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Yu L, Zhang H, Guan R, Li Y, Guo Y, Qiu L. Genome-Wide Tissue-Specific Genes Identification for Novel Tissue-Specific Promoters Discovery in Soybean. Genes (Basel) 2023; 14:1150. [PMID: 37372330 DOI: 10.3390/genes14061150] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2023] [Revised: 05/18/2023] [Accepted: 05/23/2023] [Indexed: 06/29/2023] Open
Abstract
Promoters play a crucial role in controlling the spatial and temporal expression of genes at transcriptional levels in the process of higher plant growth and development. The spatial, efficient, and correct regulation of exogenous genes expression, as desired, is the key point in plant genetic engineering research. Constitutive promoters widely used in plant genetic transformation are limited because, sometimes, they may cause potential negative effects. This issue can be solved, to a certain extent, by using tissue-specific promoters. Compared with constitutive promoters, a few tissue-specific promoters have been isolated and applied. In this study, based on the transcriptome data, a total of 288 tissue-specific genes were collected, expressed in seven tissues, including the leaves, stems, flowers, pods, seeds, roots, and nodules of soybean (Glycine max). KEGG pathway enrichment analysis was carried out, and 52 metabolites were annotated. A total of 12 tissue-specific genes were selected via the transcription expression level and validated through real-time quantitative PCR, of which 10 genes showed tissue-specific expression. The 3-kb 5' upstream regions of ten genes were obtained as putative promoters. Further analysis showed that all the 10 promoters contained many tissue-specific cis-elements. These results demonstrate that high-throughput transcriptional data can be used as effective tools, providing a guide for high-throughput novel tissue-specific promoter discovery.
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Affiliation(s)
- Lili Yu
- The National Key Facility for Crop Gene Resources and Genetic Improvement (NFCRI)/Key Laboratory of Grain Crop Genetic Resources Evaluation and Utilization, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Hao Zhang
- The National Key Facility for Crop Gene Resources and Genetic Improvement (NFCRI)/Key Laboratory of Grain Crop Genetic Resources Evaluation and Utilization, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Rongxia Guan
- The National Key Facility for Crop Gene Resources and Genetic Improvement (NFCRI)/Key Laboratory of Grain Crop Genetic Resources Evaluation and Utilization, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Yinghui Li
- The National Key Facility for Crop Gene Resources and Genetic Improvement (NFCRI)/Key Laboratory of Grain Crop Genetic Resources Evaluation and Utilization, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Yong Guo
- The National Key Facility for Crop Gene Resources and Genetic Improvement (NFCRI)/Key Laboratory of Grain Crop Genetic Resources Evaluation and Utilization, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Lijuan Qiu
- The National Key Facility for Crop Gene Resources and Genetic Improvement (NFCRI)/Key Laboratory of Grain Crop Genetic Resources Evaluation and Utilization, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
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Nucleosome Remodeling at the Yeast PHO8 and PHO84 Promoters without the Putatively Essential SWI/SNF Remodeler. Int J Mol Sci 2023; 24:ijms24054949. [PMID: 36902382 PMCID: PMC10003099 DOI: 10.3390/ijms24054949] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2022] [Revised: 02/14/2023] [Accepted: 02/19/2023] [Indexed: 03/08/2023] Open
Abstract
Chromatin remodeling by ATP-dependent remodeling enzymes is crucial for all genomic processes, like transcription or replication. Eukaryotes harbor many remodeler types, and it is unclear why a given chromatin transition requires more or less stringently one or several remodelers. As a classical example, removal of budding yeast PHO8 and PHO84 promoter nucleosomes upon physiological gene induction by phosphate starvation essentially requires the SWI/SNF remodeling complex. This dependency on SWI/SNF may indicate specificity in remodeler recruitment, in recognition of nucleosomes as remodeling substrate or in remodeling outcome. By in vivo chromatin analyses of wild type and mutant yeast under various PHO regulon induction conditions, we found that overexpression of the remodeler-recruiting transactivator Pho4 allowed removal of PHO8 promoter nucleosomes without SWI/SNF. For PHO84 promoter nucleosome removal in the absence of SWI/SNF, an intranucleosomal Pho4 site, which likely altered the remodeling outcome via factor binding competition, was required in addition to such overexpression. Therefore, an essential remodeler requirement under physiological conditions need not reflect substrate specificity, but may reflect specific recruitment and/or remodeling outcomes.
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Lu J, An J, Wang J, Cao X, Cao Y, Huang C, Jiao S, Yan D, Lin X, Zhou X. Znhit1 Regulates p21Cip1 to Control Mouse Lens Differentiation. Invest Ophthalmol Vis Sci 2022; 63:18. [PMID: 35472217 PMCID: PMC9055562 DOI: 10.1167/iovs.63.4.18] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2021] [Accepted: 04/06/2022] [Indexed: 01/22/2023] Open
Abstract
Purpose The transparency of the ocular lens is essential for refracting and focusing light onto the retina, and transparency is controlled by many factors and signaling pathways. Here we showed a critical role of chromatin remodeler zinc finger HIT-type containing 1 (Znhit1) in maintaining lens transparency. Methods To explore the roles of Znhit1 in lens development, the cre-loxp system was used to generate lens-specific Znhit1 knockout mice (Znhit1Mlr10-Cre; Znhit1 cKO). Morphological changes in mice lenses were examined using hematoxylin and eosin staining. RNA sequencing (RNA-seq) and assay for transposase accessible chromatin using sequencing (ATAC-seq) were applied to screen transcriptome changes. Immunofluorescence staining were performed to assess proteins distribution and terminal deoxynucleotidyl transferase dUTP nick-end labeling staining were used for determining apoptosis. The mRNAs expression was examined by quantitative RT-PCR and proteins expression by Western blot. Results Lens-specific conditional knockout mice had a severe cataract, microphthalmia phenotype, and seriously abnormal lens fiber cells differentiation. Deletion of Znhit1 in the lens resulted in decreased cell proliferation and increased cell apoptosis of the lens epithelia. ATAC-seq showed that Znhit1 deficiency increased chromatin accessibility of cyclin-dependent kinase inhibitors, including p57Kip2 and p21Cip1, and upregulated the expression of these genes in mRNA and protein levels. And we also showed that loss of Znhit1 lead to lens fibrosis by upregulating the expression of p21Cip1. Conclusions Our findings suggested that Znhit1 is required for the survival of lens epithelial cells. The loss of Znhit1 leads to the overexpression of p21Cip1, further resulting in lens fibrosis, and impacted the establishment of lens transparency.
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Affiliation(s)
- Juan Lu
- School of Optometry and Ophthalmology and Eye Hospital, Wenzhou Medical University, Wenzhou, Zhejiang, China
- State Key Laboratory of Optometry, Ophthalmology and Vision Science, Wenzhou, Zhejiang, China
| | - Jianhong An
- School of Optometry and Ophthalmology and Eye Hospital, Wenzhou Medical University, Wenzhou, Zhejiang, China
- State Key Laboratory of Optometry, Ophthalmology and Vision Science, Wenzhou, Zhejiang, China
| | - Jiawei Wang
- School of Optometry and Ophthalmology and Eye Hospital, Wenzhou Medical University, Wenzhou, Zhejiang, China
- State Key Laboratory of Optometry, Ophthalmology and Vision Science, Wenzhou, Zhejiang, China
| | - Xiaowen Cao
- School of Optometry and Ophthalmology and Eye Hospital, Wenzhou Medical University, Wenzhou, Zhejiang, China
- State Key Laboratory of Optometry, Ophthalmology and Vision Science, Wenzhou, Zhejiang, China
| | - Yuqing Cao
- School of Optometry and Ophthalmology and Eye Hospital, Wenzhou Medical University, Wenzhou, Zhejiang, China
- State Key Laboratory of Optometry, Ophthalmology and Vision Science, Wenzhou, Zhejiang, China
| | - Chengjie Huang
- School of Optometry and Ophthalmology and Eye Hospital, Wenzhou Medical University, Wenzhou, Zhejiang, China
- State Key Laboratory of Optometry, Ophthalmology and Vision Science, Wenzhou, Zhejiang, China
| | - Shiming Jiao
- School of Optometry and Ophthalmology and Eye Hospital, Wenzhou Medical University, Wenzhou, Zhejiang, China
- State Key Laboratory of Optometry, Ophthalmology and Vision Science, Wenzhou, Zhejiang, China
| | - Dongsheng Yan
- School of Optometry and Ophthalmology and Eye Hospital, Wenzhou Medical University, Wenzhou, Zhejiang, China
- State Key Laboratory of Optometry, Ophthalmology and Vision Science, Wenzhou, Zhejiang, China
| | - Xinhua Lin
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Xiangtian Zhou
- School of Optometry and Ophthalmology and Eye Hospital, Wenzhou Medical University, Wenzhou, Zhejiang, China
- State Key Laboratory of Optometry, Ophthalmology and Vision Science, Wenzhou, Zhejiang, China
- National Clinical Research Center for Ocular Diseases, Wenzhou, China
- Oujiang Laboratory, Zhejiang Lab for Regenerative Medicine, Vision and Brain Health, Wenzhou, Zhejiang, China
- Research Unit of Myopia Basic Research and Clinical Prevention and Control, Chinese Academy of Medical Sciences, Wenzhou, China
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Barnes T, Korber P. The Active Mechanism of Nucleosome Depletion by Poly(dA:dT) Tracts In Vivo. Int J Mol Sci 2021; 22:ijms22158233. [PMID: 34360997 PMCID: PMC8347975 DOI: 10.3390/ijms22158233] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2021] [Revised: 07/27/2021] [Accepted: 07/29/2021] [Indexed: 12/16/2022] Open
Abstract
Poly(dA:dT) tracts cause nucleosome depletion in many species, e.g., at promoters and replication origins. Their intrinsic biophysical sequence properties make them stiff and unfavorable for nucleosome assembly, as probed by in vitro nucleosome reconstitution. The mere correlation between nucleosome depletion over poly(dA:dT) tracts in in vitro reconstituted and in in vivo chromatin inspired an intrinsic nucleosome exclusion mechanism in vivo that is based only on DNA and histone properties. However, we compile here published and new evidence that this correlation does not reflect mechanistic causation. (1) Nucleosome depletion over poly(dA:dT) in vivo is not universal, e.g., very weak in S. pombe. (2) The energy penalty for incorporating poly(dA:dT) tracts into nucleosomes is modest (<10%) relative to ATP hydrolysis energy abundantly invested by chromatin remodelers. (3) Nucleosome depletion over poly(dA:dT) is much stronger in vivo than in vitro if monitored without MNase and (4) actively maintained in vivo. (5) S. cerevisiae promoters evolved a strand-biased poly(dA) versus poly(dT) distribution. (6) Nucleosome depletion over poly(dA) is directional in vivo. (7) The ATP dependent chromatin remodeler RSC preferentially and directionally displaces nucleosomes towards 5′ of poly(dA). Especially distribution strand bias and displacement directionality would not be expected for an intrinsic mechanism. Together, this argues for an in vivo mechanism where active and species-specific read out of intrinsic sequence properties, e.g., by remodelers, shapes nucleosome organization.
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Ash1 and Tup1 dependent repression of the Saccharomyces cerevisiae HO promoter requires activator-dependent nucleosome eviction. PLoS Genet 2020; 16:e1009133. [PMID: 33382702 PMCID: PMC7806131 DOI: 10.1371/journal.pgen.1009133] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2020] [Revised: 01/13/2021] [Accepted: 11/25/2020] [Indexed: 11/30/2022] Open
Abstract
Transcriptional regulation of the Saccharomyces cerevisiae HO gene is highly complex, requiring a balance of multiple activating and repressing factors to ensure that only a few transcripts are produced in mother cells within a narrow window of the cell cycle. Here, we show that the Ash1 repressor associates with two DNA sequences that are usually concealed within nucleosomes in the HO promoter and recruits the Tup1 corepressor and the Rpd3 histone deacetylase, both of which are required for full repression in daughters. Genome-wide ChIP identified greater than 200 additional sites of co-localization of these factors, primarily within large, intergenic regions from which they could regulate adjacent genes. Most Ash1 binding sites are in nucleosome depleted regions (NDRs), while a small number overlap nucleosomes, similar to HO. We demonstrate that Ash1 binding to the HO promoter does not occur in the absence of the Swi5 transcription factor, which recruits coactivators that evict nucleosomes, including the nucleosomes obscuring the Ash1 binding sites. In the absence of Swi5, artificial nucleosome depletion allowed Ash1 to bind, demonstrating that nucleosomes are inhibitory to Ash1 binding. The location of binding sites within nucleosomes may therefore be a mechanism for limiting repressive activity to periods of nucleosome eviction that are otherwise associated with activation of the promoter. Our results illustrate that activation and repression can be intricately connected, and events set in motion by an activator may also ensure the appropriate level of repression and reset the promoter for the next activation cycle. Nucleosomes inhibit both gene expression and DNA-binding by regulatory factors. Here we examine the role of nucleosomes in regulating the binding of repressive transcription factors to the complex promoter for the yeast HO gene. Ash1 is a sequence-specific DNA-binding protein, and we show that it recruits the Tup1 global repressive factor to the HO promoter. Using a method to determine where Ash1 and Tup1 are bound to DNA throughout the genome, we discovered that Tup1 is also present at most places where Ash1 binds. The majority of these sites are in “Nucleosome Depleted Regions,” or NDRs, where the absence of chromatin makes factor binding easier. We discovered that the HO promoter is an exception, in that the two places where Ash1 binds overlap nucleosomes. Activation of the HO promoter is a complex, multi-step process, and we demonstrated that chromatin factors transiently evict these nucleosomes from the HO promoter during the cell cycle, allowing Ash1 to bind and recruit Tup1. Thus, activators must evict nucleosomes from the promoter to allow the repressive machinery to bind.
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Bahna SG, Niles LP. Epigenetic regulation of melatonin receptors in neuropsychiatric disorders. Br J Pharmacol 2017; 175:3209-3219. [PMID: 28967098 DOI: 10.1111/bph.14058] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2017] [Revised: 08/17/2017] [Accepted: 09/20/2017] [Indexed: 12/29/2022] Open
Abstract
Melatonin, the primary indoleamine hormone of the mammalian pineal gland, is known to have a plethora of neuroregulatory, neuroprotective and other properties. Melatonergic signalling is mediated by its two GPCRs, MT1 and MT2 , which are widely expressed in the mammalian CNS. Melatonin levels and receptor expression often show a decrease during normal ageing, and this reduction may be accelerated in some disease states. Depleted melatonergic signalling has been associated with neuropsychiatric dysfunction and impairments in cognition, memory, neurogenesis and neurorestorative processes. The anticonvulsant and mood stabilizer, valproic acid (VPA), up-regulates melatonin MT1 and/or MT2 receptor expression in cultured cells and in the rat brain. VPA is known to affect gene expression through several mechanisms, including the modulation of intracellular kinase pathways and transcription factors, as well as the inhibition of histone deacetylase (HDAC) activity. Interestingly, other HDAC inhibitors, such as trichostatin A, which are structurally distinct from VPA, can also up-regulate melatonin receptor expression, unlike a VPA analogue, valpromide, which lacks HDAC inhibitory activity. Moreover, VPA increases histone H3 acetylation along the length of the MT1 gene promoter in rat C6 cells. These findings indicate that an epigenetic mechanism, linked to histone hyperacetylation/chromatin remodelling and associated changes in gene transcription, is involved in the up-regulation of melatonin receptors by VPA. Epigenetic induction of MT1 and/or MT2 receptor expression, in areas where these receptors are lost because of ageing, injury or disease, may be a promising therapeutic avenue for the management of CNS dysfunction and other disorders. LINKED ARTICLES: This article is part of a themed section on Recent Developments in Research of Melatonin and its Potential Therapeutic Applications. To view the other articles in this section visit http://onlinelibrary.wiley.com/doi/10.1111/bph.v175.16/issuetoc.
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Affiliation(s)
- Sarra G Bahna
- Department of Psychiatry and Behavioural Neurosciences, McMaster University, Hamilton, ON, Canada
| | - Lennard P Niles
- Department of Psychiatry and Behavioural Neurosciences, McMaster University, Hamilton, ON, Canada
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Pahi Z, Borsos BN, Vedelek B, Shidlovskii YV, Georgieva SG, Boros IM, Pankotai T. TAF10 and TAF10b partially redundant roles during Drosophila melanogaster morphogenesis. Transcription 2017; 8:297-306. [PMID: 28841365 DOI: 10.1080/21541264.2017.1327836] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022] Open
Abstract
Transcription of eukaryotic genes requires the cooperative action of the RNA polymerase complex, the general transcription factors (TFIIB, TFIID, TFIIE, TFIIF and TFIIH) and chromatin modifiers. The TFIID complex contributes to transcriptional activation by several mechanisms and has a subunit with associated histone acetyltransferase (HAT) activity. The histone modifier SAGA complex has both HAT and deubiquitylase (DUB) activities. TFIID and SAGA share several TBP-associated factors (TAFs), but not their HAT subunit. Recently, several duplicated TAF proteins have been identified in higher eukaryotes, but their functional diversity has been so far poorly characterized. Here, we report the functional similarities and differences of TAF10 and TAF10b, the two TAF10 orthologs of Drosophila melanogaster. Results from in silico modeling suggest that dTAF10 and dTAF10b have similar secondary structures characterized by the presence of a histone-fold domain. Additionally, dTAF10 and dTAF10b share interaction partners and show similar expression patterns in neuronal tissues. Nonetheless, dTAF10 and dTAF10b seem to have partly distinct functions. To investigate their roles, we generated dTaf10-dTaf10b double-mutants and rescued the mutant flies with transgenes, which allowed the translation of either dTAF10 or dTAF10b protein. We found that the loss of dTAF10b resulted in pupal lethality, while animals lacking dTAF10 were able to form puparium. dTaf10 mutant adults showed distorted eye morphology. During DNA repair, dTAF10 and dTAF10b act redundantly, suggesting that these proteins have distinct but partially overlapping functions.
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Affiliation(s)
- Z Pahi
- a Department of Biochemistry and Molecular Biology , University of Szeged , Szeged , Hungary
| | - B N Borsos
- a Department of Biochemistry and Molecular Biology , University of Szeged , Szeged , Hungary
| | - B Vedelek
- a Department of Biochemistry and Molecular Biology , University of Szeged , Szeged , Hungary
| | - Y V Shidlovskii
- b Institute of Gene Biology, Russian Academy of Sciences , Moscow , Russia
| | - S G Georgieva
- b Institute of Gene Biology, Russian Academy of Sciences , Moscow , Russia
| | - I M Boros
- a Department of Biochemistry and Molecular Biology , University of Szeged , Szeged , Hungary.,c Institute of Biochemistry, Biological Research Center , Szeged , Hungary
| | - T Pankotai
- a Department of Biochemistry and Molecular Biology , University of Szeged , Szeged , Hungary
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Kubik S, Bruzzone MJ, Shore D. Establishing nucleosome architecture and stability at promoters: Roles of pioneer transcription factors and the RSC chromatin remodeler. Bioessays 2017; 39. [PMID: 28345796 DOI: 10.1002/bies.201600237] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Improvements in deep sequencing, together with methods to rapidly deplete essential transcription factors (TFs) and chromatin remodelers, have recently led to a more detailed picture of promoter nucleosome architecture in yeast and its relationship to transcriptional regulation. These studies revealed that ∼40% of all budding yeast protein-coding genes possess a unique promoter structure, where we propose that an unusually unstable nucleosome forms immediately upstream of the transcription start site (TSS). This "fragile" nucleosome (FN) promoter architecture relies on the combined action of the essential RSC (Remodels Structure of Chromatin) nucleosome remodeler and pioneer transcription factors (PTFs). FNs are associated with genes whose expression is high, coupled to cell growth, and characterized by low cell-to-cell variability (noise), suggesting that they may promote these features. Recent studies in metazoans suggest that the presence of dynamic nucleosomes upstream of the TSS at highly expressed genes may be conserved throughout evolution.
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Affiliation(s)
- Slawomir Kubik
- Department of Molecular Biology and Institute of Genetics and Genomics in Geneva (iGE3), University of Geneva, Geneva, Switzerland
| | - Maria Jessica Bruzzone
- Department of Molecular Biology and Institute of Genetics and Genomics in Geneva (iGE3), University of Geneva, Geneva, Switzerland
| | - David Shore
- Department of Molecular Biology and Institute of Genetics and Genomics in Geneva (iGE3), University of Geneva, Geneva, Switzerland
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Regulated large-scale nucleosome density patterns and precise nucleosome positioning correlate with V(D)J recombination. Proc Natl Acad Sci U S A 2016; 113:E6427-E6436. [PMID: 27698124 DOI: 10.1073/pnas.1605543113] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Abstract
We show that the physical distribution of nucleosomes at antigen receptor loci is subject to regulated cell type-specific and lineage-specific positioning and correlates with the accessibility of these gene segments to recombination. At the Ig heavy chain locus (IgH), a nucleosome in pro-B cells is generally positioned over each IgH variable (VH) coding segment, directly adjacent to the recombination signal sequence (RSS), placing the RSS in a position accessible to the recombination activating gene (RAG) recombinase. These changes result in establishment of a specific chromatin organization at the RSS that facilitates accessibility of the genomic DNA for the RAG recombinase. In contrast, in mouse embryonic fibroblasts the coding segment is depleted of nucleosomes, which instead cover the RSS, thereby rendering it inaccessible. Pro-T cells exhibit a pattern intermediate between pro-B cells and mouse embryonic fibroblasts. We also find large-scale variations of nucleosome density over hundreds of kilobases, delineating chromosomal domains within IgH, in a cell type-dependent manner. These findings suggest that developmentally regulated changes in nucleosome location and occupancy, in addition to the known chromatin modifications, play a fundamental role in regulating V(D)J recombination. Nucleosome positioning-which has previously been observed to vary locally at individual enhancers and promoters-may be a more general mechanism by which cells can regulate the accessibility of the genome during development, at scales ranging from several hundred base pairs to many kilobases.
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Mazina MY, Vorobyeva NE. The role of ATP-dependent chromatin remodeling complexes in regulation of genetic processes. RUSS J GENET+ 2016. [DOI: 10.1134/s1022795416050082] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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Nucleosomes Are Essential for Proper Regulation of a Multigated Promoter in Saccharomyces cerevisiae. Genetics 2015; 202:551-63. [PMID: 26627840 DOI: 10.1534/genetics.115.183715] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2015] [Accepted: 11/29/2015] [Indexed: 12/22/2022] Open
Abstract
Nucleosome-depleted regions (NDRs) are present immediately adjacent to the transcription start site in most eukaryotic promoters. Here we show that NDRs in the upstream promoter region can profoundly affect gene regulation. Chromatin at the yeast HO promoter is highly repressive and numerous coactivators are required for expression. We modified the HO promoter with segments from the well-studied CLN2 NDR, creating chimeric promoters differing in nucleosome occupancy but with binding sites for the same activator, SBF. Nucleosome depletion resulted in substantial increases in both factor binding and gene expression and allowed activation from a much longer distance, probably by allowing recruited coactivators to act further downstream. Nucleosome depletion also affected sequential activation of the HO promoter; HO activation typically requires the ordered recruitment of activators first to URS1, second to the left-half of URS2 (URS2-L), and finally to the right-half of URS2 (URS2-R), with each region representing distinct gates that must be unlocked to achieve activation. The absence of nucleosomes at URS2-L resulted in promoters no longer requiring both the URS1 and URS2-L gates, as either gate alone is now sufficient to promote binding of the SBF factor to URS2-R. Furthermore, nucleosome depletion at URS2 altered the timing of HO expression and bypassed the regulation that restricts expression to mother cells. Our results reveal insight into how nucleosomes can create a requirement for ordered recruitment of factors to facilitate complex transcriptional regulation.
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Pahi Z, Kiss Z, Komonyi O, Borsos BN, Tora L, Boros IM, Pankotai T. dTAF10- and dTAF10b-Containing Complexes Are Required for Ecdysone-Driven Larval-Pupal Morphogenesis in Drosophila melanogaster. PLoS One 2015; 10:e0142226. [PMID: 26556600 PMCID: PMC4640578 DOI: 10.1371/journal.pone.0142226] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2015] [Accepted: 10/18/2015] [Indexed: 12/23/2022] Open
Abstract
In eukaryotes the TFIID complex is required for preinitiation complex assembly which positions RNA polymerase II around transcription start sites. On the other hand, histone acetyltransferase complexes including SAGA and ATAC, modulate transcription at several steps through modification of specific core histone residues. In this study we investigated the function of Drosophila melanogaster proteins TAF10 and TAF10b, which are subunits of dTFIID and dSAGA, respectively. We generated a mutation which eliminated the production of both Drosophila TAF10 orthologues. The simultaneous deletion of both dTaf10 genes impaired the recruitment of the dTFIID subunit dTAF5 to polytene chromosomes, while binding of other TFIID subunits, dTAF1 and RNAPII was not affected. The lack of both dTAF10 proteins resulted in failures in the larval-pupal transition during metamorphosis and in transcriptional reprogramming at this developmental stage. Surprisingly, unlike dSAGA mutations, dATAC subunit mutations resulted in very similar changes in the steady state mRNA levels of approximately 5000 genes as did ablation of both dTaf10 genes, indicating that dTAF10- and/or dTAF10b-containing complexes and dATAC affect similar pathways. Importantly, the phenotype resulting from dTaf10+dTaf10b mutation could be rescued by ectopically added ecdysone, suggesting that dTAF10- and/or dTAF10b-containing complexes are involved in the expression of ecdysone biosynthetic genes. Indeed, in dTaf10+dTaf10b mutants, cytochrome genes, which regulate ecdysone synthesis in the ring gland, were underrepresented. Therefore our data support the idea that the presence of dTAF10 proteins in dTFIID and/or dSAGA is required only at specific developmental steps. We propose that distinct forms of dTFIID and/or dSAGA exist during Drosophila metamorphosis, wherein different TAF compositions serve to target RNAPII at different developmental stages and tissues.
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Affiliation(s)
- Zoltan Pahi
- Department of Biochemistry and Molecular Biology, University of Szeged, Szeged, Hungary
| | - Zsuzsanna Kiss
- Department of Biochemistry and Molecular Biology, University of Szeged, Szeged, Hungary
| | - Orbán Komonyi
- Department of Biochemistry and Molecular Biology, University of Szeged, Szeged, Hungary
| | - Barbara N. Borsos
- Department of Biochemistry and Molecular Biology, University of Szeged, Szeged, Hungary
| | - Laszlo Tora
- Institut de Genetique et de Biologie Moleculaire et Cellulaire, Illkirch, France
| | - Imre M. Boros
- Department of Biochemistry and Molecular Biology, University of Szeged, Szeged, Hungary
- Institute of Biochemistry, Biological Research Center, Szeged, Hungary
| | - Tibor Pankotai
- Department of Biochemistry and Molecular Biology, University of Szeged, Szeged, Hungary
- Institute of Biochemistry, Biological Research Center, Szeged, Hungary
- * E-mail:
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Nucleosome positioning in yeasts: methods, maps, and mechanisms. Chromosoma 2014; 124:131-51. [PMID: 25529773 DOI: 10.1007/s00412-014-0501-x] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2014] [Revised: 12/02/2014] [Accepted: 12/03/2014] [Indexed: 01/23/2023]
Abstract
Eukaryotic nuclear DNA is packaged into nucleosomes. During the past decade, genome-wide nucleosome mapping across species revealed the high degree of order in nucleosome positioning. There is a conserved stereotypical nucleosome organization around transcription start sites (TSSs) with a nucleosome-depleted region (NDR) upstream of the TSS and a TSS-aligned regular array of evenly spaced nucleosomes downstream over the gene body. As nucleosomes largely impede access to DNA and thereby provide an important level of genome regulation, it is of general interest to understand the mechanisms generating nucleosome positioning and especially the stereotypical NDR-array pattern. We focus here on the most advanced models, unicellular yeasts, and review the progress in mapping nucleosomes and which nucleosome positioning mechanisms are discussed. There are four mechanistic aspects: How are NDRs generated? How are individual nucleosomes positioned, especially those flanking the NDRs? How are nucleosomes evenly spaced leading to regular arrays? How are regular arrays aligned at TSSs? The main candidates for nucleosome positioning determinants are intrinsic DNA binding preferences of the histone octamer, specific DNA binding factors, nucleosome remodeling enzymes, transcription, and statistical positioning. We summarize the state of the art in an integrative model where nucleosomes are positioned by a combination of all these candidate determinants. We highlight the predominance of active mechanisms involving nucleosome remodeling enzymes which may be recruited by DNA binding factors and the transcription machinery. While this mechanistic framework emerged clearly during recent years, the involved factors and their mechanisms are still poorly understood and require future efforts combining in vivo and in vitro approaches.
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West JA, Cook A, Alver BH, Stadtfeld M, Deaton AM, Hochedlinger K, Park PJ, Tolstorukov MY, Kingston RE. Nucleosomal occupancy changes locally over key regulatory regions during cell differentiation and reprogramming. Nat Commun 2014; 5:4719. [PMID: 25158628 PMCID: PMC4217530 DOI: 10.1038/ncomms5719] [Citation(s) in RCA: 73] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2014] [Accepted: 07/16/2014] [Indexed: 01/23/2023] Open
Abstract
Chromatin structure determines DNA accessibility. We compare nucleosome occupancy in mouse and human embryonic stem cells (ESCs), induced-pluripotent stem cells (iPSCs) and differentiated cell types using MNase-seq. To address variability inherent in this technique, we developed a bioinformatic approach to identify regions of difference (RoD) in nucleosome occupancy between pluripotent and somatic cells. Surprisingly, most chromatin remains unchanged; a majority of rearrangements appear to affect a single nucleosome. RoDs are enriched at genes and regulatory elements, including enhancers associated with pluripotency and differentiation. RoDs co-localize with binding sites of key developmental regulators, including the reprogramming factors Klf4, Oct4/Sox2 and c-Myc. Nucleosomal landscapes in ESC enhancers are extensively altered, exhibiting lower nucleosome occupancy in pluripotent cells than in somatic cells. Most changes are reset during reprogramming. We conclude that changes in nucleosome occupancy are a hallmark of cell differentiation and reprogramming and likely identify regulatory regions essential for these processes. Changes in chromatin structure impact gene expression programs by modulating accessibility to the transcription machinery. Here, West et al. explore differences in nucleosome occupancy between mammalian pluripotent and somatic cells and uncover regulatory regions likely to play key roles in determining cell identity.
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Affiliation(s)
- Jason A West
- 1] Department of Molecular Biology, Massachusetts General Hospital, Boston, Massachusetts 02114, USA [2] Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA [3] [4]
| | - April Cook
- 1] Department of Molecular Biology, Massachusetts General Hospital, Boston, Massachusetts 02114, USA [2] Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA [3]
| | - Burak H Alver
- Center for Biomedical Informatics, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Matthias Stadtfeld
- The Helen L. and Martin S. Kimmel Center for Biology and Medicine, The Skirball Institute of Biomolecular Medicine, Department of Cell Biology, New York University School of Medicine, New York, New York 10016, USA
| | - Aimee M Deaton
- 1] Department of Molecular Biology, Massachusetts General Hospital, Boston, Massachusetts 02114, USA [2] Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Konrad Hochedlinger
- 1] Howard Hughes Medical Institute and the Center for Regenerative Medicine, Massachusetts General Hospital, Boston, Massachusetts 02114, USA [2] The Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, Massachusetts 02138, USA
| | - Peter J Park
- Center for Biomedical Informatics, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Michael Y Tolstorukov
- 1] Department of Molecular Biology, Massachusetts General Hospital, Boston, Massachusetts 02114, USA [2]
| | - Robert E Kingston
- 1] Department of Molecular Biology, Massachusetts General Hospital, Boston, Massachusetts 02114, USA [2] Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA
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Site-specific association with host and viral chromatin by Kaposi's sarcoma-associated herpesvirus LANA and its reversal during lytic reactivation. J Virol 2014; 88:6762-77. [PMID: 24696474 DOI: 10.1128/jvi.00268-14] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Abstract
UNLABELLED Latency-associated nuclear antigen (LANA), a multifunctional protein expressed by the Kaposi sarcoma-associated herpesvirus (KSHV) in latently infected cells, is required for stable maintenance of the viral episome. This is mediated by two interactions: LANA binds to specific sequences (LBS1 and LBS2) on viral DNA and also engages host histones, tethering the viral genome to host chromosomes in mitosis. LANA has also been suggested to affect host gene expression, but both the mechanism(s) and role of this dysregulation in KSHV biology remain unclear. Here, we have examined LANA interactions with host chromatin on a genome-wide scale using chromatin immunoprecipitation with high-throughput sequencing (ChIP-seq) and show that LANA predominantly targets human genes near their transcriptional start sites (TSSs). These host LANA-binding sites are generally found within transcriptionally active promoters and display striking overrepresentation of a consensus DNA sequence virtually identical to the LANA-binding site 1 (LBS1) motif in KSHV DNA. Comparison of the ChIP-seq profile with whole-transcriptome (high-throughput sequencing of RNA transcripts [RNA-seq]) data reveals that few of the genes that are differentially regulated in latent infection are occupied by LANA at their promoters. This suggests that direct LANA binding to promoters is not the prime determinant of altered host transcription in KSHV-infected cells. Most surprisingly, the association of LANA to both host and viral DNA is strongly disrupted during the lytic cycle of KSHV. This disruption can be prevented by the inhibition of viral DNA synthesis, suggesting the existence of novel and potent regulatory mechanisms linked to either viral DNA replication or late gene expression. IMPORTANCE Here, we employ complementary genome-wide analyses to evaluate the distribution of the highly abundant latency-associated nuclear antigen, LANA, on the host genome and its impact on host gene expression during KSHV latent infection. Combined, ChIP-seq and RNA-seq reveal that LANA accumulates at active gene promoters that harbor specific short DNA sequences that are highly reminiscent of its cognate binding sites in the virus genome. Unexpectedly, we found that such association does not lead to remodeling of global host transcription during latency. We also report for the first time that LANA's ability to bind host and viral chromatin is highly dynamic and is disrupted in cells undergoing an extensive lytic reactivation. This therefore suggests that the association of LANA to chromatin during a productive infection cycle is controlled by a new regulatory mechanism.
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Elfving N, Chereji RV, Bharatula V, Björklund S, Morozov AV, Broach JR. A dynamic interplay of nucleosome and Msn2 binding regulates kinetics of gene activation and repression following stress. Nucleic Acids Res 2014; 42:5468-82. [PMID: 24598258 PMCID: PMC4027177 DOI: 10.1093/nar/gku176] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
The transcription factor Msn2 mediates a significant proportion of the environmental stress response, in which a common cohort of genes changes expression in a stereotypic fashion upon exposure to any of a wide variety of stresses. We have applied genome-wide chromatin immunoprecipitation and nucleosome profiling to determine where Msn2 binds under stressful conditions and how that binding affects, and is affected by, nucleosome positioning. We concurrently determined the effect of Msn2 activity on gene expression following stress and demonstrated that Msn2 stimulates both activation and repression. We found that some genes responded to both intermittent and continuous Msn2 nuclear occupancy while others responded only to continuous occupancy. Finally, these studies document a dynamic interplay between nucleosomes and Msn2 such that nucleosomes can restrict access of Msn2 to its canonical binding sites while Msn2 can promote reposition, expulsion and recruitment of nucleosomes to alter gene expression. This interplay may allow the cell to discriminate between different types of stress signaling.
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Affiliation(s)
- Nils Elfving
- Department of Medical Biochemistry and Biophysics, Umeå University, Umeå 901 87, Sweden
| | - Răzvan V Chereji
- Department of Physics and Astronomy, Rutgers University, Piscataway, NJ 08854, USA
| | - Vasudha Bharatula
- Department of Biochemistry and Molecular Biology, Penn State College of Medicine, Hershey, PA 17033, USA
| | - Stefan Björklund
- Department of Medical Biochemistry and Biophysics, Umeå University, Umeå 901 87, Sweden
| | - Alexandre V Morozov
- Department of Physics and Astronomy, Rutgers University, Piscataway, NJ 08854, USA BioMaPS Institute for Quantitative Biology, Rutgers University, Piscataway, NJ 08854, USA
| | - James R Broach
- Department of Biochemistry and Molecular Biology, Penn State College of Medicine, Hershey, PA 17033, USA
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Musladin S, Krietenstein N, Korber P, Barbaric S. The RSC chromatin remodeling complex has a crucial role in the complete remodeler set for yeast PHO5 promoter opening. Nucleic Acids Res 2014; 42:4270-82. [PMID: 24465003 PMCID: PMC3985623 DOI: 10.1093/nar/gkt1395] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Although yeast PHO5 promoter chromatin opening is a founding model for chromatin remodeling, the complete set of involved remodelers remained unknown for a long time. The SWI/SNF and INO80 remodelers cooperate here, but nonessentially, and none of the many tested single or combined remodeler gene mutations could prevent PHO5 promoter opening. RSC, the most abundant and only remodeler essential for viability, was a controversial candidate for the unrecognized remodeling activity but unassessed in vivo. Now we show that remodels the structure of chromatin (RSC) is crucially involved in PHO5 promoter opening. Further, the isw1 chd1 double deletion also delayed chromatin remodeling. Strikingly, combined absence of RSC and Isw1/Chd1 or Snf2 abolished for the first time promoter opening on otherwise sufficient induction in vivo. Together with previous findings, we recognize now a surprisingly complex network of five remodelers (RSC, SWI/SNF, INO80, Isw1 and Chd1) from four subfamilies (SWI/SNF, INO80, ISWI and CHD) as involved in PHO5 promoter chromatin remodeling. This is likely the first described complete remodeler set for a physiological chromatin transition. RSC was hardly involved at the coregulated PHO8 or PHO84 promoters despite cofactor recruitment by the same transactivator and RSC’s presence at all three promoters. Therefore, promoter-specific chromatin rather than transactivators determine remodeler requirements.
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Affiliation(s)
- Sanja Musladin
- Laboratory of Biochemistry, Faculty of Food Technology and Biotechnology, University of Zagreb, Zagreb 10000, Croatia and Molecular Biology, Adolf-Butenandt-Institut, University of Munich, Munich 80336, Germany
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Kandiah E, Trowitzsch S, Gupta K, Haffke M, Berger I. More pieces to the puzzle: recent structural insights into class II transcription initiation. Curr Opin Struct Biol 2014; 24:91-7. [PMID: 24440461 DOI: 10.1016/j.sbi.2013.12.005] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2013] [Revised: 12/19/2013] [Accepted: 12/20/2013] [Indexed: 01/17/2023]
Abstract
Class II transcription initiation is a highly regulated process and requires the assembly of a pre-initiation complex (PIC) containing DNA template, RNA polymerase II (RNAPII), general transcription factors (GTFs) TFIIA, TFIIB, TFIID, TFIIE, TFIIF, TFIIH and Mediator. RNAPII, TFIID, TFIIH and Mediator are large multiprotein complexes, each containing 10 and more subunits. Altogether, the PIC is made up of about 60 polypeptides with a combined molecular weight of close to 4MDa. Recent structural studies of key PIC components have significantly advanced our understanding of transcription initiation. TFIID was shown to bind promoter DNA in a reorganized state. The architecture of a core-TFIID complex was elucidated. Crystal structures of the TATA-binding protein (TBP) bound to TBP-associated factor 1 (TAF1), RNAPII-TFIIB complexes and the Mediator head module were solved. The overall architectures of large PIC assemblies from human and yeast have been determined by electron microscopy (EM). Here we review these latest structural insights into the architecture and assembly of the PIC, which reveal exciting new mechanistic details of transcription initiation.
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Affiliation(s)
- Eaazhisai Kandiah
- European Molecular Biology Laboratory, Grenoble Outstation, 6 rue Jules Horowitz, 38042 Grenoble, France; Unit of Virus Host-Cell Interactions, Unité Mixte Internationale UMI 3265, Université de Grenoble Alpes - EMBL - CNRS, 6 Rue Jules Horowitz, BP181, 38042 Grenoble Cedex 9, France
| | - Simon Trowitzsch
- European Molecular Biology Laboratory, Grenoble Outstation, 6 rue Jules Horowitz, 38042 Grenoble, France; Unit of Virus Host-Cell Interactions, Unité Mixte Internationale UMI 3265, Université de Grenoble Alpes - EMBL - CNRS, 6 Rue Jules Horowitz, BP181, 38042 Grenoble Cedex 9, France
| | - Kapil Gupta
- European Molecular Biology Laboratory, Grenoble Outstation, 6 rue Jules Horowitz, 38042 Grenoble, France; Unit of Virus Host-Cell Interactions, Unité Mixte Internationale UMI 3265, Université de Grenoble Alpes - EMBL - CNRS, 6 Rue Jules Horowitz, BP181, 38042 Grenoble Cedex 9, France
| | - Matthias Haffke
- European Molecular Biology Laboratory, Grenoble Outstation, 6 rue Jules Horowitz, 38042 Grenoble, France; Unit of Virus Host-Cell Interactions, Unité Mixte Internationale UMI 3265, Université de Grenoble Alpes - EMBL - CNRS, 6 Rue Jules Horowitz, BP181, 38042 Grenoble Cedex 9, France
| | - Imre Berger
- European Molecular Biology Laboratory, Grenoble Outstation, 6 rue Jules Horowitz, 38042 Grenoble, France; Unit of Virus Host-Cell Interactions, Unité Mixte Internationale UMI 3265, Université de Grenoble Alpes - EMBL - CNRS, 6 Rue Jules Horowitz, BP181, 38042 Grenoble Cedex 9, France.
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Transcriptional regulators in hepatocarcinogenesis--key integrators of malignant transformation. J Hepatol 2012; 57:186-95. [PMID: 22446689 DOI: 10.1016/j.jhep.2011.11.029] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/16/2011] [Revised: 11/28/2011] [Accepted: 11/30/2011] [Indexed: 12/26/2022]
Abstract
Hepatocellular carcinoma (HCC) is one of the most frequent human malignancies with poor prognosis and increasing incidence in the Western world. Only for a minority of HCC patients, surgical treatment options offer potential cure and therapeutic success of pharmacological approaches is limited. Highly specific approaches (e.g., kinase inhibitors) did not significantly improve the situation so far, possibly due to functional compensation, genetic heterogeneity of HCC, and development of resistance under selective pressure. In contrast, transcriptional regulators (especially transcription factors and co-factors) may integrate and process input signals of different (oncogenic) pathways and therefore represent cellular bottlenecks that regulate tumor cell biology. In this review, we want to summarize the current knowledge about central transcriptional regulators in human hepatocarcinogenesis and their potential as therapeutic target structures. Genomic and transcriptomic data of primary human HCC revealed that many of these factors showed up in subgroups of HCCs with a more aggressive phenotype, suggesting that aberrant activity of transcriptional regulators collect input information to promote tumor initiation and progression. Therefore, expression and dysfunction of transcription factors and co-factors may gain relevance for diagnostics and therapy of HCC.
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21
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Bai L, Ondracka A, Cross FR. Multiple sequence-specific factors generate the nucleosome-depleted region on CLN2 promoter. Mol Cell 2011; 42:465-76. [PMID: 21596311 DOI: 10.1016/j.molcel.2011.03.028] [Citation(s) in RCA: 82] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2010] [Revised: 03/12/2011] [Accepted: 03/30/2011] [Indexed: 01/29/2023]
Abstract
Nucleosome-depleted regions (NDRs) are ubiquitous on eukaryotic promoters. The formation of many NDRs cannot be readily explained by previously proposed mechanisms. Here, we carry out a focused study on a physiologically important NDR in the yeast CLN2 promoter (CLN2pr). We show that this NDR does not result from intrinsically unfavorable histone-DNA interaction. Instead, we identified eight conserved factor binding sites, including that of Reb1, Mcm1, and Rsc3, that cause the local nucleosome depletion. These nucleosome-depleting factors (NDFs) work redundantly, and simultaneously mutating all their binding sites eliminates CLN2pr NDR. The loss of the NDR induces unreliable "on/off" expression in individual cell cycles, but in the presence of the NDR, NDFs have little direct effect on transcription. We present bioinformatic evidence that the formation of many NDRs across the genome involves multiple NDFs. Our findings also provide significant insight into the composition and spatial organization of functional promoters.
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Affiliation(s)
- Lu Bai
- Laboratory of Cell Cycle Genetics, The Rockefeller University, New York, NY, 10065, USA.
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22
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Chevereau G, Arneodo A, Vaillant C. Influence of the genomic sequence on the primary structure of chromatin. FRONTIERS IN LIFE SCIENCE 2011. [DOI: 10.1080/21553769.2012.708882] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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23
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Tolkunov D, Zawadzki KA, Singer C, Elfving N, Morozov AV, Broach JR. Chromatin remodelers clear nucleosomes from intrinsically unfavorable sites to establish nucleosome-depleted regions at promoters. Mol Biol Cell 2011; 22:2106-18. [PMID: 21508315 PMCID: PMC3113774 DOI: 10.1091/mbc.e10-10-0826] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
Abstract
Most promoters in yeast contain a nucleosome-depleted region (NDR), but the mechanisms by which NDRs are established and maintained in vivo are currently unclear. We have examined how genome-wide nucleosome placement is altered in the absence of two distinct types of nucleosome remodeling activity. In mutants of both SNF2, which encodes the ATPase component of the Swi/Snf remodeling complex, and ASF1, which encodes a histone chaperone, distinct sets of gene promoters carry excess nucleosomes in their NDRs relative to wild-type. In snf2 mutants, excess promoter nucleosomes correlate with reduced gene expression. In both mutants, the excess nucleosomes occupy DNA sequences that are energetically less favorable for nucleosome formation, indicating that intrinsic histone-DNA interactions are not sufficient for nucleosome positioning in vivo, and that Snf2 and Asf1 promote thermodynamic equilibration of nucleosomal arrays. Cells lacking SNF2 or ASF1 still accomplish the changes in promoter nucleosome structure associated with large-scale transcriptional reprogramming. However, chromatin reorganization in the mutants is reduced in extent compared to wild-type cells, even though transcriptional changes proceed normally. In summary, active remodeling is required for distributing nucleosomes to energetically favorable positions in vivo and for reorganizing chromatin in response to changes in transcriptional activity.
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Affiliation(s)
- Denis Tolkunov
- Department of Physics and Astronomy and BioMaPS Institute for Quantitative Biology, Rutgers University, Piscataway, NJ 08854, USA
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24
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Li XY, Thomas S, Sabo PJ, Eisen MB, Stamatoyannopoulos JA, Biggin MD. The role of chromatin accessibility in directing the widespread, overlapping patterns of Drosophila transcription factor binding. Genome Biol 2011; 12:R34. [PMID: 21473766 PMCID: PMC3218860 DOI: 10.1186/gb-2011-12-4-r34] [Citation(s) in RCA: 180] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2011] [Accepted: 04/07/2011] [Indexed: 12/11/2022] Open
Abstract
Background In Drosophila embryos, many biochemically and functionally unrelated transcription factors bind quantitatively to highly overlapping sets of genomic regions, with much of the lowest levels of binding being incidental, non-functional interactions on DNA. The primary biochemical mechanisms that drive these genome-wide occupancy patterns have yet to be established. Results Here we use data resulting from the DNaseI digestion of isolated embryo nuclei to provide a biophysical measure of the degree to which proteins can access different regions of the genome. We show that the in vivo binding patterns of 21 developmental regulators are quantitatively correlated with DNA accessibility in chromatin. Furthermore, we find that levels of factor occupancy in vivo correlate much more with the degree of chromatin accessibility than with occupancy predicted from in vitro affinity measurements using purified protein and naked DNA. Within accessible regions, however, the intrinsic affinity of the factor for DNA does play a role in determining net occupancy, with even weak affinity recognition sites contributing. Finally, we show that programmed changes in chromatin accessibility between different developmental stages correlate with quantitative alterations in factor binding. Conclusions Based on these and other results, we propose a general mechanism to explain the widespread, overlapping DNA binding by animal transcription factors. In this view, transcription factors are expressed at sufficiently high concentrations in cells such that they can occupy their recognition sequences in highly accessible chromatin without the aid of physical cooperative interactions with other proteins, leading to highly overlapping, graded binding of unrelated factors.
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Affiliation(s)
- Xiao-Yong Li
- Genomics Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road MS 84-171, Berkeley, CA 94720, USA
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25
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Kaplan T, Li XY, Sabo PJ, Thomas S, Stamatoyannopoulos JA, Biggin MD, Eisen MB. Quantitative models of the mechanisms that control genome-wide patterns of transcription factor binding during early Drosophila development. PLoS Genet 2011; 7:e1001290. [PMID: 21304941 PMCID: PMC3033374 DOI: 10.1371/journal.pgen.1001290] [Citation(s) in RCA: 139] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2010] [Accepted: 01/01/2011] [Indexed: 01/01/2023] Open
Abstract
Transcription factors that drive complex patterns of gene expression during animal development bind to thousands of genomic regions, with quantitative differences in binding across bound regions mediating their activity. While we now have tools to characterize the DNA affinities of these proteins and to precisely measure their genome-wide distribution in vivo, our understanding of the forces that determine where, when, and to what extent they bind remains primitive. Here we use a thermodynamic model of transcription factor binding to evaluate the contribution of different biophysical forces to the binding of five regulators of early embryonic anterior-posterior patterning in Drosophila melanogaster. Predictions based on DNA sequence and in vitro protein-DNA affinities alone achieve a correlation of ∼0.4 with experimental measurements of in vivo binding. Incorporating cooperativity and competition among the five factors, and accounting for spatial patterning by modeling binding in every nucleus independently, had little effect on prediction accuracy. A major source of error was the prediction of binding events that do not occur in vivo, which we hypothesized reflected reduced accessibility of chromatin. To test this, we incorporated experimental measurements of genome-wide DNA accessibility into our model, effectively restricting predicted binding to regions of open chromatin. This dramatically improved our predictions to a correlation of 0.6-0.9 for various factors across known target genes. Finally, we used our model to quantify the roles of DNA sequence, accessibility, and binding competition and cooperativity. Our results show that, in regions of open chromatin, binding can be predicted almost exclusively by the sequence specificity of individual factors, with a minimal role for protein interactions. We suggest that a combination of experimentally determined chromatin accessibility data and simple computational models of transcription factor binding may be used to predict the binding landscape of any animal transcription factor with significant precision.
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Affiliation(s)
- Tommy Kaplan
- Department of Molecular and Cell Biology, California Institute of Quantitative Biosciences, University of California Berkeley, Berkeley, California, United States of America
| | - Xiao-Yong Li
- Howard Hughes Medical Institute, University of California Berkeley, Berkeley, California, United States of America
| | - Peter J. Sabo
- Department of Genome Sciences, University of Washington, Seattle, Washington, United States of America
| | - Sean Thomas
- Department of Genome Sciences, University of Washington, Seattle, Washington, United States of America
| | | | - Mark D. Biggin
- Genomics Division, Lawrence Berkeley National Laboratory, Berkeley, California, United States of America
| | - Michael B. Eisen
- Department of Molecular and Cell Biology, California Institute of Quantitative Biosciences, University of California Berkeley, Berkeley, California, United States of America
- Howard Hughes Medical Institute, University of California Berkeley, Berkeley, California, United States of America
- Genomics Division, Lawrence Berkeley National Laboratory, Berkeley, California, United States of America
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Ganapathi M, Palumbo MJ, Ansari SA, He Q, Tsui K, Nislow C, Morse RH. Extensive role of the general regulatory factors, Abf1 and Rap1, in determining genome-wide chromatin structure in budding yeast. Nucleic Acids Res 2010; 39:2032-44. [PMID: 21081559 PMCID: PMC3064788 DOI: 10.1093/nar/gkq1161] [Citation(s) in RCA: 94] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
The packaging of eukaryotic DNA into chromatin has profound consequences for gene regulation, as well as for other DNA transactions such as recombination, replication and repair. Understanding how this packaging is determined is consequently a pressing problem in molecular genetics. DNA sequence, chromatin remodelers and transcription factors affect chromatin structure, but the scope of these influences on genome-wide nucleosome occupancy patterns remains uncertain. Here, we use high resolution tiling arrays to examine the contributions of two general regulatory factors, Abf1 and Rap1, to nucleosome occupancy in Saccharomyces cerevisiae. These factors have each been shown to bind to a few hundred promoters, but we find here that thousands of loci show localized regions of altered nucleosome occupancy within 1 h of loss of Abf1 or Rap1 binding, and that altered chromatin structure can occur via binding sites having a wide range of affinities. These results indicate that DNA-binding transcription factors affect chromatin structure, and probably dynamics, throughout the genome to a much greater extent than previously appreciated.
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Affiliation(s)
- Mythily Ganapathi
- Laboratory of Molecular Genetics, New York State Department of Health, Wadsworth Center, Albany, NY 12201-0509, USA
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27
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Vorob’eva NE, Soshnikova NV, Nikolenko YV, Kuz’mina YL, Nabirochkina EN, Georgieva SG, Shidlovskii YV. A novel conserved domain of SAYP coactivator mediates the interaction of TFIID and brahma transcription complexes. Mol Biol 2010. [DOI: 10.1134/s0026893310050134] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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28
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Miki K, Shimizu M, Fujii M, Takayama S, Hossain MN, Ayusawa D. 5-bromodeoxyuridine induces transcription of repressed genes with disruption of nucleosome positioning. FEBS J 2010; 277:4539-48. [PMID: 21040474 DOI: 10.1111/j.1742-4658.2010.07868.x] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
5-Bromodeoxyuridine (BrdU) modulates the expression of particular genes associated with cellular differentiation and senescence when incorporated into DNA instead of thymidine (dThd). To date, a molecular mechanism for this phenomenon remains a mystery in spite of a large number of studies. Recently, we have demonstrated that BrdU disrupts nucleosome positioning on model plasmids mediated by specific AT-tracts in yeast cells. Here we constructed a cognate plasmid that can form an ordered array of nucleosomes determined by an α2 operator and contains the BAR1 gene as an expression marker gene to examine BAR1 expression in dThd-auxotrophic MATα cells under various conditions. In medium containing dThd, BAR1 expression was completely repressed, associated with the formation of the stable array of nucleosomes. Insertion of AT-tracts into a site of the promoter region slightly increased BAR1 expression and slightly destabilized nucleosome positioning dependent on their sequence specificity. In medium containing BrdU, BAR1 expression was further enhanced, associated with more marked disruption of nucleosome positioning on the promoter region. Disruption of nucleosome positioning seems to be sufficient for full expression of the marker gene if necessary transcription factors are supplied. Incorporation of 5-bromouracil into the plasmid did not weaken the binding of the α2/Mcm1 repressor complex to its legitimate binding site, as revealed by an in vivo UV photofootprinting assay. These results suggest that BrdU increases transcription of repressed genes by disruption of nucleosome positioning around their promoters.
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Affiliation(s)
- Kensuke Miki
- Department of Genome System Science, Yokohama City University, Yokohama, Kanagawa, Japan
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29
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De Abrew KN, Kaminski NE, Thomas RS. An integrated genomic analysis of aryl hydrocarbon receptor-mediated inhibition of B-cell differentiation. Toxicol Sci 2010; 118:454-69. [PMID: 20819909 DOI: 10.1093/toxsci/kfq265] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
The aryl hydrocarbon receptor (AHR) agonist 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD) alters differentiation of B cells and suppresses antibody production. A combination of whole-genome, microarray-based chromatin immunoprecipitation (ChIP-on-chip), and time course gene expression microarray analysis was performed on the mouse B-cell line CH12.LX following exposure to lipopolysaccharide (LPS) or LPS and TCDD to identify the primary and downstream transcriptional elements of B-cell differentiation that are altered by the AHR. ChIP-on-chip analysis identified 1893 regions with a significant increase in AHR binding with TCDD treatment. Transcription factor binding site analysis on the ChIP-on-chip data showed enrichment in AHR response elements. Other transcription factors showed significant coenrichment with AHR response elements. When ChIP-on-chip regions were compared with gene expression changes at the early time points, 78 genes were identified as potential direct targets of the AHR. AHR binding and expression changes were confirmed for a subset of genes in primary mouse B cells. Network analysis examining connections between the 78 potential AHR target genes and three transcription factors known to regulate B-cell differentiation indicated multiple paths for potential regulation by the AHR. Enrichment analysis on the differentially expressed genes at each time point evaluated the downstream impact of AHR-regulated gene expression changes on B-cell-related processes. AHR-mediated impairment of B-cell differentiation occurred at multiple nodes of the B-cell differentiation network and potentially through multiple mechanisms including direct cis-acting effects on key regulators of B-cell differentiation, indirect regulation of B-cell differentiation-related pathways, and transcriptional coregulation of target genes by AHR and other transcription factors.
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Affiliation(s)
- K Nadira De Abrew
- The Hamner Institutes for Health Sciences, Research Triangle Park, North Carolina 27709, USA
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30
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Kuzmina JL, Panov VV, Vorobyeva NE, Soshnikova NV, Kopantseva MR, Nikolenko JV, Nabirochkina EN, Georgieva SG, Shidlovskii YV. SAYP is a novel regulator of metazoan development. RUSS J GENET+ 2010. [DOI: 10.1134/s1022795410080028] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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31
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Ertel F, Dirac-Svejstrup AB, Hertel CB, Blaschke D, Svejstrup JQ, Korber P. In vitro reconstitution of PHO5 promoter chromatin remodeling points to a role for activator-nucleosome competition in vivo. Mol Cell Biol 2010; 30:4060-76. [PMID: 20566699 PMCID: PMC2916437 DOI: 10.1128/mcb.01399-09] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2009] [Revised: 12/01/2009] [Accepted: 06/09/2010] [Indexed: 11/20/2022] Open
Abstract
The yeast PHO5 promoter is a classical model for studying the role of chromatin in gene regulation. To enable biochemical dissection of the mechanism leading to PHO5 activation, we reconstituted the process in vitro. Positioned nucleosomes corresponding to the repressed PHO5 promoter state were assembled using a yeast extract-based in vitro system. Addition of the transactivator Pho4 yielded an extensive DNase I-hypersensitive site resembling induced PHO5 promoter chromatin. Importantly, this remodeling was energy dependent. In contrast, little or no chromatin remodeling was detected at the PHO8 or PHO84 promoter in this in vitro system. Only the PHO5 promoter harbors a high-affinity intranucleosomal Pho4 binding site (UASp) where Pho4 binding can compete with nucleosome formation, prompting us to test the importance of such competition for chromatin remodeling by analysis of UASp mutants in vivo. Indeed, the intranucleosomal location of the UASp element was critical, but not essential, for complete remodeling at the PHO5 promoter in vivo. Further, binding of just the Gal4 DNA binding domain to an intranucleosomal site could increase PHO5 promoter opening. These data establish an auxiliary role for DNA binding competition between Pho4 and histones in PHO5 promoter chromatin remodeling in vivo.
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Affiliation(s)
- Franziska Ertel
- Adolf-Butenandt-Institut, University of Munich, Schillerstr. 44, 80336 Munich, Germany, Cancer Research UK, London Research Institute, Clare Hall Laboratories, Blanche Lane, South Mimms, Hertfordshire EN6 3LD, United Kingdom
| | - A. Barbara Dirac-Svejstrup
- Adolf-Butenandt-Institut, University of Munich, Schillerstr. 44, 80336 Munich, Germany, Cancer Research UK, London Research Institute, Clare Hall Laboratories, Blanche Lane, South Mimms, Hertfordshire EN6 3LD, United Kingdom
| | - Christina Bech Hertel
- Adolf-Butenandt-Institut, University of Munich, Schillerstr. 44, 80336 Munich, Germany, Cancer Research UK, London Research Institute, Clare Hall Laboratories, Blanche Lane, South Mimms, Hertfordshire EN6 3LD, United Kingdom
| | - Dorothea Blaschke
- Adolf-Butenandt-Institut, University of Munich, Schillerstr. 44, 80336 Munich, Germany, Cancer Research UK, London Research Institute, Clare Hall Laboratories, Blanche Lane, South Mimms, Hertfordshire EN6 3LD, United Kingdom
| | - Jesper Q. Svejstrup
- Adolf-Butenandt-Institut, University of Munich, Schillerstr. 44, 80336 Munich, Germany, Cancer Research UK, London Research Institute, Clare Hall Laboratories, Blanche Lane, South Mimms, Hertfordshire EN6 3LD, United Kingdom
| | - Philipp Korber
- Adolf-Butenandt-Institut, University of Munich, Schillerstr. 44, 80336 Munich, Germany, Cancer Research UK, London Research Institute, Clare Hall Laboratories, Blanche Lane, South Mimms, Hertfordshire EN6 3LD, United Kingdom
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32
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Bai L, Charvin G, Siggia ED, Cross FR. Nucleosome-depleted regions in cell-cycle-regulated promoters ensure reliable gene expression in every cell cycle. Dev Cell 2010; 18:544-55. [PMID: 20412770 DOI: 10.1016/j.devcel.2010.02.007] [Citation(s) in RCA: 75] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2009] [Revised: 12/17/2009] [Accepted: 02/24/2010] [Indexed: 12/21/2022]
Abstract
Many promoters in eukaryotes have nucleosome-depleted regions (NDRs) containing transcription factor binding sites. However, the functional significance of NDRs is not well understood. Here, we examine NDR function in two cell cycle-regulated promoters, CLN2pr and HOpr, by varying nucleosomal coverage of the binding sites of their activator, Swi4/Swi6 cell-cycle box (SCB)-binding factor (SBF), and probing the corresponding transcriptional activity in individual cells with time-lapse microscopy. Nucleosome-embedded SCBs do not significantly alter peak expression levels. Instead, they induce bimodal, "on/off" activation in individual cell cycles, which displays short-term memory, or epigenetic inheritance, from the mother cycle. In striking contrast, the same SCBs localized in NDR lead to highly reliable activation, once in every cell cycle. We further demonstrate that the high variability in Cln2p expression induced by the nucleosomal SCBs reduces cell fitness. Therefore, we propose that the NDR function in limiting stochasticity in gene expression promotes the ubiquity and conservation of promoter NDR. PAPERCLIP:
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Affiliation(s)
- Lu Bai
- Center for Studies in Physics and Biology, The Rockefeller University, New York, NY 10065, USA.
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33
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Tanase JI, Mitani T, Udagawa K, Nishikawa JI, Ohyama T. Competence of an artificial bent DNA as a transcriptional activator in mouse ES cells. Mol Biol Rep 2010; 38:37-47. [PMID: 20306228 DOI: 10.1007/s11033-010-0075-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2009] [Accepted: 03/05/2010] [Indexed: 11/29/2022]
Abstract
Curved DNA structures with a left-handed superhelical conformation can activate eukaryotic transcription. However, their potency in transgene activation in embryonic stem (ES) cells has not been examined. T20 is an artificial curved DNA of 180 bp that serves as a transcriptional activator. We investigated the effect of T20 on transcription in mouse ES cell lines or hepatocytes differentiated from them. We established 10 sets of cell lines each harboring a single copy of the reporter construct. Each set comprised a T20-harboring cell line and a T20-less control cell line. Analyses showed that in ES cells and in hepatocytes originating from these cells, T20 both activated and repressed transcription in a manner that was dependent on the locus of reporter. The present and previous studies strongly suggest that in cells that have a strict gene regulation system, transcriptional activation by T20 occurs only in a transcriptionally active locus in the genome.
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Affiliation(s)
- Jun-ichi Tanase
- Department of Biology, Faculty of Education and Integrated Arts and Sciences, Waseda University, 2-2 Wakamatsu-cho, Shinjuku-ku, Tokyo, 162-8480, Japan
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34
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van Steensel B, Braunschweig U, Filion GJ, Chen M, van Bemmel JG, Ideker T. Bayesian network analysis of targeting interactions in chromatin. Genome Res 2009; 20:190-200. [PMID: 20007327 DOI: 10.1101/gr.098822.109] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
In eukaryotes, many chromatin proteins together regulate gene expression. Chromatin proteins often direct the genomic binding pattern of other chromatin proteins, for example, by recruitment or competition mechanisms. The network of such targeting interactions in chromatin is complex and still poorly understood. Based on genome-wide binding maps, we constructed a Bayesian network model of the targeting interactions among a broad set of 43 chromatin components in Drosophila cells. This model predicts many novel functional relationships. For example, we found that the homologous proteins HP1 and HP1C each target the heterochromatin protein HP3 to distinct sets of genes in a competitive manner. We also discovered a central role for the remodeling factor Brahma in the targeting of several DNA-binding factors, including GAGA factor, JRA, and SU(VAR)3-7. Our network model provides a global view of the targeting interplay among dozens of chromatin components.
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Affiliation(s)
- Bas van Steensel
- Division of Gene Regulation, Netherlands Cancer Institute, 1066 CX Amsterdam, the Netherlands.
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35
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Soshnikova NV, Vorobyeva NI, Krasnov AN, Georgieva SG, Nabirochkina EN, Shidlovskii YV. Novel complex formed by the SAYP transcriptional coactivator. Mol Biol 2009. [DOI: 10.1134/s0026893309060107] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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36
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Morris RT, O'Connor TR, Wyrick JJ. Ceres: software for the integrated analysis of transcription factor binding sites and nucleosome positions in Saccharomyces cerevisiae. ACTA ACUST UNITED AC 2009; 26:168-74. [PMID: 19959498 DOI: 10.1093/bioinformatics/btp657] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
MOTIVATION There is accumulating evidence that the chromatin environment of transcription factor (TF) binding sites in promoter regions has a critical influence on their regulatory potential. Recent studies have mapped TF binding sites and nucleosome positions throughout the yeast genome; however, there is a lack of computation tools to integrate these data types. RESULTS We have developed the Ceres software to facilitate the integrated analysis of TF binding sites and nucleosome positions in the model eukaryote S. cerevisiae. Ceres enables users to dynamically display the spatial organization of TF binding sites and nucleosome positions of individual genes, or the average profiles for large gene sets. Ceres provides novel statistical tools to test for the enrichment of TF binding sites and chromatin environments for user-selected gene sets. Ceres also enables users to search the genome for combinations of TF binding sites that are associated with specific chromatin environments. Preliminary analysis using the Ceres software indicates that functional and conserved TF binding sites are often associated with specific chromatin environments. AVAILABILITY http://bioinformatics1.smb.wsu.edu/Ceres. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Robert T Morris
- School of Molecular Biosciences and Center for Reproductive Biology, Washington State University, Pullman, WA 99164, USA
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37
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Vaillant C, Palmeira L, Chevereau G, Audit B, d'Aubenton-Carafa Y, Thermes C, Arneodo A. A novel strategy of transcription regulation by intragenic nucleosome ordering. Genome Res 2009; 20:59-67. [PMID: 19858362 DOI: 10.1101/gr.096644.109] [Citation(s) in RCA: 62] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Numerous studies of chromatin structure showed that nucleosome free regions (NFRs) located at 5' gene ends contribute to transcription initiation regulation. Here, we determine the role of intragenic chromatin structure on gene expression regulation. We show that, along Saccharomyces cerevisiae genes, nucleosomes are highly organized following two types of architecture that depend only on the distance between the NFRs located at the 5' and 3' gene ends. In the first type, this distance constrains in vivo the positioning of n nucleosomes regularly organized in a "crystal-like" array. In the second type, this distance is such that the corresponding genes can accommodate either n or (n + 1) nucleosomes, thereby displaying two possible crystal-like arrays of n weakly compacted or n + 1 highly compacted nucleosomes. This adaptability confers "bi-stable" properties to chromatin and is a key to its dynamics. Compared to crystal-like genes, bi-stable genes present higher transcriptional plasticity, higher sensitivity to chromatin regulators, higher H3 turnover rate, and lower H2A.Z enrichment. The results strongly suggest that transcription elongation is facilitated by higher chromatin compaction. The data allow us to propose a new paradigm of transcriptional control mediated by the stability and the level of compaction of the intragenic chromatin architecture and open new ways for investigating eukaryotic gene expression regulation.
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38
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Biochemical analyses of nuclear receptor-dependent transcription with chromatin templates. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2009; 87:137-92. [PMID: 20374704 DOI: 10.1016/s1877-1173(09)87005-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/18/2023]
Abstract
Chromatin, the physiological template for transcription, plays important roles in gene regulation by nuclear receptors (NRs). It can (1) restrict the binding of NRs or the transcriptional machinery to their genomic targets, (2) serve as a target of regulatory posttranslational modifications by NR coregulator proteins with histone-directed enzymatic activities, and (3) function as a binding scaffold for a variety of transcription-related proteins. The advent of in vitro or "cell-free" systems that accurately recapitulate ligand-dependent transcription by NRs with chromatin templates has allowed detailed analyses of these processes. Biochemical studies have advanced our understanding of the mechanisms of gene regulation, including the role of ligands, coregulators, and nucleosome remodeling. In addition, they have provided new insights about the dynamics of NR-mediated transcription. This chapter reviews the current methodologies for assembling, transcribing, and analyzing chromatin in vitro, as well as the new information that has been gained from these studies.
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39
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Transcription coactivator SAYP combines chromatin remodeler Brahma and transcription initiation factor TFIID into a single supercomplex. Proc Natl Acad Sci U S A 2009; 106:11049-54. [PMID: 19541607 DOI: 10.1073/pnas.0901801106] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Transcription activation by RNA polymerase II is a complicated process driven by combined, precisely coordinated action of a wide array of coactivator complexes, which carry out chromatin-directed activities and nucleate the assembly of the preinitiation complex on the promoter. Using various techniques, we have shown the existence of a stable coactivator supercomplex consisting of the chromatin-remodeling factor Brahma (SWI/SNF) and the transcription initiation factor TFIID, named BTFly (Brahma and TFIID in one assembly). The coupling of Brahma and TFIID is mediated by the SAYP factor, whose evolutionarily conserved activation domain SAY can directly bind to both BAP170 subunit of Brahma and TAF5 subunit of TFIID. The integrity of BTFly is crucial for its ability to activate transcription. BTFly is distributed genome-wide and appears to be a means of effective transcription activation.
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40
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Zawadzki KA, Morozov AV, Broach JR. Chromatin-dependent transcription factor accessibility rather than nucleosome remodeling predominates during global transcriptional restructuring in Saccharomyces cerevisiae. Mol Biol Cell 2009; 20:3503-13. [PMID: 19494041 DOI: 10.1091/mbc.e09-02-0111] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023] Open
Abstract
Several well-studied promoters in yeast lose nucleosomes upon transcriptional activation and gain them upon repression, an observation that has prompted the model that transcriptional activation and repression requires nucleosome remodeling of regulated promoters. We have examined global nucleosome positioning before and after glucose-induced transcriptional reprogramming, a condition under which more than half of all yeast genes significantly change expression. The majority of induced and repressed genes exhibit no change in promoter nucleosome arrangement, although promoters that do undergo nucleosome remodeling tend to contain a TATA box. Rather, we found multiple examples where the pre-existing accessibility of putative transcription factor binding sites before glucose addition determined whether the corresponding gene would change expression in response to glucose addition. These results suggest that selection of appropriate transcription factor binding sites may be dictated to a large extent by nucleosome prepositioning but that regulation of expression through these sites is dictated not by nucleosome repositioning but by changes in transcription factor activity.
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Affiliation(s)
- Karl A Zawadzki
- Department of Molecular Biology, Princeton University, Princeton, NJ 08544, USA
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41
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An improved method to obtain a soluble nuclear fraction from embryonic brain tissue. Neurochem Res 2009; 34:2022-9. [PMID: 19462231 DOI: 10.1007/s11064-009-9993-9] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2009] [Accepted: 05/07/2009] [Indexed: 10/20/2022]
Abstract
This paper describes modifications of the standard methods for obtaining a soluble nuclear fraction from embryonic brain tissue. The main improvements are: (1) the inclusion of a low speed centrifugation step to prevent the appearance of high density contaminants, (2) a sucrose density gradient to remove perinuclear mitochondria and ER membranes and (3) a protein extraction approach which significantly enhances protein yield. To demonstrate the effectiveness of the method, pellets were analyzed by light and electron microscopy and purity of the soluble extracts was immunologically tested. Finally, to illustrate the applicability of this approach, the induction of the transcription factor HIF-1 (hypoxia-inducible factor-1) was assessed by Western blot using soluble nuclear fractions and by immuno-electron microscopy using purified nuclear fractions, both obtained from the optic lobes of chick embryos. In conclusion, the procedure presently described appears to be reliable and convenient for obtaining a pure soluble nuclear fraction from a discrete amount of embryonic brain tissue.
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42
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Differential cofactor requirements for histone eviction from two nucleosomes at the yeast PHO84 promoter are determined by intrinsic nucleosome stability. Mol Cell Biol 2009; 29:2960-81. [PMID: 19307305 DOI: 10.1128/mcb.01054-08] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
We showed previously that the strong PHO5 promoter is less dependent on chromatin cofactors than the weaker coregulated PHO8 promoter. In this study we asked if chromatin remodeling at the even stronger PHO84 promoter was correspondingly less cofactor dependent. The repressed PHO84 promoter showed a short hypersensitive region that was flanked upstream and downstream by a positioned nucleosome and contained two transactivator Pho4 sites. Promoter induction generated an extensive hypersensitive and histone-depleted region, yielding two more Pho4 sites accessible. This remodeling was strictly Pho4 dependent, strongly dependent on the remodelers Snf2 and Ino80 and on the histone acetyltransferase Gcn5, and more weakly on the acetyltransferase Rtt109. Importantly, remodeling of each of the two positioned nucleosomes required Snf2 and Ino80 to different degrees. Only remodeling of the upstream nucleosome was strictly dependent on Snf2. Further, remodeling of the upstream nucleosome was more dependent on Ino80 than remodeling of the downstream nucleosome. Both nucleosomes differed in their intrinsic stabilities as predicted in silico and measured in vitro. The causal relationship between the different nucleosome stabilities and the different cofactor requirements was shown by introducing destabilizing mutations in vivo. Therefore, chromatin cofactor requirements were determined by intrinsic nucleosome stabilities rather than correlated to promoter strength.
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43
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Stoebel DM, Free A, Dorman CJ. Anti-silencing: overcoming H-NS-mediated repression of transcription in Gram-negative enteric bacteria. Microbiology (Reading) 2008; 154:2533-2545. [PMID: 18757787 DOI: 10.1099/mic.0.2008/020693-0] [Citation(s) in RCA: 203] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Daniel M. Stoebel
- Department of Microbiology, School of Genetics and Microbiology, Moyne Institute of Preventive Medicine, Trinity College, Dublin 2, Ireland
| | - Andrew Free
- Institute of Evolutionary Biology, University of Edinburgh, Room 714a, Darwin Building, The King's Buildings, Mayfield Road, Edinburgh EH9 3JR, UK
| | - Charles J. Dorman
- Department of Microbiology, School of Genetics and Microbiology, Moyne Institute of Preventive Medicine, Trinity College, Dublin 2, Ireland
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44
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Kharchenko PV, Woo CJ, Tolstorukov MY, Kingston RE, Park PJ. Nucleosome positioning in human HOX gene clusters. Genome Res 2008; 18:1554-61. [PMID: 18723689 DOI: 10.1101/gr.075952.107] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
The distribution of nucleosomes along the genome is a significant aspect of chromatin structure and is thought to influence gene regulation through modulation of DNA accessibility. However, properties of nucleosome organization remain poorly understood, particularly in mammalian genomes. Toward this goal we used tiled microarrays to identify stable nucleosome positions along the HOX gene clusters in human cell lines. We show that nucleosome positions exhibit sequence properties and long-range organization that are different from those characterized in other organisms. Despite overall variability of internucleosome distances, specific loci contain regular nucleosomal arrays with 195-bp periodicity. Moreover, such arrays tend to occur preferentially toward the 3' ends of genes. Through comparison of different cell lines, we find that active transcription is correlated with increased positioning of nucleosomes, suggesting an unexpected role for transcription in the establishment of well-positioned nucleosomes.
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Affiliation(s)
- Peter V Kharchenko
- Harvard Partners Center for Genetics and Genomics, Boston, Massachusetts 02115, USA
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45
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Straub T, Becker PB. DNA sequence and the organization of chromosomal domains. Curr Opin Genet Dev 2008; 18:175-80. [DOI: 10.1016/j.gde.2008.01.001] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2008] [Revised: 01/10/2008] [Accepted: 01/11/2008] [Indexed: 10/22/2022]
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46
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5-Bromouracil disrupts nucleosome positioning by inducing A-form-like DNA conformation in yeast cells. Biochem Biophys Res Commun 2008; 368:662-9. [PMID: 18258180 DOI: 10.1016/j.bbrc.2008.01.149] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2008] [Accepted: 01/26/2008] [Indexed: 11/23/2022]
Abstract
5-Bromodeoxyuridine (BrdU) modulates expression of particular genes associated with cellular differentiation and senescence. Our previous studies have suggested an involvement of chromatin structure in this phenomenon. Here, we examined the effect of 5-bromouracil on nucleosome positioning in vivo using TALS plasmid in yeast cells. This plasmid can stably and precisely be assembled nucleosomes aided by the alpha2 repressor complex bound to its alpha2 operator. Insertion of AT-rich sequences into a site near the operator destabilized nucleosome positioning dependent on their length and sequences. Addition of BrdU almost completely disrupted nucleosome positioning through specific AT-tracts. The effective AT-rich sequences migrated faster on polyacrylamide gel electrophoresis, and their mobility was further accelerated by substitution of thymine with 5-bromouracil. Since this property is indicative of a rigid conformation of DNA, our results suggest that 5-bromouracil disrupts nucleosome positioning by inducing A-form-like DNA.
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47
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Morohashi N, Nakajima K, Kurihara D, Mukai Y, Mitchell AP, Shimizu M. A nucleosome positioned by alpha2/Mcm1 prevents Hap1 activator binding in vivo. Biochem Biophys Res Commun 2007; 364:583-8. [PMID: 17959145 DOI: 10.1016/j.bbrc.2007.10.037] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2007] [Accepted: 10/09/2007] [Indexed: 11/24/2022]
Abstract
Nucleosome positioning has been proposed as a mechanism of transcriptional repression. Here, we examined whether nucleosome positioning affects activator binding in living yeast cells. We introduced the cognate Hap1 binding site (UAS1) at a location 24-43 bp, 29-48 bp, or 61-80 bp interior to the edge of a nucleosome positioned by alpha2/Mcm1 in yeast minichromosomes. Hap1 binding to the UAS1 was severely inhibited, not only at the pseudo-dyad but also in the peripheral region of the positioned nucleosome in alpha cells, while it was detectable in a cells, in which the nucleosomes were not positioned. Hap1 binding was restored in alpha cells with tup1 or isw2 mutations, which caused the loss of nucleosome positioning. These results support the mechanism in which alpha2/Mcm1-dependent nucleosome positioning has a regulatory function to limit the access of transcription factors.
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Affiliation(s)
- Nobuyuki Morohashi
- Department of Chemistry, Meisei University, 2-1-1 Hodokubo, Hino, Tokyo 191-8506, Japan
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