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Asuthkar S, Venkataraman S, Avilala J, Shishido K, Vibhakar R, Veo B, Purvis IJ, Guda MR, Velpula KK. SMYD3 Promotes Cell Cycle Progression by Inducing Cyclin D3 Transcription and Stabilizing the Cyclin D1 Protein in Medulloblastoma. Cancers (Basel) 2022; 14:cancers14071673. [PMID: 35406445 PMCID: PMC8997160 DOI: 10.3390/cancers14071673] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2022] [Revised: 03/11/2022] [Accepted: 03/22/2022] [Indexed: 12/13/2022] Open
Abstract
Simple Summary Medulloblastoma is the most common malignant pediatric brain tumor and is classified into four molecular subgroups: Wnt, Shh, Group 3, and Group 4. Of these subgroups, patients with Myc+ Group 3 MB have the worst prognosis. Using an RNAi functional genomic screen, we identified the lysine methyltransferase SMYD3 as a crucial epigenetic regulator responsible for promoting Group 3 MB cell growth. We demonstrated that SMYD3 drives MB cell cycle progression by inducing cyclin D3 transcription and preventing cyclin D1 ubiquitination. Using in vitro and ex vivo studies, we showed that SMYD3 suppression by shRNA and BCI-121 significantly impaired proliferation, resulting in the downregulation of cyclin D3, cyclin D1, and pRBSer795. Moreover, we are the first to show that SMYD3 methylates the cyclin D1 protein, indicating that the SMYD3 stabilizes cyclin D1 through post-translational modification. Collectively, our studies position SMYD3 as a promising treatment option for Group 3 Myc+ MB patients. Abstract Medulloblastoma (MB) is the most common malignant pediatric brain tumor. Maximum safe resection, postoperative craniospinal irradiation, and chemotherapy are the standard of care for MB patients. MB is classified into four subgroups: Shh, Wnt, Group 3, and Group 4. Of these subgroups, patients with Myc+ Group 3 MB have the worst prognosis, necessitating alternative therapies. There is increasing interest in targeting epigenetic modifiers for treating pediatric cancers, including MB. Using an RNAi functional genomic screen, we identified the lysine methyltransferase SMYD3, as a crucial epigenetic regulator that drives the growth of Group 3 Myc+ MB cells. We demonstrated that SMYD3 directly binds to the cyclin D3 promoter to activate its transcription. Further, SMYD3 depletion significantly reduced MB cell proliferation and led to the downregulation of cyclin D3, cyclin D1, pRBSer795, with concomitant upregulations in RB in vitro. Similar results were obtained following pharmacological inhibition of SMYD3 using BCI-121 ex vivo. SMYD3 knockdown also promoted cyclin D1 ubiquitination, indicating that SMYD3 plays a vital role in stabilizing the cyclin D1 protein. Collectively, our studies demonstrate that SMYD3 drives cell cycle progression in Group 3 Myc+ MB cells and that targeting SMYD3 has the potential to improve clinical outcomes for high-risk patients.
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Affiliation(s)
- Swapna Asuthkar
- Department of Cancer Biology and Pharmacology, University of Illinois College of Medicine at Peoria, Peoria, IL 61605, USA; (J.A.); (K.S.); (I.J.P.); (M.R.G.); (K.K.V.)
- Correspondence:
| | - Sujatha Venkataraman
- Department of Pediatrics, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA; (S.V.); (R.V.); (B.V.)
| | - Janardhan Avilala
- Department of Cancer Biology and Pharmacology, University of Illinois College of Medicine at Peoria, Peoria, IL 61605, USA; (J.A.); (K.S.); (I.J.P.); (M.R.G.); (K.K.V.)
| | - Katherine Shishido
- Department of Cancer Biology and Pharmacology, University of Illinois College of Medicine at Peoria, Peoria, IL 61605, USA; (J.A.); (K.S.); (I.J.P.); (M.R.G.); (K.K.V.)
| | - Rajeev Vibhakar
- Department of Pediatrics, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA; (S.V.); (R.V.); (B.V.)
| | - Bethany Veo
- Department of Pediatrics, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA; (S.V.); (R.V.); (B.V.)
| | - Ian J. Purvis
- Department of Cancer Biology and Pharmacology, University of Illinois College of Medicine at Peoria, Peoria, IL 61605, USA; (J.A.); (K.S.); (I.J.P.); (M.R.G.); (K.K.V.)
| | - Maheedhara R. Guda
- Department of Cancer Biology and Pharmacology, University of Illinois College of Medicine at Peoria, Peoria, IL 61605, USA; (J.A.); (K.S.); (I.J.P.); (M.R.G.); (K.K.V.)
| | - Kiran K. Velpula
- Department of Cancer Biology and Pharmacology, University of Illinois College of Medicine at Peoria, Peoria, IL 61605, USA; (J.A.); (K.S.); (I.J.P.); (M.R.G.); (K.K.V.)
- Department of Pediatrics, University of Illinois College of Medicine at Peoria, Peoria, IL 61605, USA
- Department of Neurosurgery, University of Illinois College of Medicine at Peoria, Peoria, IL 61605, USA
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P-TEFb as A Promising Therapeutic Target. Molecules 2020; 25:molecules25040838. [PMID: 32075058 PMCID: PMC7070488 DOI: 10.3390/molecules25040838] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2020] [Revised: 02/06/2020] [Accepted: 02/07/2020] [Indexed: 01/19/2023] Open
Abstract
The positive transcription elongation factor b (P-TEFb) was first identified as a general factor that stimulates transcription elongation by RNA polymerase II (RNAPII), but soon afterwards it turned out to be an essential cellular co-factor of human immunodeficiency virus (HIV) transcription mediated by viral Tat proteins. Studies on the mechanisms of Tat-dependent HIV transcription have led to radical advances in our knowledge regarding the mechanism of eukaryotic transcription, including the discoveries that P-TEFb-mediated elongation control of cellular transcription is a main regulatory step of gene expression in eukaryotes, and deregulation of P-TEFb activity plays critical roles in many human diseases and conditions in addition to HIV/AIDS. P-TEFb is now recognized as an attractive and promising therapeutic target for inflammation/autoimmune diseases, cardiac hypertrophy, cancer, infectious diseases, etc. In this review article, I will summarize our knowledge about basic P-TEFb functions, the regulatory mechanism of P-TEFb-dependent transcription, P-TEFb’s involvement in biological processes and diseases, and current approaches to manipulating P-TEFb functions for the treatment of these diseases.
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Abstract
Epigenetics is the study of heritable changes in DNA or its associated proteins except mutations in gene sequence. Epigenetic regulation plays fundamental roles in the processes of kidney cell biology through the action of DNA methylation, chromatin modifications via epigenetic regulators and interaction via transcription factors, and noncoding RNA species. Kidney diseases, including acute kidney injury, chronic kidney disease, nephritic and nephrotic syndromes, pyelonephritis and polycystic kidney diseases are driven by aberrant activity in numerous signaling pathways in even individual kidney cell. Epigenetic alterations, including DNA methylation, histone acetylation and methylation, noncoding RNAs, and protein posttranslational modifications, could disrupt essential pathways that protect the renal cells from uncontrolled growth, apoptosis and establishment of other renal associated syndromes, which have been recognized as one of the critical mechanisms for regulating functional changes that drive and maintain the kidney disease phenotype. In this chapter, we briefly summarize the epigenetic mechanisms in kidney cell biology and epigenetic basis of kidney development, and introduce epigenetic techniques that can be used in investigating the molecular mechanism of kidney cell biology and kidneys diseases, primarily focusing on the integration of DNA methylation and chromatin immunoprecipitation technologies into kidney disease associated studies. Future studies using these emerging technologies will elucidate how alterations in the renal cell epigenome cooperate with genetic aberrations for kidney disease initiation and progression. Incorporating epigenomic testing into the clinical research is essential to future studies with epigenetics biomarkers and precision medicine using emerging epigenetic therapies.
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Affiliation(s)
- Linda Xiaoyan Li
- Division of Nephrology and Hypertension, Department of Internal Medicine, Mayo Clinic, Rochester, MN, United States; Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, MN, United States
| | - Ewud Agborbesong
- Division of Nephrology and Hypertension, Department of Internal Medicine, Mayo Clinic, Rochester, MN, United States; Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, MN, United States
| | - Lu Zhang
- Division of Nephrology and Hypertension, Department of Internal Medicine, Mayo Clinic, Rochester, MN, United States; Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, MN, United States
| | - Xiaogang Li
- Division of Nephrology and Hypertension, Department of Internal Medicine, Mayo Clinic, Rochester, MN, United States; Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, MN, United States.
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Kuang JF, Chen JY, Liu XC, Han YC, Xiao YY, Shan W, Tang Y, Wu KQ, He JX, Lu WJ. The transcriptional regulatory network mediated by banana (Musa acuminata) dehydration-responsive element binding (MaDREB) transcription factors in fruit ripening. THE NEW PHYTOLOGIST 2017; 214:762-781. [PMID: 28044313 DOI: 10.1111/nph.14389] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/29/2016] [Accepted: 11/16/2016] [Indexed: 05/24/2023]
Abstract
Fruit ripening is a complex, genetically programmed process involving the action of critical transcription factors (TFs). Despite the established significance of dehydration-responsive element binding (DREB) TFs in plant abiotic stress responses, the involvement of DREBs in fruit ripening is yet to be determined. Here, we identified four genes encoding ripening-regulated DREB TFs in banana (Musa acuminata), MaDREB1, MaDREB2, MaDREB3, and MaDREB4, and demonstrated that they play regulatory roles in fruit ripening. We showed that MaDREB1-MaDREB4 are nucleus-localized, induced by ethylene and encompass transcriptional activation activities. We performed a genome-wide chromatin immunoprecipitation and high-throughput sequencing (ChIP-Seq) experiment for MaDREB2 and identified 697 genomic regions as potential targets of MaDREB2. MaDREB2 binds to hundreds of loci with diverse functions and its binding sites are distributed in the promoter regions proximal to the transcriptional start site (TSS). Most of the MaDREB2-binding targets contain the conserved (A/G)CC(G/C)AC motif and MaDREB2 appears to directly regulate the expression of a number of genes involved in fruit ripening. In combination with transcriptome profiling (RNA sequencing) data, our results indicate that MaDREB2 may serve as both transcriptional activator and repressor during banana fruit ripening. In conclusion, our study suggests a hierarchical regulatory model of fruit ripening in banana and that the MaDREB TFs may act as transcriptional regulators in the regulatory network.
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Affiliation(s)
- Jian-Fei Kuang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources/Guangdong Provincial Key Laboratory of Postharvest Science of Fruits and Vegetables, College of Horticultural Science, South China Agricultural University, Guangzhou, 510642, China
- School of Life Sciences and State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong SAR, China
| | - Jian-Ye Chen
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources/Guangdong Provincial Key Laboratory of Postharvest Science of Fruits and Vegetables, College of Horticultural Science, South China Agricultural University, Guangzhou, 510642, China
| | - Xun-Cheng Liu
- Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650, China
| | - Yan-Chao Han
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources/Guangdong Provincial Key Laboratory of Postharvest Science of Fruits and Vegetables, College of Horticultural Science, South China Agricultural University, Guangzhou, 510642, China
| | - Yun-Yi Xiao
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources/Guangdong Provincial Key Laboratory of Postharvest Science of Fruits and Vegetables, College of Horticultural Science, South China Agricultural University, Guangzhou, 510642, China
| | - Wei Shan
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources/Guangdong Provincial Key Laboratory of Postharvest Science of Fruits and Vegetables, College of Horticultural Science, South China Agricultural University, Guangzhou, 510642, China
| | - Yang Tang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources/Guangdong Provincial Key Laboratory of Postharvest Science of Fruits and Vegetables, College of Horticultural Science, South China Agricultural University, Guangzhou, 510642, China
| | - Ke-Qiang Wu
- Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650, China
| | - Jun-Xian He
- School of Life Sciences and State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong SAR, China
| | - Wang-Jin Lu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources/Guangdong Provincial Key Laboratory of Postharvest Science of Fruits and Vegetables, College of Horticultural Science, South China Agricultural University, Guangzhou, 510642, China
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Tsai SY, Chang YL, Swamy KBS, Chiang RL, Huang DH. GAGA factor, a positive regulator of global gene expression, modulates transcriptional pausing and organization of upstream nucleosomes. Epigenetics Chromatin 2016; 9:32. [PMID: 27468311 PMCID: PMC4962548 DOI: 10.1186/s13072-016-0082-4] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2016] [Accepted: 07/20/2016] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Genome-wide studies in higher eukaryotes have revealed the presence of paused RNA polymerase II (RNA-Pol) at about 30-50 bp downstream of the transcription start site of genes involved in developmental control, cell proliferation and intercellular signaling. Promoter-proximal pausing is believed to represent a critical step in transcriptional regulation. GAGA sequence motifs have frequently been found in the upstream region of paused genes in Drosophila, implicating a prevalent binding factor, GAF, in transcriptional pausing. RESULTS Using newly isolated mutants that retain only ~3 % normal GAF level, we analyzed its impacts on transcriptional regulation in whole animals. We first examined the abundance of three major isoforms of RNA-Pol on Hsp70 during heat shock. By cytogenetic analyses on polytene chromosomes and chromatin immunoprecipitation (ChIP), we show that paused RNA-Pol of Hsp70 is substantially reduced in mutants. Conversely, a global increase in paused RNA-Pol is observed when GAF is over-expressed. Coupled analyses of transcriptome and GAF genomic distribution show that 269 genes enriched for upstream GAF binding are down-regulated in mutants. Interestingly, ~15 % of them encode transcriptional factors, which might control ~2000 additional genes down-regulated in mutants. Further examination of RNA-Pol distribution in GAF targets reveals that a positive correlation exists between promoter-proximal RNA-Pol density and GAF occupancy in WT, but not in mutants. Comparison of nucleosome profiles indicates that nucleosome occupancy is preferentially attenuated by GAF in the upstream region that strongly favors nucleosome assembly. Using a dominant eye phenotype caused by GAF over-expression, we detect significant genetic interactions between GAF and the nucleosome remodeler NURF, the pausing factor NELF, and BAB1 whose binding sites are enriched specifically in genes displaying GAF-dependent pausing. CONCLUSION Our results provide direct evidence to support a critical role of GAF in global gene expression, transcriptional pausing and upstream nucleosome organization of a group of genes. By cooperating with factors acting at different levels, GAF orchestrates a series of events from local nucleosome displacement to paused transcription. The use of whole animals containing broad tissue types attests the physiological relevance of this regulatory network.
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Affiliation(s)
- Shih-Ying Tsai
- Institute of Molecular Biology, Academia Sinica, Nankang, Taipei Taiwan, ROC ; Molecular Cell Biology, Taiwan International Graduate Program, Institute of Molecular Biology, Academia Sinica, Graduate Institute of Life Sciences, National Defense Medical Center, Taipei, Taiwan, ROC
| | - Yuh-Long Chang
- Institute of Molecular Biology, Academia Sinica, Nankang, Taipei Taiwan, ROC
| | - Krishna B S Swamy
- Institute of Molecular Biology, Academia Sinica, Nankang, Taipei Taiwan, ROC
| | - Ruei-Lin Chiang
- Institute of Molecular Biology, Academia Sinica, Nankang, Taipei Taiwan, ROC
| | - Der-Hwa Huang
- Institute of Molecular Biology, Academia Sinica, Nankang, Taipei Taiwan, ROC
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Pettie KP, Dresch JM, Drewell RA. Spatial distribution of predicted transcription factor binding sites in Drosophila ChIP peaks. Mech Dev 2016; 141:51-61. [PMID: 27264535 DOI: 10.1016/j.mod.2016.06.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2015] [Revised: 04/24/2016] [Accepted: 06/01/2016] [Indexed: 11/19/2022]
Abstract
In the development of the Drosophila embryo, gene expression is directed by the sequence-specific interactions of a large network of protein transcription factors (TFs) and DNA cis-regulatory binding sites. Once the identity of the typically 8-10bp binding sites for any given TF has been determined by one of several experimental procedures, the sequences can be represented in a position weight matrix (PWM) and used to predict the location of additional TF binding sites elsewhere in the genome. Often, alignments of large (>200bp) genomic fragments that have been experimentally determined to bind the TF of interest in Chromatin Immunoprecipitation (ChIP) studies are trimmed under the assumption that the majority of the binding sites are located near the center of all the aligned fragments. In this study, ChIP/chip datasets are analyzed using the corresponding PWMs for the well-studied TFs; CAUDAL, HUNCHBACK, KNIRPS and KRUPPEL, to determine the distribution of predicted binding sites. All four TFs are critical regulators of gene expression along the anterio-posterior axis in early Drosophila development. For all four TFs, the ChIP peaks contain multiple binding sites that are broadly distributed across the genomic region represented by the peak, regardless of the prediction stringency criteria used. This result suggests that ChIP peak trimming may exclude functional binding sites from subsequent analyses.
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Affiliation(s)
- Kade P Pettie
- Department of Biology, Amherst College, Amherst, MA 01002, United States
| | - Jacqueline M Dresch
- Department of Mathematics and Computer Science, Clark University, 950 Main Street, Worcester, MA 01610, United States
| | - Robert A Drewell
- Biology Department, Clark University, 950 Main Street, Worcester, MA 01610, United States
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Ptak C, Wozniak RW. Nucleoporins and chromatin metabolism. Curr Opin Cell Biol 2016; 40:153-160. [PMID: 27085162 DOI: 10.1016/j.ceb.2016.03.024] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2016] [Revised: 03/26/2016] [Accepted: 03/31/2016] [Indexed: 01/04/2023]
Abstract
Mounting evidence has implicated a group of proteins termed nucleoporins, or Nups, in various processes that regulate chromatin structure and function. Nups were first recognized as building blocks for nuclear pore complexes, but several members of this group of proteins also reside in the cytoplasm and within the nucleus. Moreover, many are dynamic and move between these various locations. Both at the nuclear envelope, as part of nuclear pore complexes, and within the nucleoplasm, Nups interact with protein complexes that function in gene transcription, chromatin remodeling, DNA repair, and DNA replication. Here, we review recent studies that provide further insight into the molecular details of these interactions and their role in regulating the activity of chromatin modifying factors.
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Affiliation(s)
- Christopher Ptak
- Department of Cell Biology, University of Alberta, Edmonton, Alberta, Canada T6G 2H7
| | - Richard W Wozniak
- Department of Cell Biology, University of Alberta, Edmonton, Alberta, Canada T6G 2H7.
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Maurin T, Melko M, Abekhoukh S, Khalfallah O, Davidovic L, Jarjat M, D'Antoni S, Catania MV, Moine H, Bechara E, Bardoni B. The FMRP/GRK4 mRNA interaction uncovers a new mode of binding of the Fragile X mental retardation protein in cerebellum. Nucleic Acids Res 2015; 43:8540-50. [PMID: 26250109 PMCID: PMC4787806 DOI: 10.1093/nar/gkv801] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2015] [Accepted: 07/28/2015] [Indexed: 11/13/2022] Open
Abstract
Fragile X syndrome (FXS), the most common form of inherited intellectual disability, is caused by the silencing of the FMR1 gene encoding an RNA-binding protein (FMRP) mainly involved in translational control. We characterized the interaction between FMRP and the mRNA of GRK4, a member of the guanine nucleotide-binding protein (G protein)-coupled receptor kinase super-family, both in vitro and in vivo. While the mRNA level of GRK4 is unchanged in the absence or in the presence of FMRP in different regions of the brain, GRK4 protein level is increased in Fmr1-null cerebellum, suggesting that FMRP negatively modulates the expression of GRK4 at the translational level in this brain region. The C-terminal region of FMRP interacts with a domain of GRK4 mRNA, that we called G4RIF, that is folded in four stem loops. The SL1 stem loop of G4RIF is protected by FMRP and is part of the S1/S2 sub-domain that directs translation repression of a reporter mRNA by FMRP. These data confirm the role of the G4RIF/FMRP complex in translational regulation. Considering the role of GRK4 in GABAB receptors desensitization, our results suggest that an increased GRK4 levels in FXS might contribute to cerebellum-dependent phenotypes through a deregulated desensitization of GABAB receptors.
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Affiliation(s)
- Thomas Maurin
- CNRS UMR 7275, Institute of Molecular and Cellular Pharmacology, 06560 Valbonne Sophia-Antipolis, France University of Nice Sophia-Antipolis, 06103 Nice, FRANCE CNRS LIA 'Neogenex', 06560 Valbonne Sophia-Antipolis, France
| | - Mireille Melko
- CNRS UMR 7275, Institute of Molecular and Cellular Pharmacology, 06560 Valbonne Sophia-Antipolis, France University of Nice Sophia-Antipolis, 06103 Nice, FRANCE CNRS LIA 'Neogenex', 06560 Valbonne Sophia-Antipolis, France
| | - Sabiha Abekhoukh
- CNRS UMR 7275, Institute of Molecular and Cellular Pharmacology, 06560 Valbonne Sophia-Antipolis, France University of Nice Sophia-Antipolis, 06103 Nice, FRANCE CNRS LIA 'Neogenex', 06560 Valbonne Sophia-Antipolis, France
| | - Olfa Khalfallah
- CNRS UMR 7275, Institute of Molecular and Cellular Pharmacology, 06560 Valbonne Sophia-Antipolis, France University of Nice Sophia-Antipolis, 06103 Nice, FRANCE CNRS LIA 'Neogenex', 06560 Valbonne Sophia-Antipolis, France
| | - Laetitia Davidovic
- CNRS UMR 7275, Institute of Molecular and Cellular Pharmacology, 06560 Valbonne Sophia-Antipolis, France University of Nice Sophia-Antipolis, 06103 Nice, FRANCE CNRS LIA 'Neogenex', 06560 Valbonne Sophia-Antipolis, France
| | - Marielle Jarjat
- CNRS UMR 7275, Institute of Molecular and Cellular Pharmacology, 06560 Valbonne Sophia-Antipolis, France University of Nice Sophia-Antipolis, 06103 Nice, FRANCE CNRS LIA 'Neogenex', 06560 Valbonne Sophia-Antipolis, France
| | - Simona D'Antoni
- Institute of Neurological Sciences, The National Research Council of Italy, 95126 Catania, Italy
| | - Maria Vincenza Catania
- Institute of Neurological Sciences, The National Research Council of Italy, 95126 Catania, Italy IRCCS Oasi Maria SS, 94018 Troina (EN), Italy
| | - Hervé Moine
- IGBMC (Institut de Génétique et de Biologie Moléculaire et Cellulaire), CNRS, UMR7104, Inserm U596, Collège de France, Strasbourg University, 67400 Illkirch-Graffenstaden, France
| | - Elias Bechara
- CNRS UMR 7275, Institute of Molecular and Cellular Pharmacology, 06560 Valbonne Sophia-Antipolis, France University of Nice Sophia-Antipolis, 06103 Nice, FRANCE CNRS LIA 'Neogenex', 06560 Valbonne Sophia-Antipolis, France
| | - Barbara Bardoni
- CNRS UMR 7275, Institute of Molecular and Cellular Pharmacology, 06560 Valbonne Sophia-Antipolis, France University of Nice Sophia-Antipolis, 06103 Nice, FRANCE CNRS LIA 'Neogenex', 06560 Valbonne Sophia-Antipolis, France
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Chen C, Lu Y, Liu J, Li L, Zhao N, Lin B. Genome-wide ChIP-seq analysis of TCF4 binding regions in colorectal cancer cells. Int J Clin Exp Med 2014; 7:4253-9. [PMID: 25550940 PMCID: PMC4276198] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2014] [Accepted: 10/23/2014] [Indexed: 06/04/2023]
Abstract
OBJECTIVE TCF4 (transcriptional factor 4) forms a complex with its transcriptional coactivator β-catenin and the coactivator carries the final signal output from the canonical Wnt signaling pathway, which is essential for the growth of normal epithelium and also plays important roles in carcinogenesis of colon epithelium. We aimed to gain a better understanding of the genes bound by TCF4 in colorectal cancer cells. METHODS SW620 human colorectal cancer cells were cultured. The TCF4 antibody of this study was confirmed in SW620 cells by Western Blot. A ChIP-seq based genome-wide analysis of TCF4 chromatin occupancy in colorectal cancer cells was conducted and 1506 high confidence TCF4 binding sites wereidentified. RESULTS Sequence analysis revealed that the binding sites harbor a consensus sequence of C-G/C-A-G-C-T/C-C-T-T-C. Gene ontology and pathway analysis showed that TCF4 regulated 18 genes in Wnt signaling pathway and 97 other transcription factors. CONCLUSION Our results suggest TCF4 binding regions were enriched with a motif of C-G/C-A-G-C-T/C-C-T-T-C. The gene regulation of TCF4 may be conserved in colorectal cancer and glioma cells. TCF4 may be involved in a series of important biological processes such as regulation of metabolic and biosynthetic (GO: 0010604, GO: 0031328, GO: 0009891, GO: 0051173, GO: 0010557, GO: 0045935), adhesion (GO: 0007155, GO: 0022610), apoptosis (GO: 0042981, GO: 0043067, GO: 0010941), and important signaling pathways (Wnt, Chemokine, Calciu, GnRH).
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Affiliation(s)
- Chen Chen
- Systems Biology Division and Propriumbio Research Center, Zhejiang-California International Nanosystems Institute (ZCNI), Zhejiang University268 Kaixuan Road, Hangzhou 310029, China
| | - Yachun Lu
- Systems Biology Division and Propriumbio Research Center, Zhejiang-California International Nanosystems Institute (ZCNI), Zhejiang University268 Kaixuan Road, Hangzhou 310029, China
| | - Jie Liu
- Systems Biology Division and Propriumbio Research Center, Zhejiang-California International Nanosystems Institute (ZCNI), Zhejiang University268 Kaixuan Road, Hangzhou 310029, China
| | - Lisha Li
- Systems Biology Division and Propriumbio Research Center, Zhejiang-California International Nanosystems Institute (ZCNI), Zhejiang University268 Kaixuan Road, Hangzhou 310029, China
| | - Na Zhao
- Systems Biology Division and Propriumbio Research Center, Zhejiang-California International Nanosystems Institute (ZCNI), Zhejiang University268 Kaixuan Road, Hangzhou 310029, China
| | - Biaoyang Lin
- Systems Biology Division and Propriumbio Research Center, Zhejiang-California International Nanosystems Institute (ZCNI), Zhejiang University268 Kaixuan Road, Hangzhou 310029, China
- Swedish Medical CenterSeattle, WA 98122, USA
- Department of Urology, University of WashingtonSeattle, WA 98195, USA
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Markov DA, Wojtas ID, Tessitore K, Henderson S, McAllister WT. Yeast DEAD box protein Mss116p is a transcription elongation factor that modulates the activity of mitochondrial RNA polymerase. Mol Cell Biol 2014; 34:2360-9. [PMID: 24732805 PMCID: PMC4054322 DOI: 10.1128/mcb.00160-14] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2014] [Revised: 02/20/2014] [Accepted: 04/01/2014] [Indexed: 01/08/2023] Open
Abstract
DEAD box proteins have been widely implicated in regulation of gene expression. Here, we show that the yeast Saccharomyces cerevisiae DEAD box protein Mss116p, previously known as a mitochondrial splicing factor, also acts as a transcription factor that modulates the activity of the single-subunit mitochondrial RNA polymerase encoded by RPO41. Binding of Mss116p stabilizes paused mitochondrial RNA polymerase elongation complexes in vitro and favors the posttranslocated state of the enzyme, resulting in a lower concentration of nucleotide substrate required to escape the pause; this mechanism of action is similar to that of elongation factors that enhance the processivity of multisubunit RNA polymerases. In a yeast strain in which the RNA splicing-related functions of Mss116p are dispensable, overexpression of RPO41 or MSS116 increases cell survival from colonies that were exposed to low temperature, suggesting a role for Mss116p in enhancing the efficiency of mitochondrial transcription under stress conditions.
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Affiliation(s)
- Dmitriy A Markov
- Department of Cell Biology, Rowan University, School of Osteopathic Medicine, Stratford, New Jersey, USA
| | - Ireneusz D Wojtas
- Department of Cell Biology, Rowan University, School of Osteopathic Medicine, Stratford, New Jersey, USA
| | - Kassandra Tessitore
- Summer Undergraduate Research Experience Program, Rowan University, School of Osteopathic Medicine, Stratford, New Jersey, USA
| | - Simmone Henderson
- Graduate School of Biomedical Sciences, Rowan University, School of Osteopathic Medicine, Stratford, New Jersey, USA
| | - William T McAllister
- Department of Cell Biology, Rowan University, School of Osteopathic Medicine, Stratford, New Jersey, USA
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11
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Schröder S, Herker E, Itzen F, He D, Thomas S, Gilchrist DA, Kaehlcke K, Cho S, Pollard KS, Capra JA, Schnölzer M, Cole PA, Geyer M, Bruneau BG, Adelman K, Ott M. Acetylation of RNA polymerase II regulates growth-factor-induced gene transcription in mammalian cells. Mol Cell 2013; 52:314-24. [PMID: 24207025 PMCID: PMC3936344 DOI: 10.1016/j.molcel.2013.10.009] [Citation(s) in RCA: 87] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2013] [Revised: 08/26/2013] [Accepted: 09/27/2013] [Indexed: 11/17/2022]
Abstract
Lysine acetylation regulates transcription by targeting histones and nonhistone proteins. Here we report that the central regulator of transcription, RNA polymerase II, is subject to acetylation in mammalian cells. Acetylation occurs at eight lysines within the C-terminal domain (CTD) of the largest polymerase subunit and is mediated by p300/KAT3B. CTD acetylation is specifically enriched downstream of the transcription start sites of polymerase-occupied genes genome-wide, indicating a role in early stages of transcription initiation or elongation. Mutation of lysines or p300 inhibitor treatment causes the loss of epidermal growth-factor-induced expression of c-Fos and Egr2, immediate-early genes with promoter-proximally paused polymerases, but does not affect expression or polymerase occupancy at housekeeping genes. Our studies identify acetylation as a new modification of the mammalian RNA polymerase II required for the induction of growth factor response genes.
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Affiliation(s)
- Sebastian Schröder
- Gladstone Institutes, San Francisco, CA 94158, USA
- University of California, San Francisco, San Francisco, CA 94143, USA
| | - Eva Herker
- Gladstone Institutes, San Francisco, CA 94158, USA
- Heinrich-Pette-Institute, Leibniz Institute for Experimental Virology, 20251 Hamburg, Germany
| | - Friederike Itzen
- Max Planck Institute of Molecular Physiology, 44227 Dortmund, Germany
| | - Daniel He
- Gladstone Institutes, San Francisco, CA 94158, USA
- University of California, San Francisco, San Francisco, CA 94143, USA
| | - Sean Thomas
- Gladstone Institutes, San Francisco, CA 94158, USA
- University of California, San Francisco, San Francisco, CA 94143, USA
| | - Daniel A. Gilchrist
- National Institute of Environmental Health Sciences, Research Triangle Park, NC 27709, USA
| | - Katrin Kaehlcke
- Gladstone Institutes, San Francisco, CA 94158, USA
- University of California, San Francisco, San Francisco, CA 94143, USA
| | - Sungyoo Cho
- Gladstone Institutes, San Francisco, CA 94158, USA
- University of California, San Francisco, San Francisco, CA 94143, USA
| | - Katherine S. Pollard
- Gladstone Institutes, San Francisco, CA 94158, USA
- University of California, San Francisco, San Francisco, CA 94143, USA
| | - John A. Capra
- Gladstone Institutes, San Francisco, CA 94158, USA
- University of California, San Francisco, San Francisco, CA 94143, USA
| | | | | | - Matthias Geyer
- Max Planck Institute of Molecular Physiology, 44227 Dortmund, Germany
- Research Center Caesar, 53175 Bonn, Germany
| | - Benoit G. Bruneau
- Gladstone Institutes, San Francisco, CA 94158, USA
- University of California, San Francisco, San Francisco, CA 94143, USA
| | - Karen Adelman
- National Institute of Environmental Health Sciences, Research Triangle Park, NC 27709, USA
| | - Melanie Ott
- Gladstone Institutes, San Francisco, CA 94158, USA
- University of California, San Francisco, San Francisco, CA 94143, USA
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12
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Bryzgalov LO, Antontseva EV, Matveeva MY, Shilov AG, Kashina EV, Mordvinov VA, Merkulova TI. Detection of regulatory SNPs in human genome using ChIP-seq ENCODE data. PLoS One 2013; 8:e78833. [PMID: 24205329 PMCID: PMC3812152 DOI: 10.1371/journal.pone.0078833] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2012] [Accepted: 09/17/2013] [Indexed: 11/18/2022] Open
Abstract
A vast amount of SNPs derived from genome-wide association studies are represented by non-coding ones, therefore exacerbating the need for effective identification of regulatory SNPs (rSNPs) among them. However, this task remains challenging since the regulatory part of the human genome is annotated much poorly as opposed to coding regions. Here we describe an approach aggregating the whole set of ENCODE ChIP-seq data in order to search for rSNPs, and provide the experimental evidence of its efficiency. Its algorithm is based on the assumption that the enrichment of a genomic region with transcription factor binding loci (ChIP-seq peaks) indicates its regulatory function, and thereby SNPs located in this region are more likely to influence transcription regulation. To ensure that the approach preferably selects functionally meaningful SNPs, we performed enrichment analysis of several human SNP datasets associated with phenotypic manifestations. It was shown that all samples are significantly enriched with SNPs falling into the regions of multiple ChIP-seq peaks as compared with the randomly selected SNPs. For experimental verification, 40 SNPs falling into overlapping regions of at least 7 TF binding loci were selected from OMIM. The effect of SNPs on the binding of the DNA fragments containing them to the nuclear proteins from four human cell lines (HepG2, HeLaS3, HCT-116, and K562) has been tested by EMSA. A radical change in the binding pattern has been observed for 29 SNPs, besides, 6 more SNPs also demonstrated less pronounced changes. Taken together, the results demonstrate the effective way to search for potential rSNPs with the aid of ChIP-seq data provided by ENCODE project.
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Affiliation(s)
| | - Elena V. Antontseva
- Institute of Cytology and Genetics SD RAS, Novosibirsk, Russian Federation
- * E-mail:
| | | | | | - Elena V. Kashina
- Institute of Cytology and Genetics SD RAS, Novosibirsk, Russian Federation
| | | | - Tatyana I. Merkulova
- Institute of Cytology and Genetics SD RAS, Novosibirsk, Russian Federation
- Novosibirsk State University, Novosibirsk, Russian Federation
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13
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Transcriptional and epigenetic regulation of human microRNAs. Cancer Lett 2013; 331:1-10. [DOI: 10.1016/j.canlet.2012.12.006] [Citation(s) in RCA: 89] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2012] [Revised: 12/01/2012] [Accepted: 12/04/2012] [Indexed: 12/20/2022]
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14
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Schaaf CA, Kwak H, Koenig A, Misulovin Z, Gohara DW, Watson A, Zhou Y, Lis JT, Dorsett D. Genome-wide control of RNA polymerase II activity by cohesin. PLoS Genet 2013; 9:e1003382. [PMID: 23555293 PMCID: PMC3605059 DOI: 10.1371/journal.pgen.1003382] [Citation(s) in RCA: 85] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2012] [Accepted: 01/30/2013] [Indexed: 11/22/2022] Open
Abstract
Cohesin is a well-known mediator of sister chromatid cohesion, but it also influences gene expression and development. These non-canonical roles of cohesin are not well understood, but are vital: gene expression and development are altered by modest changes in cohesin function that do not disrupt chromatid cohesion. To clarify cohesin's roles in transcription, we measured how cohesin controls RNA polymerase II (Pol II) activity by genome-wide chromatin immunoprecipitation and precision global run-on sequencing. On average, cohesin-binding genes have more transcriptionally active Pol II and promoter-proximal Pol II pausing than non-binding genes, and are more efficient, producing higher steady state levels of mRNA per transcribing Pol II complex. Cohesin depletion frequently decreases gene body transcription but increases pausing at cohesin-binding genes, indicating that cohesin often facilitates transition of paused Pol II to elongation. In many cases, this likely reflects a role for cohesin in transcriptional enhancer function. Strikingly, more than 95% of predicted extragenic enhancers bind cohesin, and cohesin depletion can reduce their association with Pol II, indicating that cohesin facilitates enhancer-promoter contact. Cohesin depletion decreases the levels of transcriptionally engaged Pol II at the promoters of most genes that don't bind cohesin, suggesting that cohesin controls expression of one or more broadly acting general transcription factors. The multiple transcriptional roles of cohesin revealed by these studies likely underlie the growth and developmental deficits caused by minor changes in cohesin activity.
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Affiliation(s)
- Cheri A. Schaaf
- Edward A. Doisy Department of Biochemistry and Molecular Biology, Saint Louis University School of Medicine, Saint Louis, Missouri, United States of America
| | - Hojoong Kwak
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York, United States of America
| | - Amanda Koenig
- Edward A. Doisy Department of Biochemistry and Molecular Biology, Saint Louis University School of Medicine, Saint Louis, Missouri, United States of America
| | - Ziva Misulovin
- Edward A. Doisy Department of Biochemistry and Molecular Biology, Saint Louis University School of Medicine, Saint Louis, Missouri, United States of America
| | - David W. Gohara
- Edward A. Doisy Department of Biochemistry and Molecular Biology, Saint Louis University School of Medicine, Saint Louis, Missouri, United States of America
| | - Audrey Watson
- Edward A. Doisy Department of Biochemistry and Molecular Biology, Saint Louis University School of Medicine, Saint Louis, Missouri, United States of America
| | - Yanjiao Zhou
- The Genome Center, Department of Genetics, Washington University in St. Louis School of Medicine, Saint Louis, Missouri, United States of America
| | - John T. Lis
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York, United States of America
| | - Dale Dorsett
- Edward A. Doisy Department of Biochemistry and Molecular Biology, Saint Louis University School of Medicine, Saint Louis, Missouri, United States of America
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15
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One step back before moving forward: regulation of transcription elongation by arrest and backtracking. FEBS Lett 2012; 586:2820-5. [PMID: 22819814 DOI: 10.1016/j.febslet.2012.07.030] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2012] [Revised: 07/09/2012] [Accepted: 07/10/2012] [Indexed: 12/14/2022]
Abstract
RNA polymerase II backtracking is a well-known phenomenon, but its involvement in gene regulation is yet to be addressed. Structural studies into the backtracked complex, new reactivation mechanisms and genome-wide approaches are shedding some light on this interesting aspect of gene transcription. In this review, we briefly summarise these new findings, comment about some results recently obtained in our laboratory, and propose a new model for the influence of the chromatin context on RNA polymerase II backtracking.
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16
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Pereira LA, Wong MS, Mei Lim S, Stanley EG, Elefanty AG. The Mix family of homeobox genes—Key regulators of mesendoderm formation during vertebrate development. Dev Biol 2012; 367:163-77. [DOI: 10.1016/j.ydbio.2012.04.033] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2011] [Revised: 04/24/2012] [Accepted: 04/30/2012] [Indexed: 10/28/2022]
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17
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Kim JN, Yi JS, Lee BR, Kim EJ, Kim MW, Song Y, Cho BK, Kim BG. A versatile PCR-based tandem epitope tagging system for Streptomyces coelicolor genome. Biochem Biophys Res Commun 2012; 424:22-7. [PMID: 22704935 DOI: 10.1016/j.bbrc.2012.06.022] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2012] [Accepted: 06/06/2012] [Indexed: 10/28/2022]
Abstract
Epitope tagging approaches have been widely used for the analysis of functions, interactions and subcellular distributions of proteins. However, incorporating epitope sequence into protein loci in Streptomyces is time-consuming procedure due to the absence of the versatile tagging methods. Here, we developed a versatile PCR-based tandem epitope tagging tool for the Streptomyces genome engineering. We constructed a series of template plasmids that carry repeated sequence of c-myc epitope, Flp recombinase target (FRT) sites, and apramycin resistance marker to insert epitope tags into any desired spot of the chromosomal loci. A DNA module which includes the tandem epitope-encoding sequence and a selectable marker was amplified by PCR with primers that carry homologous extensions to the last portion and downstream region of the targeted gene. We fused the epitope tags at the 3' region of global transcription factors of Streptomyces coelicolor to test the validity of this system. The proper insertion of the epitope tag was confirmed by PCR and western blot analysis. The recombinants showed the identical phenotype to the wild-type that proved the conservation of in vivo function of the tagged proteins. Finally, the direct binding targets were successfully detected by chromatin immunoprecipitation with the increase in the signal-to-noise ratio. The epitope tagging system describes here would provide wide applications to study the protein functions in S. coelicolor.
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Affiliation(s)
- Ji-Nu Kim
- School of Chemical and Biological Engineering, Institute of Molecular Biology and Genetics, and Bioengineering Institute, Seoul National University, Seoul, Republic of Korea
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18
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Dey B, Thukral S, Krishnan S, Chakrobarty M, Gupta S, Manghani C, Rani V. DNA-protein interactions: methods for detection and analysis. Mol Cell Biochem 2012; 365:279-99. [PMID: 22399265 DOI: 10.1007/s11010-012-1269-z] [Citation(s) in RCA: 96] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2011] [Accepted: 02/16/2012] [Indexed: 12/18/2022]
Abstract
DNA-binding proteins control various cellular processes such as recombination, replication and transcription. This review is aimed to summarize some of the most commonly used techniques to determine DNA-protein interactions. In vitro techniques such as footprinting assays, electrophoretic mobility shift assay, southwestern blotting, yeast one-hybrid assay, phage display and proximity ligation assay have been discussed. The highly versatile in vivo techniques such as chromatin immunoprecipitation and its variants, DNA adenine methyl transferase identification as well as 3C and chip-loop assay have also been summarized. In addition, some in silico tools have been reviewed to provide computational basis for determining DNA-protein interactions. Biophysical techniques like fluorescence resonance energy transfer (FRET) techniques, FRET-FLIM, circular dichroism, atomic force microscopy, nuclear magnetic resonance, surface plasmon resonance, etc. have also been highlighted.
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Affiliation(s)
- Bipasha Dey
- Department of Biotechnology, Jaypee Institute of Information Technology, A-10 Sector-62, Noida 201307, Uttar Pradesh, India
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19
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Di Antonio M, Rodriguez R, Balasubramanian S. Experimental approaches to identify cellular G-quadruplex structures and functions. Methods 2012; 57:84-92. [PMID: 22343041 PMCID: PMC3563962 DOI: 10.1016/j.ymeth.2012.01.008] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2011] [Revised: 01/27/2012] [Accepted: 01/29/2012] [Indexed: 12/27/2022] Open
Abstract
Guanine-rich nucleic acids can fold into non-canonical DNA secondary structures called G-quadruplexes. The formation of these structures can interfere with the biology that is crucial to sustain cellular homeostases and metabolism via mechanisms that include transcription, translation, splicing, telomere maintenance and DNA recombination. Thus, due to their implication in several biological processes and possible role promoting genomic instability, G-quadruplex forming sequences have emerged as potential therapeutic targets. There has been a growing interest in the development of synthetic molecules and biomolecules for sensing G-quadruplex structures in cellular DNA. In this review, we summarise and discuss recent methods developed for cellular imaging of G-quadruplexes, and the application of experimental genomic approaches to detect G-quadruplexes throughout genomic DNA. In particular, we will discuss the use of engineered small molecules and natural proteins to enable pull-down, ChIP-Seq, ChIP-chip and fluorescence imaging of G-quadruplex structures in cellular DNA.
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Affiliation(s)
- Marco Di Antonio
- University of Cambridge, Department of Chemistry, Lensfield Road, Cambridge CB2 1EW, UK
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20
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Fang XF, Zhang WY, Zhao N, Yu W, Ding D, Hong X, Li LS, Zhang HR, Zheng S, Lin BY. Genome-wide analysis of OCT4 binding sites in glioblastoma cancer cells. J Zhejiang Univ Sci B 2012; 12:812-9. [PMID: 21960344 DOI: 10.1631/jzus.b1100059] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
OCT4, a member of the POU family of gene products, is an octamer motif-binding transcription factor. As it is known to play a crucial role in cancer processes including proliferation, invasion, and chemoradioresistance, it is important to identify the direct targets of OCT4 in living cancer cells. Here, chromatin immunoprecipitation-sequencing (ChIP-seq) was used to identify OCT4 binding sites in glioblastoma cancer cells. The results showed that 5438 OCT4 binding sites were localized in the glioblastoma cancer genome and that these sites contained a consensus sequence TTTkswTw (k=T or G, s=C or G, w=A or T), which occurred 3931 times in 2312 OCT4 binding regions. Furthermore, binding motifs of some other transcription factors were identified in OCT4 binding regions. Our results provide a valuable dataset for understanding gene regulation mechanisms underlying the function of OCT4 in glioblastoma cancer.
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Affiliation(s)
- Xue-feng Fang
- Key Laboratory of Cancer Prevention and Intervention of Ministry of Education, Cancer Institute, the Second Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, China
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21
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Abstract
Salt fractionation of nucleosomes, a classical method for defining "active" chromatin based on nucleosome solubility, has recently been adapted for genome-scale profiling. This method has several advantages for profiling chromatin dynamics, including general applicability to cell lines and tissues, quantitative recovery of chromatin, base-pair resolution of nucleosomes, and overall simplicity both in concept and execution. This chapter provides detailed protocols for nuclear isolation, chromatin fragmentation by micrococcal nuclease digestion, successive solubilization of chromatin fractions by addition of increasing concentrations of salt, and genome-wide analyses through microarray hybridization and next-generation sequencing.
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Affiliation(s)
- Sheila S Teves
- Division of Basic Sciences, Fred Hutchinson Cancer Research Center and Molecular and Cellular Biology Program, University of Washington, Seattle, WA, USA
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22
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Martowicz ML, Meyer MB, Pike JW. The mouse RANKL gene locus is defined by a broad pattern of histone H4 acetylation and regulated through distinct distal enhancers. J Cell Biochem 2011; 112:2030-45. [PMID: 21465526 DOI: 10.1002/jcb.23123] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
RANKL is a stromal cell-derived tumor necrosis factor (TNF)-like factor that plays a primary role in osteoclast formation and function. Recent studies suggest that 1,25(OH)(2) D(3) induces Rankl expression via vitamin D receptor (VDR) interaction at several enhancers located up to 76 kb upstream of the gene's transcriptional start site (TSS). In the current studies, we explored these interactions further using ChIP-chip and RNA analysis. We confirm VDR and RXR binding to the five enhancers described previously and identify two additional sites, one located within the Rankl coding region. We also show that RNA polymerase II is recruited to these enhancers, most likely through transcription factors TBP, TFIIB, and TAF(II) 250. Interestingly, the recruitment of these factors leads to the production of RNA transcripts, although their role at present is unknown. We also discovered that histone H4 acetylation (H4ac) marks many upstream Rankl enhancers under basal conditions and that H4ac is increased upon 1,25(OH)(2) D(3) treatment. Surprisingly, the hormone also induces C/EBPβ binding across the Rankl locus. C/EBPβ binding correlates directly with increased H4ac activity following 1,25(OH)(2) D(3) treatment. Finally, elevated H4ac is restricted to an extended region located between two potential insulator sites occupied by CTCF and Rad21. These data suggest a mechanism whereby 1,25(OH)(2) D(3) functions via the VDR and C/EBPβ to upregulate Rankl expression.
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Affiliation(s)
- Melissa L Martowicz
- Department of Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA
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23
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Molina-Navarro MM, Martinez-Jimenez CP, Rodriguez-Navarro S. Transcriptional elongation and mRNA export are coregulated processes. GENETICS RESEARCH INTERNATIONAL 2011; 2011:652461. [PMID: 22567364 PMCID: PMC3335577 DOI: 10.4061/2011/652461] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/23/2011] [Accepted: 08/10/2011] [Indexed: 01/06/2023]
Abstract
Chromatin structure complexity requires the interaction and coordinated work of a multiplicity of factors at different transcriptional regulation stages. Transcription control comprises a set of processes that ensures proper balance in the gene expression under different conditions, such as signals, metabolic states, or development. We could frame those steps from epigenetic marks to mRNA stability to support the holistic view of a fine-tune balance of final mRNA levels through mRNA transcription, export, stability, translation, and degradation. Transport of mRNA from the nucleus to the cytoplasm is a key process in regulated gene expression. Transcriptional elongation and mRNA export are coregulated steps that determine the mature mRNA levels in the cytoplasm. In this paper, recent insights into the coordination of these processes in eukaryotes will be summarised.
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24
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Kucera KS, Reddy TE, Pauli F, Gertz J, Logan JE, Myers RM, Willard HF. Allele-specific distribution of RNA polymerase II on female X chromosomes. Hum Mol Genet 2011; 20:3964-73. [PMID: 21791549 DOI: 10.1093/hmg/ddr315] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
While the distribution of RNA polymerase II (PolII) in a variety of complex genomes is correlated with gene expression, the presence of PolII at a gene does not necessarily indicate active expression. Various patterns of PolII binding have been described genome wide; however, whether or not PolII binds at transcriptionally inactive sites remains uncertain. The two X chromosomes in female cells in mammals present an opportunity to examine each of the two alleles of a given locus in both active and inactive states, depending on which X chromosome is silenced by X chromosome inactivation. Here, we investigated PolII occupancy and expression of the associated genes across the active (Xa) and inactive (Xi) X chromosomes in human female cells to elucidate the relationship of gene expression and PolII binding. We find that, while PolII in the pseudoautosomal region occupies both chromosomes at similar levels, it is significantly biased toward the Xa throughout the rest of the chromosome. The general paucity of PolII on the Xi notwithstanding, detectable (albeit significantly reduced) binding can be observed, especially on the evolutionarily younger short arm of the X. PolII levels at genes that escape inactivation correlate with the levels of their expression; however, additional PolII sites can be found at apparently silenced regions, suggesting the possibility of a subset of genes on the Xi that are poised for expression. Consistent with this hypothesis, we show that a high proportion of genes associated with PolII-accessible sites, while silenced in GM12878, are expressed in other female cell lines.
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Affiliation(s)
- Katerina S Kucera
- Genome Biology Group, Duke Institute for Genome Sciences & Policy, Duke University, CIEMAS 2376, 101 Science Drive, Durham, 27708 NC, USA
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25
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Abstract
MEME and many other popular motif finders use the expectation-maximization (EM) algorithm to optimize their parameters. Unfortunately, the running time of EM is linear in the length of the input sequences. This can prohibit its application to data sets of the size commonly generated by high-throughput biological techniques. A suffix tree is a data structure that can efficiently index a set of sequences. We describe an algorithm, Suffix Tree EM for Motif Elicitation (STEME), that approximates EM using suffix trees. To the best of our knowledge, this is the first application of suffix trees to EM. We provide an analysis of the expected running time of the algorithm and demonstrate that STEME runs an order of magnitude more quickly than the implementation of EM used by MEME. We give theoretical bounds for the quality of the approximation and show that, in practice, the approximation has a negligible effect on the outcome. We provide an open source implementation of the algorithm that we hope will be used to speed up existing and future motif search algorithms.
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Affiliation(s)
- John E Reid
- MRC Biostatistics Unit, Institute of Public Health, Forvie Site, Robinson Way, Cambridge CB2 0SR, UK.
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26
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Levine M. Paused RNA polymerase II as a developmental checkpoint. Cell 2011; 145:502-11. [PMID: 21565610 DOI: 10.1016/j.cell.2011.04.021] [Citation(s) in RCA: 220] [Impact Index Per Article: 16.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2010] [Revised: 02/18/2011] [Accepted: 04/25/2011] [Indexed: 11/18/2022]
Abstract
The textbook view of gene activation is that the rate-limiting step is the interaction of RNA polymerase II (Pol II) with the gene's promoter. However, studies in a variety of systems, including human embryonic stem cells and the early Drosophila embryo, have begun to challenge this view. There is increasing evidence that differential gene expression often depends on the regulation of transcription elongation via the release of Pol II from the proximal promoter. I review the implications of this mechanism of gene activation with respect to the orderly unfolding of complex gene networks governing animal development.
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Affiliation(s)
- Michael Levine
- Division of Genetics, Genomics, and Development, Department of Molecular and Cell Biology, Center for Integrative Biology, University of California, Berkeley, Berkeley, CA 94720, USA
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27
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Dere E, Lo R, Celius T, Matthews J, Zacharewski TR. Integration of genome-wide computation DRE search, AhR ChIP-chip and gene expression analyses of TCDD-elicited responses in the mouse liver. BMC Genomics 2011; 12:365. [PMID: 21762485 PMCID: PMC3160422 DOI: 10.1186/1471-2164-12-365] [Citation(s) in RCA: 103] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2010] [Accepted: 07/15/2011] [Indexed: 12/20/2022] Open
Abstract
Background The aryl hydrocarbon receptor (AhR) is a ligand-activated transcription factor (TF) that mediates responses to 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD). Integration of TCDD-induced genome-wide AhR enrichment, differential gene expression and computational dioxin response element (DRE) analyses further elucidate the hepatic AhR regulatory network. Results Global ChIP-chip and gene expression analyses were performed on hepatic tissue from immature ovariectomized mice orally gavaged with 30 μg/kg TCDD. ChIP-chip analysis identified 14,446 and 974 AhR enriched regions (1% false discovery rate) at 2 and 24 hrs, respectively. Enrichment density was greatest in the proximal promoter, and more specifically, within ± 1.5 kb of a transcriptional start site (TSS). AhR enrichment also occurred distal to a TSS (e.g. intergenic DNA and 3' UTR), extending the potential gene expression regulatory roles of the AhR. Although TF binding site analyses identified over-represented DRE sequences within enriched regions, approximately 50% of all AhR enriched regions lacked a DRE core (5'-GCGTG-3'). Microarray analysis identified 1,896 number of TCDD-responsive genes (|fold change| ≥ 1.5, P1(t) > 0.999). Integrating this gene expression data with our ChIP-chip and DRE analyses only identified 625 differentially expressed genes that involved an AhR interaction at a DRE. Functional annotation analysis of differentially regulated genes associated with AhR enrichment identified overrepresented processes related to fatty acid and lipid metabolism and transport, and xenobiotic metabolism, which are consistent with TCDD-elicited steatosis in the mouse liver. Conclusions Details of the AhR regulatory network have been expanded to include AhR-DNA interactions within intragenic and intergenic genomic regions. Moreover, the AhR can interact with DNA independent of a DRE core suggesting there are alternative mechanisms of AhR-mediated gene regulation.
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Affiliation(s)
- Edward Dere
- Department of Biochemistry & Molecular Biology, Michigan State University, East Lansing, MI 48824, USA
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28
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Abstract
In mammalian cells, multiple cellular processes, including gene silencing, cell growth and differentiation, pluripotency, neoplastic transformation, apoptosis, DNA repair, and maintenance of genomic integrity, converge on the evolutionarily conserved protein KAP1, which is thought to regulate the dynamic organization of chromatin structure via its ability to influence epigenetic patterns and chromatin compaction. In this minireview, we discuss how KAP1 might execute such pleiotropic effects, focusing on genomic targeting mechanisms, protein-protein interactions, specific post-translational modifications of both KAP1 and associated histones, and transcriptome analyses of cells deficient in KAP1.
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Affiliation(s)
- Sushma Iyengar
- From the Genetics Graduate Group, University of California, Davis, California 95616, USA
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McDermott JE, Yoon H, Nakayasu ES, Metz TO, Hyduke DR, Kidwai AS, Palsson BO, Adkins JN, Heffron F. Technologies and approaches to elucidate and model the virulence program of salmonella. Front Microbiol 2011; 2:121. [PMID: 21687430 PMCID: PMC3108385 DOI: 10.3389/fmicb.2011.00121] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2011] [Accepted: 05/15/2011] [Indexed: 11/13/2022] Open
Abstract
Salmonella is a primary cause of enteric diseases in a variety of animals. During its evolution into a pathogenic bacterium, Salmonella acquired an elaborate regulatory network that responds to multiple environmental stimuli within host animals and integrates them resulting in fine regulation of the virulence program. The coordinated action by this regulatory network involves numerous virulence regulators, necessitating genome-wide profiling analysis to assess and combine efforts from multiple regulons. In this review we discuss recent high-throughput analytic approaches used to understand the regulatory network of Salmonella that controls virulence processes. Application of high-throughput analyses have generated large amounts of data and necessitated the development of computational approaches for data integration. Therefore, we also cover computer-aided network analyses to infer regulatory networks, and demonstrate how genome-scale data can be used to construct regulatory and metabolic systems models of Salmonella pathogenesis. Genes that are coordinately controlled by multiple virulence regulators under infectious conditions are more likely to be important for pathogenesis. Thus, reconstructing the global regulatory network during infection or, at the very least, under conditions that mimic the host cellular environment not only provides a bird's eye view of Salmonella survival strategy in response to hostile host environments but also serves as an efficient means to identify novel virulence factors that are essential for Salmonella to accomplish systemic infection in the host.
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Affiliation(s)
- Jason E. McDermott
- Computational Biology and Bioinformatics Group, Pacific Northwest National LaboratoryRichland, WA, USA
| | - Hyunjin Yoon
- Department of Molecular Microbiology and Immunology, Oregon Health and Sciences UniversityPortland, OR, USA
| | - Ernesto S. Nakayasu
- Biological Separations and Mass Spectroscopy Group, Pacific Northwest National LaboratoryRichland WA, USA
| | - Thomas O. Metz
- Biological Separations and Mass Spectroscopy Group, Pacific Northwest National LaboratoryRichland WA, USA
| | - Daniel R. Hyduke
- Systems Biology, University of California San DiegoSan Diego, CA, USA
| | - Afshan S. Kidwai
- Department of Molecular Microbiology and Immunology, Oregon Health and Sciences UniversityPortland, OR, USA
| | | | - Joshua N. Adkins
- Biological Separations and Mass Spectroscopy Group, Pacific Northwest National LaboratoryRichland WA, USA
| | - Fred Heffron
- Department of Molecular Microbiology and Immunology, Oregon Health and Sciences UniversityPortland, OR, USA
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Horiuchi S, Onodera A, Hosokawa H, Watanabe Y, Tanaka T, Sugano S, Suzuki Y, Nakayama T. Genome-wide analysis reveals unique regulation of transcription of Th2-specific genes by GATA3. THE JOURNAL OF IMMUNOLOGY 2011; 186:6378-89. [PMID: 21536806 DOI: 10.4049/jimmunol.1100179] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
Differentiation of naive CD4 T cells into Th2 cells is accompanied by chromatin remodeling and increased expression of a set of Th2-specific genes, including those encoding Th2 cytokines. IL-4-mediated STAT6 activation induces high levels of transcription of GATA3, a master regulator of Th2 cell differentiation, and enforced expression of GATA3 induces Th2 cytokine expression. However, it remains unclear whether the expression of other Th2-specific genes is induced directly by GATA3. A genome-wide unbiased chromatin immunoprecipitation assay coupled with massive parallel sequencing analysis revealed that GATA3 bound to 1279 genes selectively in Th2 cells, and 101 genes in both Th1 and Th2 cells. Simultaneously, we identified 26 highly Th2-specific STAT6-dependent inducible genes by DNA microarray analysis-based three-step selection processes, and among them 17 genes showed GATA3 binding. We assessed dependency on GATA3 for the transcription of these 26 Th2-specific genes, and 10 genes showed increased transcription in a GATA3-dependent manner, whereas 16 genes showed no significant responses. The transcription of the 16 GATA3-nonresponding genes was clearly increased by the introduction of an active form of STAT6, STAT6VT. Therefore, although GATA3 has been recognized as a master regulator of Th2 cell differentiation, many Th2-specific genes are not regulated by GATA3 itself, but in collaboration with STAT6.
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Affiliation(s)
- Shu Horiuchi
- Department of Immunology, Graduate School of Medicine, Chiba University, Chiba 260-8670, Japan
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31
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Liu Q, Tan Y, Huang T, Ding G, Tu Z, Liu L, Li Y, Dai H, Xie L. TF-centered downstream gene set enrichment analysis: Inference of causal regulators by integrating TF-DNA interactions and protein post-translational modifications information. BMC Bioinformatics 2010; 11 Suppl 11:S5. [PMID: 21172055 PMCID: PMC3024863 DOI: 10.1186/1471-2105-11-s11-s5] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Background Inference of causal regulators responsible for gene expression changes under different conditions is of great importance but remains rather challenging. To date, most approaches use direct binding targets of transcription factors (TFs) to associate TFs with expression profiles. However, the low overlap between binding targets of a TF and the affected genes of the TF knockout limits the power of those methods. Results We developed a TF-centered downstream gene set enrichment analysis approach to identify potential causal regulators responsible for expression changes. We constructed hierarchical and multi-layer regulation models to derive possible downstream gene sets of a TF using not only TF-DNA interactions, but also, for the first time, post-translational modifications (PTM) information. We verified our method in one expression dataset of large-scale TF knockout and another dataset involving both TF knockout and TF overexpression. Compared with the flat model using TF-DNA interactions alone, our method correctly identified five more actual perturbed TFs in large-scale TF knockout data and six more perturbed TFs in overexpression data. Potential regulatory pathways downstream of three perturbed regulators— SNF1, AFT1 and SUT1 —were given to demonstrate the power of multilayer regulation models integrating TF-DNA interactions and PTM information. Additionally, our method successfully identified known important TFs and inferred some novel potential TFs involved in the transition from fermentative to glycerol-based respiratory growth and in the pheromone response. Downstream regulation pathways of SUT1 and AFT1 were also supported by the mRNA and/or phosphorylation changes of their mediating TFs and/or “modulator” proteins. Conclusions The results suggest that in addition to direct transcription, indirect transcription and post-translational regulation are also responsible for the effects of TFs perturbation, especially for TFs overexpression. Many TFs inferred by our method are supported by literature. Multiple TF regulation models could lead to new hypotheses for future experiments. Our method provides a valuable framework for analyzing gene expression data to identify causal regulators in the context of TF-DNA interactions and PTM information.
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Affiliation(s)
- Qi Liu
- School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China.
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32
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Gilchrist DA, Dos Santos G, Fargo DC, Xie B, Gao Y, Li L, Adelman K. Pausing of RNA polymerase II disrupts DNA-specified nucleosome organization to enable precise gene regulation. Cell 2010; 143:540-51. [PMID: 21074046 DOI: 10.1016/j.cell.2010.10.004] [Citation(s) in RCA: 325] [Impact Index Per Article: 23.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2010] [Revised: 08/18/2010] [Accepted: 09/27/2010] [Indexed: 11/30/2022]
Abstract
Metazoan transcription is controlled through either coordinated recruitment of transcription machinery to the gene promoter or regulated pausing of RNA polymerase II (Pol II) in early elongation. We report that a striking difference between genes that use these distinct regulatory strategies lies in the "default" chromatin architecture specified by their DNA sequences. Pol II pausing is prominent at highly regulated genes whose sequences inherently disfavor nucleosome formation within the gene but favor occlusion of the promoter by nucleosomes. In contrast, housekeeping genes that lack pronounced Pol II pausing show higher nucleosome occupancy downstream, but their promoters are deprived of nucleosomes regardless of polymerase binding. Our results indicate that a key role of paused Pol II is to compete with nucleosomes for occupancy of highly regulated promoters, thereby preventing the formation of repressive chromatin architecture to facilitate further or future gene activation.
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Affiliation(s)
- Daniel A Gilchrist
- Laboratory of Molecular Carcinogenesis, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC 27709, USA
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33
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Pearson RJ, Singh U. Approaches to characterizing Entamoeba histolytica transcriptional regulation. Cell Microbiol 2010; 12:1681-90. [DOI: 10.1111/j.1462-5822.2010.01524.x] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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JIANG LH, LI YX, LIU Q. Reconstruction of Gene Regulatory Networks by Integrating ChIP-chip, Knock out and Expression Data*. PROG BIOCHEM BIOPHYS 2010. [DOI: 10.3724/sp.j.1206.2010.00184] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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35
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Glubb DM, Innocenti F. Mechanisms of genetic regulation in gene expression: examples from drug metabolizing enzymes and transporters. WILEY INTERDISCIPLINARY REVIEWS-SYSTEMS BIOLOGY AND MEDICINE 2010; 3:299-313. [PMID: 20865777 DOI: 10.1002/wsbm.125] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
Interindividual variability in the response to drug therapy is due, in part, to genetic mechanisms which influence the expression of genes involved with drug metabolism and transport. Genetic elements and processes such as DNA methylation, histone deacetylation, transcription factors, DNA sequence variants, and microRNAs (miRNAs) can impact at either the transcriptional or translational levels to modulate gene expression. Identification of such genetic regulators has greatly advanced in the last decade. Genome-wide analyses, using different types of approaches and methodologies, have uncovered many potential regulators of the expression of drug metabolizing enzymes and transporters. However, confirming the function of these putative regulators is necessary and requires further work in the laboratory, using techniques which are still evolving. It also still remains to be seen whether these findings have clinical implications for drug therapy but the realization of personalized medicine is a possible consequence of this research.
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Affiliation(s)
- Dylan M Glubb
- Department of Medicine, University of Chicago, Chicago, IL, USA
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Ramos YFM, Hestand MS, Verlaan M, Krabbendam E, Ariyurek Y, van Galen M, van Dam H, van Ommen GJB, den Dunnen JT, Zantema A, 't Hoen PAC. Genome-wide assessment of differential roles for p300 and CBP in transcription regulation. Nucleic Acids Res 2010; 38:5396-408. [PMID: 20435671 PMCID: PMC2938195 DOI: 10.1093/nar/gkq184] [Citation(s) in RCA: 110] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2009] [Revised: 02/26/2010] [Accepted: 03/04/2010] [Indexed: 12/20/2022] Open
Abstract
Despite high levels of homology, transcription coactivators p300 and CREB binding protein (CBP) are both indispensable during embryogenesis. They are largely known to regulate the same genes. To identify genes preferentially regulated by p300 or CBP, we performed an extensive genome-wide survey using the ChIP-seq on cell-cycle synchronized cells. We found that 57% of the tags were within genes or proximal promoters, with an overall preference for binding to transcription start and end sites. The heterogeneous binding patterns possibly reflect the divergent roles of CBP and p300 in transcriptional regulation. Most of the 16 103 genes were bound by both CBP and p300. However, after stimulation 89 and 1944 genes were preferentially bound by CBP or p300, respectively. Target genes were found to be primarily involved in the regulation of metabolic and developmental processes, and transcription, with CBP showing a stronger preference than p300 for genes active in negative regulation of transcription. Analysis of transcription factor binding sites suggest that CBP and p300 have many partners in common, but AP-1 and Serum Response Factor (SRF) appear to be more prominent in CBP-specific sequences, whereas AP-2 and SP1 are enriched in p300-specific targets. Taken together, our findings further elucidate the distinct roles of coactivators p300 and CBP in transcriptional regulation.
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Affiliation(s)
- Yolande F M Ramos
- Department of Molecular Cell Biology, Leiden University Medical Center, Postzone S4-0P, PO Box 9600, 2300 RC Leiden, The Netherlands.
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Rodríguez-Gil A, García-Martínez J, Pelechano V, Muñoz-Centeno MDLC, Geli V, Pérez-Ortín JE, Chávez S. The distribution of active RNA polymerase II along the transcribed region is gene-specific and controlled by elongation factors. Nucleic Acids Res 2010; 38:4651-64. [PMID: 20385590 PMCID: PMC2919717 DOI: 10.1093/nar/gkq215] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
In order to study the intragenic profiles of active transcription, we determined the relative levels of active RNA polymerase II present at the 3′- and 5′-ends of 261 yeast genes by run-on. The results obtained indicate that the 3′/5′ run-on ratio varies among the genes studied by over 12 log2 units. This ratio seems to be an intrinsic characteristic of each transcriptional unit and does not significantly correlate with gene length, G + C content or level of expression. The correlation between the 3′/5′ RNA polymerase II ratios measured by run-on and those obtained by chromatin immunoprecipitation is poor, although the genes encoding ribosomal proteins present exceptionally low ratios in both cases. We detected a subset of elongation-related factors that are important for maintaining the wild-type profiles of active transcription, including DSIF, Mediator, factors related to the methylation of histone H3-lysine 4, the Bur CDK and the RNA polymerase II subunit Rpb9. We conducted a more detailed investigation of the alterations caused by rpb9Δ to find that Rpb9 contributes to the intragenic profiles of active transcription by influencing the probability of arrest of RNA polymerase II.
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Affiliation(s)
- Alfonso Rodríguez-Gil
- Departamento de Genética, Facultad de Biología, Universidad de Sevilla, Sevilla, Spain
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38
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Zhao Y, Granas D, Stormo GD. Inferring binding energies from selected binding sites. PLoS Comput Biol 2009; 5:e1000590. [PMID: 19997485 PMCID: PMC2777355 DOI: 10.1371/journal.pcbi.1000590] [Citation(s) in RCA: 159] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2009] [Accepted: 11/02/2009] [Indexed: 11/18/2022] Open
Abstract
We employ a biophysical model that accounts for the non-linear relationship between binding energy and the statistics of selected binding sites. The model includes the chemical potential of the transcription factor, non-specific binding affinity of the protein for DNA, as well as sequence-specific parameters that may include non-independent contributions of bases to the interaction. We obtain maximum likelihood estimates for all of the parameters and compare the results to standard probabilistic methods of parameter estimation. On simulated data, where the true energy model is known and samples are generated with a variety of parameter values, we show that our method returns much more accurate estimates of the true parameters and much better predictions of the selected binding site distributions. We also introduce a new high-throughput SELEX (HT-SELEX) procedure to determine the binding specificity of a transcription factor in which the initial randomized library and the selected sites are sequenced with next generation methods that return hundreds of thousands of sites. We show that after a single round of selection our method can estimate binding parameters that give very good fits to the selected site distributions, much better than standard motif identification algorithms. The DNA binding sites of transcription factors that control gene expression are often predicted based on a collection of known or selected binding sites. The most commonly used methods for inferring the binding site pattern, or sequence motif, assume that the sites are selected in proportion to their affinity for the transcription factor, ignoring the effect of the transcription factor concentration. We have developed a new maximum likelihood approach, in a program called BEEML, that directly takes into account the transcription factor concentration as well as non-specific contributions to the binding affinity, and we show in simulation studies that it gives a much more accurate model of the transcription factor binding sites than previous methods. We also develop a new method for extracting binding sites for a transcription factor from a random pool of DNA sequences, called high-throughput SELEX (HT-SELEX), and we show that after a single round of selection BEEML can obtain an accurate model of the transcription factor binding sites.
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Affiliation(s)
- Yue Zhao
- Department of Genetics, Washington University School of Medicine, St. Louis, Missouri, United States of America
| | - David Granas
- Department of Genetics, Washington University School of Medicine, St. Louis, Missouri, United States of America
| | - Gary D. Stormo
- Department of Genetics, Washington University School of Medicine, St. Louis, Missouri, United States of America
- * E-mail:
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39
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Interindividual variation in epigenomic phenomena in humans. Mamm Genome 2009; 20:604-11. [PMID: 19763687 DOI: 10.1007/s00335-009-9219-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2009] [Accepted: 08/18/2009] [Indexed: 12/20/2022]
Abstract
Our knowledge of regulatory mechanisms of gene expression and other chromosomal processes related to DNA methylation and chromatin state is continuing to grow at a rapid pace. Understanding how these epigenomic phenomena vary between individuals will have an impact on understanding their broader role in determining variation in gene expression and biochemical, physiological, and behavioural phenotypes. In this review we survey recent progress in this area, focusing on data available from humans. We highlight the role of obligatory (sequence-dependent) epigenomic variation as an important mechanism for generating interindividual variation that could impact our understanding of the mechanistic basis of complex trait architecture.
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40
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Barr CS. Strategies for performing genotype-phenotype association studies in nonhuman primates. Methods 2009; 49:56-62. [PMID: 19505576 PMCID: PMC2739376 DOI: 10.1016/j.ymeth.2009.05.014] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2009] [Revised: 05/20/2009] [Accepted: 05/22/2009] [Indexed: 01/21/2023] Open
Abstract
Anthropoid primate models offer opportunities to study genetic influence on alcohol consumption and alcohol-related intermediate phenotypes in socially and behaviorally complex animal models that are closely related to humans, and in which functionally equivalent or orthologous genetic variants exist. This review will discuss the methods commonly used for performing candidate gene-based studies in rhesus macaques in order to model how functional genetic variation moderates risk for human psychiatric disorders. Various in silico and in vitro approaches to identifying functional genetic variants for performance of these studies will be discussed. Next, I will provide examples of how this approach can be used for performing candidate gene-based studies and for examining gene by environment interactions. Finally, these approaches will then be placed in the context of how function-guided studies can inform us of genetic variants that may be under selection across species, demonstrating how functional genetic variants that may have conferred selective advantage at some point in the evolutionary history of humans could increase risk for addictive disorders in modern society.
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Affiliation(s)
- Christina S Barr
- Laboratories of Neurogenetics and Clinical and Translational Studies, NIH/NIAAA, 5625 Fishers Lane, Rm. 3S-32, Rockville, MD 20852, USA.
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