1
|
Serra-Cardona A, Hua X, McNutt SW, Zhou H, Toda T, Jia S, Chu F, Zhang Z. The PCNA-Pol δ complex couples lagging strand DNA synthesis to parental histone transfer for epigenetic inheritance. SCIENCE ADVANCES 2024; 10:eadn5175. [PMID: 38838138 PMCID: PMC11152121 DOI: 10.1126/sciadv.adn5175] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/14/2023] [Accepted: 05/01/2024] [Indexed: 06/07/2024]
Abstract
Inheritance of epigenetic information is critical for maintaining cell identity. The transfer of parental histone H3-H4 tetramers, the primary carrier of epigenetic modifications on histone proteins, represents a crucial yet poorly understood step in the inheritance of epigenetic information. Here, we show the lagging strand DNA polymerase, Pol δ, interacts directly with H3-H4 and that the interaction between Pol δ and the sliding clamp PCNA regulates parental histone transfer to lagging strands, most likely independent of their roles in DNA synthesis. When combined, mutations at Pol δ and Mcm2 that compromise parental histone transfer result in a greater reduction in nucleosome occupancy at nascent chromatin than mutations in either alone. Last, PCNA contributes to nucleosome positioning on nascent chromatin. On the basis of these results, we suggest that the PCNA-Pol δ complex couples lagging strand DNA synthesis to parental H3-H4 transfer, facilitating epigenetic inheritance.
Collapse
Affiliation(s)
- Albert Serra-Cardona
- Institute for Cancer Genetics, Department of Pediatrics and Department of Genetics and Development, Columbia University Irving Medical Center, New York, NY 10019, USA
| | - Xu Hua
- Institute for Cancer Genetics, Department of Pediatrics and Department of Genetics and Development, Columbia University Irving Medical Center, New York, NY 10019, USA
| | - Seth W. McNutt
- Department of Molecular, Cellular, and Biomedical Sciences, University of New Hampshire, Durham, NH 03824, USA
| | - Hui Zhou
- Institute for Cancer Genetics, Department of Pediatrics and Department of Genetics and Development, Columbia University Irving Medical Center, New York, NY 10019, USA
| | - Takenori Toda
- Department of Biological Sciences, Columbia University, New York, NY 10027, USA
| | - Songtao Jia
- Department of Biological Sciences, Columbia University, New York, NY 10027, USA
| | - Feixia Chu
- Department of Molecular, Cellular, and Biomedical Sciences, University of New Hampshire, Durham, NH 03824, USA
| | - Zhiguo Zhang
- Institute for Cancer Genetics, Department of Pediatrics and Department of Genetics and Development, Columbia University Irving Medical Center, New York, NY 10019, USA
| |
Collapse
|
2
|
Battistini F, Sala A, Hospital A, Orozco M. Sequence-Dependent Properties of the RNA Duplex. J Chem Inf Model 2023; 63:5259-5271. [PMID: 37577978 DOI: 10.1021/acs.jcim.3c00741] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/15/2023]
Abstract
Sequence-dependent properties of the DNA duplex have been accurately described using extensive molecular dynamics simulations. The RNA duplex meanwhile─which is typically represented as a sequence-averaged rigid rod─does not benefit from having equivalent molecular dynamics simulations. In this paper, we present a massive simulation effort using a set of ABC-optimized duplexes from which we derived tetramer-resolution properties of the RNA duplex and a simple mesoscopic model that can represent elastic properties of long RNA duplexes. Despite the extreme chemical similarity between DNA and RNA, the local and global elastic properties of the duplexes are very different. DNA duplexes show a complex and nonelastic pattern of flexibility, for instance, while RNA duplexes behave as an elastic system whose deformations can be represented by simple harmonic potentials. In RNA duplexes (RNA2), not only are intra- and interbase pair parameters (equilibrium and mechanical) different from those in the equivalent DNA duplex sequences (DNA2) but the correlations between movements also differ. Simple statements on the relative flexibility or stability of both polymers are meaningless and should be substituted by a more detailed description depending on the sequence and the type of deformation considered.
Collapse
Affiliation(s)
- Federica Battistini
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology (BIST), Baldiri Reixac 10, Barcelona 08028, Spain
- Departament de Bioquímica i Biomedicina. Facultat de Biologia, Universitat de Barcelona, Avgda Diagonal 647, Barcelona 08028, Spain
| | - Alba Sala
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology (BIST), Baldiri Reixac 10, Barcelona 08028, Spain
| | - Adam Hospital
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology (BIST), Baldiri Reixac 10, Barcelona 08028, Spain
| | - Modesto Orozco
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology (BIST), Baldiri Reixac 10, Barcelona 08028, Spain
- Departament de Bioquímica i Biomedicina. Facultat de Biologia, Universitat de Barcelona, Avgda Diagonal 647, Barcelona 08028, Spain
| |
Collapse
|
3
|
Barissi S, Sala A, Wieczór M, Battistini F, Orozco M. DNAffinity: a machine-learning approach to predict DNA binding affinities of transcription factors. Nucleic Acids Res 2022; 50:9105-9114. [PMID: 36018808 PMCID: PMC9458447 DOI: 10.1093/nar/gkac708] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2022] [Revised: 07/21/2022] [Accepted: 08/08/2022] [Indexed: 12/24/2022] Open
Abstract
We present a physics-based machine learning approach to predict in vitro transcription factor binding affinities from structural and mechanical DNA properties directly derived from atomistic molecular dynamics simulations. The method is able to predict affinities obtained with techniques as different as uPBM, gcPBM and HT-SELEX with an excellent performance, much better than existing algorithms. Due to its nature, the method can be extended to epigenetic variants, mismatches, mutations, or any non-coding nucleobases. When complemented with chromatin structure information, our in vitro trained method provides also good estimates of in vivo binding sites in yeast.
Collapse
Affiliation(s)
| | | | - Miłosz Wieczór
- Institute for Research in Biomedicine (IRB Barcelona). The Barcelona Institute of Science and Technology. Baldiri Reixac 10–12, 08028 Barcelona, Spain,Department of Physical Chemistry. Gdansk University of Technology, 80-233 Gdańsk, Poland
| | | | - Modesto Orozco
- Correspondence may also be addressed to Modesto Orozco. Tel: +34 934 037 156;
| |
Collapse
|
4
|
A study of strong nucleosomes in the human genome. iScience 2022; 25:104593. [PMID: 35789840 PMCID: PMC9249913 DOI: 10.1016/j.isci.2022.104593] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2021] [Revised: 03/03/2022] [Accepted: 06/08/2022] [Indexed: 11/30/2022] Open
Abstract
Micrococcal nuclease (MNase) is widely used to map nucleosomes. However, nucleosomes are highly dynamic and susceptible to experimental conditions, resulting in extreme variability across nucleosome maps, which complicates the generation of accurate nucleosome organization data. We mapped nucleosomes from different individuals using improved MNase-seq. The improvements included setting different digestion levels (low, medium, high) and naked DNA correction to remove the noise caused by experimental manipulation and comparing maps to obtain the accurate position and occupancy of strong nucleosomes (SNs) in the whole genome. In addition, the characteristics of SNs were further excavated. SNs were enriched in Alu elements and near the centromere of Chr12. SNs contain some specific sequences, and the GC content of SNs is different from that of dynamic nucleosomes. The findings suggest that nucleosome location in the genome and the DNA sequence may affect nucleosome stability. Naked DNA correction improved the accuracy of nucleosome map in partial digestion Level of MNase digestion has effects on nucleosome organization A type of strong nucleosomes (SNs) exist across different nucleosome maps Nucleosome stability may be related to its location and the DNA sequence
Collapse
|
5
|
Liu G, Zhao H, Meng H, Xing Y, Yang H, Lin H. Deform-nu: A DNA Deformation Energy-Based Predictor for Nucleosome Positioning. Front Cell Dev Biol 2021; 8:596341. [PMID: 33425904 PMCID: PMC7785812 DOI: 10.3389/fcell.2020.596341] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2020] [Accepted: 11/26/2020] [Indexed: 12/01/2022] Open
Abstract
The structure and function of chromatin can be regulated through positioning patterns of nucleosomes. DNA-based processes are regulated via nucleosomes. Therefore, it is significant to determine nucleosome positions in DNA-based processes. A deformation energy model was proposed to predict nucleosome positions in our previous study. A free web server based on the model (http://lin-group.cn/server/deform-nu/) was firstly established to estimate the occupancy and rotational positioning of nucleosomes in the study. Then, the performance of the model was verified by several examples. The results indicated that nucleosome positioning relied on the physical properties of DNA, such as deformation energy.
Collapse
Affiliation(s)
- Guoqing Liu
- School of Life Sciences and Technology, Inner Mongolia University of Science and Technology, Baotou, China
| | - Hongyu Zhao
- School of Life Sciences and Technology, Inner Mongolia University of Science and Technology, Baotou, China
| | - Hu Meng
- School of Life Sciences and Technology, Inner Mongolia University of Science and Technology, Baotou, China
| | - Yongqiang Xing
- School of Life Sciences and Technology, Inner Mongolia University of Science and Technology, Baotou, China
| | - Hui Yang
- School of Life Sciences and Technology, Inner Mongolia University of Science and Technology, Baotou, China
| | - Hao Lin
- Center for Informational Biology, University of Electronic Science and Technology of China, Chengdu, China
| |
Collapse
|
6
|
Melters DP, Dalal Y. Nano-Surveillance: Tracking Individual Molecules in a Sea of Chromatin. J Mol Biol 2020; 433:166720. [PMID: 33221335 PMCID: PMC8770095 DOI: 10.1016/j.jmb.2020.11.019] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2020] [Revised: 11/06/2020] [Accepted: 11/16/2020] [Indexed: 01/12/2023]
Abstract
Chromatin is the epigenomic platform for diverse nuclear processes such as DNA repair, replication, transcription, telomere, and centromere function. In cancer cells, mutations in key processes result in DNA amplification, chromosome translocations, and chromothripsis, severely distorting the natural chromatin state. In normal and diseased states, dozens of chromatin effectors alter the physical integrity and dynamics of chromatin at the level of both single nucleosomes and arrays of nucleosomes folded into 3-dimensional shapes. Integrating these length scales, from the 10 nm sized nucleosome to mitotic chromosomes, whilst jostling within the crowded environment of the cell, cannot yet be achieved by a single technology. In this review, we discuss tools that have proven powerful in the investigation of nucleosome and chromatin fiber dynamics. We also provide a deeper focus into atomic force microscopy (AFM) applications that can bridge diverse length and time scales. Using time course AFM, we observe that chromatin condensation by H1.5 is dynamic, whereas using nano-indentation force spectroscopy we observe that both histone variants and nucleosome binding partners alter material properties of individual nucleosomes. Finally, we demonstrate how high-speed AFM can visualize plasmid DNA dynamics, intermittent nucleosome-nucleosome contacts, and changes in nucleosome phasing along a contiguous chromatin fiber. Altogether, the development of innovative technologies holds the promise of revealing the secret lives of nucleosomes, potentially bridging the gaps in our understanding of how chromatin works within living cells and tissues.
Collapse
Affiliation(s)
- Daniël P Melters
- National Cancer Institute, Center for Cancer Research, Laboratory of Receptor Biology and Gene Expression, Bethesda, MD, United States.
| | - Yamini Dalal
- National Cancer Institute, Center for Cancer Research, Laboratory of Receptor Biology and Gene Expression, Bethesda, MD, United States.
| |
Collapse
|
7
|
Myrum C, Kittleson J, De S, Fletcher BR, Castellano J, Kundu G, Becker KG, Rapp PR. Survey of the Arc Epigenetic Landscape in Normal Cognitive Aging. Mol Neurobiol 2020; 57:2727-2740. [PMID: 32333254 DOI: 10.1007/s12035-020-01915-4] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2019] [Accepted: 03/30/2020] [Indexed: 01/21/2023]
Abstract
Aging is accompanied by aberrant gene expression that ultimately affects brain plasticity and the capacity to form long-term memories. Immediate-early genes (IEGs) play an active role in these processes. Using a rat model of normal cognitive aging, we found that the expression of Egr1 and c-Fos was associated with chronological age, whereas Arc was more tightly linked to cognitive outcomes in aging. More specifically, constitutive Arc expression was significantly elevated in aged rats with memory impairment compared to cognitively intact aged rats and young adult animals. Since alterations in the neuroepigenetic mechanisms that gate hippocampal gene expression are also associated with cognitive outcome in aging, we narrowed our focus on examining potential epigenetic mechanisms that may lead to aberrant Arc expression. Employing a multilevel analytical approach using bisulfite sequencing, chromatin immunoprecipitations, and micrococcal nuclease digestion, we identified CpG sites in the Arc promoter that were coupled to poor cognitive outcomes in aging, histone marks that were similarly coupled to spatial memory deficits, and nucleosome positioning that also varied depending on cognitive status. Together, these findings paint a diverse and complex picture of the Arc epigenetic landscape in cognitive aging and bolster a body of work, indicating that dysfunctional epigenetic regulation is associated with memory impairment in the aged brain.
Collapse
Affiliation(s)
- Craig Myrum
- Neurocognitive Aging Section, Laboratory of Behavioral Neuroscience, National Institute on Aging, National Institutes of Health (NIH), 251 Bayview Blvd., Baltimore, MD, 21224, USA
| | - Joshua Kittleson
- Neurocognitive Aging Section, Laboratory of Behavioral Neuroscience, National Institute on Aging, National Institutes of Health (NIH), 251 Bayview Blvd., Baltimore, MD, 21224, USA
| | - Supriyo De
- Computational Biology Core, Laboratory of Genetics & Genomics (LGG), National Institute on Aging (NIA), National Institutes of Health (NIH), Baltimore, MD, USA
| | - Bonnie R Fletcher
- Neurocognitive Aging Section, Laboratory of Behavioral Neuroscience, National Institute on Aging, National Institutes of Health (NIH), 251 Bayview Blvd., Baltimore, MD, 21224, USA
| | - James Castellano
- Neurocognitive Aging Section, Laboratory of Behavioral Neuroscience, National Institute on Aging, National Institutes of Health (NIH), 251 Bayview Blvd., Baltimore, MD, 21224, USA
| | - Gautam Kundu
- Computational Biology Core, Laboratory of Genetics & Genomics (LGG), National Institute on Aging (NIA), National Institutes of Health (NIH), Baltimore, MD, USA
| | - Kevin G Becker
- Gene Expression and Genomics Unit, National Institute on Aging (NIA), National Institutes of Health (NIH), Baltimore, MD, USA
| | - Peter R Rapp
- Neurocognitive Aging Section, Laboratory of Behavioral Neuroscience, National Institute on Aging, National Institutes of Health (NIH), 251 Bayview Blvd., Baltimore, MD, 21224, USA.
| |
Collapse
|
8
|
Buitrago D, Codó L, Illa R, de Jorge P, Battistini F, Flores O, Bayarri G, Royo R, Del Pino M, Heath S, Hospital A, Gelpí JL, Heath IB, Orozco M. Nucleosome Dynamics: a new tool for the dynamic analysis of nucleosome positioning. Nucleic Acids Res 2019; 47:9511-9523. [PMID: 31504766 PMCID: PMC6765203 DOI: 10.1093/nar/gkz759] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2019] [Revised: 07/23/2019] [Accepted: 08/22/2019] [Indexed: 02/03/2023] Open
Abstract
We present Nucleosome Dynamics, a suite of programs integrated into a virtual research environment and created to define nucleosome architecture and dynamics from noisy experimental data. The package allows both the definition of nucleosome architectures and the detection of changes in nucleosomal organization due to changes in cellular conditions. Results are displayed in the context of genomic information thanks to different visualizers and browsers, allowing the user a holistic, multidimensional view of the genome/transcriptome. The package shows good performance for both locating equilibrium nucleosome architecture and nucleosome dynamics and provides abundant useful information in several test cases, where experimental data on nucleosome position (and for some cases expression level) have been collected for cells under different external conditions (cell cycle phase, yeast metabolic cycle progression, changes in nutrients or difference in MNase digestion level). Nucleosome Dynamics is a free software and is provided under several distribution models.
Collapse
Affiliation(s)
- Diana Buitrago
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Baldiri Reixac 10, Barcelona 08028, Spain
| | - Laia Codó
- Barcelona Supercomputing Center (BSC), Jordi Girona 31, Barcelona 08028. Spain
| | - Ricard Illa
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Baldiri Reixac 10, Barcelona 08028, Spain
| | - Pau de Jorge
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Baldiri Reixac 10, Barcelona 08028, Spain
| | - Federica Battistini
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Baldiri Reixac 10, Barcelona 08028, Spain
| | - Oscar Flores
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Baldiri Reixac 10, Barcelona 08028, Spain
| | - Genis Bayarri
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Baldiri Reixac 10, Barcelona 08028, Spain
| | - Romina Royo
- Barcelona Supercomputing Center (BSC), Jordi Girona 31, Barcelona 08028. Spain
| | - Marc Del Pino
- Barcelona Supercomputing Center (BSC), Jordi Girona 31, Barcelona 08028. Spain
| | - Simon Heath
- Centro Nacional de Análisis Genómico (CNAG-CRG), Centre de Regulacio Genómico (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Adam Hospital
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Baldiri Reixac 10, Barcelona 08028, Spain
| | - Josep Lluís Gelpí
- Barcelona Supercomputing Center (BSC), Jordi Girona 31, Barcelona 08028. Spain.,Departament de Bioquímica i Biomedicina. Facultat de Biologia, Universitat de Barcelona, Avgda Diagonal 647, Barcelona 08028, Spain
| | - Isabelle Brun Heath
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Baldiri Reixac 10, Barcelona 08028, Spain
| | - Modesto Orozco
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Baldiri Reixac 10, Barcelona 08028, Spain.,Departament de Bioquímica i Biomedicina. Facultat de Biologia, Universitat de Barcelona, Avgda Diagonal 647, Barcelona 08028, Spain
| |
Collapse
|
9
|
Oberbeckmann E, Wolff M, Krietenstein N, Heron M, Ellins JL, Schmid A, Krebs S, Blum H, Gerland U, Korber P. Absolute nucleosome occupancy map for the Saccharomyces cerevisiae genome. Genome Res 2019; 29:1996-2009. [PMID: 31694866 PMCID: PMC6886505 DOI: 10.1101/gr.253419.119] [Citation(s) in RCA: 56] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2019] [Accepted: 10/31/2019] [Indexed: 12/23/2022]
Abstract
Mapping of nucleosomes, the basic DNA packaging unit in eukaryotes, is fundamental for understanding genome regulation because nucleosomes modulate DNA access by their positioning along the genome. A cell-population nucleosome map requires two observables: nucleosome positions along the DNA ("Where?") and nucleosome occupancies across the population ("In how many cells?"). All available genome-wide nucleosome mapping techniques are yield methods because they score either nucleosomal (e.g., MNase-seq, chemical cleavage-seq) or nonnucleosomal (e.g., ATAC-seq) DNA but lose track of the total DNA population for each genomic region. Therefore, they only provide nucleosome positions and maybe compare relative occupancies between positions, but cannot measure absolute nucleosome occupancy, which is the fraction of all DNA molecules occupied at a given position and time by a nucleosome. Here, we established two orthogonal and thereby cross-validating approaches to measure absolute nucleosome occupancy across the Saccharomyces cerevisiae genome via restriction enzymes and DNA methyltransferases. The resulting high-resolution (9-bp) map shows uniform absolute occupancies. Most nucleosome positions are occupied in most cells: 97% of all nucleosomes called by chemical cleavage-seq have a mean absolute occupancy of 90 ± 6% (±SD). Depending on nucleosome position calling procedures, there are 57,000 to 60,000 nucleosomes per yeast cell. The few low absolute occupancy nucleosomes do not correlate with highly transcribed gene bodies, but correlate with increased presence of the nucleosome-evicting chromatin structure remodeling (RSC) complex, and are enriched upstream of highly transcribed or regulated genes. Our work provides a quantitative method and reference frame in absolute terms for future chromatin studies.
Collapse
Affiliation(s)
- Elisa Oberbeckmann
- Molecular Biology Division, Biomedical Center, Faculty of Medicine, Ludwig-Maximilians-Universität München, 82152 Planegg-Martinsried, Germany
| | - Michael Wolff
- Physik Department, Technische Universität München, 85748 Garching, Germany
| | - Nils Krietenstein
- Molecular Biology Division, Biomedical Center, Faculty of Medicine, Ludwig-Maximilians-Universität München, 82152 Planegg-Martinsried, Germany.,Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, Massachusetts 01605, USA
| | - Mark Heron
- Quantitative and Computational Biology, Max Planck Institute for Biophysical Chemistry, 37077 Göttingen, Germany.,Gene Center, Faculty of Chemistry and Pharmacy, Ludwig-Maximilians-Universität München, 81377 Munich, Germany
| | - Jessica L Ellins
- Department of Biochemistry, University of Oxford, Oxford, OX1 3QU, United Kingdom
| | - Andrea Schmid
- Molecular Biology Division, Biomedical Center, Faculty of Medicine, Ludwig-Maximilians-Universität München, 82152 Planegg-Martinsried, Germany
| | - Stefan Krebs
- Laboratory of Functional Genome Analysis (LAFUGA), Gene Center, Faculty of Chemistry and Pharmacy, Ludwig-Maximilians-Universität München, 81377 Munich, Germany
| | - Helmut Blum
- Laboratory of Functional Genome Analysis (LAFUGA), Gene Center, Faculty of Chemistry and Pharmacy, Ludwig-Maximilians-Universität München, 81377 Munich, Germany
| | - Ulrich Gerland
- Physik Department, Technische Universität München, 85748 Garching, Germany
| | - Philipp Korber
- Molecular Biology Division, Biomedical Center, Faculty of Medicine, Ludwig-Maximilians-Universität München, 82152 Planegg-Martinsried, Germany
| |
Collapse
|
10
|
Dronamraju R, Hepperla AJ, Shibata Y, Adams AT, Magnuson T, Davis IJ, Strahl BD. Spt6 Association with RNA Polymerase II Directs mRNA Turnover During Transcription. Mol Cell 2019; 70:1054-1066.e4. [PMID: 29932900 DOI: 10.1016/j.molcel.2018.05.020] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2017] [Revised: 03/23/2018] [Accepted: 05/17/2018] [Indexed: 10/28/2022]
Abstract
Spt6 is an essential histone chaperone that mediates nucleosome reassembly during gene transcription. Spt6 also associates with RNA polymerase II (RNAPII) via a tandem Src2 homology domain. However, the significance of Spt6-RNAPII interaction is not well understood. Here, we show that Spt6 recruitment to genes and the nucleosome reassembly functions of Spt6 can still occur in the absence of its association with RNAPII. Surprisingly, we found that Spt6-RNAPII association is required for efficient recruitment of the Ccr4-Not de-adenylation complex to transcribed genes for essential degradation of a range of mRNAs, including mRNAs required for cell-cycle progression. These findings reveal an unexpected control mechanism for mRNA turnover during transcription facilitated by a histone chaperone.
Collapse
Affiliation(s)
- Raghuvar Dronamraju
- Department of Biochemistry & Biophysics, University of North Carolina School of Medicine, Chapel Hill, NC 27599, USA; Lineberger Comprehensive Cancer Center, University of North Carolina School of Medicine, Chapel Hill, NC 27599, USA
| | - Austin J Hepperla
- Curriculum in Genetics and Molecular Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Yoichiro Shibata
- Lineberger Comprehensive Cancer Center, University of North Carolina School of Medicine, Chapel Hill, NC 27599, USA; Curriculum in Genetics and Molecular Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Alexander T Adams
- Department of Biochemistry & Biophysics, University of North Carolina School of Medicine, Chapel Hill, NC 27599, USA
| | - Terry Magnuson
- Lineberger Comprehensive Cancer Center, University of North Carolina School of Medicine, Chapel Hill, NC 27599, USA; Curriculum in Genetics and Molecular Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA; Department of Genetics, The Carolina Center for Genome Sciences, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Ian J Davis
- Lineberger Comprehensive Cancer Center, University of North Carolina School of Medicine, Chapel Hill, NC 27599, USA; Curriculum in Genetics and Molecular Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA; Department of Genetics, The Carolina Center for Genome Sciences, University of North Carolina, Chapel Hill, NC 27599, USA; Departments of Pediatrics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Brian D Strahl
- Department of Biochemistry & Biophysics, University of North Carolina School of Medicine, Chapel Hill, NC 27599, USA; Lineberger Comprehensive Cancer Center, University of North Carolina School of Medicine, Chapel Hill, NC 27599, USA; Curriculum in Genetics and Molecular Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA.
| |
Collapse
|
11
|
Kumar MA, Kasti K, Balakrishnan L, Milavetz B. Directed Nucleosome Sliding during the Formation of the Simian Virus 40 Particle Exposes DNA Sequences Required for Early Transcription. J Virol 2019; 93:e01678-18. [PMID: 30518654 PMCID: PMC6364036 DOI: 10.1128/jvi.01678-18] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2018] [Accepted: 11/23/2018] [Indexed: 12/14/2022] Open
Abstract
Simian virus 40 (SV40) exists as chromatin throughout its life cycle and undergoes typical epigenetic regulation mediated by changes in nucleosome location and associated histone modifications. In order to investigate the role of epigenetic regulation during the encapsidation of late-stage minichromosomes into virions, we mapped the locations of nucleosomes containing acetylated or methylated lysines in the histone tails of H3 and H4 present in the chromatin from 48-h-postinfection minichromosomes and disrupted virions. In minichromosomes obtained late in infection, nucleosomes were found carrying various histone modifications primarily in the regulatory region, with a major nucleosome located within the enhancer and other nucleosomes at the early and late transcriptional start sites. The nucleosome found in the enhancer would be expected to repress early transcription by blocking access to part of the SP1 binding sites and the left side of the enhancer in late-stage minichromosomes while also allowing late transcription. In chromatin from virions, the principal nucleosome located in the enhancer was shifted ∼70 bases in the late direction from what was found in minichromosomes, and the level of modified histones was increased throughout the genome. The shifting of the enhancer-associated nucleosome to the late side would effectively serve as a switch to relieve the repression of early transcription found in late minichromosomes while likely also repressing late transcription by blocking access to necessary regulatory sequences. This epigenetic switch appeared to occur during the final stage of virion formation.IMPORTANCE For a virus to complete infection, it must produce a new virus particle in which the genome is able to support a new infection. This is particularly important for viruses like simian virus 40 (SV40), which exist as chromatin throughout their life cycles, since chromatin structure plays a major role in the regulation of the life cycle. In order to determine the role of SV40 chromatin structure late in infection, we mapped the locations of nucleosomes and their histone tail modifications in SV40 minichromosomes and in the SV40 chromatin found in virions using chromatin immunoprecipitation-DNA sequencing (ChIP-Seq). We have identified a novel viral transcriptional control mechanism in which a nucleosome found in the regulatory region of the SV40 minichromosome is directed to slide during the formation of the virus particle, exposing transcription factor binding sites required for early transcription that were previously blocked by the presence of the nucleosome.
Collapse
Affiliation(s)
- Meera Ajeet Kumar
- Department of Biomedical Sciences, University of North Dakota School of Medicine and Health Sciences, Grand Forks, North Dakota, USA
| | - Karine Kasti
- Department of Biomedical Sciences, University of North Dakota School of Medicine and Health Sciences, Grand Forks, North Dakota, USA
| | - Lata Balakrishnan
- Department of Biology, Indiana University Purdue University Indianapolis, Indianapolis, Indiana, USA
| | - Barry Milavetz
- Department of Biomedical Sciences, University of North Dakota School of Medicine and Health Sciences, Grand Forks, North Dakota, USA
| |
Collapse
|
12
|
The implication of DNA bending energy for nucleosome positioning and sliding. Sci Rep 2018; 8:8853. [PMID: 29891930 PMCID: PMC5995830 DOI: 10.1038/s41598-018-27247-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2017] [Accepted: 05/24/2018] [Indexed: 11/24/2022] Open
Abstract
Nucleosome not only directly affects cellular processes, such as DNA replication, recombination, and transcription, but also severs as a fundamentally important target of epigenetic modifications. Our previous study indicated that the bending property of DNA is important in nucleosome formation, particularly in predicting the dyad positions of nucleosomes on a DNA segment. Here, we investigated the role of bending energy in nucleosome positioning and sliding in depth to decipher sequence-directed mechanism. The results show that bending energy is a good physical index to predict the free energy in the process of nucleosome reconstitution in vitro. Our data also imply that there are at least 20% of the nucleosomes in budding yeast do not adopt canonical positioning, in which underlying sequences wrapped around histones are structurally symmetric. We also revealed distinct patterns of bending energy profile for distinctly organized chromatin structures, such as well-positioned nucleosomes, fuzzy nucleosomes, and linker regions and discussed nucleosome sliding in terms of bending energy. We proposed that the stability of a nucleosome is positively correlated with the strength of the bending anisotropy of DNA segment, and both accessibility and directionality of nucleosome sliding is likely to be modulated by diverse patterns of DNA bending energy profile.
Collapse
|
13
|
Piao Y, Lee SK, Lee EJ, Robertson KD, Shi H, Ryu KH, Choi JH. CAME: identification of chromatin accessibility from nucleosome occupancy and methylome sequencing. Bioinformatics 2017; 33:1139-1146. [PMID: 28035030 DOI: 10.1093/bioinformatics/btw785] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2016] [Accepted: 12/09/2016] [Indexed: 11/15/2022] Open
Abstract
Motivation Chromatin accessibility plays a key role in epigenetic regulation of gene activation and silencing. Open chromatin regions allow regulatory elements such as transcription factors and polymerases to bind for gene expression while closed chromatin regions prevent the activity of transcriptional machinery. Recently, Methyltransferase Accessibility Protocol for individual templates-Bisulfite Genome Sequencing (MAPit-BGS) and nucleosome occupancy and methylome sequencing (NOMe-seq) have been developed for simultaneously profiling chromatin accessibility and DNA methylation on single molecules. Therefore, there is a great demand in developing computational methods to identify chromatin accessibility from MAPit-BGS and NOMe-seq. Results In this article, we present CAME (Chromatin Accessibility and Methylation), a seed-extension based approach that identifies chromatin accessibility from NOMe-seq. The efficiency and effectiveness of CAME were demonstrated through comparisons with other existing techniques on both simulated and real data, and the results show that our method not only can precisely identify chromatin accessibility but also outperforms other methods. Availability and Implementation CAME is implemented in java and the program is freely available online at http://sourceforge.net/projects/came/. Contacts jechoi@gru.edu or khryu@dblab.chungbuk.ac.kr. Supplementary information Supplementary data are available at Bioinformatics online.
Collapse
Affiliation(s)
- Yongjun Piao
- Cancer Center, Georgia Regents University, Augusta, GA, USA.,College of Electrical and Computer Engineering, Chungbuk National University, Cheongju, Republic of Korea
| | - Seong Keon Lee
- Department of Statistics, Sungshin Women's University, Seoul, Republic of Korea
| | - Eun-Joon Lee
- Cancer Center, Georgia Regents University, Augusta, GA, USA
| | - Keith D Robertson
- Department of Molecular Pharmacology and Experimental Therapeutics, Center for Individualized Medicine, Mayo Clinic, Rochester, MN, USA
| | - Huidong Shi
- Cancer Center, Georgia Regents University, Augusta, GA, USA.,Department of Biochemistry and Molecular Biology
| | - Keun Ho Ryu
- College of Electrical and Computer Engineering, Chungbuk National University, Cheongju, Republic of Korea
| | - Jeong-Hyeon Choi
- Cancer Center, Georgia Regents University, Augusta, GA, USA.,Department of Biostatistics and Epidemiology, Georgia Regents University, Augusta, GA, USA.,Department of Applied Research, Marine Biodiversity Institute of Korea, Seocheon, Republic of Korea
| |
Collapse
|
14
|
Nagari A, Murakami S, Malladi VS, Kraus WL. Computational Approaches for Mining GRO-Seq Data to Identify and Characterize Active Enhancers. Methods Mol Biol 2017; 1468:121-138. [PMID: 27662874 PMCID: PMC5522910 DOI: 10.1007/978-1-4939-4035-6_10] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Transcriptional enhancers are DNA regulatory elements that are bound by transcription factors and act to positively regulate the expression of nearby or distally located target genes. Enhancers have many features that have been discovered using genomic analyses. Recent studies have shown that active enhancers recruit RNA polymerase II (Pol II) and are transcribed, producing enhancer RNAs (eRNAs). GRO-seq, a method for identifying the location and orientation of all actively transcribing RNA polymerases across the genome, is a powerful approach for monitoring nascent enhancer transcription. Furthermore, the unique pattern of enhancer transcription can be used to identify enhancers in the absence of any information about the underlying transcription factors. Here, we describe the computational approaches required to identify and analyze active enhancers using GRO-seq data, including data pre-processing, alignment, and transcript calling. In addition, we describe protocols and computational pipelines for mining GRO-seq data to identify active enhancers, as well as known transcription factor binding sites that are transcribed. Furthermore, we discuss approaches for integrating GRO-seq-based enhancer data with other genomic data, including target gene expression and function. Finally, we describe molecular biology assays that can be used to confirm and explore further the function of enhancers that have been identified using genomic assays. Together, these approaches should allow the user to identify and explore the features and biological functions of new cell type-specific enhancers.
Collapse
Affiliation(s)
- Anusha Nagari
- The Laboratory of Signaling and Gene Expression, Cecil H. and Ida Green Center for Reproductive Biology Sciences, University of Texas Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, TX, 75390-8511, USA
- The Division of Basic Research, Department of Obstetrics and Gynecology, University of Texas Southwestern Medical Center, Dallas, TX, 75390-8511, USA
| | - Shino Murakami
- The Laboratory of Signaling and Gene Expression, Cecil H. and Ida Green Center for Reproductive Biology Sciences, University of Texas Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, TX, 75390-8511, USA
- The Division of Basic Research, Department of Obstetrics and Gynecology, University of Texas Southwestern Medical Center, Dallas, TX, 75390-8511, USA
- Program in Genetics, Development and Disease, Graduate School of Biomedical Sciences, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA
| | - Venkat S Malladi
- The Laboratory of Signaling and Gene Expression, Cecil H. and Ida Green Center for Reproductive Biology Sciences, University of Texas Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, TX, 75390-8511, USA
- The Division of Basic Research, Department of Obstetrics and Gynecology, University of Texas Southwestern Medical Center, Dallas, TX, 75390-8511, USA
| | - W Lee Kraus
- The Laboratory of Signaling and Gene Expression, Cecil H. and Ida Green Center for Reproductive Biology Sciences, University of Texas Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, TX, 75390-8511, USA.
- The Division of Basic Research, Department of Obstetrics and Gynecology, University of Texas Southwestern Medical Center, Dallas, TX, 75390-8511, USA.
- Program in Genetics, Development and Disease, Graduate School of Biomedical Sciences, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA.
| |
Collapse
|
15
|
Liu G, Xing Y, Zhao H, Wang J, Shang Y, Cai L. A deformation energy-based model for predicting nucleosome dyads and occupancy. Sci Rep 2016; 6:24133. [PMID: 27053067 PMCID: PMC4823781 DOI: 10.1038/srep24133] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2016] [Accepted: 03/21/2016] [Indexed: 12/14/2022] Open
Abstract
Nucleosome plays an essential role in various cellular processes, such as DNA replication, recombination, and transcription. Hence, it is important to decode the mechanism of nucleosome positioning and identify nucleosome positions in the genome. In this paper, we present a model for predicting nucleosome positioning based on DNA deformation, in which both bending and shearing of the nucleosomal DNA are considered. The model successfully predicted the dyad positions of nucleosomes assembled in vitro and the in vitro map of nucleosomes in Saccharomyces cerevisiae. Applying the model to Caenorhabditis elegans and Drosophila melanogaster, we achieved satisfactory results. Our data also show that shearing energy of nucleosomal DNA outperforms bending energy in nucleosome occupancy prediction and the ability to predict nucleosome dyad positions is attributed to bending energy that is associated with rotational positioning of nucleosomes.
Collapse
Affiliation(s)
- Guoqing Liu
- The Institute of Bioengineering and Technology, Inner Mongolia University of Science and Technology, Baotou, 014010, China.,Computational Systems Biology Lab, Department of Biochemistry and Molecular Biology, Institute of Bioinformatics, University of Georgia, Athens, GA 30602, USA
| | - Yongqiang Xing
- The Institute of Bioengineering and Technology, Inner Mongolia University of Science and Technology, Baotou, 014010, China
| | - Hongyu Zhao
- The Institute of Bioengineering and Technology, Inner Mongolia University of Science and Technology, Baotou, 014010, China
| | - Jianying Wang
- The Institute of Bioengineering and Technology, Inner Mongolia University of Science and Technology, Baotou, 014010, China.,State Key Laboratory for Utilization of Bayan Obo Multi-Metallic Resources, Inner Mongolia University of Science and Technology, Baotou, 014010, China
| | - Yu Shang
- Computational Systems Biology Lab, Department of Biochemistry and Molecular Biology, Institute of Bioinformatics, University of Georgia, Athens, GA 30602, USA.,College of Computer Science and Technology, Jilin University, Changchun, Jilin 130021, China
| | - Lu Cai
- The Institute of Bioengineering and Technology, Inner Mongolia University of Science and Technology, Baotou, 014010, China
| |
Collapse
|
16
|
Chereji RV, Kan TW, Grudniewska MK, Romashchenko AV, Berezikov E, Zhimulev IF, Guryev V, Morozov AV, Moshkin YM. Genome-wide profiling of nucleosome sensitivity and chromatin accessibility in Drosophila melanogaster. Nucleic Acids Res 2016; 44:1036-51. [PMID: 26429969 PMCID: PMC4756854 DOI: 10.1093/nar/gkv978] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2015] [Revised: 08/27/2015] [Accepted: 09/16/2015] [Indexed: 01/09/2023] Open
Abstract
Nucleosomal DNA is thought to be generally inaccessible to DNA-binding factors, such as micrococcal nuclease (MNase). Here, we digest Drosophila chromatin with high and low concentrations of MNase to reveal two distinct nucleosome types: MNase-sensitive and MNase-resistant. MNase-resistant nucleosomes assemble on sequences depleted of A/T and enriched in G/C-containing dinucleotides, whereas MNase-sensitive nucleosomes form on A/T-rich sequences found at transcription start and termination sites, enhancers and DNase I hypersensitive sites. Estimates of nucleosome formation energies indicate that MNase-sensitive nucleosomes tend to be less stable than MNase-resistant ones. Strikingly, a decrease in cell growth temperature of about 10°C makes MNase-sensitive nucleosomes less accessible, suggesting that observed variations in MNase sensitivity are related to either thermal fluctuations of chromatin fibers or the activity of enzymatic machinery. In the vicinity of active genes and DNase I hypersensitive sites nucleosomes are organized into periodic arrays, likely due to 'phasing' off potential barriers formed by DNA-bound factors or by nucleosomes anchored to their positions through external interactions. The latter idea is substantiated by our biophysical model of nucleosome positioning and energetics, which predicts that nucleosomes immediately downstream of transcription start sites are anchored and recapitulates nucleosome phasing at active genes significantly better than sequence-dependent models.
Collapse
Affiliation(s)
- Răzvan V Chereji
- Program in Genomics of Differentiation, Eunice Kennedy Shriver National Institute for Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892, USA
| | - Tsung-Wai Kan
- Department of Biochemistry, Erasmus Medical Center, P.O. Box 2040, 3000 CA Rotterdam, The Netherlands
| | - Magda K Grudniewska
- European Research Institute for the Biology of Ageing, University of Groningen, University Medical Center Groningen, Groningen, 9713AD, The Netherlands
| | | | - Eugene Berezikov
- European Research Institute for the Biology of Ageing, University of Groningen, University Medical Center Groningen, Groningen, 9713AD, The Netherlands
| | - Igor F Zhimulev
- Institute of Molecular and Cellular Biology, Siberian Branch of RAS, Novosibirsk 630090, Russia
| | - Victor Guryev
- European Research Institute for the Biology of Ageing, University of Groningen, University Medical Center Groningen, Groningen, 9713AD, The Netherlands
| | - Alexandre V Morozov
- Department of Physics and Astronomy and BioMaPS Institute for Quantitative Biology, Rutgers University, Piscataway, NJ 08854, USA
| | - Yuri M Moshkin
- Department of Biochemistry, Erasmus Medical Center, P.O. Box 2040, 3000 CA Rotterdam, The Netherlands Institute of Cytology and Genetics, Siberian Branch of RAS, Novosibirsk 630090, Russia Institute of Molecular and Cellular Biology, Siberian Branch of RAS, Novosibirsk 630090, Russia
| |
Collapse
|
17
|
Deniz Ö, Flores O, Aldea M, Soler-López M, Orozco M. Nucleosome architecture throughout the cell cycle. Sci Rep 2016; 6:19729. [PMID: 26818620 PMCID: PMC4730144 DOI: 10.1038/srep19729] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2015] [Accepted: 09/29/2015] [Indexed: 11/09/2022] Open
Abstract
Nucleosomes provide additional regulatory mechanisms to transcription and DNA replication by mediating the access of proteins to DNA. During the cell cycle chromatin undergoes several conformational changes, however the functional significance of these changes to cellular processes are largely unexplored. Here, we present the first comprehensive genome-wide study of nucleosome plasticity at single base-pair resolution along the cell cycle in Saccharomyces cerevisiae. We determined nucleosome organization with a specific focus on two regulatory regions: transcription start sites (TSSs) and replication origins (ORIs). During the cell cycle, nucleosomes around TSSs display rearrangements in a cyclic manner. In contrast to gap (G1 and G2) phases, nucleosomes have a fuzzier organization during S and M phases, Moreover, the choreography of nucleosome rearrangements correlate with changes in gene expression during the cell cycle, indicating a strong association between nucleosomes and cell cycle-dependent gene functionality. On the other hand, nucleosomes are more dynamic around ORIs along the cell cycle, albeit with tighter regulation in early firing origins, implying the functional role of nucleosomes on replication origins. Our study provides a dynamic picture of nucleosome organization throughout the cell cycle and highlights the subsequent impact on transcription and replication activity.
Collapse
Affiliation(s)
- Özgen Deniz
- Institute for Research in Biomedicine (IRB Barcelona). Baldiri Reixac 10-12. 08028 Barcelona, Spain.,Joint BSC-CRG-IRB Program in Computational Biology. Baldiri Reixac 10-12. 08028 Barcelona, Spain
| | - Oscar Flores
- Institute for Research in Biomedicine (IRB Barcelona). Baldiri Reixac 10-12. 08028 Barcelona, Spain.,Joint BSC-CRG-IRB Program in Computational Biology. Baldiri Reixac 10-12. 08028 Barcelona, Spain
| | - Martí Aldea
- Molecular Biology Institute of Barcelona (IBMB) CSIC. Baldiri Reixac 4. 08028 Barcelona, Spain
| | - Montserrat Soler-López
- Institute for Research in Biomedicine (IRB Barcelona). Baldiri Reixac 10-12. 08028 Barcelona, Spain.,Joint BSC-CRG-IRB Program in Computational Biology. Baldiri Reixac 10-12. 08028 Barcelona, Spain
| | - Modesto Orozco
- Institute for Research in Biomedicine (IRB Barcelona). Baldiri Reixac 10-12. 08028 Barcelona, Spain.,Joint BSC-CRG-IRB Program in Computational Biology. Baldiri Reixac 10-12. 08028 Barcelona, Spain.,Department of Biochemistry and Molecular Biology. University of Barcelona, 08028 Barcelona, Spain
| |
Collapse
|
18
|
Abstract
Nucleosome positioning is an important process required for proper genome packing and its accessibility to execute the genetic program in a cell-specific, timely manner. In the recent years hundreds of papers have been devoted to the bioinformatics, physics and biology of nucleosome positioning. The purpose of this review is to cover a practical aspect of this field, namely, to provide a guide to the multitude of nucleosome positioning resources available online. These include almost 300 experimental datasets of genome-wide nucleosome occupancy profiles determined in different cell types and more than 40 computational tools for the analysis of experimental nucleosome positioning data and prediction of intrinsic nucleosome formation probabilities from the DNA sequence. A manually curated, up to date list of these resources will be maintained at http://generegulation.info.
Collapse
|
19
|
Yoo EJ, Brown CD, Tsai YC, Cooke NE, Liebhaber SA. Autonomous actions of the human growth hormone long-range enhancer. Nucleic Acids Res 2015; 43:2091-101. [PMID: 25662214 PMCID: PMC4344525 DOI: 10.1093/nar/gkv093] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The human growth hormone (hGH) gene is controlled by a long-range enhancer, HSI, located 14.5 kb 5′ to the hGH promoter. HSI establishes a domain of noncoding transcription that is ‘looped’ to the hGH promoter as an essential step in initiating hGH gene expression. Thus, defining how HSI generates its domain of noncoding transcription is central to understanding its long-range function. Here, we demonstrate that activation of noncoding transcription reflects an HSI-autonomous activity fully independent of interactions with linked gene promoters and occurring in spatial and temporal synchrony with initiation of GH expression in the embryonic pituitary. HSI establishes its noncoding transcription start sites (TSS) over a defined distance from its core determinants and in a manner independent of local primary sequences. The interval between HSI and it TSS co-maps with a domain of disordered and/or highly mobile nucleosomes specific to the pituitary locus. Thus, a localized chromatin reconfiguration by HSI and consequent establishment of an adjacent domain of noncoding transcription constitute initiating events in long-range enhancer function within the hGH locus.
Collapse
Affiliation(s)
- Eung Jae Yoo
- Department of Genetics, Perelman School of Medicine University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Christopher D Brown
- Department of Genetics, Perelman School of Medicine University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Yu-Cheng Tsai
- Department of Genetics, Perelman School of Medicine University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Nancy E Cooke
- Department of Genetics, Perelman School of Medicine University of Pennsylvania, Philadelphia, PA 19104, USA Department of Medicine, Perelman School of Medicine University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Stephen A Liebhaber
- Department of Genetics, Perelman School of Medicine University of Pennsylvania, Philadelphia, PA 19104, USA Department of Medicine, Perelman School of Medicine University of Pennsylvania, Philadelphia, PA 19104, USA
| |
Collapse
|
20
|
Nucleosome positioning in yeasts: methods, maps, and mechanisms. Chromosoma 2014; 124:131-51. [PMID: 25529773 DOI: 10.1007/s00412-014-0501-x] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2014] [Revised: 12/02/2014] [Accepted: 12/03/2014] [Indexed: 01/23/2023]
Abstract
Eukaryotic nuclear DNA is packaged into nucleosomes. During the past decade, genome-wide nucleosome mapping across species revealed the high degree of order in nucleosome positioning. There is a conserved stereotypical nucleosome organization around transcription start sites (TSSs) with a nucleosome-depleted region (NDR) upstream of the TSS and a TSS-aligned regular array of evenly spaced nucleosomes downstream over the gene body. As nucleosomes largely impede access to DNA and thereby provide an important level of genome regulation, it is of general interest to understand the mechanisms generating nucleosome positioning and especially the stereotypical NDR-array pattern. We focus here on the most advanced models, unicellular yeasts, and review the progress in mapping nucleosomes and which nucleosome positioning mechanisms are discussed. There are four mechanistic aspects: How are NDRs generated? How are individual nucleosomes positioned, especially those flanking the NDRs? How are nucleosomes evenly spaced leading to regular arrays? How are regular arrays aligned at TSSs? The main candidates for nucleosome positioning determinants are intrinsic DNA binding preferences of the histone octamer, specific DNA binding factors, nucleosome remodeling enzymes, transcription, and statistical positioning. We summarize the state of the art in an integrative model where nucleosomes are positioned by a combination of all these candidate determinants. We highlight the predominance of active mechanisms involving nucleosome remodeling enzymes which may be recruited by DNA binding factors and the transcription machinery. While this mechanistic framework emerged clearly during recent years, the involved factors and their mechanisms are still poorly understood and require future efforts combining in vivo and in vitro approaches.
Collapse
|
21
|
'Memory and molecular turnover,' 30 years after inception. Epigenetics Chromatin 2014; 7:37. [PMID: 25525471 PMCID: PMC4269865 DOI: 10.1186/1756-8935-7-37] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2014] [Accepted: 11/28/2014] [Indexed: 12/28/2022] Open
Abstract
In 1984 Sir Francis Crick hypothesized that memory is recorded in the brain as reversible modifications to DNA and protein, but acknowledged that most biomolecules turn over too rapidly to account for long-term memories. To accommodate this possible paradox he modeled an enzymatic mechanism to maintain modifications on hemi-modified multimeric symmetrical molecules. While studies on the turnover of chromatin modifications that may be involved in memory are in their infancy, an exploration of his model in the light of modern epigenetics produced somewhat surprising results. The molecular turnover rates for two classes of chromatin modifications believed to record and store durable memories were approximated from experiments using diverse approaches and were found to be remarkably short. The half-lives of DNA cytosine methylation and post-translationally modified nucleosomal histones are measured in hours and minutes, respectively, for a subset of sites on chromatin controlling gene expression. It appears likely that the turnover of DNA methylation in the brain and in neurons, in particular, is even more rapid than in other cell types and organs, perhaps accommodating neuronal plasticity, learning, and memory. The machinery responsible for the rapid turnover of DNA methylation and nucleosomal histone modifications is highly complex, partially redundant, and appears to act in a sequence specific manner. Molecular symmetry plays an important part in maintaining site-specific turnover, but its particular role in memory maintenance is unknown. Elucidating Crick’s paradox, the contradiction between rapid molecular turnover of modified biomolecules and long-term memory storage, appears fundamental to understanding cognitive function and neurodegenerative disease.
Collapse
|