1
|
Abstract
Real-time quantitative polymerase chain reaction (qPCR) is a powerful tool for analyzing and quantifying gene expression, and its primer design is the first and most important step. In order to improve the efficiency and effectiveness of primer design, we designed a database qPrimerDB, based on thermodynamics gene-specific for multispecies qPCR primers design.In this chapter, we explained the working principle of the database and detailed the step-by-step practical steps with examples. The valuable and time-saving qPrimerDB database is publicly accessible at http://biodb.swu.edu.cn/qprimerdb and will be routinely updated.
Collapse
|
2
|
Blumberg A, Zhao Y, Huang YF, Dukler N, Rice EJ, Chivu AG, Krumholz K, Danko CG, Siepel A. Characterizing RNA stability genome-wide through combined analysis of PRO-seq and RNA-seq data. BMC Biol 2021; 19:30. [PMID: 33588838 PMCID: PMC7885420 DOI: 10.1186/s12915-021-00949-x] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2020] [Accepted: 01/05/2021] [Indexed: 01/03/2023] Open
Abstract
BACKGROUND The concentrations of distinct types of RNA in cells result from a dynamic equilibrium between RNA synthesis and decay. Despite the critical importance of RNA decay rates, current approaches for measuring them are generally labor-intensive, limited in sensitivity, and/or disruptive to normal cellular processes. Here, we introduce a simple method for estimating relative RNA half-lives that is based on two standard and widely available high-throughput assays: Precision Run-On sequencing (PRO-seq) and RNA sequencing (RNA-seq). RESULTS Our method treats PRO-seq as a measure of transcription rate and RNA-seq as a measure of RNA concentration, and estimates the rate of RNA decay required for a steady-state equilibrium. We show that this approach can be used to assay relative RNA half-lives genome-wide, with good accuracy and sensitivity for both coding and noncoding transcription units. Using a structural equation model (SEM), we test several features of transcription units, nearby DNA sequences, and nearby epigenomic marks for associations with RNA stability after controlling for their effects on transcription. We find that RNA splicing-related features are positively correlated with RNA stability, whereas features related to miRNA binding and DNA methylation are negatively correlated with RNA stability. Furthermore, we find that a measure based on U1 binding and polyadenylation sites distinguishes between unstable noncoding and stable coding transcripts but is not predictive of relative stability within the mRNA or lincRNA classes. We also identify several histone modifications that are associated with RNA stability. CONCLUSION We introduce an approach for estimating the relative half-lives of individual RNAs. Together, our estimation method and systematic analysis shed light on the pervasive impacts of RNA stability on cellular RNA concentrations.
Collapse
Affiliation(s)
- Amit Blumberg
- Simons Center for Quantitative Biology, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA
| | - Yixin Zhao
- Simons Center for Quantitative Biology, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA
| | - Yi-Fei Huang
- Simons Center for Quantitative Biology, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA
- Present Address: Department of Biology and Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, PA, USA
| | - Noah Dukler
- Simons Center for Quantitative Biology, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA
| | - Edward J Rice
- Baker Institute for Animal Health, College of Veterinary Medicine, Cornell University, Ithaca, NY, USA
| | - Alexandra G Chivu
- Baker Institute for Animal Health, College of Veterinary Medicine, Cornell University, Ithaca, NY, USA
| | - Katie Krumholz
- Simons Center for Quantitative Biology, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA
| | - Charles G Danko
- Baker Institute for Animal Health, College of Veterinary Medicine, Cornell University, Ithaca, NY, USA
| | - Adam Siepel
- Simons Center for Quantitative Biology, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA.
| |
Collapse
|
3
|
Reshetniak S, Ußling J, Perego E, Rammner B, Schikorski T, Fornasiero EF, Truckenbrodt S, Köster S, Rizzoli SO. A comparative analysis of the mobility of 45 proteins in the synaptic bouton. EMBO J 2020; 39:e104596. [PMID: 32627850 PMCID: PMC7429486 DOI: 10.15252/embj.2020104596] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2020] [Revised: 05/20/2020] [Accepted: 05/29/2020] [Indexed: 02/01/2023] Open
Abstract
Many proteins involved in synaptic transmission are well known, and their features, as their abundance or spatial distribution, have been analyzed in systematic studies. This has not been the case, however, for their mobility. To solve this, we analyzed the motion of 45 GFP-tagged synaptic proteins expressed in cultured hippocampal neurons, using fluorescence recovery after photobleaching, particle tracking, and modeling. We compared synaptic vesicle proteins, endo- and exocytosis cofactors, cytoskeleton components, and trafficking proteins. We found that movement was influenced by the protein association with synaptic vesicles, especially for membrane proteins. Surprisingly, protein mobility also correlated significantly with parameters as the protein lifetimes, or the nucleotide composition of their mRNAs. We then analyzed protein movement thoroughly, taking into account the spatial characteristics of the system. This resulted in a first visualization of overall protein motion in the synapse, which should enable future modeling studies of synaptic physiology.
Collapse
Affiliation(s)
- Sofiia Reshetniak
- Institute for Neuro‐ and Sensory Physiology and Biostructural Imaging of Neurodegeneration (BIN) CenterUniversity Medical Center GöttingenGöttingenGermany
- International Max Planck Research School for Molecular BiologyGöttingenGermany
| | - Jan‐Eike Ußling
- Institute for Neuro‐ and Sensory Physiology and Biostructural Imaging of Neurodegeneration (BIN) CenterUniversity Medical Center GöttingenGöttingenGermany
| | - Eleonora Perego
- Institute for X‐Ray PhysicsUniversity of GöttingenGöttingenGermany
| | - Burkhard Rammner
- Institute for Neuro‐ and Sensory Physiology and Biostructural Imaging of Neurodegeneration (BIN) CenterUniversity Medical Center GöttingenGöttingenGermany
| | - Thomas Schikorski
- Department of NeuroscienceUniversidad Central del CaribeBayamonPRUSA
| | - Eugenio F Fornasiero
- Institute for Neuro‐ and Sensory Physiology and Biostructural Imaging of Neurodegeneration (BIN) CenterUniversity Medical Center GöttingenGöttingenGermany
| | - Sven Truckenbrodt
- Institute for Neuro‐ and Sensory Physiology and Biostructural Imaging of Neurodegeneration (BIN) CenterUniversity Medical Center GöttingenGöttingenGermany
- International Max Planck Research School for Molecular BiologyGöttingenGermany
| | - Sarah Köster
- Institute for X‐Ray PhysicsUniversity of GöttingenGöttingenGermany
- Cluster of Excellence “Multiscale Bioimaging: from Molecular Machines to Networks of Excitable Cells” (MBExC)University of GöttingenGöttingenGermany
| | - Silvio O Rizzoli
- Institute for Neuro‐ and Sensory Physiology and Biostructural Imaging of Neurodegeneration (BIN) CenterUniversity Medical Center GöttingenGöttingenGermany
- Cluster of Excellence “Multiscale Bioimaging: from Molecular Machines to Networks of Excitable Cells” (MBExC)University of GöttingenGöttingenGermany
| |
Collapse
|
4
|
Arhondakis S, Milanesi M, Castrignanò T, Gioiosa S, Valentini A, Chillemi G. Evidence of distinct gene functional patterns in GC-poor and GC-rich isochores in Bos taurus. Anim Genet 2020; 51:358-368. [PMID: 32069522 DOI: 10.1111/age.12917] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/20/2020] [Indexed: 01/10/2023]
Abstract
Vertebrate genomes are mosaics of megabase-size DNA segments with a fairly homogeneous base composition, called isochores. They are divided into five families characterized by different guanine-cytosine (GC) levels and linked to several functional and structural properties. The increased availability of fully sequenced genomes allows the investigation of isochores in several species, assessing their level of conservation across vertebrate genomes. In this work, we characterized the isochores in Bos taurus using the ARS-UCD1.2 genome version. The comparison of our results with the well-studied human isochores and those of other mammals revealed a large conservation in isochore families, in number, average GC levels and gene density. Exceptions to the established increase in gene density with the increase in isochores (GC%) were observed for the following gene biotypes: tRNA, small nuclear RNA, small nucleolar RNA and pseudogenes that have their maximum number in H2 and H1 isochores. Subsequently, we assessed the ontology of all gene biotypes looking for functional classes that are statistically over- or under-represented in each isochore. Receptor activity and sensory perception pathways were significantly over-represented in L1 and L2 (GC-poor) isochores. This was also validated for the horse genome. Our analysis of housekeeping genes confirmed a preferential localization in GC-rich isochores, as reported in other species. Finally, we assessed the SNP distribution of a bovine high-density SNP chip across the isochores, finding a higher density in the GC-rich families, reflecting a potential bias in the chip, widely used for genetic selection and biodiversity studies.
Collapse
Affiliation(s)
- S Arhondakis
- Bioinformatics and Computational Science (BioCoS), Boniali 11-19, Chania, 73134, Crete, Greece
| | - M Milanesi
- Department of Support, Production and Animal Health, School of Veterinary Medicine, São Paulo State University, 16050-680 R. Clóvis Pestana 793 - Dona Amelia, Araçatuba, SP, Brazil.,International Atomic Energy Agency Collaborating Centre on Animal Genomics and Bioinformatics, 16050-680 R. Clóvis Pestana 793 - Dona Amelia, Araçatuba, SP, Brazil
| | - T Castrignanò
- SCAI - Super Computing Applications and Innovation Department, CINECA, Rome, Italy
| | - S Gioiosa
- SCAI - Super Computing Applications and Innovation Department, CINECA, Rome, Italy
| | - A Valentini
- Department for Innovation in Biological, Agro-food and Forest Systems, DIBAF, University of Tuscia, via S. Camillo de Lellis s.n.c, 01100, Viterbo, Italy
| | - G Chillemi
- Department for Innovation in Biological, Agro-food and Forest Systems, DIBAF, University of Tuscia, via S. Camillo de Lellis s.n.c, 01100, Viterbo, Italy.,Institute of Biomembranes, Bioenergetics and Molecular Biotechnologies, IBIOM, CNR, Bari, Italy
| |
Collapse
|
5
|
Lu K, Li T, He J, Chang W, Zhang R, Liu M, Yu M, Fan Y, Ma J, Sun W, Qu C, Liu L, Li N, Liang Y, Wang R, Qian W, Tang Z, Xu X, Lei B, Zhang K, Li J. qPrimerDB: a thermodynamics-based gene-specific qPCR primer database for 147 organisms. Nucleic Acids Res 2019; 46:D1229-D1236. [PMID: 28977518 PMCID: PMC5753361 DOI: 10.1093/nar/gkx725] [Citation(s) in RCA: 92] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2017] [Accepted: 08/08/2017] [Indexed: 01/09/2023] Open
Abstract
Real-time quantitative polymerase chain reaction (qPCR) is one of the most important methods for analyzing the expression patterns of target genes. However, successful qPCR experiments rely heavily on the use of high-quality primers. Various qPCR primer databases have been developed to address this issue, but these databases target only a few important organisms. Here, we developed the qPrimerDB database, founded on an automatic gene-specific qPCR primer design and thermodynamics-based validation workflow. The qPrimerDB database is the most comprehensive qPCR primer database available to date, with a web front-end providing gene-specific and pre-computed primer pairs across 147 important organisms, including human, mouse, zebrafish, yeast, thale cress, rice and maize. In this database, we provide 3331426 of the best primer pairs for each gene, based on primer pair coverage, as well as 47760359 alternative gene-specific primer pairs, which can be conveniently batch downloaded. The specificity and efficiency was validated for qPCR primer pairs for 66 randomly selected genes, in six different organisms, through qPCR assays and gel electrophoresis. The qPrimerDB database represents a valuable, timesaving resource for gene expression analysis. This resource, which will be routinely updated, is publically accessible at http://biodb.swu.edu.cn/qprimerdb.
Collapse
Affiliation(s)
- Kun Lu
- College of Agronomy and Biotechnology, Southwest University, Beibei, Chongqing 400715, China.,Academy of Agricultural Sciences, Southwest University, Beibei, Chongqing 400715, China
| | - Tian Li
- State Key Laboratory of Silkworm Genome Biology, Southwest University, Chongqing 400715, China
| | - Jian He
- Shennong Class, Southwest University, Beibei, Chongqing 400715, China.,College of Resources and Environment, Southwest University, Chongqing 400715, China
| | - Wei Chang
- College of Agronomy and Biotechnology, Southwest University, Beibei, Chongqing 400715, China.,Shennong Class, Southwest University, Beibei, Chongqing 400715, China
| | - Rui Zhang
- College of Agronomy and Biotechnology, Southwest University, Beibei, Chongqing 400715, China
| | - Miao Liu
- College of Agronomy and Biotechnology, Southwest University, Beibei, Chongqing 400715, China
| | - Mengna Yu
- College of Agronomy and Biotechnology, Southwest University, Beibei, Chongqing 400715, China
| | - Yonghai Fan
- College of Agronomy and Biotechnology, Southwest University, Beibei, Chongqing 400715, China
| | - Jinqi Ma
- College of Agronomy and Biotechnology, Southwest University, Beibei, Chongqing 400715, China.,Shennong Class, Southwest University, Beibei, Chongqing 400715, China
| | - Wei Sun
- College of Agronomy and Biotechnology, Southwest University, Beibei, Chongqing 400715, China
| | - Cunmin Qu
- College of Agronomy and Biotechnology, Southwest University, Beibei, Chongqing 400715, China.,Academy of Agricultural Sciences, Southwest University, Beibei, Chongqing 400715, China
| | - Liezhao Liu
- College of Agronomy and Biotechnology, Southwest University, Beibei, Chongqing 400715, China.,Academy of Agricultural Sciences, Southwest University, Beibei, Chongqing 400715, China
| | - Nannan Li
- Academy of Agricultural Sciences, Southwest University, Beibei, Chongqing 400715, China.,College of Resources and Environment, Southwest University, Chongqing 400715, China
| | - Ying Liang
- College of Agronomy and Biotechnology, Southwest University, Beibei, Chongqing 400715, China.,Academy of Agricultural Sciences, Southwest University, Beibei, Chongqing 400715, China
| | - Rui Wang
- College of Agronomy and Biotechnology, Southwest University, Beibei, Chongqing 400715, China.,Academy of Agricultural Sciences, Southwest University, Beibei, Chongqing 400715, China
| | - Wei Qian
- College of Agronomy and Biotechnology, Southwest University, Beibei, Chongqing 400715, China
| | - Zhanglin Tang
- College of Agronomy and Biotechnology, Southwest University, Beibei, Chongqing 400715, China
| | - Xinfu Xu
- College of Agronomy and Biotechnology, Southwest University, Beibei, Chongqing 400715, China.,Academy of Agricultural Sciences, Southwest University, Beibei, Chongqing 400715, China
| | - Bo Lei
- Key Laboratory of Molecular Genetics, China National Tobacco Corporation, Guizhou Academy of Tobacco Science, Guiyang 550081, China.,Upland Flue-Cured Tobacco Quality and Ecology Key Laboratory of China Tobacco, Guizhou Academy of Tobacco Science, Guiyang 550081, China
| | - Kai Zhang
- College of Agronomy and Biotechnology, Southwest University, Beibei, Chongqing 400715, China
| | - Jiana Li
- College of Agronomy and Biotechnology, Southwest University, Beibei, Chongqing 400715, China.,Academy of Agricultural Sciences, Southwest University, Beibei, Chongqing 400715, China
| |
Collapse
|
6
|
Mandad S, Rahman RU, Centeno TP, Vidal RO, Wildhagen H, Rammner B, Keihani S, Opazo F, Urban I, Ischebeck T, Kirli K, Benito E, Fischer A, Yousefi RY, Dennerlein S, Rehling P, Feussner I, Urlaub H, Bonn S, Rizzoli SO, Fornasiero EF. The codon sequences predict protein lifetimes and other parameters of the protein life cycle in the mouse brain. Sci Rep 2018; 8:16913. [PMID: 30443017 PMCID: PMC6237891 DOI: 10.1038/s41598-018-35277-8] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2018] [Accepted: 11/02/2018] [Indexed: 12/14/2022] Open
Abstract
The homeostasis of the proteome depends on the tight regulation of the mRNA and protein abundances, of the translation rates, and of the protein lifetimes. Results from several studies on prokaryotes or eukaryotic cell cultures have suggested that protein homeostasis is connected to, and perhaps regulated by, the protein and the codon sequences. However, this has been little investigated for mammals in vivo. Moreover, the link between the coding sequences and one critical parameter, the protein lifetime, has remained largely unexplored, both in vivo and in vitro. We tested this in the mouse brain, and found that the percentages of amino acids and codons in the sequences could predict all of the homeostasis parameters with a precision approaching experimental measurements. A key predictive element was the wobble nucleotide. G-/C-ending codons correlated with higher protein lifetimes, protein abundances, mRNA abundances and translation rates than A-/U-ending codons. Modifying the proportions of G-/C-ending codons could tune these parameters in cell cultures, in a proof-of-principle experiment. We suggest that the coding sequences are strongly linked to protein homeostasis in vivo, albeit it still remains to be determined whether this relation is causal in nature.
Collapse
Affiliation(s)
- Sunit Mandad
- Department of Neuro- and Sensory Physiology, University Medical Center Göttingen, Cluster of Excellence Nanoscale Microscopy and Molecular Physiology of the Brain, 37073, Göttingen, Germany
- Bioanalytical Mass Spectrometry Group, Max Planck Institute of Biophysical Chemistry, 37077, Göttingen, Germany
| | - Raza-Ur Rahman
- Laboratory of Computational Systems Biology, German Center for Neurodegenerative Diseases (DZNE), 37075, Göttingen, Germany
- Institute of Medical Systems Biology, Center for Molecular Neurobiology (ZMNH), University Medical Center Hamburg-Eppendorf (UKE), 20246, Hamburg, Germany
| | - Tonatiuh Pena Centeno
- Laboratory of Computational Systems Biology, German Center for Neurodegenerative Diseases (DZNE), 37075, Göttingen, Germany
| | - Ramon O Vidal
- Laboratory of Computational Systems Biology, German Center for Neurodegenerative Diseases (DZNE), 37075, Göttingen, Germany
| | - Hanna Wildhagen
- Department of Neuro- and Sensory Physiology, University Medical Center Göttingen, Cluster of Excellence Nanoscale Microscopy and Molecular Physiology of the Brain, 37073, Göttingen, Germany
| | - Burkhard Rammner
- Department of Neuro- and Sensory Physiology, University Medical Center Göttingen, Cluster of Excellence Nanoscale Microscopy and Molecular Physiology of the Brain, 37073, Göttingen, Germany
| | - Sarva Keihani
- Department of Neuro- and Sensory Physiology, University Medical Center Göttingen, Cluster of Excellence Nanoscale Microscopy and Molecular Physiology of the Brain, 37073, Göttingen, Germany
| | - Felipe Opazo
- Department of Neuro- and Sensory Physiology, University Medical Center Göttingen, Cluster of Excellence Nanoscale Microscopy and Molecular Physiology of the Brain, 37073, Göttingen, Germany
| | - Inga Urban
- Genes and Behavior Department, Max Planck Institute of Biophysical Chemistry, 37073, Göttingen, Germany
| | - Till Ischebeck
- Department of Plant Biochemistry, Albrecht-von-Haller-Institute, Georg-August-University, 37073, Göttingen, Germany
| | - Koray Kirli
- Department of Cellular Logistics, Max Planck Institute for Biophysical Chemistry, 37073, Göttingen, Germany
| | - Eva Benito
- Laboratory of Epigenetics in Neurodegenerative Diseases, German Center for Neurodegenerative Diseases (DZNE), 37075, Göttingen, Germany
| | - André Fischer
- Laboratory of Epigenetics in Neurodegenerative Diseases, German Center for Neurodegenerative Diseases (DZNE), 37075, Göttingen, Germany
- Department of Psychiatry and Psychotherapy, University Medical Center Göttingen, 37075, Göttingen, Germany
| | - Roya Y Yousefi
- Department of Cellular Biochemistry, University Medical Center Göttingen, Göttingen, 37073, Germany
| | - Sven Dennerlein
- Department of Cellular Biochemistry, University Medical Center Göttingen, Göttingen, 37073, Germany
| | - Peter Rehling
- Department of Cellular Biochemistry, University Medical Center Göttingen, Göttingen, 37073, Germany
- Max Planck Institute for Biophysical Chemistry, 37073, Göttingen, Germany
| | - Ivo Feussner
- Department of Plant Biochemistry, Albrecht-von-Haller-Institute, Georg-August-University, 37073, Göttingen, Germany
| | - Henning Urlaub
- Department of Clinical Chemistry, University Medical Center Göttingen, 37077, Göttingen, Germany
- Bioanalytical Mass Spectrometry Group, Max Planck Institute of Biophysical Chemistry, 37077, Göttingen, Germany
| | - Stefan Bonn
- Laboratory of Computational Systems Biology, German Center for Neurodegenerative Diseases (DZNE), 37075, Göttingen, Germany.
- Institute of Medical Systems Biology, Center for Molecular Neurobiology (ZMNH), University Medical Center Hamburg-Eppendorf (UKE), 20246, Hamburg, Germany.
- German Center for Neurodegenerative Diseases (DZNE), 72076, Tübingen, Germany.
| | - Silvio O Rizzoli
- Department of Neuro- and Sensory Physiology, University Medical Center Göttingen, Cluster of Excellence Nanoscale Microscopy and Molecular Physiology of the Brain, 37073, Göttingen, Germany.
- Center for Biostructural Imaging of Neurodegeneration (BIN), 37075, Göttingen, Germany.
| | - Eugenio F Fornasiero
- Department of Neuro- and Sensory Physiology, University Medical Center Göttingen, Cluster of Excellence Nanoscale Microscopy and Molecular Physiology of the Brain, 37073, Göttingen, Germany.
| |
Collapse
|
7
|
Budzinska MA, Shackel NA, Urban S, Tu T. Cellular Genomic Sites of Hepatitis B Virus DNA Integration. Genes (Basel) 2018; 9:E365. [PMID: 30037029 PMCID: PMC6071206 DOI: 10.3390/genes9070365] [Citation(s) in RCA: 49] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2018] [Revised: 07/12/2018] [Accepted: 07/12/2018] [Indexed: 12/14/2022] Open
Abstract
Infection with the Hepatitis B Virus (HBV) is one of the strongest risk-factors for liver cancer (hepatocellular carcinoma, HCC). One of the reported drivers of HCC is the integration of HBV DNA into the host cell genome, which may induce pro-carcinogenic pathways. These reported pathways include: induction of chromosomal instability; generation of insertional mutagenesis in key cancer-associated genes; transcription of downstream cancer-associated cellular genes; and/or formation of a persistent source of viral protein expression (particularly HBV surface and X proteins). The contribution of each of these specific mechanisms towards carcinogenesis is currently unclear. Here, we review the current knowledge of specific sites of HBV DNA integration into the host genome, which sheds light on these mechanisms. We give an overview of previously-used methods to detect HBV DNA integration and the enrichment of integration events in specific functional and structural cellular genomic sites. Finally, we posit a theoretical model of HBV DNA integration during disease progression and highlight open questions in the field.
Collapse
Affiliation(s)
| | - Nicholas A Shackel
- Centenary Institute, University of Sydney, Sydney NSW 2050, Australia.
- South Western Sydney Clinical School, University of New South Wales, Liverpool NSW 2170, Australia.
- Gastroenterology, Liverpool Hospital, Liverpool NSW 2170, Australia.
| | - Stephan Urban
- Department of Infectious Diseases, Molecular Virology, Heidelberg Hospital University, D-69120 Heidelberg, Germany.
- German Center for Infection Research (DZIF), Partner Site Heidelberg, D-69120 Heidelberg, Germany.
| | - Thomas Tu
- Department of Infectious Diseases, Molecular Virology, Heidelberg Hospital University, D-69120 Heidelberg, Germany.
| |
Collapse
|
8
|
Barton C, Iliopoulos CS, Pissis SP, Arhondakis S. Transcriptome activity of isochores during preimplantation process in human and mouse. FEBS Lett 2016; 590:2297-306. [PMID: 27279593 DOI: 10.1002/1873-3468.12245] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2016] [Revised: 05/27/2016] [Accepted: 06/03/2016] [Indexed: 12/17/2022]
Abstract
This work investigates the role of isochores during preimplantation process. Using RNA-seq data from human and mouse preimplantation stages, we created the spatio-temporal transcriptional profiles of the isochores during preimplantation. We found that from early to late stages, GC-rich isochores increase their expression while GC-poor ones decrease it. Network analysis revealed that modules with few coexpressed isochores are GC-poorer than medium-large ones, characterized by an opposite expression as preimplantation advances, decreasing and increasing respectively. Our results reveal a functional contribution of the isochores, supporting the presence of structural-functional interactions during maturation and early-embryonic development.
Collapse
Affiliation(s)
- Carl Barton
- The Blizard Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, UK
| | | | | | - Stilianos Arhondakis
- Institute of Molecular Biology and Biotechnology (IMBB), Foundation for Research and Technology - Hellas (FORTH), Heraklion, Crete, Greece
| |
Collapse
|
9
|
Kutzner A, Pramanik S, Kim PS, Heese K. All-or-(N)One - an epistemological characterization of the human tumorigenic neuronal paralogous FAM72 gene loci. Genomics 2015; 106:278-285. [PMID: 26206078 DOI: 10.1016/j.ygeno.2015.07.003] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2015] [Revised: 05/26/2015] [Accepted: 07/13/2015] [Indexed: 12/21/2022]
Abstract
FAM72 is a novel neuronal progenitor cell (NPC) self-renewal supporting protein expressed under physiological conditions at low levels in other tissues. Accumulating data indicate the potential pivotal tumourigenic effects of FAM72. Our in silico human genome-wide analysis (GWA) revealed that the FAM72 gene family consists of four human-specific paralogous members, all of which are located on chromosome (chr) 1. Unique asymmetric FAM72 segmental gene duplications are most likely to have occurred in conjunction with the paired genomic neighbour SRGAP2 (SLIT-ROBO Rho GTPase activating protein), as both genes have four paralogues in humans but only one vertebra-emerging orthologue in all other species. No species with two or three FAM72/SRGAP2 gene pairs could be identified, and the four exclusively human-defining ohnologues, with different mutation patterns in Homo neanderthalensis and Denisova hominin, may remain under epigenetic control through long non-coding (lnc) RNAs.
Collapse
Affiliation(s)
- Arne Kutzner
- Department of Information Systems, College of Engineering, Hanyang University, 222 Wangsimni-ro, Seongdong-gu, Seoul 133-791, Republic of Korea
| | - Subrata Pramanik
- Graduate School of Biomedical Science and Engineering, Hanyang University, 222 Wangsimni-ro, Seongdong-gu, Seoul 133-791, Republic of Korea
| | - Pok-Son Kim
- Department of Mathematics, Kookmin University, 77 Jeongneung-ro, Seongbuk-gu, Seoul 136-702, Republic of Korea
| | - Klaus Heese
- Graduate School of Biomedical Science and Engineering, Hanyang University, 222 Wangsimni-ro, Seongdong-gu, Seoul 133-791, Republic of Korea.
| |
Collapse
|
10
|
Elhaik E, Graur D. A comparative study and a phylogenetic exploration of the compositional architectures of mammalian nuclear genomes. PLoS Comput Biol 2014; 10:e1003925. [PMID: 25375262 PMCID: PMC4222635 DOI: 10.1371/journal.pcbi.1003925] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2014] [Accepted: 09/18/2014] [Indexed: 11/18/2022] Open
Abstract
For the past four decades the compositional organization of the mammalian genome posed a formidable challenge to molecular evolutionists attempting to explain it from an evolutionary perspective. Unfortunately, most of the explanations adhered to the "isochore theory," which has long been rebutted. Recently, an alternative compositional domain model was proposed depicting the human and cow genomes as composed mostly of short compositionally homogeneous and nonhomogeneous domains and a few long ones. We test the validity of this model through a rigorous sequence-based analysis of eleven completely sequenced mammalian and avian genomes. Seven attributes of compositional domains are used in the analyses: (1) the number of compositional domains, (2) compositional domain-length distribution, (3) density of compositional domains, (4) genome coverage by the different domain types, (5) degree of fit to a power-law distribution, (6) compositional domain GC content, and (7) the joint distribution of GC content and length of the different domain types. We discuss the evolution of these attributes in light of two competing phylogenetic hypotheses that differ from each other in the validity of clade Euarchontoglires. If valid, the murid genome compositional organization would be a derived state and exhibit a high similarity to that of other mammals. If invalid, the murid genome compositional organization would be closer to an ancestral state. We demonstrate that the compositional organization of the murid genome differs from those of primates and laurasiatherians, a phenomenon previously termed the "murid shift," and in many ways resembles the genome of opossum. We find no support to the "isochore theory." Instead, our findings depict the mammalian genome as a tapestry of mostly short homogeneous and nonhomogeneous domains and few long ones thus providing strong evidence in favor of the compositional domain model and seem to invalidate clade Euarchontoglires.
Collapse
Affiliation(s)
- Eran Elhaik
- Department of Animal and Plant Sciences, University of Sheffield, Sheffield, United Kingdom
- * E-mail:
| | - Dan Graur
- Department of Biology & Biochemistry, University of Houston, Houston, Texas, United States of America
| |
Collapse
|
11
|
Rao YS, Chai XW, Wang ZF, Nie QH, Zhang XQ. Impact of GC content on gene expression pattern in chicken. Genet Sel Evol 2013; 45:9. [PMID: 23557030 PMCID: PMC3641017 DOI: 10.1186/1297-9686-45-9] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2012] [Accepted: 03/16/2013] [Indexed: 11/21/2022] Open
Abstract
Background GC content varies greatly between different genomic regions in many eukaryotes. In order to determine whether this organization named isochore organization influences gene expression patterns, the relationship between GC content and gene expression has been investigated in man and mouse. However, to date, this question is still a matter for debate. Among the avian species, chicken (Gallus gallus) is the best studied representative with a complete genome sequence. The distinctive features and organization of its sequence make it a good model to explore important issues in genome structure and evolution. Methods Only nuclear genes with complete information on protein-coding sequence with no evidence of multiple-splicing forms were included in this study. Chicken protein coding sequences, complete mRNA sequences (or full length cDNA sequences), and 5′ untranslated region sequences (5′ UTR) were downloaded from Ensembl and chicken expression data originated from a previous work. Three indices i.e. expression level, expression breadth and maximum expression level were used to measure the expression pattern of a given gene. CpG islands were identified using hgTables of the UCSC Genome Browser. Correlation analysis between variables was performed by SAS Proprietary Software Release 8.1. Results In chicken, the GC content of 5′ UTR is significantly and positively correlated with expression level, expression breadth, and maximum expression level, whereas that of coding sequences and introns and at the third coding position are negatively correlated with expression level and expression breadth, and not correlated with maximum expression level. These significant trends are independent of recombination rate, chromosome size and gene density. Furthermore, multiple linear regression analysis indicated that GC content in genes could explain approximately 10% of the variation in gene expression. Conclusions GC content is significantly associated with gene expression pattern and could be one of the important regulation factors in the chicken genome.
Collapse
Affiliation(s)
- You Sheng Rao
- Department of Biological Technology, Jiangxi Educational Institute, Jiangxi, Nanchang 330029, China
| | | | | | | | | |
Collapse
|
12
|
Frousios K, Iliopoulos CS, Tischler G, Kossida S, Pissis SP, Arhondakis S. Transcriptome map of mouse isochores in embryonic and neonatal cortex. Genomics 2012. [PMID: 23195409 DOI: 10.1016/j.ygeno.2012.11.006] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Several studies on adult tissues agree on the presence of a positive effect of the genomic and genic base composition on mammalian gene expression. Recent literature supports the idea that during developmental processes GC-poor genomic regions are preferentially implicated. We investigate the relationship between the compositional properties of the isochores and of the genes with their respective expression activity during developmental processes. Using RNA-seq data from two distinct developmental stages of the mouse cortex, embryonic day 18 (E18) and postnatal day 7 (P7), we established for the first time a developmental-related transcriptome map of the mouse isochores. Additionally, for each stage we estimated the correlation between isochores' GC level and their expression activity, and the genes' expression patterns for each isochore family. Our analyses add evidence supporting the idea that during development GC-poor isochores are preferentially implicated, and confirm the positive effect of genes' GC level on their expression activity.
Collapse
Affiliation(s)
- Kimon Frousios
- Department of Informatics, King's College London, The Strand, London WC2R 2LS, UK
| | - Costas S Iliopoulos
- Department of Informatics, King's College London, The Strand, London WC2R 2LS, UK; School of Mathematics and Statistics, University of Western Australia, 35 Stirling Highway, Crawley, Perth WA 6009, Australia
| | - German Tischler
- Lehrstuhl für Informatik 2, Universität Würzburg, Am Hubland, 97074 Würzburg, Germany
| | - Sophia Kossida
- Biomedical Research Foundation of the Academy of Athens, 4 Soranou Ephessiou, Athens 115 27, Greece
| | - Solon P Pissis
- Florida Museum of Natural History, University of Florida, 1659 Museum Road, Gainesville, FL 32611, USA; Heidelberg Institute for Theoretical Studies, 35 Schloss-Wolfsbrunnenweg, Heidelberg D-69118, Germany
| | - Stilianos Arhondakis
- Biomedical Research Foundation of the Academy of Athens, 4 Soranou Ephessiou, Athens 115 27, Greece.
| |
Collapse
|
13
|
Chojnowski JL, Braun EL. An unbiased approach to identify genes involved in development in a turtle with temperature-dependent sex determination. BMC Genomics 2012; 13:308. [PMID: 22793670 PMCID: PMC3434017 DOI: 10.1186/1471-2164-13-308] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2011] [Accepted: 07/15/2012] [Indexed: 02/08/2023] Open
Abstract
BACKGROUND Many reptiles exhibit temperature-dependent sex determination (TSD). The initial cue in TSD is incubation temperature, unlike genotypic sex determination (GSD) where it is determined by the presence of specific alleles (or genetic loci). We used patterns of gene expression to identify candidates for genes with a role in TSD and other developmental processes without making a priori assumptions about the identity of these genes (ortholog-based approach). We identified genes with sexually dimorphic mRNA accumulation during the temperature sensitive period of development in the Red-eared slider turtle (Trachemys scripta), a turtle with TSD. Genes with differential mRNA accumulation in response to estrogen (estradiol-17β; E(2)) exposure and developmental stages were also identified. RESULTS Sequencing 767 clones from three suppression-subtractive hybridization libraries yielded a total of 581 unique sequences. Screening a macroarray with a subset of those sequences revealed a total of 26 genes that exhibited differential mRNA accumulation: 16 female biased and 10 male biased. Additional analyses revealed that C16ORF62 (an unknown gene) and MALAT1 (a long noncoding RNA) exhibited increased mRNA accumulation at the male producing temperature relative to the female producing temperature during embryonic sexual development. Finally, we identified four genes (C16ORF62, CCT3, MMP2, and NFIB) that exhibited a stage effect and five genes (C16ORF62, CCT3, MMP2, NFIB and NOTCH2) showed a response to E(2) exposure. CONCLUSIONS Here we report a survey of genes identified using patterns of mRNA accumulation during embryonic development in a turtle with TSD. Many previous studies have focused on examining the turtle orthologs of genes involved in mammalian development. Although valuable, the limitations of this approach are exemplified by our identification of two genes (MALAT1 and C16ORF62) that are sexually dimorphic during embryonic development. MALAT1 is a noncoding RNA that has not been implicated in sexual differentiation in other vertebrates and C16ORF62 has an unknown function. Our results revealed genes that are candidates for having roles in turtle embryonic development, including TSD, and highlight the need to expand our search parameters beyond protein-coding genes.
Collapse
Affiliation(s)
- Jena L Chojnowski
- Genetics Department, University of Georgia, 500 DW Brooks Dr., Coverdell Center Rm270, Athens, GA, 30602, USA
- Department of Biology, University of Florida, PO Box 118525, Gainesville, FL, 32607, USA
| | - Edward L Braun
- Department of Biology, University of Florida, PO Box 118525, Gainesville, FL, 32607, USA
| |
Collapse
|
14
|
Arhondakis S, Frousios K, Iliopoulos CS, Pissis SP, Tischler G, Kossida S. Transcriptome map of mouse isochores. BMC Genomics 2011; 12:511. [PMID: 22004510 PMCID: PMC3215772 DOI: 10.1186/1471-2164-12-511] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2011] [Accepted: 10/17/2011] [Indexed: 12/28/2022] Open
Abstract
Background The availability of fully sequenced genomes and the implementation of transcriptome technologies have increased the studies investigating the expression profiles for a variety of tissues, conditions, and species. In this study, using RNA-seq data for three distinct tissues (brain, liver, and muscle), we investigate how base composition affects mammalian gene expression, an issue of prime practical and evolutionary interest. Results We present the transcriptome map of the mouse isochores (DNA segments with a fairly homogeneous base composition) for the three different tissues and the effects of isochores' base composition on their expression activity. Our analyses also cover the relations between the genes' expression activity and their localization in the isochore families. Conclusions This study is the first where next-generation sequencing data are used to associate the effects of both genomic and genic compositional properties to their corresponding expression activity. Our findings confirm previous results, and further support the existence of a relationship between isochores and gene expression. This relationship corroborates that isochores are primarily a product of evolutionary adaptation rather than a simple by-product of neutral evolutionary processes.
Collapse
Affiliation(s)
- Stilianos Arhondakis
- Biomedical Research Foundation of the Academy of Athens, 4 Soranou Ephessiou, 115 27, Athens, Greece.
| | | | | | | | | | | |
Collapse
|
15
|
Ferguson AA, Jiang N. Pack-MULEs: Recycling and reshaping genes through GC-biased acquisition. Mob Genet Elements 2011; 1:135-138. [PMID: 22016862 DOI: 10.4161/mge.1.2.16948] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2011] [Revised: 06/13/2011] [Accepted: 06/14/2011] [Indexed: 11/19/2022] Open
Abstract
The availability of genomic sequences provided new opportunities to decipher how plant genomes evolve. One recent discovery about plant genomes is the abundance of Pack-MULEs, a special group of transposable elements that duplicate, amplify and recombine gene fragments in many species at a very large scale. Despite the widespread occurrence of Pack-MULEs, their function remains an enigma. Our analysis using maize, rice and Arabidopsis genomic sequences indicates that the acquisition of genic sequences by Pack-MULEs is not random. Pack-MULEs in grasses specifically acquire and amplify GC-rich gene fragments. The resulting GC-rich elements have the ability to form independent transcripts with negative GC gradient, which refers to the decline of GC content along the orientation of transcription of genes. In other cases, Pack-MULEs insert near the 5' region of "normal" genes, and consequently form additional 5' exons or replace the original 5' exon of genes. In this manner, Pack-MULEs raise the GC content of the 5' termini of genes, modify the gene structure and contribute to the increased number of genes with negative GC gradient in grasses. The possible consequence of such activity is discussed.
Collapse
Affiliation(s)
- Ann A Ferguson
- Department of Horticulture; Michigan State University; East Lansing, MI USA
| | | |
Collapse
|
16
|
Transcriptome sequencing of a highly salt tolerant mangrove species Sonneratia alba using Illumina platform. Mar Genomics 2011; 4:129-36. [PMID: 21620334 DOI: 10.1016/j.margen.2011.03.005] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2011] [Revised: 03/19/2011] [Accepted: 03/27/2011] [Indexed: 12/24/2022]
Abstract
Mangroves are critical and threatened marine resources, yet few transcriptomic and genomic data are available in public databases. The transcriptome of a highly salt tolerant mangrove species, Sonneratia alba, was sequenced using the Illumina Genome Analyzer in this study. Over 15 million 75-bp paired-end reads were assembled into 30,628 unique sequences with an average length of 581 bp. Of them, 2358 SSRs were detected, with di-nucleotide repeats (59.2%) and tri-nucleotide repeats (37.7%) being the most common. Analysis of codon usage bias based on 20,945 coding sequences indicated that genes of S. alba were less biased than those of some microorganisms and Drosophila and that codon usage variation in S. alba was due primarily to compositional mutation bias, while translational selection has a relatively weak effect. Genome-wide gene ontology (GO) assignments showed that S. alba shared a similar GO slim classification with Arabidopsis thaliana. High percentages of sequences assigned to GO slim category 'mitochondrion' and four KEGG pathways, such as carbohydrates and secondary metabolites metabolism, may contribute to salt adaptation of S. alba. In addition, 1266 unique sequences matched to 273 known salt responsive genes (gene families) in other species were screened as candidates for salt tolerance of S. alba, and some of these genes showed fairly high coverage depth. At last, we identified four genes with signals of strong diversifying selection (K(a)/K(s)>1) by comparing the transcriptome sequences of S. alba with 249 known ESTs from its congener S. caseolaris. This study demonstrated a successful application of the Illumina platform to de novo assembly of the transcriptome of a non-model organism. Abundant SSR markers, salt responsive genes and four genes with signature of natural selection obtained from S. alba provide abundant sequence sources for future genetic diversity, salt adaptation and speciation studies.
Collapse
|
17
|
Tatarinova TV, Alexandrov NN, Bouck JB, Feldmann KA. GC3 biology in corn, rice, sorghum and other grasses. BMC Genomics 2010; 11:308. [PMID: 20470436 PMCID: PMC2895627 DOI: 10.1186/1471-2164-11-308] [Citation(s) in RCA: 105] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2009] [Accepted: 05/16/2010] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The third, or wobble, position in a codon provides a high degree of possible degeneracy and is an elegant fault-tolerance mechanism. Nucleotide biases between organisms at the wobble position have been documented and correlated with the abundances of the complementary tRNAs. We and others have noticed a bias for cytosine and guanine at the third position in a subset of transcripts within a single organism. The bias is present in some plant species and warm-blooded vertebrates but not in all plants, or in invertebrates or cold-blooded vertebrates. RESULTS Here we demonstrate that in certain organisms the amount of GC at the wobble position (GC3) can be used to distinguish two classes of genes. We highlight the following features of genes with high GC3 content: they (1) provide more targets for methylation, (2) exhibit more variable expression, (3) more frequently possess upstream TATA boxes, (4) are predominant in certain classes of genes (e.g., stress responsive genes) and (5) have a GC3 content that increases from 5'to 3'. These observations led us to formulate a hypothesis to explain GC3 bimodality in grasses. CONCLUSIONS Our findings suggest that high levels of GC3 typify a class of genes whose expression is regulated through DNA methylation or are a legacy of accelerated evolution through gene conversion. We discuss the three most probable explanations for GC3 bimodality: biased gene conversion, transcriptional and translational advantage and gene methylation.
Collapse
Affiliation(s)
- Tatiana V Tatarinova
- Department of Biomedical Engineering, Georgia Institute of Technology, Atlanta, Georgia 30332, USA.
| | | | | | | |
Collapse
|
18
|
Sabbbia V, Romero H, Musto H, Naya H. Composition Profile of the Human Genome at the Chromosome Level. J Biomol Struct Dyn 2009; 27:361-70. [DOI: 10.1080/07391102.2009.10507322] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
|
19
|
Bucciarelli G, Di Filippo M, Costagliola D, Alvarez-Valin F, Bernardi G, Bernardi G. Environmental Genomics: A Tale of Two Fishes. Mol Biol Evol 2009; 26:1235-43. [DOI: 10.1093/molbev/msp041] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
|
20
|
Mahmud AA, Amore G, Bernardi G. Compositional genome contexts affect gene expression control in sea urchin embryo. PLoS One 2008; 3:e4025. [PMID: 19112499 PMCID: PMC2603317 DOI: 10.1371/journal.pone.0004025] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2008] [Accepted: 11/21/2008] [Indexed: 11/18/2022] Open
Abstract
Gene expression is widely perceived as exclusively controlled by the information contained in cis-regulatory regions. These are built in a modular way, each module being a cluster of binding sites for the transcription factors that control the level, the location and the time at which gene transcription takes place. On the other hand, results from our laboratory have shown that gene expression is affected by the compositional properties (GC levels) of the isochores in which genes are embedded, i.e. the genome context. To clarify how compositional genomic properties affect the way cis-regulatory information is utilized, we have changed the genome context of a GFP-reporter gene containing the complete cis-regulatory region of the gene spdeadringer (spdri), expressed during sea urchin embryogenesis. We have observed that GC levels higher or lower than those found in the natural genome context can alter the reporter expression pattern. We explain this as the result of an interference with the functionality of specific modules in the gene's cis-regulatory region. From these observations we derive the notion that the compositional properties of the genome context can affect cis-regulatory control of gene expression. Therefore although the way a gene works depends on the information contained in its cis-regulatory region, availability of such information depends on the compositional properties of the genomic context.
Collapse
Affiliation(s)
| | - Gabriele Amore
- Stazione Zoologica “Anton Dohrn” Napoli, Villa Comunale, Napoli, Italy
- * E-mail:
| | - Giorgio Bernardi
- Stazione Zoologica “Anton Dohrn” Napoli, Villa Comunale, Napoli, Italy
| |
Collapse
|