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Kato H, Shimizu M, Urano T. Chemical map-based prediction of nucleosome positioning using the Bioconductor package nuCpos. BMC Bioinformatics 2021; 22:322. [PMID: 34120589 PMCID: PMC8201924 DOI: 10.1186/s12859-021-04240-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2020] [Accepted: 06/06/2021] [Indexed: 11/10/2022] Open
Abstract
Background Assessing the nucleosome-forming potential of specific DNA sequences is important for understanding complex chromatin organization. Methods for predicting nucleosome positioning include bioinformatics and biophysical approaches. An advantage of bioinformatics methods, which are based on in vivo nucleosome maps, is the use of natural sequences that may contain previously unknown elements involved in nucleosome positioning in vivo. The accuracy of such prediction attempts reflects the genomic coordinate resolution of the nucleosome maps applied. Nucleosome maps are constructed using micrococcal nuclease digestion followed by high-throughput sequencing (MNase-seq). However, as MNase has a strong preference for A/T-rich sequences, MNase-seq may not be appropriate for this purpose. In addition to MNase-seq-based maps, base pair-resolution chemical maps of in vivo nucleosomes from three different species (budding and fission yeasts, and mice) are currently available. However, these chemical maps have yet to be integrated into publicly available computational methods. Results We developed a Bioconductor package (named nuCpos) to demonstrate the superiority of chemical maps in predicting nucleosome positioning. The accuracy of chemical map-based prediction in rotational settings was higher than that of the previously developed MNase-seq-based approach. With our method, predicted nucleosome occupancy reasonably matched in vivo observations and was not affected by A/T nucleotide frequency. Effects of genetic alterations on nucleosome positioning that had been observed in living yeast cells could also be predicted. nuCpos calculates individual histone binding affinity (HBA) scores for given 147-bp sequences to examine their suitability for nucleosome formation. We also established local HBA as a new parameter to predict nucleosome formation, which was calculated for 13 overlapping nucleosomal DNA subsequences. HBA and local HBA scores for various sequences agreed well with previous in vitro and in vivo studies. Furthermore, our results suggest that nucleosomal subsegments that are disfavored in different rotational settings contribute to the defined positioning of nucleosomes. Conclusions Our results demonstrate that chemical map-based statistical models are beneficial for studying nucleosomal DNA features. Studies employing nuCpos software can enhance understanding of chromatin regulation and the interpretation of genetic alterations and facilitate the design of artificial sequences. Supplementary Information The online version contains supplementary material available at 10.1186/s12859-021-04240-2.
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Affiliation(s)
- Hiroaki Kato
- Department of Biochemistry, Shimane University School of Medicine, 89-1 Enya-cho, Izumo, Shimane, 693-8501, Japan.
| | - Mitsuhiro Shimizu
- Department of Chemistry, Graduate School of Science and Engineering, Program in Chemistry and Life Science, School of Science and Engineering, Meisei University, 2-1-1 Hodokubo, Hino, Tokyo, 191-8506, Japan
| | - Takeshi Urano
- Department of Biochemistry, Shimane University School of Medicine, 89-1 Enya-cho, Izumo, Shimane, 693-8501, Japan
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Katsumata K, Ichikawa Y, Fuse T, Kurumizaka H, Yanagida A, Urano T, Kato H, Shimizu M. Sequence-dependent nucleosome formation in trinucleotide repeats evaluated by in vivo chemical mapping. Biochem Biophys Res Commun 2021; 556:179-184. [PMID: 33839413 DOI: 10.1016/j.bbrc.2021.03.155] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2021] [Accepted: 03/28/2021] [Indexed: 11/18/2022]
Abstract
Trinucleotide repeat sequences (TRSs), consisting of 10 unique classes of repeats in DNA, are members of microsatellites and abundantly and non-randomly distributed in many eukaryotic genomes. The lengths of TRSs are mutable, and the expansions of several TRSs are implicated in hereditary neurological diseases. However, the underlying causes of the biased distribution and the dynamic properties of TRSs in the genome remain elusive. Here, we examined the effects of TRSs on nucleosome formation in vivo by histone H4-S47C site-directed chemical cleavages, using well-defined yeast minichromosomes in which each of the ten TRS classes resided in the central region of a positioned nucleosome. We showed that (AAT)12 and (ACT)12 act as strong nucleosome-promoting sequences, while (AGG)12 and (CCG)12 act as nucleosome-excluding sequences in vivo. The local histone binding affinity scores support the idea that nucleosome formation in TRSs, except for (AGG)12, is mainly determined by the affinity for the histone octamers. Overall, our study presents a framework for understanding the nucleosome-forming abilities of TRSs.
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Affiliation(s)
- Koji Katsumata
- Department of Chemistry, Graduate School of Science and Engineering, Meisei University, 2-1-1 Hodokubo, Hino, Tokyo, 191-8506, Japan
| | - Yuichi Ichikawa
- Division of Cancer Biology, The Cancer Institute of JFCR, 3-8-31 Ariake, Koto-ku, Tokyo, 135-8550, Japan
| | - Tomohiro Fuse
- Department of Chemistry, Graduate School of Science and Engineering, Meisei University, 2-1-1 Hodokubo, Hino, Tokyo, 191-8506, Japan
| | - Hitoshi Kurumizaka
- Laboratory of Chromatin Structure and Function, Institute for Quantitative Biosciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo, 113-0032, Japan
| | - Akio Yanagida
- School of Pharmacy, Tokyo University of Pharmacy and Life Sciences, 1432-1 Horinouchi, Hachioji, Tokyo, 192-0392, Japan
| | - Takeshi Urano
- Department of Biochemistry, Shimane University School of Medicine, 89-1 Enya-cho, Izumo, Shimane, 693-8501, Japan
| | - Hiroaki Kato
- Department of Biochemistry, Shimane University School of Medicine, 89-1 Enya-cho, Izumo, Shimane, 693-8501, Japan
| | - Mitsuhiro Shimizu
- Department of Chemistry, Graduate School of Science and Engineering, Meisei University, 2-1-1 Hodokubo, Hino, Tokyo, 191-8506, Japan.
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3
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Fuse T, Katsumata K, Morohoshi K, Mukai Y, Ichikawa Y, Kurumizaka H, Yanagida A, Urano T, Kato H, Shimizu M. Parallel mapping with site-directed hydroxyl radicals and micrococcal nuclease reveals structural features of positioned nucleosomes in vivo. PLoS One 2017; 12:e0186974. [PMID: 29073207 PMCID: PMC5658119 DOI: 10.1371/journal.pone.0186974] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2017] [Accepted: 10/11/2017] [Indexed: 12/17/2022] Open
Abstract
Micrococcal nuclease (MNase) has been widely used for analyses of nucleosome locations in many organisms. However, due to its sequence preference, the interpretations of the positions and occupancies of nucleosomes using MNase have remained controversial. Next-generation sequencing (NGS) has also been utilized for analyses of MNase-digests, but some technical biases are commonly present in the NGS experiments. Here, we established a gel-based method to map nucleosome positions in Saccharomyces cerevisiae, using isolated nuclei as the substrate for the histone H4 S47C-site-directed chemical cleavage in parallel with MNase digestion. The parallel mapping allowed us to compare the chemically and enzymatically cleaved sites by indirect end-labeling and primer extension mapping, and thus we could determine the nucleosome positions and the sizes of the nucleosome-free regions (or nucleosome-depleted regions) more accurately, as compared to nucleosome mapping by MNase alone. The analysis also revealed that the structural features of the nucleosomes flanked by the nucleosome-free region were different from those within regularly arrayed nucleosomes, showing that the structures and dynamics of individual nucleosomes strongly depend on their locations. Moreover, we demonstrated that the parallel mapping results were generally consistent with the previous genome-wide chemical mapping and MNase-Seq results. Thus, the gel-based parallel mapping will be useful for the analysis of a specific locus under various conditions.
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Affiliation(s)
- Tomohiro Fuse
- Department of Chemistry, Graduate School of Science and Engineering, Program in Chemistry and Life Science, School of Science and Engineering, Meisei University, Hino, Tokyo, Japan
| | - Koji Katsumata
- Department of Chemistry, Graduate School of Science and Engineering, Program in Chemistry and Life Science, School of Science and Engineering, Meisei University, Hino, Tokyo, Japan
| | - Koya Morohoshi
- Department of Chemistry, Graduate School of Science and Engineering, Program in Chemistry and Life Science, School of Science and Engineering, Meisei University, Hino, Tokyo, Japan
| | - Yukio Mukai
- Department of Bioscience, Faculty of Bioscience, Nagahama Institute of Bio-Science and Technology, Nagahama, Shiga, Japan
| | - Yuichi Ichikawa
- Graduate School of Advanced Science and Engineering/RISE/IMSB, Waseda University, Shinjuku-ku, Tokyo, Japan
| | - Hitoshi Kurumizaka
- Graduate School of Advanced Science and Engineering/RISE/IMSB, Waseda University, Shinjuku-ku, Tokyo, Japan
| | - Akio Yanagida
- School of Pharmacy, Tokyo University of Pharmacy and Life Science, Hachioji, Tokyo, Japan
| | - Takeshi Urano
- Department of Biochemistry, Shimane University School of Medicine, Izumo, Shimane, Japan
| | - Hiroaki Kato
- Department of Biochemistry, Shimane University School of Medicine, Izumo, Shimane, Japan
| | - Mitsuhiro Shimizu
- Department of Chemistry, Graduate School of Science and Engineering, Program in Chemistry and Life Science, School of Science and Engineering, Meisei University, Hino, Tokyo, Japan
- * E-mail:
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4
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Ichikawa Y, Connelly CF, Appleboim A, Miller TC, Jacobi H, Abshiru NA, Chou HJ, Chen Y, Sharma U, Zheng Y, Thomas PM, Chen HV, Bajaj V, Müller CW, Kelleher NL, Friedman N, Bolon DN, Rando OJ, Kaufman PD. A synthetic biology approach to probing nucleosome symmetry. eLife 2017; 6:28836. [PMID: 28895528 PMCID: PMC5626479 DOI: 10.7554/elife.28836] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2017] [Accepted: 09/12/2017] [Indexed: 11/13/2022] Open
Abstract
The repeating subunit of chromatin, the nucleosome, includes two copies of each of the four core histones, and several recent studies have reported that asymmetrically-modified nucleosomes occur at regulatory elements in vivo. To probe the mechanisms by which histone modifications are read out, we designed an obligate pair of H3 heterodimers, termed H3X and H3Y, which we extensively validated genetically and biochemically. Comparing the effects of asymmetric histone tail point mutants with those of symmetric double mutants revealed that a single methylated H3K36 per nucleosome was sufficient to silence cryptic transcription in vivo. We also demonstrate the utility of this system for analysis of histone modification crosstalk, using mass spectrometry to separately identify modifications on each H3 molecule within asymmetric nucleosomes. The ability to generate asymmetric nucleosomes in vivo and in vitro provides a powerful and generalizable tool to probe the mechanisms by which H3 tails are read out by effector proteins in the cell.
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Affiliation(s)
- Yuichi Ichikawa
- Department of Molecular, Cell and Cancer Biology, University of Massachusetts Medical School, Worcester, United States
| | - Caitlin F Connelly
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, United States
| | - Alon Appleboim
- School of Computer Science and Engineering, The Hebrew University of Jerusalem, Jerusalem, Israel.,The Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Thomas Cr Miller
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Hadas Jacobi
- School of Computer Science and Engineering, The Hebrew University of Jerusalem, Jerusalem, Israel.,The Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Nebiyu A Abshiru
- National Resource for Translational and Developmental Proteomics, Northwestern University, Evanston, United States
| | - Hsin-Jung Chou
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, United States
| | - Yuanyuan Chen
- Department of Molecular, Cell and Cancer Biology, University of Massachusetts Medical School, Worcester, United States
| | - Upasna Sharma
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, United States
| | - Yupeng Zheng
- National Resource for Translational and Developmental Proteomics, Northwestern University, Evanston, United States
| | - Paul M Thomas
- National Resource for Translational and Developmental Proteomics, Northwestern University, Evanston, United States
| | - Hsuiyi V Chen
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, United States
| | - Vineeta Bajaj
- Department of Molecular, Cell and Cancer Biology, University of Massachusetts Medical School, Worcester, United States
| | - Christoph W Müller
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Neil L Kelleher
- National Resource for Translational and Developmental Proteomics, Northwestern University, Evanston, United States
| | - Nir Friedman
- School of Computer Science and Engineering, The Hebrew University of Jerusalem, Jerusalem, Israel.,The Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Daniel Na Bolon
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, United States
| | - Oliver J Rando
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, United States
| | - Paul D Kaufman
- Department of Molecular, Cell and Cancer Biology, University of Massachusetts Medical School, Worcester, United States
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5
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Kushwaha M, Rostain W, Prakash S, Duncan JN, Jaramillo A. Using RNA as Molecular Code for Programming Cellular Function. ACS Synth Biol 2016; 5:795-809. [PMID: 26999422 DOI: 10.1021/acssynbio.5b00297] [Citation(s) in RCA: 42] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
RNA is involved in a wide-range of important molecular processes in the cell, serving diverse functions: regulatory, enzymatic, and structural. Together with its ease and predictability of design, these properties can lead RNA to become a useful handle for biological engineers with which to control the cellular machinery. By modifying the many RNA links in cellular processes, it is possible to reprogram cells toward specific design goals. We propose that RNA can be viewed as a molecular programming language that, together with protein-based execution platforms, can be used to rewrite wide ranging aspects of cellular function. In this review, we catalogue developments in the use of RNA parts, methods, and associated computational models that have contributed to the programmability of biology. We discuss how RNA part repertoires have been combined to build complex genetic circuits, and review recent applications of RNA-based parts and circuitry. We explore the future potential of RNA engineering and posit that RNA programmability is an important resource for firmly establishing an era of rationally designed synthetic biology.
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Affiliation(s)
- Manish Kushwaha
- Warwick
Integrative Synthetic Biology Centre (WISB) and School of Life Sciences, University of Warwick, Coventry, CV4 7AL, U.K
| | - William Rostain
- Warwick
Integrative Synthetic Biology Centre (WISB) and School of Life Sciences, University of Warwick, Coventry, CV4 7AL, U.K
- iSSB, Genopole,
CNRS, UEVE, Université Paris-Saclay, Évry, France
| | - Satya Prakash
- Warwick
Integrative Synthetic Biology Centre (WISB) and School of Life Sciences, University of Warwick, Coventry, CV4 7AL, U.K
| | - John N. Duncan
- Warwick
Integrative Synthetic Biology Centre (WISB) and School of Life Sciences, University of Warwick, Coventry, CV4 7AL, U.K
| | - Alfonso Jaramillo
- Warwick
Integrative Synthetic Biology Centre (WISB) and School of Life Sciences, University of Warwick, Coventry, CV4 7AL, U.K
- iSSB, Genopole,
CNRS, UEVE, Université Paris-Saclay, Évry, France
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6
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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.
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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.
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7
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Lopez-Serra L, Kelly G, Patel H, Stewart A, Uhlmann F. The Scc2-Scc4 complex acts in sister chromatid cohesion and transcriptional regulation by maintaining nucleosome-free regions. Nat Genet 2014; 46:1147-51. [PMID: 25173104 PMCID: PMC4177232 DOI: 10.1038/ng.3080] [Citation(s) in RCA: 104] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2014] [Accepted: 08/06/2014] [Indexed: 12/14/2022]
Abstract
The cohesin complex is at the heart of many chromosomal activities, including sister chromatid cohesion and transcriptional regulation. Cohesin loading onto chromosomes depends on the Scc2-Scc4 cohesin loader complex, but the chromatin features that form cohesin loading sites remain poorly understood. Here we show that the RSC chromatin remodeling complex recruits budding yeast Scc2-Scc4 to broad nucleosome-free regions, which the cohesin loader helps to maintain. Consequently, inactivation of either the cohesin loader or the RSC complex has similar effects on nucleosome positioning, gene expression and sister chromatid cohesion. These results show an intimate link between local chromatin structure and higher-order chromosome architecture. Our findings pertain to the similarities between two severe human disorders, Cornelia de Lange syndrome, which is caused by alterations in the human cohesin loader, and Coffin-Siris syndrome, which results from alterations in human RSC complex components. Both syndromes can arise from gene misregulation due to related changes in the nucleosome landscape.
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MESH Headings
- Abnormalities, Multiple/genetics
- Abnormalities, Multiple/metabolism
- Binding Sites/genetics
- Chromatids/genetics
- Chromatids/metabolism
- Chromatin/genetics
- Chromatin/metabolism
- Chromosomal Proteins, Non-Histone/genetics
- Chromosomal Proteins, Non-Histone/metabolism
- Chromosomes, Fungal/genetics
- Chromosomes, Fungal/metabolism
- De Lange Syndrome/genetics
- De Lange Syndrome/metabolism
- Face/abnormalities
- Gene Expression Profiling
- Gene Expression Regulation, Fungal
- Hand Deformities, Congenital/genetics
- Hand Deformities, Congenital/metabolism
- Humans
- Intellectual Disability/genetics
- Intellectual Disability/metabolism
- Micrognathism/genetics
- Micrognathism/metabolism
- Neck/abnormalities
- Nucleosomes/genetics
- Nucleosomes/metabolism
- Oligonucleotide Array Sequence Analysis
- Promoter Regions, Genetic/genetics
- Protein Binding
- Saccharomyces cerevisiae Proteins/genetics
- Saccharomyces cerevisiae Proteins/metabolism
- Transcription Initiation Site
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Affiliation(s)
- Lidia Lopez-Serra
- Chromosome Segregation Laboratory, Cancer Research UK London Research Institute, London, UK
| | - Gavin Kelly
- Bioinformatics and Biostatistics Service, Cancer Research UK London Research Institute, London, UK
| | - Harshil Patel
- Bioinformatics and Biostatistics Service, Cancer Research UK London Research Institute, London, UK
| | - Aengus Stewart
- Bioinformatics and Biostatistics Service, Cancer Research UK London Research Institute, London, UK
| | - Frank Uhlmann
- Chromosome Segregation Laboratory, Cancer Research UK London Research Institute, London, UK
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Ichikawa Y, Morohashi N, Nishimura Y, Kurumizaka H, Shimizu M. Telomeric repeats act as nucleosome-disfavouring sequences in vivo. Nucleic Acids Res 2013; 42:1541-52. [PMID: 24174540 PMCID: PMC3919577 DOI: 10.1093/nar/gkt1006] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
Telomeric DNAs consist of tandem repeats of G-clusters such as TTAGGG and TG1-3, which are the human and yeast repeat sequences, respectively. In the yeast Saccharomyces cerevisiae, the telomeric repeats are non-nucleosomal, whereas in humans, they are organized in tightly packaged nucleosomes. However, previous in vitro studies revealed that the binding affinities of human and yeast telomeric repeat sequences to histone octamers in vitro were similar, which is apparently inconsistent with the differences in the human and yeast telomeric chromatin structures. To further investigate the relationship between telomeric sequences and chromatin structure, we examined the effect of telomeric repeats on the formation of positioned nucleosomes in vivo by indirect end-label mapping, primer extension mapping and nucleosome repeat analyses, using a defined minichromosome in yeast cells. We found that the human and yeast telomeric repeat sequences both disfavour nucleosome assembly and alter nucleosome positioning in the yeast minichromosome. We further demonstrated that the G-clusters in the telomeric repeats are required for the nucleosome-disfavouring properties. Thus, our results suggest that this inherent structural feature of the telomeric repeat sequences is involved in the functional dynamics of the telomeric chromatin structure.
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Affiliation(s)
- Yuichi Ichikawa
- Laboratory of Structural Biology, Graduate School of Advanced Science and Engineering/RISE, Waseda University, 2-2 Wakamatsu-cho, Shinjuku-ku, Tokyo 162-8640, Japan, 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 and Graduate School of Medical Life Science, Yokohama City University, 1-7-29 Suehiro-cho, Tsurumi-ku, Yokohama 230-0045, Japan
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9
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The MAT locus genes play different roles in sexual reproduction and pathogenesis in Fusarium graminearum. PLoS One 2013; 8:e66980. [PMID: 23826182 PMCID: PMC3691137 DOI: 10.1371/journal.pone.0066980] [Citation(s) in RCA: 62] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2013] [Accepted: 05/13/2013] [Indexed: 12/18/2022] Open
Abstract
Sexual reproduction plays a critical role in the infection cycle of Fusarium graminearum because ascospores are the primary inoculum. As a homothallic ascomycete, F. graminearum contains both the MAT1-1 and MAT1-2-1 loci in the genome. To better understand their functions and regulations in sexual reproduction and pathogenesis, in this study we assayed the expression, interactions, and mutant phenotypes of individual MAT locus genes. Whereas the expression of MAT1-1-1 and MAT12-1 rapidly increased after perithecial induction and began to decline after 1 day post-perithecial induction (dpi), the expression of MAT1-1-2 and MAT1-1-3 peaked at 4 dpi. MAT1-1-2 and MAT1-1-3 had a similar expression profile and likely are controlled by a bidirectional promoter. Although none of the MAT locus genes were essential for perithecium formation, all of them were required for ascosporogenesis in self-crosses. In outcrosses, the mat11-1-2 and mat11-1-3 mutants were fertile but the mat1-1-1 and mat1-2-1 mutants displayed male- and female-specific defects, respectively. The mat1-2-1 mutant was reduced in FgSO expression and hyphal fusion. Mat1-1-2 interacted with all other MAT locus transcription factors, suggesting that they may form a protein complex during sexual reproduction. Mat1-1-1 also interacted with FgMcm1, which may play a role in controlling cell identity and sexual development. Interestingly, the mat1-1-1 and mat1-2-1 mutants were reduced in virulence in corn stalk rot assays although none of the MAT locus genes was important for wheat infection. The MAT1-1-1 and MAT1-2-1 genes may play a host-specific role in colonization of corn stalks.
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10
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Nalabothula N, Xi L, Bhattacharyya S, Widom J, Wang JP, Reeve JN, Santangelo TJ, Fondufe-Mittendorf YN. Archaeal nucleosome positioning in vivo and in vitro is directed by primary sequence motifs. BMC Genomics 2013; 14:391. [PMID: 23758892 PMCID: PMC3691661 DOI: 10.1186/1471-2164-14-391] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2013] [Accepted: 05/31/2013] [Indexed: 02/03/2023] Open
Abstract
Background Histone wrapping of DNA into nucleosomes almost certainly evolved in the Archaea, and predates Eukaryotes. In Eukaryotes, nucleosome positioning plays a central role in regulating gene expression and is directed by primary sequence motifs that together form a nucleosome positioning code. The experiments reported were undertaken to determine if archaeal histone assembly conforms to the nucleosome positioning code. Results Eukaryotic nucleosome positioning is favored and directed by phased helical repeats of AA/TT/AT/TA and CC/GG/CG/GC dinucleotides, and disfavored by longer AT-rich oligonucleotides. Deep sequencing of genomic DNA protected from micrococcal nuclease digestion by assembly into archaeal nucleosomes has established that archaeal nucleosome assembly is also directed and positioned by these sequence motifs, both in vivo in Methanothermobacter thermautotrophicus and Thermococcus kodakarensis and in vitro in reaction mixtures containing only one purified archaeal histone and genomic DNA. Archaeal nucleosomes assembled at the same locations in vivo and in vitro, with much reduced assembly immediately upstream of open reading frames and throughout the ribosomal rDNA operons. Providing further support for a common positioning code, archaeal histones assembled into nucleosomes on eukaryotic DNA and eukaryotic histones into nucleosomes on archaeal DNA at the same locations. T. kodakarensis has two histones, designated HTkA and HTkB, and strains with either but not both histones deleted grow normally but do exhibit transcriptome differences. Comparisons of the archaeal nucleosome profiles in the intergenic regions immediately upstream of genes that exhibited increased or decreased transcription in the absence of HTkA or HTkB revealed substantial differences but no consistent pattern of changes that would correlate directly with archaeal nucleosome positioning inhibiting or stimulating transcription. Conclusions The results obtained establish that an archaeal histone and a genome sequence together are sufficient to determine where archaeal nucleosomes preferentially assemble and where they avoid assembly. We confirm that the same nucleosome positioning code operates in Archaea as in Eukaryotes and presumably therefore evolved with the histone-fold mechanism of DNA binding and compaction early in the archaeal lineage, before the divergence of Eukaryotes.
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Affiliation(s)
- Narasimharao Nalabothula
- Department of Molecular and Cellular Biochemistry, College of Medicine, University of Kentucky, Lexington, KY 40536, USA
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Parnell EJ, Stillman DJ. Shields up: the Tup1-Cyc8 repressor complex blocks coactivator recruitment. Genes Dev 2012; 25:2429-35. [PMID: 22156205 DOI: 10.1101/gad.181768.111] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
The Tup1-Cyc8 complex is responsible for repression of a large and diverse collection of genes in Saccharomyces cerevisiae. The predominant view has been that Tup1-Cyc8 functions as a corepressor, actively associating with regulatory proteins and organizing chromatin to block transcription. A new study by Wong and Struhl in this issue of Genes & Development (pp. 2525-2539) challenges nearly 20 years of models by demonstrating that Tup1-Cyc8 functions primarily as a shield to block DNA-binding proteins from recruiting transcriptional coactivators.
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Affiliation(s)
- Emily J Parnell
- Department of Pathology, University of Utah Health Sciences Center, Salt Lake City, Utah 84112, USA
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12
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Hashimoto T, Kawazu T, Nagasaki T, Murakami A, Yamaoka T. Quantitative comparison between poly(L-arginine) and poly(L-lysine) at each step of polyplex-based gene transfection using a microinjection technique. SCIENCE AND TECHNOLOGY OF ADVANCED MATERIALS 2012; 13:015009. [PMID: 27877476 PMCID: PMC5090301 DOI: 10.1088/1468-6996/13/1/015009] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/06/2011] [Revised: 02/09/2012] [Accepted: 01/17/2012] [Indexed: 05/29/2023]
Abstract
Among the well-studied polypeptide-type gene carriers, transfection efficiency is empirically known to be higher for poly(L-arginine) (PR) than poly(L-lysine) (PK). The big difference between PR and PK should be determined at one of the intracellular trafficking steps based on the different charge densities, structures or PKa values. However, the endosomal escape and the intranuclear transcription efficiency in living cells have not been clarified yet. In this study, a novel method for quantifying the intranuclear transcription efficiency and the nuclear transport of the polyplex is established based on the nuclear and the cytosolic microinjection technique, and the results for PK and PR with different molecular weights (MWs) are compared in living cells. The intranuclear transcription efficiency is the same in PR and PK and it decreases rapidly with increasing MW, in spite of the commonly measured transfection efficiency. The transcription efficiency is strongly suppressed at high MW and strongly correlates with the polyplex forming ability expressed as a critical ratio of the number of polypeptide cationic groups to the number of pDNA anionic groups. When considered with the results of the cellular uptake and in vitro transfection with or without chloroquine, the rate-limiting step for their gene transfer is the buffering effect-independent endosomal escape.
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Affiliation(s)
- Tomoko Hashimoto
- Department of Biomedical Engineering, National Cerebral and Cardiovascular Center Research Institute, 5-7-1 Fujishiro-dai, Suita, Osaka, 565-8585, Japan
| | - Takeshi Kawazu
- Department of Applied and Bioapplied Chemistry, Graduate School of Engineering, Osaka City University, 3-3-138 Sugimoto, Sumiyoshi, Osaka, 558-8585, Japan
| | - Takeshi Nagasaki
- Silk Materials Research Unit, National Institute of Agrobiological Sciences, 1-2 Owashi, Tsukuba, Ibaraki, 305-8634, Japan
| | - Akira Murakami
- Department of Biomolecular Engineering, Kyoto Institute of Technology, Matsugasaki, Sakyo-ku, Kyoto, 606-8585, Japan
| | - Tetsuji Yamaoka
- Department of Biomedical Engineering, National Cerebral and Cardiovascular Center Research Institute, 5-7-1 Fujishiro-dai, Suita, Osaka, 565-8585, Japan
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13
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Piccirillo S, Wang HL, Fisher TJ, Honigberg SM. GAL1-SceI directed site-specific genomic (gsSSG) mutagenesis: a method for precisely targeting point mutations in S. cerevisiae. BMC Biotechnol 2011; 11:120. [PMID: 22141399 PMCID: PMC3251539 DOI: 10.1186/1472-6750-11-120] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2011] [Accepted: 12/05/2011] [Indexed: 12/18/2022] Open
Abstract
Background Precise targeted mutations are defined as targeted mutations that do not require the retention of other genetic changes, such as marker genes, near the mutation site. In the yeast, S. cerevisiae, there are several methods for introducing precise targeted mutations, all of which depend on inserting both a counter-selectable marker and DNA bearing the mutation. For example, the marker can first be inserted, and then replaced with either a long oligonucleotide carrying the mutation (delitto perfetto) or a PCR fragment synthesized with one primer containing the mutation (SSG mutagenesis). Results A hybrid method for targeting precise mutation into the genomes uses PCR fragments as in SSG mutagenesis together with a CORE cassette devised for delitto perfetto that contains the homing endonuclease SceI. This method, termed gsSSG mutagenesis, is much more efficient than standard SSG mutagenesis, allowing replacements to be identified without extensive screening of isolates. In gsSSG, recombination between the PCR fragment and the genome occurs equally efficiently regardless of the size of the fragment or the distance between the fragment end and the site of marker insertion. In contrast, the efficiency of incorporating targeted mutations by this method increases as the distance between the mutation and the marker insertion site decreases. Conclusion gsSSG is an efficient way of introducing precise mutations into the genome of S. cerevisiae. The frequency of incorporating the targeted mutation remains efficient at least as far as 460 bp from the insertion site meaning that a single insertion can be used to create many different mutants. The overall efficiency of gsSSG can be estimated based on the distance between the mutation and the marker insertion, and this efficiency can be maximized by limiting the number of untargeted mutations. Thus, a single insertion of marker genes plus homing endonuclease cassette can be used to efficiently introduce precise point mutations through a region of > 900 bp.
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Affiliation(s)
- Sarah Piccirillo
- School of Biological Sciences, University of Missouri-Kansas City, Kansas City, MO 64110, USA
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14
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Miki K, Shimizu M, Fujii M, Takayama S, Hossain MN, Ayusawa D. 5-bromodeoxyuridine induces transcription of repressed genes with disruption of nucleosome positioning. FEBS J 2010; 277:4539-48. [PMID: 21040474 DOI: 10.1111/j.1742-4658.2010.07868.x] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
5-Bromodeoxyuridine (BrdU) modulates the expression of particular genes associated with cellular differentiation and senescence when incorporated into DNA instead of thymidine (dThd). To date, a molecular mechanism for this phenomenon remains a mystery in spite of a large number of studies. Recently, we have demonstrated that BrdU disrupts nucleosome positioning on model plasmids mediated by specific AT-tracts in yeast cells. Here we constructed a cognate plasmid that can form an ordered array of nucleosomes determined by an α2 operator and contains the BAR1 gene as an expression marker gene to examine BAR1 expression in dThd-auxotrophic MATα cells under various conditions. In medium containing dThd, BAR1 expression was completely repressed, associated with the formation of the stable array of nucleosomes. Insertion of AT-tracts into a site of the promoter region slightly increased BAR1 expression and slightly destabilized nucleosome positioning dependent on their sequence specificity. In medium containing BrdU, BAR1 expression was further enhanced, associated with more marked disruption of nucleosome positioning on the promoter region. Disruption of nucleosome positioning seems to be sufficient for full expression of the marker gene if necessary transcription factors are supplied. Incorporation of 5-bromouracil into the plasmid did not weaken the binding of the α2/Mcm1 repressor complex to its legitimate binding site, as revealed by an in vivo UV photofootprinting assay. These results suggest that BrdU increases transcription of repressed genes by disruption of nucleosome positioning around their promoters.
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Affiliation(s)
- Kensuke Miki
- Department of Genome System Science, Yokohama City University, Yokohama, Kanagawa, Japan
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15
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Tanaka Y, Yamashita R, Suzuki Y, Nakai K. Effects of Alu elements on global nucleosome positioning in the human genome. BMC Genomics 2010; 11:309. [PMID: 20478020 PMCID: PMC2878307 DOI: 10.1186/1471-2164-11-309] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2009] [Accepted: 05/17/2010] [Indexed: 11/14/2022] Open
Abstract
Background Understanding the genome sequence-specific positioning of nucleosomes is essential to understand various cellular processes, such as transcriptional regulation and replication. As a typical example, the 10-bp periodicity of AA/TT and GC dinucleotides has been reported in several species, but it is still unclear whether this feature can be observed in the whole genomes of all eukaryotes. Results With Fourier analysis, we found that this is not the case: 84-bp and 167-bp periodicities are prevalent in primates. The 167-bp periodicity is intriguing because it is almost equal to the sum of the lengths of a nucleosomal unit and its linker region. After masking Alu elements, these periodicities were greatly diminished. Next, using two independent large-scale sets of nucleosome mapping data, we analyzed the distribution of nucleosomes in the vicinity of Alu elements and showed that (1) there are one or two fixed slot(s) for nucleosome positioning within the Alu element and (2) the positioning of neighboring nucleosomes seems to be in phase, more or less, with the presence of Alu elements. Furthermore, (3) these effects of Alu elements on nucleosome positioning are consistent with inactivation of promoter activity in Alu elements. Conclusions Our discoveries suggest that the principle governing nucleosome positioning differs greatly across species and that the Alu family is an important factor in primate genomes.
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Affiliation(s)
- Yoshiaki Tanaka
- Department of Medical Genome Sciences, University of Tokyo, Minato-ku, Japan
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16
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Effects of non-B DNA sequences on transgene expression. J Biosci Bioeng 2009; 108:20-3. [PMID: 19577186 DOI: 10.1016/j.jbiosc.2009.02.013] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2009] [Revised: 02/13/2009] [Accepted: 02/16/2009] [Indexed: 11/21/2022]
Abstract
DNA conformation may be an important factor affecting gene transcription. In this study, we examined how DNA sequences with unusual conformations affect transgene expression. A(30) and (CG)(15) sequences that can adopt the B' and Z conformations, respectively, were introduced into a beta-actin promoter. Luciferase plasmids containing the manipulated promoter were transfected into NIH3T3 cells by electroporation and were delivered into mouse livers with a hydrodynamics-based injection. Expression from plasmid with the (CG)(15) sequence was multiple times higher than expression from control plasmid DNA. The A(30) sequence also tended to enhance expression. These results suggest that non-B DNA sequences could improve transgene expression in cells.
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17
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Field Y, Kaplan N, Fondufe-Mittendorf Y, Moore IK, Sharon E, Lubling Y, Widom J, Segal E. Distinct modes of regulation by chromatin encoded through nucleosome positioning signals. PLoS Comput Biol 2008; 4:e1000216. [PMID: 18989395 PMCID: PMC2570626 DOI: 10.1371/journal.pcbi.1000216] [Citation(s) in RCA: 365] [Impact Index Per Article: 22.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2008] [Accepted: 09/24/2008] [Indexed: 11/19/2022] Open
Abstract
The detailed positions of nucleosomes profoundly impact gene regulation and are partly encoded by the genomic DNA sequence. However, less is known about the functional consequences of this encoding. Here, we address this question using a genome-wide map of ∼380,000 yeast nucleosomes that we sequenced in their entirety. Utilizing the high resolution of our map, we refine our understanding of how nucleosome organizations are encoded by the DNA sequence and demonstrate that the genomic sequence is highly predictive of the in vivo nucleosome organization, even across new nucleosome-bound sequences that we isolated from fly and human. We find that Poly(dA:dT) tracts are an important component of these nucleosome positioning signals and that their nucleosome-disfavoring action results in large nucleosome depletion over them and over their flanking regions and enhances the accessibility of transcription factors to their cognate sites. Our results suggest that the yeast genome may utilize these nucleosome positioning signals to regulate gene expression with different transcriptional noise and activation kinetics and DNA replication with different origin efficiency. These distinct functions may be achieved by encoding both relatively closed (nucleosome-covered) chromatin organizations over some factor binding sites, where factors must compete with nucleosomes for DNA access, and relatively open (nucleosome-depleted) organizations over other factor sites, where factors bind without competition. The detailed positions of nucleosomes along genomes have critical roles in transcriptional regulation. Consequently, it is important to understand the principles that govern the organization of nucleosomes in vivo and the functional consequences of this organization. Here we report on progress in identifying the functional consequences of nucleosome organization, in understanding the way in which nucleosome organization is encoded in the DNA, and in linking the two, by suggesting that distinct transcriptional behaviors are encoded through the genome's intrinsic nucleosome organization. Our results thus provide insight on the broader question of understanding how transcriptional programs are encoded in the DNA sequence. These new insights were enabled by individually sequencing ∼380,000 nucleosomes from yeast in their entirety. Using this map, we refine our previous model for predicting nucleosome positions and demonstrate that our new model predicts nucleosome organizations in yeast with high accuracy and that its nucleosome positioning signals are predictive across eukaryotes. We show that the yeast genome may utilize these nucleosome positioning signals to encode regions with both relatively open (nucleosome-depleted) chromatin organizations and relatively closed (nucleosome-covered) chromatin organizations and that this encoding can partly explain aspects of transcription factor binding, gene expression, transcriptional noise, and DNA replication.
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Affiliation(s)
- Yair Field
- Department of Computer Science and Applied Mathematics, Weizmann Institute of Science, Rehovot, Israel
| | - Noam Kaplan
- Department of Computer Science and Applied Mathematics, Weizmann Institute of Science, Rehovot, Israel
| | - Yvonne Fondufe-Mittendorf
- Department of Biochemistry, Molecular Biology, and Cell Biology, Northwestern University, Evanston, Illinois, United States of America
| | - Irene K. Moore
- Department of Biochemistry, Molecular Biology, and Cell Biology, Northwestern University, Evanston, Illinois, United States of America
| | - Eilon Sharon
- Department of Computer Science and Applied Mathematics, Weizmann Institute of Science, Rehovot, Israel
| | - Yaniv Lubling
- Department of Computer Science and Applied Mathematics, Weizmann Institute of Science, Rehovot, Israel
| | - Jonathan Widom
- Department of Biochemistry, Molecular Biology, and Cell Biology, Northwestern University, Evanston, Illinois, United States of America
- * E-mail: (JW); (ES)
| | - Eran Segal
- Department of Computer Science and Applied Mathematics, Weizmann Institute of Science, Rehovot, Israel
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
- * E-mail: (JW); (ES)
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18
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Endoh M, Kobayashi Y, Yamakami Y, Yonekura R, Fujii M, Ayusawa D. Coordinate expression of the human pregnancy-specific glycoprotein gene family during induced and replicative senescence. Biogerontology 2008; 10:213-21. [PMID: 18792801 DOI: 10.1007/s10522-008-9173-3] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2008] [Accepted: 08/18/2008] [Indexed: 10/21/2022]
Abstract
Pregnancy-specific glycoproteins (PSGs) comprise a family of highly similar polypeptides encoded by 11 transcriptionally active genes that compactly cluster on band 19q13.2. All members of the PSG family were found to be markedly up-regulated by addition of 5-bromodeoxyuridine in HeLa cells. Similarly, all of the members were markedly up-regulated during replicative senescence in normal human fibroblasts. Promoter analysis of the PSG1, 4, and 11 genes in HeLa cells did not reveal a cis-regulatory element responsive to 5-bromodeoxyuridine in their 5'-flanking sequences. These results suggest that the PSG genes are regulated at a level of higher order chromatin structure besides by a signal of pregnancy.
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Affiliation(s)
- Morio Endoh
- International Graduate School of Arts and Sciences, Yokohama City University, Seto 22-2, Kanazawa-ku, Yokohama, Kanagawa, 236-0027, Japan
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19
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Schnitzler GR. Control of Nucleosome Positions by DNA Sequence and Remodeling Machines. Cell Biochem Biophys 2008; 51:67-80. [DOI: 10.1007/s12013-008-9015-6] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/06/2008] [Indexed: 12/24/2022]
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20
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Transcriptional repression by the Pho4 transcription factor controls the timing of SNZ1 expression. EUKARYOTIC CELL 2008; 7:949-57. [PMID: 18408055 DOI: 10.1128/ec.00366-07] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Nutrient-sensing kinases play important roles for the yeast Saccharomyces cerevisiae to adapt to new nutrient conditions when the nutrient status changes. Our previous global gene expression analysis revealed that the Pho85 kinase, one of the yeast nutrient-sensing kinases, is involved in the changes in gene expression profiles when yeast cells undergo a diauxic shift. We also found that the stationary phase-specific genes SNZ1 and SNO1, which share a common promoter, are not properly induced when Pho85 is absent. To examine the role of the kinase in SNZ1/SNO1 regulation, we analyzed their expression during the growth of various yeast mutants, including those affecting Pho85 function or lacking the Pho4 transcription factor, an in vivo substrate of Pho85, and tested Pho4 binding by chromatin immunoprecipitation. Pho4 exhibits temporal binding to the SNZ1/SNO1 promoter to down-regulate the promoter activity, and a Deltapho4 mutation advances the timing of SNZ1/SNO1 expression. SNZ2, another member of the SNZ/SNO family, is expressed at an earlier growth stage than SNZ1, and Pho4 does not affect this timing, although Pho85 is required for SNZ2 expression. Thus, Pho4 appears to regulate the different timing of the expression of the SNZ/SNO family members. Pho4 binding to the SNZ1/SNO1 promoter is accompanied by alterations in chromatin structure, and Rpd3 histone deacetylase is required for the proper timing of SNZ1/SNO1 expression, while Asf1 histone chaperone is indispensable for their expression. These results imply that Pho4 plays positive and negative roles in transcriptional regulation, with both cases involving structural changes in its target chromatin.
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21
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Morohashi N, Nakajima K, Kuwana S, Tachiwana H, Kurumizaka H, Shimizu M. In vivo and in vitro footprinting of nucleosomes and transcriptional activators using an infrared-fluorescence DNA sequencer. Biol Pharm Bull 2008; 31:187-92. [PMID: 18239271 DOI: 10.1248/bpb.31.187] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The analysis of nucleosome positions and transcription factor binding in chromatin is a central issue for understanding the mechanisms of gene expression in eukaryotes. Here, we have developed a footprinting technique, using multi-cycle primer extension with an infrared-fluorescence DNA sequencer, to analyze chromatin structure in isolated yeast nuclei and transcriptional activator binding in living yeast cells. Using this technique, the binding of the yeast activators Hap1 and Hap2/3/4/5 to their cognate sites was detectable as hypersensitive sites by in vivo UV-photofootprinting, and the locations of nucleosomes in yeast minichromosomes were determined by micrococcal nuclease mapping. We also applied this method to determine the position of the nucleosome in the 5S DNA fragment reconstituted in vitro. This technique allowed us to eliminate the use of radioactive materials and to perform experiments on common benches. Thus, the footprinting procedure established in this study will be useful to researchers studying DNA-protein interactions and chromatin structure in vivo and in vitro.
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Affiliation(s)
- Nobuyuki Morohashi
- Department of Chemistry, Graduate School of Science and Engineering, Meisei University, Hino, Tokyo, Japan
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22
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Morohashi N, Nakajima K, Kurihara D, Mukai Y, Mitchell AP, Shimizu M. A nucleosome positioned by alpha2/Mcm1 prevents Hap1 activator binding in vivo. Biochem Biophys Res Commun 2007; 364:583-8. [PMID: 17959145 DOI: 10.1016/j.bbrc.2007.10.037] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2007] [Accepted: 10/09/2007] [Indexed: 11/24/2022]
Abstract
Nucleosome positioning has been proposed as a mechanism of transcriptional repression. Here, we examined whether nucleosome positioning affects activator binding in living yeast cells. We introduced the cognate Hap1 binding site (UAS1) at a location 24-43 bp, 29-48 bp, or 61-80 bp interior to the edge of a nucleosome positioned by alpha2/Mcm1 in yeast minichromosomes. Hap1 binding to the UAS1 was severely inhibited, not only at the pseudo-dyad but also in the peripheral region of the positioned nucleosome in alpha cells, while it was detectable in a cells, in which the nucleosomes were not positioned. Hap1 binding was restored in alpha cells with tup1 or isw2 mutations, which caused the loss of nucleosome positioning. These results support the mechanism in which alpha2/Mcm1-dependent nucleosome positioning has a regulatory function to limit the access of transcription factors.
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Affiliation(s)
- Nobuyuki Morohashi
- Department of Chemistry, Meisei University, 2-1-1 Hodokubo, Hino, Tokyo 191-8506, Japan
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23
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Frýdlová I, Basler M, Vasicová P, Malcová I, Hasek J. Special type of pheromone-induced invasive growth in Saccharomyces cerevisiae. Curr Genet 2007; 52:87-95. [PMID: 17639399 DOI: 10.1007/s00294-007-0141-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2007] [Revised: 06/22/2007] [Accepted: 06/28/2007] [Indexed: 10/23/2022]
Abstract
The ability to invade a solid substrate is an important phenomenon due to its connection with pathogenic activity of fungi. We report here on invasion displayed by MATalpha cells of Saccharomyces cerevisiae lacking Isw2p, a subunit of the ISW2 chromatin remodelling complex. We found that on minimal medium, where the isw2Delta MATalpha mutant is not invasive, additional absence of another ISW2 complex subunit, Dls1p or Dpb4p, promoted invasion. Our microarray data showed that derepression of MAT a-specific genes caused by absence of Isw2p is very low. Their expression is increased only by the autocrine activation of the mating pathway. Invasion of isw2Delta MATalpha cells thus resembles the pheromone-induced invasion, including dependence on Fig2p. We show here that another pheromone-induced protein, mating agglutinin Aga1p, can play a role in the agar adhesion necessary for invasion. In contrast with MAT a-cells invading agar under low alpha-pheromone concentration, the invasive growth of isw2Delta cells specifically requires Fus3 kinase. Its function in the invasion of isw2Delta MATalpha cells cannot be completely substituted by Kss1 kinase, which plays a basic role in invasive growth signalling. We suggest that partial dependence of the isw2Delta MATalpha invasion on Fus3p and Aga1p corresponds to a weaker pheromone response of this mutant.
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Affiliation(s)
- Ivana Frýdlová
- Institute of Microbiology of AS CR, v.v.i, Vídenská 1083, 142 20 Prague 4, Czech Republic
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24
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Current awareness on yeast. Yeast 2007. [DOI: 10.1002/yea.1328] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
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25
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Zhang H, Reese JC. Exposing the core promoter is sufficient to activate transcription and alter coactivator requirement at RNR3. Proc Natl Acad Sci U S A 2007; 104:8833-8. [PMID: 17502614 PMCID: PMC1885588 DOI: 10.1073/pnas.0701666104] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Chromatin is a formidable barrier to transcription. Nucleosome density is lowest over the regulatory regions of active genes, and many repressed genes have a tightly positioned nucleosome over their core promoter. However, it has not been shown that nucleosome positioning is sufficient for repression or whether disrupting a core promoter nucleosome specifically can activate gene expression in the absence of activating signals. Here we show that disrupting the nucleosome over the core promoter of RNR3 is sufficient to drive preinitiation complex assembly and activate transcription in the absence of activating signals. Remodeling of chromatin over the RNR3 promoter requires the recruitment of the SWI/SNF complex by the general transcription factor TFIID. We found that disrupting the nucleosome over the RNR3 core promoter relieves its dependence on TFIID and SWI/SNF, indicating a functional link between these two complexes. These results suggest that the specific function of TAF(II)s is to direct the chromatin remodeling step through SWI/SNF recruitment, and not core promoter selectivity. Our results indicate that nucleosome placement plays a dominant role in repression and that the ability of the core promoter to position a nucleosome is a major determinant in TAF(II) dependency of genes in vivo.
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Affiliation(s)
- Hesheng Zhang
- Department of Biochemistry and Molecular Biology, Center for Gene Regulation, Pennsylvania State University, University Park, PA 16802
| | - Joseph C. Reese
- Department of Biochemistry and Molecular Biology, Center for Gene Regulation, Pennsylvania State University, University Park, PA 16802
- *To whom correspondence should be addressed. E-mail:
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