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Kwon AT, Chou AY, Arenillas DJ, Wasserman WW. Validation of skeletal muscle cis-regulatory module predictions reveals nucleotide composition bias in functional enhancers. PLoS Comput Biol 2011; 7:e1002256. [PMID: 22144875 PMCID: PMC3228787 DOI: 10.1371/journal.pcbi.1002256] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2011] [Accepted: 09/16/2011] [Indexed: 11/19/2022] Open
Abstract
We performed a genome-wide scan for muscle-specific cis-regulatory modules (CRMs) using three computational prediction programs. Based on the predictions, 339 candidate CRMs were tested in cell culture with NIH3T3 fibroblasts and C2C12 myoblasts for capacity to direct selective reporter gene expression to differentiated C2C12 myotubes. A subset of 19 CRMs validated as functional in the assay. The rate of predictive success reveals striking limitations of computational regulatory sequence analysis methods for CRM discovery. Motif-based methods performed no better than predictions based only on sequence conservation. Analysis of the properties of the functional sequences relative to inactive sequences identifies nucleotide sequence composition can be an important characteristic to incorporate in future methods for improved predictive specificity. Muscle-related TFBSs predicted within the functional sequences display greater sequence conservation than non-TFBS flanking regions. Comparison with recent MyoD and histone modification ChIP-Seq data supports the validity of the functional regions. For efficient identification of genomic sequences responsible for regulating gene expression, a number of computer programs have been developed for automatic annotation of these regulatory regions. We searched for potential regulatory regions responsible for controlling the expression of skeletal muscle-specific genes using these programs, and validated the predictions in a popular cell culture model for muscle. We were able to identify 19 previously uncharacterized regulatory regions for muscle genes. The accuracy of the predictions made by these programs leaves much to be desired, leading us to conclude that other signals in addition to the sequence information will be required to achieve sufficient predictive power for genome annotation. Genomic regions with confirmed regulatory function were compared against non-functional sequences, revealing sequence conservation, composition and chromatin modification properties as important signals in determining regulatory region functionality.
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Affiliation(s)
- Andrew T. Kwon
- Centre for Molecular Medicine and Therapeutics, Child and Family Research Institute, Genetics Graduate Program, and Department of Medical Genetics, University of British Columbia, Vancouver, British Columbia, Canada
| | - Alice Yi Chou
- Centre for Molecular Medicine and Therapeutics, Child and Family Research Institute, Genetics Graduate Program, and Department of Medical Genetics, University of British Columbia, Vancouver, British Columbia, Canada
| | - David J. Arenillas
- Centre for Molecular Medicine and Therapeutics, Child and Family Research Institute, Genetics Graduate Program, and Department of Medical Genetics, University of British Columbia, Vancouver, British Columbia, Canada
| | - Wyeth W. Wasserman
- Centre for Molecular Medicine and Therapeutics, Child and Family Research Institute, Genetics Graduate Program, and Department of Medical Genetics, University of British Columbia, Vancouver, British Columbia, Canada
- * E-mail:
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Miyaguchi K, Fukuoka Y, Mizushima H, Yasen M, Nemoto S, Ishikawa T, Uetake H, Tanaka S, Sugihara K, Arii S, Tanaka H. Genome-wide integrative analysis revealed a correlation between lengths of copy number segments and corresponding gene expression profile. Bioinformation 2011; 7:280-4. [PMID: 22355221 PMCID: PMC3280495 DOI: 10.6026/97320630007280] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2011] [Accepted: 11/08/2011] [Indexed: 12/31/2022] Open
Abstract
Microarray analysis has been applied to comprehensively reveal the abnormalities of DNA copy number (CN) and gene expression in human cancer research during the last decade. These analyses have individually contributed to identify the genes associated with carcinogenesis, progression, metastasis of tumor cells and poor prognosis of cancer patients. However, it is known that the correlation between profiles of CN and gene expression does not highly correlate. Factors which determine the degree of correlation remain largely unexplained. To investigate one such factor, we performed trend analyses between the lengths of CN segments and corresponding gene expression profiles from microarray data in hepatocellular carcinoma (HCC) and colorectal carcinoma (CRC). Significant correlations were observed in CN gain of HCC and CRC (p<0.05). The trend of the CN loss showed a significant correlation in HCC although there was no correlation between the length of CN loss segments and gene expression in CRC. Our findings suggest that the influence of CN on gene expression highly depends on the length of CN region, especially in the case of CN gain. To the best of our knowledge, this is the first study describing the correlation between lengths of CNA segments and expression profiles of corresponding genes.
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Affiliation(s)
| | - Yutaka Fukuoka
- Department of Biosystem Modeling, Graduate School of Biomedical Science, Tokyo Medical and Dental University, Japan
| | - Hiroshi Mizushima
- Center for Public Health Informatics, National Institute of Public Health, Japan
| | | | | | | | | | | | - Kenichi Sugihara
- Department of Surgical Oncology, Graduate School, Tokyo Medical and Dental University, Japan
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3
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AtFKBP53 is a histone chaperone required for repression of ribosomal RNA gene expression in Arabidopsis. Cell Res 2010; 20:357-66. [DOI: 10.1038/cr.2010.22] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
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Hagerman TA, Fu Q, Molinié B, Denvir J, Lindsay S, Georgel PT. Chromatin stability at low concentration depends on histone octamer saturation levels. Biophys J 2009; 96:1944-51. [PMID: 19254554 DOI: 10.1016/j.bpj.2008.10.070] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2008] [Accepted: 10/31/2008] [Indexed: 01/01/2023] Open
Abstract
Studies on the stability of nucleosome core particles as a function of concentration have indicated a lower limit of approximately 5 ng/microL, below which the complexes start to spontaneously destabilize. Until recently little information was available on the effect of low concentration on chromatin. Using the well-characterized array of tandemly repeated 5S rDNA reconstituted into chromatin, we have investigated the effect of dilution. In this study, we demonstrate that the stability of saturated nucleosomal arrays and that of nucleosome core particles are within the same order of magnitude, and no significant loss of histones is monitored down to a concentration of 2.5 ng/microL. We observed that levels of subsaturation of the nucleosomal arrays were directly correlated with an increased sensitivity to histone loss, suggesting a shielding effect. The loss of histones from our linear nucleosomal arrays was shown not to be random, with a significant likelihood to occur at the end of the template than toward the center. This observation indicates that centrally located nucleosomes are more stable than those close to the end of the DNA templates. Itis important to take this information into account for the proper design of experiments pertaining to histone composition and the folding ability of chromatin samples.
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Affiliation(s)
- Thomas A Hagerman
- Marshall University, Department of Biological Sciences, Byrd Biotechnology Science Center, Huntington, West Virginia 25755, USA
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Lee CW, Kim NH, Choi HK, Sun Y, Nam JS, Rhee HJ, Chun J, Huh SO. Lysophosphatidic acid-induced c-fos up-regulation involves cyclic AMP response element-binding protein activated by mitogen- and stress-activated protein kinase-1. J Cell Biochem 2008; 104:785-94. [PMID: 18172855 DOI: 10.1002/jcb.21663] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
Lysophosphatidic acid (LPA) is a lipid growth factor that exerts diverse biological effects through its cognate receptor-mediated signaling cascades. Recently, we reported that LPA stimulates cAMP response element-binding protein (CREB) through mitogen- and stress-activated protein kinase-1 (MSK1). Previously, LPA has been shown to stimulate c-fos mRNA expression in Rat-2 fibroblast cells via a serum response element binding protein (SRF). However, involvement of CREB in LPA-stimulated c-fos gene expression is not elucidated yet. To investigate the CREB-mediated c-fos activation by LPA, various c-fos promoter-reporter constructs containing wild-type and mutated SRE and CRE were tested for their inducibility by LPA in transient transfection assays. LPA-stimulated c-fos promoter activation was markedly decreased when SRE and CRE were mutated. A dominant negative CREB significantly down-regulated the LPA-stimulated c-fos promoter activation. Chromatin immunoprecipitation assay revealed that LPA induced an increased binding of phosphorylated CREB and CREB-binding protein (CBP) to the CRE region of the endogenous c-fos promoter. Immunoblot analyses with various pharmacological inhibitors further showed that LPA induces up-regulation of c-fos mRNA level by activation of ERK, p38 MAPK, and MSK1. Taken together, our results suggest that CREB plays an important role in up-regulation of c-fos mRNA level in LPA-stimulated Rat-2 fibroblast cells.
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Affiliation(s)
- Chang-Wook Lee
- Department of Molecular Biology, Helen L. Dorris Child and Adolescent Neuropsychiatric Disorder Institute, The Scripps Research Institute, La Jolla, California 92037, USA
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Gershenzon NI, Trifonov EN, Ioshikhes IP. The features of Drosophila core promoters revealed by statistical analysis. BMC Genomics 2006; 7:161. [PMID: 16790048 PMCID: PMC1538597 DOI: 10.1186/1471-2164-7-161] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2006] [Accepted: 06/21/2006] [Indexed: 11/19/2022] Open
Abstract
BACKGROUND Experimental investigation of transcription is still a very labor- and time-consuming process. Only a few transcription initiation scenarios have been studied in detail. The mechanism of interaction between basal machinery and promoter, in particular core promoter elements, is not known for the majority of identified promoters. In this study, we reveal various transcription initiation mechanisms by statistical analysis of 3393 nonredundant Drosophila promoters. RESULTS Using Drosophila-specific position-weight matrices, we identified promoters containing TATA box, Initiator, Downstream Promoter Element (DPE), and Motif Ten Element (MTE), as well as core elements discovered in Human (TFIIB Recognition Element (BRE) and Downstream Core Element (DCE)). Promoters utilizing known synergetic combinations of two core elements (TATA_Inr, Inr_MTE, Inr_DPE, and DPE_MTE) were identified. We also establish the existence of promoters with potentially novel synergetic combinations: TATA_DPE and TATA_MTE. Our analysis revealed several motifs with the features of promoter elements, including possible novel core promoter element(s). Comparison of Human and Drosophila showed consistent percentages of promoters with TATA, Inr, DPE, and synergetic combinations thereof, as well as most of the same functional and mutual positions of the core elements. No statistical evidence of MTE utilization in Human was found. Distinct nucleosome positioning in particular promoter classes was revealed. CONCLUSION We present lists of promoters that potentially utilize the aforementioned elements/combinations. The number of these promoters is two orders of magnitude larger than the number of promoters in which transcription initiation was experimentally studied. The sequences are ready to be experimentally tested or used for further statistical analysis. The developed approach may be utilized for other species.
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Affiliation(s)
- Naum I Gershenzon
- Department of Biomedical Informatics, The Ohio State University, 333 West 10Avenue, Columbus OH 43210, USA
- Department of Physics, Wright State University, Dayton OH 45435, USA
| | - Edward N Trifonov
- Genome Diversity Center, Institute of Evolution, University of Haifa, Haifa 31905, Israel
| | - Ilya P Ioshikhes
- Department of Biomedical Informatics, The Ohio State University, 333 West 10Avenue, Columbus OH 43210, USA
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Georgel PT. Chromatin potentiation of the hsp70 promoter is linked to GAGA-factor recruitment. Biochem Cell Biol 2005; 83:555-65. [PMID: 16094459 DOI: 10.1139/o05-060] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
The events leading to transcription initiation of the Drosophila melanogaster heat-shock protein (hsp)70 gene have been demonstrated to be directly connected with nucleosome remodeling factor and GAGA-dependent chromatin remodeling on its promoter region. To investigate the relative importance of the multiple GAGA-factor binding sites in the process of chromatin remodeling and their effect on DNA conformation, the position of nucleosomes over the proximal region of the promoter was mapped. No real-positioned nucleosome was detected. By matching the relative position of the GAGA-factor binding sites with the distribution of nucleosomes over the hsp70 promoter, the GAGA site 2 appeared to be the most accessible, i.e., located close to a nucleosomal edge or within the linker DNA. This result, combined with previous observations, suggest a link between increased GAGA-factor accessibility and efficiency of transcription initiation. The effect of GAGA-binding-site mutations, both individually and in combination, on DNA structure and nucleosome remodeling was assessed using free DNA and fly embryo extract chromatin templates assembled in vitro. Results indicated that both the number of functional sites and their positions within the chromatin were important determinants for nucleosome-remodeling efficiency. Ultimately, the degree of accessibility of the GAGA factor to its cognate binding site(s) appears to be proportional to chromatin-remodeling competency of the hsp70 promoter.
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Affiliation(s)
- Philippe T Georgel
- Department of Biological Sciences, Marshall University, Huntington, WV 25755, USA.
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Lund CV, Blancafort P, Popkov M, Barbas CF. Promoter-targeted phage display selections with preassembled synthetic zinc finger libraries for endogenous gene regulation. J Mol Biol 2004; 340:599-613. [PMID: 15210357 DOI: 10.1016/j.jmb.2004.04.057] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2004] [Revised: 04/21/2004] [Accepted: 04/22/2004] [Indexed: 11/30/2022]
Abstract
Regulation of endogenous gene expression has been achieved using synthetic zinc finger proteins fused to activation or repression domains, zinc finger transcription factors (TFZFs). Two key aspects of selective gene regulation using TFZFs are the accessibility of a zinc finger protein to its target DNA sequence and the interaction of the fused activation or repression domain with endogenous proteins. Previous work has shown that predicting a biologically active binding site at which a TF(ZF) can control gene expression is not always straightforward. Here, we used a library of preassembled three-finger zinc finger proteins (ZFPs) displayed on filamentous phage, and selected for ZFPs that bound along a 1.4 kb promoter fragment of the human ErbB-2 gene. Following affinity selection by phage display, 13 ZFPs were isolated and sequenced. Transcription factors were prepared by fusion of the zinc finger proteins with a VP64 activation domain or a KRAB repression domain and the transcriptional control imposed by these TFZFs was evaluated using luciferase reporter assays. Endogenous gene regulation activity was studied following retroviral delivery into A431 cells. Additional ZFP characterization included DNaseI footprinting to evaluate the integrity of each predicted protein:DNA interaction. The most promising TFZFs able to both up-regulate and down-regulate ErbB-2 expression were extended to six-finger proteins. The increased affinity and refined specificity demonstrated by the six-finger proteins provided reliable transcriptional control. As a result of studies with the six-finger proteins, the specific region of the promoter most accessible to transcriptional control by VP64-ZFP and KRAB-ZFP fusion proteins was elucidated and confirmed by DNaseI footprinting, flow cytometric analysis and immunofluorescence. The ZFP phage display library strategy disclosed here, coupled with the growing availability of genome sequencing information, provides a route to identifying gene-regulating TFZFs without the prerequisite of well-defined promoter elements.
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Affiliation(s)
- Caren V Lund
- The Skaggs Institute for Chemical Biology and Department of Molecular Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA
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McManus KJ, Hendzel MJ. Quantitative analysis of CBP- and P300-induced histone acetylations in vivo using native chromatin. Mol Cell Biol 2003; 23:7611-27. [PMID: 14560007 PMCID: PMC207635 DOI: 10.1128/mcb.23.21.7611-7627.2003] [Citation(s) in RCA: 68] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2003] [Revised: 07/02/2003] [Accepted: 07/17/2003] [Indexed: 11/20/2022] Open
Abstract
In vivo, histone tails are involved in numerous interactions, including those with DNA, adjacent histones, and other, nonhistone proteins. The amino termini are also the substrates for a number of enzymes, including histone acetyltransferases (HATs), histone deacetylases, and histone methyltransferases. Traditional biochemical approaches defining the substrate specificity profiles of HATs have been performed using purified histone tails, recombinant histones, or purified mononucleosomes as substrates. It is clear that the in vivo presentation of the substrate cannot be accurately represented by using these in vitro approaches. Because of the difficulty in translating in vitro results into in vivo situations, we developed a novel single-cell HAT assay that provides quantitative measurements of endogenous HAT activity. The HAT assay is performed under in vivo conditions by using the native chromatin structure as the physiological substrate. The assay combines the spatial resolving power of laser scanning confocal microscopy with simple statistical analyses to characterize CREB binding protein (CBP)- and P300-induced changes in global histone acetylation levels at specific lysine residues. Here we show that CBP and P300 exhibit unique substrate specificity profiles, consistent with the developmental and functional differences between the two HATs.
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Affiliation(s)
- Kirk J McManus
- Department of Oncology, Cross Cancer Institute, University of Alberta, Edmonton, Alberta, Canada T6G 1Z2
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McCall GE, Allen DL, Haddad F, Baldwin KM. Transcriptional regulation of IGF-I expression in skeletal muscle. Am J Physiol Cell Physiol 2003; 285:C831-9. [PMID: 12773315 DOI: 10.1152/ajpcell.00047.2003] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The present study investigated the role of transcription in the regulation of insulin-like growth factor (IGF)-I expression in skeletal muscle. RT-PCR was used to determine endogenous expression of IGF-I pre-mRNA and mRNA in control (Con) and functionally overloaded (FO) rat plantaris. The transcriptional activities of five different-length IGF-I promoter fragments controlling transcription of a firefly luciferase (FLuc) reporter gene were tested in vitro by transfection of myoblasts or in vivo during FO by direct gene transfer into the plantaris. Increased endogenous IGF-I gene transcription during 7 days of plantaris FO was evidenced by an approximately 140-160% increase (P < 0.0001) in IGF-I pre-mRNA (a transcriptional marker). IGF-I mRNA expression also increased by approximately 90% (P < 0.0001), and it was correlated (R = 0.93; P < 0.0001) with the pre-mRNA increases. The three longest IGF-I exon 1 promoters induced reporter gene expression in proliferating C2C12 and L6E9 myoblasts. In differentiated L6E9 myotubes, promoter activity increased approximately two- to threefold over myoblasts. Overexpression of calcineurin and MyoD increased the activity of the -852/+192 promoter in C2C12 myotubes by approximately 5- and approximately 18-fold, respectively. However, FO did not induce these exogenous promoter fragments. Nevertheless, the present findings are consistent with the hypothesis that the IGF-I gene is transcriptionally regulated during muscle hypertrophy in vivo as evidenced by the induction of the endogenous IGF-I pre-mRNA during plantaris FO. The exon 1 promoter region of the IGF-I gene is sufficient to direct inducible expression in vitro; however, an in vivo response to FO may require elements outside the -852/+346 region of the exon 1 IGF-I promoter or features inherent to the endogenous IGF-I gene.
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Affiliation(s)
- G E McCall
- University of California, Irvine, CA 92697-4560, USA
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Georgel PT, Fletcher TM, Hager GL, Hansen JC. Formation of higher-order secondary and tertiary chromatin structures by genomic mouse mammary tumor virus promoters. Genes Dev 2003; 17:1617-29. [PMID: 12842912 PMCID: PMC196134 DOI: 10.1101/gad.1097603] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
Agarose multigel electrophoresis has been used to characterize the structural features of isolated genomic mouse mammary tumor virus (MMTV) promoters. The mouse 3134 cells used for these studies contain approximately 200 stably integrated tandem repeats of a 2.4-kb MMTV promoter fragment. Inactive, basally active, and hormonally activated genomic promoters were liberated by restriction digestion of isolated nuclei, recovered in low-salt nuclear extracts, and electrophoresed in multigels consisting of nine individual agarose running gels. Specific bands were detected and characterized by Southern and Western blotting. We find that transcriptionally inactive promoters contain TBP and high levels of histone H1, and are present to varying extents in both untreated and dexamethasone (DEX)-treated 3134 cells. In contrast, the basally active promoter, present in untreated cells, is bound to RNA Pol II, TBP, and Oct1, contains acetylated H3 tail domains, and is depleted of histone H1. The DEX-activated promoter possessed similar composition as the basal promoter, but also contains stably bound Brg1. Strikingly, all forms of the MMTV promoter condense into higher-order secondary and/or tertiary chromatin structures in vitro in the presence of Mg2+. Thus, genomic MMTV promoter chromatin retains the ability to form classical higher-order structures under physiological salt conditions, even after dissociation of H1 and binding of several transcription factors and multiprotein complexes. These results suggest that transcriptionally active eukaryotic promoters may function in a locally folded chromatin environment in vivo.
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Affiliation(s)
- Philippe T Georgel
- Department of Biochemistry, University of Texas Health Science Center at San Antonio, San Antonio, Texas 78229-3900, USA
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Benecke A. Genomic Plasticity and Information Processing by Transcription Coregulators. ACTA ACUST UNITED AC 2003. [DOI: 10.1159/000070463] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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