1
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Guo J, Li P, Yu A, Chapman MA, Liu A. Genome-wide characterization and evolutionary analysis of linker histones in castor bean ( Ricinus communis). FRONTIERS IN PLANT SCIENCE 2022; 13:1014418. [PMID: 36340363 PMCID: PMC9635857 DOI: 10.3389/fpls.2022.1014418] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/08/2022] [Accepted: 09/30/2022] [Indexed: 06/16/2023]
Abstract
H1s, or linker histones, are ubiquitous proteins in eukaryotic cells, consisting of a globular GH1 domain flanked by two unstructured tails. Whilst it is known that numerous non-allelic variants exist within the same species, the degree of interspecific and intraspecific variation and divergence of linker histones remain unknown. The conserved basic binding sites in GH1 and evenly distributed strong positive charges on the C-terminal domain (CTD) are key structural characters for linker histones to bind chromatin. Based on these features, we identified five linker histones from 13 GH1-containing proteins in castor bean (Ricinus communis), which were named as RcH1.1, RcH1.2a, RcH1.2b, RcH1.3, and RcH1.4 based on their phylogenetic relationships with the H1s from five other economically important Euphorbiaceae species (Hevea brasiliensis Jatropha curcas, Manihot esculenta Mercurialis annua, and Vernicia fordii) and Arabidopsis thaliana. The expression profiles of RcH1 genes in a variety of tissues and stresses were determined from RNA-seq data. We found three RcH1 genes (RcH1.1, RcH1.2a, and RcH1.3) were broadly expressed in all tissues, suggesting a conserved role in stabilizing and organizing the nuclear DNA. RcH1.2a and RcH1.4 was preferentially expressed in floral tissues, indicating potential involvement in floral development in castor bean. Lack of non-coding region and no expression detected in any tissue tested suggest that RcH1.2b is a pseudogene. RcH1.3 was salt stress inducible, but not induced by cold, heat and drought in our investigation. Structural comparison confirmed that GH1 domain was highly evolutionarily conserved and revealed that N- and C-terminal domains of linker histones are divergent between variants, but highly conserved between species for a given variant. Although the number of H1 genes varies between species, the number of H1 variants is relatively conserved in more closely related species (such as within the same family). Through comparison of nucleotide diversity of linker histone genes and oil-related genes, we found similar mutation rate of these two groups of genes. Using Tajima's D and ML-HKA tests, we found RcH1.1 and RcH1.3 may be under balancing selection.
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Affiliation(s)
- Jiayu Guo
- Key Laboratory for Forest Resource Conservation and Utilization in the Southwest Mountains of China, Ministry of Education, Southwest Forestry University, Kunming, China
| | - Ping Li
- Key Laboratory for Forest Resource Conservation and Utilization in the Southwest Mountains of China, Ministry of Education, Southwest Forestry University, Kunming, China
| | - Anmin Yu
- Key Laboratory for Forest Resource Conservation and Utilization in the Southwest Mountains of China, Ministry of Education, Southwest Forestry University, Kunming, China
| | - Mark A. Chapman
- Biological Sciences and Centre for Underutilised Crops, University of Southampton, Southampton, United Kingdom
| | - Aizhong Liu
- Key Laboratory for Forest Resource Conservation and Utilization in the Southwest Mountains of China, Ministry of Education, Southwest Forestry University, Kunming, China
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2
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Zhang H, Huo QY, Gao YQ. DNA Sequence-Dependent Binding of Linker Histone gH1 Regulates Nucleosome Conformations. J Phys Chem B 2022; 126:6771-6779. [PMID: 36062461 DOI: 10.1021/acs.jpcb.2c03785] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Sequence-dependent binding between DNA and proteins in chromatin is an essential part of gene expression. Linker histone H1 is an important protein in the regulation of chromatin compartmentalization and compaction, and its binding with the nucleosome is sensitive to the DNA sequence. Although the interactions of H1 and DNA have been widely investigated, the mechanism of nucleosome conformation changes induced by the DNA-sequence-dependent binding with gH1 (globular H1.0) remains largely unclear at the atomic level. In the present molecular dynamics simulations, both linker and dyad DNAs were mutated to investigate the conformational changes of the nucleosome induced by the sequence-dependent binding of gH1 based on the on-dyad binding mode. Our results indicate that gH1 is insensitive to the DNA sequence of the dyad DNA but presents an apparent preference to linker DNA with an AT-rich sequence. Moreover, this specific binding induces the entry/exit region of a nucleosome to a tight conformation and regulates the accessibility of core histones. Considering that the entry/exit region of the nucleosome is a crucial binding site for many functional proteins related to gene expression, the conformational change at this region could represent an important gene regulation signal.
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Affiliation(s)
- Hong Zhang
- Beijing National Laboratory for Molecular Sciences, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Qin Yuan Huo
- Beijing National Laboratory for Molecular Sciences, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Yi Qin Gao
- Beijing National Laboratory for Molecular Sciences, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China.,Biomedical Pioneering Innovation Center (BIOPIC), Peking University, Beijing 100871, China
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3
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Abstract
In eukaryotic cells, protein and RNA factors involved in genome activities like transcription, RNA processing, DNA replication, and repair accumulate in self-organizing membraneless chromatin subcompartments. These structures contribute to efficiently conduct chromatin-mediated reactions and to establish specific cellular programs. However, the underlying mechanisms for their formation are only partly understood. Recent studies invoke liquid-liquid phase separation (LLPS) of proteins and RNAs in the establishment of chromatin activity patterns. At the same time, the folding of chromatin in the nucleus can drive genome partitioning into spatially distinct domains. Here, the interplay between chromatin organization, chromatin binding, and LLPS is discussed by comparing and contrasting three prototypical chromatin subcompartments: the nucleolus, clusters of active RNA polymerase II, and pericentric heterochromatin domains. It is discussed how the different ways of chromatin compartmentalization are linked to transcription regulation, the targeting of soluble factors to certain parts of the genome, and to disease-causing genetic aberrations.
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Affiliation(s)
- Karsten Rippe
- Division of Chromatin Networks, German Cancer Research Center (DKFZ) and Bioquant, 69120 Heidelberg, Germany
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4
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Soshnev AA, Allis CD, Cesarman E, Melnick AM. Histone H1 Mutations in Lymphoma: A Link(er) between Chromatin Organization, Developmental Reprogramming, and Cancer. Cancer Res 2021; 81:6061-6070. [PMID: 34580064 PMCID: PMC8678342 DOI: 10.1158/0008-5472.can-21-2619] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2021] [Revised: 09/10/2021] [Accepted: 09/23/2021] [Indexed: 11/16/2022]
Abstract
Aberrant cell fate decisions due to transcriptional misregulation are central to malignant transformation. Histones are the major constituents of chromatin, and mutations in histone-encoding genes are increasingly recognized as drivers of oncogenic transformation. Mutations in linker histone H1 genes were recently identified as drivers of peripheral lymphoid malignancy. Loss of H1 in germinal center B cells results in widespread chromatin decompaction, redistribution of core histone modifications, and reactivation of stem cell-specific transcriptional programs. This review explores how linker histones and mutations therein regulate chromatin structure, highlighting reciprocal relationships between epigenetic circuits, and discusses the emerging role of aberrant three-dimensional chromatin architecture in malignancy.
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Affiliation(s)
- Alexey A Soshnev
- Laboratory of Chromatin Biology and Epigenetics, The Rockefeller University, New York, New York.
| | - C David Allis
- Laboratory of Chromatin Biology and Epigenetics, The Rockefeller University, New York, New York
| | - Ethel Cesarman
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, New York
| | - Ari M Melnick
- Division of Hematology & Medical Oncology, Sanford I. Weill Department of Medicine, Weill Cornell Medicine, New York, New York.
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5
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Saha A, Dalal Y. A glitch in the snitch: the role of linker histone H1 in shaping the epigenome in normal and diseased cells. Open Biol 2021; 11:210124. [PMID: 34343462 PMCID: PMC8331230 DOI: 10.1098/rsob.210124] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
Histone H1s or the linker histones are a family of dynamic chromatin compacting proteins that are essential for higher-order chromatin organization. These highly positively charged proteins were previously thought to function solely as repressors of transcription. However, over the last decade, there is a growing interest in understanding this multi-protein family, finding that not all variants act as repressors. Indeed, the H1 family members appear to have distinct affinities for chromatin and may potentially affect distinct functions. This would suggest a more nuanced contribution of H1 to chromatin organization. The advent of new technologies to probe H1 dynamics in vivo, combined with powerful computational biology, and in vitro imaging tools have greatly enhanced our knowledge of the mechanisms by which H1 interacts with chromatin. This family of proteins can be metaphorically compared to the Golden Snitch from the Harry Potter series, buzzing on and off several regions of the chromatin, in combat with competing transcription factors and chromatin remodellers, thereby critical to the epigenetic endgame on short and long temporal scales in the life of the nucleus. Here, we summarize recent efforts spanning structural, computational, genomic and genetic experiments which examine the linker histone as an unseen architect of chromatin fibre in normal and diseased cells and explore unanswered fundamental questions in the field.
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Affiliation(s)
- Ankita Saha
- Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD 20892, USA
| | - Yamini Dalal
- Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD 20892, USA
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6
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Zhao B, Xi Y, Kim J, Sung S. Chromatin architectural proteins regulate flowering time by precluding gene looping. SCIENCE ADVANCES 2021; 7:eabg3097. [PMID: 34117065 PMCID: PMC8195489 DOI: 10.1126/sciadv.abg3097] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/24/2020] [Accepted: 04/28/2021] [Indexed: 05/03/2023]
Abstract
Chromatin structure is critical for gene expression and many other cellular processes. In Arabidopsis thaliana, the floral repressor FLC adopts a self-loop chromatin structure via bridging of its flanking regions. This local gene loop is necessary for active FLC expression. However, the molecular mechanism underlying the formation of this class of gene loops is unknown. Here, we report the characterization of a group of linker histone-like proteins, named the GH1-HMGA family in Arabidopsis, which act as chromatin architecture modulators. We demonstrate that these family members redundantly promote the floral transition through the repression of FLC A genome-wide study revealed that this family preferentially binds to the 5' and 3' ends of gene bodies. The loss of this binding increases FLC expression by stabilizing the FLC 5' to 3' gene looping. Our study provides mechanistic insights into how a family of evolutionarily conserved proteins regulates the formation of local gene loops.
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Affiliation(s)
- Bo Zhao
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX 78712, USA
| | - Yanpeng Xi
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX 78712, USA
| | - Junghyun Kim
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX 78712, USA
| | - Sibum Sung
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX 78712, USA.
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7
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Site-Specific Phosphorylation of Histone H1.4 Is Associated with Transcription Activation. Int J Mol Sci 2020; 21:ijms21228861. [PMID: 33238524 PMCID: PMC7700352 DOI: 10.3390/ijms21228861] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2020] [Revised: 11/12/2020] [Accepted: 11/16/2020] [Indexed: 01/05/2023] Open
Abstract
Core histone variants, such as H2A.X and H3.3, serve specialized roles in chromatin processes that depend on the genomic distributions and amino acid sequence differences of the variant proteins. Modifications of these variants alter interactions with other chromatin components and thus the protein’s functions. These inferences add to the growing arsenal of evidence against the older generic view of those linker histones as redundant repressors. Furthermore, certain modifications of specific H1 variants can confer distinct roles. On the one hand, it has been reported that the phosphorylation of H1 results in its release from chromatin and the subsequent transcription of HIV-1 genes. On the other hand, recent evidence indicates that phosphorylated H1 may in fact be associated with active promoters. This conflict suggests that different H1 isoforms and modified versions of these variants are not redundant when together but may play distinct functional roles. Here, we provide the first genome-wide evidence that when phosphorylated, the H1.4 variant remains associated with active promoters and may even play a role in transcription activation. Using novel, highly specific antibodies, we generated the first genome-wide view of the H1.4 isoform phosphorylated at serine 187 (pS187-H1.4) in estradiol-inducible MCF7 cells. We observe that pS187-H1.4 is enriched primarily at the transcription start sites (TSSs) of genes activated by estradiol treatment and depleted from those that are repressed. We also show that pS187-H1.4 associates with ‘early estrogen response’ genes and stably interacts with RNAPII. Based on the observations presented here, we propose that phosphorylation at S187 by CDK9 represents an early event required for gene activation. This event may also be involved in the release of promoter-proximal polymerases to begin elongation by interacting directly with the polymerase or other parts of the transcription machinery. Although we focused on estrogen-responsive genes, taking into account previous evidence of H1.4′s enrichment of promoters of pluripotency genes, and its involvement with rDNA activation, we propose that H1.4 phosphorylation for gene activation may be a more global observation.
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8
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Computation of FRAP recovery times for linker histone – chromatin binding on the basis of Brownian dynamics simulations. Biochim Biophys Acta Gen Subj 2020; 1864:129653. [DOI: 10.1016/j.bbagen.2020.129653] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2020] [Revised: 04/22/2020] [Accepted: 05/28/2020] [Indexed: 11/22/2022]
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9
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Franklin JM, Ghosh RP, Shi Q, Reddick MP, Liphardt JT. Concerted localization-resets precede YAP-dependent transcription. Nat Commun 2020; 11:4581. [PMID: 32917893 PMCID: PMC7486942 DOI: 10.1038/s41467-020-18368-x] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2019] [Accepted: 07/13/2020] [Indexed: 02/07/2023] Open
Abstract
Yes-associated protein 1 (YAP) is a transcriptional regulator with critical roles in mechanotransduction, organ size control, and regeneration. Here, using advanced tools for real-time visualization of native YAP and target gene transcription dynamics, we show that a cycle of fast exodus of nuclear YAP to the cytoplasm followed by fast reentry to the nucleus ("localization-resets") activates YAP target genes. These "resets" are induced by calcium signaling, modulation of actomyosin contractility, or mitosis. Using nascent-transcription reporter knock-ins of YAP target genes, we show a strict association between these resets and downstream transcription. Oncogenically-transformed cell lines lack localization-resets and instead show dramatically elevated rates of nucleocytoplasmic shuttling of YAP, suggesting an escape from compartmentalization-based control. The single-cell localization and transcription traces suggest that YAP activity is not a simple linear function of nuclear enrichment and point to a model of transcriptional activation based on nucleocytoplasmic exchange properties of YAP.
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Affiliation(s)
- J Matthew Franklin
- Bioengineering, Stanford University, Stanford, CA, 94305, USA
- BioX Institute, Stanford University, Stanford, CA, 94305, USA
- ChEM-H, Stanford University, Stanford, CA, 94305, USA
- Cell Biology Division, Stanford Cancer Institute, Stanford, CA, 94305, USA
- Chemical Engineering, Stanford University, Stanford, CA, 94305, USA
| | - Rajarshi P Ghosh
- Bioengineering, Stanford University, Stanford, CA, 94305, USA.
- BioX Institute, Stanford University, Stanford, CA, 94305, USA.
- ChEM-H, Stanford University, Stanford, CA, 94305, USA.
- Cell Biology Division, Stanford Cancer Institute, Stanford, CA, 94305, USA.
| | - Quanming Shi
- Bioengineering, Stanford University, Stanford, CA, 94305, USA
- BioX Institute, Stanford University, Stanford, CA, 94305, USA
- ChEM-H, Stanford University, Stanford, CA, 94305, USA
- Cell Biology Division, Stanford Cancer Institute, Stanford, CA, 94305, USA
| | - Michael P Reddick
- Bioengineering, Stanford University, Stanford, CA, 94305, USA
- BioX Institute, Stanford University, Stanford, CA, 94305, USA
- ChEM-H, Stanford University, Stanford, CA, 94305, USA
- Cell Biology Division, Stanford Cancer Institute, Stanford, CA, 94305, USA
- Chemical Engineering, Stanford University, Stanford, CA, 94305, USA
| | - Jan T Liphardt
- Bioengineering, Stanford University, Stanford, CA, 94305, USA.
- BioX Institute, Stanford University, Stanford, CA, 94305, USA.
- ChEM-H, Stanford University, Stanford, CA, 94305, USA.
- Cell Biology Division, Stanford Cancer Institute, Stanford, CA, 94305, USA.
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10
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Sridhar A, Orozco M, Collepardo-Guevara R. Protein disorder-to-order transition enhances the nucleosome-binding affinity of H1. Nucleic Acids Res 2020; 48:5318-5331. [PMID: 32356891 PMCID: PMC7261198 DOI: 10.1093/nar/gkaa285] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2020] [Revised: 04/02/2020] [Accepted: 04/14/2020] [Indexed: 12/18/2022] Open
Abstract
Intrinsically disordered proteins are crucial elements of chromatin heterogenous organization. While disorder in the histone tails enables a large variation of inter-nucleosome arrangements, disorder within the chromatin-binding proteins facilitates promiscuous binding to a wide range of different molecular targets, consistent with structural heterogeneity. Among the partially disordered chromatin-binding proteins, the H1 linker histone influences a myriad of chromatin characteristics including compaction, nucleosome spacing, transcription regulation, and the recruitment of other chromatin regulating proteins. Although it is now established that the long C-terminal domain (CTD) of H1 remains disordered upon nucleosome binding and that such disorder favours chromatin fluidity, the structural behaviour and thereby the role/function of the N-terminal domain (NTD) within chromatin is yet unresolved. On the basis of microsecond-long parallel-tempering metadynamics and temperature-replica exchange atomistic molecular dynamics simulations of different H1 NTD subtypes, we demonstrate that the NTD is completely unstructured in solution but undergoes an important disorder-to-order transition upon nucleosome binding: it forms a helix that enhances its DNA binding ability. Further, we show that the helical propensity of the H1 NTD is subtype-dependent and correlates with the experimentally observed binding affinity of H1 subtypes, suggesting an important functional implication of this disorder-to-order transition.
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Affiliation(s)
- Akshay Sridhar
- Maxwell Centre, Cavendish Laboratory, University of Cambridge, JJ Thomson Avenue, Cambridge CB3 0HE, UK
| | - Modesto Orozco
- Institute for Research in Biomedicine, The Barcelona Institute of Science and Technology, Baldiri i Reixac, 19, 08028 Barcelona, Spain
- Department of Biochemistry and Biomedicine, University of Barcelona, Av. Diagonal 647. 08028 Barcelona, Spain
| | - Rosana Collepardo-Guevara
- Maxwell Centre, Cavendish Laboratory, University of Cambridge, JJ Thomson Avenue, Cambridge CB3 0HE, UK
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, UK
- Department of Genetics, University of Cambridge, Cambridge CB2 3EH, UK
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11
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Maguire L, Betterton MD, Hough LE. Bound-State Diffusion due to Binding to Flexible Polymers in a Selective Biofilter. Biophys J 2019; 118:376-385. [PMID: 31858976 DOI: 10.1016/j.bpj.2019.11.026] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2019] [Revised: 11/05/2019] [Accepted: 11/14/2019] [Indexed: 01/02/2023] Open
Abstract
Selective biofilters are used by cells to control the transport of proteins, nucleic acids, and other macromolecules. Biological filters demonstrate both high specificity and rapid motion or high flux of proteins. In contrast, high flux comes at the expense of selectivity in many synthetic filters. Binding can lead to selective transport in systems in which the bound particle can diffuse, but the mechanisms that lead to bound diffusion remain unclear. Previous theory has proposed a molecular mechanism of bound-state mobility based only on transient binding to flexible polymers. However, this mechanism has not been directly tested in experiments. We demonstrate that bound mobility via tethered diffusion can be engineered into a synthetic gel using protein fragments derived from the nuclear pore complex. The resulting bound-state diffusion is quantitatively consistent with theory. Our results suggest that synthetic biological filters can be designed to take advantage of tethered diffusion to give rapid, selective transport.
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Affiliation(s)
- Laura Maguire
- Department of Physics, University of Colorado Boulder, Boulder, Colorado; BioFrontiers Institute, University of Colorado Boulder, Boulder, Colorado
| | - Meredith D Betterton
- Department of Physics, University of Colorado Boulder, Boulder, Colorado; Molecular, Cellular and Developmental Biology, University of Colorado Boulder, Boulder, Colorado
| | - Loren E Hough
- Department of Physics, University of Colorado Boulder, Boulder, Colorado; BioFrontiers Institute, University of Colorado Boulder, Boulder, Colorado.
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12
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Perišić O, Portillo-Ledesma S, Schlick T. Sensitive effect of linker histone binding mode and subtype on chromatin condensation. Nucleic Acids Res 2019; 47:4948-4957. [PMID: 30968131 PMCID: PMC6547455 DOI: 10.1093/nar/gkz234] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2019] [Revised: 03/19/2019] [Accepted: 03/22/2019] [Indexed: 12/14/2022] Open
Abstract
The complex role of linker histone (LH) on chromatin compaction regulation has been highlighted by recent discoveries of the effect of LH binding variability and isoforms on genome structure and function. Here we examine the effect of two LH variants and variable binding modes on the structure of chromatin fibers. Our mesoscale modeling considers oligonucleosomes with H1C and H1E, bound in three different on and off-dyad modes, and spanning different LH densities (0.5–1.6 per nucleosome), over a wide range of physiologically relevant nucleosome repeat lengths (NRLs). Our studies reveal an LH-variant and binding-mode dependent heterogeneous ensemble of fiber structures with variable packing ratios, sedimentation coefficients, and persistence lengths. For maximal compaction, besides dominantly interacting with parental DNA, LHs must have strong interactions with nonparental DNA and promote tail/nonparental core interactions. An off-dyad binding of H1E enables both; others compromise compaction for bendability. We also find that an increase of LH density beyond 1 is best accommodated in chromatosomes with one on-dyad and one off-dyad LH. We suggest that variable LH binding modes and concentrations are advantageous, allowing tunable levels of chromatin condensation and DNA accessibility/interactions. Thus, LHs add another level of epigenetic regulation of chromatin.
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Affiliation(s)
- Ognjen Perišić
- Department of Chemistry, New York University, 1001 Silver, 100 Washington Square East, New York, NY 10003, USA
| | - Stephanie Portillo-Ledesma
- Department of Chemistry, New York University, 1001 Silver, 100 Washington Square East, New York, NY 10003, USA
| | - Tamar Schlick
- Department of Chemistry, New York University, 1001 Silver, 100 Washington Square East, New York, NY 10003, USA.,Courant Institute of Mathematical Sciences, New York University, 251 Mercer Street, New York, NY 10012, USA.,New York University ECNU - Center for Computational Chemistry at NYU Shanghai, 3663 North Zhongshan Road, Shanghai, 200062, China
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13
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Li Y, Li Z, Dong L, Tang M, Zhang P, Zhang C, Cao Z, Zhu Q, Chen Y, Wang H, Wang T, Lv D, Wang L, Zhao Y, Yang Y, Wang H, Zhang H, Roeder RG, Zhu WG. Histone H1 acetylation at lysine 85 regulates chromatin condensation and genome stability upon DNA damage. Nucleic Acids Res 2019; 46:7716-7730. [PMID: 29982688 PMCID: PMC6125638 DOI: 10.1093/nar/gky568] [Citation(s) in RCA: 45] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2018] [Accepted: 06/14/2018] [Indexed: 12/22/2022] Open
Abstract
Linker histone H1 has a key role in maintaining higher order chromatin structure and genome stability, but how H1 functions in these processes is elusive. Here, we report that acetylation of lysine 85 (K85) within the H1 globular domain is a critical post-translational modification that regulates chromatin organization. H1K85 is dynamically acetylated by the acetyltransferase PCAF in response to DNA damage, and this effect is counterbalanced by the histone deacetylase HDAC1. Notably, an acetylation-mimic mutation of H1K85 (H1K85Q) alters H1 binding to the nucleosome and leads to condensed chromatin as a result of increased H1 binding to core histones. In addition, H1K85 acetylation promotes heterochromatin protein 1 (HP1) recruitment to facilitate chromatin compaction. Consequently, H1K85 mutation leads to genomic instability and decreased cell survival upon DNA damage. Together, our data suggest a novel model whereby H1K85 acetylation regulates chromatin structure and preserves chromosome integrity upon DNA damage.
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Affiliation(s)
- Yinglu Li
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Beijing Key Laboratory of Protein Posttranslational Modifications and Cell Function, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Peking University Health Science Center, Beijing 100191, China.,Guangdong Key Laboratory of Genome Instability and Human Disease Prevention, Shenzhen University Carson Cancer Center, Department of Biochemistry and Molecular Biology, School of Medicine, Shenzhen University, Shenzhen 518060, China
| | - Zhiming Li
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Beijing Key Laboratory of Protein Posttranslational Modifications and Cell Function, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Peking University Health Science Center, Beijing 100191, China.,Guangdong Key Laboratory of Genome Instability and Human Disease Prevention, Shenzhen University Carson Cancer Center, Department of Biochemistry and Molecular Biology, School of Medicine, Shenzhen University, Shenzhen 518060, China
| | - Liping Dong
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Ming Tang
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Beijing Key Laboratory of Protein Posttranslational Modifications and Cell Function, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Peking University Health Science Center, Beijing 100191, China
| | - Ping Zhang
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Beijing Key Laboratory of Protein Posttranslational Modifications and Cell Function, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Peking University Health Science Center, Beijing 100191, China
| | - Chaohua Zhang
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Beijing Key Laboratory of Protein Posttranslational Modifications and Cell Function, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Peking University Health Science Center, Beijing 100191, China
| | - Ziyang Cao
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Beijing Key Laboratory of Protein Posttranslational Modifications and Cell Function, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Peking University Health Science Center, Beijing 100191, China
| | - Qian Zhu
- Guangdong Key Laboratory of Genome Instability and Human Disease Prevention, Shenzhen University Carson Cancer Center, Department of Biochemistry and Molecular Biology, School of Medicine, Shenzhen University, Shenzhen 518060, China
| | - Yongcan Chen
- Guangdong Key Laboratory of Genome Instability and Human Disease Prevention, Shenzhen University Carson Cancer Center, Department of Biochemistry and Molecular Biology, School of Medicine, Shenzhen University, Shenzhen 518060, China.,Peking University-Tsinghua University Center for Life Sciences, Beijing 100871, China
| | - Hui Wang
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Beijing Key Laboratory of Protein Posttranslational Modifications and Cell Function, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Peking University Health Science Center, Beijing 100191, China.,Guangdong Key Laboratory of Genome Instability and Human Disease Prevention, Shenzhen University Carson Cancer Center, Department of Biochemistry and Molecular Biology, School of Medicine, Shenzhen University, Shenzhen 518060, China
| | - Tianzhuo Wang
- Department of Anatomy, Histology and Embryology, Peking University Health Science Center, Beijing 100191, China
| | - Danyu Lv
- Department of Anatomy, Histology and Embryology, Peking University Health Science Center, Beijing 100191, China
| | - Lina Wang
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Beijing Key Laboratory of Protein Posttranslational Modifications and Cell Function, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Peking University Health Science Center, Beijing 100191, China
| | - Ying Zhao
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Beijing Key Laboratory of Protein Posttranslational Modifications and Cell Function, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Peking University Health Science Center, Beijing 100191, China
| | - Yang Yang
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Beijing Key Laboratory of Protein Posttranslational Modifications and Cell Function, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Peking University Health Science Center, Beijing 100191, China
| | - Haiying Wang
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Beijing Key Laboratory of Protein Posttranslational Modifications and Cell Function, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Peking University Health Science Center, Beijing 100191, China
| | - Hongquan Zhang
- Department of Anatomy, Histology and Embryology, Peking University Health Science Center, Beijing 100191, China
| | - Robert G Roeder
- Laboratory of Biochemistry and Molecular Biology, The Rockefeller University, New York, NY 10065, USA
| | - Wei-Guo Zhu
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Beijing Key Laboratory of Protein Posttranslational Modifications and Cell Function, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Peking University Health Science Center, Beijing 100191, China.,Guangdong Key Laboratory of Genome Instability and Human Disease Prevention, Shenzhen University Carson Cancer Center, Department of Biochemistry and Molecular Biology, School of Medicine, Shenzhen University, Shenzhen 518060, China.,Peking University-Tsinghua University Center for Life Sciences, Beijing 100871, China
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14
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Ghosh RP, Shi Q, Yang L, Reddick MP, Nikitina T, Zhurkin VB, Fordyce P, Stasevich TJ, Chang HY, Greenleaf WJ, Liphardt JT. Satb1 integrates DNA binding site geometry and torsional stress to differentially target nucleosome-dense regions. Nat Commun 2019; 10:3221. [PMID: 31324780 PMCID: PMC6642133 DOI: 10.1038/s41467-019-11118-8] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2018] [Accepted: 06/20/2019] [Indexed: 01/12/2023] Open
Abstract
The Satb1 genome organizer regulates multiple cellular and developmental processes. It is not yet clear how Satb1 selects different sets of targets throughout the genome. Here we have used live-cell single molecule imaging and deep sequencing to assess determinants of Satb1 binding-site selectivity. We have found that Satb1 preferentially targets nucleosome-dense regions and can directly bind consensus motifs within nucleosomes. Some genomic regions harbor multiple, regularly spaced Satb1 binding motifs (typical separation ~1 turn of the DNA helix) characterized by highly cooperative binding. The Satb1 homeodomain is dispensable for high affinity binding but is essential for specificity. Finally, we find that Satb1-DNA interactions are mechanosensitive. Increasing negative torsional stress in DNA enhances Satb1 binding and Satb1 stabilizes base unpairing regions against melting by molecular machines. The ability of Satb1 to control diverse biological programs may reflect its ability to combinatorially use multiple site selection criteria.
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Affiliation(s)
- Rajarshi P Ghosh
- Bioengineering, Stanford University, Stanford, CA, 94305, USA
- BioX Institute, Stanford University, Stanford, CA, 94305, USA
- ChEM-H, Stanford University, Stanford, CA, 94305, USA
- Cell Biology Division, Stanford Cancer Institute, Stanford, CA, 94305, USA
| | - Quanming Shi
- Bioengineering, Stanford University, Stanford, CA, 94305, USA
- BioX Institute, Stanford University, Stanford, CA, 94305, USA
- ChEM-H, Stanford University, Stanford, CA, 94305, USA
- Cell Biology Division, Stanford Cancer Institute, Stanford, CA, 94305, USA
| | - Linfeng Yang
- Bioengineering, Stanford University, Stanford, CA, 94305, USA
- BioX Institute, Stanford University, Stanford, CA, 94305, USA
- ChEM-H, Stanford University, Stanford, CA, 94305, USA
- Cell Biology Division, Stanford Cancer Institute, Stanford, CA, 94305, USA
| | - Michael P Reddick
- Bioengineering, Stanford University, Stanford, CA, 94305, USA
- BioX Institute, Stanford University, Stanford, CA, 94305, USA
- ChEM-H, Stanford University, Stanford, CA, 94305, USA
- Cell Biology Division, Stanford Cancer Institute, Stanford, CA, 94305, USA
- Chemical Engineering, Stanford University, Stanford, CA, 94305, USA
| | - Tatiana Nikitina
- Laboratory of Cell Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Victor B Zhurkin
- Laboratory of Cell Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Polly Fordyce
- Bioengineering, Stanford University, Stanford, CA, 94305, USA
- ChEM-H, Stanford University, Stanford, CA, 94305, USA
- Department of Genetics, Stanford University, Stanford, CA, 94305, USA
- Chan Zuckerberg Biohub, San Francisco, CA, 94158, USA
| | - Timothy J Stasevich
- Department of Biochemistry and Molecular Biology and the Institute for Genome Architecture and Function, Colorado State University, Fort Collins, CO, USA
| | - Howard Y Chang
- Department of Genetics, Stanford University, Stanford, CA, 94305, USA
- Center for Personal Dynamic Regulomes, Stanford University, Stanford, CA, 94305, USA
- Program in Epithelial Biology, Stanford University School of Medicine, Stanford, CA, 94305, USA
- Howard Hughes Medical Institute, Stanford University, Stanford, CA, USA
| | - William J Greenleaf
- Department of Genetics, Stanford University, Stanford, CA, 94305, USA
- Department of Applied Physics, Stanford University, Stanford, United States
| | - Jan T Liphardt
- Bioengineering, Stanford University, Stanford, CA, 94305, USA.
- BioX Institute, Stanford University, Stanford, CA, 94305, USA.
- ChEM-H, Stanford University, Stanford, CA, 94305, USA.
- Cell Biology Division, Stanford Cancer Institute, Stanford, CA, 94305, USA.
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15
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Fluorescence fluctuation spectroscopy: an invaluable microscopy tool for uncovering the biophysical rules for navigating the nuclear landscape. Biochem Soc Trans 2019; 47:1117-1129. [DOI: 10.1042/bst20180604] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2019] [Revised: 06/03/2019] [Accepted: 06/05/2019] [Indexed: 11/17/2022]
Abstract
Abstract
Nuclear architecture is fundamental to the manner by which molecules traverse the nucleus. The nucleoplasm is a crowded environment where dynamic rearrangements in local chromatin compaction locally redefine the space accessible toward nuclear protein diffusion. Here, we review a suite of methods based on fluorescence fluctuation spectroscopy (FFS) and how they have been employed to interrogate chromatin organization, as well as the impact this structural framework has on nuclear protein target search. From first focusing on a set of studies that apply FFS to an inert fluorescent tracer diffusing inside the nucleus of a living cell, we demonstrate the capacity of this technology to measure the accessibility of the nucleoplasm. Then with a baseline understanding of the exploration volume available to nuclear proteins during target search, we review direct applications of FFS to fluorescently labeled transcription factors (TFs). FFS can detect changes in TF mobility due to DNA binding, as well as the formation of TF complexes via changes in brightness due to oligomerization. Collectively, we find that FFS-based methods can uncover how nuclear proteins in general navigate the nuclear landscape.
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16
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Unraveling the multiplex folding of nucleosome chains in higher order chromatin. Essays Biochem 2019; 63:109-121. [PMID: 31015386 DOI: 10.1042/ebc20180066] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2018] [Revised: 02/25/2019] [Accepted: 03/01/2019] [Indexed: 12/19/2022]
Abstract
The DNA of eukaryotic chromatin and chromosomes is repeatedly supercoiled around histone octamers forming 'beads-on-a-string' chains of nucleosomes. The extent of nucleosome chain folding and DNA accessibility vary between different functional and epigenetic states of nuclear chromatin and change dramatically upon cell differentiation, but the molecular mechanisms that direct 3D folding of the nucleosome chain in vivo are still enigmatic. Recent advances in cell imaging and chromosome capture techniques have radically challenged the established paradigm of regular and hierarchical chromatin fibers by highlighting irregular chromatin organization and the importance of the nuclear skeletal structures hoisting the nucleosome chains. Here, we argue that, by analyzing individual structural elements of the nucleosome chain - nucleosome spacing, linker DNA conformations, internucleosomal interactions, and nucleosome chain flexibility - and integrating these elements in multiplex 3D structural models, we can predict the features of the multiplex chromatin folding assemblies underlying distinct developmental and epigenetic states in living cells. Furthermore, partial disassembly of the nuclear structures suspending chromatin fibers may reveal the intrinsic mechanisms of nucleosome chain folding. These mechanisms and structures are expected to provide molecular cues to modify chromatin structure and functions related to developmental and disease processes.
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17
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A Discontinuous Galerkin Model for Fluorescence Loss in Photobleaching. Sci Rep 2018; 8:1387. [PMID: 29362364 PMCID: PMC5780497 DOI: 10.1038/s41598-018-19159-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2017] [Accepted: 12/21/2017] [Indexed: 11/09/2022] Open
Abstract
Fluorescence loss in photobleaching (FLIP) is a modern microscopy method for visualization of transport processes in living cells. This paper presents the simulation of FLIP sequences based on a calibrated reaction-diffusion system defined on segmented cell images. By the use of a discontinuous Galerkin method, the computational complexity is drastically reduced compared to continuous Galerkin methods. Using this approach on green fluorescent protein (GFP), we can determine its intracellular diffusion constant, the strength of localized hindrance to diffusion as well as the permeability of the nuclear membrane for GFP passage, directly from the FLIP image series. Thus, we present for the first time, to our knowledge, a quantitative computational FLIP method for inferring several molecular transport parameters in parallel from FLIP image data acquired at commercial microscope systems.
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18
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Using a model comparison approach to describe the assembly pathway for histone H1. PLoS One 2018; 13:e0191562. [PMID: 29352283 PMCID: PMC5774818 DOI: 10.1371/journal.pone.0191562] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2017] [Accepted: 01/08/2018] [Indexed: 11/30/2022] Open
Abstract
Histones H1 or linker histones are highly dynamic proteins that diffuse throughout the cell nucleus and associate with chromatin (DNA and associated proteins). This binding interaction of histone H1 with the chromatin is thought to regulate chromatin organization and DNA accessibility to transcription factors and has been proven to involve a kinetic process characterized by a population that associates weakly with chromatin and rapidly dissociates and another population that resides at a binding site for up to several minutes before dissociating. When considering differences between these two classes of interactions in a mathematical model for the purpose of describing and quantifying the dynamics of histone H1, it becomes apparent that there could be several assembly pathways that explain the kinetic data obtained in living cells. In this work, we model these different pathways using systems of reaction-diffusion equations and carry out a model comparison analysis using FRAP (fluorescence recovery after photobleaching) experimental data from different histone H1 variants to determine the most feasible mechanism to explain histone H1 binding to chromatin. The analysis favors four different chromatin assembly pathways for histone H1 which share common features and provide meaningful biological information on histone H1 dynamics. We show, using perturbation analysis, that the explicit consideration of high- and low-affinity associations of histone H1 with chromatin in the favored assembly pathways improves the interpretation of histone H1 experimental FRAP data. To illustrate the results, we use one of the favored models to assess the kinetic changes of histone H1 after core histone hyperacetylation, and conclude that this post-transcriptional modification does not affect significantly the transition of histone H1 from a weakly bound state to a tightly bound state.
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19
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Kotliński M, Jerzmanowski A. Histone H1 Purification and Post-Translational Modification Profiling by High-Resolution Mass Spectrometry. METHODS IN MOLECULAR BIOLOGY (CLIFTON, N.J.) 2017; 1675:147-166. [PMID: 29052191 DOI: 10.1007/978-1-4939-7318-7_10] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
It has proven particularly difficult to purify Linker (H1) histones from the model plant Arabidopsis thaliana. This is most likely due to its low nuclear DNA content and the abundance of substances that interfere with protein isolation. These problems have hindered the use of Arabidopsis for in-depth characterization of nuclear proteins by modern techniques based on mass spectrometry (MS). Here, we describe an improved methodology for preparing pure Arabidopsis H1s and separating them by HPLC into fractions corresponding to nonallelic variants. In addition, we outline basic approaches enabling the identification of posttranslational modifications of H1 by MS and their mapping by digestion with different proteases. We also discuss the analysis and interpretation of the acquired data.
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Affiliation(s)
- Maciej Kotliński
- Laboratory of Systems Biology, Faculty of Biology, University of Warsaw, Pawinskiego 5a, Warsaw, Poland
| | - Andrzej Jerzmanowski
- Laboratory of Systems Biology, Faculty of Biology, University of Warsaw, Pawinskiego 5a, Warsaw, Poland.
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawinskiego 5a, 02-106, Warsaw, Poland.
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20
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Kotliński M, Knizewski L, Muszewska A, Rutowicz K, Lirski M, Schmidt A, Baroux C, Ginalski K, Jerzmanowski A. Phylogeny-Based Systematization of Arabidopsis Proteins with Histone H1 Globular Domain. PLANT PHYSIOLOGY 2017; 174:27-34. [PMID: 28298478 PMCID: PMC5411143 DOI: 10.1104/pp.16.00214] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/13/2017] [Accepted: 03/10/2017] [Indexed: 05/19/2023]
Abstract
H1 (or linker) histones are basic nuclear proteins that possess an evolutionarily conserved nucleosome-binding globular domain, GH1. They perform critical functions in determining the accessibility of chromatin DNA to trans-acting factors. In most metazoan species studied so far, linker histones are highly heterogenous, with numerous nonallelic variants cooccurring in the same cells. The phylogenetic relationships among these variants as well as their structural and functional properties have been relatively well established. This contrasts markedly with the rather limited knowledge concerning the phylogeny and structural and functional roles of an unusually diverse group of GH1-containing proteins in plants. The dearth of information and the lack of a coherent phylogeny-based nomenclature of these proteins can lead to misunderstandings regarding their identity and possible relationships, thereby hampering plant chromatin research. Based on published data and our in silico and high-throughput analyses, we propose a systematization and coherent nomenclature of GH1-containing proteins of Arabidopsis (Arabidopsis thaliana [L.] Heynh) that will be useful for both the identification and structural and functional characterization of homologous proteins from other plant species.
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Affiliation(s)
- Maciej Kotliński
- Laboratory of Systems Biology, Faculty of Biology, University of Warsaw, 02-106 Warsaw, Poland (M.K., A.J.)
- Laboratory of Bioinformatics and Systems Biology, Centre of New Technologies, University of Warsaw, 02-089 Warsaw, Poland (L.K., K.G.)
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, 02-106 Warsaw, Poland (A.M., K.R., M.L., A.J.)
- Institute of Plant Biology and Zürich-Basel Plant Science Center, University of Zürich, 8008 Zurich, Switzerland (K.R., C.B.); and
- Centre for Organismal Studies, Heidelberg University, 69120 Heidelberg, Germany (A.S.)
| | - Lukasz Knizewski
- Laboratory of Systems Biology, Faculty of Biology, University of Warsaw, 02-106 Warsaw, Poland (M.K., A.J.)
- Laboratory of Bioinformatics and Systems Biology, Centre of New Technologies, University of Warsaw, 02-089 Warsaw, Poland (L.K., K.G.)
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, 02-106 Warsaw, Poland (A.M., K.R., M.L., A.J.)
- Institute of Plant Biology and Zürich-Basel Plant Science Center, University of Zürich, 8008 Zurich, Switzerland (K.R., C.B.); and
- Centre for Organismal Studies, Heidelberg University, 69120 Heidelberg, Germany (A.S.)
| | - Anna Muszewska
- Laboratory of Systems Biology, Faculty of Biology, University of Warsaw, 02-106 Warsaw, Poland (M.K., A.J.)
- Laboratory of Bioinformatics and Systems Biology, Centre of New Technologies, University of Warsaw, 02-089 Warsaw, Poland (L.K., K.G.)
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, 02-106 Warsaw, Poland (A.M., K.R., M.L., A.J.)
- Institute of Plant Biology and Zürich-Basel Plant Science Center, University of Zürich, 8008 Zurich, Switzerland (K.R., C.B.); and
- Centre for Organismal Studies, Heidelberg University, 69120 Heidelberg, Germany (A.S.)
| | - Kinga Rutowicz
- Laboratory of Systems Biology, Faculty of Biology, University of Warsaw, 02-106 Warsaw, Poland (M.K., A.J.)
- Laboratory of Bioinformatics and Systems Biology, Centre of New Technologies, University of Warsaw, 02-089 Warsaw, Poland (L.K., K.G.)
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, 02-106 Warsaw, Poland (A.M., K.R., M.L., A.J.)
- Institute of Plant Biology and Zürich-Basel Plant Science Center, University of Zürich, 8008 Zurich, Switzerland (K.R., C.B.); and
- Centre for Organismal Studies, Heidelberg University, 69120 Heidelberg, Germany (A.S.)
| | - Maciej Lirski
- Laboratory of Systems Biology, Faculty of Biology, University of Warsaw, 02-106 Warsaw, Poland (M.K., A.J.)
- Laboratory of Bioinformatics and Systems Biology, Centre of New Technologies, University of Warsaw, 02-089 Warsaw, Poland (L.K., K.G.)
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, 02-106 Warsaw, Poland (A.M., K.R., M.L., A.J.)
- Institute of Plant Biology and Zürich-Basel Plant Science Center, University of Zürich, 8008 Zurich, Switzerland (K.R., C.B.); and
- Centre for Organismal Studies, Heidelberg University, 69120 Heidelberg, Germany (A.S.)
| | - Anja Schmidt
- Laboratory of Systems Biology, Faculty of Biology, University of Warsaw, 02-106 Warsaw, Poland (M.K., A.J.)
- Laboratory of Bioinformatics and Systems Biology, Centre of New Technologies, University of Warsaw, 02-089 Warsaw, Poland (L.K., K.G.)
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, 02-106 Warsaw, Poland (A.M., K.R., M.L., A.J.)
- Institute of Plant Biology and Zürich-Basel Plant Science Center, University of Zürich, 8008 Zurich, Switzerland (K.R., C.B.); and
- Centre for Organismal Studies, Heidelberg University, 69120 Heidelberg, Germany (A.S.)
| | - Célia Baroux
- Laboratory of Systems Biology, Faculty of Biology, University of Warsaw, 02-106 Warsaw, Poland (M.K., A.J.);
- Laboratory of Bioinformatics and Systems Biology, Centre of New Technologies, University of Warsaw, 02-089 Warsaw, Poland (L.K., K.G.);
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, 02-106 Warsaw, Poland (A.M., K.R., M.L., A.J.);
- Institute of Plant Biology and Zürich-Basel Plant Science Center, University of Zürich, 8008 Zurich, Switzerland (K.R., C.B.); and
- Centre for Organismal Studies, Heidelberg University, 69120 Heidelberg, Germany (A.S.)
| | - Krzysztof Ginalski
- Laboratory of Systems Biology, Faculty of Biology, University of Warsaw, 02-106 Warsaw, Poland (M.K., A.J.)
- Laboratory of Bioinformatics and Systems Biology, Centre of New Technologies, University of Warsaw, 02-089 Warsaw, Poland (L.K., K.G.)
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, 02-106 Warsaw, Poland (A.M., K.R., M.L., A.J.)
- Institute of Plant Biology and Zürich-Basel Plant Science Center, University of Zürich, 8008 Zurich, Switzerland (K.R., C.B.); and
- Centre for Organismal Studies, Heidelberg University, 69120 Heidelberg, Germany (A.S.)
| | - Andrzej Jerzmanowski
- Laboratory of Systems Biology, Faculty of Biology, University of Warsaw, 02-106 Warsaw, Poland (M.K., A.J.);
- Laboratory of Bioinformatics and Systems Biology, Centre of New Technologies, University of Warsaw, 02-089 Warsaw, Poland (L.K., K.G.);
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, 02-106 Warsaw, Poland (A.M., K.R., M.L., A.J.);
- Institute of Plant Biology and Zürich-Basel Plant Science Center, University of Zürich, 8008 Zurich, Switzerland (K.R., C.B.); and
- Centre for Organismal Studies, Heidelberg University, 69120 Heidelberg, Germany (A.S.)
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21
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Wachsmuth M, Knoch TA, Rippe K. Dynamic properties of independent chromatin domains measured by correlation spectroscopy in living cells. Epigenetics Chromatin 2016; 9:57. [PMID: 28035241 PMCID: PMC5192577 DOI: 10.1186/s13072-016-0093-1] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2016] [Accepted: 09/12/2016] [Indexed: 01/08/2023] Open
Abstract
Background Genome organization into subchromosomal topologically associating domains (TADs) is linked to cell-type-specific gene expression programs. However, dynamic properties of such domains remain elusive, and it is unclear how domain plasticity modulates genomic accessibility for soluble factors. Results Here, we combine and compare a high-resolution topology analysis of interacting chromatin loci with fluorescence correlation spectroscopy measurements of domain dynamics in single living cells. We identify topologically and dynamically independent chromatin domains of ~1 Mb in size that are best described by a loop-cluster polymer model. Hydrodynamic relaxation times and gyration radii of domains are larger for open (161 ± 15 ms, 297 ± 9 nm) than for dense chromatin (88 ± 7 ms, 243 ± 6 nm) and increase globally upon chromatin hyperacetylation or ATP depletion. Conclusions Based on the domain structure and dynamics measurements, we propose a loop-cluster model for chromatin domains. It suggests that the regulation of chromatin accessibility for soluble factors displays a significantly stronger dependence on factor concentration than search processes within a static network. Electronic supplementary material The online version of this article (doi:10.1186/s13072-016-0093-1) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Malte Wachsmuth
- Cell Biology and Biophysics Unit, European Molecular Biology Laboratory (EMBL), Meyerhofstrasse 1, 69117 Heidelberg, Germany
| | - Tobias A Knoch
- Biophysical Genomics Group, Department of Cell Biology and Genetics, Erasmus Medical Center, Dr. Molewaterplein 50, 3015 GE Rotterdam, The Netherlands
| | - Karsten Rippe
- Research Group Genome Organization and Function, Deutsches Krebsforschungszentrum (DKFZ) & BioQuant, Im Neuenheimer Feld 280, 69120 Heidelberg, Germany
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22
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Regulation of Cellular Dynamics and Chromosomal Binding Site Preference of Linker Histones H1.0 and H1.X. Mol Cell Biol 2016; 36:2681-2696. [PMID: 27528617 DOI: 10.1128/mcb.00200-16] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2016] [Accepted: 08/08/2016] [Indexed: 01/01/2023] Open
Abstract
Linker histones play important roles in the genomic organization of mammalian cells. Of the linker histone variants, H1.X shows the most dynamic behavior in the nucleus. Recent research has suggested that the linker histone variants H1.X and H1.0 have different chromosomal binding site preferences. However, it remains unclear how the dynamics and binding site preferences of linker histones are determined. Here, we biochemically demonstrated that the DNA/nucleosome and histone chaperone binding activities of H1.X are significantly lower than those of other linker histones. This explains why H1.X moves more rapidly than other linker histones in vivo Domain swapping between H1.0 and H1.X suggests that the globular domain (GD) and C-terminal domain (CTD) of H1.X independently contribute to the dynamic behavior of H1.X. Our results also suggest that the N-terminal domain (NTD), GD, and CTD cooperatively determine the preferential binding sites, and the contribution of each domain for this determination is different depending on the target genes. We also found that linker histones accumulate in the nucleoli when the nucleosome binding activities of the GDs are weak. Our results contribute to understanding the molecular mechanisms of dynamic behaviors, binding site selection, and localization of linker histones.
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23
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Kowalski A, Pałyga J. Modulation of chromatin function through linker histone H1 variants. Biol Cell 2016; 108:339-356. [PMID: 27412812 DOI: 10.1111/boc.201600007] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2016] [Revised: 07/08/2016] [Accepted: 07/08/2016] [Indexed: 12/30/2022]
Abstract
In this review, the structural aspects of linker H1 histones are presented as a background for characterization of the factors influencing their function in animal and human chromatin. The action of H1 histone variants is largely determined by dynamic alterations of their intrinsically disordered tail domains, posttranslational modifications and allelic diversification. The interdependent effects of these factors can establish dynamic histone H1 states that may affect the organization and function of chromatin regions.
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Affiliation(s)
- Andrzej Kowalski
- Department of Biochemistry and Genetics, Institute of Biology, Jan Kochanowski University, 25-406 Kielce, Poland
| | - Jan Pałyga
- Department of Biochemistry and Genetics, Institute of Biology, Jan Kochanowski University, 25-406 Kielce, Poland
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24
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Cutter AR, Hayes JJ. Linker histones: novel insights into structure-specific recognition of the nucleosome. Biochem Cell Biol 2016; 95:171-178. [PMID: 28177778 DOI: 10.1139/bcb-2016-0097] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
Linker histones (H1s) are a primary component of metazoan chromatin, fulfilling numerous functions, both in vitro and in vivo, including stabilizing the wrapping of DNA around the nucleosome, promoting folding and assembly of higher order chromatin structures, influencing nucleosome spacing on DNA, and regulating specific gene expression. However, many molecular details of how H1 binds to nucleosomes and recognizes unique structural features on the nucleosome surface remain undefined. Numerous, confounding studies are complicated not only by experimental limitations, but the use of different linker histone isoforms and nucleosome constructions. This review summarizes the decades of research that has resulted in several models of H1 association with nucleosomes, with a focus on recent advances that suggest multiple modes of H1 interaction in chromatin, while highlighting the remaining questions.
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Affiliation(s)
- Amber R Cutter
- Department of Biochemistry & Biophysics, University of Rochester Medical Center, Rochester, NY 14642, USA.,Department of Biochemistry & Biophysics, University of Rochester Medical Center, Rochester, NY 14642, USA
| | - Jeffrey J Hayes
- Department of Biochemistry & Biophysics, University of Rochester Medical Center, Rochester, NY 14642, USA.,Department of Biochemistry & Biophysics, University of Rochester Medical Center, Rochester, NY 14642, USA
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25
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Staneva D, Georgieva M, Miloshev G. Kluyveromyces lactis genome harbours a functional linker histone encoding gene. FEMS Yeast Res 2016; 16:fow034. [PMID: 27189369 DOI: 10.1093/femsyr/fow034] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/02/2016] [Indexed: 11/14/2022] Open
Abstract
Linker histones are essential components of chromatin in eukaryotes. Through interactions with linker DNA and nucleosomes they facilitate folding and maintenance of higher-order chromatin structures and thus delicately modulate gene activity. The necessity of linker histones in lower eukaryotes appears controversial and dubious. Genomic data have shown that Schizosaccharomyces pombe does not possess genes encoding linker histones while Kluyveromyces lactis has been reported to have a pseudogene. Regarding this controversy, we have provided the first direct experimental evidence for the existence of a functional linker histone gene, KlLH1, in K. lactis genome. Sequencing of KlLH1 from both genomic DNA and copy DNA confirmed the presence of an intact open reading frame. Transcription and splicing of the KlLH1 sequence as well as translation of its mRNA have been studied. In silico analysis revealed homology of KlLH1p to the histone H1/H5 protein family with predicted three domain structure characteristic for the linker histones of higher eukaryotes. This strongly proves that the yeast K. lactis does indeed possess a functional linker histone gene thus entailing the evolutionary preservation and significance of linker histones. The nucleotide sequences of KlLH1 are deposited in the GenBank under accession numbers KT826576, KT826577 and KT826578.
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Affiliation(s)
- Dessislava Staneva
- Laboratory of Yeast Molecular Genetics, Institute of Molecular Biology, Bulgarian Academy of Sciences, 'Acad. Roumen Tsanev', Sofia 1113, Bulgaria
| | - Milena Georgieva
- Laboratory of Yeast Molecular Genetics, Institute of Molecular Biology, Bulgarian Academy of Sciences, 'Acad. Roumen Tsanev', Sofia 1113, Bulgaria
| | - George Miloshev
- Laboratory of Yeast Molecular Genetics, Institute of Molecular Biology, Bulgarian Academy of Sciences, 'Acad. Roumen Tsanev', Sofia 1113, Bulgaria
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26
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Roque A, Ponte I, Suau P. Post-translational modifications of the intrinsically disordered terminal domains of histone H1: effects on secondary structure and chromatin dynamics. Chromosoma 2016; 126:83-91. [DOI: 10.1007/s00412-016-0591-8] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2016] [Revised: 04/05/2016] [Accepted: 04/07/2016] [Indexed: 01/14/2023]
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Kotliński M, Rutowicz K, Kniżewski Ł, Palusiński A, Olędzki J, Fogtman A, Rubel T, Koblowska M, Dadlez M, Ginalski K, Jerzmanowski A. Histone H1 Variants in Arabidopsis Are Subject to Numerous Post-Translational Modifications, Both Conserved and Previously Unknown in Histones, Suggesting Complex Functions of H1 in Plants. PLoS One 2016; 11:e0147908. [PMID: 26820416 PMCID: PMC4731575 DOI: 10.1371/journal.pone.0147908] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2015] [Accepted: 01/10/2016] [Indexed: 12/24/2022] Open
Abstract
Linker histones (H1s) are conserved and ubiquitous structural components of eukaryotic chromatin. Multiple non-allelic variants of H1, which differ in their DNA/nucleosome binding properties, co-exist in animal and plant cells and have been implicated in the control of genetic programs during development and differentiation. Studies in mammals and Drosophila have revealed diverse post-translational modifications of H1s, most of which are of unknown function. So far, it is not known how this pattern compares with that of H1s from other major lineages of multicellular Eukaryotes. Here, we show that the two main H1variants of a model flowering plant Arabidopsis thaliana are subject to a rich and diverse array of post-translational modifications. The distribution of these modifications in the H1 molecule, especially in its globular domain (GH1), resembles that occurring in mammalian H1s, suggesting that their functional significance is likely to be conserved. While the majority of modifications detected in Arabidopsis H1s, including phosphorylation, acetylation, mono- and dimethylation, formylation, crotonylation and propionylation, have also been reported in H1s of other species, some others have not been previously identified in histones.
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Affiliation(s)
- Maciej Kotliński
- Laboratory of Systems Biology, Faculty of Biology, University of Warsaw, Warsaw, Poland
| | - Kinga Rutowicz
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw, Poland
| | - Łukasz Kniżewski
- Laboratory of Bioinformatics and Systems Biology, Centre of New Technologies, University of Warsaw, Warsaw, Poland
| | - Antoni Palusiński
- Laboratory of Systems Biology, Faculty of Biology, University of Warsaw, Warsaw, Poland
| | - Jacek Olędzki
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw, Poland
| | - Anna Fogtman
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw, Poland
| | - Tymon Rubel
- Institute of Radioelectronic and Multimedia Technology, Warsaw University of Technology, Warsaw, Poland
| | - Marta Koblowska
- Laboratory of Systems Biology, Faculty of Biology, University of Warsaw, Warsaw, Poland
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw, Poland
| | - Michał Dadlez
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw, Poland
- Institute of Genetics and Biotechnology, Faculty of Biology, University of Warsaw, Warsaw, Poland
| | - Krzysztof Ginalski
- Laboratory of Bioinformatics and Systems Biology, Centre of New Technologies, University of Warsaw, Warsaw, Poland
| | - Andrzej Jerzmanowski
- Laboratory of Systems Biology, Faculty of Biology, University of Warsaw, Warsaw, Poland
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw, Poland
- * E-mail:
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Coleman RA, Liu Z, Darzacq X, Tjian R, Singer RH, Lionnet T. Imaging Transcription: Past, Present, and Future. COLD SPRING HARBOR SYMPOSIA ON QUANTITATIVE BIOLOGY 2016; 80:1-8. [PMID: 26763984 DOI: 10.1101/sqb.2015.80.027201] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Transcription, the first step of gene expression, is exquisitely regulated in higher eukaryotes to ensure correct development and homeostasis. Traditional biochemical, genetic, and genomic approaches have proved successful at identifying factors, regulatory sequences, and potential pathways that modulate transcription. However, they typically only provide snapshots or population averages of the highly dynamic, stochastic biochemical processes involved in transcriptional regulation. Single-molecule live-cell imaging has, therefore, emerged as a complementary approach capable of circumventing these limitations. By observing sequences of molecular events in real time as they occur in their native context, imaging has the power to derive cause-and-effect relationships and quantitative kinetics to build predictive models of transcription. Ongoing progress in fluorescence imaging technology has brought new microscopes and labeling technologies that now make it possible to visualize and quantify the transcription process with single-molecule resolution in living cells and animals. Here we provide an overview of the evolution and current state of transcription imaging technologies. We discuss some of the important concepts they uncovered and present possible future developments that might solve long-standing questions in transcriptional regulation.
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Affiliation(s)
- Robert A Coleman
- Department of Anatomy and Structural Biology, Albert Einstein College of Medicine, Bronx, New York 10461
| | - Zhe Liu
- HHMI Janelia Research Campus, Ashburn, Virginia 20147
| | - Xavier Darzacq
- HHMI Janelia Research Campus, Ashburn, Virginia 20147 Department of MCB, LKS Biomedical and Health Sciences Center, CIRM Center of Excellence, University of California, Berkeley, California 94720
| | - Robert Tjian
- HHMI Janelia Research Campus, Ashburn, Virginia 20147 Department of MCB, LKS Biomedical and Health Sciences Center, CIRM Center of Excellence, University of California, Berkeley, California 94720
| | - Robert H Singer
- Department of Anatomy and Structural Biology, Albert Einstein College of Medicine, Bronx, New York 10461 HHMI Janelia Research Campus, Ashburn, Virginia 20147
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A quantitative investigation of linker histone interactions with nucleosomes and chromatin. Sci Rep 2016; 6:19122. [PMID: 26750377 PMCID: PMC4707517 DOI: 10.1038/srep19122] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2015] [Accepted: 12/07/2015] [Indexed: 12/20/2022] Open
Abstract
Linker histones such as H1 are abundant basic proteins that bind tightly to nucleosomes, thereby acting as key organizers of chromatin structure. The molecular details of linker histone interactions with the nucleosome, and in particular the contributions of linker DNA and of the basic C-terminal tail of H1, are controversial. Here we combine rigorous solution-state binding assays with native gel electrophoresis and Atomic Force Microscopy, to quantify the interaction of H1 with chromatin. We find that H1 binds nucleosomes and nucleosomal arrays with very tight affinity by recognizing a specific DNA geometry minimally consisting of a solitary nucleosome with a single ~18 base pair DNA linker arm. The association of H1 alters the conformation of trinucleosomes so that only one H1 can bind to the two available linker DNA regions. Neither incorporation of the histone variant H2A.Z, nor the presence of neighboring nucleosomes affects H1 affinity. Our data provide a comprehensive thermodynamic framework for this ubiquitous chromatin architectural protein.
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30
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Kim JM, Kim K, Punj V, Liang G, Ulmer TS, Lu W, An W. Linker histone H1.2 establishes chromatin compaction and gene silencing through recognition of H3K27me3. Sci Rep 2015; 5:16714. [PMID: 26581166 PMCID: PMC4652225 DOI: 10.1038/srep16714] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2015] [Accepted: 10/19/2015] [Indexed: 12/21/2022] Open
Abstract
Linker histone H1 is a protein component of chromatin and has been linked to higher-order chromatin compaction and global gene silencing. However, a growing body of evidence suggests that H1 plays a gene-specific role, regulating a relatively small number of genes. Here we show that H1.2, one of the H1 subtypes, is overexpressed in cancer cells and contributes to gene silencing. H1.2 gets recruited to distinct chromatin regions in a manner dependent on EZH2-mediated H3K27me3, and inhibits transcription of multiple growth suppressive genes via modulation of chromatin architecture. The C-terminal tail of H1.2 is critical for the observed effects, because mutations of three H1.2-specific amino acids in this domain abrogate the ability of H1.2 to bind H3K27me3 nucleosomes and inactivate target genes. Collectively, these results provide a molecular explanation for H1.2 functions in the regulation of chromatin folding and indicate that H3K27me3 is a key mechanism governing the recruitment and activity of H1.2 at target loci.
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Affiliation(s)
- Jin-Man Kim
- Department of Biochemistry and Molecular Biology, University of Southern California, Los Angeles, CA 90033, USA.,Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, CA 90033, USA
| | - Kyunghwan Kim
- Department of Biochemistry and Molecular Biology, University of Southern California, Los Angeles, CA 90033, USA.,Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, CA 90033, USA.,Department of Biology, College of Natural Sciences, Chungbuk National University, Cheongju, Chungbuk 361-763, Republic of Korea
| | - Vasu Punj
- Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, CA 90033, USA.,Department of Medicine, University of Southern California, Los Angeles, CA 90033, USA
| | - Gangning Liang
- Department of Urology, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA
| | - Tobias S Ulmer
- Department of Biochemistry and Molecular Biology, University of Southern California, Los Angeles, CA 90033, USA.,Zilkha Neurogenetic Institute, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA
| | - Wange Lu
- Department of Biochemistry and Molecular Biology, University of Southern California, Los Angeles, CA 90033, USA.,Eli and Edythe Broad Center for Regenerative Medicine and Stem Cell Research, University of Southern California, Los Angeles, CA 90033, USA
| | - Woojin An
- Department of Biochemistry and Molecular Biology, University of Southern California, Los Angeles, CA 90033, USA.,Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, CA 90033, USA
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31
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Parseghian MH. What is the role of histone H1 heterogeneity? A functional model emerges from a 50 year mystery. AIMS BIOPHYSICS 2015; 2:724-772. [PMID: 31289748 PMCID: PMC6615755 DOI: 10.3934/biophy.2015.4.724] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
For the past 50 years, understanding the function of histone H1 heterogeneity has been mired in confusion and contradiction. Part of the reason for this is the lack of a working model that tries to explain the large body of data that has been collected about the H1 subtypes so far. In this review, a global model is described largely based on published data from the author and other researchers over the past 20 years. The intrinsic disorder built into H1 protein structure is discussed to help the reader understand that these histones are multi-conformational and adaptable to interactions with different targets. We discuss the role of each structural section of H1 (as we currently understand it), but we focus on the H1's C-terminal domain and its effect on each subtype's affinity, mobility and compaction of chromatin. We review the multiple ways these characteristics have been measured from circular dichroism to FRAP analysis, which has added to the sometimes contradictory assumptions made about each subtype. Based on a tabulation of these measurements, we then organize the H1 variants according to their ability to condense chromatin and produce nucleosome repeat lengths amenable to that compaction. This subtype variation generates a continuum of different chromatin states allowing for fine regulatory control and some overlap in the event one or two subtypes are lost to mutation. We also review the myriad of disparate observations made about each subtype, both somatic and germline specific ones, that lend support to the proposed model. Finally, to demonstrate its adaptability as new data further refines our understanding of H1 subtypes, we show how the model can be applied to experimental observations of telomeric heterochromatin in aging cells.
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Rutowicz K, Puzio M, Halibart-Puzio J, Lirski M, Kotliński M, Kroteń MA, Knizewski L, Lange B, Muszewska A, Śniegowska-Świerk K, Kościelniak J, Iwanicka-Nowicka R, Buza K, Janowiak F, Żmuda K, Jõesaar I, Laskowska-Kaszub K, Fogtman A, Kollist H, Zielenkiewicz P, Tiuryn J, Siedlecki P, Swiezewski S, Ginalski K, Koblowska M, Archacki R, Wilczynski B, Rapacz M, Jerzmanowski A. A Specialized Histone H1 Variant Is Required for Adaptive Responses to Complex Abiotic Stress and Related DNA Methylation in Arabidopsis. PLANT PHYSIOLOGY 2015; 169:2080-101. [PMID: 26351307 PMCID: PMC4634048 DOI: 10.1104/pp.15.00493] [Citation(s) in RCA: 56] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/31/2015] [Accepted: 09/07/2015] [Indexed: 05/18/2023]
Abstract
Linker (H1) histones play critical roles in chromatin compaction in higher eukaryotes. They are also the most variable of the histones, with numerous nonallelic variants cooccurring in the same cell. Plants contain a distinct subclass of minor H1 variants that are induced by drought and abscisic acid and have been implicated in mediating adaptive responses to stress. However, how these variants facilitate adaptation remains poorly understood. Here, we show that the single Arabidopsis (Arabidopsis thaliana) stress-inducible variant H1.3 occurs in plants in two separate and most likely autonomous pools: a constitutive guard cell-specific pool and a facultative environmentally controlled pool localized in other tissues. Physiological and transcriptomic analyses of h1.3 null mutants demonstrate that H1.3 is required for both proper stomatal functioning under normal growth conditions and adaptive developmental responses to combined light and water deficiency. Using fluorescence recovery after photobleaching analysis, we show that H1.3 has superfast chromatin dynamics, and in contrast to the main Arabidopsis H1 variants H1.1 and H1.2, it has no stable bound fraction. The results of global occupancy studies demonstrate that, while H1.3 has the same overall binding properties as the main H1 variants, including predominant heterochromatin localization, it differs from them in its preferences for chromatin regions with epigenetic signatures of active and repressed transcription. We also show that H1.3 is required for a substantial part of DNA methylation associated with environmental stress, suggesting that the likely mechanism underlying H1.3 function may be the facilitation of chromatin accessibility by direct competition with the main H1 variants.
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Affiliation(s)
- Kinga Rutowicz
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, 02-106 Warsaw, Poland (K.R., J.H.-P., M.L., M.Kot., A.M., R.I.-N., A.F., P.Z., P.S., S.S., M.Kob., A.J.);Laboratory of Systems Biology, University of Warsaw, 02-106 Warsaw, Poland (M.P., M.Kot., B.L., R.I.-N., K.L.-K., P.S., M.Kob., R.A., A.J.);Institute of Plant Physiology, University of Rzeszów, 36-100 Kolbuszowa, Poland (J.H.-P.);College of Inter-Faculty Individual Studies in Mathematics and Natural Sciences, University of Warsaw, 02-089 Warsaw, Poland (M.A.K.);Laboratory of Bioinformatics and Systems Biology, Center of New Technologies (L.K., A.M., K.G.), and Institute of Informatics (K.B., J.T., B.W.), University of Warsaw, 02-097 Warsaw, Poland;Department of Plant Physiology, University of Agriculture in Cracow, 30-239 Cracow, Poland (K.Ś.-Ś., J.K., K.Ż., M.R.);Institute of Plant Physiology, Polish Academy of Sciences, 30-239 Cracow, Poland (F.J.); andInstitute of Technology, University of Tartu, 50411 Tartu, Tartumaa, Estonia (I.J., H.K.)
| | - Marcin Puzio
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, 02-106 Warsaw, Poland (K.R., J.H.-P., M.L., M.Kot., A.M., R.I.-N., A.F., P.Z., P.S., S.S., M.Kob., A.J.);Laboratory of Systems Biology, University of Warsaw, 02-106 Warsaw, Poland (M.P., M.Kot., B.L., R.I.-N., K.L.-K., P.S., M.Kob., R.A., A.J.);Institute of Plant Physiology, University of Rzeszów, 36-100 Kolbuszowa, Poland (J.H.-P.);College of Inter-Faculty Individual Studies in Mathematics and Natural Sciences, University of Warsaw, 02-089 Warsaw, Poland (M.A.K.);Laboratory of Bioinformatics and Systems Biology, Center of New Technologies (L.K., A.M., K.G.), and Institute of Informatics (K.B., J.T., B.W.), University of Warsaw, 02-097 Warsaw, Poland;Department of Plant Physiology, University of Agriculture in Cracow, 30-239 Cracow, Poland (K.Ś.-Ś., J.K., K.Ż., M.R.);Institute of Plant Physiology, Polish Academy of Sciences, 30-239 Cracow, Poland (F.J.); andInstitute of Technology, University of Tartu, 50411 Tartu, Tartumaa, Estonia (I.J., H.K.)
| | - Joanna Halibart-Puzio
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, 02-106 Warsaw, Poland (K.R., J.H.-P., M.L., M.Kot., A.M., R.I.-N., A.F., P.Z., P.S., S.S., M.Kob., A.J.);Laboratory of Systems Biology, University of Warsaw, 02-106 Warsaw, Poland (M.P., M.Kot., B.L., R.I.-N., K.L.-K., P.S., M.Kob., R.A., A.J.);Institute of Plant Physiology, University of Rzeszów, 36-100 Kolbuszowa, Poland (J.H.-P.);College of Inter-Faculty Individual Studies in Mathematics and Natural Sciences, University of Warsaw, 02-089 Warsaw, Poland (M.A.K.);Laboratory of Bioinformatics and Systems Biology, Center of New Technologies (L.K., A.M., K.G.), and Institute of Informatics (K.B., J.T., B.W.), University of Warsaw, 02-097 Warsaw, Poland;Department of Plant Physiology, University of Agriculture in Cracow, 30-239 Cracow, Poland (K.Ś.-Ś., J.K., K.Ż., M.R.);Institute of Plant Physiology, Polish Academy of Sciences, 30-239 Cracow, Poland (F.J.); andInstitute of Technology, University of Tartu, 50411 Tartu, Tartumaa, Estonia (I.J., H.K.)
| | - Maciej Lirski
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, 02-106 Warsaw, Poland (K.R., J.H.-P., M.L., M.Kot., A.M., R.I.-N., A.F., P.Z., P.S., S.S., M.Kob., A.J.);Laboratory of Systems Biology, University of Warsaw, 02-106 Warsaw, Poland (M.P., M.Kot., B.L., R.I.-N., K.L.-K., P.S., M.Kob., R.A., A.J.);Institute of Plant Physiology, University of Rzeszów, 36-100 Kolbuszowa, Poland (J.H.-P.);College of Inter-Faculty Individual Studies in Mathematics and Natural Sciences, University of Warsaw, 02-089 Warsaw, Poland (M.A.K.);Laboratory of Bioinformatics and Systems Biology, Center of New Technologies (L.K., A.M., K.G.), and Institute of Informatics (K.B., J.T., B.W.), University of Warsaw, 02-097 Warsaw, Poland;Department of Plant Physiology, University of Agriculture in Cracow, 30-239 Cracow, Poland (K.Ś.-Ś., J.K., K.Ż., M.R.);Institute of Plant Physiology, Polish Academy of Sciences, 30-239 Cracow, Poland (F.J.); andInstitute of Technology, University of Tartu, 50411 Tartu, Tartumaa, Estonia (I.J., H.K.)
| | - Maciej Kotliński
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, 02-106 Warsaw, Poland (K.R., J.H.-P., M.L., M.Kot., A.M., R.I.-N., A.F., P.Z., P.S., S.S., M.Kob., A.J.);Laboratory of Systems Biology, University of Warsaw, 02-106 Warsaw, Poland (M.P., M.Kot., B.L., R.I.-N., K.L.-K., P.S., M.Kob., R.A., A.J.);Institute of Plant Physiology, University of Rzeszów, 36-100 Kolbuszowa, Poland (J.H.-P.);College of Inter-Faculty Individual Studies in Mathematics and Natural Sciences, University of Warsaw, 02-089 Warsaw, Poland (M.A.K.);Laboratory of Bioinformatics and Systems Biology, Center of New Technologies (L.K., A.M., K.G.), and Institute of Informatics (K.B., J.T., B.W.), University of Warsaw, 02-097 Warsaw, Poland;Department of Plant Physiology, University of Agriculture in Cracow, 30-239 Cracow, Poland (K.Ś.-Ś., J.K., K.Ż., M.R.);Institute of Plant Physiology, Polish Academy of Sciences, 30-239 Cracow, Poland (F.J.); andInstitute of Technology, University of Tartu, 50411 Tartu, Tartumaa, Estonia (I.J., H.K.)
| | - Magdalena A Kroteń
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, 02-106 Warsaw, Poland (K.R., J.H.-P., M.L., M.Kot., A.M., R.I.-N., A.F., P.Z., P.S., S.S., M.Kob., A.J.);Laboratory of Systems Biology, University of Warsaw, 02-106 Warsaw, Poland (M.P., M.Kot., B.L., R.I.-N., K.L.-K., P.S., M.Kob., R.A., A.J.);Institute of Plant Physiology, University of Rzeszów, 36-100 Kolbuszowa, Poland (J.H.-P.);College of Inter-Faculty Individual Studies in Mathematics and Natural Sciences, University of Warsaw, 02-089 Warsaw, Poland (M.A.K.);Laboratory of Bioinformatics and Systems Biology, Center of New Technologies (L.K., A.M., K.G.), and Institute of Informatics (K.B., J.T., B.W.), University of Warsaw, 02-097 Warsaw, Poland;Department of Plant Physiology, University of Agriculture in Cracow, 30-239 Cracow, Poland (K.Ś.-Ś., J.K., K.Ż., M.R.);Institute of Plant Physiology, Polish Academy of Sciences, 30-239 Cracow, Poland (F.J.); andInstitute of Technology, University of Tartu, 50411 Tartu, Tartumaa, Estonia (I.J., H.K.)
| | - Lukasz Knizewski
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, 02-106 Warsaw, Poland (K.R., J.H.-P., M.L., M.Kot., A.M., R.I.-N., A.F., P.Z., P.S., S.S., M.Kob., A.J.);Laboratory of Systems Biology, University of Warsaw, 02-106 Warsaw, Poland (M.P., M.Kot., B.L., R.I.-N., K.L.-K., P.S., M.Kob., R.A., A.J.);Institute of Plant Physiology, University of Rzeszów, 36-100 Kolbuszowa, Poland (J.H.-P.);College of Inter-Faculty Individual Studies in Mathematics and Natural Sciences, University of Warsaw, 02-089 Warsaw, Poland (M.A.K.);Laboratory of Bioinformatics and Systems Biology, Center of New Technologies (L.K., A.M., K.G.), and Institute of Informatics (K.B., J.T., B.W.), University of Warsaw, 02-097 Warsaw, Poland;Department of Plant Physiology, University of Agriculture in Cracow, 30-239 Cracow, Poland (K.Ś.-Ś., J.K., K.Ż., M.R.);Institute of Plant Physiology, Polish Academy of Sciences, 30-239 Cracow, Poland (F.J.); andInstitute of Technology, University of Tartu, 50411 Tartu, Tartumaa, Estonia (I.J., H.K.)
| | - Bartosz Lange
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, 02-106 Warsaw, Poland (K.R., J.H.-P., M.L., M.Kot., A.M., R.I.-N., A.F., P.Z., P.S., S.S., M.Kob., A.J.);Laboratory of Systems Biology, University of Warsaw, 02-106 Warsaw, Poland (M.P., M.Kot., B.L., R.I.-N., K.L.-K., P.S., M.Kob., R.A., A.J.);Institute of Plant Physiology, University of Rzeszów, 36-100 Kolbuszowa, Poland (J.H.-P.);College of Inter-Faculty Individual Studies in Mathematics and Natural Sciences, University of Warsaw, 02-089 Warsaw, Poland (M.A.K.);Laboratory of Bioinformatics and Systems Biology, Center of New Technologies (L.K., A.M., K.G.), and Institute of Informatics (K.B., J.T., B.W.), University of Warsaw, 02-097 Warsaw, Poland;Department of Plant Physiology, University of Agriculture in Cracow, 30-239 Cracow, Poland (K.Ś.-Ś., J.K., K.Ż., M.R.);Institute of Plant Physiology, Polish Academy of Sciences, 30-239 Cracow, Poland (F.J.); andInstitute of Technology, University of Tartu, 50411 Tartu, Tartumaa, Estonia (I.J., H.K.)
| | - Anna Muszewska
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, 02-106 Warsaw, Poland (K.R., J.H.-P., M.L., M.Kot., A.M., R.I.-N., A.F., P.Z., P.S., S.S., M.Kob., A.J.);Laboratory of Systems Biology, University of Warsaw, 02-106 Warsaw, Poland (M.P., M.Kot., B.L., R.I.-N., K.L.-K., P.S., M.Kob., R.A., A.J.);Institute of Plant Physiology, University of Rzeszów, 36-100 Kolbuszowa, Poland (J.H.-P.);College of Inter-Faculty Individual Studies in Mathematics and Natural Sciences, University of Warsaw, 02-089 Warsaw, Poland (M.A.K.);Laboratory of Bioinformatics and Systems Biology, Center of New Technologies (L.K., A.M., K.G.), and Institute of Informatics (K.B., J.T., B.W.), University of Warsaw, 02-097 Warsaw, Poland;Department of Plant Physiology, University of Agriculture in Cracow, 30-239 Cracow, Poland (K.Ś.-Ś., J.K., K.Ż., M.R.);Institute of Plant Physiology, Polish Academy of Sciences, 30-239 Cracow, Poland (F.J.); andInstitute of Technology, University of Tartu, 50411 Tartu, Tartumaa, Estonia (I.J., H.K.)
| | - Katarzyna Śniegowska-Świerk
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, 02-106 Warsaw, Poland (K.R., J.H.-P., M.L., M.Kot., A.M., R.I.-N., A.F., P.Z., P.S., S.S., M.Kob., A.J.);Laboratory of Systems Biology, University of Warsaw, 02-106 Warsaw, Poland (M.P., M.Kot., B.L., R.I.-N., K.L.-K., P.S., M.Kob., R.A., A.J.);Institute of Plant Physiology, University of Rzeszów, 36-100 Kolbuszowa, Poland (J.H.-P.);College of Inter-Faculty Individual Studies in Mathematics and Natural Sciences, University of Warsaw, 02-089 Warsaw, Poland (M.A.K.);Laboratory of Bioinformatics and Systems Biology, Center of New Technologies (L.K., A.M., K.G.), and Institute of Informatics (K.B., J.T., B.W.), University of Warsaw, 02-097 Warsaw, Poland;Department of Plant Physiology, University of Agriculture in Cracow, 30-239 Cracow, Poland (K.Ś.-Ś., J.K., K.Ż., M.R.);Institute of Plant Physiology, Polish Academy of Sciences, 30-239 Cracow, Poland (F.J.); andInstitute of Technology, University of Tartu, 50411 Tartu, Tartumaa, Estonia (I.J., H.K.)
| | - Janusz Kościelniak
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, 02-106 Warsaw, Poland (K.R., J.H.-P., M.L., M.Kot., A.M., R.I.-N., A.F., P.Z., P.S., S.S., M.Kob., A.J.);Laboratory of Systems Biology, University of Warsaw, 02-106 Warsaw, Poland (M.P., M.Kot., B.L., R.I.-N., K.L.-K., P.S., M.Kob., R.A., A.J.);Institute of Plant Physiology, University of Rzeszów, 36-100 Kolbuszowa, Poland (J.H.-P.);College of Inter-Faculty Individual Studies in Mathematics and Natural Sciences, University of Warsaw, 02-089 Warsaw, Poland (M.A.K.);Laboratory of Bioinformatics and Systems Biology, Center of New Technologies (L.K., A.M., K.G.), and Institute of Informatics (K.B., J.T., B.W.), University of Warsaw, 02-097 Warsaw, Poland;Department of Plant Physiology, University of Agriculture in Cracow, 30-239 Cracow, Poland (K.Ś.-Ś., J.K., K.Ż., M.R.);Institute of Plant Physiology, Polish Academy of Sciences, 30-239 Cracow, Poland (F.J.); andInstitute of Technology, University of Tartu, 50411 Tartu, Tartumaa, Estonia (I.J., H.K.)
| | - Roksana Iwanicka-Nowicka
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, 02-106 Warsaw, Poland (K.R., J.H.-P., M.L., M.Kot., A.M., R.I.-N., A.F., P.Z., P.S., S.S., M.Kob., A.J.);Laboratory of Systems Biology, University of Warsaw, 02-106 Warsaw, Poland (M.P., M.Kot., B.L., R.I.-N., K.L.-K., P.S., M.Kob., R.A., A.J.);Institute of Plant Physiology, University of Rzeszów, 36-100 Kolbuszowa, Poland (J.H.-P.);College of Inter-Faculty Individual Studies in Mathematics and Natural Sciences, University of Warsaw, 02-089 Warsaw, Poland (M.A.K.);Laboratory of Bioinformatics and Systems Biology, Center of New Technologies (L.K., A.M., K.G.), and Institute of Informatics (K.B., J.T., B.W.), University of Warsaw, 02-097 Warsaw, Poland;Department of Plant Physiology, University of Agriculture in Cracow, 30-239 Cracow, Poland (K.Ś.-Ś., J.K., K.Ż., M.R.);Institute of Plant Physiology, Polish Academy of Sciences, 30-239 Cracow, Poland (F.J.); andInstitute of Technology, University of Tartu, 50411 Tartu, Tartumaa, Estonia (I.J., H.K.)
| | - Krisztián Buza
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, 02-106 Warsaw, Poland (K.R., J.H.-P., M.L., M.Kot., A.M., R.I.-N., A.F., P.Z., P.S., S.S., M.Kob., A.J.);Laboratory of Systems Biology, University of Warsaw, 02-106 Warsaw, Poland (M.P., M.Kot., B.L., R.I.-N., K.L.-K., P.S., M.Kob., R.A., A.J.);Institute of Plant Physiology, University of Rzeszów, 36-100 Kolbuszowa, Poland (J.H.-P.);College of Inter-Faculty Individual Studies in Mathematics and Natural Sciences, University of Warsaw, 02-089 Warsaw, Poland (M.A.K.);Laboratory of Bioinformatics and Systems Biology, Center of New Technologies (L.K., A.M., K.G.), and Institute of Informatics (K.B., J.T., B.W.), University of Warsaw, 02-097 Warsaw, Poland;Department of Plant Physiology, University of Agriculture in Cracow, 30-239 Cracow, Poland (K.Ś.-Ś., J.K., K.Ż., M.R.);Institute of Plant Physiology, Polish Academy of Sciences, 30-239 Cracow, Poland (F.J.); andInstitute of Technology, University of Tartu, 50411 Tartu, Tartumaa, Estonia (I.J., H.K.)
| | - Franciszek Janowiak
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, 02-106 Warsaw, Poland (K.R., J.H.-P., M.L., M.Kot., A.M., R.I.-N., A.F., P.Z., P.S., S.S., M.Kob., A.J.);Laboratory of Systems Biology, University of Warsaw, 02-106 Warsaw, Poland (M.P., M.Kot., B.L., R.I.-N., K.L.-K., P.S., M.Kob., R.A., A.J.);Institute of Plant Physiology, University of Rzeszów, 36-100 Kolbuszowa, Poland (J.H.-P.);College of Inter-Faculty Individual Studies in Mathematics and Natural Sciences, University of Warsaw, 02-089 Warsaw, Poland (M.A.K.);Laboratory of Bioinformatics and Systems Biology, Center of New Technologies (L.K., A.M., K.G.), and Institute of Informatics (K.B., J.T., B.W.), University of Warsaw, 02-097 Warsaw, Poland;Department of Plant Physiology, University of Agriculture in Cracow, 30-239 Cracow, Poland (K.Ś.-Ś., J.K., K.Ż., M.R.);Institute of Plant Physiology, Polish Academy of Sciences, 30-239 Cracow, Poland (F.J.); andInstitute of Technology, University of Tartu, 50411 Tartu, Tartumaa, Estonia (I.J., H.K.)
| | - Katarzyna Żmuda
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, 02-106 Warsaw, Poland (K.R., J.H.-P., M.L., M.Kot., A.M., R.I.-N., A.F., P.Z., P.S., S.S., M.Kob., A.J.);Laboratory of Systems Biology, University of Warsaw, 02-106 Warsaw, Poland (M.P., M.Kot., B.L., R.I.-N., K.L.-K., P.S., M.Kob., R.A., A.J.);Institute of Plant Physiology, University of Rzeszów, 36-100 Kolbuszowa, Poland (J.H.-P.);College of Inter-Faculty Individual Studies in Mathematics and Natural Sciences, University of Warsaw, 02-089 Warsaw, Poland (M.A.K.);Laboratory of Bioinformatics and Systems Biology, Center of New Technologies (L.K., A.M., K.G.), and Institute of Informatics (K.B., J.T., B.W.), University of Warsaw, 02-097 Warsaw, Poland;Department of Plant Physiology, University of Agriculture in Cracow, 30-239 Cracow, Poland (K.Ś.-Ś., J.K., K.Ż., M.R.);Institute of Plant Physiology, Polish Academy of Sciences, 30-239 Cracow, Poland (F.J.); andInstitute of Technology, University of Tartu, 50411 Tartu, Tartumaa, Estonia (I.J., H.K.)
| | - Indrek Jõesaar
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, 02-106 Warsaw, Poland (K.R., J.H.-P., M.L., M.Kot., A.M., R.I.-N., A.F., P.Z., P.S., S.S., M.Kob., A.J.);Laboratory of Systems Biology, University of Warsaw, 02-106 Warsaw, Poland (M.P., M.Kot., B.L., R.I.-N., K.L.-K., P.S., M.Kob., R.A., A.J.);Institute of Plant Physiology, University of Rzeszów, 36-100 Kolbuszowa, Poland (J.H.-P.);College of Inter-Faculty Individual Studies in Mathematics and Natural Sciences, University of Warsaw, 02-089 Warsaw, Poland (M.A.K.);Laboratory of Bioinformatics and Systems Biology, Center of New Technologies (L.K., A.M., K.G.), and Institute of Informatics (K.B., J.T., B.W.), University of Warsaw, 02-097 Warsaw, Poland;Department of Plant Physiology, University of Agriculture in Cracow, 30-239 Cracow, Poland (K.Ś.-Ś., J.K., K.Ż., M.R.);Institute of Plant Physiology, Polish Academy of Sciences, 30-239 Cracow, Poland (F.J.); andInstitute of Technology, University of Tartu, 50411 Tartu, Tartumaa, Estonia (I.J., H.K.)
| | - Katarzyna Laskowska-Kaszub
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, 02-106 Warsaw, Poland (K.R., J.H.-P., M.L., M.Kot., A.M., R.I.-N., A.F., P.Z., P.S., S.S., M.Kob., A.J.);Laboratory of Systems Biology, University of Warsaw, 02-106 Warsaw, Poland (M.P., M.Kot., B.L., R.I.-N., K.L.-K., P.S., M.Kob., R.A., A.J.);Institute of Plant Physiology, University of Rzeszów, 36-100 Kolbuszowa, Poland (J.H.-P.);College of Inter-Faculty Individual Studies in Mathematics and Natural Sciences, University of Warsaw, 02-089 Warsaw, Poland (M.A.K.);Laboratory of Bioinformatics and Systems Biology, Center of New Technologies (L.K., A.M., K.G.), and Institute of Informatics (K.B., J.T., B.W.), University of Warsaw, 02-097 Warsaw, Poland;Department of Plant Physiology, University of Agriculture in Cracow, 30-239 Cracow, Poland (K.Ś.-Ś., J.K., K.Ż., M.R.);Institute of Plant Physiology, Polish Academy of Sciences, 30-239 Cracow, Poland (F.J.); andInstitute of Technology, University of Tartu, 50411 Tartu, Tartumaa, Estonia (I.J., H.K.)
| | - Anna Fogtman
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, 02-106 Warsaw, Poland (K.R., J.H.-P., M.L., M.Kot., A.M., R.I.-N., A.F., P.Z., P.S., S.S., M.Kob., A.J.);Laboratory of Systems Biology, University of Warsaw, 02-106 Warsaw, Poland (M.P., M.Kot., B.L., R.I.-N., K.L.-K., P.S., M.Kob., R.A., A.J.);Institute of Plant Physiology, University of Rzeszów, 36-100 Kolbuszowa, Poland (J.H.-P.);College of Inter-Faculty Individual Studies in Mathematics and Natural Sciences, University of Warsaw, 02-089 Warsaw, Poland (M.A.K.);Laboratory of Bioinformatics and Systems Biology, Center of New Technologies (L.K., A.M., K.G.), and Institute of Informatics (K.B., J.T., B.W.), University of Warsaw, 02-097 Warsaw, Poland;Department of Plant Physiology, University of Agriculture in Cracow, 30-239 Cracow, Poland (K.Ś.-Ś., J.K., K.Ż., M.R.);Institute of Plant Physiology, Polish Academy of Sciences, 30-239 Cracow, Poland (F.J.); andInstitute of Technology, University of Tartu, 50411 Tartu, Tartumaa, Estonia (I.J., H.K.)
| | - Hannes Kollist
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, 02-106 Warsaw, Poland (K.R., J.H.-P., M.L., M.Kot., A.M., R.I.-N., A.F., P.Z., P.S., S.S., M.Kob., A.J.);Laboratory of Systems Biology, University of Warsaw, 02-106 Warsaw, Poland (M.P., M.Kot., B.L., R.I.-N., K.L.-K., P.S., M.Kob., R.A., A.J.);Institute of Plant Physiology, University of Rzeszów, 36-100 Kolbuszowa, Poland (J.H.-P.);College of Inter-Faculty Individual Studies in Mathematics and Natural Sciences, University of Warsaw, 02-089 Warsaw, Poland (M.A.K.);Laboratory of Bioinformatics and Systems Biology, Center of New Technologies (L.K., A.M., K.G.), and Institute of Informatics (K.B., J.T., B.W.), University of Warsaw, 02-097 Warsaw, Poland;Department of Plant Physiology, University of Agriculture in Cracow, 30-239 Cracow, Poland (K.Ś.-Ś., J.K., K.Ż., M.R.);Institute of Plant Physiology, Polish Academy of Sciences, 30-239 Cracow, Poland (F.J.); andInstitute of Technology, University of Tartu, 50411 Tartu, Tartumaa, Estonia (I.J., H.K.)
| | - Piotr Zielenkiewicz
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, 02-106 Warsaw, Poland (K.R., J.H.-P., M.L., M.Kot., A.M., R.I.-N., A.F., P.Z., P.S., S.S., M.Kob., A.J.);Laboratory of Systems Biology, University of Warsaw, 02-106 Warsaw, Poland (M.P., M.Kot., B.L., R.I.-N., K.L.-K., P.S., M.Kob., R.A., A.J.);Institute of Plant Physiology, University of Rzeszów, 36-100 Kolbuszowa, Poland (J.H.-P.);College of Inter-Faculty Individual Studies in Mathematics and Natural Sciences, University of Warsaw, 02-089 Warsaw, Poland (M.A.K.);Laboratory of Bioinformatics and Systems Biology, Center of New Technologies (L.K., A.M., K.G.), and Institute of Informatics (K.B., J.T., B.W.), University of Warsaw, 02-097 Warsaw, Poland;Department of Plant Physiology, University of Agriculture in Cracow, 30-239 Cracow, Poland (K.Ś.-Ś., J.K., K.Ż., M.R.);Institute of Plant Physiology, Polish Academy of Sciences, 30-239 Cracow, Poland (F.J.); andInstitute of Technology, University of Tartu, 50411 Tartu, Tartumaa, Estonia (I.J., H.K.)
| | - Jerzy Tiuryn
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, 02-106 Warsaw, Poland (K.R., J.H.-P., M.L., M.Kot., A.M., R.I.-N., A.F., P.Z., P.S., S.S., M.Kob., A.J.);Laboratory of Systems Biology, University of Warsaw, 02-106 Warsaw, Poland (M.P., M.Kot., B.L., R.I.-N., K.L.-K., P.S., M.Kob., R.A., A.J.);Institute of Plant Physiology, University of Rzeszów, 36-100 Kolbuszowa, Poland (J.H.-P.);College of Inter-Faculty Individual Studies in Mathematics and Natural Sciences, University of Warsaw, 02-089 Warsaw, Poland (M.A.K.);Laboratory of Bioinformatics and Systems Biology, Center of New Technologies (L.K., A.M., K.G.), and Institute of Informatics (K.B., J.T., B.W.), University of Warsaw, 02-097 Warsaw, Poland;Department of Plant Physiology, University of Agriculture in Cracow, 30-239 Cracow, Poland (K.Ś.-Ś., J.K., K.Ż., M.R.);Institute of Plant Physiology, Polish Academy of Sciences, 30-239 Cracow, Poland (F.J.); andInstitute of Technology, University of Tartu, 50411 Tartu, Tartumaa, Estonia (I.J., H.K.)
| | - Paweł Siedlecki
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, 02-106 Warsaw, Poland (K.R., J.H.-P., M.L., M.Kot., A.M., R.I.-N., A.F., P.Z., P.S., S.S., M.Kob., A.J.);Laboratory of Systems Biology, University of Warsaw, 02-106 Warsaw, Poland (M.P., M.Kot., B.L., R.I.-N., K.L.-K., P.S., M.Kob., R.A., A.J.);Institute of Plant Physiology, University of Rzeszów, 36-100 Kolbuszowa, Poland (J.H.-P.);College of Inter-Faculty Individual Studies in Mathematics and Natural Sciences, University of Warsaw, 02-089 Warsaw, Poland (M.A.K.);Laboratory of Bioinformatics and Systems Biology, Center of New Technologies (L.K., A.M., K.G.), and Institute of Informatics (K.B., J.T., B.W.), University of Warsaw, 02-097 Warsaw, Poland;Department of Plant Physiology, University of Agriculture in Cracow, 30-239 Cracow, Poland (K.Ś.-Ś., J.K., K.Ż., M.R.);Institute of Plant Physiology, Polish Academy of Sciences, 30-239 Cracow, Poland (F.J.); andInstitute of Technology, University of Tartu, 50411 Tartu, Tartumaa, Estonia (I.J., H.K.)
| | - Szymon Swiezewski
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, 02-106 Warsaw, Poland (K.R., J.H.-P., M.L., M.Kot., A.M., R.I.-N., A.F., P.Z., P.S., S.S., M.Kob., A.J.);Laboratory of Systems Biology, University of Warsaw, 02-106 Warsaw, Poland (M.P., M.Kot., B.L., R.I.-N., K.L.-K., P.S., M.Kob., R.A., A.J.);Institute of Plant Physiology, University of Rzeszów, 36-100 Kolbuszowa, Poland (J.H.-P.);College of Inter-Faculty Individual Studies in Mathematics and Natural Sciences, University of Warsaw, 02-089 Warsaw, Poland (M.A.K.);Laboratory of Bioinformatics and Systems Biology, Center of New Technologies (L.K., A.M., K.G.), and Institute of Informatics (K.B., J.T., B.W.), University of Warsaw, 02-097 Warsaw, Poland;Department of Plant Physiology, University of Agriculture in Cracow, 30-239 Cracow, Poland (K.Ś.-Ś., J.K., K.Ż., M.R.);Institute of Plant Physiology, Polish Academy of Sciences, 30-239 Cracow, Poland (F.J.); andInstitute of Technology, University of Tartu, 50411 Tartu, Tartumaa, Estonia (I.J., H.K.)
| | - Krzysztof Ginalski
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, 02-106 Warsaw, Poland (K.R., J.H.-P., M.L., M.Kot., A.M., R.I.-N., A.F., P.Z., P.S., S.S., M.Kob., A.J.);Laboratory of Systems Biology, University of Warsaw, 02-106 Warsaw, Poland (M.P., M.Kot., B.L., R.I.-N., K.L.-K., P.S., M.Kob., R.A., A.J.);Institute of Plant Physiology, University of Rzeszów, 36-100 Kolbuszowa, Poland (J.H.-P.);College of Inter-Faculty Individual Studies in Mathematics and Natural Sciences, University of Warsaw, 02-089 Warsaw, Poland (M.A.K.);Laboratory of Bioinformatics and Systems Biology, Center of New Technologies (L.K., A.M., K.G.), and Institute of Informatics (K.B., J.T., B.W.), University of Warsaw, 02-097 Warsaw, Poland;Department of Plant Physiology, University of Agriculture in Cracow, 30-239 Cracow, Poland (K.Ś.-Ś., J.K., K.Ż., M.R.);Institute of Plant Physiology, Polish Academy of Sciences, 30-239 Cracow, Poland (F.J.); andInstitute of Technology, University of Tartu, 50411 Tartu, Tartumaa, Estonia (I.J., H.K.)
| | - Marta Koblowska
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, 02-106 Warsaw, Poland (K.R., J.H.-P., M.L., M.Kot., A.M., R.I.-N., A.F., P.Z., P.S., S.S., M.Kob., A.J.);Laboratory of Systems Biology, University of Warsaw, 02-106 Warsaw, Poland (M.P., M.Kot., B.L., R.I.-N., K.L.-K., P.S., M.Kob., R.A., A.J.);Institute of Plant Physiology, University of Rzeszów, 36-100 Kolbuszowa, Poland (J.H.-P.);College of Inter-Faculty Individual Studies in Mathematics and Natural Sciences, University of Warsaw, 02-089 Warsaw, Poland (M.A.K.);Laboratory of Bioinformatics and Systems Biology, Center of New Technologies (L.K., A.M., K.G.), and Institute of Informatics (K.B., J.T., B.W.), University of Warsaw, 02-097 Warsaw, Poland;Department of Plant Physiology, University of Agriculture in Cracow, 30-239 Cracow, Poland (K.Ś.-Ś., J.K., K.Ż., M.R.);Institute of Plant Physiology, Polish Academy of Sciences, 30-239 Cracow, Poland (F.J.); andInstitute of Technology, University of Tartu, 50411 Tartu, Tartumaa, Estonia (I.J., H.K.)
| | - Rafał Archacki
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, 02-106 Warsaw, Poland (K.R., J.H.-P., M.L., M.Kot., A.M., R.I.-N., A.F., P.Z., P.S., S.S., M.Kob., A.J.);Laboratory of Systems Biology, University of Warsaw, 02-106 Warsaw, Poland (M.P., M.Kot., B.L., R.I.-N., K.L.-K., P.S., M.Kob., R.A., A.J.);Institute of Plant Physiology, University of Rzeszów, 36-100 Kolbuszowa, Poland (J.H.-P.);College of Inter-Faculty Individual Studies in Mathematics and Natural Sciences, University of Warsaw, 02-089 Warsaw, Poland (M.A.K.);Laboratory of Bioinformatics and Systems Biology, Center of New Technologies (L.K., A.M., K.G.), and Institute of Informatics (K.B., J.T., B.W.), University of Warsaw, 02-097 Warsaw, Poland;Department of Plant Physiology, University of Agriculture in Cracow, 30-239 Cracow, Poland (K.Ś.-Ś., J.K., K.Ż., M.R.);Institute of Plant Physiology, Polish Academy of Sciences, 30-239 Cracow, Poland (F.J.); andInstitute of Technology, University of Tartu, 50411 Tartu, Tartumaa, Estonia (I.J., H.K.)
| | - Bartek Wilczynski
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, 02-106 Warsaw, Poland (K.R., J.H.-P., M.L., M.Kot., A.M., R.I.-N., A.F., P.Z., P.S., S.S., M.Kob., A.J.);Laboratory of Systems Biology, University of Warsaw, 02-106 Warsaw, Poland (M.P., M.Kot., B.L., R.I.-N., K.L.-K., P.S., M.Kob., R.A., A.J.);Institute of Plant Physiology, University of Rzeszów, 36-100 Kolbuszowa, Poland (J.H.-P.);College of Inter-Faculty Individual Studies in Mathematics and Natural Sciences, University of Warsaw, 02-089 Warsaw, Poland (M.A.K.);Laboratory of Bioinformatics and Systems Biology, Center of New Technologies (L.K., A.M., K.G.), and Institute of Informatics (K.B., J.T., B.W.), University of Warsaw, 02-097 Warsaw, Poland;Department of Plant Physiology, University of Agriculture in Cracow, 30-239 Cracow, Poland (K.Ś.-Ś., J.K., K.Ż., M.R.);Institute of Plant Physiology, Polish Academy of Sciences, 30-239 Cracow, Poland (F.J.); andInstitute of Technology, University of Tartu, 50411 Tartu, Tartumaa, Estonia (I.J., H.K.)
| | - Marcin Rapacz
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, 02-106 Warsaw, Poland (K.R., J.H.-P., M.L., M.Kot., A.M., R.I.-N., A.F., P.Z., P.S., S.S., M.Kob., A.J.);Laboratory of Systems Biology, University of Warsaw, 02-106 Warsaw, Poland (M.P., M.Kot., B.L., R.I.-N., K.L.-K., P.S., M.Kob., R.A., A.J.);Institute of Plant Physiology, University of Rzeszów, 36-100 Kolbuszowa, Poland (J.H.-P.);College of Inter-Faculty Individual Studies in Mathematics and Natural Sciences, University of Warsaw, 02-089 Warsaw, Poland (M.A.K.);Laboratory of Bioinformatics and Systems Biology, Center of New Technologies (L.K., A.M., K.G.), and Institute of Informatics (K.B., J.T., B.W.), University of Warsaw, 02-097 Warsaw, Poland;Department of Plant Physiology, University of Agriculture in Cracow, 30-239 Cracow, Poland (K.Ś.-Ś., J.K., K.Ż., M.R.);Institute of Plant Physiology, Polish Academy of Sciences, 30-239 Cracow, Poland (F.J.); andInstitute of Technology, University of Tartu, 50411 Tartu, Tartumaa, Estonia (I.J., H.K.)
| | - Andrzej Jerzmanowski
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, 02-106 Warsaw, Poland (K.R., J.H.-P., M.L., M.Kot., A.M., R.I.-N., A.F., P.Z., P.S., S.S., M.Kob., A.J.);Laboratory of Systems Biology, University of Warsaw, 02-106 Warsaw, Poland (M.P., M.Kot., B.L., R.I.-N., K.L.-K., P.S., M.Kob., R.A., A.J.);Institute of Plant Physiology, University of Rzeszów, 36-100 Kolbuszowa, Poland (J.H.-P.);College of Inter-Faculty Individual Studies in Mathematics and Natural Sciences, University of Warsaw, 02-089 Warsaw, Poland (M.A.K.);Laboratory of Bioinformatics and Systems Biology, Center of New Technologies (L.K., A.M., K.G.), and Institute of Informatics (K.B., J.T., B.W.), University of Warsaw, 02-097 Warsaw, Poland;Department of Plant Physiology, University of Agriculture in Cracow, 30-239 Cracow, Poland (K.Ś.-Ś., J.K., K.Ż., M.R.);Institute of Plant Physiology, Polish Academy of Sciences, 30-239 Cracow, Poland (F.J.); andInstitute of Technology, University of Tartu, 50411 Tartu, Tartumaa, Estonia (I.J., H.K.)
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Flanagan TW, Brown DT. Molecular dynamics of histone H1. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2015; 1859:468-75. [PMID: 26454113 DOI: 10.1016/j.bbagrm.2015.10.005] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/11/2015] [Revised: 09/17/2015] [Accepted: 10/05/2015] [Indexed: 12/28/2022]
Abstract
The H1 or linker histones bind dynamically to chromatin in living cells via a process that involves transient association with the nucleosome near the DNA entry/exit site followed by dissociation, translocation to a new location, and rebinding. The mean residency time of H1 on any given nucleosome is about a minute, which is much shorter than that of most core histones but considerably longer than that of most other chromatin-binding proteins, including transcription factors. Here we review recent advances in understanding the kinetic pathway of H1 binding and how it relates to linker histone structure and function. We also describe potential mechanisms by which the dynamic binding of H1 might contribute directly to the regulation of gene expression and discuss several situations for which there is experimental evidence to support these mechanisms. Finally, we review the evidence for the participation of linker histone chaperones in mediating H1 exchange.
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Affiliation(s)
- Thomas W Flanagan
- Department of Biochemistry, University of Mississippi Medical Center, 2500 North State Street, Jackson, MS 39216, USA
| | - David T Brown
- Department of Biochemistry, University of Mississippi Medical Center, 2500 North State Street, Jackson, MS 39216, USA.
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Fluorescence recovery after photobleaching in material and life sciences: putting theory into practice. Q Rev Biophys 2015; 48:323-87. [PMID: 26314367 DOI: 10.1017/s0033583515000013] [Citation(s) in RCA: 89] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
AbstractFluorescence recovery after photobleaching (FRAP) is a versatile tool for determining diffusion and interaction/binding properties in biological and material sciences. An understanding of the mechanisms controlling the diffusion requires a deep understanding of structure–interaction–diffusion relationships. In cell biology, for instance, this applies to the movement of proteins and lipids in the plasma membrane, cytoplasm and nucleus. In industrial applications related to pharmaceutics, foods, textiles, hygiene products and cosmetics, the diffusion of solutes and solvent molecules contributes strongly to the properties and functionality of the final product. All these systems are heterogeneous, and accurate quantification of the mass transport processes at the local level is therefore essential to the understanding of the properties of soft (bio)materials. FRAP is a commonly used fluorescence microscopy-based technique to determine local molecular transport at the micrometer scale. A brief high-intensity laser pulse is locally applied to the sample, causing substantial photobleaching of the fluorescent molecules within the illuminated area. This causes a local concentration gradient of fluorescent molecules, leading to diffusional influx of intact fluorophores from the local surroundings into the bleached area. Quantitative information on the molecular transport can be extracted from the time evolution of the fluorescence recovery in the bleached area using a suitable model. A multitude of FRAP models has been developed over the years, each based on specific assumptions. This makes it challenging for the non-specialist to decide which model is best suited for a particular application. Furthermore, there are many subtleties in performing accurate FRAP experiments. For these reasons, this review aims to provide an extensive tutorial covering the essential theoretical and practical aspects so as to enable accurate quantitative FRAP experiments for molecular transport measurements in soft (bio)materials.
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Interaction of chromatin with a histone H1 containing swapped N- and C-terminal domains. Biosci Rep 2015; 35:BSR20150087. [PMID: 26182371 PMCID: PMC4613717 DOI: 10.1042/bsr20150087] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2015] [Accepted: 04/27/2015] [Indexed: 12/12/2022] Open
Abstract
The present study was to understand whether the globular or C-terminal linker histone domain is more important for its binding to chromatin. Using histone H1, with swapped domain orientation,
we found that both domains are equally important for nucleosome binding. Although the details of the structural involvement of histone H1 in the organization of the nucleosome are quite well understood, the sequential events involved in the recognition of its binding site are not as well known. We have used a recombinant human histone H1 (H1.1) in which the N- and C-terminal domains (NTD/CTD) have been swapped and we have reconstituted it on to a 208-bp nucleosome. We have shown that the swapped version of the protein is still able to bind to nucleosomes through its structurally folded wing helix domain (WHD); however, analytical ultracentrifuge analysis demonstrates its ability to properly fold the chromatin fibre is impaired. Furthermore, FRAP analysis shows that the highly dynamic binding association of histone H1 with the chromatin fibre is altered, with a severely decreased half time of residence. All of this suggests that proper binding of histone H1 to chromatin is determined by the simultaneous and synergistic binding of its WHD–CTD to the nucleosome.
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Garfinkel BP, Melamed-Book N, Anuka E, Bustin M, Orly J. HP1BP3 is a novel histone H1 related protein with essential roles in viability and growth. Nucleic Acids Res 2015; 43:2074-90. [PMID: 25662603 PMCID: PMC4344522 DOI: 10.1093/nar/gkv089] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2014] [Revised: 12/17/2014] [Accepted: 01/23/2015] [Indexed: 12/28/2022] Open
Abstract
The dynamic architecture of chromatin is vital for proper cellular function, and is maintained by the concerted action of numerous nuclear proteins, including that of the linker histone H1 variants, the most abundant family of nucleosome-binding proteins. Here we show that the nuclear protein HP1BP3 is widely expressed in most vertebrate tissues and is evolutionarily and structurally related to the H1 family. HP1BP3 contains three globular domains and a highly positively charged C-terminal domain, resembling similar domains in H1. Fluorescence recovery after photobleaching (FRAP) studies indicate that like H1, binding of HP1BP3 to chromatin depends on both its C and N terminal regions and is affected by the cell cycle and post translational modifications. HP1BP3 contains functional motifs not found in H1 histones, including an acidic stretch and a consensus HP1-binding motif. Transcriptional profiling of HeLa cells lacking HP1BP3 showed altered expression of 383 genes, suggesting a role for HP1BP3 in modulation of gene expression. Significantly, Hp1bp3(-/-) mice present a dramatic phenotype with 60% of pups dying within 24 h of birth and the surviving animals exhibiting a lifelong 20% growth retardation. We suggest that HP1BP3 is a ubiquitous histone H1 like nuclear protein with distinct and non-redundant functions necessary for survival and growth.
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Affiliation(s)
- Benjamin P Garfinkel
- Department of Biological Chemistry, The Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem 91904, Israel
| | - Naomi Melamed-Book
- Bio-Imaging Unit, The Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem 91904, Israel
| | - Eli Anuka
- Department of Biological Chemistry, The Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem 91904, Israel
| | - Michael Bustin
- Protein Section, Laboratory of Metabolism, Center for Cancer Research, NCI, National Institutes of Health, Bethesda, MD 20892, USA
| | - Joseph Orly
- Department of Biological Chemistry, The Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem 91904, Israel
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Stasevich TJ, Hayashi-Takanaka Y, Sato Y, Maehara K, Ohkawa Y, Sakata-Sogawa K, Tokunaga M, Nagase T, Nozaki N, McNally JG, Kimura H. Regulation of RNA polymerase II activation by histone acetylation in single living cells. Nature 2014; 516:272-5. [PMID: 25252976 DOI: 10.1038/nature13714] [Citation(s) in RCA: 191] [Impact Index Per Article: 19.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2014] [Accepted: 07/25/2014] [Indexed: 12/31/2022]
Abstract
In eukaryotic cells, post-translational histone modifications have an important role in gene regulation. Starting with early work on histone acetylation, a variety of residue-specific modifications have now been linked to RNA polymerase II (RNAP2) activity, but it remains unclear if these markers are active regulators of transcription or just passive byproducts. This is because studies have traditionally relied on fixed cell populations, meaning temporal resolution is limited to minutes at best, and correlated factors may not actually be present in the same cell at the same time. Complementary approaches are therefore needed to probe the dynamic interplay of histone modifications and RNAP2 with higher temporal resolution in single living cells. Here we address this problem by developing a system to track residue-specific histone modifications and RNAP2 phosphorylation in living cells by fluorescence microscopy. This increases temporal resolution to the tens-of-seconds range. Our single-cell analysis reveals histone H3 lysine-27 acetylation at a gene locus can alter downstream transcription kinetics by as much as 50%, affecting two temporally separate events. First acetylation enhances the search kinetics of transcriptional activators, and later the acetylation accelerates the transition of RNAP2 from initiation to elongation. Signatures of the latter can be found genome-wide using chromatin immunoprecipitation followed by sequencing. We argue that this regulation leads to a robust and potentially tunable transcriptional response.
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Affiliation(s)
- Timothy J Stasevich
- 1] Graduate School of Frontier Biosciences, Osaka University, Osaka, 565-0871, Japan [2] Department of Biochemistry and Molecular Biology, Colorado State University, Fort Collins, Colorado 80523-1870, USA [3] Transcription Imaging Consortium, Janelia Farm Research Campus, Howard Hughes Medical Institute, Ashburn, Virginia 20147, USA
| | - Yoko Hayashi-Takanaka
- 1] Graduate School of Frontier Biosciences, Osaka University, Osaka, 565-0871, Japan [2] Japan Science and Technology Agency (JST), Core Research for Evolutional Science and Technology (CREST), Kawaguchi, Saitama, 332-0012, Japan [3] Department of Biological Sciences, Graduate School of Bioscience and Biotechnology, Tokyo Institute of Technology, Yokohama, 226-8501, Japan
| | - Yuko Sato
- 1] Graduate School of Frontier Biosciences, Osaka University, Osaka, 565-0871, Japan [2] Department of Biological Sciences, Graduate School of Bioscience and Biotechnology, Tokyo Institute of Technology, Yokohama, 226-8501, Japan
| | - Kazumitsu Maehara
- Department of Advanced Medical Initiatives, Faculty of Medicine, Kyushu University, Fukuoka, 812-8582, Japan
| | - Yasuyuki Ohkawa
- 1] Japan Science and Technology Agency (JST), Core Research for Evolutional Science and Technology (CREST), Kawaguchi, Saitama, 332-0012, Japan [2] Department of Advanced Medical Initiatives, Faculty of Medicine, Kyushu University, Fukuoka, 812-8582, Japan
| | - Kumiko Sakata-Sogawa
- 1] Department of Biological Information, Graduate School of Bioscience and Biotechnology, Tokyo Institute of Technology, Yokohama, 226-8501, Japan [2] RIKEN Center for Integrative Medical Sciences (IMS), Yokohama, 230-0045, Japan
| | - Makio Tokunaga
- 1] Department of Biological Information, Graduate School of Bioscience and Biotechnology, Tokyo Institute of Technology, Yokohama, 226-8501, Japan [2] RIKEN Center for Integrative Medical Sciences (IMS), Yokohama, 230-0045, Japan
| | - Takahiro Nagase
- Department of Biotechnology Research, Kazusa DNA Research Institute, Chiba, 292-0818, Japan
| | | | - James G McNally
- 1] Laboratory of Receptor Biology and Gene Expression, National Cancer Institute, National Institutes of Health, Bethesda, Maryland 20892, USA [2] Institute for Soft Matter and Functional Materials, Helmholtz Zentrum Berlin, Berlin, 14109, Germany
| | - Hiroshi Kimura
- 1] Graduate School of Frontier Biosciences, Osaka University, Osaka, 565-0871, Japan [2] Japan Science and Technology Agency (JST), Core Research for Evolutional Science and Technology (CREST), Kawaguchi, Saitama, 332-0012, Japan [3] Department of Biological Sciences, Graduate School of Bioscience and Biotechnology, Tokyo Institute of Technology, Yokohama, 226-8501, Japan
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Alvarez-Saavedra M, De Repentigny Y, Lagali PS, Raghu Ram EVS, Yan K, Hashem E, Ivanochko D, Huh MS, Yang D, Mears AJ, Todd MAM, Corcoran CP, Bassett EA, Tokarew NJA, Kokavec J, Majumder R, Ioshikhes I, Wallace VA, Kothary R, Meshorer E, Stopka T, Skoultchi AI, Picketts DJ. Snf2h-mediated chromatin organization and histone H1 dynamics govern cerebellar morphogenesis and neural maturation. Nat Commun 2014; 5:4181. [PMID: 24946904 PMCID: PMC4083431 DOI: 10.1038/ncomms5181] [Citation(s) in RCA: 60] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2014] [Accepted: 05/15/2014] [Indexed: 12/28/2022] Open
Abstract
Chromatin compaction mediates progenitor to post-mitotic cell transitions and modulates gene expression programs, yet the mechanisms are poorly defined. Snf2h and Snf2l are ATP-dependent chromatin remodelling proteins that assemble, reposition and space nucleosomes, and are robustly expressed in the brain. Here we show that mice conditionally inactivated for Snf2h in neural progenitors have reduced levels of histone H1 and H2A variants that compromise chromatin fluidity and transcriptional programs within the developing cerebellum. Disorganized chromatin limits Purkinje and granule neuron progenitor expansion, resulting in abnormal post-natal foliation, while deregulated transcriptional programs contribute to altered neural maturation, motor dysfunction and death. However, mice survive to young adulthood, in part from Snf2l compensation that restores Engrailed-1 expression. Similarly, Purkinje-specific Snf2h ablation affects chromatin ultrastructure and dendritic arborization, but alters cognitive skills rather than motor control. Our studies reveal that Snf2h controls chromatin organization and histone H1 dynamics for the establishment of gene expression programs underlying cerebellar morphogenesis and neural maturation.
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Affiliation(s)
- Matías Alvarez-Saavedra
- 1] Regenerative Medicine Program, Ottawa Hospital Research Institute, Ottawa, Ontario, Canada K1H 8L6 [2] Department of Cellular and Molecular Medicine, University of Ottawa, Ottawa, Ontario, Canada K1H 8M5
| | - Yves De Repentigny
- Regenerative Medicine Program, Ottawa Hospital Research Institute, Ottawa, Ontario, Canada K1H 8L6
| | - Pamela S Lagali
- Regenerative Medicine Program, Ottawa Hospital Research Institute, Ottawa, Ontario, Canada K1H 8L6
| | - Edupuganti V S Raghu Ram
- Department of Genetics, The Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem 91904, Israel
| | - Keqin Yan
- Regenerative Medicine Program, Ottawa Hospital Research Institute, Ottawa, Ontario, Canada K1H 8L6
| | - Emile Hashem
- 1] Regenerative Medicine Program, Ottawa Hospital Research Institute, Ottawa, Ontario, Canada K1H 8L6 [2] Department of Cellular and Molecular Medicine, University of Ottawa, Ottawa, Ontario, Canada K1H 8M5
| | - Danton Ivanochko
- 1] Regenerative Medicine Program, Ottawa Hospital Research Institute, Ottawa, Ontario, Canada K1H 8L6 [2] Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, Ontario, Canada K1H 8M5
| | - Michael S Huh
- Regenerative Medicine Program, Ottawa Hospital Research Institute, Ottawa, Ontario, Canada K1H 8L6
| | - Doo Yang
- 1] Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, Ontario, Canada K1H 8M5 [2] Institute of Systems Biology, University of Ottawa, Ottawa, Ontario, Canada K1H 8M5
| | - Alan J Mears
- Vision Program, Ottawa Hospital Research Institute, Ottawa, Ontario, Canada K1H 8L6
| | - Matthew A M Todd
- 1] Regenerative Medicine Program, Ottawa Hospital Research Institute, Ottawa, Ontario, Canada K1H 8L6 [2] Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, Ontario, Canada K1H 8M5
| | - Chelsea P Corcoran
- Regenerative Medicine Program, Ottawa Hospital Research Institute, Ottawa, Ontario, Canada K1H 8L6
| | - Erin A Bassett
- Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, Ontario, Canada K1H 8M5
| | - Nicholas J A Tokarew
- Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, Ontario, Canada K1H 8M5
| | - Juraj Kokavec
- Institute of Pathologic Physiology, First Faculty of Medicine, Charles University in Prague, Prague 12853, Czech Republic
| | - Romit Majumder
- Department of Cell Biology, Albert Einstein College of Medicine, Bronx, New York 10461, USA
| | - Ilya Ioshikhes
- 1] Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, Ontario, Canada K1H 8M5 [2] Institute of Systems Biology, University of Ottawa, Ottawa, Ontario, Canada K1H 8M5
| | - Valerie A Wallace
- 1] Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, Ontario, Canada K1H 8M5 [2] Vision Program, Ottawa Hospital Research Institute, Ottawa, Ontario, Canada K1H 8L6
| | - Rashmi Kothary
- 1] Regenerative Medicine Program, Ottawa Hospital Research Institute, Ottawa, Ontario, Canada K1H 8L6 [2] Department of Cellular and Molecular Medicine, University of Ottawa, Ottawa, Ontario, Canada K1H 8M5
| | - Eran Meshorer
- Department of Genetics, The Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem 91904, Israel
| | - Tomas Stopka
- Institute of Pathologic Physiology, First Faculty of Medicine, Charles University in Prague, Prague 12853, Czech Republic
| | - Arthur I Skoultchi
- Department of Cell Biology, Albert Einstein College of Medicine, Bronx, New York 10461, USA
| | - David J Picketts
- 1] Regenerative Medicine Program, Ottawa Hospital Research Institute, Ottawa, Ontario, Canada K1H 8L6 [2] Department of Cellular and Molecular Medicine, University of Ottawa, Ottawa, Ontario, Canada K1H 8M5 [3] Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, Ontario, Canada K1H 8M5
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Bernas T, Brutkowski W, Zarębski M, Dobrucki J. Spatial heterogeneity of dynamics of H1 linker histone. EUROPEAN BIOPHYSICS JOURNAL: EBJ 2014; 43:287-300. [PMID: 24830851 PMCID: PMC4053610 DOI: 10.1007/s00249-014-0962-0] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/08/2013] [Revised: 04/10/2014] [Accepted: 04/25/2014] [Indexed: 02/04/2023]
Abstract
Linker histone H1 participates in maintaining higher order chromatin structures. It is a dynamic protein that binds to DNA and exchanges rapidly with a mobile pool. Therefore, the dynamics of H1 were probed in the nuclei of intact, live cells, using an array of microscopy techniques: fluorescence recovery after photobleaching (FRAP), raster image correlation spectroscopy (RICS), fluorescence correlation spectroscopy (FCS), pair correlation functions (pCF) and fluorescence anisotropy. Combination of these techniques yielded information on H1 dynamics at small (1–100 μs: FCS, RICS, anisotropy), moderate (1–100 ms: FCS, RICS, pCF) and large (1–100 s: pCF and FRAP) time scales. These results indicate that the global movement of H1 in nuclei (at distances >1 µm) occurs at the time scale of seconds and is determined by processes other than diffusion. Moreover, a fraction of H1, which remains immobile at the time scale of tenths of seconds, is detectable. However, local (at distances <0.7 µm) H1 dynamics comprises a process occurring at a short (~3 ms) time scale and multiple processes occurring at longer (10–2,500 ms) scales. The former (fast) process (corresponding probably to H1 diffusion) is more pronounced in the nuclear regions characterized by low H1 concentration, but the latter (slow, attributable to H1 binding) in the regions of high H1 concentration. Furthermore, some regions in nuclei (possibly containing dense chromatin) may constitute barriers that impair or block movement of H1 histones within short (<1 µm) distances.
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Affiliation(s)
- T Bernas
- Nencki Institute of Experimental Biology, Polish Academy of Sciences, Warsaw, Poland,
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40
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Sato Y, Mukai M, Ueda J, Muraki M, Stasevich TJ, Horikoshi N, Kujirai T, Kita H, Kimura T, Hira S, Okada Y, Hayashi-Takanaka Y, Obuse C, Kurumizaka H, Kawahara A, Yamagata K, Nozaki N, Kimura H. Genetically encoded system to track histone modification in vivo. Sci Rep 2014; 3:2436. [PMID: 23942372 PMCID: PMC3743053 DOI: 10.1038/srep02436] [Citation(s) in RCA: 75] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2013] [Accepted: 07/29/2013] [Indexed: 01/25/2023] Open
Abstract
Post-translational histone modifications play key roles in gene regulation, development, and differentiation, but their dynamics in living organisms remain almost completely unknown. To address this problem, we developed a genetically encoded system for tracking histone modifications by generating fluorescent modification-specific intracellular antibodies (mintbodies) that can be expressed in vivo. To demonstrate, an H3 lysine 9 acetylation specific mintbody (H3K9ac-mintbody) was engineered and stably expressed in human cells. In good agreement with the localization of its target acetylation, H3K9ac-mintbody was enriched in euchromatin, and its kinetics measurably changed upon treatment with a histone deacetylase inhibitor. We also generated transgenic fruit fly and zebrafish stably expressing H3K9ac-mintbody for in vivo tracking. Dramatic changes in H3K9ac-mintbody localization during Drosophila embryogenesis could highlight enhanced acetylation at the start of zygotic transcription around mitotic cycle 7. Together, this work demonstrates the broad potential of mintbody and lays the foundation for epigenetic analysis in vivo.
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Affiliation(s)
- Yuko Sato
- 1] Graduate School of Frontier Biosciences, Osaka University, Suita. 565-0871, Japan [2] JST, CREST, Suita. 565-0871, Japan
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Hendrix J, van Heertum B, Vanstreels E, Daelemans D, De Rijck J. Dynamics of the ternary complex formed by c-Myc interactor JPO2, transcriptional co-activator LEDGF/p75, and chromatin. J Biol Chem 2014; 289:12494-506. [PMID: 24634210 DOI: 10.1074/jbc.m113.525964] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
Abstract
Lens epithelium-derived growth factor (LEDGF/p75) is a transcriptional co-activator involved in targeting human immunodeficiency virus (HIV) integration and the development of MLL fusion-mediated acute leukemia. A previous study revealed that LEDGF/p75 dynamically scans the chromatin, and upon interaction with HIV-1 integrase, their complex is locked on chromatin. At present, it is not known whether LEDGF/p75-mediated chromatin locking is typical for interacting proteins. Here, we employed continuous photobleaching and fluorescence correlation and cross-correlation spectroscopy to investigate in vivo chromatin binding of JPO2, a LEDGF/p75- and c-Myc-interacting protein involved in transcriptional regulation. In the absence of LEDGF/p75, JPO2 performs chromatin scanning inherent to transcription factors. However, whereas the dynamics of JPO2 chromatin binding are decelerated upon interaction with LEDGF/p75, very strong locking of their complex onto chromatin is absent. Similar results were obtained with the domesticated transposase PogZ, another cellular interaction partner of LEDGF/p75. We furthermore show that diffusive JPO2 can oligomerize; that JPO2 and LEDGF/p75 interact directly and specifically in vivo through the specific interaction domain of JPO2 and the C-terminal domain of LEDGF/p75, comprising the integrase-binding domain; and that modulation of JPO2 dynamics requires a functional PWWP domain in LEDGF/p75. Our results suggest that the dynamics of the LEDGF/p75-chromatin interaction depend on the specific partner and that strong chromatin locking is not a property of all LEDGF/p75-binding proteins.
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Affiliation(s)
- Jelle Hendrix
- From the Laboratory for Photochemistry and Spectroscopy, Department of Chemistry, University of Leuven, Celestijnenlaan 200F, B-3001 Leuven, Belgium
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González-Romero R, Ausio J. dBigH1, a second histone H1 in Drosophila, and the consequences for histone fold nomenclature. Epigenetics 2014; 9:791-7. [PMID: 24622397 DOI: 10.4161/epi.28427] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Abstract
Recently, Pérez-Montero and colleagues (Developmental cell, 26: 578-590, 2013) described the occurrence of a new histone H1 variant (dBigH1) in Drosophila. The presence of unusual acidic amino acid patches at the N-terminal end of dBigH1 is in contrast to the arginine patches that exist at the N- and C-terminal domains of other histone H1-related proteins found in the sperm of some organisms. This departure from the strictly lysine-rich composition of the somatic histone H1 raises a question about the true definition of its protein members. Their minimal essential requirements appear to be the presence of a lysine- and alanine-rich, intrinsically disordered C-terminal domain, with a highly helicogenic potential upon binding to the linker DNA regions of chromatin. In metazoans, specific targeting of these regions is further achieved by a linker histone fold domain (LHFD), distinctively different from the characteristic core histone fold domain (CHFD) of the nucleosome core histones.
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Affiliation(s)
| | - Juan Ausio
- Department of Biochemistry and Microbiology; University of Victoria; Victoria, BC, Canada
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Wachsmuth M. Molecular diffusion and binding analyzed with FRAP. PROTOPLASMA 2014; 251:373-382. [PMID: 24390250 DOI: 10.1007/s00709-013-0604-x] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/15/2013] [Accepted: 12/16/2013] [Indexed: 06/03/2023]
Abstract
Intracellular molecular transport and localization are crucial for cells (plant cells as much as mammalian cells) to proliferate and to adapt to diverse environmental conditions. Here, some aspects of the microscopy-based method of fluorescence recovery after photobleaching (FRAP) are introduced. In the course of the last years, this has become a very powerful tool to study dynamic processes in living cells and tissue, and it is expected to experience further increasing demand because quantitative information on biological systems becomes more and more important. This review introduces the FRAP methodology, including some theoretical background, describes challenges and pitfalls, and presents some recent advanced applications.
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Affiliation(s)
- Malte Wachsmuth
- Cell Biology and Biophysics Unit, European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117, Heidelberg, Germany,
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Raghuram N, Strickfaden H, McDonald D, Williams K, Fang H, Mizzen C, Hayes JJ, Th'ng J, Hendzel MJ. Pin1 promotes histone H1 dephosphorylation and stabilizes its binding to chromatin. ACTA ACUST UNITED AC 2013; 203:57-71. [PMID: 24100296 PMCID: PMC3798258 DOI: 10.1083/jcb.201305159] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
The prolyl isomerase Pin1 stimulates the dephosphorylation of histone H1, stabilizing its binding to chromatin at transcriptionally active chromatin. Histone H1 plays a crucial role in stabilizing higher order chromatin structure. Transcriptional activation, DNA replication, and chromosome condensation all require changes in chromatin structure and are correlated with the phosphorylation of histone H1. In this study, we describe a novel interaction between Pin1, a phosphorylation-specific prolyl isomerase, and phosphorylated histone H1. A sub-stoichiometric amount of Pin1 stimulated the dephosphorylation of H1 in vitro and modulated the structure of the C-terminal domain of H1 in a phosphorylation-dependent manner. Depletion of Pin1 destabilized H1 binding to chromatin only when Pin1 binding sites on H1 were present. Pin1 recruitment and localized histone H1 phosphorylation were associated with transcriptional activation independent of RNA polymerase II. We thus identify a novel form of histone H1 regulation through phosphorylation-dependent proline isomerization, which has consequences on overall H1 phosphorylation levels and the stability of H1 binding to chromatin.
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Affiliation(s)
- Nikhil Raghuram
- Department of Oncology, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, Alberta T6G 2R7, Canada
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Ferrando-May E, Tomas M, Blumhardt P, Stöckl M, Fuchs M, Leitenstorfer A. Highlighting the DNA damage response with ultrashort laser pulses in the near infrared and kinetic modeling. Front Genet 2013; 4:135. [PMID: 23882280 PMCID: PMC3712194 DOI: 10.3389/fgene.2013.00135] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2013] [Accepted: 06/25/2013] [Indexed: 12/13/2022] Open
Abstract
Our understanding of the mechanisms governing the response to DNA damage in higher eucaryotes crucially depends on our ability to dissect the temporal and spatial organization of the cellular machinery responsible for maintaining genomic integrity. To achieve this goal, we need experimental tools to inflict DNA lesions with high spatial precision at pre-defined locations, and to visualize the ensuing reactions with adequate temporal resolution. Near-infrared femtosecond laser pulses focused through high-aperture objective lenses of advanced scanning microscopes offer the advantage of inducing DNA damage in a 3D-confined volume of subnuclear dimensions. This high spatial resolution results from the highly non-linear nature of the excitation process. Here we review recent progress based on the increasing availability of widely tunable and user-friendly technology of ultrafast lasers in the near infrared. We present a critical evaluation of this approach for DNA microdamage as compared to the currently prevalent use of UV or VIS laser irradiation, the latter in combination with photosensitizers. Current and future applications in the field of DNA repair and DNA-damage dependent chromatin dynamics are outlined. Finally, we discuss the requirement for proper simulation and quantitative modeling. We focus in particular on approaches to measure the effect of DNA damage on the mobility of nuclear proteins and consider the pros and cons of frequently used analysis models for FRAP and photoactivation and their applicability to non-linear photoperturbation experiments.
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Affiliation(s)
- Elisa Ferrando-May
- Department of Biology, Bioimaging Center and Center for Applied Photonics, University of Konstanz Konstanz, Germany
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Herbomel G, Kloster-Landsberg M, Folco EG, Col E, Usson Y, Vourc’h C, Delon A, Souchier C. Dynamics of the full length and mutated heat shock factor 1 in human cells. PLoS One 2013; 8:e67566. [PMID: 23861773 PMCID: PMC3704536 DOI: 10.1371/journal.pone.0067566] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2013] [Accepted: 05/23/2013] [Indexed: 11/24/2022] Open
Abstract
Heat shock factor 1 is the key transcription factor of the heat shock response. Its function is to protect the cell against the deleterious effects of stress. Upon stress, HSF1 binds to and transcribes hsp genes and repeated satellite III (sat III) sequences present at the 9q12 locus. HSF1 binding to pericentric sat III sequences forms structures known as nuclear stress bodies (nSBs). nSBs represent a natural amplification of RNA pol II dependent transcription sites. Dynamics of HSF1 and of deletion mutants were studied in living cells using multi-confocal Fluorescence Correlation Spectroscopy (mFCS) and Fluorescence Recovery After Photobleaching (FRAP). In this paper, we show that HSF1 dynamics modifications upon heat shock result from both formation of high molecular weight complexes and increased HSF1 interactions with chromatin. These interactions involve both DNA binding with Heat Shock Element (HSE) and sat III sequences and a more transient sequence-independent binding likely corresponding to a search for more specific targets. We find that the trimerization domain is required for low affinity interactions with chromatin while the DNA binding domain is required for site-specific interactions of HSF1 with DNA.
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Affiliation(s)
- Gaëtan Herbomel
- INSERM, University Grenoble 1, IAB CRI U823 team 10, La Tronche, France
| | | | - Eric G. Folco
- INSERM, University Grenoble 1, IAB CRI U823 team 10, La Tronche, France
| | - Edwige Col
- INSERM, University Grenoble 1, IAB CRI U823 team 10, La Tronche, France
| | - Yves Usson
- University Grenoble I, CNRS, TIMC-IMAG UMR5525, La Tronche, France
| | - Claire Vourc’h
- INSERM, University Grenoble 1, IAB CRI U823 team 10, La Tronche, France
| | - Antoine Delon
- University Grenoble 1, CNRS, LIPhy UMR 5588, St Martin d’Hères, France
| | - Catherine Souchier
- INSERM, University Grenoble 1, IAB CRI U823 team 10, La Tronche, France
- * E-mail:
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Schneider K, Fuchs C, Dobay A, Rottach A, Qin W, Wolf P, Álvarez-Castro JM, Nalaskowski MM, Kremmer E, Schmid V, Leonhardt H, Schermelleh L. Dissection of cell cycle-dependent dynamics of Dnmt1 by FRAP and diffusion-coupled modeling. Nucleic Acids Res 2013; 41:4860-76. [PMID: 23535145 PMCID: PMC3643600 DOI: 10.1093/nar/gkt191] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
DNA methyltransferase 1 (Dnmt1) reestablishes methylation of hemimethylated CpG sites generated during DNA replication in mammalian cells. Two subdomains, the proliferating cell nuclear antigen (PCNA)-binding domain (PBD) and the targeting sequence (TS) domain, target Dnmt1 to the replication sites in S phase. We aimed to dissect the details of the cell cycle–dependent coordinated activity of both domains. To that end, we combined super-resolution 3D-structured illumination microscopy and fluorescence recovery after photobleaching (FRAP) experiments of GFP-Dnmt1 wild type and mutant constructs in somatic mouse cells. To interpret the differences in FRAP kinetics, we refined existing data analysis and modeling approaches to (i) account for the heterogeneous and variable distribution of Dnmt1-binding sites in different cell cycle stages; (ii) allow diffusion-coupled dynamics; (iii) accommodate multiple binding classes. We find that transient PBD-dependent interaction directly at replication sites is the predominant specific interaction in early S phase (residence time Tres ≤10 s). In late S phase, this binding class is taken over by a substantially stronger (Tres ∼22 s) TS domain-dependent interaction at PCNA-enriched replication sites and at nearby pericentromeric heterochromatin subregions. We propose a two-loading-platform-model of additional PCNA-independent loading at postreplicative, heterochromatic Dnmt1 target sites to ensure faithful maintenance of densely methylated genomic regions.
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Affiliation(s)
- Katrin Schneider
- Department of Biology and Center for Integrated Protein Science, Ludwig Maximilians University Munich (LMU), 82152 Planegg-Martinsried, Germany
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48
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Kloster-Landsberg M, Herbomel G, Wang I, Derouard J, Vourc'h C, Usson Y, Souchier C, Delon A. Cellular response to heat shock studied by multiconfocal fluorescence correlation spectroscopy. Biophys J 2012; 103:1110-9. [PMID: 22995483 PMCID: PMC3446677 DOI: 10.1016/j.bpj.2012.07.041] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2011] [Revised: 07/21/2012] [Accepted: 07/27/2012] [Indexed: 10/27/2022] Open
Abstract
Heat shock triggers a transient and ubiquitous response, the function of which is to protect cells against stress-induced damage. The heat-shock response is controlled by a key transcription factor known as heat shock factor 1 (HSF1). We have developed a multiconfocal fluorescence correlation spectroscopy setup to measure the dynamics of HSF1 during the course of the heat-shock response. The system combines a spatial light modulator, to address several points of interest, and an electron-multiplying charge-coupled camera for fast multiconfocal recording of the photon streams. Autocorrelation curves with a temporal resolution of 14 μs were analyzed before and after heat shock on eGFP and HSF1-eGFP-expressing cells. Evaluation of the dynamic parameters of a diffusion-and-binding model showed a slower HSF1 diffusion after heat shock. It is also observed that the dissociation rate decreases after heat shock, whereas the association rate is not affected. In addition, thanks to the multiconfocal fluorescence correlation spectroscopy system, up to five spots could be simultaneously located in each cell nucleus. This made it possible to quantify the intracellular variability of the diffusion constant of HSF1, which is higher than that of inert eGFP molecules and increases after heat shock. This finding is consistent with the fact that heat-shock response is associated with an increase of HSF1 interactions with DNA and cannot be explained even partially by heat-induced modifications of nuclear organization.
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Affiliation(s)
- Meike Kloster-Landsberg
- University of Grenoble I/Centre National de la Recherche Scientifique, Laboratoire Interdisciplinaire de Physique, Grenoble, France
| | - Gaëtan Herbomel
- University of Grenoble I/Institut National de la Santé et de la Recherche Médicale, Institut Albert Bonniot, U823 team 10, Grenoble, France
| | - Irène Wang
- University of Grenoble I/Centre National de la Recherche Scientifique, Laboratoire Interdisciplinaire de Physique, Grenoble, France
| | - Jacques Derouard
- University of Grenoble I/Centre National de la Recherche Scientifique, Laboratoire Interdisciplinaire de Physique, Grenoble, France
| | - Claire Vourc'h
- University of Grenoble I/Institut National de la Santé et de la Recherche Médicale, Institut Albert Bonniot, U823 team 10, Grenoble, France
| | - Yves Usson
- University of Grenoble I/Centre National de la Recherche Scientifique, Laboratoire TIMC-IMAG, Grenoble, France
| | - Catherine Souchier
- University of Grenoble I/Institut National de la Santé et de la Recherche Médicale, Institut Albert Bonniot, U823 team 10, Grenoble, France
| | - Antoine Delon
- University of Grenoble I/Centre National de la Recherche Scientifique, Laboratoire Interdisciplinaire de Physique, Grenoble, France
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49
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Steffen PA, Fonseca JP, Ringrose L. Epigenetics meets mathematics: towards a quantitative understanding of chromatin biology. Bioessays 2012; 34:901-13. [PMID: 22911103 DOI: 10.1002/bies.201200076] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
How fast? How strong? How many? So what? Why do numbers matter in biology? Chromatin binding proteins are forever in motion, exchanging rapidly between bound and free pools. How do regulatory systems whose components are in constant flux ensure stability and flexibility? This review explores the application of quantitative and mathematical approaches to mechanisms of epigenetic regulation. We discuss methods for measuring kinetic parameters and protein quantities in living cells, and explore the insights that have been gained by quantifying and modelling dynamics of chromatin binding proteins.
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50
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Contribution of hydrophobic interactions to the folding and fibrillation of histone H1 and its carboxy-terminal domain. J Struct Biol 2012; 180:101-9. [PMID: 22813934 DOI: 10.1016/j.jsb.2012.07.004] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2012] [Revised: 05/31/2012] [Accepted: 07/06/2012] [Indexed: 11/23/2022]
Abstract
Histone H1 is involved in chromatin structure and gene regulation. H1 also performs functions outside cell nuclei, which may depend on its properties as a lipid-binding protein. The H1 CTD behaves as an intrinsically disordered protein (IDP) with coupled binding and folding. Here, we used neutral detergents and anionic SDS to study the contribution of hydrophobic interactions to the folding of the CTD. In the presence of neutral detergents, the CTD folded with proportions of secondary structure motifs similar to those observed in the DNA complexes. These results identify a folding pathway for the CTD based on hydrophobic interactions, and independent of charge compensation. The CTD is phosphorylated to different extents by cyclin-dependent kinases. The general effect of phosphorylation in the presence of detergents was a decrease in the α-helix content and an increase in that of the β-structure. The greatest effect was observed in the fully phosphorylated CTD (three phosphate groups) in the presence of anionic SDS (7:1, detergent/CTD molar ratio); in these conditions, the CTD became an all-β protein, with 83% β-structure and no α-helix. The CTD in all-β conformation readily formed ribbon-like fibers. The entire H1 also formed fibers when fully phosphorylated in the CTD. Fibers were of the amyloid type, as judged by strong birefringence in the presence of Congo red and thioflavin fluorescence enhancement. Amyloid fiber formation was only observed in SDS, suggesting that it requires the joint effects of partial charge neutralization and hydrophobic interactions, together with the all-β potential provided by full phosphorylation.
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