1
|
Onufriev AV. Biologically relevant small variations of intra-cellular pH can have significant effect on stability of protein-DNA complexes, including the nucleosome. Front Mol Biosci 2023; 10:1067787. [PMID: 37143824 PMCID: PMC10151541 DOI: 10.3389/fmolb.2023.1067787] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2022] [Accepted: 01/16/2023] [Indexed: 05/06/2023] Open
Abstract
Stability of a protein-ligand complex may be sensitive to pH of its environment. Here we explore, computationally, stability of a set of protein-nucleic acid complexes using fundamental thermodynamic linkage relationship. The nucleosome, as well as an essentially random selection of 20 protein complexes with DNA or RNA, are included in the analysis. An increase in intra-cellular/intra-nuclear pH destabilizes most complexes, including the nucleosome. We propose to quantify the effect by ΔΔG0.3-the change in the binding free energy due to pH increase of 0.3 units, corresponding to doubling of the H + activity; variations of pH of this amplitude can occur in living cells, including in the course of the cell cycle, and in cancer cells relative to normal ones. We suggest, based on relevant experimental findings, a threshold of biological significance of 1 2 k B T ( ∼ 0.3 k c a l / m o l ) for changes of stability of chromatin-related protein-DNA complexes: a change in the binding affinity above the threshold may have biological consequences. We find that for 70% of the examined complexes, Δ Δ G 0.3 > 1 2 k B T (for 10%, ΔΔG0.3 is between 3 and 4 k B T). Thus, small but relevant variations of intra-nuclear pH of 0.3 may have biological consequences for many protein-nucleic acid complexes. The binding affinity between the histone octamer and its DNA, which directly affects the DNA accessibility in the nucleosome, is predicted to be highly sensitive to intra-nuclear pH. A variation of 0.3 units results in ΔΔG0.3 ∼ 10k B T ( ∼ 6 k c a l / m o l ) ; for spontaneous unwrapping of 20 bp long entry/exit fragments of the nucleosomal DNA, ΔΔG0.3 = 2.2k B T; partial disassembly of the nucleosome into the tetrasome is characterized by ΔΔG0.3 = 5.2k B T. The predicted pH -induced modulations of the nucleosome stability are significant enough to suggest that they may have consequences relevant to the biological function of the nucleosome. Accessibility of the nucleosomal DNA is predicted to positively correlate with pH variations during the cell cycle; an increase in intra-cellular pH seen in cancer cells is predicted to lead to a more accessible nucleosomal DNA; a drop in pH associated with apoptosis is predicted to make nucleosomal DNA less accessible. We speculate that processes that depend on accessibility to the DNA in the nucleosomes, such as transcription or DNA replication, might become upregulated due to relatively small, but nevertheless realistic increases of intra-nuclear pH.
Collapse
Affiliation(s)
- Alexey V. Onufriev
- Department of Physics, Virginia Tech, Blacksburg, Blacksburg, VA, United States
- Department of Computer Science, Virginia Tech, Blacksburg, Blacksburg, VA, United States
- Center from Soft Matter and Biological Physics, Virginia Tech, Blacksburg, VA, United States
- *Correspondence: Alexey V. Onufriev,
| |
Collapse
|
2
|
Onufriev AV, Schiessel H. The nucleosome: from structure to function through physics. Curr Opin Struct Biol 2019; 56:119-130. [DOI: 10.1016/j.sbi.2018.11.003] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2018] [Revised: 11/07/2018] [Accepted: 11/13/2018] [Indexed: 02/07/2023]
|
3
|
Fonseca M, Molina M, Winnik D, Busi M, Fariña J, Villalba L, Zapata P. Isolation of a laccase-coding gene from the lignin-degrading fungusPhlebia brevisporaBAFC 633 and heterologous expression inPichia pastoris. J Appl Microbiol 2018; 124:1454-1468. [DOI: 10.1111/jam.13720] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2017] [Revised: 01/26/2018] [Accepted: 01/29/2018] [Indexed: 11/28/2022]
Affiliation(s)
- M.I. Fonseca
- Laboratorio de Biotecnología Molecular; Instituto de Biotecnología Misiones; Facultad de Ciencias Exactas Químicas y Naturales; Universidad Nacional de Misiones; Posadas Misiones Argentina
| | - M.A. Molina
- Laboratorio de Biotecnología Molecular; Instituto de Biotecnología Misiones; Facultad de Ciencias Exactas Químicas y Naturales; Universidad Nacional de Misiones; Posadas Misiones Argentina
| | - D.L. Winnik
- Laboratorio de Biotecnología Molecular; Instituto de Biotecnología Misiones; Facultad de Ciencias Exactas Químicas y Naturales; Universidad Nacional de Misiones; Posadas Misiones Argentina
| | - M.V. Busi
- Centro de Estudios Fotosintéticos y Bioquímicos (CEFOBI-CONICET); Universidad Nacional de Rosario; Rosario Argentina
| | - J.I. Fariña
- Laboratorio de Biotecnología Fúngica; PROIMI-CONICET; Tucumán Argentina
| | - L.L. Villalba
- Laboratorio de Biotecnología Molecular; Instituto de Biotecnología Misiones; Facultad de Ciencias Exactas Químicas y Naturales; Universidad Nacional de Misiones; Posadas Misiones Argentina
| | - P.D. Zapata
- Laboratorio de Biotecnología Molecular; Instituto de Biotecnología Misiones; Facultad de Ciencias Exactas Químicas y Naturales; Universidad Nacional de Misiones; Posadas Misiones Argentina
| |
Collapse
|
4
|
Fenley AT, Anandakrishnan R, Kidane YH, Onufriev AV. Modulation of nucleosomal DNA accessibility via charge-altering post-translational modifications in histone core. Epigenetics Chromatin 2018; 11:11. [PMID: 29548294 PMCID: PMC5856334 DOI: 10.1186/s13072-018-0181-5] [Citation(s) in RCA: 58] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2017] [Accepted: 03/06/2018] [Indexed: 12/20/2022] Open
Abstract
BACKGROUND Controlled modulation of nucleosomal DNA accessibility via post-translational modifications (PTM) is a critical component to many cellular functions. Charge-altering PTMs in the globular histone core-including acetylation, phosphorylation, crotonylation, propionylation, butyrylation, formylation, and citrullination-can alter the strong electrostatic interactions between the oppositely charged nucleosomal DNA and the histone proteins and thus modulate accessibility of the nucleosomal DNA, affecting processes that depend on access to the genetic information, such as transcription. However, direct experimental investigation of the effects of these PTMs is very difficult. Theoretical models can rationalize existing observations, suggest working hypotheses for future experiments, and provide a unifying framework for connecting PTMs with the observed effects. RESULTS A physics-based framework is proposed that predicts the effect of charge-altering PTMs in the histone core, quantitatively for several types of lysine charge-neutralizing PTMs including acetylation, and qualitatively for all phosphorylations, on the nucleosome stability and subsequent changes in DNA accessibility, making a connection to resulting biological phenotypes. The framework takes into account multiple partially assembled states of the nucleosome at the atomic resolution. The framework is validated against experimentally known nucleosome stability changes due to the acetylation of specific lysines, and their effect on transcription. The predicted effect of charge-altering PTMs on DNA accessibility can vary dramatically, from virtually none to a strong, region-dependent increase in accessibility of the nucleosomal DNA; in some cases, e.g., H4K44, H2AK75, and H2BK57, the effect is significantly stronger than that of the extensively studied acetylation sites such H3K56, H3K115 or H3K122. Proximity to the DNA is suggestive of the strength of the PTM effect, but there are many exceptions. For the vast majority of charge-altering PTMs, the predicted increase in the DNA accessibility should be large enough to result in a measurable modulation of transcription. However, a few possible PTMs, such as acetylation of H4K77, counterintuitively decrease the DNA accessibility, suggestive of the repressed chromatin. A structural explanation for the phenomenon is provided. For the majority of charge-altering PTMs, the effect on DNA accessibility is simply additive (noncooperative), but there are exceptions, e.g., simultaneous acetylation of H4K79 and H3K122, where the combined effect is amplified. The amplification is a direct consequence of the nucleosome-DNA complex having more than two structural states. The effect of individual PTMs is classified based on changes in the accessibility of various regions throughout the nucleosomal DNA. The PTM's resulting imprint on the DNA accessibility, "PTMprint," is used to predict effects of many yet unexplored PTMs. For example, acetylation of H4K44 yields a PTMprint similar to the PTMprint of H3K56, and thus acetylation of H4K44 is predicted to lead to a wide range of strong biological effects. CONCLUSION Charge-altering post-translational modifications in the relatively unexplored globular histone core may provide a precision mechanism for controlling accessibility to the nucleosomal DNA.
Collapse
Affiliation(s)
- Andrew T. Fenley
- Department of Physics, Virginia Tech, 2160C Torgersen Hall, Blacksburg, VA 24061 USA
| | | | - Yared H. Kidane
- Genetics, Bioinformatics and Computational Biology Program, Virginia Tech, Blacksburg, VA 24061 USA
| | - Alexey V. Onufriev
- Department of Physics, Virginia Tech, 2160C Torgersen Hall, Blacksburg, VA 24061 USA
- Genetics, Bioinformatics and Computational Biology Program, Virginia Tech, Blacksburg, VA 24061 USA
- Department of Computer Science, Virginia Tech, Blacksburg, VA 24061 USA
- Center for Soft Matter and Biological Physics, Virginia Tech, Blacksburg, VA 24061 USA
| |
Collapse
|
5
|
Ichikawa Y, Morohashi N, Tomita N, Mitchell AP, Kurumizaka H, Shimizu M. Sequence-directed nucleosome-depletion is sufficient to activate transcription from a yeast core promoter in vivo. Biochem Biophys Res Commun 2016; 476:57-62. [PMID: 27208777 DOI: 10.1016/j.bbrc.2016.05.063] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2016] [Accepted: 05/12/2016] [Indexed: 11/18/2022]
Abstract
Nucleosome-depleted regions (NDRs) (also called nucleosome-free regions or NFRs) are often found in the promoter regions of many yeast genes, and are formed by multiple mechanisms, including the binding of activators and enhancers, the actions of chromatin remodeling complexes, and the specific DNA sequences themselves. However, it remains unclear whether NDR formation per se is essential for transcriptional activation. Here, we examined the relationship between nucleosome organization and gene expression using a defined yeast reporter system, consisting of the CYC1 minimal core promoter and the lacZ gene. We introduced simple repeated sequences that should be either incorporated in nucleosomes or excluded from nucleosomes in the site upstream of the TATA boxes. The (CTG)12, (GAA)12 and (TGTAGG)6 inserts were incorporated into a positioned nucleosome in the core promoter region, and did not affect the reporter gene expression. In contrast, the insertion of (CGG)12, (TTAGGG)6, (A)34 or (CG)8 induced lacZ expression by 10-20 fold. Nucleosome mapping analyses revealed that the inserts that induced the reporter gene expression prevented nucleosome formation, and created an NDR upstream of the TATA boxes. Thus, our results demonstrated that NDR formation dictated by DNA sequences is sufficient for transcriptional activation from the core promoter in vivo.
Collapse
Affiliation(s)
- Yuichi Ichikawa
- Graduate School of Advanced Science and Engineering/RISE, Waseda University, 2-2 Wakamatsu-cho, Shinjuku-ku, Tokyo 162-8640, Japan; Department of Biological Sciences, Carnegie Mellon University, 4400 Fifth Avenue, Pittsburgh, PA 15213, USA
| | - Nobuyuki Morohashi
- Program in Chemistry and Life Science, School of Science and Engineering, Department of Chemistry, Graduate School of Science and Engineering, Meisei University, 2-1-1 Hodokubo, Hino, Tokyo 191-8506, Japan
| | - Nobuyuki Tomita
- Program in Chemistry and Life Science, School of Science and Engineering, Department of Chemistry, Graduate School of Science and Engineering, Meisei University, 2-1-1 Hodokubo, Hino, Tokyo 191-8506, Japan
| | - Aaron P Mitchell
- Department of Biological Sciences, Carnegie Mellon University, 4400 Fifth Avenue, Pittsburgh, PA 15213, USA
| | - Hitoshi Kurumizaka
- Graduate School of Advanced Science and Engineering/RISE, Waseda University, 2-2 Wakamatsu-cho, Shinjuku-ku, Tokyo 162-8640, Japan
| | - Mitsuhiro Shimizu
- Program in Chemistry and Life Science, School of Science and Engineering, Department of Chemistry, Graduate School of Science and Engineering, Meisei University, 2-1-1 Hodokubo, Hino, Tokyo 191-8506, Japan.
| |
Collapse
|
6
|
Zheng Y, Li X, Hu H. Computational discovery of feature patterns in nucleosomal DNA sequences. Genomics 2014; 104:87-95. [PMID: 25063528 DOI: 10.1016/j.ygeno.2014.07.002] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2013] [Revised: 04/18/2014] [Accepted: 07/15/2014] [Indexed: 11/27/2022]
Abstract
The identification of important factors that affect nucleosome formation is critical to clarify nucleosome-forming mechanisms and the role of the nucleosome in gene regulation. Various features reported in the literature led to our hypothesis that multiple features can together contribute to nucleosome formation. Therefore, we compiled 779 features and developed a pattern discovery and scoring algorithm FFN (Finding Features for Nucleosomes) to identify feature patterns that are differentially enriched in nucleosome-forming sequences and nucleosome-depletion sequences. Applying FFN to genome-wide nucleosome occupancy data in yeast and human, we identified statistically significant feature patterns that may influence nucleosome formation, many of which are common to the two species. We found that both sequence and structural features are important in nucleosome occupancy prediction. We discovered that, even for the same feature combinations, variations in feature values may lead to differences in predictive power. We demonstrated that the identified feature patterns could be used to assist nucleosomal sequence prediction.
Collapse
Affiliation(s)
- Yiyu Zheng
- Department of Electrical Engineering and Computer Science, University Of Central Florida, Orlando, FL 32816, USA
| | - Xiaoman Li
- Department of Electrical Engineering and Computer Science, University Of Central Florida, Orlando, FL 32816, USA; Burnett School of Biomedical Science, University Of Central Florida, Orlando, FL 32816, USA
| | - Haiyan Hu
- Department of Electrical Engineering and Computer Science, University Of Central Florida, Orlando, FL 32816, USA.
| |
Collapse
|
7
|
Determinants of nucleosome positioning. Nat Struct Mol Biol 2013; 20:267-73. [PMID: 23463311 DOI: 10.1038/nsmb.2506] [Citation(s) in RCA: 452] [Impact Index Per Article: 41.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2012] [Accepted: 01/03/2013] [Indexed: 01/09/2023]
Abstract
Nucleosome positioning is critical for gene expression and most DNA-related processes. Here we review the dominant patterns of nucleosome positioning that have been observed and summarize the current understanding of their underlying determinants. The genome-wide pattern of nucleosome positioning is determined by the combination of DNA sequence, ATP-dependent nucleosome remodeling enzymes and transcription factors that include activators, components of the preinitiation complex and elongating RNA polymerase II. These determinants influence each other such that the resulting nucleosome positioning patterns are likely to differ among genes and among cells in a population, with consequent effects on gene expression.
Collapse
|
8
|
Rodriguez J, Tsukiyama T. ATR-like kinase Mec1 facilitates both chromatin accessibility at DNA replication forks and replication fork progression during replication stress. Genes Dev 2013; 27:74-86. [PMID: 23307868 DOI: 10.1101/gad.202978.112] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Faithful DNA replication is essential for normal cell division and differentiation. In eukaryotic cells, DNA replication takes place on chromatin. This poses the critical question as to how DNA replication can progress through chromatin, which is inhibitory to all DNA-dependent processes. Here, we developed a novel genome-wide method to measure chromatin accessibility to micrococcal nuclease (MNase) that is normalized for nucleosome density, the NCAM (normalized chromatin accessibility to MNase) assay. This method enabled us to discover that chromatin accessibility increases specifically at and ahead of DNA replication forks in normal S phase and during replication stress. We further found that Mec1, a key regulatory ATR-like kinase in the S-phase checkpoint, is required for both normal chromatin accessibility around replication forks and replication fork rate during replication stress, revealing novel functions for the kinase in replication stress response. These results suggest a possibility that Mec1 may facilitate DNA replication fork progression during replication stress by increasing chromatin accessibility around replication forks.
Collapse
Affiliation(s)
- Jairo Rodriguez
- Fred Hutchinson Cancer Research Center, Division of Basic Sciences, Seattle, Washington 98109, USA
| | | |
Collapse
|
9
|
Vedel V, Scotti I. Promoting the promoter. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2011; 180:182-189. [PMID: 21421359 DOI: 10.1016/j.plantsci.2010.09.009] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/01/2010] [Revised: 09/23/2010] [Accepted: 09/27/2010] [Indexed: 05/28/2023]
Abstract
Recent evolutionary studies clearly indicate that evolution is mainly driven by changes in the complex mechanisms of gene regulation and not solely by polymorphism in protein-encoding genes themselves. After a short description of the cis-regulatory mechanism, we intend in this review to argue that by applying newly available technologies and by merging research areas such as evolutionary and developmental biology, population genetics, ecology and molecular cell biology it is now possible to study evolution in an integrative way. We contend that, by analysing the effects of promoter sequence variation on phenotypic diversity in natural populations, we will soon be able to break the barrier between the study of extant genetic variability and the study of major developmental changes. This will lead to an integrative view of evolution at different scales. Because of their sessile nature and their continuous development, plants must permanently regulate their gene expression to react to their environment, and can, therefore, be considered as a remarkable model for these types of studies.
Collapse
Affiliation(s)
- Vincent Vedel
- UMR ECOFOG, INRA, Ecological genetic, Campus Agronomique de Kourou, BP 709, 97387 Kourou, French Guiana.
| | | |
Collapse
|
10
|
Abstract
Sequence-specific transcription factors (TFs) play a central role in regulating transcription initiation by directing the recruitment and activity of the general transcription machinery and accessory factors. It is now well established that many of the effects exerted by TFs in eukaryotes are mediated through interactions with a host of coregulators that modify the chromatin state, resulting in a more open (in case of activation) or closed conformation (in case of repression). The relationship between TFs and chromatin is a two-way street, however, as chromatin can in turn influence the recognition and binding of target sequences by TFs. The aim of this chapter is to highlight how this dynamic interplay between TF-directed remodelling of chromatin and chromatin-adjusted targeting of TF binding determines where and how transcription is initiated, and to what degree it is productive.
Collapse
|
11
|
Determination of the core promoter regions of the Saccharomyces cerevisiae RPS3 gene. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2009; 1789:741-50. [PMID: 19853675 DOI: 10.1016/j.bbagrm.2009.10.002] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/09/2009] [Revised: 10/12/2009] [Accepted: 10/13/2009] [Indexed: 12/13/2022]
Abstract
Ribosomal protein genes (RPG), which are scattered throughout the genomes of all eukaryotes, are subjected to coordinated expression. In yeast, the expression of RPGs is highly regulated, mainly at the transcriptional level. Recent research has found that many ribosomal proteins (RPs) function in multiple processes in addition to protein synthesis. Therefore, detailed knowledge of promoter architecture as well as gene regulation is important in understanding the multiple cellular processes mediated by RPGs. In this study, we investigated the functional architecture of the yeast RPS3 promoter and identified many putative cis-elements. Using beta-galactosidase reporter analysis and EMSA, the core promoter of RPS3 containing UASrpg and T-rich regions was corroborated. Moreover, the promoter occupancy of RPS3 by three transcription factors was confirmed. Taken together, our results further the current understanding of the promoter architecture and trans-elements of the Saccharomyces cerevisiae RPS3 gene.
Collapse
|
12
|
Ransom M, Williams SK, Dechassa ML, Das C, Linger J, Adkins M, Liu C, Bartholomew B, Tyler JK. FACT and the proteasome promote promoter chromatin disassembly and transcriptional initiation. J Biol Chem 2009; 284:23461-71. [PMID: 19574230 DOI: 10.1074/jbc.m109.019562] [Citation(s) in RCA: 52] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
The packaging of the eukaryotic genome into chromatin represses gene expression by blocking access of the general transcription machinery to the underlying DNA sequences. Accordingly, eukaryotes have developed a variety of mechanisms to disrupt, alter, or disassemble nucleosomes from promoter regions and open reading frames to allow transcription to occur. Although we know that chromatin disassembly from the yeast PHO5 promoter is triggered by the Pho4 activator, the mechanism is far from clear. Here we show that the Pho4 activator can occupy its nucleosome-bound DNA binding site within the PHO5 promoter. In contrast to the role of Saccharomyces cerevisiae FACT (facilitates chromatin transcription) complex in assembling chromatin within open reading frames, we find that FACT is involved in the disassembly of histones H2A/H2B from the PHO5 promoter during transcriptional induction. We have also discovered that the proteasome is required for efficient chromatin disassembly and transcriptional induction from the PHO5 promoter. Mutants of the degradation function of the proteasome have a defect in recruitment of the Pho4 activator, whereas mutants of the ATPase cap of the proteasome do recruit Pho4 but are still delayed for chromatin assembly. Finally, we rule out the possibility that the proteasome or ATPase cap is driving chromatin disassembly via a potential ATP-dependent chromatin remodeling activity.
Collapse
Affiliation(s)
- Monica Ransom
- Department of Biochemistry, University of Colorado School of Medicine, Aurora, Colorado 80045, USA
| | | | | | | | | | | | | | | | | |
Collapse
|
13
|
Ababneh AM. The role of polarization interactions in the wrapping/unwrapping of nucleosomal DNA around the histone octamer: Implications to gene regulation. J Theor Biol 2009; 258:229-39. [DOI: 10.1016/j.jtbi.2009.02.006] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2008] [Revised: 02/10/2009] [Accepted: 02/12/2009] [Indexed: 10/21/2022]
|
14
|
Bomble YJ, Case DA. Multiscale modeling of nucleic acids: insights into DNA flexibility. Biopolymers 2008; 89:722-31. [PMID: 18412139 DOI: 10.1002/bip.21000] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
The elastic rod theory is used together with all-atom normal mode analysis in implicit solvent to characterize the mechanical flexibility of duplex DNA. The bending, twisting, stretching rigidities extracted from all-atom simulations (on linear duplexes from 60 to 150 base pairs in length and from 94-bp minicircles) are in reasonable agreement with experimental results. We focus on salt concentration and sequence effects on the overall flexibility. Bending persistence lengths are about 20% higher than most experimental estimates, but the transition from low-salt to high-salt behavior is reproduced well, as is the dependence of the stretching modulus on salt (which is opposite to that of bending). CTG and CGG trinucleotide repeats, responsible for several degenerative disorders, are found to be more flexible than random DNA, in agreement with several recent studies, whereas poly(dA).poly(dT) is the stiffest sequence we have encountered. The results suggest that current all-atom potentials, which were parameterized on small molecules and short oligonucleotides, also provide a useful description of duplex DNA at much longer length scales.
Collapse
Affiliation(s)
- Yannick J Bomble
- Department of Molecular Biology, The Scripps Research Institute, La Jolla, CA 92122, USA
| | | |
Collapse
|
15
|
Sumida N, Nishikawa JI, Kishi H, Amano M, Furuya T, Sonobe H, Ohyama T. A designed curved DNA segment that is a remarkable activator of eukaryotic transcription. FEBS J 2006; 273:5691-702. [PMID: 17212784 DOI: 10.1111/j.1742-4658.2006.05557.x] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
To identify artificial DNA segments that can stably express transgenes in the genome of host cells, we built a series of curved DNA segments that mimic a left-handed superhelical structure. Curved DNA segments of 288 bp (T32) and 180 bp (T20) were able to activate transcription from the herpes simplex virus thymidine kinase (tk) promoter by approximately 150-fold and 70-fold, respectively, compared to a control in a transient transfection assay in COS-7 cells. The T20 segment was also able to activate transcription from the human adenovirus type 2 E1A promoter with an 18-fold increase in the same assay system, and also activated transcription from the tk promoter on episomes in COS-7 cells. We also established five HeLa cell lines with genomes containing T20 upstream of the transgene promoter and control cell lines with T20 deleted from the transgene locus. Interestingly, T20 was found to activate transcription in all the stable transformants, irrespective of the locus. This suggests that the T20 segment may allow stable expression of transgenes, which is of importance in many fields, and may also be useful for the construction of nonviral vectors for gene therapy.
Collapse
Affiliation(s)
- Noriyuki Sumida
- Department of Biology, Faculty of Science and Engineering, Konan University, Kobe, Japan
| | | | | | | | | | | | | |
Collapse
|
16
|
Morohashi N, Yamamoto Y, Kuwana S, Morita W, Shindo H, Mitchell AP, Shimizu M. Effect of sequence-directed nucleosome disruption on cell-type-specific repression by alpha2/Mcm1 in the yeast genome. EUKARYOTIC CELL 2006; 5:1925-33. [PMID: 16980406 PMCID: PMC1694797 DOI: 10.1128/ec.00105-06] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
In Saccharomyces cerevisiae, a-cell-specific genes are repressed in MATalpha cells by alpha2/Mcm1, acting in concert with the Ssn6-Tup1 corepressors and the Isw2 chromatin remodeling complex, and nucleosome positioning has been proposed as one mechanism of repression. However, prior studies showed that nucleosome positioning is not essential for repression by alpha2/Mcm1 in artificial reporter plasmids, and the importance of the nucleosome positioning remains questionable. We have tested the function of positioned nucleosomes through alteration of genomic chromatin at the a-cell-specific gene BAR1. We report here that a positioned nucleosome in the BAR1 promoter is disrupted in cis by the insertion of diverse DNA sequences such as poly(dA) . poly(dT) and poly(dC-dG) . poly(dC-dG), leading to inappropriate partial derepression of BAR1. Also, we show that isw2 mutation causes loss of nucleosome positioning in BAR1 in MATalpha cells as well as partial disruption of repression. Thus, nucleosome positioning is required for full repression, but loss of nucleosome positioning is not sufficient to relieve repression completely. Even though disruption of nucleosome positioning by the cis- and trans-acting modulators of chromatin has a modest effect on the level of transcription, it causes significant degradation of the alpha-mating pheromone in MATalpha cells, thereby affecting its cell type identity. Our results illustrate a useful paradigm for analysis of chromatin structural effects at genomic loci.
Collapse
Affiliation(s)
- Nobuyuki Morohashi
- Department of Chemistry, Meisei University, 2-1-1 Hodokubo, Hino, Tokyo 191-8506, Japan
| | | | | | | | | | | | | |
Collapse
|
17
|
Bao Y, White CL, Luger K. Nucleosome core particles containing a poly(dA.dT) sequence element exhibit a locally distorted DNA structure. J Mol Biol 2006; 361:617-24. [PMID: 16860337 DOI: 10.1016/j.jmb.2006.06.051] [Citation(s) in RCA: 65] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2006] [Revised: 06/15/2006] [Accepted: 06/21/2006] [Indexed: 11/29/2022]
Abstract
Poly(dA.dT) DNA sequence elements are thought to promote transcription by either excluding nucleosomes or by altering their structural or dynamic properties. Here, the stability and structure of a defined nucleosome core particle containing a 16 base-pair poly(dA.dT) element (A16 NCP) was investigated. The A16 NCP requires a significantly higher temperature for histone octamer sliding in vitro compared to comparable nucleosomes that do not contain a poly(dA.dT) element. Fluorescence resonance energy transfer showed that the interactions between the nucleosomal DNA ends and the histone octamer were destabilized in A16 NCP. The crystal structure of A16 NCP was determined to a resolution of 3.2 A. The overall structure was maintained except for local deviations in DNA conformation. These results are consistent with previous in vivo and in vitro observations that poly(dA.dT) elements cause only modest changes in DNA accessibility and modest increases in steady-state transcription levels.
Collapse
Affiliation(s)
- Yunhe Bao
- Howard Hughes Medical Institute and Department of Biochemistry and Molecular Biology, Colorado State University, Fort Collins, CO 80523-1870, USA
| | | | | |
Collapse
|
18
|
Ishida C, Aranda C, Valenzuela L, Riego L, Deluna A, Recillas-Targa F, Filetici P, López-Revilla R, González A. The UGA3-GLT1 intergenic region constitutes a promoter whose bidirectional nature is determined by chromatin organization in Saccharomyces cerevisiae. Mol Microbiol 2006; 59:1790-806. [PMID: 16553884 DOI: 10.1111/j.1365-2958.2006.05055.x] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Transcription of an important number of divergent genes of Saccharomyces cerevisiae is controlled by intergenic regions, which constitute factual bidirectional promoters. However, few of such promoters have been characterized in detail. The analysis of the UGA3-GLT1 intergenic region has provided an interesting model to study the joint action of two global transcriptional activators that had been considered to act independently. Our results show that Gln3p and Gcn4p exert their effect upon cis-acting elements, which are shared in a bidirectional promoter. Accordingly, when yeast is grown on a low-quality nitrogen source, or under amino acid deprivation, the expression of both UGA3 and GLT1 is induced through the action of both these global transcriptional modulators that bind to a region of the bidirectional promoter. In addition, we demonstrate that chromatin organization plays a major role in the bidirectional properties of the UGA3-GLT1 promoter, through the action of an upstream Abf1p-binding consensus sequence and a polydAdT(tract). Mutations in these cis-elements differentially affect transcription of UGA3 and GLT1, and thus alter the overall relative expression. This is the first example of an intergenic region constituting a promoter whose bidirectional character is determined by chromatin organization.
Collapse
Affiliation(s)
- Cecilia Ishida
- Departamento de Genética Molecular, Instituto de Fisiología Celular, Universidad Nacional Autónoma de México, México
| | | | | | | | | | | | | | | | | |
Collapse
|
19
|
Chodaparambil JV, Edayathumangalam RS, Bao Y, Park YJ, Luger K. Nucleosome structure and function. ERNST SCHERING RESEARCH FOUNDATION WORKSHOP 2006:29-46. [PMID: 16568947 DOI: 10.1007/3-540-37633-x_2] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
It is now widely recognized that the packaging of genomic DNA, together with core histones, linker histones, and other functional proteins into chromatin profoundly influences nuclear processes such as transcription, replication, DNA repair, and recombination. How chromatin structure modulates the expression of knowledge encoded in eukaryotic genomes, and how these processes take place within the context of a highly complex and compacted genomic chromatin environment remains a major unresolved question in biology. Here we review recent advances in nucleosome structure and dynamics.
Collapse
Affiliation(s)
- J V Chodaparambil
- Department of Biochemistry and Molecular Biology, Colorado State University, Fort Collins 80523-1870, USA
| | | | | | | | | |
Collapse
|
20
|
Kanhere A, Bansal M. Structural properties of promoters: similarities and differences between prokaryotes and eukaryotes. Nucleic Acids Res 2005; 33:3165-75. [PMID: 15939933 PMCID: PMC1143579 DOI: 10.1093/nar/gki627] [Citation(s) in RCA: 92] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
During the process of transcription, RNA polymerase can exactly locate a promoter sequence in the complex maze of a genome. Several experimental studies and computational analyses have shown that the promoter sequences apparently possess some special properties, such as unusual DNA structures and low stability, which make them distinct from the rest of the genome. But most of these studies have been carried out on a particular set of promoter sequences or on promoter sequences from similar organisms. To examine whether the promoters from a wide variety of organisms share these special properties, we have carried out an analysis of sets of promoters from bacteria, vertebrates and plants. These promoters were analyzed with respect to the prediction of three different properties, such as DNA curvature, bendability and stability, which are relevant to transcription. All the promoter sequences are predicted to share certain features, such as stability and bendability profiles, but there are significant differences in DNA curvature profiles and nucleotide composition between the different organisms. These similarities and differences are correlated with some of the known facts about transcription process in the promoters from the three groups of organisms.
Collapse
Affiliation(s)
| | - Manju Bansal
- To whom correspondence should be addressed. Tel: +91 80 2293 2534; Fax: +91 80 2360 0535;
| |
Collapse
|
21
|
Chakravarthy S, Park YJ, Chodaparambil J, Edayathumangalam RS, Luger K. Structure and dynamic properties of nucleosome core particles. FEBS Lett 2004; 579:895-8. [PMID: 15680970 DOI: 10.1016/j.febslet.2004.11.030] [Citation(s) in RCA: 62] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2004] [Accepted: 11/04/2004] [Indexed: 11/16/2022]
Abstract
It is now widely recognized that the packaging of genomic DNA, together with core histones, linker histones, and other functional proteins into chromatin profoundly influences nuclear processes such as transcription, replication, DNA repair, and recombination. Whereas earlier structural studies portrayed nucleosomes (the basic repeating unit of chromatin) as monolithic and static macromolecular assemblies, we now know that they are highly dynamic and capable of extensive crosstalk with the cellular machinery. Histone variants have evolved to locally alter chromatin structure, whereas histone chaperones and other cellular factors promote histone exchange and chromatin fluidity. Both of these phenomena likely facilitate interconversion between different chromatin states that show varying degrees of transcriptional activity.
Collapse
Affiliation(s)
- Srinivas Chakravarthy
- Department of Biochemistry and Molecular Biology, Colorado State University, Fort Collins, CO 80523-1870, USA
| | | | | | | | | |
Collapse
|
22
|
White CL, Luger K. Defined structural changes occur in a nucleosome upon Amt1 transcription factor binding. J Mol Biol 2004; 342:1391-402. [PMID: 15364568 DOI: 10.1016/j.jmb.2004.07.080] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2004] [Revised: 07/17/2004] [Accepted: 07/20/2004] [Indexed: 11/19/2022]
Abstract
Here, we study the binding of the transcription factor Amt1 to its recognition site near the dyad of a highly positioned nucleosome. We find that the DNA binding domain of Amt1 binds to nucleosomes with only threefold reduced affinity compared to free DNA. We show by fluorescence resonance energy transfer that factor binding at the nucleosomal dyad is accompanied by the partial dissociation of the DNA ends from the histone octamer surface; however, no dissociation or subtle rearrangements of histone subunits is observed. A poly(dA.dT) DNA sequence element adjacent to the transcription factor binding site appears to facilitate factor binding, but is not essential. The methods that we describe here characterize for the first time the subtle structural changes that occur upon transcription factor binding to nucleosomes, and demonstrate the ability of the nucleosome to structurally adapt in response to outside influences.
Collapse
Affiliation(s)
- Cindy L White
- Department of Biochemistry and Molecular Biology, Colorado State University, Fort Collins, CO-80523-1870, USA
| | | |
Collapse
|
23
|
Shivaswamy S, Kassavetis GA, Bhargava P. High-level activation of transcription of the yeast U6 snRNA gene in chromatin by the basal RNA polymerase III transcription factor TFIIIC. Mol Cell Biol 2004; 24:3596-606. [PMID: 15082757 PMCID: PMC387771 DOI: 10.1128/mcb.24.9.3596-3606.2004] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Transcription of the U6 snRNA gene (SNR6) in Saccharomyces cerevisiae by RNA polymerase III (pol III) requires TFIIIC and its box A and B binding sites. In contrast, TFIIIC has little or no effect on SNR6 transcription with purified components in vitro due to direct recognition of the SNR6 TATA box by TFIIIB. When SNR6 was assembled into chromatin in vitro by use of the Drosophila melanogaster S-190 extract, transcription of these templates with highly purified yeast pol III, TFIIIC, and TFIIIB displayed a near-absolute requirement for TFIIIC but yielded a 5- to 15-fold-higher level of transcription relative to naked DNA (>100-fold activation over repressed chromatin). Analysis of chromatin structure demonstrated that TFIIIC binding leads to remodeling of U6 gene chromatin, resulting in positioning of a nucleosome between boxes A and B. The resulting folding of the intervening DNA into the nucleosome could bring the suboptimally spaced SNR6 box A and B elements into greater proximity and thus facilitate activation of transcription. In the absence of ATP, however, the binding of TFIIIC to box B in chromatin was not accompanied by remodeling and the transcription activation was approximately 35% of that seen in its presence, implying that both TFIIIC binding and ATP-dependent chromatin remodeling were required for the full activation of the gene. Our results suggest that TFIIIC, which is a basal transcription factor of pol III, also plays a direct role in remodeling chromatin on the SNR6 gene.
Collapse
Affiliation(s)
- Sushma Shivaswamy
- Centre for Cellular and Molecular Biology, Tarnaka, Hyderabad 500007, India
| | | | | |
Collapse
|
24
|
Nishikawa JI, Amano M, Fukue Y, Tanaka S, Kishi H, Hirota Y, Yoda K, Ohyama T. Left-handedly curved DNA regulates accessibility to cis-DNA elements in chromatin. Nucleic Acids Res 2004; 31:6651-62. [PMID: 14602926 PMCID: PMC275550 DOI: 10.1093/nar/gkg854] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
There is little information on chromatin structure that allows access of trans-acting transcription factors. Logically, the target DNA elements become accessible by either exposing themselves towards the environment on the surface of the nucleosome, or making the regulatory region free of the nucleosome. Here, we demonstrate that curved DNA that mimics a negative supercoil can play both roles in the promoter region. By constructing 35 reporter plasmids and using in vivo assay systems, we scrutinized the relationships between upstream DNA geometry, nucleosome positioning and promoter activity. When the left-handedly curved DNA was linked to the herpes simplex virus thymidine kinase (HSV tk) promoter at a specific rotational phase and distance, the curved DNA attracted the nucleosome and the TATA box was thereby left in the linker DNA with its minor groove facing outwards, which led to the activation of transcription. Neither planar curving, nor right-handedly curved DNA nor straight DNA had this effect. Our results seem to provide a clue for solving the problem of why curved DNA is often located near transcriptional control regions.
Collapse
Affiliation(s)
- Jun-ichi Nishikawa
- Department of Biology, Faculty of Science and Engineering, Konan University, 8-9-1 Okamoto, Higashinada-ku, Kobe 658-8501, Japan
| | | | | | | | | | | | | | | |
Collapse
|
25
|
Bi X, Yu Q, Sandmeier JJ, Zou Y. Formation of boundaries of transcriptionally silent chromatin by nucleosome-excluding structures. Mol Cell Biol 2004; 24:2118-31. [PMID: 14966290 PMCID: PMC350542 DOI: 10.1128/mcb.24.5.2118-2131.2004] [Citation(s) in RCA: 71] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The eukaryotic genome is divided into chromosomal domains of distinct gene activities. Transcriptionally silent chromatin tends to encroach upon active chromatin. Barrier elements that can block the spread of silent chromatin have been documented, but the mechanisms of their function are not resolved. We show that the prokaryotic LexA protein can function as a barrier to the propagation of transcriptionally silent chromatin in yeast. The barrier function of LexA correlates with its ability to disrupt local chromatin structure. In accord with this, (CCGNN)(n) and poly(dA-dT), both of which do not favor nucleosome formation, can also act as efficient boundaries of silent chromatin. Moreover, we show that a Rap1p-binding barrier element also disrupts chromatin structure. These results demonstrate that nucleosome exclusion is one of the mechanisms for the establishment of boundaries of silent chromatin domains.
Collapse
Affiliation(s)
- Xin Bi
- Department of Biochemistry, University of Nebraska-Lincoln, Lincoln, Nebraska 68588, USA.
| | | | | | | |
Collapse
|
26
|
Morse RH. Getting into chromatin: how do transcription factors get past the histones? Biochem Cell Biol 2003; 81:101-12. [PMID: 12897843 DOI: 10.1139/o03-039] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
Transcriptional activators and the general transcription machinery must gain access to DNA that in eukaryotes may be packaged into nucleosomes. In this review, I discuss this problem from the standpoint of the types of chromatin structures that these DNA-binding proteins may encounter, and the mechanisms by which they may contend with various chromatin structures. The discussion includes consideration of experiments in which chromatin structure is manipulated in vivo to confront activators with nucleosomal binding sites, and the roles of nucleosome dynamics and activation domains in facilitating access to such sites. Finally, the role of activators in facilitating access of the general transcriptional machinery to sites in chromatin is discussed.
Collapse
Affiliation(s)
- Randall H Morse
- Wadsworth Center, New York State Department of Health and Department of Biomedical Sciences, University at Albany School of Public Health, 12201-2002, USA.
| |
Collapse
|
27
|
Kwik-Uribe CL, Reaney S, Zhu Z, Smith D. Alterations in cellular IRP-dependent iron regulation by in vitro manganese exposure in undifferentiated PC12 cells. Brain Res 2003; 973:1-15. [PMID: 12729948 DOI: 10.1016/s0006-8993(03)02457-0] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
Manganese (Mn) may interfere with iron regulation by altering the binding of iron regulatory proteins (IRPs) to their response elements found on the mRNA encoding proteins critical to iron homeostasis. To explore this, the effects of 24-h in vitro manganese exposure (1, 10, 50, and 200 microM Mn) on: (i) total intracellular and labile iron concentrations; (ii) the cellular abundance of transferrin receptor (TfR), H- and L-ferritin, and mitochondrial aconitase proteins; and (iii) IRP binding to a [32P](-) labeled mRNA sequence of L-ferritin were evaluated in undifferentiated PC12 cells. In vitro manganese exposure altered the cellular abundance of TfR, H-/L-ferritin, and m-aconitase, resulting in an increase in labile iron. This latter effect led to a decrease in IRP binding activity at the lower (10 and 50 microM) manganese exposures. In contrast, 200 microM manganese exposure increased IRP binding, in spite of the significant increase in labile iron. These data indicate that at lower exposures, manganese directly interfered with IRP-dependent translational events, producing an increase in labile iron, which in turn signaled a decrease in IRP binding at 24 h. At higher exposures, the intracellular burden of manganese resulted in overt cytotoxicity and appeared to compromise the normal compensatory response to increased labile iron, producing increased IRP binding. We conclude that low to moderate manganese exposure interferes with cellular iron regulation, and thus may serve as a contributory mechanism underlying manganese neurotoxicity.
Collapse
Affiliation(s)
- Catherine L Kwik-Uribe
- Department of Environmental Toxicology, University of California, 1156 High Street, Santa Cruz, CA 95064, USA
| | | | | | | |
Collapse
|
28
|
Affiliation(s)
- Dennis R Winge
- University of Utah Health Sciences Center, Salt Lake City, Utah 84132, USA
| |
Collapse
|
29
|
Abstract
Genetic studies have identified residues in the structured regions of the histones that are critically involved in the formation of heterochromatin. Any investigation of the events that regulate access to the chromatin substrate must take into account the dynamic nature of the nucleosome, and the regulated inter-conversion between various levels of chromatin higher-order structure.
Collapse
Affiliation(s)
- Karolin Luger
- Department for Biochemistry and Molecular Biology, Colorado State University, Fort Collins, Colorado 80523-1870, USA.
| |
Collapse
|
30
|
Suto RK, Edayathumangalam RS, White CL, Melander C, Gottesfeld JM, Dervan PB, Luger K. Crystal structures of nucleosome core particles in complex with minor groove DNA-binding ligands. J Mol Biol 2003; 326:371-80. [PMID: 12559907 DOI: 10.1016/s0022-2836(02)01407-9] [Citation(s) in RCA: 116] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
We determined the crystal structures of three nucleosome core particles in complex with site-specific DNA-binding ligands, the pyrrole-imidazole polyamides. While the structure of the histone octamer and its interaction with the DNA remain unaffected by ligand binding, nucleosomal DNA undergoes significant structural changes at the ligand-binding sites and in adjacent regions to accommodate the ligands. Our findings suggest that twist diffusion occurs over long distances through tightly bound nucleosomal DNA. This may be relevant to the mechanism of ATP-dependent and spontaneous nucleosome translocation, and to the effect of bound factors on nucleosome dynamics.
Collapse
Affiliation(s)
- Robert K Suto
- Department of Biochemistry and Molecular Biology, Colorado State University, Fort Collins, CO 80523-1870, USA
| | | | | | | | | | | | | |
Collapse
|
31
|
Spontaneous access of proteins to buried nucleosomal DNA target sites occurs via a mechanism that is distinct from nucleosome translocation. Mol Cell Biol 2002. [PMID: 12242292 DOI: 10.1128/mbc.22.20.7147-7157.2002] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
Intrinsic nucleosome dynamics termed "site exposure" provides spontaneous and cooperative access to buried regions of nucleosomal DNA in vitro. Two different mechanisms for site exposure have been proposed, one based on nucleosome translocation, the other on dynamic nucleosome conformational changes in which a stretch of the nucleosomal DNA is transiently released off the histone surface. Here we report on three experiments that distinguish between these mechanisms. One experiment investigates the effects on the accessibilities of restriction enzyme target sites inside nucleosomes when extra DNA (onto which the nucleosome may move at low energetic cost) is appended onto one end. The other two experiments test directly for nucleosome mobility under the conditions used to probe accessibility to restriction enzymes: one on a selected nonnatural nucleosome positioning sequence, the other on the well-studied 5S rRNA gene nucleosome positioning sequence. We find from all three assays that restriction enzymes gain access to sites throughout the entire length of the nucleosomal DNA without contribution from nucleosome translocation. We conclude that site exposure in nucleosomes in vitro occurs via a nucleosome conformational change that leads to transient release of a stretch of DNA from the histone surface, most likely involving progressive uncoiling from an end. Recapture at a distal site along DNA that has partially uncoiled would result in looped structures which are believed to contribute to RNA polymerase elongation and may contribute to spontaneous or ATP-driven nucleosome mobility. Transient open states may facilitate the initial entry of transcription factors and enzymes in vivo.
Collapse
|
32
|
Anderson JD, Thåström A, Widom J. Spontaneous access of proteins to buried nucleosomal DNA target sites occurs via a mechanism that is distinct from nucleosome translocation. Mol Cell Biol 2002; 22:7147-57. [PMID: 12242292 PMCID: PMC139820 DOI: 10.1128/mcb.22.20.7147-7157.2002] [Citation(s) in RCA: 97] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Intrinsic nucleosome dynamics termed "site exposure" provides spontaneous and cooperative access to buried regions of nucleosomal DNA in vitro. Two different mechanisms for site exposure have been proposed, one based on nucleosome translocation, the other on dynamic nucleosome conformational changes in which a stretch of the nucleosomal DNA is transiently released off the histone surface. Here we report on three experiments that distinguish between these mechanisms. One experiment investigates the effects on the accessibilities of restriction enzyme target sites inside nucleosomes when extra DNA (onto which the nucleosome may move at low energetic cost) is appended onto one end. The other two experiments test directly for nucleosome mobility under the conditions used to probe accessibility to restriction enzymes: one on a selected nonnatural nucleosome positioning sequence, the other on the well-studied 5S rRNA gene nucleosome positioning sequence. We find from all three assays that restriction enzymes gain access to sites throughout the entire length of the nucleosomal DNA without contribution from nucleosome translocation. We conclude that site exposure in nucleosomes in vitro occurs via a nucleosome conformational change that leads to transient release of a stretch of DNA from the histone surface, most likely involving progressive uncoiling from an end. Recapture at a distal site along DNA that has partially uncoiled would result in looped structures which are believed to contribute to RNA polymerase elongation and may contribute to spontaneous or ATP-driven nucleosome mobility. Transient open states may facilitate the initial entry of transcription factors and enzymes in vivo.
Collapse
Affiliation(s)
- J D Anderson
- Department of Biochemistry, Molecular Biology, and Cell Biology and Department of Chemistry, Northwestern University, Evanston, Illinois 60208-3500, USA
| | | | | |
Collapse
|
33
|
Deckert J, Struhl K. Targeted recruitment of Rpd3 histone deacetylase represses transcription by inhibiting recruitment of Swi/Snf, SAGA, and TATA binding protein. Mol Cell Biol 2002; 22:6458-70. [PMID: 12192044 PMCID: PMC135627 DOI: 10.1128/mcb.22.18.6458-6470.2002] [Citation(s) in RCA: 50] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
Certain DNA-binding repressors inhibit transcription by recruiting Rpd3 histone deacetylase complexes to promoters and generating domains of histone deacetylation that extend over a limited number of nucleosomes. Here, we show that the degree of Rpd3-dependent repression depends on the activator and the level of activation, not the extent of histone deacetylation. In all cases tested, activator binding is unaffected by histone deacetylation. In contrast, Rpd3-dependent repression is associated with decreased occupancy by TATA binding protein (TBP), the Swi/Snf nucleosome-remodeling complex, and the SAGA histone acetylase complex. Transcriptional repression is bypassed by direct recruitment of TBP and several TBP-associated factors, but not by natural activation domains or direct recruitment of polymerase II holoenzyme components. These results suggest that the domain of localized histone deacetylation generated by recruitment of Rpd3 mediates repression by inhibiting recruitment of chromatin-modifying activities and TBP.
Collapse
Affiliation(s)
- Jutta Deckert
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts 02115, USA
| | | |
Collapse
|
34
|
Abstract
We describe an original approach to determining sequence-structure relationships for DNA. This approach, termed ADAPT, combines all-atom molecular mechanics with a multicopy algorithm to build nucleotides that contain all four standard bases in variable proportions. These nucleotides enable us to search very rapidly for base sequences that energetically favor chosen types of DNA deformation or chosen DNA-protein or DNA-ligand interactions. Sequences satisfying the chosen criteria can be found by energy minimization, combinatorial sequence searching, or genome scanning, in a manner similar to the threading approaches developed for protein structure prediction. In the latter case, we are able to analyze roughly 2000 base pairs per second. Applications of the method to DNA allomorphic transitions, DNA deformation, and specific DNA interactions are presented.
Collapse
Affiliation(s)
- I Lafontaine
- Laboratoire de Biochimie Théorique, CNRS UPR 9080, Institut de Biologie Physico-Chimique, 13 rue Pierre et Marie Curie, Paris 75005, France
| | | |
Collapse
|
35
|
Martin MP, Gerlach VL, Brow DA. A novel upstream RNA polymerase III promoter element becomes essential when the chromatin structure of the yeast U6 RNA gene is altered. Mol Cell Biol 2001; 21:6429-39. [PMID: 11533232 PMCID: PMC99790 DOI: 10.1128/mcb.21.19.6429-6439.2001] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The Saccharomyces cerevisiae U6 RNA gene, SNR6, possesses upstream sequences that allow productive binding in vitro of the RNA polymerase III (Pol III) transcription initiation factor IIIB (TFIIIB) in the absence of TFIIIC or other assembly factors. TFIIIC-independent transcription of SNR6 in vitro is highly sensitive to point mutations in a consensus TATA box at position -30. In contrast, the TATA box is dispensable for SNR6 transcription in vivo, apparently because TFIIIC bound to the intragenic A block and downstream B block can recruit TFIIIB via protein-protein interactions. A mutant allele of SNR6 with decreased spacing between the A and B blocks, snr6-Delta42, exhibits increased dependence on the upstream sequences in vivo. Unexpectedly, we find that in vivo expression of snr6-Delta42 is much more sensitive to mutations in a (dT-dA)(7) tract between the TATA box and transcription start site than to mutations in the TATA box itself. Inversion of single base pairs in the center of the dT-dA tract nearly abolishes transcription of snr6-Delta42, yet inversion of all 7 base pairs has little effect on expression, indicating that the dA-dT tract is relatively orientation independent. Although it is within the TFIIIB footprint, point mutations in the dT-dA tract do not inhibit TFIIIB binding or TFIIIC-independent transcription of SNR6 in vitro. In the absence of the chromatin architectural protein Nhp6, dT-dA tract mutations are lethal even when A-to-B block spacing is wild type. We conclude that the (dT-dA)(7) tract and Nhp6 cooperate to direct productive transcription complex assembly on SNR6 in vivo.
Collapse
Affiliation(s)
- M P Martin
- Department of Biomolecular Chemistry, University of Wisconsin Medical School, Madison, Wisconsin 53706-1532, USA
| | | | | |
Collapse
|
36
|
Stafford GA, Morse RH. GCN5 dependence of chromatin remodeling and transcriptional activation by the GAL4 and VP16 activation domains in budding yeast. Mol Cell Biol 2001; 21:4568-78. [PMID: 11416135 PMCID: PMC87115 DOI: 10.1128/mcb.21.14.4568-4578.2001] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Chromatin-modifying enzymes such as the histone acetyltransferase GCN5 can contribute to transcriptional activation at steps subsequent to the initial binding of transcriptional activators. However, few studies have directly examined dependence of chromatin remodeling in vivo on GCN5 or other acetyltransferases, and none have examined remodeling via nucleosomal activator binding sites. In this study, we have monitored chromatin perturbation via nucleosomal binding sites in the yeast episome TALS by GAL4 derivatives in GCN5(+) and gcn5Delta yeast cells. The strong activator GAL4 shows no dependence on GCN5 for remodeling TALS chromatin, whereas GAL4-estrogen receptor-VP16 shows substantial, albeit not complete, GCN5 dependence. Mini-GAL4 derivatives having weakened interactions with TATA-binding protein and TFIIB exhibit a strong dependence on GCN5 for both transcriptional activation and TALS remodeling not seen for native GAL4. These results indicate that GCN5 can contribute to chromatin remodeling at activator binding sites and that dependence on coactivator function for a given activator can vary according to the type and strength of contacts that it makes with other factors. We also found a weaker dependence for chromatin remodeling on SPT7 than on GCN5, indicating that GCN5 can function via pathways independent of the SAGA complex. Finally, we examine dependence on GCN5 and SWI-SNF at two model promoters and find that although these two chromatin-remodeling and/or modification activities may sometimes work together, in other instances they act in complementary fashion.
Collapse
Affiliation(s)
- G A Stafford
- Department of Biomedical Sciences, State University of New York at Albany School of Public Health, Albany, New York 12201-2002, USA
| | | |
Collapse
|
37
|
Anderson JD, Widom J. Poly(dA-dT) promoter elements increase the equilibrium accessibility of nucleosomal DNA target sites. Mol Cell Biol 2001; 21:3830-9. [PMID: 11340174 PMCID: PMC87046 DOI: 10.1128/mcb.21.11.3830-3839.2001] [Citation(s) in RCA: 129] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Polypurine tracts are important elements of eukaryotic promoters. They are believed to somehow destabilize chromatin, but the mechanism of their action is not known. We show that incorporating an A(16) element at an end of the nucleosomal DNA and further inward destabilizes histone-DNA interactions by 0.1 +/- 0.03 and 0.35 +/- 0.04 kcal mol(-1), respectively, and is accompanied by 1.5- +/- 0.1-fold and 1.7- +/- 0.1-fold increases in position-averaged equilibrium accessibility of nucleosomal DNA target sites. These effects are comparable in magnitude to effects of A(16) elements that correlate with transcription in vivo, suggesting that our system may capture most of their physiological role. These results point to two distinct but interrelated models for the mechanism of action of polypurine tract promoter elements in vivo. Given a nucleosome positioned over a promoter region, the presence of a polypurine tract in that nucleosome's DNA decreases the stability of the DNA wrapping, increasing the equilibrium accessibility of other DNA target sites buried inside that nucleosome. Alternatively (if nucleosomes are freely mobile), the presence of a polypurine tract provides a free energy bias for the nucleosome to move to alternative locations, thereby changing the equilibrium accessibilities of other nearby DNA target sites.
Collapse
Affiliation(s)
- J D Anderson
- Department of Biochemistry, Molecular Biology, and Cell Biology, Illinois 60208, USA
| | | |
Collapse
|
38
|
Koch KA, Allard S, Santoro N, Côté J, Thiele DJ. The Candida glabrata Amt1 copper-sensing transcription factor requires Swi/Snf and Gcn5 at a critical step in copper detoxification. Mol Microbiol 2001; 40:1165-74. [PMID: 11401720 DOI: 10.1046/j.1365-2958.2001.02458.x] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
The yeast Candida glabrata rapidly autoactivates transcription of the AMT1 gene in response to potentially toxic copper levels through the copper-inducible binding of the Amt1 transcription factor to a metal response element (MRE) within a positioned nucleosome. Our previous studies have characterized the role of a 16 bp homopolymeric dA:dT DNA structural element in facilitating rapid Amt1 access to the AMT1 promoter nucleosomal MRE. In this study, we have used the genetically more facile yeast Saccharomyces cerevisiae to identify additional cellular factors that are important for promoting rapid autoactivation of the AMT1 gene in response to toxic copper levels. We demonstrate that the Swi/Snf nucleosome remodelling complex and the histone acetyltransferase Gcn5 are both essential for AMT1 gene autoregulation, and that the requirement for these chromatin remodelling factors is target gene specific. Chromatin accessibility measurements performed in vitro and in vivo indicate that part of the absolute requirement for these factors is derived from their involvement in facilitating nucleosomal access to the AMT1 promoter MRE. Additionally, these data implicate the involvement of Swi/Snf and Gcn5 at multiple levels of AMT1 gene autoregulation.
Collapse
Affiliation(s)
- K A Koch
- Department of Biological Chemistry, University of Michigan Medical School, Ann Arbor, MI 48109-0606, USA
| | | | | | | | | |
Collapse
|
39
|
Beaudoin J, Labbé S. The fission yeast copper-sensing transcription factor Cuf1 regulates the copper transporter gene expression through an Ace1/Amt1-like recognition sequence. J Biol Chem 2001; 276:15472-80. [PMID: 11278870 DOI: 10.1074/jbc.m011256200] [Citation(s) in RCA: 60] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Transcriptional regulation of genes encoding critical components of copper transport is essential for copper homeostasis and growth in yeast. Analysis of regulatory regions in the promoter of the ctr4(+) copper transporter gene in fission yeast Schizosaccharomyces pombe reveals the identity of a conserved copper-signaling element (CuSE), which is recognized by the transcription factor Cuf1. We demonstrate that CuSE is necessary for transcriptional activation in response to copper deprivation conditions. Interestingly, the CuSE element bears a strong sequence similarity to the recognition site, denoted MRE (metal regulatory element), which is recognized by a distinct class of copper sensors required for copper detoxification, including Ace1 from Saccharomyces cerevisiae and Amt1 from Candida glabrata. When a consensus MRE from S. cerevisiae is introduced into S. pombe, transcription is induced by copper deprivation in a Cuf1-dependent manner, similar to regulation by Mac1, the nuclear sensor for regulating the expression of genes encoding components involved in copper transport in S. cerevisiae. UV-cross-linking experiments show that the Cuf1 protein directly binds the CuSE. These results demonstrate that the Cuf1 nutritional copper-sensing factor possesses a module that functions similarly to domains found in the Ace1/Amt1 class of metalloregulatory factors, which allows the protein to act through a closely related MRE-like sequence to regulate copper transport gene expression in S. pombe.
Collapse
Affiliation(s)
- J Beaudoin
- Département de Biochimie, Université de Sherbrooke, Sherbrooke, Québec, J1H 5N4, Canada
| | | |
Collapse
|
40
|
Heredia J, Crooks M, Zhu Z. Phosphorylation and Cu+ coordination-dependent DNA binding of the transcription factor Mac1p in the regulation of copper transport. J Biol Chem 2001; 276:8793-7. [PMID: 11134042 DOI: 10.1074/jbc.m008179200] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Copper ions are essential at a proper level yet toxic when present in excess. To maintain a proper intracellular level, cells must be able to sense the changes in copper ion concentrations. The yeast transcription factor Mac1p plays a critical role in the transcriptional regulation of CTR1 and CTR3, both encoding high affinity copper ion transporters. Here we report that the Mac1p binding of the copper ion-responsive elements (CuREs) in the promoters of CTR1 and CTR3 is affected by copper ions. On one hand, the Mac1p DNA binding is Cu(+) coordination-dependent, and on the other hand, exogenous Cu(+) and isoelectronic Ag(+) ions disrupt the DNA binding of Mac1p. These results suggest that the Mac1p is able to sense two different levels of copper ions. These two levels are probably the physiological and toxic copper levels in yeast cells. Furthermore, we found that Mac1p undergoes posttranslational phosphorylation modification in yeast and that the phosphorylation is required for the Mac1p to become DNA-binding active. Nonphosphorylated Mac1p is unable to bind the CTR1 promoter DNA. The data support the model of intradomain interactions and indicate further that the phosphorylation probably prevents the inhibition of DNA-binding domain activity by the activation domain of Mac1p. Taken together, these findings demonstrate that Mac1p functions critically in maintaining a proper intracellular concentration of copper ions.
Collapse
Affiliation(s)
- J Heredia
- Department of Environmental Toxicology, University of California, Santa Cruz, California 95064, USA
| | | | | |
Collapse
|
41
|
Kumar MJ, Jamaluddin MS, Natarajan K, Kaur D, Datta A. The inducible N-acetylglucosamine catabolic pathway gene cluster in Candida albicans: discrete N-acetylglucosamine-inducible factors interact at the promoter of NAG1. Proc Natl Acad Sci U S A 2000; 97:14218-23. [PMID: 11114181 PMCID: PMC18898 DOI: 10.1073/pnas.250452997] [Citation(s) in RCA: 65] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
The catabolic pathway of N-acetylglucosamine (GlcNAc) in Candida albicans is an important facet of its pathogenicity. One of the pathway genes, encoding glucosamine-6-phosphate deaminase (NAG1) is transcriptionally regulated by GlcNAc. Sequence analysis of a 4-kb genomic clone containing NAG1 indicates that this gene is part of a cluster containing two other genes of the GlcNAc catabolic pathway, i.e., DAC1, GlcNAc-6-phosphate deacetylase, and HXK1, hexokinase. All three genes are temporally and coordinately induced by GlcNAc suggesting a common regulatory mechanism for these genes. The NAG1 promoter is up-regulated when induced by GlcNAc in C. albicans but not in Saccharomyces cerevisiae. In vivo analysis of the deletion constructs delineated the minimal promoter to -130 bp and mapped two regions at -200 and -400 bp upstream of +1 (ATG) responsible for GlcNAc induction. Gel mobility-shift assays and "footprinting" (DNase protection method) analyses revealed two regions, 5'-GGAGCAAAAAAATGT 3' (-164 to -150, box A) and 5'-ACGGTGAGTTG 3' (-291 to -281, box B), that are recognized and bound by at least two inducible activator proteins directing the regulation of gene expression.
Collapse
Affiliation(s)
- M J Kumar
- Molecular Biology Laboratory, School of Life Sciences, Jawaharlal Nehru University, New Delhi, 110067, India
| | | | | | | | | |
Collapse
|
42
|
Suter B, Schnappauf G, Thoma F. Poly(dA.dT) sequences exist as rigid DNA structures in nucleosome-free yeast promoters in vivo. Nucleic Acids Res 2000; 28:4083-9. [PMID: 11058103 PMCID: PMC113125 DOI: 10.1093/nar/28.21.4083] [Citation(s) in RCA: 114] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Poly(dA.dT) sequences (T-tracts) are abundant genomic DNA elements with unusual properties in vitro and an established role in transcriptional regulation of yeast genes. In vitro T-tracts are rigid, contribute to DNA bending, affect assembly in nucleosomes and generate a characteristic pattern of CPDs (cyclobutane pyrimidine dimers) upon irradiation with UV light (UV photofootprint). In eukaryotic cells, where DNA is packaged in chromatin, the DNA structure of T-tracts is unknown. Here we have used in vivo UV photofootprinting and DNA repair by photolyase to investigate the structure and accessibility of T-tracts in yeast promoters (HIS3, URA3 and ILV1). The same characteristic photofootprints were obtained in yeast and in naked DNA, demonstrating that the unusual T-tract structure exists in living cells. Rapid repair of CPDs in the T-tracts demonstrates that these T-tracts were not folded in nucleosomes. Moreover, neither datin, a T-tract binding protein, nor Gcn5p, a histone acetyltransferase involved in nucleosome remodelling, showed an influence on the structure and accessibility of T-tracts. The data support a contribution of this unusual DNA structure to transcriptional regulation.
Collapse
MESH Headings
- Acetyltransferases/genetics
- Acetyltransferases/metabolism
- Base Sequence
- Chromosomes, Fungal/chemistry
- Chromosomes, Fungal/genetics
- Chromosomes, Fungal/metabolism
- Chromosomes, Fungal/radiation effects
- DNA Damage/genetics
- DNA Damage/radiation effects
- DNA Footprinting
- DNA Repair/genetics
- DNA, Fungal/chemistry
- DNA, Fungal/genetics
- DNA, Fungal/metabolism
- DNA, Fungal/radiation effects
- DNA-Binding Proteins/genetics
- DNA-Binding Proteins/metabolism
- Deoxyribodipyrimidine Photo-Lyase/metabolism
- Dopamine Plasma Membrane Transport Proteins
- Fungal Proteins/genetics
- Fungal Proteins/metabolism
- Gene Expression Regulation, Fungal
- Genes, Fungal/genetics
- Genome, Fungal
- Histone Acetyltransferases
- Hydro-Lyases/genetics
- Membrane Glycoproteins
- Membrane Transport Proteins
- Nerve Tissue Proteins
- Nucleic Acid Conformation
- Nucleosomes/physiology
- Pliability
- Poly A/genetics
- Poly T/genetics
- Promoter Regions, Genetic/genetics
- Protein Kinases/genetics
- Protein Kinases/metabolism
- Saccharomyces cerevisiae Proteins
- Ultraviolet Rays
- Yeasts/enzymology
- Yeasts/genetics
- Yeasts/radiation effects
Collapse
Affiliation(s)
- B Suter
- Institut für Zellbiologie, ETH-Zürich, Hönggerberg, CH-8093 Zürich, Switzerland
| | | | | |
Collapse
|
43
|
Mai X, Chou S, Struhl K. Preferential accessibility of the yeast his3 promoter is determined by a general property of the DNA sequence, not by specific elements. Mol Cell Biol 2000; 20:6668-76. [PMID: 10958664 PMCID: PMC86173 DOI: 10.1128/mcb.20.18.6668-6676.2000] [Citation(s) in RCA: 44] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Yeast promoter regions are often more accessible to nuclear proteins than are nonpromoter regions. As assayed by HinfI endonuclease cleavage in living yeast cells, HinfI sites located in the promoters of all seven genes tested were 5- to 20-fold more accessible than sites in adjacent nonpromoter regions. HinfI hypersensitivity within the his3 promoter region is locally determined, since it was observed when this region was translocated to the middle of the ade2 structural gene. Detailed analysis of the his3 promoter indicated that preferential accessibility is not determined by specific elements such as the Gcn4 binding site, poly(dA-dT) sequences, TATA elements, or initiator elements or by transcriptional activity. However, progressive deletion of the promoter region in either direction resulted in a progressive loss of HinfI accessibility. Preferential accessibility is independent of the Swi-Snf chromatin remodeling complex, Gcn5 histone acetylase complexes Ada and SAGA, and Rad6, which ubiquitinates histone H2B. These results suggest that preferential accessibility of the his3 (and presumably other) promoter regions is determined by a general property of the DNA sequence (e.g., base composition or a related feature) rather than by defined sequence elements. The organization of the compact yeast genome into inherently distinct promoter and nonpromoter regions may ensure that transcription factors bind preferentially to appropriate sites in promoters rather than to the excess of irrelevant but equally high-affinity sites in nonpromoter regions.
Collapse
Affiliation(s)
- X Mai
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts 02115, USA
| | | | | |
Collapse
|
44
|
Shimizu M, Mori T, Sakurai T, Shindo H. Destabilization of nucleosomes by an unusual DNA conformation adopted by poly(dA) small middle dotpoly(dT) tracts in vivo. EMBO J 2000; 19:3358-65. [PMID: 10880448 PMCID: PMC313933 DOI: 10.1093/emboj/19.13.3358] [Citation(s) in RCA: 51] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Poly(dA) small middle dotpoly(dT) tracts are common and often found upstream of genes in eukaryotes. It has been suggested that poly(dA) small middle dotpoly(dT) promotes transcription in vivo by affecting nucleosome formation. On the other hand, in vitro studies show that poly(dA) small middle dotpoly(dT) can be easily incorporated into nucleosomes. Therefore, the roles of these tracts in nucleosome organization in vivo remain to be established. We have developed an assay system that can evaluate nucleosome formation in yeast cells, and demonstrated that relatively longer tracts such as A(15)TATA(16) and A(34) disrupt an array of positioned nucleosomes, whereas a shorter A(5)TATA(4) tract is incorporated in positioned nucleosomes of yeast minichromosomes. Thus, nucleosomes are destabilized by poly(dA) small middle dotpoly(dT) in vivo in a length-dependent manner. Furthermore, in vivo UV footprinting revealed that the longer tracts adopt an unusual DNA structure in yeast cells that corresponds to the B' conformation described in vitro. Our results support a mechanism in which a unique poly(dA) small middle dot poly(dT) conformation presets chromatin structure to which transcription factors are accessible.
Collapse
Affiliation(s)
- M Shimizu
- Department of Chemistry, Meisei University, Hino, Tokyo 191-8506 and School of Pharmacy, Tokyo University of Pharmacy and Life Science, Hachioji, Tokyo 192-0392, Japan.
| | | | | | | |
Collapse
|
45
|
Reeves R, Leonard WJ, Nissen MS. Binding of HMG-I(Y) imparts architectural specificity to a positioned nucleosome on the promoter of the human interleukin-2 receptor alpha gene. Mol Cell Biol 2000; 20:4666-79. [PMID: 10848593 PMCID: PMC85880 DOI: 10.1128/mcb.20.13.4666-4679.2000] [Citation(s) in RCA: 49] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Transcriptional induction of the interleukin-2 receptor alpha-chain (IL-2Ralpha) gene is a key event regulating T-cell-mediated immunity in mammals. In vivo, the T-cell-restricted protein Elf-1 and the general architectural transcription factor HMG-I(Y) cooperate in transcriptional regulation of the human IL-2Ralpha gene by binding to a specific positive regulatory region (PRRII) in its proximal promoter. Employing chromatin reconstitution analyses, we demonstrate that the binding sites for both HMG-I(Y) and Elf-1 in the PRRII element are incorporated into a strongly positioned nucleosome in vitro. A variety of analytical techniques was used to determine that a stable core particle is positioned over most of the PRRII element and that this nucleosome exhibits only a limited amount of lateral translational mobility. Regardless of its translational setting, the in vitro position of the nucleosome is such that DNA recognition sequences for both HMG-I(Y) and Elf-1 are located on the surface of the core particle. Restriction nuclease accessibility analyses indicate that a similarly positioned nucleosome also exists on the PRRII element in unstimulated lymphocytes when the IL-2Ralpha gene is silent and suggest that this core particle is remodeled following transcriptional activation of the gene in vivo. In vitro experiments employing the chemical cleavage reagent 1,10-phenanthroline copper (II) covalently attached to its C-terminal end demonstrate that HMG-I(Y) protein binds to the positioned PRRII nucleosome in a direction-specific manner, thus imparting a distinct architectural configuration to the core particle. Together, these findings suggest a role for the HMG-I(Y) protein in assisting the remodeling of a critically positioned nucleosome on the PRRII promoter element during IL-2Ralpha transcriptional activation in lymphocytes in vivo.
Collapse
Affiliation(s)
- R Reeves
- Biochemistry/Biophysics, School of Molecular Biosciences, Washington State University, Pullman 99164, USA.
| | | | | |
Collapse
|
46
|
Pedersen AG, Jensen LJ, Brunak S, Staerfeldt HH, Ussery DW. A DNA structural atlas for Escherichia coli. J Mol Biol 2000; 299:907-30. [PMID: 10843847 DOI: 10.1006/jmbi.2000.3787] [Citation(s) in RCA: 178] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
We have performed a computational analysis of DNA structural features in 18 fully sequenced prokaryotic genomes using models for DNA curvature, DNA flexibility, and DNA stability. The structural values that are computed for the Escherichia coli chromosome are significantly different from (and generally more extreme than) that expected from the nucleotide composition. To aid this analysis, we have constructed tools that plot structural measures for all positions in a long DNA sequence (e.g. an entire chromosome) in the form of color-coded wheels (http://www.cbs.dtu. dk/services/GenomeAtlas/). We find that these "structural atlases" are useful for the discovery of interesting features that may then be investigated in more depth using statistical methods. From investigation of the E. coli structural atlas, we discovered a genome-wide trend, where an extended region encompassing the terminus displays a high of level curvature, a low level of flexibility, and a low degree of helix stability. The same situation is found in the distantly related Gram-positive bacterium Bacillus subtilis, suggesting that the phenomenon is biologically relevant. Based on a search for long DNA segments where all the independent structural measures agree, we have found a set of 20 regions with identical and very extreme structural properties. Due to their strong inherent curvature, we suggest that these may function as topological domain boundaries by efficiently organizing plectonemically supercoiled DNA. Interestingly, we find that in practically all the investigated eubacterial and archaeal genomes, there is a trend for promoter DNA being more curved, less flexible, and less stable than DNA in coding regions and in intergenic DNA without promoters. This trend is present regardless of the absolute levels of the structural parameters, and we suggest that this may be related to the requirement for helix unwinding during initiation of transcription, or perhaps to the previously observed location of promoters at the apex of plectonemically supercoiled DNA. We have also analyzed the structural similarities between groups of genes by clustering all RNA and protein-encoding genes in E. coli, based on the average structural parameters. We find that most ribosomal genes (protein-encoding as well as rRNA genes) cluster together, and we suggest that DNA structure may play a role in the transcription of these highly expressed genes.
Collapse
MESH Headings
- Bacterial Proteins/genetics
- Base Pairing/genetics
- Color
- Computational Biology
- Computer Simulation
- Crystallography, X-Ray
- DNA, Bacterial/chemistry
- DNA, Bacterial/genetics
- DNA, Superhelical/chemistry
- DNA, Superhelical/genetics
- Deoxyribonuclease I/metabolism
- Escherichia coli/genetics
- Genes, Bacterial/genetics
- Genome, Bacterial
- Models, Molecular
- Nucleic Acid Conformation
- Nucleosomes/chemistry
- Nucleosomes/genetics
- Pattern Recognition, Automated
- Phylogeny
- Pliability
- Promoter Regions, Genetic/genetics
- RNA, Bacterial/genetics
- Software
- Statistics as Topic
- Thermodynamics
Collapse
Affiliation(s)
- A G Pedersen
- Center for Biological Sequence Analysis, Department of Biotechnology, The Technical University of Denmark, Building 208, DK-2800 Lyngby, Denmark
| | | | | | | | | |
Collapse
|
47
|
El Barkani A, Haynes K, Mösch H, Frosch M, Mühlschlegel FA. Candida glabrata shuttle vectors suitable for translational fusions to lacZ and use of beta-galactosidase as a reporter of gene expression. Gene 2000; 246:151-5. [PMID: 10767536 DOI: 10.1016/s0378-1119(00)00065-2] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
The functionality of beta-galactosidase encoded by the E. coli lacZ gene as a reporter of gene expression in C. glabrata was investigated. C. glabrata/E. coli shuttle vectors were constructed, containing both a C. glabrata CEN-ARS cassette, to allow regular segregation and episomal replication of the plasmids, and the lacZ coding sequence of E. coli. The functionality of beta-galactosidase in C. glabrata was verified by inserting the promoter and the 5' coding region of the HIS3 gene from C. glabrata directionally upstream of the lacZ gene. By fusing the promoter of the copper-controlled MTII gene to the lacZ reporter, we showed that beta-galactosidase activity can be differentially induced in C. glabrata. beta-galactosidase reporter activities were detected qualitatively by an indirect filter assay and quantitatively from permeabilized cells.
Collapse
Affiliation(s)
- A El Barkani
- Institut für Hygiene und Mikrobiologie, Universität Würzburg, Josef-Schneider-Strasse 2, 97080, Würzburg, Germany
| | | | | | | | | |
Collapse
|
48
|
Lascaris RF, Groot E, Hoen PB, Mager WH, Planta RJ. Different roles for abf1p and a T-rich promoter element in nucleosome organization of the yeast RPS28A gene. Nucleic Acids Res 2000; 28:1390-6. [PMID: 10684934 PMCID: PMC111049 DOI: 10.1093/nar/28.6.1390] [Citation(s) in RCA: 46] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
In vivo mutational analysis of the yeast RPS28A ribosomal protein (rp-)gene promoter demonstrated that both the Abf1p binding site and the adjacent T-rich element are essential for efficient transcription. In vivo Mnase and DNaseI digestion showed that the RPS28A promoter contains a 50-60 bp long nucleosome-free region directly downstream from the Abf1p binding site, followed by an ordered array of nucleosomes. Mutating either the Abf1p binding site or the T-rich element has dramatic, but different, effects on the local chromatin structure. Failure to bind Abf1p appears to cause nucleosome positioning to become disorganized as concluded from the complete disappearance of Mnase hypersensitive sites. On the other hand, mutation of the T-rich element causes the downstream nucleosomal array to shift by approximately 50 bp towards the Abf1p site, resulting in loss of the nucleosome-free region downstream of Abf1p. We conclude that Abf1p is a strong organizer of local chromatin structure that appears to act as a nucleosomal boundary factor requiring the downstream T-rich element to create a nucleosome-free region.
Collapse
Affiliation(s)
- R F Lascaris
- Department of Biochemistry and Molecular Biology, IMBW, Biocentrum Amsterdam, Vrije Universiteit, de Boelelaan 1083, 1081 HV Amsterdam, The Netherlands
| | | | | | | | | |
Collapse
|
49
|
Zhan XL, Hong Y, Zhu T, Mitchell AP, Deschenes RJ, Guan KL. Essential functions of protein tyrosine phosphatases PTP2 and PTP3 and RIM11 tyrosine phosphorylation in Saccharomyces cerevisiae meiosis and sporulation. Mol Biol Cell 2000; 11:663-76. [PMID: 10679022 PMCID: PMC14801 DOI: 10.1091/mbc.11.2.663] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
Abstract
Tyrosine phosphorylation plays a central role in eukaryotic signal transduction. In yeast, MAP kinase pathways are regulated by tyrosine phosphorylation, and it has been speculated that other biochemical processes may also be regulated by tyrosine phosphorylation. Previous genetic and biochemical studies demonstrate that protein tyrosine phosphatases (PTPases) negatively regulate yeast MAP kinases. Here we report that deletion of PTP2 and PTP3 results in a sporulation defect, suggesting that tyrosine phosphorylation is involved in regulation of meiosis and sporulation. Deletion of PTP2 and PTP3 blocks cells at an early stage of sporulation before premeiotic DNA synthesis and induction of meiotic-specific genes. We observed that tyrosine phosphorylation of several proteins, including 52-, 43-, and 42-kDa proteins, was changed in ptp2Deltaptp3Delta homozygous deletion cells under sporulation conditions. The 42-kDa tyrosine-phosphorylated protein was identified as Mck1, which is a member of the GSK3 family of protein kinases and previously known to be phosphorylated on tyrosine. Mutation of MCK1 decreases sporulation efficiency, whereas mutation of RIM11, another GSK3 member, specifically abolishes sporulation; therefore, we investigated regulation of Rim11 by Tyr phosphorylation during sporulation. We demonstrated that Rim11 is phosphorylated on Tyr-199, and the Tyr phosphorylation is essential for its in vivo function, although Rim11 appears not to be directly regulated by Ptp2 and Ptp3. Biochemical characterizations indicate that tyrosine phosphorylation of Rim11 is essential for the activity of Rim11 to phosphorylate substrates. Our data demonstrate important roles of protein tyrosine phosphorylation in meiosis and sporulation
Collapse
Affiliation(s)
- X L Zhan
- Department of Biological Chemistry, University of Michigan, Ann Arbor, Michigan 48109, USA
| | | | | | | | | | | |
Collapse
|
50
|
Fojta M, Brazdova M, Cernocka H, Pecinka P, Brazda V, Palecek J, Jagelska E, Vojtesek B, Pospisilova S, Subramaniam V, Jovin TM, Palecek E. Effects of Oxidation Agents and Metal Ions on Binding of p53 to Supercoiled DNA. J Biomol Struct Dyn 2000; 17 Suppl 1:177-83. [DOI: 10.1080/07391102.2000.10506618] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
|