16 different scaffoldin proteins were identified in the genome, representing a broader diversity and modularity than those of Clostridium thermocellum. Although many of the A. cellulolyticus scaffoldins appear in unconventional modular combinations, elements of the basic structural scaffoldins are maintained in both species. In addition, both species exhibit similarly elaborate cell-anchoring and cellulosome-related gene-regulatory elements. Conclusions: This work portrays a particularly intricate, cell-surface cellulosome system in A. cellulolyticus and provides a blueprint for examining the specific roles of the various cellulosomal components in the degradation of complex carbohydrate substrates of the plant cell wall by the bacterium. http://www.biomedcentral.com/1471-2164/13/210 Bareket Dassa Ilya Borovok Raphael Lamed Bernard Henrissat Pedro Coutinho Christopher Hemme Yue Huang Jizhong Zhou Edward Bayer BMC Genomics 2012, null:210 2012-05-30T00:00:00Z doi:10.1186/1471-2164-13-210 /content/figures/1471-2164-13-210-toc.gif BMC Genomics 1471-2164 ${item.volume} 210 2012-05-30T00:00:00Z PDF Background: The biphasic life cycle with pelagic larva and benthic adult stages is widely observed in the animal kingdom, including the Porifera (sponges), which are the earliest branching metazoans. The demosponge, Amphimedon queenslandica, undergoes metamorphosis from a free-swimming larva into a sessile adult that bears no morphological resemblance to other animals. While the genome of A. queenslandica contains an extensive repertoire of genes very similar to that of complex bilaterians, it is as yet unclear how this is drawn upon to coordinate changing morphological features and ecological demands throughout the sponge life cycle. Results: To identify genome-wide events that accompany the pelagobenthic transition in A. queenslandica, we compared global gene expression profiles at four key developmental stages by sequencing the poly(A) transcriptome using SOLiD technology. Large-scale changes in transcription were observed as sponge larvae settled on the benthos and began metamorphosis. Although previous systematics suggest that the only clear homology between Porifera and other animals is in the embryonic and larval stages, we observed extensive use of genes involved in metazoan-associated cellular processes throughout the sponge life cycle. Sponge-specific transcripts are not over-represented in the morphologically distinct adult; rather, many genes that encode typical metazoan features, such as cell adhesion and immunity, are upregulated. Our analysis further revealed gene families with candidate roles in competence, settlement, and metamorphosis in the sponge, including transcription factors, G-protein coupled receptors and other signaling molecules. Conclusions: This first genome-wide study of the developmental transcriptome in an early branching metazoan highlights major transcriptional events that accompany the pelagobenthic transition and point to a network of regulatory mechanisms that coordinate changes in morphology with shifting environmental demands. Metazoan developmental and structural gene orthologs are well-integrated into the expression profiles at every stage of sponge development, including the adult. The utilization of genes involved in metazoan-associated processes throughout sponge development emphasizes the potential of the genome of the last common ancestor of animals to generate phenotypic complexity. http://www.biomedcentral.com/1471-2164/13/209 Cecilia Conaco Pierre Neveu Hongjun Zhou Mary Luz Arcila Sandie Degnan Bernard Degnan Kenneth Kosik BMC Genomics 2012, null:209 2012-05-30T00:00:00Z doi:10.1186/1471-2164-13-209 /content/figures/1471-2164-13-209-toc.gif BMC Genomics 1471-2164 ${item.volume} 209 2012-05-30T00:00:00Z PDF Background: Although the Ciona intestinalis genome contains many allelic polymorphisms, there is only limited data analyzed systematically. Establishing a dense map of genetic variations in C. intestinalis is necessary not only for linkage analysis, but also for other experimental biology including molecular developmental and evolutionary studies, because animals from natural populations are typically used for experiments. Results: Here, we identified over three million candidate short genomic variations within a 110 Mb euchromatin region among five C. intestinalis individuals. The average nucleotide diversity was approximately 1.1%. Genetic variations were found at a similar density in intergenic and gene regions. Non-synonymous and nonsense nucleotide substitutions were found in 12,493 and 1,214 genes accounting for 81.9% and 8.0% of the entire gene set, respectively, and over 60% of genes in the single animal encode non-identical proteins between maternal and paternal alleles. Conclusions: Our results provide a framework for studying evolution of the animal genome, as well as a useful resource for a wide range of C. intestinalis researchers. http://www.biomedcentral.com/1471-2164/13/208 Yutaka Satou Tadasu Shin-i Yuji Kohara Nori Satoh Shota Chiba BMC Genomics 2012, null:208 2012-05-30T00:00:00Z doi:10.1186/1471-2164-13-208 /content/figures/1471-2164-13-208-toc.gif BMC Genomics 1471-2164 ${item.volume} 208 2012-05-30T00:00:00Z PDF