Journal articles: 'Mammalian genomics'

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Wayne, R. K., and E. A. Ostrander. "Mammalian genomics:." Heredity 92, no. 4 (March 24, 2004): 273–74. http://dx.doi.org/10.1038/sj.hdy.6800428.

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O'Brien, S. J. "GENOMICS: On Choosing Mammalian Genomes for Sequencing." Science 292, no. 5525 (June 22, 2001): 2264–66. http://dx.doi.org/10.1126/science.1059393.

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Jones, N. C., and P. A. Pevzner. "Comparative genomics reveals unusually long motifs in mammalian genomes." Bioinformatics 22, no. 14 (July 15, 2006): e236-e242. http://dx.doi.org/10.1093/bioinformatics/btl265.

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Wuest, Diane M., Sarah W. Harcum, and Kelvin H. Lee. "Genomics in mammalian cell culture bioprocessing." Biotechnology Advances 30, no. 3 (May 2012): 629–38. http://dx.doi.org/10.1016/j.biotechadv.2011.10.010.

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Wixon, Jo. "Meeting Highlights: Genome Sequencing and Biology 2001." Comparative and Functional Genomics 2, no. 4 (2001): 243–51. http://dx.doi.org/10.1002/cfg.97.

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We bring you a report from the CSHL Genome Sequencing and Biology Meeting, which has a long and prestigious history. This year there were sessions on large-scale sequencing and analysis, polymorphisms (covering discovery and technologies and mapping and analysis), comparative genomics of mammalian and model organism genomes, functional genomics and bioinformatics.

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Madende, Moses, and Gernot Osthoff. "Comparative genomics of casein genes." Journal of Dairy Research 86, no. 3 (July 24, 2019): 323–30. http://dx.doi.org/10.1017/s0022029919000414.

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AbstractThis research paper addresses the hypothesis that comparative genomics can give a new insight into the functionality of casein genes with respect to the casein micelle. Comparative genomics is a rapidly emerging field in computational biology whereby two or more genomes are compared in order to obtain a global view on genomes as well as assigning previously unknown functions for genes. Casein genes are among the most rapidly evolving mammalian genes, with the gene products mainly grouped into four types (αs1-, αs2-, β- and κ-casein). Functionally, casein genes are central to the casein micelle, the exact structure of which is still a subject of intense debate. Moreover, and adding to this complexity, some mammals lack some of the casein genes, although casein micelles have been observed in their milk. This observation has prompted an investigation into the distribution of casein genes across a host of mammalian species. It was apparent from this study that casein gene sequences are very diverse from each other and we confirmed that many mammalian species lack one or more of the casein genes. The genes encoding β- and κ-caseins are present in most mammals whereas α-casein encoding genes are less represented. This suggests different mechanisms for casein micelle formation in different species as well as the functions that are assigned to each individual casein.

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Rodriguez-Osorio, Nelida, Hongfeng Wang, Jennifer Rupinski, Susan M. Bridges, and Erdogan Memili. "Comparative functional genomics of mammalian DNA methyltransferases." Reproductive BioMedicine Online 20, no. 2 (February 2010): 243–55. http://dx.doi.org/10.1016/j.rbmo.2009.11.006.

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Holmes, Roger S., Laura A. Cox, and John L. VandeBerg. "Mammalian carboxylesterase 3: comparative genomics and proteomics." Genetica 138, no. 7 (April 28, 2010): 695–708. http://dx.doi.org/10.1007/s10709-010-9438-z.

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Holmes, Roger S., Laura A. Cox, and John L. VandeBerg. "Mammalian carboxylesterase 5: Comparative biochemistry and genomics." Comparative Biochemistry and Physiology Part D: Genomics and Proteomics 3, no. 3 (September 2008): 195–204. http://dx.doi.org/10.1016/j.cbd.2008.05.002.

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Li, W. H., J. Nadeau, E. Ostrander, B. Van Valkenburgh, and P. Waddell. "Comparative Genomics: Mammalian Radiations -- Genome Maps 10." Science 286, no. 5439 (October 15, 1999): 463–78. http://dx.doi.org/10.1126/science.286.5439.463.

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Hochgeschwender, Ute, and Miles B. Brennan. "The impact of genomics on mammalian neurobiology." BioEssays 21, no. 2 (February 12, 1999): 157–63. http://dx.doi.org/10.1002/(sici)1521-1878(199902)21:2<157::aid-bies9>3.0.co;2-0.

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Stefen, Clara, Franziska Wagner, Marika Asztalos, Peter Giere, Peter Grobe, Michael Hiller, Rebecca Hofmann, et al. "Phenotyping in the era of genomics: MaTrics—a digital character matrix to document mammalian phenotypic traits." Mammalian Biology 102, no. 1 (December 7, 2021): 235–49. http://dx.doi.org/10.1007/s42991-021-00192-5.

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AbstractA new and uniquely structured matrix of mammalian phenotypes, MaTrics (Mammalian Traits for Comparative Genomics) in a digital form is presented. By focussing on mammalian species for which genome assemblies are available, MaTrics provides an interface between mammalogy and comparative genomics.MaTrics was developed within a project aimed to find genetic causes of phenotypic traits of mammals using Forward Genomics. This approach requires genomes and comprehensive and recorded information on homologous phenotypes that are coded as discrete categories in a matrix. MaTrics is an evolving online resource providing information on phenotypic traits in numeric code; traits are coded either as absent/present or with several states as multistate. The state record for each species is linked to at least one reference (e.g., literature, photographs, histological sections, CT scans, or museum specimens) and so MaTrics contributes to digitalization of museum collections. Currently, MaTrics covers 147 mammalian species and includes 231 characters related to structure, morphology, physiology, ecology, and ethology and available in a machine actionable NEXUS-format*. Filling MaTrics revealed substantial knowledge gaps, highlighting the need for phenotyping efforts. Studies based on selected data from MaTrics and using Forward Genomics identified associations between genes and certain phenotypes ranging from lifestyles (e.g., aquatic) to dietary specializations (e.g., herbivory, carnivory). These findings motivate the expansion of phenotyping in MaTrics by filling research gaps and by adding taxa and traits. Only databases like MaTrics will provide machine actionable information on phenotypic traits, an important limitation to genomics. MaTrics is available within the data repository Morph·D·Base (www.morphdbase.de).

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Villanueva-Canas, J. L., S. L. Faherty, A. D. Yoder, and M. M. Alba. "Comparative Genomics of Mammalian Hibernators Using Gene Networks." Integrative and Comparative Biology 54, no. 3 (May 31, 2014): 452–62. http://dx.doi.org/10.1093/icb/icu048.

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O'Brien, Stephen J., Marilyn Menotti-Raymond, William J. Murphy, William G. Nash, Johannes Wienberg, Roscoe Stanyon, Neal G. Copeland, Nancy A. Jenkins, James E. Womack, and Jennifer A. Marshall Graves. "The Promise of Comparative Genomics in Mammals." Science 286, no. 5439 (October 15, 1999): 458–81. http://dx.doi.org/10.1126/science.286.5439.458.

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Dense genetic maps of human, mouse, and rat genomes that are based on coding genes and on microsatellite and single-nucleotide polymorphism markers have been complemented by precise gene homolog alignment with moderate-resolution maps of livestock, companion animals, and additional mammal species. Comparative genetic assessment expands the utility of these maps in gene discovery, in functional genomics, and in tracking the evolutionary forces that sculpted the genome organization of modern mammalian species.

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Cissé, Ousmane H., Liang Ma, Da Wei Huang, Pavel P. Khil, John P. Dekker, Geetha Kutty, Lisa Bishop, et al. "Comparative Population Genomics Analysis of the Mammalian Fungal PathogenPneumocystis." mBio 9, no. 3 (May 8, 2018): e00381-18. http://dx.doi.org/10.1128/mbio.00381-18.

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ABSTRACTPneumocystisspecies are opportunistic mammalian pathogens that cause severe pneumonia in immunocompromised individuals. These fungi are highly host specific and uncultivablein vitro. HumanPneumocystisinfections present major challenges because of a limited therapeutic arsenal and the rise of drug resistance. To investigate the diversity and demographic history of natural populations ofPneumocystisinfecting humans, rats, and mice, we performed whole-genome and large-scale multilocus sequencing of infected tissues collected in various geographic locations. Here, we detected reduced levels of recombination and variations in historical demography, which shape the global population structures. We report estimates of evolutionary rates, levels of genetic diversity, and population sizes. Molecular clock estimates indicate thatPneumocystisspecies diverged before their hosts, while the asynchronous timing of population declines suggests host shifts. Our results have uncovered complex patterns of genetic variation influenced by multiple factors that shaped the adaptation ofPneumocystispopulations during their spread across mammals.IMPORTANCEUnderstanding how natural pathogen populations evolve and identifying the determinants of genetic variation are central issues in evolutionary biology.Pneumocystis, a fungal pathogen which infects mammals exclusively, provides opportunities to explore these issues. In humans,Pneumocystiscan cause a life-threatening pneumonia in immunosuppressed individuals. In analysis of differentPneumocystisspecies infecting humans, rats, and mice, we found that there are high infection rates and that natural populations maintain a high level of genetic variation despite low levels of recombination. We found no evidence of population structuring by geography. Our comparisons of the times of divergence of these species to their respective hosts suggest thatPneumocystismay have undergone recent host shifts. The results demonstrate thatPneumocystisstrains are widely disseminated geographically and provide a new understanding of the evolution of these pathogens.

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Zhou, Fu-lai, Sheena C. Li, Yue Zhu, Wan-jing Guo, Li-jun Shao, Justin Nelson, Scott Simpkins, et al. "Integrating yeast chemical genomics and mammalian cell pathway analysis." Acta Pharmacologica Sinica 40, no. 9 (May 28, 2019): 1245–55. http://dx.doi.org/10.1038/s41401-019-0231-y.

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Barnes, Brian M. "Targets and terminology for comparative genomics in mammalian hibernators." Comparative Biochemistry and Physiology Part C: Toxicology & Pharmacology 148, no. 4 (November 2008): 447. http://dx.doi.org/10.1016/j.cbpc.2008.10.004.

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18

Baggs, Julie E., and John B. Hogenesch. "Genomics and systems approaches in the mammalian circadian clock." Current Opinion in Genetics & Development 20, no. 6 (December 2010): 581–87. http://dx.doi.org/10.1016/j.gde.2010.08.009.

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Cowley, Allen W. "Genomics and homeostasis." American Journal of Physiology-Regulatory, Integrative and Comparative Physiology 284, no. 3 (March 1, 2003): R611—R627. http://dx.doi.org/10.1152/ajpregu.00567.2002.

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The Cannon lecture this year illustrates how knowledge of DNA sequences of complex living organisms is beginning to shape the landscape of physiology in the 21st century. Enormous challenges and opportunities now exist for physiologists to relate the galaxy of genes to normal and pathological functions. The first extensive genomic systems biology map for cardiovascular and renal function was completed last year as well as a new hypothesis-generating tool (“physiological profiling”) that enables us to hypothesize relationships between specific genes responsible for the regulation of regulatory pathways. Techniques of chromosomal substitution (consomic and congenic rats) are beginning to confirm statistical results from linkage analysis studies, narrow the regions of genetic interest for positional cloning, and provide genetically well-defined control strains for physiological studies. Patterns of gene expression identified by microarray and mapping of expressed genes to chromosomal sites are adding to the understanding of systems physiology. The previously unimaginable goal of connecting ∼36,000 genes to the complex functions of mammalian systems is indeed well underway.

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Hiller, Michael, Hermann Ansorge, Triantafyllos Chavakis, Jörns Fickel, Peter Giere, Peter Grobe, Jochen Hampe, et al. "Discovering the genomic basis of morphological and physiological differences between mammalian species with Forward Genomics." Mammalian Biology 81 (September 2016): 9–10. http://dx.doi.org/10.1016/j.mambio.2016.07.027.

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Kulyyassov, Arman, and Ruslan Kalendar. "In Silico Estimation of the Abundance and Phylogenetic Significance of the Composite Oct4-Sox2 Binding Motifs within a Wide Range of Species." Data 5, no. 4 (November 29, 2020): 111. http://dx.doi.org/10.3390/data5040111.

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High-throughput sequencing technologies have greatly accelerated the progress of genomics, transcriptomics, and metagenomics. Currently, a large amount of genomic data from various organisms is being generated, the volume of which is increasing every year. Therefore, the development of methods that allow the rapid search and analysis of DNA sequences is urgent. Here, we present a novel motif-based high-throughput sequence scoring method that generates genome information. We found and identified Utf1-like, Fgf4-like, and Hoxb1-like motifs, which are cis-regulatory elements for the pluripotency transcription factors Sox2 and Oct4 within the genomes of different eukaryotic organisms. The genome-wide analysis of these motifs was performed to understand the impact of their diversification on mammalian genome evolution. Utf1-like, Fgf4-like, and Hoxb1-like motif diversity was evaluated across genomes from multiple species.

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Samusik, Nikolay A., Yuriy P. Galachyants, and Andrey P. Kozlov. "Evolutionary analysis of sequences expressed in tumors." Ecological genetics 7, no. 2 (June 15, 2009): 26–37. http://dx.doi.org/10.17816/ecogen7226-37.

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Earlier we have identified a new class of human genomic sequences expressed preferentially in tumors. Here we use a comparative genomics approach and conservation analysis to study evolutionary specificity of nine human tumor-specific sequences, described previously. Three sequences had originated in the primate lineage. The other three had mammalian orthologs, but conservation analysis has shown that these sequences evolved neutrally. Three sequences were conservative. These data confirm previously formulated hypothesis that evolutionarily new genes are expressed in tumors.

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Uzun, Alper, Nelida Rodriguez-Osorio, Abdullah Kaya, Hongfeng Wang, John J. Parrish, Valentin A. Ilyin, and Erdogan Memili. "Functional genomics of HMGN3a and SMARCAL1 in early mammalian embryogenesis." BMC Genomics 10, no. 1 (2009): 183. http://dx.doi.org/10.1186/1471-2164-10-183.

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Tollis, Marc, Joshua D. Schiffman, and Amy M. Boddy. "Evolution of cancer suppression as revealed by mammalian comparative genomics." Current Opinion in Genetics & Development 42 (February 2017): 40–47. http://dx.doi.org/10.1016/j.gde.2016.12.004.

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Klysik, Jan. "Mice and humans: chromosome engineering and its application to functional genomics." Acta Biochimica Polonica 49, no. 3 (September 30, 2002): 553–69. http://dx.doi.org/10.18388/abp.2002_3766.

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Functional modeling of human genes and diseases requires suitable mammalian model organisms. For its genetic malleability, the mouse is likely to continue to play a major role in defining basic genetic traits and complex pathological disorders. Recently, gene targeting techniques have been extended towards developing new engineering strategies for generating extensive lesions and rearrangements in mouse chromosomes. While these advances create new opportunities to address similar aberrations observed in human diseases, they also open new ways of scaling-up mutagenesis projects that try to catalogue and annotate cellular functions of mammalian genes.

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Dalrymple, B. P. "Harnessing the bovine genome sequence for the Australian cattle and sheep industries." Australian Journal of Experimental Agriculture 45, no. 8 (2005): 1011. http://dx.doi.org/10.1071/ea05043.

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Genomics is an emerging science and the release of the human and mouse genomes has significantly altered our picture of the information content of mammalian genomes. A smaller number of protein coding genes, and a larger number of genes that do not appear to encode protein products, the so-called non-coding RNAs (ncRNAs), have been identified. The first 2 drafts of the bovine genome sequence have been released, and work to utilise the framework of the bovine genome to facilitate ovine genomics is underway. In anticipation of the requirement for a detailed analysis of the ruminant genomes, their transcriptomes, interactomes, regulomes and similar, we have been developing the informatics platform for the analysis and integration of genome sequences and expression data for cattle and sheep. This resource will enable us to utilise the ruminant datasets and integrate them with equivalent data from other mammals for the advancement of animal scientific research for applications in the cattle and sheep industries in Australia.

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Sánchez-Andrade, Gabriela, Jacob Moskowitz, Selene Howe, and Teresa M. Gunn. "Meeting report: 31st International Mammalian Genome Conference, Mammalian Genetics and Genomics: From Molecular Mechanisms to Translational Applications." Mammalian Genome 29, no. 5-6 (May 8, 2018): 299–309. http://dx.doi.org/10.1007/s00335-018-9747-6.

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Church, Philip C., and Andrzej M. Goscinski. "A Survey of Cloud-Based Service Computing Solutions for Mammalian Genomics." IEEE Transactions on Services Computing 7, no. 4 (October 1, 2014): 726–40. http://dx.doi.org/10.1109/tsc.2014.2353645.

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Zhou, Fu-lai, Sheena C. Li, Yue Zhu, Wan-jing Guo, Li-jun Shao, Justin Nelson, Scott Simpkins, et al. "Publisher Correction: Integrating yeast chemical genomics and mammalian cell pathway analysis." Acta Pharmacologica Sinica 41, no. 5 (February 21, 2020): 729. http://dx.doi.org/10.1038/s41401-019-0355-0.

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Ui-Tei, Kumiko, Yuki Naito, and Kaoru Saigo. "Essential Notes Regarding the Design of Functional siRNAs for Efficient Mammalian RNAi." Journal of Biomedicine and Biotechnology 2006 (2006): 1–8. http://dx.doi.org/10.1155/jbb/2006/65052.

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Short interfering RNAs (siRNAs) are widely used to bring about RNA interference (RNAi) in mammalian cells. Numerous siRNAs may be designed for any target gene though most of which would be incapable of efficiently inducing mammalian RNAi. Certain highly functional siRNAs designed for knockout of a particular gene may render unrelated endogenous genes nonfunctional. These major bottlenecks should be properly eliminated when RNAi technologies are employed for any experiment in mammalian functional genomics. This paper thus presents essential notes and findings regarding the proper choice of siRNA-sequence selection algorithms and web-based online software systems.

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Amare, Andinet, Amanda B. Hummon, Bruce R. Southey, Tyler A. Zimmerman, Sandra L. Rodriguez-Zas, and Jonathan V. Sweedler. "Bridging Neuropeptidomics and Genomics with Bioinformatics: Prediction of Mammalian Neuropeptide Prohormone Processing." Journal of Proteome Research 5, no. 5 (May 2006): 1162–67. http://dx.doi.org/10.1021/pr0504541.

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Alekseyev, Max A., and Pavel A. Pevzner. "Comparative genomics reveals birth and death of fragile regions in mammalian evolution." Genome Biology 11, no. 11 (2010): R117. http://dx.doi.org/10.1186/gb-2010-11-11-r117.

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Genov, Nikolai, Stefano Castellana, Felix Scholkmann, Daniele Capocefalo, Mauro Truglio, Jessica Rosati, Elisa Maria Turco, et al. "A Multi-Layered Study on Harmonic Oscillations in Mammalian Genomics and Proteomics." International Journal of Molecular Sciences 20, no. 18 (September 17, 2019): 4585. http://dx.doi.org/10.3390/ijms20184585.

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Cellular, organ, and whole animal physiology show temporal variation predominantly featuring 24-h (circadian) periodicity. Time-course mRNA gene expression profiling in mouse liver showed two subsets of genes oscillating at the second (12-h) and third (8-h) harmonic of the prime (24-h) frequency. The aim of our study was to identify specific genomic, proteomic, and functional properties of ultradian and circadian subsets. We found hallmarks of the three oscillating gene subsets, including different (i) functional annotation, (ii) proteomic and electrochemical features, and (iii) transcription factor binding motifs in upstream regions of 8-h and 12-h oscillating genes that seemingly allow the link of the ultradian gene sets to a known circadian network. Our multifaceted bioinformatics analysis of circadian and ultradian genes suggests that the different rhythmicity of gene expression impacts physiological outcomes and may be related to transcriptional, translational and post-translational dynamics, as well as to phylogenetic and evolutionary components.

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Mallon, Ann-Marie. "Introduction to Mammalian Genome special issue: Informatics and Integrative Genomics—Part 1." Mammalian Genome 26, no. 7-8 (August 2015): 271. http://dx.doi.org/10.1007/s00335-015-9594-7.

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Mallon, Ann-Marie. "Introduction to Mammalian Genome special issue: Informatics and Integrative Genomics—Part 2." Mammalian Genome 26, no. 9-10 (September 28, 2015): 365. http://dx.doi.org/10.1007/s00335-015-9604-9.

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Dow, Lukas E., and Scott W. Lowe. "Life in the Fast Lane: Mammalian Disease Models in the Genomics Era." Cell 148, no. 6 (March 2012): 1099–109. http://dx.doi.org/10.1016/j.cell.2012.02.023.

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Fontanesi, Luca, Federica Di Palma, Paul Flicek, Andrew T. Smith, Carl-Gustaf Thulin, and Paulo C. Alves. "LaGomiCs—Lagomorph Genomics Consortium: An International Collaborative Effort for Sequencing the Genomes of an Entire Mammalian Order." Journal of Heredity 107, no. 4 (February 26, 2016): 295–308. http://dx.doi.org/10.1093/jhered/esw010.

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Kalbfleisch, Ted, and Michael P. Heaton. "Mapping whole genome shotgun sequence and variant calling in mammalian species without their reference genomes." F1000Research 2 (November 14, 2013): 244. http://dx.doi.org/10.12688/f1000research.2-244.v1.

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Genomics research in mammals has produced reference genome sequences that are essential for identifying variation associated with disease. High quality reference genome sequences are now available for humans, model species, and economically important agricultural animals. Comparisons between these species have provided unique insights into mammalian gene function. However, the number of species with reference genomes is small compared to those needed for studying molecular evolutionary relationships in the tree of life. For example, among the even-toed ungulates there are approximately 300 species whose phylogenetic relationships have been calculated in the 10k trees project. Only six of these have reference genomes: cattle, swine, sheep, goat, water buffalo, and bison. Although reference sequences will eventually be developed for additional hoof stock, the resources in terms of time, money, infrastructure and expertise required to develop a quality reference genome may be unattainable for most species for at least another decade. In this work we mapped 35 Gb of next generation sequence data of a Katahdin sheep to its own species’ reference genome (Ovis aries Oar3.1) and to that of a species that diverged 15 to 30 million years ago (Bos taurus UMD3.1). In total, 56% of reads covered 76% of UMD3.1 to an average depth of 6.8 reads per site, 83 million variants were identified, of which 78 million were homozygous and likely represent interspecies nucleotide differences. Excluding genome repeat regions and sex chromosomes, approximately 3.7 million heterozygous sites were identified in this animal vs. bovine UMD3.1, representing polymorphisms occurring in sheep. Of these, 41% could be readily mapped to orthologous positions in ovine Oar3.1 with 80% corroborated as heterozygous. These variant sites, identified via interspecies mapping could be used for comparative genomics, disease association studies, and ultimately to understand mammalian gene function.

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Kalbfleisch, Ted, and Michael P. Heaton. "Mapping whole genome shotgun sequence and variant calling in mammalian species without their reference genomes." F1000Research 2 (February 10, 2014): 244. http://dx.doi.org/10.12688/f1000research.2-244.v2.

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Genomics research in mammals has produced reference genome sequences that are essential for identifying variation associated with disease. High quality reference genome sequences are now available for humans, model species, and economically important agricultural animals. Comparisons between these species have provided unique insights into mammalian gene function. However, the number of species with reference genomes is small compared to those needed for studying molecular evolutionary relationships in the tree of life. For example, among the even-toed ungulates there are approximately 300 species whose phylogenetic relationships have been calculated in the 10k trees project. Only six of these have reference genomes: cattle, swine, sheep, goat, water buffalo, and bison. Although reference sequences will eventually be developed for additional hoof stock, the resources in terms of time, money, infrastructure and expertise required to develop a quality reference genome may be unattainable for most species for at least another decade. In this work we mapped 35 Gb of next generation sequence data of a Katahdin sheep to its own species’ reference genome (Ovis aries Oar3.1) and to that of a species that diverged 15 to 30 million years ago (Bos taurus UMD3.1). In total, 56% of reads covered 76% of UMD3.1 to an average depth of 6.8 reads per site, 83 million variants were identified, of which 78 million were homozygous and likely represent interspecies nucleotide differences. Excluding repeat regions and sex chromosomes, nearly 3.7 million heterozygous sites were identified in this animal vs. bovine UMD3.1, representing polymorphisms occurring in sheep. Of these, 41% could be readily mapped to orthologous positions in ovine Oar3.1 with 80% corroborated as heterozygous. These variant sites, identified via interspecies mapping could be used for comparative genomics, disease association studies, and ultimately to understand mammalian gene function.

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Oluwole, O. O. "Computational Genomics of RELA gene of Pig and its protein prescription." Nigerian Journal of Animal Production 45, no. 1 (December 27, 2020): 9–17. http://dx.doi.org/10.51791/njap.v45i1.378.

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RELA gene is a pleiotropic transcription that is present in almost all living cells where several signal transduction events end points were initiated by many arrays of stimuli that were related to many biological processes such as inflammation, immunity, differentiation, cell growth, tumorigenesis and apoptosis in the cells. The nucleotide and amino acid sequence (AAS) of RELA gene of pig and other mammalian species were downloaded from the National Center for Biotechnology information (NCBI) data base, United State of America and Universal protein resources (Uniprot) database, United Kingdom. Data generated were analyzed by bioinformatics tools. The results showed a high variation of AAS among the mammals where only four mammals have the same AAS length (551) with pig while others were not. The RELA gene of pig shared very high percent identity with all mammals ranging from 95.5% (warthog) to 83.5% (guinea pig) and similarity percentage ranged from 85.1 to 99.5% where the warthog had the highest percentage value while the least mammal was Guinea pig. The tree showed RELA gene with two clades; the first for mammals and the second for non-mammals. The RELA gene of pig was in the same cluster with the other Suidae family, warthog and babirusa. For the protein structure obtained, only 43% can be meaningfully predicted from the 61% residues modelled at more than 90%. The domain architecture of RELA protein structure contained mainly RNA Recognition motif and region of low complexity. The domainstarting position of all the organisms ranged from 191 to 210 while the termination of all the mammals ranged from 102 to 306 amino acids.The region of low complexity starting point ranged from position 173 to 462while termination positions ranged from 184 to 474. The evolution relationship of RELA gene of pig and other mammalian species were highly related and conserved among the mammalian species; they have high comparability and they evolved from common ancestors.

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Keniry, Andrew, and Marnie E. Blewitt. "Studying X chromosome inactivation in the single-cell genomic era." Biochemical Society Transactions 46, no. 3 (April 20, 2018): 577–86. http://dx.doi.org/10.1042/bst20170346.

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Single-cell genomics is set to revolutionise our understanding of how epigenetic silencing works; by studying specific epigenetic marks or chromatin conformations in single cells, it is possible to ask whether they cause transcriptional silencing or are instead a consequence of the silent state. Here, we review what single-cell genomics has revealed about X chromosome inactivation, perhaps the best characterised mammalian epigenetic process, highlighting the novel findings and important differences between mouse and human X inactivation uncovered through these studies. We consider what fundamental questions these techniques are set to answer in coming years and propose that X chromosome inactivation is an ideal model to study gene silencing by single-cell genomics as technical limitations are minimised through the co-analysis of hundreds of genes.

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Kampmann, Martin, Michael C. Bassik, and Jonathan S. Weissman. "Functional genomics platform for pooled screening and generation of mammalian genetic interaction maps." Nature Protocols 9, no. 8 (July 3, 2014): 1825–47. http://dx.doi.org/10.1038/nprot.2014.103.

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El-Shazly, S., S. Ahmad, A. S. Mustafa, R. Al-Attiya, and D. Krajci. "PP-226 Functional genomics of Mammalian cell entry-3 proteins of Mycobacterium tuberculosis." International Journal of Infectious Diseases 14 (July 2010): S93. http://dx.doi.org/10.1016/s1201-9712(10)60294-9.

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Silva, Jose, Kenneth Chang, Gregory J. Hannon, and Fabiola V. Rivas. "RNA-interference-based functional genomics in mammalian cells: reverse genetics coming of age." Oncogene 23, no. 51 (November 2004): 8401–9. http://dx.doi.org/10.1038/sj.onc.1208176.

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Barturen, Guillermo, Stefanie Geisen, Francisco Dios, E. J. Maarten Hamberg, Michael Hackenberg, and José L. Oliver. "CpGislandEVO: A Database and Genome Browser for Comparative Evolutionary Genomics of CpG Islands." BioMed Research International 2013 (2013): 1–6. http://dx.doi.org/10.1155/2013/709042.

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Hypomethylated, CpG-rich DNA segments (CpG islands, CGIs) are epigenome markers involved in key biological processes. Aberrant methylation is implicated in the appearance of several disorders as cancer, immunodeficiency, or centromere instability. Furthermore, methylation differences at promoter regions between human and chimpanzee strongly associate with genes involved in neurological/psychological disorders and cancers. Therefore, the evolutionary comparative analyses of CGIs can provide insights on the functional role of these epigenome markers in both health and disease. Given the lack of specific tools, we developedCpGislandEVO. Briefly, we first compile a database of statistically significant CGIs for the best assembled mammalian genome sequences available to date. Second, by means of a coupled browser front-end, we focus on the CGIs overlapping orthologous genes extracted fromOrthoDB, thus ensuring the comparison between CGIs located on truly homologous genome segments. This allows comparing the main compositional features between homologous CGIs. Finally, to facilitate nucleotide comparisons, we lifted genome coordinates between assemblies from different species, which enables the analysis of sequence divergence by direct count of nucleotide substitutions and indels occurring between homologous CGIs. The resultingCpGislandEVOdatabase, linking together CGIs and single-cytosine DNA methylation data from several mammalian species, is freely available at our website.

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Seta, Karen A., and David E. Millhorn. "Functional genomics approach to hypoxia signaling." Journal of Applied Physiology 96, no. 2 (February 2004): 765–73. http://dx.doi.org/10.1152/japplphysiol.00836.2003.

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Mammalian cells require a constant supply of oxygen to maintain energy balance, and sustained hypoxia can result in cell death. It is therefore not surprising that sophisticated adaptive mechanisms have evolved that enhance cell survival during hypoxia. During the past few years, there have been a growing number of reports on hypoxia-induced transcription of specific genes. In this review, we describe a unique experimental approach that utilizes focused cDNA libraries coupled to microarray analyses to identify hypoxia-responsive signal transduction pathways and genes that confer the hypoxia-tolerant phenotype. We have used the subtractive suppression hybridization (SSH) method to create a cDNA library enriched in hypoxia-regulated genes in oxygen-sensing pheochromocytoma cells and have used this library to create microarrays that allow us to examine hundreds of genes at a time. This library contains over 300 genes and expressed sequence tags upregulated by hypoxia, including tyrosine hydroxylase, vascular endothelial growth factor, and junB. Hypoxic regulation of these and other genes in the library has been confirmed by microarray, Northern blot, and real-time PCR analyses. Coupling focused SSH libraries with microarray analyses allows one to specifically study genes relevant to a phenotype of interest while reducing much of the biological noise associated with these types of studies. When used in conjunction with high-throughput, dye-based assays for cell survival and apoptosis, this approach offers a rapid method for discovering validated therapeutic targets for the treatment of cardiovascular disease, stroke, and tumors.

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Hao, Yue, Hyuk Jin Lee, Michael Baraboo, Katherine Burch, Taylor Maurer, Jason A. Somarelli, and Gavin C. Conant. "Baby Genomics: Tracing the Evolutionary Changes That Gave Rise to Placentation." Genome Biology and Evolution 12, no. 3 (February 13, 2020): 35–47. http://dx.doi.org/10.1093/gbe/evaa026.

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Abstract It has long been challenging to uncover the molecular mechanisms behind striking morphological innovations such as mammalian pregnancy. We studied the power of a robust comparative orthology pipeline based on gene synteny to address such problems. We inferred orthology relations between human genes and genes from each of 43 other vertebrate genomes, resulting in ∼18,000 orthologous pairs for each genome comparison. By identifying genes that first appear coincident with origin of the placental mammals, we hypothesized that we would define a subset of the genome enriched for genes that played a role in placental evolution. We thus pinpointed orthologs that appeared before and after the divergence of eutherian mammals from marsupials. Reinforcing previous work, we found instead that much of the genetic toolkit of mammalian pregnancy evolved through the repurposing of preexisting genes to new roles. These genes acquired regulatory controls for their novel roles from a group of regulatory genes, many of which did in fact originate at the appearance of the eutherians. Thus, orthologs appearing at the origin of the eutherians are enriched in functions such as transcriptional regulation by Krüppel-associated box-zinc-finger proteins, innate immune responses, keratinization, and the melanoma-associated antigen protein class. Because the cellular mechanisms of invasive placentae are similar to those of metastatic cancers, we then used our orthology inferences to explore the association between placenta invasion and cancer metastasis. Again echoing previous work, we find that genes that are phylogenetically older are more likely to be implicated in cancer development.

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Lo, Albert, and Lei Qi. "Genetic and epigenetic control of gene expression by CRISPR–Cas systems." F1000Research 6 (May 25, 2017): 747. http://dx.doi.org/10.12688/f1000research.11113.1.

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The discovery and adaption of bacterial clustered regularly interspaced short palindromic repeats (CRISPR)–CRISPR-associated (Cas) systems has revolutionized the way researchers edit genomes. Engineering of catalytically inactivated Cas variants (nuclease-deficient or nuclease-deactivated [dCas]) combined with transcriptional repressors, activators, or epigenetic modifiers enable sequence-specific regulation of gene expression and chromatin state. These CRISPR–Cas-based technologies have contributed to the rapid development of disease models and functional genomics screening approaches, which can facilitate genetic target identification and drug discovery. In this short review, we will cover recent advances of CRISPR–dCas9 systems and their use for transcriptional repression and activation, epigenome editing, and engineered synthetic circuits for complex control of the mammalian genome.

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Womack, J. E. "The impact of sequencing the bovine genome." Australian Journal of Experimental Agriculture 46, no. 2 (2006): 151. http://dx.doi.org/10.1071/ea05229.

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Sequencing the bovine genome is the culmination of more than a decade of international collaboration to bring together resources to chart the genome of an economically important and biologically interesting species. Although considerable sequence is available at the publication of these proceedings, much work remains in annotation of the genome and the discovery of DNA polymorphisms within and between breeds. Nonetheless, the public availability of this sequence has already enhanced our ability to identify genes underlying phenotypes and to understand evolutionary relationships with other mammalian species. The accelerated rate of gene discovery in humans and laboratory animals following the sequencing of their genomes promises an exciting post-sequencing era for bovine genomics.

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Blake, J. A., C. J. Bult, J. A. Kadin, J. E. Richardson, and J. T. Eppig. "The Mouse Genome Database (MGD): premier model organism resource for mammalian genomics and genetics." Nucleic Acids Research 39, Database (November 3, 2010): D842—D848. http://dx.doi.org/10.1093/nar/gkq1008.

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Journal articles on the topic 'Mammalian genomics'

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