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Tombácz D, Kakuk B, Torma G, Csabai Z, Gulyás G, Tamás V, Zádori Z, Jefferson VA, Meyer F, Boldogkői Z. In-Depth Temporal Transcriptome Profiling of an Alphaherpesvirus Using Nanopore Sequencing. Viruses 2022; 14:v14061289. [PMID: 35746760 PMCID: PMC9229804 DOI: 10.3390/v14061289] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2022] [Revised: 06/05/2022] [Accepted: 06/08/2022] [Indexed: 12/10/2022] Open
Abstract
In this work, a long-read sequencing (LRS) technique based on the Oxford Nanopore Technology MinION platform was used for quantifying and kinetic characterization of the poly(A) fraction of bovine alphaherpesvirus type 1 (BoHV-1) lytic transcriptome across a 12-h infection period. Amplification-based LRS techniques frequently generate artefactual transcription reads and are biased towards the production of shorter amplicons. To avoid these undesired effects, we applied direct cDNA sequencing, an amplification-free technique. Here, we show that a single promoter can produce multiple transcription start sites whose distribution patterns differ among the viral genes but are similar in the same gene at different timepoints. Our investigations revealed that the circ gene is expressed with immediate–early (IE) kinetics by utilizing a special mechanism based on the use of the promoter of another IE gene (bicp4) for the transcriptional control. Furthermore, we detected an overlap between the initiation of DNA replication and the transcription from the bicp22 gene, which suggests an interaction between the two molecular machineries. This study developed a generally applicable LRS-based method for the time-course characterization of transcriptomes of any organism.
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Affiliation(s)
- Dóra Tombácz
- Department of Medical Biology, Albert Szent-Györgyi Medical School, University of Szeged, Somogyi u. 4, 6720 Szeged, Hungary; (D.T.); (B.K.); (G.T.); (Z.C.); (G.G.)
| | - Balázs Kakuk
- Department of Medical Biology, Albert Szent-Györgyi Medical School, University of Szeged, Somogyi u. 4, 6720 Szeged, Hungary; (D.T.); (B.K.); (G.T.); (Z.C.); (G.G.)
| | - Gábor Torma
- Department of Medical Biology, Albert Szent-Györgyi Medical School, University of Szeged, Somogyi u. 4, 6720 Szeged, Hungary; (D.T.); (B.K.); (G.T.); (Z.C.); (G.G.)
| | - Zsolt Csabai
- Department of Medical Biology, Albert Szent-Györgyi Medical School, University of Szeged, Somogyi u. 4, 6720 Szeged, Hungary; (D.T.); (B.K.); (G.T.); (Z.C.); (G.G.)
| | - Gábor Gulyás
- Department of Medical Biology, Albert Szent-Györgyi Medical School, University of Szeged, Somogyi u. 4, 6720 Szeged, Hungary; (D.T.); (B.K.); (G.T.); (Z.C.); (G.G.)
| | - Vivien Tamás
- Institute for Veterinary Medical Research, Centre for Agricultural Research, Hungária krt. 21, 1143 Budapest, Hungary; (V.T.); (Z.Z.)
| | - Zoltán Zádori
- Institute for Veterinary Medical Research, Centre for Agricultural Research, Hungária krt. 21, 1143 Budapest, Hungary; (V.T.); (Z.Z.)
| | - Victoria A. Jefferson
- Department of Biochemistry & Molecular Biology, Entomology & Plant Pathology, Mississippi State University, 408 Dorman P.O. Box 9655, 32 Creelman St., Starkville, MS 39762, USA; (V.A.J.); (F.M.)
| | - Florencia Meyer
- Department of Biochemistry & Molecular Biology, Entomology & Plant Pathology, Mississippi State University, 408 Dorman P.O. Box 9655, 32 Creelman St., Starkville, MS 39762, USA; (V.A.J.); (F.M.)
| | - Zsolt Boldogkői
- Department of Medical Biology, Albert Szent-Györgyi Medical School, University of Szeged, Somogyi u. 4, 6720 Szeged, Hungary; (D.T.); (B.K.); (G.T.); (Z.C.); (G.G.)
- Correspondence:
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Einarsson H, Salvatore M, Vaagensø C, Alcaraz N, Bornholdt J, Rennie S, Andersson R. Promoter sequence and architecture determine expression variability and confer robustness to genetic variants. eLife 2022; 11:80943. [PMID: 36377861 PMCID: PMC9844987 DOI: 10.7554/elife.80943] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2022] [Accepted: 11/14/2022] [Indexed: 11/16/2022] Open
Abstract
Genetic and environmental exposures cause variability in gene expression. Although most genes are affected in a population, their effect sizes vary greatly, indicating the existence of regulatory mechanisms that could amplify or attenuate expression variability. Here, we investigate the relationship between the sequence and transcription start site architectures of promoters and their expression variability across human individuals. We find that expression variability can be largely explained by a promoter's DNA sequence and its binding sites for specific transcription factors. We show that promoter expression variability reflects the biological process of a gene, demonstrating a selective trade-off between stability for metabolic genes and plasticity for responsive genes and those involved in signaling. Promoters with a rigid transcription start site architecture are more prone to have variable expression and to be associated with genetic variants with large effect sizes, while a flexible usage of transcription start sites within a promoter attenuates expression variability and limits genotypic effects. Our work provides insights into the variable nature of responsive genes and reveals a novel mechanism for supplying transcriptional and mutational robustness to essential genes through multiple transcription start site regions within a promoter.
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Affiliation(s)
| | - Marco Salvatore
- Department of Biology, University of CopenhagenCopenhagenDenmark
| | | | - Nicolas Alcaraz
- Department of Biology, University of CopenhagenCopenhagenDenmark
| | - Jette Bornholdt
- Department of Biology, University of CopenhagenCopenhagenDenmark
| | - Sarah Rennie
- Department of Biology, University of CopenhagenCopenhagenDenmark
| | - Robin Andersson
- Department of Biology, University of CopenhagenCopenhagenDenmark
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3
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Zhao T, Vvedenskaya IO, Lai WKM, Basu S, Pugh BF, Nickels BE, Kaplan CD. Ssl2/TFIIH function in transcription start site scanning by RNA polymerase II in Saccharomyces cerevisiae. eLife 2021; 10:e71013. [PMID: 34652274 PMCID: PMC8589449 DOI: 10.7554/elife.71013] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2021] [Accepted: 10/14/2021] [Indexed: 12/31/2022] Open
Abstract
In Saccharomyces cerevisiae, RNA polymerase II (Pol II) selects transcription start sites (TSSs) by a unidirectional scanning process. During scanning, a preinitiation complex (PIC) assembled at an upstream core promoter initiates at select positions within a window ~40-120 bp downstream. Several lines of evidence indicate that Ssl2, the yeast homolog of XPB and an essential and conserved subunit of the general transcription factor (GTF) TFIIH, drives scanning through its DNA-dependent ATPase activity, therefore potentially controlling both scanning rate and scanning extent (processivity). To address questions of how Ssl2 functions in promoter scanning and interacts with other initiation activities, we leveraged distinct initiation-sensitive reporters to identify novel ssl2 alleles. These ssl2 alleles, many of which alter residues conserved from yeast to human, confer either upstream or downstream TSS shifts at the model promoter ADH1 and genome-wide. Specifically, tested ssl2 alleles alter TSS selection by increasing or narrowing the distribution of TSSs used at individual promoters. Genetic interactions of ssl2 alleles with other initiation factors are consistent with ssl2 allele classes functioning through increasing or decreasing scanning processivity but not necessarily scanning rate. These alleles underpin a residue interaction network that likely modulates Ssl2 activity and TFIIH function in promoter scanning. We propose that the outcome of promoter scanning is determined by two functional networks, the first being Pol II activity and factors that modulate it to determine initiation efficiency within a scanning window, and the second being Ssl2/TFIIH and factors that modulate scanning processivity to determine the width of the scanning widow.
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Affiliation(s)
- Tingting Zhao
- Department of Biological Sciences, University of PittsburghPittsburghUnited States
| | - Irina O Vvedenskaya
- Department of Genetics and Waksman Institute, Rutgers UniversityPiscatawayUnited States
| | - William KM Lai
- Department of Molecular Biology and Genetics, Cornell UniversityIthacaUnited States
| | - Shrabani Basu
- Department of Biological Sciences, University of PittsburghPittsburghUnited States
| | - B Franklin Pugh
- Department of Molecular Biology and Genetics, Cornell UniversityIthacaUnited States
| | - Bryce E Nickels
- Department of Genetics and Waksman Institute, Rutgers UniversityPiscatawayUnited States
| | - Craig D Kaplan
- Department of Biological Sciences, University of PittsburghPittsburghUnited States
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4
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Liu Q, Jiang F, Zhang J, Li X, Kang L. Transcription initiation of distant core promoters in a large-sized genome of an insect. BMC Biol 2021; 19:62. [PMID: 33785021 PMCID: PMC8011201 DOI: 10.1186/s12915-021-01004-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2020] [Accepted: 03/16/2021] [Indexed: 12/30/2022] Open
Abstract
Background Core promoters have a substantial influence on various steps of transcription, including initiation, elongation, termination, polyadenylation, and finally, translation. The characterization of core promoters is crucial for exploring the regulatory code of transcription initiation. However, the current understanding of insect core promoters is focused on those of Diptera (especially Drosophila) species with small genome sizes. Results Here, we present an analysis of the transcription start sites (TSSs) in the migratory locust, Locusta migratoria, which has a genome size of 6.5 Gb. The genomic differences, including lower precision of transcription initiation and fewer constraints on the distance from transcription factor binding sites or regulatory elements to TSSs, were revealed in locusts compared with Drosophila insects. Furthermore, we found a distinct bimodal log distribution of the distances from the start codons to the core promoters of locust genes. We found stricter constraints on the exon length of mRNA leaders and widespread expression activity of the distant core promoters in locusts compared with fruit flies. We further compared core promoters in seven arthropod species across a broad range of genome sizes to reinforce our results on the emergence of distant core promoters in large-sized genomes. Conclusions In summary, our results provide novel insights into the effects of genome size expansion on distant transcription initiation. Supplementary Information The online version contains supplementary material available at 10.1186/s12915-021-01004-5.
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Affiliation(s)
- Qing Liu
- Beijing Institutes of Life Science, Chinese Academy of Sciences, Beijing, China.,Sino-Danish College, University of Chinese Academy of Sciences, Beijing, China.,Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Feng Jiang
- Beijing Institutes of Life Science, Chinese Academy of Sciences, Beijing, China.,CAS Center for Excellence in Biotic Interactions, University of Chinese Academy of Sciences, Beijing, China
| | - Jie Zhang
- Beijing Institutes of Life Science, Chinese Academy of Sciences, Beijing, China
| | - Xiao Li
- State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Le Kang
- Beijing Institutes of Life Science, Chinese Academy of Sciences, Beijing, China. .,CAS Center for Excellence in Biotic Interactions, University of Chinese Academy of Sciences, Beijing, China. .,State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China.
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5
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Cha M, Zheng H, Talukder A, Barham C, Li X, Hu H. A two-stream convolutional neural network for microRNA transcription start site feature integration and identification. Sci Rep 2021; 11:5625. [PMID: 33707582 PMCID: PMC7952457 DOI: 10.1038/s41598-021-85173-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2020] [Accepted: 02/24/2021] [Indexed: 12/31/2022] Open
Abstract
MicroRNAs (miRNAs) play important roles in post-transcriptional gene regulation and phenotype development. Understanding the regulation of miRNA genes is critical to understand gene regulation. One of the challenges to study miRNA gene regulation is the lack of condition-specific annotation of miRNA transcription start sites (TSSs). Unlike protein-coding genes, miRNA TSSs can be tens of thousands of nucleotides away from the precursor miRNAs and they are hard to be detected by conventional RNA-Seq experiments. A number of studies have been attempted to computationally predict miRNA TSSs. However, high-resolution condition-specific miRNA TSS prediction remains a challenging problem. Recently, deep learning models have been successfully applied to various bioinformatics problems but have not been effectively created for condition-specific miRNA TSS prediction. Here we created a two-stream deep learning model called D-miRT for computational prediction of condition-specific miRNA TSSs ( http://hulab.ucf.edu/research/projects/DmiRT/ ). D-miRT is a natural fit for the integration of low-resolution epigenetic features (DNase-Seq and histone modification data) and high-resolution sequence features. Compared with alternative computational models on different sets of training data, D-miRT outperformed all baseline models and demonstrated high accuracy for condition-specific miRNA TSS prediction tasks. Comparing with the most recent approaches on cell-specific miRNA TSS identification using cell lines that were unseen to the model training processes, D-miRT also showed superior performance.
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Affiliation(s)
- Mingyu Cha
- Department of Computer Science, University of Central Florida, Orlando, FL, USA
| | - Hansi Zheng
- Department of Computer Science, University of Central Florida, Orlando, FL, USA
| | - Amlan Talukder
- Department of Computer Science, University of Central Florida, Orlando, FL, USA
| | - Clayton Barham
- Department of Computer Science, University of Central Florida, Orlando, FL, USA
| | - Xiaoman Li
- Burnett School of Biomedical Science, College of Medicine, University of Central Florida, Orlando, FL, USA.
| | - Haiyan Hu
- Department of Computer Science, University of Central Florida, Orlando, FL, USA.
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6
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Qiu C, Jin H, Vvedenskaya I, Llenas JA, Zhao T, Malik I, Visbisky AM, Schwartz SL, Cui P, Čabart P, Han KH, Lai WKM, Metz RP, Johnson CD, Sze SH, Pugh BF, Nickels BE, Kaplan CD. Universal promoter scanning by Pol II during transcription initiation in Saccharomyces cerevisiae. Genome Biol 2020; 21:132. [PMID: 32487207 PMCID: PMC7265651 DOI: 10.1186/s13059-020-02040-0] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2019] [Accepted: 05/08/2020] [Indexed: 12/15/2022] Open
Abstract
BACKGROUND The majority of eukaryotic promoters utilize multiple transcription start sites (TSSs). How multiple TSSs are specified at individual promoters across eukaryotes is not understood for most species. In Saccharomyces cerevisiae, a pre-initiation complex (PIC) comprised of Pol II and conserved general transcription factors (GTFs) assembles and opens DNA upstream of TSSs. Evidence from model promoters indicates that the PIC scans from upstream to downstream to identify TSSs. Prior results suggest that TSS distributions at promoters where scanning occurs shift in a polar fashion upon alteration in Pol II catalytic activity or GTF function. RESULTS To determine the extent of promoter scanning across promoter classes in S. cerevisiae, we perturb Pol II catalytic activity and GTF function and analyze their effects on TSS usage genome-wide. We find that alterations to Pol II, TFIIB, or TFIIF function widely alter the initiation landscape consistent with promoter scanning operating at all yeast promoters, regardless of promoter class. Promoter architecture, however, can determine the extent of promoter sensitivity to altered Pol II activity in ways that are predicted by a scanning model. CONCLUSIONS Our observations coupled with previous data validate key predictions of the scanning model for Pol II initiation in yeast, which we term the shooting gallery. In this model, Pol II catalytic activity and the rate and processivity of Pol II scanning together with promoter sequence determine the distribution of TSSs and their usage.
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Affiliation(s)
- Chenxi Qiu
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX, 77843-2128, USA
- Present Address: Department of Medicine, Division of Translational Therapeutics, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, 02215, USA
| | - Huiyan Jin
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX, 77843-2128, USA
| | - Irina Vvedenskaya
- Waksman Institute of Microbiology, Rutgers University, Piscataway, NJ, 08854, USA
- Department of Genetics, Rutgers University, Piscataway, NJ, 08854, USA
| | - Jordi Abante Llenas
- Department of Electrical and Computer Engineering, Texas A&M University, College Station, TX, 77843-3128, USA
- Present Address: Whitaker Biomedical Engineering Institute, Johns Hopkins University, Baltimore, MD, 21218, USA
| | - Tingting Zhao
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA, 15260, USA
| | - Indranil Malik
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX, 77843-2128, USA
- Present Address: Department of Neurology, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Alex M Visbisky
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA, 15260, USA
| | - Scott L Schwartz
- Genomics and Bioinformatics Service, Texas A&M AgriLife, College Station, TX, 77845, USA
| | - Ping Cui
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX, 77843-2128, USA
| | - Pavel Čabart
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX, 77843-2128, USA
- Present Address: First Faculty of Medicine, Charles University, BIOCEV, 252 42, Vestec, Czech Republic
| | - Kang Hoo Han
- Department of Biochemistry and Molecular Biology, Penn State University, University Park, PA, 16802, USA
| | - William K M Lai
- Department of Biochemistry and Molecular Biology, Penn State University, University Park, PA, 16802, USA
- Present Address: Department of Molecular Biology and Genetics, 458 Biotechnology, Cornell University, New York, 14853, USA
| | - Richard P Metz
- Genomics and Bioinformatics Service, Texas A&M AgriLife, College Station, TX, 77845, USA
| | - Charles D Johnson
- Genomics and Bioinformatics Service, Texas A&M AgriLife, College Station, TX, 77845, USA
| | - Sing-Hoi Sze
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX, 77843-2128, USA
- Department of Computer Science and Engineering, Texas A&M University, College Station, TX, 77843-3127, USA
| | - B Franklin Pugh
- Department of Biochemistry and Molecular Biology, Penn State University, University Park, PA, 16802, USA
- Present Address: Department of Molecular Biology and Genetics, 458 Biotechnology, Cornell University, New York, 14853, USA
| | - Bryce E Nickels
- Waksman Institute of Microbiology, Rutgers University, Piscataway, NJ, 08854, USA
- Department of Genetics, Rutgers University, Piscataway, NJ, 08854, USA
| | - Craig D Kaplan
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA, 15260, USA.
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7
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Forstnerič V, Oven I, Ogorevc J, Lainšček D, Praznik A, Lebar T, Jerala R, Horvat S. CRISPRa-mediated FOXP3 gene upregulation in mammalian cells. Cell Biosci 2019; 9:93. [PMID: 31832140 PMCID: PMC6873431 DOI: 10.1186/s13578-019-0357-0] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2019] [Accepted: 11/15/2019] [Indexed: 12/18/2022] Open
Abstract
BACKGROUND Forkhead box P3+ (FOXP3 +) regulatory T cells (Tregs) are a subset of lymphocytes, critical for the maintenance of immune homeostasis. Loss-of-function mutations of the FOXP3 gene in animal models and humans results in loss of differentiation potential into Treg cells and are responsible for several immune-mediated inflammatory diseases. Strategies of increasing FOXP3 expression represent a potential approach to increase the pool of Tregs within the lymphocyte population and may be employed in therapies of diverse autoimmune conditions. In the present study, a dCas9 CRISPR-based method was systematically employed to achieve upregulation and sustained high expression of endogenous FOXP3 in HEK293 and human Jurkat T cell lines through targeting of the core promotor, three known regulatory regions of the FOXP3 gene (CNS1-3), and two additional regions selected through extensive bioinformatics analysis (Cage1 and Cage2). RESULTS Using an activator-domain fusion based dCas9 transcription activator, robust upregulation of FOXP3 was achieved, and an optimal combination of single guide RNAs was selected, which exerted an additive effect on FOXP3 gene upregulation. Simultaneous targeting of FOXP3 and EOS, a transcription factor known to act in concert with FOXP3 in initiating a Treg phenotype, resulted in upregulation of FOXP3 downstream genes CD25 and TNFR2. When compared to ectopic expression of FOXP3 via plasmid electroporation, upregulation of endogenous FOXP3 via the Cas9-based method resulted in prolonged expression of FOXP3 in Jurkat cells. CONCLUSIONS Transfection of both HEK293 and Jurkat cells with dCas9-activators showed that regulatory regions downstream and upstream of FOXP3 promoter can be very potent transcription inducers in comparison to targeting the core promoter. While introduction of genes by conventional methods of gene therapy may involve a risk of insertional mutagenesis due to viral integration into the genome, transient up- or down-regulation of transcription by a CRISPR-dCas9 approach may resolve this safety concern. dCas9-based systems provide great promise in DNA footprint-free phenotype perturbations (perturbation without the risk of DNA damage) to drive development of transcription modulation-based therapies.
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Affiliation(s)
- Vida Forstnerič
- Department of Synthetic Biology and Immunology, National Institute of Chemistry, Ljubljana, Hajdrihova 19, 1000 Ljubljana, Slovenia
| | - Irena Oven
- Department of Animal Science, Biotechnical Faculty, University of Ljubljana, Groblje 3, 1230 Domžale, Slovenia
| | - Jernej Ogorevc
- Department of Animal Science, Biotechnical Faculty, University of Ljubljana, Groblje 3, 1230 Domžale, Slovenia
| | - Duško Lainšček
- Department of Synthetic Biology and Immunology, National Institute of Chemistry, Ljubljana, Hajdrihova 19, 1000 Ljubljana, Slovenia
| | - Arne Praznik
- Department of Synthetic Biology and Immunology, National Institute of Chemistry, Ljubljana, Hajdrihova 19, 1000 Ljubljana, Slovenia
| | - Tina Lebar
- Department of Synthetic Biology and Immunology, National Institute of Chemistry, Ljubljana, Hajdrihova 19, 1000 Ljubljana, Slovenia
| | - Roman Jerala
- Department of Synthetic Biology and Immunology, National Institute of Chemistry, Ljubljana, Hajdrihova 19, 1000 Ljubljana, Slovenia
- EN-FIST Centre of Excellence, Trg Osvobodilne fronte 13, 1000 Ljubljana, Slovenia
| | - Simon Horvat
- Department of Animal Science, Biotechnical Faculty, University of Ljubljana, Groblje 3, 1230 Domžale, Slovenia
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Kumar V, Saha D, Thakare DR, Jajoo A, Jain PK, Bhat SR, Srinivasan R. A part of the upstream promoter region of SHN2 gene directs trichome specific expression in Arabidopsis thaliana and heterologous plants. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2017; 264:138-148. [PMID: 28969794 DOI: 10.1016/j.plantsci.2017.09.005] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/26/2017] [Revised: 09/06/2017] [Accepted: 09/06/2017] [Indexed: 06/07/2023]
Abstract
A promoter trap mutant line of Arabidopsis carrying a promoterless β-glucuronidase (uidA) gene exhibited GUS expression predominantly in all the trichomes. In this mutant, the T-DNA insertion was localized at 147bp upstream of the putative start codon, ATG, of the At5g11190 (SHN2) gene. Transcript profiling of the SHN2 suggested a constitutive expression of the gene in all the tissues. Deletion analysis of the upstream sequences established that a 565bp (-594/-30) region confers trichome-specific gene expression. The trichomes isolated from young, mature and senesced leaf tissues also showed the presence of SHN2 transcript. The occurrence of multiple TSSs on the SHN2 gene sequence, presence of the SHN2 transcript in the homozygous trip mutant, despite an insertional mutation event, and diverse reporter gene expression pattern driven by 5' and 3' promoter deletion fragments, suggest a complex transcriptional regulation of SHN2 gene in Arabidopsis. The promoter sequence -594/-30 showed a conserved functional role in conferring non-glandular trichome-specific expression in other heterologous systems like Brassica juncea and Solanum lycopersicon. Thus, in the present study T-DNA tagging has led to the identification of a trichome-specific regulatory sequence in the upstream region of a constitutively expressed SHN2 gene. The study also suggests a complex regulation of SHN2 gene. Isolated trichome specific region retains its functions in other systems like Brassica and tomato, hence could be effectively exploited in engineering trichome cells in heterologous crop plants to manipulate traits like biopharming and insect herbivory.
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Affiliation(s)
- Vajinder Kumar
- ICAR-National Research Centre on Plant Biotechnology, Pusa Campus, New Delhi, 110012, India.
| | - Dipnarayan Saha
- ICAR-National Research Centre on Plant Biotechnology, Pusa Campus, New Delhi, 110012, India.
| | - Dhiraj Ramesh Thakare
- ICAR-National Research Centre on Plant Biotechnology, Pusa Campus, New Delhi, 110012, India.
| | - Anjana Jajoo
- School of Life Sciences, Devi Ahilya Vishwavidyalaya, Indore, Madhya Pradesh, 452010, India.
| | - Pradeep Kumar Jain
- ICAR-National Research Centre on Plant Biotechnology, Pusa Campus, New Delhi, 110012, India.
| | | | - Ramamurthy Srinivasan
- ICAR-National Research Centre on Plant Biotechnology, Pusa Campus, New Delhi, 110012, India.
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9
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Badaoui B, Fougeroux A, Petit F, Anselmo A, Gorni C, Cucurachi M, Cersini A, Granato A, Cardeti G, Formato G, Mutinelli F, Giuffra E, Williams JL, Botti S. RNA-sequence analysis of gene expression from honeybees (Apis mellifera) infected with Nosema ceranae. PLoS One 2017; 12:e0173438. [PMID: 28350872 PMCID: PMC5370102 DOI: 10.1371/journal.pone.0173438] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2015] [Accepted: 02/22/2017] [Indexed: 12/22/2022] Open
Abstract
Honeybees (Apis mellifera) are constantly subjected to many biotic stressors including parasites. This study examined honeybees infected with Nosema ceranae (N. ceranae). N. ceranae infection increases the bees energy requirements and may contribute to their decreased survival. RNA-seq was used to investigate gene expression at days 5, 10 and 15 Post Infection (P.I) with N. ceranae. The expression levels of genes, isoforms, alternative transcription start sites (TSS) and differential promoter usage revealed a complex pattern of transcriptional and post-transcriptional gene regulation suggesting that bees use a range of tactics to cope with the stress of N. ceranae infection. N. ceranae infection may cause reduced immune function in the bees by: (i)disturbing the host amino acids metabolism (ii) down-regulating expression of antimicrobial peptides (iii) down-regulation of cuticle coatings and (iv) down-regulation of odorant binding proteins.
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Affiliation(s)
- Bouabid Badaoui
- Parco Tecnologico Padano - CERSA, Integrative Biology Group, Lodi, Italy
| | | | | | - Anna Anselmo
- Parco Tecnologico Padano - CERSA, Integrative Biology Group, Lodi, Italy
| | - Chiara Gorni
- Parco Tecnologico Padano - CERSA, Integrative Biology Group, Lodi, Italy
| | - Marco Cucurachi
- Parco Tecnologico Padano - CERSA, Integrative Biology Group, Lodi, Italy
| | - Antonella Cersini
- Istituto Zooprofilattico Sperimentale del Lazio e della Toscana, Roma, Italy
| | - Anna Granato
- Istituto Zooprofilattico Sperimentale delle Venezie, Legnaro, Padua, Italy
| | - Giusy Cardeti
- Istituto Zooprofilattico Sperimentale del Lazio e della Toscana, Roma, Italy
| | - Giovanni Formato
- Istituto Zooprofilattico Sperimentale del Lazio e della Toscana, Roma, Italy
| | - Franco Mutinelli
- Istituto Zooprofilattico Sperimentale delle Venezie, Legnaro, Padua, Italy
| | - Elisabetta Giuffra
- Parco Tecnologico Padano - CERSA, Integrative Biology Group, Lodi, Italy
| | - John L. Williams
- Davies Research Centre, University of Adelaide, Roseworthy, South Australia, Australia
| | - Sara Botti
- Parco Tecnologico Padano - CERSA, Integrative Biology Group, Lodi, Italy
- * E-mail:
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10
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Lai WKM, Pugh BF. Genome-wide uniformity of human 'open' pre-initiation complexes. Genome Res 2016; 27:15-26. [PMID: 27927716 PMCID: PMC5204339 DOI: 10.1101/gr.210955.116] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2016] [Accepted: 11/03/2016] [Indexed: 01/05/2023]
Abstract
Transcription of protein-coding and noncoding DNA occurs pervasively throughout the mammalian genome. Their sites of initiation are generally inferred from transcript 5' ends and are thought to be either locally dispersed or focused. How these two modes of initiation relate is unclear. Here, we apply permanganate treatment and chromatin immunoprecipitation (PIP-seq) of initiation factors to identify the precise location of melted DNA separately associated with the preinitiation complex (PIC) and the adjacent paused complex (PC). This approach revealed the two known modes of transcription initiation. However, in contrast to prevailing views, they co-occurred within the same promoter region: initiation originating from a focused PIC, and broad nucleosome-linked initiation. PIP-seq allowed transcriptional orientation of Pol II to be determined, which may be useful near promoters where sufficient sense/anti-sense transcript mapping information is lacking. PIP-seq detected divergently oriented Pol II at both coding and noncoding promoters, as well as at enhancers. Their occupancy levels were not necessarily coupled in the two orientations. DNA sequence and shape analysis of initiation complex sites suggest that both sequence and shape contribute to specificity, but in a context-restricted manner. That is, initiation sites have the locally "best" initiator (INR) sequence and/or shape. These findings reveal a common core to pervasive Pol II initiation throughout the human genome.
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Affiliation(s)
- William K M Lai
- Center for Eukaryotic Gene Regulation, Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania 16802, USA
| | - B Franklin Pugh
- Center for Eukaryotic Gene Regulation, Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania 16802, USA
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11
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Raborn RT, Spitze K, Brendel VP, Lynch M. Promoter Architecture and Sex-Specific Gene Expression in Daphnia pulex. Genetics 2016; 204:593-612. [PMID: 27585846 PMCID: PMC5068849 DOI: 10.1534/genetics.116.193334] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2016] [Accepted: 07/29/2016] [Indexed: 11/18/2022] Open
Abstract
Large-scale transcription start site (TSS) profiling produces a high-resolution, quantitative picture of transcription initiation and core promoter locations within a genome. However, application of TSS profiling to date has largely been restricted to a small set of prominent model systems. We sought to characterize the cis-regulatory landscape of the water flea Daphnia pulex, an emerging model arthropod that reproduces both asexually (via parthenogenesis) and sexually (via meiosis). We performed Cap Analysis of Gene Expression (CAGE) with RNA isolated from D. pulex within three developmental states: sexual females, asexual females, and males. Identified TSSs were utilized to generate a "Daphnia Promoter Atlas," i.e., a catalog of active promoters across the surveyed states. Analysis of the distribution of promoters revealed evidence for widespread alternative promoter usage in D. pulex, in addition to a prominent fraction of compactly-arranged promoters in divergent orientations. We carried out de novo motif discovery using CAGE-defined TSSs and identified eight candidate core promoter motifs; this collection includes canonical promoter elements (e.g., TATA and Initiator) in addition to others lacking obvious orthologs. A comparison of promoter activities found evidence for considerable state-specific differential gene expression between states. Our work represents the first global definition of transcription initiation and promoter architecture in crustaceans. The Daphnia Promoter Atlas presented here provides a valuable resource for comparative study of cis-regulatory regions in metazoans, as well as for investigations into the circuitries that underpin meiosis and parthenogenesis.
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Affiliation(s)
- R Taylor Raborn
- Department of Biology, Indiana University, Bloomington, Indiana 47405 School of Informatics and Computing, Indiana University, Bloomington, Indiana 47405
| | - Ken Spitze
- Department of Biology, Indiana University, Bloomington, Indiana 47405
| | - Volker P Brendel
- Department of Biology, Indiana University, Bloomington, Indiana 47405 School of Informatics and Computing, Indiana University, Bloomington, Indiana 47405
| | - Michael Lynch
- Department of Biology, Indiana University, Bloomington, Indiana 47405
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12
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Merenciano M, Ullastres A, de Cara MAR, Barrón MG, González J. Multiple Independent Retroelement Insertions in the Promoter of a Stress Response Gene Have Variable Molecular and Functional Effects in Drosophila. PLoS Genet 2016; 12:e1006249. [PMID: 27517860 PMCID: PMC4982627 DOI: 10.1371/journal.pgen.1006249] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2015] [Accepted: 07/18/2016] [Indexed: 12/20/2022] Open
Abstract
Promoters are structurally and functionally diverse gene regulatory regions. The presence or absence of sequence motifs and the spacing between the motifs defines the properties of promoters. Recent alternative promoter usage analyses in Drosophila melanogaster revealed that transposable elements significantly contribute to promote diversity. In this work, we analyzed in detail one of the transposable element insertions, named FBti0019985, that has been co-opted to drive expression of CG18446, a candidate stress response gene. We analyzed strains from different natural populations and we found that besides FBti0019985, there are another eight independent transposable elements inserted in the proximal promoter region of CG18446. All nine insertions are solo-LTRs that belong to the roo family. We analyzed the sequence of the nine roo insertions and we investigated whether the different insertions were functionally equivalent by performing 5'-RACE, gene expression, and cold-stress survival experiments. We found that different insertions have different molecular and functional consequences. The exact position where the transposable elements are inserted matters, as they all showed highly conserved sequences but only two of the analyzed insertions provided alternative transcription start sites, and only the FBti0019985 insertion consistently affects CG18446 expression. The phenotypic consequences of the different insertions also vary: only FBti0019985 was associated with cold-stress tolerance. Interestingly, the only previous report of transposable elements inserting repeatedly and independently in a promoter region in D. melanogaster, were also located upstream of a stress response gene. Our results suggest that functional validation of individual structural variants is needed to resolve the complexity of insertion clusters.
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Affiliation(s)
- Miriam Merenciano
- Institute of Evolutionary Biology (CSIC-Universitat Pompeu Fabra), Barcelona. Spain
| | - Anna Ullastres
- Institute of Evolutionary Biology (CSIC-Universitat Pompeu Fabra), Barcelona. Spain
| | - M. A. R. de Cara
- Laboratoire d’Eco-anthropologie et Ethnobiologie, UMR 7206, CNRS/MNHN/Universite Paris 7, Museum National d’Histoire Naturelle, F-75116 Paris, France
| | - Maite G. Barrón
- Institute of Evolutionary Biology (CSIC-Universitat Pompeu Fabra), Barcelona. Spain
| | - Josefa González
- Institute of Evolutionary Biology (CSIC-Universitat Pompeu Fabra), Barcelona. Spain
- * E-mail:
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13
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Wang X, Zheng ZM. Construction of a Transcription Map for Papillomaviruses using RACE, RNase Protection, and Primer Extension Assays. ACTA ACUST UNITED AC 2016; 40:14B.6.1-14B.6.29. [PMID: 26855281 DOI: 10.1002/9780471729259.mc14b06s40] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Papillomaviruses are a family of small, non-enveloped DNA tumor viruses. Knowing a complete transcription map of each papillomavirus genome can provide guidance for various papillomavirus studies. This unit provides detailed protocols to construct a transcription map of human papillomavirus type 18. The same approach can be easily adapted to other transcription map studies of any other papillomavirus genotype due to the high degree of conservation in genome structure, organization, and gene expression among papillomaviruses. The focused methods are 5'- and 3'-rapid amplification of cDNA ends (RACE), which are techniques commonly used in molecular biology to obtain full-length RNA transcript or to map a transcription start site (TSS) or an RNA polyadenylation (pA) cleavage site. Primer walking RT-PCR is a method for studying the splicing junction of RACE products. In addition, RNase protection assay and primer extension are also introduced as alternative methods in the mapping analysis.
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Affiliation(s)
- Xiaohong Wang
- Tumor Virus RNA Biology Section, Gene Regulation and Chromosome Biology Laboratory, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, Maryland
| | - Zhi-Ming Zheng
- Tumor Virus RNA Biology Section, Gene Regulation and Chromosome Biology Laboratory, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, Maryland
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14
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Haberle V, Lenhard B. Promoter architectures and developmental gene regulation. Semin Cell Dev Biol 2016; 57:11-23. [PMID: 26783721 DOI: 10.1016/j.semcdb.2016.01.014] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2015] [Revised: 01/08/2016] [Accepted: 01/11/2016] [Indexed: 01/03/2023]
Abstract
Core promoters are minimal regions sufficient to direct accurate initiation of transcription and are crucial for regulation of gene expression. They are highly diverse in terms of associated core promoter motifs, underlying sequence composition and patterns of transcription initiation. Distinctive features of promoters are also seen at the chromatin level, including nucleosome positioning patterns and presence of specific histone modifications. Recent advances in identifying and characterizing promoters using next-generation sequencing-based technologies have provided the basis for their classification into functional groups and have shed light on their modes of regulation, with important implications for transcriptional regulation in development. This review discusses the methodology and the results of genome-wide studies that provided insight into the diversity of RNA polymerase II promoter architectures in vertebrates and other Metazoa, and the association of these architectures with distinct modes of regulation in embryonic development and differentiation.
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Affiliation(s)
- Vanja Haberle
- Institute of Clinical Sciences and MRC Clinical Sciences Center, Faculty of Medicine, Imperial College London, Hammersmith Hospital, Du Cane Road, London W12 0NN, UK; Department of Biology, University of Bergen, Thormøhlensgate 53A, N-5008 Bergen, Norway
| | - Boris Lenhard
- Institute of Clinical Sciences and MRC Clinical Sciences Center, Faculty of Medicine, Imperial College London, Hammersmith Hospital, Du Cane Road, London W12 0NN, UK.
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15
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16
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Yokomori R, Shimai K, Nishitsuji K, Suzuki Y, Kusakabe TG, Nakai K. Genome-wide identification and characterization of transcription start sites and promoters in the tunicate Ciona intestinalis. Genome Res 2015; 26:140-50. [PMID: 26668163 PMCID: PMC4691747 DOI: 10.1101/gr.184648.114] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2014] [Accepted: 10/13/2015] [Indexed: 02/05/2023]
Abstract
The tunicate Ciona intestinalis, an invertebrate chordate, has recently emerged as a powerful model organism for gene regulation analysis. However, few studies have been conducted to identify and characterize its transcription start sites (TSSs) and promoters at the genome-wide level. Here, using TSS-seq, we identified TSSs at the genome-wide scale and characterized promoters in C. intestinalis. Specifically, we identified TSS clusters (TSCs), high-density regions of TSS-seq tags, each of which appears to originate from an identical promoter. TSCs were found not only at known TSSs but also in other regions, suggesting the existence of many unknown transcription units in the genome. We also identified candidate promoters of 79 ribosomal protein (RP) genes, each of which had the major TSS in a polypyrimidine tract and showed a sharp TSS distribution like human RP gene promoters. Ciona RP gene promoters, however, did not appear to have typical TATA boxes, unlike human RP gene promoters. In Ciona non-RP promoters, two pyrimidine-purine dinucleotides, CA and TA, were frequently used as TSSs. Despite the absence of CpG islands, Ciona TATA-less promoters showed low expression specificity like CpG-associated human TATA-less promoters. By using TSS-seq, we also predicted trans-spliced gene TSSs and found that their downstream regions had higher G+T content than those of non-trans-spliced gene TSSs. Furthermore, we identified many putative alternative promoters, some of which were regulated in a tissue-specific manner. Our results provide valuable information about TSSs and promoter characteristics in C. intestinalis and will be helpful in future analysis of transcriptional regulation in chordates.
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Affiliation(s)
- Rui Yokomori
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa 277-8568, Japan
| | - Kotaro Shimai
- Institute for Integrative Neurobiology, Graduate School of Natural Science, Konan University, Kobe 658-8501, Japan
| | - Koki Nishitsuji
- Graduate School of Life Science, University of Hyogo, Kamigori, Hyogo 678-1297, Japan
| | - Yutaka Suzuki
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa 277-8568, Japan
| | - Takehiro G Kusakabe
- Institute for Integrative Neurobiology, Graduate School of Natural Science, Konan University, Kobe 658-8501, Japan; Department of Biology, Faculty of Science and Engineering, Konan University, Kobe 658-8501, Japan
| | - Kenta Nakai
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa 277-8568, Japan; Institute for Integrative Neurobiology, Graduate School of Natural Science, Konan University, Kobe 658-8501, Japan; Human Genome Center, Institute of Medical Science, The University of Tokyo, Tokyo 108-8639, Japan
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17
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Mejía-Guerra MK, Li W, Galeano NF, Vidal M, Gray J, Doseff AI, Grotewold E. Core Promoter Plasticity Between Maize Tissues and Genotypes Contrasts with Predominance of Sharp Transcription Initiation Sites. THE PLANT CELL 2015; 27:3309-20. [PMID: 26628745 PMCID: PMC4707454 DOI: 10.1105/tpc.15.00630] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/16/2015] [Accepted: 11/11/2015] [Indexed: 05/03/2023]
Abstract
Core promoters are crucial for gene regulation, providing blueprints for the assembly of transcriptional machinery at transcription start sites (TSSs). Empirically, TSSs define the coordinates of core promoters and other regulatory sequences. Thus, experimental TSS identification provides an essential step in the characterization of promoters and their features. Here, we describe the application of CAGE (cap analysis of gene expression) to identify genome-wide TSSs used in root and shoot tissues of two maize (Zea mays) inbred lines (B73 and Mo17). Our studies indicate that most TSS clusters are sharp in maize, similar to mice, but distinct from Arabidopsis thaliana, Drosophila melanogaster, or zebra fish, in which a majority of genes have broad-shaped TSS clusters. We established that ∼38% of maize promoters are characterized by a broader TATA-motif consensus, and this motif is significantly enriched in genes with sharp TSSs. A noteworthy plasticity in TSS usage between tissues and inbreds was uncovered, with ∼1500 genes showing significantly different dominant TSSs, sometimes affecting protein sequence by providing alternate translation initiation codons. We experimentally characterized instances in which this differential TSS utilization results in protein isoforms with additional domains or targeted to distinct subcellular compartments. These results provide important insights into TSS selection and gene expression in an agronomically important crop.
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Affiliation(s)
- María Katherine Mejía-Guerra
- Center for Applied Plant Sciences, The Ohio State University, Columbus, Ohio 43210 Molecular Cellular and Developmental Biology Graduate Program, The Ohio State University, Columbus, Ohio 43210
| | - Wei Li
- Department of Physiology and Cell Biology, 305B Heart and Lung Research Institute, The Ohio State University, Columbus, Ohio 43210 Department of Molecular Genetics, The Ohio State University, Columbus, Ohio 43210
| | - Narmer F Galeano
- Center for Applied Plant Sciences, The Ohio State University, Columbus, Ohio 43210 Instituto de Investigación en Microbiología y Biotecnología Agroindustrial, Universidad Católica de Manizales, Carrera 23 No 60-63 Manizales, Colombia
| | - Mabel Vidal
- Center for Applied Plant Sciences, The Ohio State University, Columbus, Ohio 43210
| | - John Gray
- Department of Biological Sciences, University of Toledo, Toledo, Ohio 43606
| | - Andrea I Doseff
- Department of Physiology and Cell Biology, 305B Heart and Lung Research Institute, The Ohio State University, Columbus, Ohio 43210 Department of Molecular Genetics, The Ohio State University, Columbus, Ohio 43210
| | - Erich Grotewold
- Center for Applied Plant Sciences, The Ohio State University, Columbus, Ohio 43210 Department of Molecular Genetics, The Ohio State University, Columbus, Ohio 43210
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18
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Ratliff WA, Athanason MG, Chechele AC, Kuehl MN, Fernandez AM, MarElia CB, Burkhardt BR. Hepatic nutrient and hormonal regulation of the PANcreatic-DERived factor (PANDER) promoter. Mol Cell Endocrinol 2015; 413:101-12. [PMID: 26123584 DOI: 10.1016/j.mce.2015.05.040] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/06/2014] [Revised: 04/29/2015] [Accepted: 05/28/2015] [Indexed: 11/24/2022]
Abstract
PANcreatic-DERived factor (PANDER, FAM3B) has been shown to regulate glycemic levels via interactions with both pancreatic islets and the liver. Although PANDER is predominantly expressed from the endocrine pancreas, recent work has provided sufficient evidence that the liver may also be an additional tissue source of PANDER production. At physiological levels, PANDER is capable of disrupting insulin signaling and promoting increased hepatic glucose production. As shown in some animal models, strong expression of PANDER, induced by viral delivery within the liver, induces hepatic steatosis. However, no studies to date have explicitly characterized the transcriptional regulation of PANDER from the liver. Therefore, our investigation elucidated the nutrient and hormonal regulation of the hepatic PANDER promoter. Initial RNA-ligated rapid amplification of cDNA ends identified a novel transcription start site (TSS) approximately 26 bp upstream of the PANDER translational start codon not previously revealed in pancreatic β-cell lines. Western evaluation of various murine tissues demonstrated robust expression in the liver and brain. Promoter analysis identified strong tissue-specific activity of the PANDER promoter in both human and murine liver-derived cell lines. The minimal element responsible for maximal promoter activity within hepatic cell lines was located between -293 and -3 of the identified TSS. PANDER promoter activity was inhibited by both insulin and palmitate, whereas glucose strongly increased expression. The minimal element was responsible for maximal glucose-responsive and basal activity. Co-transfection reporter assays, chromatin-immunoprecipitation (ChIP) and site-directed mutagenesis revealed that the carbohydrate-responsive element binding protein (ChREBP) increased PANDER promoter activity and interacted with the PANDER promoter. E-box 3 was shown to be critical for basal and glucose responsive expression. In summary, in-vitro and in-vivo glucose is a potent stimulator of the PANDER promoter within the liver and this response may be facilitated by ChREBP.
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Affiliation(s)
- Whitney A Ratliff
- Department of Cell Biology, Microbiology and Molecular Biology, University of South Florida, 4202 East Fowler Avenue, Tampa, FL 33620, USA
| | - Mark G Athanason
- Department of Cell Biology, Microbiology and Molecular Biology, University of South Florida, 4202 East Fowler Avenue, Tampa, FL 33620, USA
| | - Alicia C Chechele
- Department of Cell Biology, Microbiology and Molecular Biology, University of South Florida, 4202 East Fowler Avenue, Tampa, FL 33620, USA
| | - Melanie N Kuehl
- Department of Cell Biology, Microbiology and Molecular Biology, University of South Florida, 4202 East Fowler Avenue, Tampa, FL 33620, USA
| | - Amanda M Fernandez
- Department of Cell Biology, Microbiology and Molecular Biology, University of South Florida, 4202 East Fowler Avenue, Tampa, FL 33620, USA
| | - Catherine B MarElia
- Department of Cell Biology, Microbiology and Molecular Biology, University of South Florida, 4202 East Fowler Avenue, Tampa, FL 33620, USA
| | - Brant R Burkhardt
- Department of Cell Biology, Microbiology and Molecular Biology, University of South Florida, 4202 East Fowler Avenue, Tampa, FL 33620, USA.
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19
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Russo MT, Annunziata R, Sanges R, Ferrante MI, Falciatore A. The upstream regulatory sequence of the light harvesting complex Lhcf2 gene of the marine diatom Phaeodactylum tricornutum enhances transcription in an orientation- and distance-independent fashion. Mar Genomics 2015; 24 Pt 1:69-79. [PMID: 26117181 DOI: 10.1016/j.margen.2015.06.010] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2015] [Revised: 05/31/2015] [Accepted: 06/17/2015] [Indexed: 10/23/2022]
Abstract
Diatoms are a key phytoplankton group in the contemporary ocean, showing extraordinary adaptation capacities to rapidly changing environments. The recent availability of whole genome sequences from representative species has revealed distinct features in their genomes, like novel combinations of genes encoding distinct metabolisms and a significant number of diatom-specific genes. However, the regulatory mechanisms driving diatom gene expression are still largely uncharacterized. Considering the wide variety of fields of study orbiting diatoms, ranging from ecology, evolutionary biology to biotechnology, it is thus essential to increase our understanding of fundamental gene regulatory processes such as transcriptional regulation. To this aim, we explored the functional properties of the 5'-flanking region of the Phaeodatylum tricornutum Lhcf2 gene, encoding a member of the Light Harvesting Complex superfamily and we showed that this region enhances transcription of a GUS reporter gene in an orientation- and distance-independent fashion. This represents the first example of a cis-regulatory sequence with enhancer-like features discovered in diatoms and it is instrumental for the generation of novel genetic tools and diatom exploitation in different areas of study.
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Affiliation(s)
| | - Rossella Annunziata
- Sorbonne Universités, UPMC Univ Paris 06, Institut de Biologie Paris-Seine, UMR 7238, F-75006 Paris, France; CNRS, UMR 7238, F-75006 Paris, France
| | - Remo Sanges
- Stazione Zoologica Anton Dohrn, Villa Comunale, 80121 Naples, Italy
| | | | - Angela Falciatore
- Sorbonne Universités, UPMC Univ Paris 06, Institut de Biologie Paris-Seine, UMR 7238, F-75006 Paris, France; CNRS, UMR 7238, F-75006 Paris, France.
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20
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Khamis AM, Hamilton AR, Medvedeva YA, Alam T, Alam I, Essack M, Umylny B, Jankovic BR, Naeger NL, Suzuki M, Harbers M, Robinson GE, Bajic VB. Insights into the Transcriptional Architecture of Behavioral Plasticity in the Honey Bee Apis mellifera. Sci Rep 2015; 5:11136. [PMID: 26073445 PMCID: PMC4466890 DOI: 10.1038/srep11136] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2014] [Accepted: 05/01/2015] [Indexed: 12/30/2022] Open
Abstract
Honey bee colonies exhibit an age-related division of labor, with worker bees performing discrete sets of behaviors throughout their lifespan. These behavioral states are associated with distinct brain transcriptomic states, yet little is known about the regulatory mechanisms governing them. We used CAGEscan (a variant of the Cap Analysis of Gene Expression technique) for the first time to characterize the promoter regions of differentially expressed brain genes during two behavioral states (brood care (aka “nursing”) and foraging) and identified transcription factors (TFs) that may govern their expression. More than half of the differentially expressed TFs were associated with motifs enriched in the promoter regions of differentially expressed genes (DEGs), suggesting they are regulators of behavioral state. Strikingly, five TFs (nf-kb, egr, pax6, hairy, and clockwork orange) were predicted to co-regulate nearly half of the genes that were upregulated in foragers. Finally, differences in alternative TSS usage between nurses and foragers were detected upstream of 646 genes, whose functional analysis revealed enrichment for Gene Ontology terms associated with neural function and plasticity. This demonstrates for the first time that alternative TSSs are associated with stable differences in behavior, suggesting they may play a role in organizing behavioral state.
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Affiliation(s)
- Abdullah M Khamis
- Computational Bioscience Research Center, Computer, Electrical and Mathematical Sciences and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia
| | - Adam R Hamilton
- Departments of Entomology and Institute for Genomic Biology, Urbana, IL 61801; and Neuroscience Program, University of Illinois at Urbana-Champaign, Urbana, IL 61801
| | - Yulia A Medvedeva
- Computational Bioscience Research Center, Computer, Electrical and Mathematical Sciences and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia
| | - Tanvir Alam
- Computational Bioscience Research Center, Computer, Electrical and Mathematical Sciences and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia
| | - Intikhab Alam
- Computational Bioscience Research Center, Computer, Electrical and Mathematical Sciences and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia
| | - Magbubah Essack
- Computational Bioscience Research Center, Computer, Electrical and Mathematical Sciences and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia
| | - Boris Umylny
- Lumenogix Inc., 2935 Rodeo Park Drive East, Santa Fe NM, 87505, USA
| | - Boris R Jankovic
- Computational Bioscience Research Center, Computer, Electrical and Mathematical Sciences and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia
| | - Nicholas L Naeger
- Departments of Entomology and Institute for Genomic Biology, Urbana, IL 61801; and Neuroscience Program, University of Illinois at Urbana-Champaign, Urbana, IL 61801
| | - Makoto Suzuki
- DNAFORM Inc., Leading Venture Plaza-2, 75-1, Ono-cho, Tsurumi-ku, Yokohama City, Kanagawa, 230-0046, Japan
| | - Matthias Harbers
- 1] DNAFORM Inc., Leading Venture Plaza-2, 75-1, Ono-cho, Tsurumi-ku, Yokohama City, Kanagawa, 230-0046, Japan [2] RIKEN Center for Life Science Technologies, Suehiro-cho, Tsurumi-ku, Yokohama City, Kanagawa, 230-0045, Japan
| | - Gene E Robinson
- Departments of Entomology and Institute for Genomic Biology, Urbana, IL 61801; and Neuroscience Program, University of Illinois at Urbana-Champaign, Urbana, IL 61801
| | - Vladimir B Bajic
- Computational Bioscience Research Center, Computer, Electrical and Mathematical Sciences and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia
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21
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Razin SV, Gavrilov AA, Ulyanov SV. Transcription-controlling regulatory elements of the eukaryotic genome. Mol Biol 2015. [DOI: 10.1134/s0026893315020119] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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22
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Haberle V, Forrest ARR, Hayashizaki Y, Carninci P, Lenhard B. CAGEr: precise TSS data retrieval and high-resolution promoterome mining for integrative analyses. Nucleic Acids Res 2015; 43:e51. [PMID: 25653163 PMCID: PMC4417143 DOI: 10.1093/nar/gkv054] [Citation(s) in RCA: 134] [Impact Index Per Article: 14.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2015] [Accepted: 01/15/2015] [Indexed: 12/21/2022] Open
Abstract
Cap analysis of gene expression (CAGE) is a high-throughput method for transcriptome analysis that provides a single base-pair resolution map of transcription start sites (TSS) and their relative usage. Despite their high resolution and functional significance, published CAGE data are still underused in promoter analysis due to the absence of tools that enable its efficient manipulation and integration with other genome data types. Here we present CAGEr, an R implementation of novel methods for the analysis of differential TSS usage and promoter dynamics, integrated with CAGE data processing and promoterome mining into a first comprehensive CAGE toolbox on a common analysis platform. Crucially, we provide collections of TSSs derived from most published CAGE datasets, as well as direct access to FANTOM5 resource of TSSs for numerous human and mouse cell/tissue types from within R, greatly increasing the accessibility of precise context-specific TSS data for integrative analyses. The CAGEr package is freely available from Bioconductor at http://www.bioconductor.org/packages/release/bioc/html/CAGEr.html.
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Affiliation(s)
- Vanja Haberle
- Department of Biology, University of Bergen, Thormøhlensgate 53 A & B, N-5008 Bergen, Norway Department of Molecular Sciences, Institute of Clinical Sciences, Faculty of Medicine, Imperial College London and MRC Clinical Sciences Centre, Hammersmith Hospital Campus, Du Cane Road, London W12 0NN, UK
| | - Alistair R R Forrest
- RIKEN Center for Life Science Technologies, Division of Genomic Technologies (CLST DGT), RIKEN Yokohama Campus, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
| | - Yoshihide Hayashizaki
- RIKEN Preventive Medicine and Diagnosis Innovation Program (PMI), 2-1 Hirosawa, Wako-shi, Saitama 351-0198, Japan
| | - Piero Carninci
- RIKEN Center for Life Science Technologies, Division of Genomic Technologies (CLST DGT), RIKEN Yokohama Campus, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
| | - Boris Lenhard
- Department of Molecular Sciences, Institute of Clinical Sciences, Faculty of Medicine, Imperial College London and MRC Clinical Sciences Centre, Hammersmith Hospital Campus, Du Cane Road, London W12 0NN, UK Department of Informatics, University of Bergen, Høyteknologisenteret, Thormøhlensgate 55, N-5008 Bergen, Norway
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Xu Y, Jin C, Liu Z, Pan J, Li H, Zhang Z, Bi S, Yokoyama KK. Cloning and characterization of the mouse JDP2 gene promoter reveal negative regulation by p53. Biochem Biophys Res Commun 2014; 450:1531-6. [PMID: 25026555 DOI: 10.1016/j.bbrc.2014.07.034] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2014] [Accepted: 07/06/2014] [Indexed: 01/22/2023]
Abstract
Jun dimerization protein 2 (JDP2) is a repressor of transcription factor AP-1. To investigate the transcriptional regulation of the JDP2 gene, we cloned the 5'-flanking region of the mouse JDP2 gene. Primer extension analysis revealed a new transcription start site (+1). Promoter analysis showed that the region from nt -343 to nt +177 contains basal transcriptional activity. Interestingly, the tumor suppressor p53 significantly repressed the transcriptional activity of the JDP2 promoter. Given that JDP2 inhibits expression of p53, our results suggest a negative feedback loop between JDP2 and p53, and a direct link between JDP2 and a key oncogenic pathway.
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Affiliation(s)
- Yuanhong Xu
- Department of Pancreatic Gastroenterologic Surgery, First Hospital of China Medical University, No. 92, Nanjing Rd, Shenyang 110001, China.
| | - Chunyuan Jin
- Department of Environmental Medicine, New York University School of Medicine, 57 Old Forge Rd, Tuxedo Park, NY 10987, USA
| | - Zhe Liu
- Department of Pancreatic Gastroenterologic Surgery, First Hospital of China Medical University, No. 92, Nanjing Rd, Shenyang 110001, China
| | - Jianzhi Pan
- Institute of Animal Husbandry and Veterinary, Zhejiang Academy of Agricultural Sciences, China
| | - Hongjie Li
- Department of Environmental Medicine, New York University School of Medicine, 57 Old Forge Rd, Tuxedo Park, NY 10987, USA
| | - Zhongbo Zhang
- Department of Pancreatic Gastroenterologic Surgery, First Hospital of China Medical University, No. 92, Nanjing Rd, Shenyang 110001, China
| | - Shulong Bi
- Department of Pancreatic Gastroenterologic Surgery, First Hospital of China Medical University, No. 92, Nanjing Rd, Shenyang 110001, China
| | - Kazunari K Yokoyama
- Graduate Institute of Medicine, Kaohsiung Medical University, 100 Shih-Chuan 1st Rd, San-Ming District, Kaohsiung 807, Taiwan.
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24
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Liang KC, Suzuki Y, Kumagai Y, Nakai K. Analysis of changes in transcription start site distribution by a classification approach. Gene 2014; 537:29-40. [DOI: 10.1016/j.gene.2013.12.038] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2013] [Accepted: 12/16/2013] [Indexed: 10/25/2022]
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25
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Bhatt D, Ghosh S. Regulation of the NF-κB-Mediated Transcription of Inflammatory Genes. Front Immunol 2014; 5:71. [PMID: 24611065 PMCID: PMC3933792 DOI: 10.3389/fimmu.2014.00071] [Citation(s) in RCA: 168] [Impact Index Per Article: 16.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2014] [Accepted: 02/10/2014] [Indexed: 12/12/2022] Open
Abstract
The NF-κB family of transcription factors plays a central role in the inducible expression of inflammatory genes during the immune response, and the proper regulation of these genes is a critical factor in the maintenance of immune homeostasis. The chromatin environment at stimulus-responsive NF-κB sites is a major determinant in transcription factor binding, and dynamic alteration of the chromatin state to facilitate transcription factor binding is a key regulatory mechanism. NF-κB is in turn able to influence the chromatin state through a variety of mechanisms, including the recruitment of chromatin modifying co-activator complexes such as p300, the competitive eviction of negative chromatin modifications, and the recruitment of components of the general transcriptional machinery. Frequently, the selective interaction with these co-activators is dependent on specific post-translational modification of NF-κB subunits. Finally, the mechanisms of inducible NF-κB activity in different immune cell types seem to be largely conserved. The diversity of cell-specific NF-κB-mediated transcriptional programs is established at the chromatin level during cell differentiation by lineage-defining transcription factors. These factors generate and maintain a cell-specific chromatin landscape that is accessible to NF-κB, thus restricting the inducible transcriptional response to a cell-appropriate output.
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Affiliation(s)
- Dev Bhatt
- Department of Microbiology and Immunology, College of Physicians and Surgeons, Columbia University , New York, NY , USA
| | - Sankar Ghosh
- Department of Microbiology and Immunology, College of Physicians and Surgeons, Columbia University , New York, NY , USA
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26
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Murata M, Nishiyori-Sueki H, Kojima-Ishiyama M, Carninci P, Hayashizaki Y, Itoh M. Detecting expressed genes using CAGE. Methods Mol Biol 2014; 1164:67-85. [PMID: 24927836 DOI: 10.1007/978-1-4939-0805-9_7] [Citation(s) in RCA: 114] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
Cap analysis of gene expression (CAGE) provides accurate high-throughput measurement of RNA expression. By the large-scale analysis of 5' end of transcripts using CAGE method, it enables not only determination of the transcription start site but also prediction of promoter region. Here we provide a protocol for the construction of no-amplification non-tagging CAGE libraries for Illumina next-generation sequencers (nAnT-iCAGE). We have excluded the commonly used PCR amplification and cleavage of restriction enzyme to eliminate any potential biases. As a result, we achieved less biased simple preparation process.
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Affiliation(s)
- Mitsuyoshi Murata
- Division of Genomic Technologies, RIKEN Center for Life Science Technologies, RIKEN Yokohama Institute, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa, 230-0045, Japan
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27
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Su S, Omiecinski CJ. Sp1 and Sp3 transcription factors regulate the basal expression of human microsomal epoxide hydrolase (EPHX1) through interaction with the E1b far upstream promoter. Gene 2013; 536:135-44. [PMID: 24315822 DOI: 10.1016/j.gene.2013.11.053] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2013] [Revised: 10/28/2013] [Accepted: 11/18/2013] [Indexed: 11/24/2022]
Abstract
Microsomal epoxide hydrolase (mEH, EPHX1) is a critical biotransformation enzyme, catalyzing the metabolism of many xenobiotics. Human mEH is transcribed using alternative promoters. The upstream E1 promoter is active in liver while the far upstream E1b promoter drives the expression of mEH in all tissues, including liver. Although several liver-specific transcription factors have been identified in the regulation of E1 transcription, little is known regarding the mechanisms of E1b transcriptional regulation. Genome-wide mapping of DNase I hypersensitive sites revealed an open chromatin region between nucleotide -300 upstream and +400 downstream of E1b. This area coincides with a previously described promoter region responsible for maintaining high basal promoter activity. In silico analysis of this location revealed several Sp1/Sp3 binding sites. Site-directed mutagenesis of these motifs suppressed the transactivation activity of the E1b proximal promoter, indicating their importance as contributors to E1b promoter regulation. Further, E1b promoter activities were increased significantly following Sp1 and Sp3 overexpression, while Mithramycin A, a selective Sp1 inhibitor, reduced the promoter activities. EMSA studies demonstrated that Sp1 bound to two putative Sp1/Sp3 binding sites. ChIP analysis confirmed that both endogenous Sp1 and Sp3 were bound to the proximal promoter region of E1b. Knockdown of Sp1 expression using siRNA did not alter the endogenous E1b transcriptional level, while knockdown of Sp3 greatly decreased E1b expression in different human cell lines. Taken together, these results support the concept that Sp1 and Sp3 are functionally involved as transcriptional integrators regulating the basal expression of the derived mEH E1b variant transcript.
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Affiliation(s)
- Shengzhong Su
- Center for Molecular Toxicology and Carcinogenesis, The Pennsylvania State University, 101 Life Sciences Bldg, University Park, PA 16802, USA
| | - Curtis J Omiecinski
- Center for Molecular Toxicology and Carcinogenesis, The Pennsylvania State University, 101 Life Sciences Bldg, University Park, PA 16802, USA.
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The fate of the messenger is pre-determined: a new model for regulation of gene expression. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2013; 1829:643-53. [PMID: 23337853 DOI: 10.1016/j.bbagrm.2013.01.004] [Citation(s) in RCA: 85] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/22/2012] [Revised: 01/07/2013] [Accepted: 01/08/2013] [Indexed: 02/08/2023]
Abstract
Recent years have seen a rise in publications demonstrating coupling between transcription and mRNA decay. This coupling most often accompanies cellular processes that involve transitions in gene expression patterns, for example during mitotic division and cellular differentiation and in response to cellular stress. Transcription can affect the mRNA fate by multiple mechanisms. The most novel finding is the process of co-transcriptional imprinting of mRNAs with proteins, which in turn regulate cytoplasmic mRNA stability. Transcription therefore is not only a catalyst of mRNA synthesis but also provides a platform that enables imprinting, which coordinates between transcription and mRNA decay. Here we present an overview of the literature, which provides the evidence of coupling between transcription and decay, review the mechanisms and regulators by which the two processes are coupled, discuss why such coupling is beneficial and present a new model for regulation of gene expression. This article is part of a Special Issue entitled: RNA Decay mechanisms.
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29
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Kim D, Hong JSJ, Qiu Y, Nagarajan H, Seo JH, Cho BK, Tsai SF, Palsson BØ. Comparative analysis of regulatory elements between Escherichia coli and Klebsiella pneumoniae by genome-wide transcription start site profiling. PLoS Genet 2012; 8:e1002867. [PMID: 22912590 PMCID: PMC3415461 DOI: 10.1371/journal.pgen.1002867] [Citation(s) in RCA: 111] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2012] [Accepted: 06/14/2012] [Indexed: 01/08/2023] Open
Abstract
Genome-wide transcription start site (TSS) profiles of the enterobacteria Escherichia coli and Klebsiella pneumoniae were experimentally determined through modified 5′ RACE followed by deep sequencing of intact primary mRNA. This identified 3,746 and 3,143 TSSs for E. coli and K. pneumoniae, respectively. Experimentally determined TSSs were then used to define promoter regions and 5′ UTRs upstream of coding genes. Comparative analysis of these regulatory elements revealed the use of multiple TSSs, identical sequence motifs of promoter and Shine-Dalgarno sequence, reflecting conserved gene expression apparatuses between the two species. In both species, over 70% of primary transcripts were expressed from operons having orthologous genes during exponential growth. However, expressed orthologous genes in E. coli and K. pneumoniae showed a strikingly different organization of upstream regulatory regions with only 20% identical promoters with TSSs in both species. Over 40% of promoters had TSSs identified in only one species, despite conserved promoter sequences existing in the other species. 662 conserved promoters having TSSs in both species resulted in the same number of comparable 5′ UTR pairs, and that regulatory element was found to be the most variant region in sequence among promoter, 5′ UTR, and ORF. In K. pneumoniae, 48 sRNAs were predicted and 36 of them were expressed during exponential growth. Among them, 34 orthologous sRNAs between two species were analyzed in depth, and the analysis showed that many sRNAs of K. pneumoniae, including pleiotropic sRNAs such as rprA, arcZ, and sgrS, may work in the same way as in E. coli. These results reveal a new dimension of comparative genomics such that a comparison of two genomes needs to be comprehensive over all levels of genome organization. In order to investigate similarities and differences of closely related species, most of the comparative genomics studies focus on comparing the gene contents either shared or specific for each genome. However, it is also important to investigate the differences in non-coding regulatory elements because they influence the transcriptional and post-transcriptional processes. Thus, we performed a genome-wide profiling of transcription start sites (TSSs) in two species, E. coli K-12 MG1655 and K. pneumoniae MGH78578. Experimental identification of TSSs is important for precise definition of promoter regions and 5′ untranslated regions upstream of coding genes. Comparative analysis of these regulatory elements revealed the use of multiple TSSs, identical sequence motifs of promoter and Shine-Dalgarno sequence. However, we observed that the upstream regulatory regions of the majority of operons having orthologous genes were organized with different usage of promoters and TSSs, resulting in diverse and complex gene regulation. We also found that the 5′ UTR is the least conserved regulatory element in sequence between the two species. Moreover, 34 orthologous sRNAs between E. coli and K. pneumoniae were analyzed in depth. The analysis suggested many of K. pneumoniae sRNAs might regulate the target genes as in E. coli.
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Affiliation(s)
- Donghyuk Kim
- Department of Bioengineering, University of California San Diego, La Jolla, California, United States of America
| | - Jay Sung-Joong Hong
- Department of Bioengineering, University of California San Diego, La Jolla, California, United States of America
| | - Yu Qiu
- Department of Bioengineering, University of California San Diego, La Jolla, California, United States of America
| | - Harish Nagarajan
- Department of Bioengineering, University of California San Diego, La Jolla, California, United States of America
| | - Joo-Hyun Seo
- Department of Bioengineering, University of California San Diego, La Jolla, California, United States of America
| | - Byung-Kwan Cho
- Department of Bioengineering, University of California San Diego, La Jolla, California, United States of America
| | - Shih-Feng Tsai
- Division of Molecular and Genomic Medicine, National Health Research Institutes, Miaoli, Taiwan
| | - Bernhard Ø. Palsson
- Department of Bioengineering, University of California San Diego, La Jolla, California, United States of America
- * E-mail:
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30
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Zhang Z, Ma X, Zhang MQ. Bivalent-like chromatin markers are predictive for transcription start site distribution in human. PLoS One 2012; 7:e38112. [PMID: 22768038 PMCID: PMC3387189 DOI: 10.1371/journal.pone.0038112] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2011] [Accepted: 05/01/2012] [Indexed: 11/24/2022] Open
Abstract
Deep sequencing of 5′ capped transcripts has revealed a variety of transcription initiation patterns, from narrow, focused promoters to wide, broad promoters. Attempts have already been made to model empirically classified patterns, but virtually no quantitative models for transcription initiation have been reported. Even though both genetic and epigenetic elements have been associated with such patterns, the organization of regulatory elements is largely unknown. Here, linear regression models were derived from a pool of regulatory elements, including genomic DNA features, nucleosome organization, and histone modifications, to predict the distribution of transcription start sites (TSS). Importantly, models including both active and repressive histone modification markers, e.g. H3K4me3 and H4K20me1, were consistently found to be much more predictive than models with only single-type histone modification markers, indicating the possibility of “bivalent-like” epigenetic control of transcription initiation. The nucleosome positions are proposed to be coded in the active component of such bivalent-like histone modification markers. Finally, we demonstrated that models trained on one cell type could successfully predict TSS distribution in other cell types, suggesting that these models may have a broader application range.
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Affiliation(s)
- Zhihua Zhang
- Department of Molecular Cell Biology, Center for Systems Biology, University of Texas at Dallas, Richardson, Texas, United States of America
- Center for Computational Biology, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, People’s Republic of China
- Laboratory of Disease Genomics and Personalized Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, People’s Republic of China
| | - Xiaotu Ma
- Department of Molecular Cell Biology, Center for Systems Biology, University of Texas at Dallas, Richardson, Texas, United States of America
| | - Michael Q. Zhang
- Department of Molecular Cell Biology, Center for Systems Biology, University of Texas at Dallas, Richardson, Texas, United States of America
- Bioinformatics Division, Center for Synthetic and Systems Biology, TNLIST, Tsinghua University, Beijing, China
- * E-mail:
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31
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Pereira-Castro I, Costa LTD, Amorim A, Azevedo L. Transcriptional regulation of the human mitochondrial peptide deformylase (PDF). Biochem Biophys Res Commun 2012; 421:825-31. [PMID: 22554513 DOI: 10.1016/j.bbrc.2012.04.097] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2012] [Accepted: 04/18/2012] [Indexed: 11/30/2022]
Abstract
The last years of research have been particularly dynamic in establishing the importance of peptide deformylase (PDF), a protein of the N-terminal methionine excision (NME) pathway that removes formyl-methionine from mitochondrial-encoded proteins. The genomic sequence of the human PDF gene is shared with the COG8 gene, which encodes a component of the oligomeric golgi complex, a very unusual case in Eukaryotic genomes. Since PDF is crucial in maintaining mitochondrial function and given the atypical short distance between the end of COG8 coding sequence and the PDF initiation codon, we investigated whether the regulation of the human PDF is affected by the COG8 overlapping partner. Our data reveals that PDF has several transcription start sites, the most important of which only 18 bp from the initiation codon. Furthermore, luciferase-activation assays using differently-sized fragments defined a 97 bp minimal promoter region for human PDF, which is capable of very strong transcriptional activity. This fragment contains a potential Sp1 binding site highly conserved in mammalian species. We show that this binding site, whose mutation significantly reduces transcription activation, is a target for the Sp1 transcription factor, and possibly of other members of the Sp family. Importantly, the entire minimal promoter region is located after the end of COG8's coding region, strongly suggesting that the human PDF preserves an independent regulation from its overlapping partner.
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Affiliation(s)
- Isabel Pereira-Castro
- IPATIMUP-Institute of Molecular Pathology and Immunology of University of Porto, Portugal.
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Le HTT, Sorrell AM, Siddle K. Two isoforms of the mRNA binding protein IGF2BP2 are generated by alternative translational initiation. PLoS One 2012; 7:e33140. [PMID: 22427968 PMCID: PMC3299737 DOI: 10.1371/journal.pone.0033140] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2011] [Accepted: 02/09/2012] [Indexed: 12/11/2022] Open
Abstract
IGF2BP2 is a member of a family of mRNA binding proteins that, collectively, have been shown to bind to several different mRNAs in mammalian cells, including one of the mRNAs encoding insulin-like growth factor-2. Polymorphisms in the Igf2bp2 gene are associated with risk of developing type 2 diabetes, but detailed functional characterisation of IGF2BP2 protein is lacking. By immunoblotting with C-terminally reactive antibodies we identified a novel IGF2BP2 isoform with a molecular weight of 58 kDa in both human and rodents, that is expressed at somewhat lower levels than the full-length 65 kDa protein. We demonstrated by mutagenesis that this isoform is generated by alternative translation initiation at the internal Met69. It lacks a conserved N-terminal RNA Recognition Motif (RRM) and would be predicted to differ functionally from the canonical full length isoform. We further investigated IGF2BP2 mRNA transcripts by amplification of cDNA using 5'-RACE. We identified multiple transcription start sites of the human, mouse and rat Igf2bp2 genes in a highly conserved region only 50-90 nts upstream of the major translation start site, ruling out the existence of N-terminally extended isoforms. We conclude that structural heterogeneity of IGF2BP2 protein should be taken into account when considering cellular function.
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Affiliation(s)
| | | | - Kenneth Siddle
- University of Cambridge Metabolic Research Laboratories and Department of Clinical Biochemistry, Institute of Metabolic Science, Addenbrooke's Hospital, Cambridge, United Kingdom
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33
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5' end-centered expression profiling using cap-analysis gene expression and next-generation sequencing. Nat Protoc 2012; 7:542-61. [PMID: 22362160 DOI: 10.1038/nprot.2012.005] [Citation(s) in RCA: 182] [Impact Index Per Article: 15.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Cap-analysis gene expression (CAGE) provides accurate high-throughput measurement of RNA expression. CAGE allows mapping of all the initiation sites of both capped coding and noncoding RNAs. In addition, transcriptional start sites within promoters are characterized at single-nucleotide resolution. The latter allows the regulatory inputs driving gene expression to be studied, which in turn enables the construction of transcriptional networks. Here we provide an optimized protocol for the construction of CAGE libraries on the basis of the preparation of 27-nt-long tags corresponding to initial bases at the 5' ends of capped RNAs. We have optimized the methods using simple steps based on filtration, which altogether takes 4 d to complete. The CAGE tags can be readily sequenced with Illumina sequencers, and upon modification they are also amenable to sequencing using other platforms.
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Zhao X, Valen E, Parker BJ, Sandelin A. Systematic clustering of transcription start site landscapes. PLoS One 2011; 6:e23409. [PMID: 21887249 PMCID: PMC3160847 DOI: 10.1371/journal.pone.0023409] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2011] [Accepted: 07/15/2011] [Indexed: 12/27/2022] Open
Abstract
Genome-wide, high-throughput methods for transcription start site (TSS) detection have shown that most promoters have an array of neighboring TSSs where some are used more than others, forming a distribution of initiation propensities. TSS distributions (TSSDs) vary widely between promoters and earlier studies have shown that the TSSDs have biological implications in both regulation and function. However, no systematic study has been made to explore how many types of TSSDs and by extension core promoters exist and to understand which biological features distinguish them. In this study, we developed a new non-parametric dissimilarity measure and clustering approach to explore the similarities and stabilities of clusters of TSSDs. Previous studies have used arbitrary thresholds to arrive at two general classes: broad and sharp. We demonstrated that in addition to the previous broad/sharp dichotomy an additional category of promoters exists. Unlike typical TATA-driven sharp TSSDs where the TSS position can vary a few nucleotides, in this category virtually all TSSs originate from the same genomic position. These promoters lack epigenetic signatures of typical mRNA promoters and a substantial subset of them are mapping upstream of ribosomal protein pseudogenes. We present evidence that these are likely mapping errors, which have confounded earlier analyses, due to the high similarity of ribosomal gene promoters in combination with known G addition bias in the CAGE libraries. Thus, previous two-class separations of promoter based on TSS distributions are motivated, but the ultra-sharp TSS distributions will confound downstream analyses if not removed.
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Affiliation(s)
- Xiaobei Zhao
- Department of Biology and Biotech Research and Innovation Centre, The Bioinformatics Centre, Copenhagen University, Copenhagen, Denmark
| | - Eivind Valen
- Department of Biology and Biotech Research and Innovation Centre, The Bioinformatics Centre, Copenhagen University, Copenhagen, Denmark
| | - Brian J. Parker
- Department of Biology and Biotech Research and Innovation Centre, The Bioinformatics Centre, Copenhagen University, Copenhagen, Denmark
| | - Albin Sandelin
- Department of Biology and Biotech Research and Innovation Centre, The Bioinformatics Centre, Copenhagen University, Copenhagen, Denmark
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Nozaki T, Yachie N, Ogawa R, Kratz A, Saito R, Tomita M. Tight associations between transcription promoter type and epigenetic variation in histone positioning and modification. BMC Genomics 2011; 12:416. [PMID: 21846408 PMCID: PMC3170308 DOI: 10.1186/1471-2164-12-416] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2010] [Accepted: 08/17/2011] [Indexed: 11/19/2022] Open
Abstract
Background Transcription promoters are fundamental genomic cis-elements controlling gene expression. They can be classified into two types by the degree of imprecision of their transcription start sites: peak promoters, which initiate transcription from a narrow genomic region; and broad promoters, which initiate transcription from a wide-ranging region. Eukaryotic transcription initiation is suggested to be associated with the genomic positions and modifications of nucleosomes. For instance, it has been recently shown that histone with H3K9 acetylation (H3K9ac) is more likely to be distributed around broad promoters rather than peak promoters; it can thus be inferred that there is an association between histone H3K9 and promoter architecture. Results Here, we performed a systematic analysis of transcription promoters and gene expression, as well as of epigenetic histone behaviors, including genomic position, stability within the chromatin, and several modifications. We found that, in humans, broad promoters, but not peak promoters, generally had significant associations with nucleosome positioning and modification. Specifically, around broad promoters histones were highly distributed and aligned in an orderly fashion. This feature was more evident with histones that were methylated or acetylated; moreover, the nucleosome positions around the broad promoters were more stable than those around the peak ones. More strikingly, the overall expression levels of genes associated with broad promoters (but not peak promoters) with modified histones were significantly higher than the levels of genes associated with broad promoters with unmodified histones. Conclusion These results shed light on how epigenetic regulatory networks of histone modifications are associated with promoter architecture.
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Affiliation(s)
- Tadasu Nozaki
- Institute for Advanced Biosciences, Keio University, Tsuruoka, 997-0017, Japan
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36
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Two proteins with different functions are derived from the KlHEM13 gene. EUKARYOTIC CELL 2011; 10:1331-9. [PMID: 21821717 DOI: 10.1128/ec.05108-11] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Two proteins that differ at the N terminus (l-KlCpo and s-KlCpo) are derived from KlHEM13, a single-copy-number gene in the haploid genome of Kluyveromyces lactis. Two transcriptional start site (tss) pools are detectable using primer extension, and their selection is heme dependent. One of these tss pools is located 5' of the first translation initiation codon (TIC) in the open reading frame of KlHEM13, while the other is located between the first and second TICs. In terms of functional significance, only s-KlCpo complements the heme deficiency caused by the Δhem13 deletion in K. lactis. Data obtained from immune detection in subcellular fractions, directed mutagenesis, chromatin immunoprecipitation (ChIP) assays, and the functional relevance of ΔKlhem13 deletion for KlHEM13 promoter activity suggest that l-KlCpo regulates KlHEM13 transcription. A hypothetical model of the evolutionary origins and coexistence of these two proteins in K. lactis is discussed.
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37
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Green VA, Weinberg MS. Small RNA-induced transcriptional gene regulation in mammals mechanisms, therapeutic applications, and scope within the genome. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2011; 102:11-46. [PMID: 21846568 DOI: 10.1016/b978-0-12-415795-8.00005-2] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Argonaute-bound small RNAs, derived from RNA interference and related pathways, are well-known effectors of posttranscriptional gene silencing (PTGS). Yet, these complexes also play an important role in affecting gene expression at the transcriptional level, either by transcriptional gene silencing (TGS) or activation (TGA). Our current understanding of how small RNAs are able to both activate and suppress transcription is unclear. In this review, we briefly outline the biogenesis of small RNAs and explore the mechanisms behind the various phenomena attributed to AGO-bound small RNA-mediated transcriptional regulation. The therapeutic potential of TGS and TGA is examined, emphasizing the distinct advantages over PTGS approaches with examples of application to cancer and diseases associated with viruses, aberrant splicing, and dysregulated heterochromatin. Finally, the influence of promoter architecture on gene susceptibility to transcriptional regulation is discussed in the light of how this impacts the scope of small RNA-induced transcriptional regulation within the genome.
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Affiliation(s)
- Victoria A Green
- Department of Molecular Medicine and Haematology, University of the Witwatersrand, Johannesburg, South Africa
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Schaefer U, Kodzius R, Kai C, Kawai J, Carninci P, Hayashizaki Y, Bajic VB. High sensitivity TSS prediction: estimates of locations where TSS cannot occur. PLoS One 2010; 5:e13934. [PMID: 21085627 PMCID: PMC2981523 DOI: 10.1371/journal.pone.0013934] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2010] [Accepted: 10/19/2010] [Indexed: 11/26/2022] Open
Abstract
Background Although transcription in mammalian genomes can initiate from various genomic positions (e.g., 3′UTR, coding exons, etc.), most locations on genomes are not prone to transcription initiation. It is of practical and theoretical interest to be able to estimate such collections of non-TSS locations (NTLs). The identification of large portions of NTLs can contribute to better focusing the search for TSS locations and thus contribute to promoter and gene finding. It can help in the assessment of 5′ completeness of expressed sequences, contribute to more successful experimental designs, as well as more accurate gene annotation. Methodology Using comprehensive collections of Cap Analysis of Gene Expression (CAGE) and other transcript data from mouse and human genomes, we developed a methodology that allows us, by performing computational TSS prediction with very high sensitivity, to annotate, with a high accuracy in a strand specific manner, locations of mammalian genomes that are highly unlikely to harbor transcription start sites (TSSs). The properties of the immediate genomic neighborhood of 98,682 accurately determined mouse and 113,814 human TSSs are used to determine features that distinguish genomic transcription initiation locations from those that are not likely to initiate transcription. In our algorithm we utilize various constraining properties of features identified in the upstream and downstream regions around TSSs, as well as statistical analyses of these surrounding regions. Conclusions Our analysis of human chromosomes 4, 21 and 22 estimates ∼46%, ∼41% and ∼27% of these chromosomes, respectively, as being NTLs. This suggests that on average more than 40% of the human genome can be expected to be highly unlikely to initiate transcription. Our method represents the first one that utilizes high-sensitivity TSS prediction to identify, with high accuracy, large portions of mammalian genomes as NTLs. The server with our algorithm implemented is available at http://cbrc.kaust.edu.sa/ddm/.
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MESH Headings
- Algorithms
- Animals
- Base Sequence
- Chromosomes, Human, Pair 21/genetics
- Chromosomes, Human, Pair 22/genetics
- Chromosomes, Human, Pair 4/genetics
- Computational Biology/methods
- Genome/genetics
- Genome, Human/genetics
- Humans
- Internet
- Mice
- Molecular Sequence Data
- Promoter Regions, Genetic/genetics
- Receptors, Opioid, mu/genetics
- Reproducibility of Results
- Transcription Initiation Site
- Transcription, Genetic
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Affiliation(s)
- Ulf Schaefer
- Computational Bioscience Research Center (CBRC), King Abdullah University of Science and Technology, Thuwal, Kingdom of Saudi Arabia
| | - Rimantas Kodzius
- Division of Physical Sciences and Engineering, King Abdullah University of Science and Technology, Thuwal, Kingdom of Saudi Arabia
| | - Chikatoshi Kai
- Genome Exploration Research Group (Genome Network Project Core Group), RIKEN Genomic Sciences Center (GSC), RIKEN Yokohama Institute, Yokohama, Kanagawa, Japan
| | - Jun Kawai
- Genome Exploration Research Group (Genome Network Project Core Group), RIKEN Genomic Sciences Center (GSC), RIKEN Yokohama Institute, Yokohama, Kanagawa, Japan
| | - Piero Carninci
- Genome Science Laboratory, Discovery Research Institute, RIKEN Wako Institute, Wako, Saitama, Japan
| | - Yoshihide Hayashizaki
- Genome Exploration Research Group (Genome Network Project Core Group), RIKEN Genomic Sciences Center (GSC), RIKEN Yokohama Institute, Yokohama, Kanagawa, Japan
| | - Vladimir B. Bajic
- Computational Bioscience Research Center (CBRC), King Abdullah University of Science and Technology, Thuwal, Kingdom of Saudi Arabia
- * E-mail:
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Troukhan M, Tatarinova T, Bouck J, Flavell RB, Alexandrov NN. Genome-wide discovery of cis-elements in promoter sequences using gene expression. OMICS-A JOURNAL OF INTEGRATIVE BIOLOGY 2010; 13:139-51. [PMID: 19231992 DOI: 10.1089/omi.2008.0034] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
The availability of complete or nearly complete genome sequences, a large number of 5' expressed sequence tags, and significant public expression data allow for a more accurate identification of cis-elements regulating gene expression. We have implemented a global approach that takes advantage of available expression data, genomic sequences, and transcript information to predict cis-elements associated with specific expression patterns. The key components of our approach are: (1) precise identification of transcription start sites, (2) specific locations of cis-elements relative to the transcription start site, and (3) assessment of statistical significance for all sequence motifs. By applying our method to promoters of Arabidopsis thaliana and Mus musculus, we have identified motifs that affect gene expression under specific environmental conditions or in certain tissues. We also found that the presence of the TATA box is associated with increased variability of gene expression. Strong correlation between our results and experimentally determined motifs shows that the method is capable of predicting new functionally important cis-elements in promoter sequences.
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Affiliation(s)
- Maxim Troukhan
- Ceres, Inc. 1535 Rancho Conejo Road, Thousand Oaks, CA 91310, USA
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Natoli G. Maintaining cell identity through global control of genomic organization. Immunity 2010; 33:12-24. [PMID: 20643336 DOI: 10.1016/j.immuni.2010.07.006] [Citation(s) in RCA: 149] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2010] [Indexed: 02/06/2023]
Abstract
Cell differentiation entails early lineage choices leading to the activation, and the subsequent maintenance, of the gene expression program characteristic of each cell type. Alternative lineage choices involve the activation of different regulatory and coding regions of the genome, a process instructed by lineage-determining transcription factors, and at least in part mediated by the deposition of chromatin marks that modify functionality and accessibility of the underlying genome. According to classic epigenetics, subsequent maintenance of chromatin marks across mitoses and in spite of environmental perturbations occurs largely through autonomous and unsupervised mechanisms. However, paradigmatic genetic and biochemical studies in immune system and hematopoietic cells strongly point to the concept that both induction and maintenance of the differentiated state require constant supervision by lineage-determining transcription factors, which may act to globally organize the genome in both the one- and the three-dimensional space.
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Affiliation(s)
- Gioacchino Natoli
- Department of Experimental Oncology, European Institute of Oncology, IFOM-IEO Campus, Via Adamello 16, 20139 Milan, Italy
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Blomquist TM, Crawford EL, Willey JC. Cis-acting genetic variation at an E2F1/YY1 response site and putative p53 site is associated with altered allele-specific expression of ERCC5 (XPG) transcript in normal human bronchial epithelium. Carcinogenesis 2010; 31:1242-50. [PMID: 20233728 DOI: 10.1093/carcin/bgq057] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
ERCC5 (XPG) is a key component of the nucleotide excision DNA repair pathway. In two recent case-control studies, we determined that ERCC5 transcript expression pattern in grossly normal human bronchial epithelial cells (NBEC) was different in individuals diagnosed with lung cancer compared with non-lung cancer controls. In this study, we tested the hypothesis that variation at cis-acting sites contributed to observed variation in ERCC5 transcript expression in NBEC. Allele-specific expression (ASE) was measured at transcribed polymorphic site rs1047768 in exon 2 of ERCC5 in NBEC complementary DNA (cDNA) of 22 individuals using allele-specific competitive polymerase chain reaction. ASE at rs1047768 was then assessed for association with allelotype at polymorphic sites rs751402 (E2F1 and YY1 recognition and response site) and rs2296147 (putative P53 recognition site) in the proximal promoter and 5' untranslated region, respectively, of ERCC5. Interindividual variation in recombination between rs751402, rs2296147 and rs1047768 in poly-heterozygotes was controlled for by allele-specific sequencing. Measured rs1047768 T:C allelic ratio was (i) significantly higher in NBEC cDNA compared with genomic DNA controls (P < 0.001) among samples heterozygous at both rs751402 and rs2296147; (ii) less high (P = 0.02) for samples homozygous at rs751402 but heterozygous at rs2296147 and (iii) not significantly different (P = 0.18) for doubly homozygous individuals. Here, we demonstrate that rs751402 A allele and rs2296147 T allele are associated with higher ASE of ERCC5 T allele transcript at rs1047768 in NBEC.
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Affiliation(s)
- Thomas M Blomquist
- Department of Medicine, University of Toledo Medical Center, Toledo, OH 43614, USA
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Abstract
Animal growth and development depend on the precise control of gene expression at the level of transcription. A central role in the regulation of developmental transcription is attributed to transcription factors that bind DNA enhancer elements, which are often located far from gene transcription start sites. Here, we review recent studies that have uncovered significant regulatory functions in developmental transcription for the TFIID basal transcription factors and for the DNA core promoter elements that are located close to transcription start sites.
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Affiliation(s)
- Uwe Ohler
- Institute for Genome Sciences & Policy, Departments of Biostatistics & Bioinformatics and Computer Science, Duke University, Durham, NC 27708, USA
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44
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Rach EA, Yuan HY, Majoros WH, Tomancak P, Ohler U. Motif composition, conservation and condition-specificity of single and alternative transcription start sites in the Drosophila genome. Genome Biol 2009; 10:R73. [PMID: 19589141 PMCID: PMC2728527 DOI: 10.1186/gb-2009-10-7-r73] [Citation(s) in RCA: 76] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2008] [Revised: 04/21/2009] [Accepted: 07/09/2009] [Indexed: 01/05/2023] Open
Abstract
A map of transcription start sites across the Drosophila genome, providing insights into initiation patterns and spatiotemporal conditions. Background Transcription initiation is a key component in the regulation of gene expression. mRNA 5' full-length sequencing techniques have enhanced our understanding of mammalian transcription start sites (TSSs), revealing different initiation patterns on a genomic scale. Results To identify TSSs in Drosophila melanogaster, we applied a hierarchical clustering strategy on available 5' expressed sequence tags (ESTs) and identified a high quality set of 5,665 TSSs for approximately 4,000 genes. We distinguished two initiation patterns: 'peaked' TSSs, and 'broad' TSS cluster groups. Peaked promoters were found to contain location-specific sequence elements; conversely, broad promoters were associated with non-location-specific elements. In alignments across other Drosophila genomes, conservation levels of sequence elements exceeded 90% within the melanogaster subgroup, but dropped considerably for distal species. Elements in broad promoters had lower levels of conservation than those in peaked promoters. When characterizing the distributions of ESTs, 64% of TSSs showed distinct associations to one out of eight different spatiotemporal conditions. Available whole-genome tiling array time series data revealed different temporal patterns of embryonic activity across the majority of genes with distinct alternative promoters. Many genes with maternally inherited transcripts were found to have alternative promoters utilized later in development. Core promoters of maternally inherited transcripts showed differences in motif composition compared to zygotically active promoters. Conclusions Our study provides a comprehensive map of Drosophila TSSs and the conditions under which they are utilized. Distinct differences in motif associations with initiation pattern and spatiotemporal utilization illustrate the complex regulatory code of transcription initiation.
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Affiliation(s)
- Elizabeth A Rach
- Program in Computational Biology and Bioinformatics, Duke University, Science Drive, Durham, NC 27708, USA
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Han L, Zhao Z. CpG islands or CpG clusters: how to identify functional GC-rich regions in a genome? BMC Bioinformatics 2009; 10:65. [PMID: 19232104 PMCID: PMC2652441 DOI: 10.1186/1471-2105-10-65] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2008] [Accepted: 02/20/2009] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND CpG islands (CGIs), clusters of CpG dinucleotides in GC-rich regions, are often located in the 5' end of genes and considered gene markers. Hackenberg et al. (2006) recently developed a new algorithm, CpGcluster, which uses a completely different mathematical approach from previous traditional algorithms. Their evaluation suggests that CpGcluster provides a much more efficient approach to detecting functional clusters or islands of CpGs. RESULTS We systematically compared CpGcluster with the traditional algorithm by Takai and Jones (2002). Our comparisons of (1) the number of islands versus the number of genes in a genome, (2) the distribution of islands in different genomic regions, (3) island length, (4) the distance between two neighboring islands, and (5) methylation status suggest that Takai and Jones' algorithm is overall more appropriate for identifying promoter-associated islands of CpGs in vertebrate genomes. CONCLUSION The generation of genome sequence and DNA methylation data is expected to accelerate greatly. The information in this study is important for its extensive utility in gene feature analysis and epigenomics including gene prediction and methylation chip design in different genomes.
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Affiliation(s)
- Leng Han
- Virginia Institute for Psychiatric and Behavioral Genetics, Virginia Commonwealth University, Richmond, VA 23298, USA.
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46
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Brick K, Watanabe J, Pizzi E. Core promoters are predicted by their distinct physicochemical properties in the genome of Plasmodium falciparum. Genome Biol 2008; 9:R178. [PMID: 19094208 PMCID: PMC2646282 DOI: 10.1186/gb-2008-9-12-r178] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2008] [Revised: 11/03/2008] [Accepted: 12/18/2008] [Indexed: 11/23/2022] Open
Abstract
A method is presented to computationally identify core promoters in the Plasmodium falciparum genome using only DNA physicochemical properties. Little is known about the structure and distinguishing features of core promoters in Plasmodium falciparum. In this work, we describe the first method to computationally identify core promoters in this AT-rich genome. This prediction algorithm uses solely DNA physicochemical properties as descriptors. Our results add to a growing body of evidence that a physicochemical code for eukaryotic genomes plays a crucial role in core promoter recognition.
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Affiliation(s)
- Kevin Brick
- Dipartimento di Malattie Infettive, Parassitarie ed Immunomediate - Istituto Superiore di Sanità, Viale Regina Elena, 299, 00161 Rome, Italy.
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Valen E, Pascarella G, Chalk A, Maeda N, Kojima M, Kawazu C, Murata M, Nishiyori H, Lazarevic D, Motti D, Marstrand TT, Tang MHE, Zhao X, Krogh A, Winther O, Arakawa T, Kawai J, Wells C, Daub C, Harbers M, Hayashizaki Y, Gustincich S, Sandelin A, Carninci P. Genome-wide detection and analysis of hippocampus core promoters using DeepCAGE. Genome Res 2008; 19:255-65. [PMID: 19074369 DOI: 10.1101/gr.084541.108] [Citation(s) in RCA: 123] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Finding and characterizing mRNAs, their transcription start sites (TSS), and their associated promoters is a major focus in post-genome biology. Mammalian cells have at least 5-10 magnitudes more TSS than previously believed, and deeper sequencing is necessary to detect all active promoters in a given tissue. Here, we present a new method for high-throughput sequencing of 5' cDNA tags-DeepCAGE: merging the Cap Analysis of Gene Expression method with ultra-high-throughput sequence technology. We apply DeepCAGE to characterize 1.4 million sequenced TSS from mouse hippocampus and reveal a wealth of novel core promoters that are preferentially used in hippocampus: This is the most comprehensive promoter data set for any tissue to date. Using these data, we present evidence indicating a key role for the Arnt2 transcription factor in hippocampus gene regulation. DeepCAGE can also detect promoters used only in a small subset of cells within the complex tissue.
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Affiliation(s)
- Eivind Valen
- The Bioinformatics Centre, Department of Biology and Biotech Research and Innovation Centre, University of Copenhagen, Ole Maaloes vej 5, DK-2200, Denmark
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Abeel T, Saeys Y, Rouzé P, Van de Peer Y. ProSOM: core promoter prediction based on unsupervised clustering of DNA physical profiles. Bioinformatics 2008; 24:i24-31. [PMID: 18586720 PMCID: PMC2718650 DOI: 10.1093/bioinformatics/btn172] [Citation(s) in RCA: 53] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
MOTIVATION More and more genomes are being sequenced, and to keep up with the pace of sequencing projects, automated annotation techniques are required. One of the most challenging problems in genome annotation is the identification of the core promoter. Because the identification of the transcription initiation region is such a challenging problem, it is not yet a common practice to integrate transcription start site prediction in genome annotation projects. Nevertheless, better core promoter prediction can improve genome annotation and can be used to guide experimental work. RESULTS Comparing the average structural profile based on base stacking energy of transcribed, promoter and intergenic sequences demonstrates that the core promoter has unique features that cannot be found in other sequences. We show that unsupervised clustering by using self-organizing maps can clearly distinguish between the structural profiles of promoter sequences and other genomic sequences. An implementation of this promoter prediction program, called ProSOM, is available and has been compared with the state-of-the-art. We propose an objective, accurate and biologically sound validation scheme for core promoter predictors. ProSOM performs at least as well as the software currently available, but our technique is more balanced in terms of the number of predicted sites and the number of false predictions, resulting in a better all-round performance. Additional tests on the ENCODE regions of the human genome show that 98% of all predictions made by ProSOM can be associated with transcriptionally active regions, which demonstrates the high precision. AVAILABILITY Predictions for the human genome, the validation datasets and the program (ProSOM) are available upon request.
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Affiliation(s)
- Thomas Abeel
- Department of Plant Systems Biology, VIB, 9052 Gent, Belgium
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Philibert RA, Gunter TD, Beach SR, Brody G, Madan A. MAOA methylation is associated with nicotine and alcohol dependence in women. Am J Med Genet B Neuropsychiatr Genet 2008; 147B:565-70. [PMID: 18454435 PMCID: PMC3685146 DOI: 10.1002/ajmg.b.30778] [Citation(s) in RCA: 122] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
In recent years, the role of epigenetic phenomenon, such as methylation, in mediating vulnerability to behavioral illness has become increasingly appreciated. One prominent locus at which epigenetic phenomena are thought to be in play is the monoamine oxidase A (MAOA) locus. In order to examine the role of methylation at this locus, we performed quantitative methylation analysis across the promoter region of this gene in lymphoblast lines derived from 191 subjects participating in the Iowa Adoption Studies (IAS). We analyzed the resulting data with respect to genotype and lifetime symptom counts for the more common major behavioral disorders in the IAS, antisocial personality disorder (ASPD), and substance use disorders (alcohol (AD) and nicotine dependence (ND)). We found that methylation status was significantly associated with lifetime symptom counts for ND (P < 0.001) and AD (P < 0.008) in women, but not men. Furthermore, a trend was found for women homozygous for the 3,3 allele to have a higher degree of overall methylation than women homozygous for the 4,4 allele (P < 0.10). We conclude that methylation of MAOA may play a significant role in common psychiatric illness and that further examination of epigenetic processes at this locus is in order.
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Affiliation(s)
- Robert A. Philibert
- Department of Psychiatry, The University of Iowa, Iowa City, IA
,Neuroscience and Genetics Programs, The University of Iowa, Iowa City, IA
,To whom correspondence should be addressed. Rm 2-126 MEB Psychiatry Research/MEB, Iowa City, IA, USA. 52242-1000 TEL 319-353-4986, FAX 301-353-3003,
| | - Tracy D. Gunter
- Department of Psychiatry, The University of Iowa, Iowa City, IA
| | | | | | - Anup Madan
- The Institute for Systems Biology, Seattle, WA
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Borel C, Gagnebin M, Gehrig C, Kriventseva EV, Zdobnov EM, Antonarakis SE. Mapping of small RNAs in the human ENCODE regions. Am J Hum Genet 2008; 82:971-81. [PMID: 18394580 DOI: 10.1016/j.ajhg.2008.02.016] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2007] [Revised: 01/28/2008] [Accepted: 02/26/2008] [Indexed: 10/22/2022] Open
Abstract
The elucidation of the largely unknown transcriptome of small RNAs is crucial for the understanding of genome and cellular function. We report here the results of the analysis of small RNAs (< 50 nt) in the ENCODE regions of the human genome. Size-fractionated RNAs from four different cell lines (HepG2, HelaS3, GM06990, SK-N-SH) were mapped with the forward and reverse ENCODE high-density resolution tiling arrays. The top 1% of hybridization signals are termed SmRfrags (Small RNA fragments). Eight percent of SmRfrags overlap the GENCODE genes (CDS), given that the majority map to intergenic regions (34%), intronic regions (53%), and untranslated regions (UTRs) (5%). In addition, 9.6% and 16.8% of SmRfrags in the 5' UTR regions overlap significantly with His/Pol II/TAF250 binding sites and DNase I Hypersensitive sites, respectively (compared to the 5.3% and 9% expected). Interestingly, 17%-24% (depending on the cell line) of SmRfrags are sense-antisense strand pairs that show evidence of overlapping transcription. Only 3.4% and 7.2% of SmRfrags in intergenic regions overlap transcribed fragments (Txfrags) in HeLa and GM06990 cell lines, respectively. We hypothesized that a fraction of the identified SmRfrags corresponded to microRNAs. We tested by Northern blot a set of 15 high-likelihood predictions of microRNA candidates that overlap with smRfrags and validated three potential microRNAs ( approximately 20 nt length). Notably, most of the remaining candidates showed a larger hybridizing band ( approximately 100 nt) that could be a microRNA precursor. The small RNA transcriptome is emerging as an important and abundant component of the genome function.
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