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MAHDAVI MR, POURFARZAD F, KOSARYAN M, AKBARI MT. In Vitro Hb Production in B-thalassemia Patients Is Not a Predictor of Clinical Responsiveness to Hydroxyurea. IRANIAN JOURNAL OF PUBLIC HEALTH 2017; 46:948-956. [PMID: 28845406 PMCID: PMC5563877] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
BACKGROUND The hematologic response to hydroxyurea (HU) is varied among β-thalassemia (BT) patients. The BCL11A and SOX6 genes are involved in response to HU. This study aimed to investigate the in-vitro responsiveness of HU among BT major patients homozygote for IVSII-1G>A mutation and XmnI single nucleotide polymorphism (SNP) in order to find whether the in-vitro Hb concentration is a predictor of clinical (HU) responsiveness. METHODS In this case-control study, twenty BT patients homozygote for IVSII-1G>A mutation and XmnI SNP from Thalassemia Research Center, Sari, Iran in 2015 were selected and categorized into two groups of 10 Responder (R) and 10 Non-Responder (NR) according to their clinical HU response. Ten healthy individuals as a control group were also selected. Hematopoietic erythroid progenitors were expanded from peripheral blood. Hb concentration was measured using photometry method. The flow cytometry and real-time PCR methods were applied for the analysis of cell surface markers (CD71 and CD235a) and gene expression (BCL11A and SOX6), respectively. RESULTS R and NR groups produced higher amount of Basic Hb than C group in cell culture medium at day 14 (P<0.05). After HU treatment, in R group, Hb levels was significantly elevated in comparison to NR and C group (P<0.05). BCL11A expression was decreased after exposure to HU in all groups while SOX6 expression was only down-regulated in C group, and its expression was increased in R and NR groups after HU treatment. CONCLUSION Since different factors including wide networks of intracellular factors and individual differences between patients can affect response to HU in patients, the increasing Hemoglobin on culture medium alone cannot predict clinical responsiveness to that drug.
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152
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Du M, Bai L. 3D clustering of co-regulated genes and its effect on gene expression. Curr Genet 2017; 63:1017-1021. [PMID: 28551816 DOI: 10.1007/s00294-017-0712-9] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2017] [Revised: 05/22/2017] [Accepted: 05/24/2017] [Indexed: 01/29/2023]
Abstract
There are extensive long-distance chromosomal interactions in eukaryotic genomes, but to what extent these interactions affect gene expression is not clear. Recent works have identified several cases where clustering of co-regulated genes leads to enhanced gene expression in budding yeast. Similar phenomenon was also observed in mammalian cells. These results challenge widely held views of gene regulation in yeast and further our understanding of how the 3D organization of the genome contribute to gene regulation in eukaryotes.
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Affiliation(s)
- Manyu Du
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, State College, PA, USA.,Center for Eukaryotic Gene Regulation, The Pennsylvania State University, University Park, State College, PA, USA
| | - Lu Bai
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, State College, PA, USA. .,Center for Eukaryotic Gene Regulation, The Pennsylvania State University, University Park, State College, PA, USA. .,Department of Physics, The Pennsylvania State University, University Park, State College, PA, USA.
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153
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Wang Y, Jain N, Nagarajan M, Maharana S, Iyer KV, Talwar S, Shivashankar GV. Coupling between chromosome intermingling and gene regulation during cellular differentiation. Methods 2017; 123:66-75. [PMID: 28554525 DOI: 10.1016/j.ymeth.2017.05.022] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2017] [Revised: 04/04/2017] [Accepted: 05/24/2017] [Indexed: 11/19/2022] Open
Abstract
In this article, we summarize current findings for the emergence of biophysical properties such as nuclear stiffness, chromatin compaction, chromosome positioning, and chromosome intermingling during stem cell differentiation, which eventually correlated with the changes of gene expression profiles during cellular differentiation. An overview is first provided to link stem cell differentiation with alterations in nuclear architecture, chromatin compaction, along with nuclear and chromatin dynamics. Further, we highlight the recent biophysical and molecular approaches, imaging methods and computational developments in characterizing transcription-related chromosome organization especially chromosome intermingling and nano-scale chromosomal contacts. Finally, the article ends with an outlook towards the emergence of a functional roadmap in setting up chromosome positioning and intermingling in a cell type specific manner during cellular differentiation.
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Affiliation(s)
- Yejun Wang
- Mechanobiology Institute and Department of Biological Sciences, National University of Singapore, 117411 Singapore, Singapore
| | - Nikhil Jain
- Mechanobiology Institute and Department of Biological Sciences, National University of Singapore, 117411 Singapore, Singapore
| | - Mallika Nagarajan
- Mechanobiology Institute and Department of Biological Sciences, National University of Singapore, 117411 Singapore, Singapore
| | - Shovamayee Maharana
- Mechanobiology Institute and Department of Biological Sciences, National University of Singapore, 117411 Singapore, Singapore
| | - K Venkatesan Iyer
- Mechanobiology Institute and Department of Biological Sciences, National University of Singapore, 117411 Singapore, Singapore
| | - Shefali Talwar
- Mechanobiology Institute and Department of Biological Sciences, National University of Singapore, 117411 Singapore, Singapore
| | - G V Shivashankar
- Mechanobiology Institute and Department of Biological Sciences, National University of Singapore, 117411 Singapore, Singapore; FIRC Institute for Molecular Oncology (IFOM), Milan 20139, Italy.
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154
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Active and poised promoter states drive folding of the extended HoxB locus in mouse embryonic stem cells. Nat Struct Mol Biol 2017; 24:515-524. [DOI: 10.1038/nsmb.3402] [Citation(s) in RCA: 64] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2016] [Accepted: 03/27/2017] [Indexed: 12/30/2022]
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155
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Du M, Zhang Q, Bai L. Three distinct mechanisms of long-distance modulation of gene expression in yeast. PLoS Genet 2017; 13:e1006736. [PMID: 28426659 PMCID: PMC5417705 DOI: 10.1371/journal.pgen.1006736] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2017] [Revised: 05/04/2017] [Accepted: 04/05/2017] [Indexed: 12/04/2022] Open
Abstract
Recent Hi-C measurements have revealed numerous intra- and inter-chromosomal interactions in various eukaryotic cells. To what extent these interactions regulate gene expression is not clear. This question is particularly intriguing in budding yeast because it has extensive long-distance chromosomal interactions but few cases of gene regulation over-a-distance. Here, we developed a medium-throughput assay to screen for functional long-distance interactions that affect the average expression level of a reporter gene as well as its cell-to-cell variability (noise). We ectopically inserted an insulated MET3 promoter (MET3pr) flanked by ~1kb invariable sequences into thousands of genomic loci, allowing it to make contacts with different parts of the genome, and assayed the MET3pr activity in single cells. Changes of MET3pr activity in this case necessarily involve mechanisms that function over a distance. MET3pr has similar activities at most locations. However, at some locations, they deviate from the norm and exhibit three distinct patterns including low expression / high noise, low expression / low noise, and high expression / low noise. We provided evidence that these three patterns of MET3pr expression are caused by Sir2-mediated silencing, transcriptional interference, and 3D clustering. The clustering also occurs in the native genome and enhances the transcription of endogenous Met4-targeted genes. Overall, our results demonstrate that a small fraction of long-distance chromosomal interactions can affect gene expression in yeast. Eukaryotic transcription occurs within the nucleus where DNA is packaged into high order chromosome structures. Some long-distance chromosomal interactions play an important role in gene regulation in higher eukaryotic species, such as mouse and human. In budding yeast, gene expression is traditionally thought to be regulated over short distances because the upstream regulatory sequences (URSs) are usually located close to the core promoters. However, recent chromosome conformation capture experiments have detected numerous long-distance chromosomal interactions in the yeast genome. The function of these interactions in gene regulation remains unclear. Here, we developed a new assay to screen for long-distance interactions that affect the activity of a reporter gene. We found three regulatory mechanisms that act from a distance: silencing, transcriptional interference, and 3D clustering, which alter expression level of the reporter gene as well as its cell-to-cell variability. Our results demonstrate that transcription in budding yeast, similar to transcription in higher eukaryotes, can be regulated over long distances. We anticipate our assay can be used as a general platform to screen for functional long-distance chromosomal interactions that affect gene expression.
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Affiliation(s)
- Manyu Du
- Department of Biochemistry and Molecular Biology, the Pennsylvania State University, University Park, State College, PA, United States of America
- Center for Eukaryotic Gene Regulation, the Pennsylvania State University, University Park, PA, State College, United States of America
| | - Qian Zhang
- Department of Biochemistry and Molecular Biology, the Pennsylvania State University, University Park, State College, PA, United States of America
- Center for Eukaryotic Gene Regulation, the Pennsylvania State University, University Park, PA, State College, United States of America
| | - Lu Bai
- Department of Biochemistry and Molecular Biology, the Pennsylvania State University, University Park, State College, PA, United States of America
- Center for Eukaryotic Gene Regulation, the Pennsylvania State University, University Park, PA, State College, United States of America
- Department of Physics, the Pennsylvania State University, University Park, State College, PA, United States of America
- * E-mail:
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156
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Yang C, Ma R, Axton RA, Jackson M, Taylor AH, Fidanza A, Marenah L, Frayne J, Mountford JC, Forrester LM. Activation of KLF1 Enhances the Differentiation and Maturation of Red Blood Cells from Human Pluripotent Stem Cells. Stem Cells 2017; 35:886-897. [PMID: 28026072 PMCID: PMC5396323 DOI: 10.1002/stem.2562] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2016] [Revised: 11/17/2016] [Accepted: 12/08/2016] [Indexed: 01/23/2023]
Abstract
Blood transfusion is widely used in the clinic but the source of red blood cells (RBCs) is dependent on donors, procedures are susceptible to transfusion-transmitted infections and complications can arise from immunological incompatibility. Clinically-compatible and scalable protocols that allow the production of RBCs from human embryonic stem cells (hESCs) and induced pluripotent stem cells (iPSCs) have been described but progress to translation has been hampered by poor maturation and fragility of the resultant cells. Genetic programming using transcription factors has been used to drive lineage determination and differentiation so we used this approach to assess whether exogenous expression of the Erythroid Krüppel-like factor 1 (EKLF/KLF1) could augment the differentiation and stability of iPSC-derived RBCs. To activate KLF1 at defined time points during later stages of the differentiation process and to avoid transgene silencing that is commonly observed in differentiating pluripotent stem cells, we targeted a tamoxifen-inducible KLF1-ERT2 expression cassette into the AAVS1 locus. Activation of KLF1 at day 10 of the differentiation process when hematopoietic progenitor cells were present, enhanced erythroid commitment and differentiation. Continued culture resulted the appearance of more enucleated cells when KLF1 was activated which is possibly due to their more robust morphology. Globin profiling indicated that these conditions produced embryonic-like erythroid cells. This study demonstrates the successful use of an inducible genetic programing strategy that could be applied to the production of many other cell lineages from human induced pluripotent stem cells with the integration of programming factors into the AAVS1 locus providing a safer and more reproducible route to the clinic. Stem Cells 2017;35:886-897.
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Affiliation(s)
- Cheng‐Tao Yang
- Centre for Regenerative MedicineUniversity of EdinburghEdinburghUnited Kingdom
| | - Rui Ma
- Centre for Regenerative MedicineUniversity of EdinburghEdinburghUnited Kingdom
| | - Richard A. Axton
- Centre for Regenerative MedicineUniversity of EdinburghEdinburghUnited Kingdom
| | - Melany Jackson
- Centre for Regenerative MedicineUniversity of EdinburghEdinburghUnited Kingdom
| | - A. Helen Taylor
- Centre for Regenerative MedicineUniversity of EdinburghEdinburghUnited Kingdom
| | - Antonella Fidanza
- Centre for Regenerative MedicineUniversity of EdinburghEdinburghUnited Kingdom
| | - Lamin Marenah
- Institute of Cardiovascular & Medical Sciences, University of GlasgowGlasgowUnited Kingdom
- Scottish National Blood Transfusion ServiceScotlandUnited Kingdom
| | - Jan Frayne
- Department of BiochemistryUniversity of BristolUnited Kingdom
| | - Joanne C. Mountford
- Institute of Cardiovascular & Medical Sciences, University of GlasgowGlasgowUnited Kingdom
- Scottish National Blood Transfusion ServiceScotlandUnited Kingdom
| | - Lesley M. Forrester
- Centre for Regenerative MedicineUniversity of EdinburghEdinburghUnited Kingdom
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157
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van de Werken HJG, Haan JC, Feodorova Y, Bijos D, Weuts A, Theunis K, Holwerda SJB, Meuleman W, Pagie L, Thanisch K, Kumar P, Leonhardt H, Marynen P, van Steensel B, Voet T, de Laat W, Solovei I, Joffe B. Small chromosomal regions position themselves autonomously according to their chromatin class. Genome Res 2017; 27:922-933. [PMID: 28341771 PMCID: PMC5453326 DOI: 10.1101/gr.213751.116] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2016] [Accepted: 03/22/2017] [Indexed: 11/24/2022]
Abstract
The spatial arrangement of chromatin is linked to the regulation of nuclear processes. One striking aspect of nuclear organization is the spatial segregation of heterochromatic and euchromatic domains. The mechanisms of this chromatin segregation are still poorly understood. In this work, we investigated the link between the primary genomic sequence and chromatin domains. We analyzed the spatial intranuclear arrangement of a human artificial chromosome (HAC) in a xenospecific mouse background in comparison to an orthologous region of native mouse chromosome. The two orthologous regions include segments that can be assigned to three major chromatin classes according to their gene abundance and repeat repertoire: (1) gene-rich and SINE-rich euchromatin; (2) gene-poor and LINE/LTR-rich heterochromatin; and (3) gene-depleted and satellite DNA-containing constitutive heterochromatin. We show, using fluorescence in situ hybridization (FISH) and 4C-seq technologies, that chromatin segments ranging from 0.6 to 3 Mb cluster with segments of the same chromatin class. As a consequence, the chromatin segments acquire corresponding positions in the nucleus irrespective of their chromosomal context, thereby strongly suggesting that this is their autonomous property. Interactions with the nuclear lamina, although largely retained in the HAC, reveal less autonomy. Taken together, our results suggest that building of a functional nucleus is largely a self-organizing process based on mutual recognition of chromosome segments belonging to the major chromatin classes.
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Affiliation(s)
- Harmen J G van de Werken
- Cancer Computational Biology Center, Erasmus MC Cancer Institute & Department of Urology, Erasmus MC Cancer Institute, Erasmus University Medical Center, 3015 CN, Rotterdam, The Netherlands.,Hubrecht Institute-KNAW & University Medical Center Utrecht, 3584 CT Utrecht, The Netherlands
| | - Josien C Haan
- Laboratory of Reproductive Genomics, Department of Human Genetics, KU Leuven, Leuven, 3000, Belgium
| | - Yana Feodorova
- Department of Biology II, Ludwig Maximilians University Munich, 82152 Planegg-Martinsried, Germany
| | - Dominika Bijos
- Division of Gene Regulation, Netherlands Cancer Institute, 1066 CX Amsterdam, The Netherlands
| | - An Weuts
- Laboratory of Reproductive Genomics, Department of Human Genetics, KU Leuven, Leuven, 3000, Belgium
| | - Koen Theunis
- Laboratory of Reproductive Genomics, Department of Human Genetics, KU Leuven, Leuven, 3000, Belgium
| | - Sjoerd J B Holwerda
- Hubrecht Institute-KNAW & University Medical Center Utrecht, 3584 CT Utrecht, The Netherlands
| | - Wouter Meuleman
- Division of Gene Regulation, Netherlands Cancer Institute, 1066 CX Amsterdam, The Netherlands
| | - Ludo Pagie
- Division of Gene Regulation, Netherlands Cancer Institute, 1066 CX Amsterdam, The Netherlands
| | - Katharina Thanisch
- Department of Biology II, Ludwig Maximilians University Munich, 82152 Planegg-Martinsried, Germany
| | - Parveen Kumar
- Laboratory of Reproductive Genomics, Department of Human Genetics, KU Leuven, Leuven, 3000, Belgium
| | - Heinrich Leonhardt
- Department of Biology II, Ludwig Maximilians University Munich, 82152 Planegg-Martinsried, Germany
| | - Peter Marynen
- Human Genome Laboratory, Department of Human Genetics, KU Leuven, Leuven, 3000, Belgium
| | - Bas van Steensel
- Division of Gene Regulation, Netherlands Cancer Institute, 1066 CX Amsterdam, The Netherlands
| | - Thierry Voet
- Laboratory of Reproductive Genomics, Department of Human Genetics, KU Leuven, Leuven, 3000, Belgium
| | - Wouter de Laat
- Hubrecht Institute-KNAW & University Medical Center Utrecht, 3584 CT Utrecht, The Netherlands
| | - Irina Solovei
- Department of Biology II, Ludwig Maximilians University Munich, 82152 Planegg-Martinsried, Germany
| | - Boris Joffe
- Department of Biology II, Ludwig Maximilians University Munich, 82152 Planegg-Martinsried, Germany
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158
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Superresolution imaging of nanoscale chromosome contacts. Sci Rep 2017; 7:42422. [PMID: 28186153 PMCID: PMC5301241 DOI: 10.1038/srep42422] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2016] [Accepted: 01/09/2017] [Indexed: 12/29/2022] Open
Abstract
Co-expression of a specific group of genes requires physical associations among these genes, which form functional chromosomal contacts. While DNA fluorescence in situ hybridization (FISH) pinpoints the localization of genes within the 3D nuclear architecture, direct evidence of physical chromosomal contacts is still lacking. Here, we report a method for the direct visualization of transcription-dependent chromosomal contacts formed in two distinct mechanical states of cells. We prepared open chromatin spreads from isolated nuclei, ensuring 2D rendering of chromosome organization. Superresolution imaging of these chromatin spreads resolved the nanoscale organization of genome contacts. We optimized our imaging method using chromatin spreads from serum+/− cells. We then showed direct visualization of functional gene clusters targeted by YAP (Yes-associated protein) and SRF (Serum response factor) transcription factors. In addition, we showed the association of NF-κB bound gene clusters induced by TNF-α addition. Furthermore, EpiTect ChIP qPCR results showed that these nanoscale clusters were enriched with corresponding transcription factors. Taken together, our method provides a robust platform to directly visualize and study specific genome-wide chromosomal contacts.
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159
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Osborne CS, Mifsud B. Capturing genomic relationships that matter. Chromosome Res 2017; 25:15-24. [PMID: 28078515 PMCID: PMC5346121 DOI: 10.1007/s10577-016-9546-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2016] [Revised: 12/08/2016] [Accepted: 12/19/2016] [Indexed: 12/16/2022]
Abstract
There is a strong interrelationship within the cell nucleus between form and function of the genome. This connection is exhibited across multiple hierarchies, ranging from grand-scale positioning of chromosomes and their intersection with specific nuclear functional activities, the segregation of chromosome structure into distinct domains and long-range regulatory contacts that drive spatial and temporal expression patterns of genes. Fifteen years ago, the development of the chromosome conformation capture method placed the nature of specific, long-range regulatory interactions under scrutiny. However, its development and integration with next-generation sequencing technologies has greatly expanded the breadth and scope of what is detected. The sheer scale of data offered by these important advances has come with new and challenging bottlenecks that are both experimental and bioinformatical. Here, we discuss the recent and prospective development and implementation of new methodologies and analytical tools that are allowing an in-depth, yet focussed characterisation of genomic contacts that are associated with functional activities in the nucleus.
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Affiliation(s)
- Cameron S Osborne
- Department of Medical and Molecular Genetics, King's College London, London, UK.
| | - Borbála Mifsud
- William Harvey Research Institute, Queen Mary University London, London, UK
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160
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Wang J, Zhou Y, Li X, Meng X, Fan M, Chen H, Xue J, Chen M. Genome-Wide Analysis of the Distinct Types of Chromatin Interactions in Arabidopsis thaliana. PLANT & CELL PHYSIOLOGY 2017; 58:57-70. [PMID: 28064247 DOI: 10.1093/pcp/pcw194] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/22/2015] [Accepted: 06/15/2016] [Indexed: 06/06/2023]
Abstract
The three-dimensional shapes of chromosomes regulate gene expression and genome function. Our knowledge of the role of chromatin interaction is evolving rapidly. Here, we present a study of global chromatin interaction patterns in Arabidopsis thaliana. High-throughput experimental techniques have been developed to map long-range interactions within chromatin. We have integrated data from multiple experimental sources including Hi-C, BS-seq, ChIP-chip and ChIP-seq data for 17 epigenetic marks and 35 transcription factors. We identified seven groups of interacting loci, which can be distinguished by their epigenetic profiles. Furthermore, the seven groups of interacting loci can be divided into three types of chromatin linkages based on expression status. We observed that two interacting loci sometimes share common epigenetic and transcription factor-binding profiles. Different groups of loci display very different relationships between epigenetic marks and the binding of transcription factors. Distinctive types of chromatin linkages exhibit different gene expression profiles. Our study unveils an entirely unexplored regulatory interaction, linking epigenetic profiles, transcription factor binding and the three-dimensional spatial organization of the Arabidopsis nuclear genome.
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Affiliation(s)
- Jingjing Wang
- Department of Bioinformatics, The State Key Laboratory of Plant Physiology and Biochemistry, Institute of Plant Science, PR China
- James D. Watson Institute of Genome Sciences, Zhejiang University, Hangzhou, PR China
- College of Life Sciences, Zhejiang University, Hangzhou, PR China
| | - Yincong Zhou
- Department of Bioinformatics, The State Key Laboratory of Plant Physiology and Biochemistry, Institute of Plant Science, PR China
- College of Life Sciences, Zhejiang University, Hangzhou, PR China
| | - Xue Li
- Department of Bioinformatics, The State Key Laboratory of Plant Physiology and Biochemistry, Institute of Plant Science, PR China
- James D. Watson Institute of Genome Sciences, Zhejiang University, Hangzhou, PR China
- College of Life Sciences, Zhejiang University, Hangzhou, PR China
| | - Xianwen Meng
- Department of Bioinformatics, The State Key Laboratory of Plant Physiology and Biochemistry, Institute of Plant Science, PR China
- College of Life Sciences, Zhejiang University, Hangzhou, PR China
| | - Miao Fan
- Department of Bioinformatics, The State Key Laboratory of Plant Physiology and Biochemistry, Institute of Plant Science, PR China
- Institute of Crop Science, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, PR China
- College of Life Sciences, Zhejiang University, Hangzhou, PR China
| | - Hongjun Chen
- Department of Bioinformatics, The State Key Laboratory of Plant Physiology and Biochemistry, Institute of Plant Science, PR China
- College of Life Sciences, Zhejiang University, Hangzhou, PR China
| | - Jitong Xue
- Department of Bioinformatics, The State Key Laboratory of Plant Physiology and Biochemistry, Institute of Plant Science, PR China
- James D. Watson Institute of Genome Sciences, Zhejiang University, Hangzhou, PR China
- College of Life Sciences, Zhejiang University, Hangzhou, PR China
| | - Ming Chen
- Department of Bioinformatics, The State Key Laboratory of Plant Physiology and Biochemistry, Institute of Plant Science, PR China
- James D. Watson Institute of Genome Sciences, Zhejiang University, Hangzhou, PR China
- College of Life Sciences, Zhejiang University, Hangzhou, PR China
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161
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TAKOUDA J, KATADA S, NAKASHIMA K. Emerging mechanisms underlying astrogenesis in the developing mammalian brain. PROCEEDINGS OF THE JAPAN ACADEMY. SERIES B, PHYSICAL AND BIOLOGICAL SCIENCES 2017; 93:386-398. [PMID: 28603210 PMCID: PMC5709539 DOI: 10.2183/pjab.93.024] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/05/2017] [Accepted: 03/31/2017] [Indexed: 06/06/2023]
Abstract
In the developing brain, the three major cell types, i.e., neurons, astrocytes and oligodendrocytes, are generated from common multipotent neural stem cells (NSCs). In particular, astrocytes eventually occupy a great fraction of the brain and play pivotal roles in the brain development and functions. However, NSCs cannot produce the three major cell types simultaneously from the beginning; e.g., it is known that neurogenesis precedes astrogenesis during brain development. How is this fate switching achieved? Many studies have revealed that extracellular cues and intracellular programs are involved in the transition of NSC fate specification. The former include growth factor- and cytokine-signaling, and the latter involve epigenetic machinery, including DNA methylation, histone modifications, and non-coding RNAs. Accumulating evidence has identified a complex array of epigenetic modifications that control the timing of astrocytic differentiation of NSCs. In this review, we introduce recent progress in identifying the molecular mechanisms of astrogenesis underlying the tight regulation of neuronal-astrocytic fate switching of NSCs.
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Affiliation(s)
- Jun TAKOUDA
- Division of Basic Stem Cell Biology, Department of Stem Cell Biology and Medicine, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Sayako KATADA
- Division of Basic Stem Cell Biology, Department of Stem Cell Biology and Medicine, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Kinichi NAKASHIMA
- Division of Basic Stem Cell Biology, Department of Stem Cell Biology and Medicine, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
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162
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Yang YP, Magnuson MA, Stein R, Wright CVE. The mammal-specific Pdx1 Area II enhancer has multiple essential functions in early endocrine cell specification and postnatal β-cell maturation. Development 2016; 144:248-257. [PMID: 27993987 DOI: 10.1242/dev.143123] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2016] [Accepted: 12/07/2016] [Indexed: 01/19/2023]
Abstract
The transcription factor Pdx1 is required for multiple aspects of pancreatic organogenesis. It remains unclear to what extent Pdx1 expression and function depend upon trans-activation through 5' conserved cis-regulatory regions and, in particular, whether the mammal-specific Area II (-2139 to -1958 bp) affects minor or major aspects of organogenesis. We show that Area II is a primary effector of endocrine-selective transcription in epithelial multipotent cells, nascent endocrine progenitors, and differentiating and mature β cells in vivo Pdx1ΔAREAII/- mice exhibit a massive reduction in endocrine progenitor cells and progeny hormone-producing cells, indicating that Area II activity is fundamental to mounting an effective endocrine lineage-specification program within the multipotent cell population. Creating an Area II-deleted state within already specified Neurog3-expressing endocrine progenitor cells increased the proportion of glucagon+ α relative to insulin+ β cells, associated with the transcriptional and epigenetic derepression of the α-cell-determining Arx gene in endocrine progenitors. There were also glucagon and insulin co-expressing cells, and β cells that were incapable of maturation. Creating the Pdx1ΔAREAII state after cells entered an insulin-expressing stage led to immature and dysfunctional islet β cells carrying abnormal chromatin marking in vital β-cell-associated genes. Therefore, trans-regulatory integration through Area II mediates a surprisingly extensive range of progenitor and β-cell-specific Pdx1 functions.
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Affiliation(s)
- Yu-Ping Yang
- Vanderbilt University Program in Developmental Biology and Department of Cell and Developmental Biology, Vanderbilt University, Nashville, TN 37232 USA.,Vanderbilt Center for Stem Cell Biology, Vanderbilt University, Nashville, TN 37232, USA
| | - Mark A Magnuson
- Vanderbilt University Program in Developmental Biology and Department of Cell and Developmental Biology, Vanderbilt University, Nashville, TN 37232 USA.,Vanderbilt Center for Stem Cell Biology, Vanderbilt University, Nashville, TN 37232, USA.,Department of Molecular Physiology and Biophysics, Vanderbilt University, Nashville, TN 37232, USA
| | - Roland Stein
- Vanderbilt University Program in Developmental Biology and Department of Cell and Developmental Biology, Vanderbilt University, Nashville, TN 37232 USA.,Department of Molecular Physiology and Biophysics, Vanderbilt University, Nashville, TN 37232, USA
| | - Christopher V E Wright
- Vanderbilt University Program in Developmental Biology and Department of Cell and Developmental Biology, Vanderbilt University, Nashville, TN 37232 USA .,Vanderbilt Center for Stem Cell Biology, Vanderbilt University, Nashville, TN 37232, USA
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163
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Duffy MF, Tang J, Sumardy F, Nguyen HHT, Selvarajah SA, Josling GA, Day KP, Petter M, Brown GV. Activation and clustering of a Plasmodium falciparum var gene are affected by subtelomeric sequences. FEBS J 2016; 284:237-257. [PMID: 27860263 DOI: 10.1111/febs.13967] [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] [Received: 06/07/2016] [Revised: 10/12/2016] [Accepted: 11/15/2016] [Indexed: 11/30/2022]
Abstract
The Plasmodium falciparum var multigene family encodes the cytoadhesive, variant antigen PfEMP1. P. falciparum antigenic variation and cytoadhesion specificity are controlled by epigenetic switching between the single, or few, simultaneously expressed var genes. Most var genes are maintained in perinuclear clusters of heterochromatic telomeres. The active var gene(s) occupy a single, perinuclear var expression site. It is unresolved whether the var expression site forms in situ at a telomeric cluster or whether it is an extant compartment to which single chromosomes travel, thus controlling var switching. Here we show that transcription of a var gene did not require decreased colocalisation with clusters of telomeres, supporting var expression site formation in situ. However following recombination within adjacent subtelomeric sequences, the same var gene was persistently activated and did colocalise less with telomeric clusters. Thus, participation in stable, heterochromatic, telomere clusters and var switching are independent but are both affected by subtelomeric sequences. The var expression site colocalised with the euchromatic mark H3K27ac to a greater extent than it did with heterochromatic H3K9me3. H3K27ac was enriched within the active var gene promoter even when the var gene was transiently repressed in mature parasites and thus H3K27ac may contribute to var gene epigenetic memory.
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Affiliation(s)
- Michael F Duffy
- Department of Medicine, Royal Melbourne Hospital, The University of Melbourne at The Peter Doherty Institute for Infection and Immunity, Victoria, Australia.,The School of BioSciences, Bio21, The University of Melbourne, Victoria, Australia
| | - Jingyi Tang
- Department of Medicine, Royal Melbourne Hospital, The University of Melbourne at The Peter Doherty Institute for Infection and Immunity, Victoria, Australia.,The School of BioSciences, Bio21, The University of Melbourne, Victoria, Australia
| | - Fransisca Sumardy
- Department of Medicine, Royal Melbourne Hospital, The University of Melbourne at The Peter Doherty Institute for Infection and Immunity, Victoria, Australia.,The Florey Institute of Neuroscience and Mental Health, Parkville, Victoria, Australia
| | - Hanh H T Nguyen
- Department of Medicine, Royal Melbourne Hospital, The University of Melbourne at The Peter Doherty Institute for Infection and Immunity, Victoria, Australia.,The School of BioSciences, Bio21, The University of Melbourne, Victoria, Australia
| | - Shamista A Selvarajah
- Department of Medicine, Royal Melbourne Hospital, The University of Melbourne at The Peter Doherty Institute for Infection and Immunity, Victoria, Australia.,The School of BioSciences, Bio21, The University of Melbourne, Victoria, Australia
| | - Gabrielle A Josling
- Department of Medicine, Royal Melbourne Hospital, The University of Melbourne at The Peter Doherty Institute for Infection and Immunity, Victoria, Australia.,Department of Biochemistry and Molecular Biology, The Pennsylvania State University, State College, PA, USA
| | - Karen P Day
- The School of BioSciences, Bio21, The University of Melbourne, Victoria, Australia
| | - Michaela Petter
- Department of Medicine, Royal Melbourne Hospital, The University of Melbourne at The Peter Doherty Institute for Infection and Immunity, Victoria, Australia.,The School of BioSciences, Bio21, The University of Melbourne, Victoria, Australia
| | - Graham V Brown
- The Nossal Institute for Global Health, The University of Melbourne, Victoria, Australia
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164
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Abstract
Chromosomes of eukaryotes adopt highly dynamic and complex hierarchical structures in the nucleus. The three-dimensional (3D) organization of chromosomes profoundly affects DNA replication, transcription and the repair of DNA damage. Thus, a thorough understanding of nuclear architecture is fundamental to the study of nuclear processes in eukaryotic cells. Recent years have seen rapid proliferation of technologies to investigate genome organization and function. Here, we review experimental and computational methodologies for 3D genome analysis, with special focus on recent advances in high-throughput chromatin conformation capture (3C) techniques and data analysis.
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Affiliation(s)
- Anthony D Schmitt
- Ludwig Institute for Cancer Research and the University of California, San Diego (UCSD) Biomedical Sciences Graduate Program, 9500 Gilman Drive, La Jolla, California 92093, USA
| | - Ming Hu
- Department of Population Health, Division of Biostatistics, New York University School of Medicine, 650 First Avenue, Room 540, New York, New York 10016, USA
- Present address: Department of Quantitative Health Sciences, Lerner Research Institute, Cleveland Clinic Foundation, 9500 Euclid Avenue, Cleveland, Ohio 44195, USA
| | - Bing Ren
- Ludwig Institute for Cancer Research, Department of Cellular and Molecular Medicine, Moores Cancer Center and Institute of Genomic Medicine, University of California, San Diego (UCSD) School of Medicine, 9500 Gilman Drive, La Jolla, California 92093, USA
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165
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Martin P, McGovern A, Massey J, Schoenfelder S, Duffus K, Yarwood A, Barton A, Worthington J, Fraser P, Eyre S, Orozco G. Identifying Causal Genes at the Multiple Sclerosis Associated Region 6q23 Using Capture Hi-C. PLoS One 2016; 11:e0166923. [PMID: 27861577 PMCID: PMC5115837 DOI: 10.1371/journal.pone.0166923] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2016] [Accepted: 11/06/2016] [Indexed: 12/21/2022] Open
Abstract
Background The chromosomal region 6q23 has been found to be associated with multiple sclerosis (MS) predisposition through genome wide association studies (GWAS). There are four independent single nucleotide polymorphisms (SNPs) associated with MS in this region, which spans around 2.5 Mb. Most GWAS variants associated with complex traits, including these four MS associated SNPs, are non-coding and their function is currently unknown. However, GWAS variants have been found to be enriched in enhancers and there is evidence that they may be involved in transcriptional regulation of their distant target genes through long range chromatin looping. Aim The aim of this work is to identify causal disease genes in the 6q23 locus by studying long range chromatin interactions, using the recently developed Capture Hi-C method in human T and B-cell lines. Interactions involving four independent associations unique to MS, tagged by rs11154801, rs17066096, rs7769192 and rs67297943 were analysed using Capture Hi-C Analysis of Genomic Organisation (CHiCAGO). Results We found that the pattern of chromatin looping interactions in the MS 6q23 associated region is complex. Interactions cluster in two regions, the first involving the rs11154801 region and a second containing the rs17066096, rs7769192 and rs67297943 SNPs. Firstly, SNPs located within the AHI1 gene, tagged by rs11154801, are correlated with expression of AHI1 and interact with its promoter. These SNPs also interact with other potential candidate genes such as SGK1 and BCLAF1. Secondly, the rs17066096, rs7769192 and rs67297943 SNPs interact with each other and with immune-related genes such as IL20RA, IL22RA2, IFNGR1 and TNFAIP3. Finally, the above-mentioned regions interact with each other and therefore, may co-regulate these target genes. Conclusion These results suggest that the four 6q23 variants, independently associated with MS, are involved in the regulation of several genes, including immune genes. These findings could help understand mechanisms of disease and suggest potential novel therapeutic targets.
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Affiliation(s)
- Paul Martin
- Arthritis Research UK Centre for Genetics and Genomics, Centre for Musculoskeletal Research, Division of Musculoskeletal and Dermatological Siences, Faculty of Biology, Medicine and Health, Manchester Academic Health Science Centre, The University of Manchester, Stopford Building, Oxford Road, Manchester, M13 9PT, United Kingdom
| | - Amanda McGovern
- Arthritis Research UK Centre for Genetics and Genomics, Centre for Musculoskeletal Research, Division of Musculoskeletal and Dermatological Siences, Faculty of Biology, Medicine and Health, Manchester Academic Health Science Centre, The University of Manchester, Stopford Building, Oxford Road, Manchester, M13 9PT, United Kingdom
| | - Jonathan Massey
- Arthritis Research UK Centre for Genetics and Genomics, Centre for Musculoskeletal Research, Division of Musculoskeletal and Dermatological Siences, Faculty of Biology, Medicine and Health, Manchester Academic Health Science Centre, The University of Manchester, Stopford Building, Oxford Road, Manchester, M13 9PT, United Kingdom
| | - Stefan Schoenfelder
- Nuclear Dynamics Programme, The Babraham Institute, Cambridge CB22 3AT, United Kingdom
| | - Kate Duffus
- Arthritis Research UK Centre for Genetics and Genomics, Centre for Musculoskeletal Research, Division of Musculoskeletal and Dermatological Siences, Faculty of Biology, Medicine and Health, Manchester Academic Health Science Centre, The University of Manchester, Stopford Building, Oxford Road, Manchester, M13 9PT, United Kingdom
| | - Annie Yarwood
- Arthritis Research UK Centre for Genetics and Genomics, Centre for Musculoskeletal Research, Division of Musculoskeletal and Dermatological Siences, Faculty of Biology, Medicine and Health, Manchester Academic Health Science Centre, The University of Manchester, Stopford Building, Oxford Road, Manchester, M13 9PT, United Kingdom
| | - Anne Barton
- Arthritis Research UK Centre for Genetics and Genomics, Centre for Musculoskeletal Research, Division of Musculoskeletal and Dermatological Siences, Faculty of Biology, Medicine and Health, Manchester Academic Health Science Centre, The University of Manchester, Stopford Building, Oxford Road, Manchester, M13 9PT, United Kingdom
- NIHR Manchester Musculoskeletal BRU, Manchester Academic Health Sciences Centre, Central Manchester Foundation Trust, Manchester, United Kingdom
| | - Jane Worthington
- Arthritis Research UK Centre for Genetics and Genomics, Centre for Musculoskeletal Research, Division of Musculoskeletal and Dermatological Siences, Faculty of Biology, Medicine and Health, Manchester Academic Health Science Centre, The University of Manchester, Stopford Building, Oxford Road, Manchester, M13 9PT, United Kingdom
- NIHR Manchester Musculoskeletal BRU, Manchester Academic Health Sciences Centre, Central Manchester Foundation Trust, Manchester, United Kingdom
| | - Peter Fraser
- Nuclear Dynamics Programme, The Babraham Institute, Cambridge CB22 3AT, United Kingdom
| | - Stephen Eyre
- Arthritis Research UK Centre for Genetics and Genomics, Centre for Musculoskeletal Research, Division of Musculoskeletal and Dermatological Siences, Faculty of Biology, Medicine and Health, Manchester Academic Health Science Centre, The University of Manchester, Stopford Building, Oxford Road, Manchester, M13 9PT, United Kingdom
| | - Gisela Orozco
- Arthritis Research UK Centre for Genetics and Genomics, Centre for Musculoskeletal Research, Division of Musculoskeletal and Dermatological Siences, Faculty of Biology, Medicine and Health, Manchester Academic Health Science Centre, The University of Manchester, Stopford Building, Oxford Road, Manchester, M13 9PT, United Kingdom
- * E-mail:
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166
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Tordini F, Aldinucci M, Milanesi L, Liò P, Merelli I. The Genome Conformation As an Integrator of Multi-Omic Data: The Example of Damage Spreading in Cancer. Front Genet 2016; 7:194. [PMID: 27895661 PMCID: PMC5108817 DOI: 10.3389/fgene.2016.00194] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2016] [Accepted: 10/24/2016] [Indexed: 12/17/2022] Open
Abstract
Publicly available multi-omic databases, in particular if associated with medical annotations, are rich resources with the potential to lead a rapid transition from high-throughput molecular biology experiments to better clinical outcomes for patients. In this work, we propose a model for multi-omic data integration (i.e., genetic variations, gene expression, genome conformation, and epigenetic patterns), which exploits a multi-layer network approach to analyse, visualize, and obtain insights from such biological information, in order to use achieved results at a macroscopic level. Using this representation, we can describe how driver and passenger mutations accumulate during the development of diseases providing, for example, a tool able to characterize the evolution of cancer. Indeed, our test case concerns the MCF-7 breast cancer cell line, before and after the stimulation with estrogen, since many datasets are available for this case study. In particular, the integration of data about cancer mutations, gene functional annotations, genome conformation, epigenetic patterns, gene expression, and metabolic pathways in our multi-layer representation will allow a better interpretation of the mechanisms behind a complex disease such as cancer. Thanks to this multi-layer approach, we focus on the interplay of chromatin conformation and cancer mutations in different pathways, such as metabolic processes, that are very important for tumor development. Working on this model, a variance analysis can be implemented to identify normal variations within each omics and to characterize, by contrast, variations that can be accounted to pathological samples compared to normal ones. This integrative model can be used to identify novel biomarkers and to provide innovative omic-based guidelines for treating many diseases, improving the efficacy of decision trees currently used in clinic.
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Affiliation(s)
- Fabio Tordini
- Computer Science Department, University of Torino Torino, Italy
| | - Marco Aldinucci
- Computer Science Department, University of Torino Torino, Italy
| | - Luciano Milanesi
- Institute of Biomedical Technologies, Italian National Research Council Milan, Italy
| | - Pietro Liò
- Computer Laboratory, University of Cambridge Cambridge, UK
| | - Ivan Merelli
- Institute of Biomedical Technologies, Italian National Research Council Milan, Italy
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167
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Mahdieh N, Rabbani B. Beta thalassemia in 31,734 cases with HBB gene mutations: Pathogenic and structural analysis of the common mutations; Iran as the crossroads of the Middle East. Blood Rev 2016; 30:493-508. [DOI: 10.1016/j.blre.2016.07.001] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2015] [Revised: 06/13/2016] [Accepted: 07/08/2016] [Indexed: 12/16/2022]
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168
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169
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Lahbib-Mansais Y, Barasc H, Marti-Marimon M, Mompart F, Iannuccelli E, Robelin D, Riquet J, Yerle-Bouissou M. Expressed alleles of imprinted IGF2, DLK1 and MEG3 colocalize in 3D-preserved nuclei of porcine fetal cells. BMC Cell Biol 2016; 17:35. [PMID: 27716032 PMCID: PMC5045652 DOI: 10.1186/s12860-016-0113-9] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2016] [Accepted: 09/20/2016] [Indexed: 11/23/2022] Open
Abstract
Background To explore the relationship between spatial genome organization and gene expression in the interphase nucleus, we used a genomic imprinting model, which offers parental-specific gene expression. Using 3D FISH in porcine fetal liver cells, we compared the nuclear organization of the two parental alleles (expressed or not) of insulin-like growth factor 2 (IGF2), a paternally imprinted gene located on chromosome 2. We investigated whether its nuclear positioning favors specific locus associations. We also tested whether IGF2 is implicated in long-range chromatin trans-associations as previously shown in the mouse model species for its reciprocal imprinted gene H19. Results We focused on the 3D position of IGF2 alleles, with respect to their individual chromosome 2 territories. The paternally expressed allele was tagged with nascent RNA. There were no significant differences in the position of the two alleles (p = 0.06). To determine long-range chromatin trans-interactions, we chose 12 genes, some of which are known to be imprinted in mammalian model species and belong to a network of imprinted genes (i.e. SLC38A4, DLK1, MEG3, and ZAC1). We screened them and ABCG2, OSBP2, OSBPL1, RPL32, NF1, ZAR1, SEP15, GPC3 for associations with IGF2 in liver cells. All imprinted genes tested showed an association with IGF2. The DLK1/MEG3 locus showed the highest rate of colocalization. This gene association was confirmed by 3D FISH (in 20 % of the nuclei analyzed), revealing also the close proximity of chromosomes 2 and 7 (in 60 % of nuclei). Furthermore, our observations showed that the expressed paternal IGF2 allele is involved in this association. This IGF2-(DLK1/MEG3) association also occurred in a high percentage of fetal muscle cells (36 % of nuclei). Finally, we showed that nascent IGF2, DLK1 and MEG3 RNAs can associate in pairs or in a three-way combination. Conclusion Our results show that trans-associations occur between three imprinted genes IGF2, DLK1 and MEG3 both in fetal liver and muscle cells. All three expressed alleles associated in muscle cells. Our findings suggest that the 3D nuclear organization is linked to the transcriptional state of these genes. Electronic supplementary material The online version of this article (doi:10.1186/s12860-016-0113-9) contains supplementary material, which is available to authorized users.
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Affiliation(s)
| | - Harmonie Barasc
- GenPhySE, Université de Toulouse, INRA, INPT, ENVT, Castanet Tolosan, France
| | - Maria Marti-Marimon
- GenPhySE, Université de Toulouse, INRA, INPT, ENVT, Castanet Tolosan, France
| | - Florence Mompart
- GenPhySE, Université de Toulouse, INRA, INPT, ENVT, Castanet Tolosan, France
| | - Eddie Iannuccelli
- GenPhySE, Université de Toulouse, INRA, INPT, ENVT, Castanet Tolosan, France
| | - David Robelin
- GenPhySE, Université de Toulouse, INRA, INPT, ENVT, Castanet Tolosan, France
| | - Juliette Riquet
- GenPhySE, Université de Toulouse, INRA, INPT, ENVT, Castanet Tolosan, France
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170
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Buxa MK, Slotman JA, van Royen ME, Paul MW, Houtsmuller AB, Renkawitz R. Insulator speckles associated with long-distance chromatin contacts. Biol Open 2016; 5:1266-74. [PMID: 27464669 PMCID: PMC5051650 DOI: 10.1242/bio.019455] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Nuclear foci of chromatin binding factors are, in many cases, discussed as sites of long-range chromatin interaction in the three-dimensional nuclear space. Insulator binding proteins have been shown to aggregate into insulator bodies, which are large structures not involved in insulation; however, the more diffusely distributed insulator speckles have not been analysed in this respect. Furthermore, insulator binding proteins have been shown to drive binding sites for Polycomb group proteins into Polycomb bodies. Here we find that insulator speckles, marked by the insulator binding protein dCTCF, and Polycomb bodies show differential association with the insulator protein CP190. They differ in number and three-dimensional location with only 26% of the Polycomb bodies overlapping with CP190. By using fluorescence in situ hybridization (FISH) probes to identify long-range interaction (kissing) of the Hox gene clusters Antennapedia complex (ANT-C) and Bithorax complex (BX-C), we found the frequency of interaction to be very low. However, these rare kissing events were associated with insulator speckles at a significantly shorter distance and an increased speckle number. This suggests that insulator speckles are associated with long-distance interaction.
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Affiliation(s)
- Melanie K Buxa
- Institute for Genetics, Justus-Liebig-University, Heinrich-Buff-Ring 58, Giessen D35392, Germany
| | - Johan A Slotman
- Department of Pathology, Josephine Nefkens Institute, Erasmus Optical Imaging Centre, Erasmus MC, Postbus 2040, Rotterdam 3000 CA, The Netherlands
| | - Martin E van Royen
- Department of Pathology, Josephine Nefkens Institute, Erasmus Optical Imaging Centre, Erasmus MC, Postbus 2040, Rotterdam 3000 CA, The Netherlands
| | - Maarten W Paul
- Department of Pathology, Josephine Nefkens Institute, Erasmus Optical Imaging Centre, Erasmus MC, Postbus 2040, Rotterdam 3000 CA, The Netherlands
| | - Adriaan B Houtsmuller
- Department of Pathology, Josephine Nefkens Institute, Erasmus Optical Imaging Centre, Erasmus MC, Postbus 2040, Rotterdam 3000 CA, The Netherlands
| | - Rainer Renkawitz
- Institute for Genetics, Justus-Liebig-University, Heinrich-Buff-Ring 58, Giessen D35392, Germany
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171
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Letsou W, Cai L. Noncommutative Biology: Sequential Regulation of Complex Networks. PLoS Comput Biol 2016; 12:e1005089. [PMID: 27560383 PMCID: PMC4999240 DOI: 10.1371/journal.pcbi.1005089] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2016] [Accepted: 07/28/2016] [Indexed: 12/21/2022] Open
Abstract
Single-cell variability in gene expression is important for generating distinct cell types, but it is unclear how cells use the same set of regulatory molecules to specifically control similarly regulated genes. While combinatorial binding of transcription factors at promoters has been proposed as a solution for cell-type specific gene expression, we found that such models resulted in substantial information bottlenecks. We sought to understand the consequences of adopting sequential logic wherein the time-ordering of factors informs the final outcome. We showed that with noncommutative control, it is possible to independently control targets that would otherwise be activated simultaneously using combinatorial logic. Consequently, sequential logic overcomes the information bottleneck inherent in complex networks. We derived scaling laws for two noncommutative models of regulation, motivated by phosphorylation/neural networks and chromosome folding, respectively, and showed that they scale super-exponentially in the number of regulators. We also showed that specificity in control is robust to the loss of a regulator. Lastly, we connected these theoretical results to real biological networks that demonstrate specificity in the context of promiscuity. These results show that achieving a desired outcome often necessitates roundabout steps. DNA is the blueprint of life. Yet the order in which a cell follows these instructions makes it capable of generating thousands of different fates. How this information is extracted from underlying gene regulatory networks is unclear, especially given that biological networks are highly interconnected, and that the number of signaling pathways is relatively small (approximately 5–10). The conventional approach for increasing the information capacity of a limited set of regulators is to use them in combination. Surprisingly, combinatorial logic does not increase the diversity of target configurations or cell fates, but instead causes information bottlenecks. A different approach, called sequential logic, uses noncommutative sequences of a small set of regulators to drive networks to a large number of novel configurations. If certain targets are first protected, then even promiscuous regulators can activate specific subsets of lineage-specific targets. In this paper we show how sequential logic outperforms combinatorial logic, and argue that noncommutative sequences underlie a number of cases of biological regulation, e.g. how a small number of signaling pathways generates a large diversity of cell types in development. In addition to explaining biological networks, sequential logic may be a general experimental design strategy in synthetic and single-cell biology.
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Affiliation(s)
- William Letsou
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California, United States of America
| | - Long Cai
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California, United States of America
- * E-mail:
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172
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Gillespie ZE, Pickering J, Eskiw CH. Better Living through Chemistry: Caloric Restriction (CR) and CR Mimetics Alter Genome Function to Promote Increased Health and Lifespan. Front Genet 2016; 7:142. [PMID: 27588026 PMCID: PMC4988992 DOI: 10.3389/fgene.2016.00142] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2016] [Accepted: 07/21/2016] [Indexed: 12/19/2022] Open
Abstract
Caloric restriction (CR), defined as decreased nutrient intake without causing malnutrition, has been documented to increase both health and lifespan across numerous organisms, including humans. Many drugs and other compounds naturally occurring in our diet (nutraceuticals) have been postulated to act as mimetics of caloric restriction, leading to a wave of research investigating the efficacy of these compounds in preventing age-related diseases and promoting healthier, longer lifespans. Although well studied at the biochemical level, there are still many unanswered questions about how CR and CR mimetics impact genome function and structure. Here we discuss how genome function and structure are influenced by CR and potential CR mimetics, including changes in gene expression profiles and epigenetic modifications and their potential to identify the genetic fountain of youth.
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Affiliation(s)
- Zoe E Gillespie
- Department of Food and Bioproduct Sciences, University of Saskatchewan Saskatoon, SK, Canada
| | - Joshua Pickering
- Department of Biochemistry, University of Saskatchewan Saskatoon, SK, Canada
| | - Christopher H Eskiw
- Department of Food and Bioproduct Sciences, University of SaskatchewanSaskatoon, SK, Canada; Department of Biochemistry, University of SaskatchewanSaskatoon, SK, Canada
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173
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Brickner DG, Sood V, Tutucci E, Coukos R, Viets K, Singer RH, Brickner JH. Subnuclear positioning and interchromosomal clustering of the GAL1-10 locus are controlled by separable, interdependent mechanisms. Mol Biol Cell 2016; 27:2980-93. [PMID: 27489341 PMCID: PMC5042583 DOI: 10.1091/mbc.e16-03-0174] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2016] [Accepted: 07/27/2016] [Indexed: 01/10/2023] Open
Abstract
“DNA zip codes” control positioning and interchromosomal clustering of GAL1-10 in yeast. However, these two phenomena have distinct molecular mechanisms, requiring different nuclear pore proteins, and are regulated differently by transcription and the cell cycle. On activation, the GAL genes in yeast are targeted to the nuclear periphery through interaction with the nuclear pore complex. Here we identify two cis-acting “DNA zip codes” from the GAL1-10 promoter that are necessary and sufficient to induce repositioning to the nuclear periphery. One of these zip codes, GRS4, is also necessary and sufficient to promote clustering of GAL1-10 alleles. GRS4, and to a lesser extent GRS5, contribute to stronger expression of GAL1 and GAL10 by increasing the fraction of cells that respond to the inducer. The molecular mechanism controlling targeting to the NPC is distinct from the molecular mechanism controlling interchromosomal clustering. Targeting to the nuclear periphery and interaction with the nuclear pore complex are prerequisites for gene clustering. However, once formed, clustering can be maintained in the nucleoplasm, requires distinct nuclear pore proteins, and is regulated differently through the cell cycle. In addition, whereas targeting of genes to the NPC is independent of transcription, interchromosomal clustering requires transcription. These results argue that zip code–dependent gene positioning at the nuclear periphery and interchromosomal clustering represent interdependent phenomena with distinct molecular mechanisms.
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Affiliation(s)
| | - Varun Sood
- Department of Molecular Biosciences, Northwestern University, Evanston, IL 60208
| | - Evelina Tutucci
- Department of Anatomy and Structural Biology, Albert Einstein College of Medicine, Bronx, NY 10461
| | - Robert Coukos
- Department of Molecular Biosciences, Northwestern University, Evanston, IL 60208
| | - Kayla Viets
- Department of Molecular Biosciences, Northwestern University, Evanston, IL 60208
| | - Robert H Singer
- Department of Anatomy and Structural Biology, Albert Einstein College of Medicine, Bronx, NY 10461 Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA 20147
| | - Jason H Brickner
- Department of Molecular Biosciences, Northwestern University, Evanston, IL 60208
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174
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Tomita S, Abdalla MOA, Fujiwara S, Yamamoto T, Iwase H, Nakao M, Saitoh N. Roles of long noncoding RNAs in chromosome domains. WILEY INTERDISCIPLINARY REVIEWS-RNA 2016; 8. [DOI: 10.1002/wrna.1384] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/30/2016] [Revised: 06/30/2016] [Accepted: 07/07/2016] [Indexed: 12/26/2022]
Affiliation(s)
- Saori Tomita
- Department of Medical Cell Biology, Institute of Molecular Embryology and Genetics; Kumamoto University; Kumamoto Japan
- Department of Breast and Endocrine Surgery, Graduate School of Medical Sciences; Kumamoto University; Kumamoto Japan
| | - Mohamed Osama Ali Abdalla
- Department of Medical Cell Biology, Institute of Molecular Embryology and Genetics; Kumamoto University; Kumamoto Japan
- Department of Clinical Pathology, Faculty of Medicine; Suez Canal University; Ismailia Egypt
| | - Saori Fujiwara
- Department of Medical Cell Biology, Institute of Molecular Embryology and Genetics; Kumamoto University; Kumamoto Japan
- Department of Breast and Endocrine Surgery, Graduate School of Medical Sciences; Kumamoto University; Kumamoto Japan
| | - Tatsuro Yamamoto
- Department of Medical Cell Biology, Institute of Molecular Embryology and Genetics; Kumamoto University; Kumamoto Japan
| | - Hirotaka Iwase
- Department of Breast and Endocrine Surgery, Graduate School of Medical Sciences; Kumamoto University; Kumamoto Japan
| | - Mitsuyoshi Nakao
- Department of Medical Cell Biology, Institute of Molecular Embryology and Genetics; Kumamoto University; Kumamoto Japan
- Core Research for Evolutional Science and Technology (CREST), Japan Agency for Medical Research and Development; Tokyo Japan
| | - Noriko Saitoh
- Department of Medical Cell Biology, Institute of Molecular Embryology and Genetics; Kumamoto University; Kumamoto Japan
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175
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Pueschel R, Coraggio F, Meister P. From single genes to entire genomes: the search for a function of nuclear organization. Development 2016; 143:910-23. [PMID: 26980791 DOI: 10.1242/dev.129007] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
The existence of different domains within the nucleus has been clear from the time, in the late 1920s, that heterochromatin and euchromatin were discovered. The observation that heterochromatin is less transcribed than euchromatin suggested that microscopically identifiable structures might correspond to functionally different domains of the nucleus. Until 15 years ago, studies linking gene expression and subnuclear localization were limited to a few genes. As we discuss in this Review, new genome-wide techniques have now radically changed the way nuclear organization is analyzed. These have provided a much more detailed view of functional nuclear architecture, leading to the emergence of a number of new paradigms of chromatin folding and how this folding evolves during development.
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Affiliation(s)
- Ringo Pueschel
- Cell Fate and Nuclear Organization, Institute of Cell Biology, University of Bern, 3012 Bern, Switzerland Graduate School for Cellular and Biomedical Sciences, University of Bern, Switzerland
| | - Francesca Coraggio
- Cell Fate and Nuclear Organization, Institute of Cell Biology, University of Bern, 3012 Bern, Switzerland Graduate School for Cellular and Biomedical Sciences, University of Bern, Switzerland
| | - Peter Meister
- Cell Fate and Nuclear Organization, Institute of Cell Biology, University of Bern, 3012 Bern, Switzerland
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176
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Meaburn KJ. Spatial Genome Organization and Its Emerging Role as a Potential Diagnosis Tool. Front Genet 2016; 7:134. [PMID: 27507988 PMCID: PMC4961005 DOI: 10.3389/fgene.2016.00134] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2016] [Accepted: 07/13/2016] [Indexed: 12/12/2022] Open
Abstract
In eukaryotic cells the genome is highly spatially organized. Functional relevance of higher order genome organization is implied by the fact that specific genes, and even whole chromosomes, alter spatial position in concert with functional changes within the nucleus, for example with modifications to chromatin or transcription. The exact molecular pathways that regulate spatial genome organization and the full implication to the cell of such an organization remain to be determined. However, there is a growing realization that the spatial organization of the genome can be used as a marker of disease. While global genome organization patterns remain largely conserved in disease, some genes and chromosomes occupy distinct nuclear positions in diseased cells compared to their normal counterparts, with the patterns of reorganization differing between diseases. Importantly, mapping the spatial positioning patterns of specific genomic loci can distinguish cancerous tissue from benign with high accuracy. Genome positioning is an attractive novel biomarker since additional quantitative biomarkers are urgently required in many cancer types. Current diagnostic techniques are often subjective and generally lack the ability to identify aggressive cancer from indolent, which can lead to over- or under-treatment of patients. Proof-of-principle for the use of genome positioning as a diagnostic tool has been provided based on small scale retrospective studies. Future large-scale studies are required to assess the feasibility of bringing spatial genome organization-based diagnostics to the clinical setting and to determine if the positioning patterns of specific loci can be useful biomarkers for cancer prognosis. Since spatial reorganization of the genome has been identified in multiple human diseases, it is likely that spatial genome positioning patterns as a diagnostic biomarker may be applied to many diseases.
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Affiliation(s)
- Karen J. Meaburn
- Cell Biology of Genomes Group, National Cancer Institute, National Institutes of HealthBethesda, MD, USA
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177
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Randise-Hinchliff C, Brickner JH. Transcription factors dynamically control the spatial organization of the yeast genome. Nucleus 2016; 7:369-74. [PMID: 27442220 PMCID: PMC5039007 DOI: 10.1080/19491034.2016.1212797] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/04/2022] Open
Abstract
In yeast, inducible genes such as INO1, PRM1 and HIS4 reposition from the nucleoplasm to nuclear periphery upon activation. This leads to a physical interaction with nuclear pore complex (NPC), interchromosomal clustering, and stronger transcription. Repositioning to the nuclear periphery is controlled by cis-acting transcription factor (TF) binding sites located within the promoters of these genes and the TFs that bind to them. Such elements are both necessary and sufficient to control positioning of genes to the nuclear periphery. We have identified 4 TFs capable of controlling the regulated positioning of genes to the nuclear periphery in budding yeast under different conditions: Put3, Cbf1, Gcn4 and Ste12. In each case, we have defined the molecular basis of regulated relocalization to the nuclear periphery. Put3- and Cbf1-mediated targeting to nuclear periphery is regulated through local recruitment of Rpd3(L) histone deacetylase complex by transcriptional repressors. Rpd3(L), through its histone deacetylase activity, prevents TF-mediated gene positioning by blocking TF binding. Many yeast transcriptional repressors were capable of blocking Put3-mediated recruitment; 11 of these required Rpd3. Thus, it is a general function of transcription repressors to regulate TF-mediated recruitment. However, Ste12 and Gcn4-mediated recruitment is regulated independently of Rpd3(L) and transcriptional repressors. Ste12-mediated recruitment is regulated by phosphorylation of an inhibitor called Dig2, and Gcn4-mediated gene targeting is up-regulated by increasing Gcn4 protein levels. The ability to control spatial position of genes in yeast represents a novel function for TFs and different regulatory strategies provide dynamic control of the yeast genome through different time scales.
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Affiliation(s)
| | - Jason H Brickner
- a Department of Molecular Biosciences , Northwestern University , Evanston , IL , USA
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178
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Jiang T, Raviram R, Snetkova V, Rocha PP, Proudhon C, Badri S, Bonneau R, Skok JA, Kluger Y. Identification of multi-loci hubs from 4C-seq demonstrates the functional importance of simultaneous interactions. Nucleic Acids Res 2016; 44:8714-8725. [PMID: 27439714 PMCID: PMC5062970 DOI: 10.1093/nar/gkw568] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2015] [Accepted: 06/13/2016] [Indexed: 12/29/2022] Open
Abstract
Use of low resolution single cell DNA FISH and population based high resolution chromosome conformation capture techniques have highlighted the importance of pairwise chromatin interactions in gene regulation. However, it is unlikely that associations involving regulatory elements act in isolation of other interacting partners that also influence their impact. Indeed, the influence of multi-loci interactions remains something of an enigma as beyond low-resolution DNA FISH we do not have the appropriate tools to analyze these. Here we present a method that uses standard 4C-seq data to identify multi-loci interactions from the same cell. We demonstrate the feasibility of our method using 4C-seq data sets that identify known pairwise and novel tri-loci interactions involving the Tcrb and Igk antigen receptor enhancers. We further show that the three Igk enhancers, MiEκ, 3′Eκ and Edκ, interact simultaneously in this super-enhancer cluster, which add to our previous findings showing that loss of one element decreases interactions between all three elements as well as reducing their transcriptional output. These findings underscore the functional importance of simultaneous interactions and provide new insight into the relationship between enhancer elements. Our method opens the door for studying multi-loci interactions and their impact on gene regulation in other biological settings.
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Affiliation(s)
- Tingting Jiang
- Interdepartmental Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT 06511, USA
| | - Ramya Raviram
- Department of Pathology, New York University School of Medicine, New York, NY, USA Department of Biology, New York University, New York, NY, USA
| | - Valentina Snetkova
- Department of Pathology, New York University School of Medicine, New York, NY, USA
| | - Pedro P Rocha
- Department of Pathology, New York University School of Medicine, New York, NY, USA
| | - Charlotte Proudhon
- Department of Pathology, New York University School of Medicine, New York, NY, USA
| | - Sana Badri
- Department of Pathology, New York University School of Medicine, New York, NY, USA Department of Biology, New York University, New York, NY, USA
| | - Richard Bonneau
- Department of Biology, New York University, New York, NY, USA Department of Computer Science, Courant Institute of Mathematical Sciences, New York, NY, USA Simons Center for Data Analysis, New York, NY 10010, USA
| | - Jane A Skok
- Department of Pathology, New York University School of Medicine, New York, NY, USA
| | - Yuval Kluger
- Interdepartmental Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT 06511, USA Department of Pathology and Yale Cancer Center, Yale University School of Medicine, New Haven, CT, USA Program of Applied Mathematics, Yale university, New Haven, CT, USA
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179
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Abstract
Epigenetic regulatory mechanisms play key roles in cardiac development, differentiation, homeostasis, response to stress and injury, and disease. Human heart failure (HF) epigenetic regulatory mechanisms have not been deciphered to date. This 2-part review distills the rapidly evolving research focused on human HF epigenetic regulatory mechanisms. Part I, which was published in the September/October issue, focused on epigenetic regulatory mechanisms involving RNA, specifically the role of short, intermediate, and long noncoding RNAs (lncRNAs) and endogenous competing RNA regulatory networks. Part II, now in the November/December issue, focuses on the epigenetic regulatory mechanisms involving DNA, including DNA methylation, histone modifications, and chromatin conformational changes. Part II concludes with 2 examples of well-studied integrated epigenetic regulatory mechanisms: the structural and functional roles of the Mediator complex in regulating transcription and the epigenetic networked "cross-talk" regulating atrial natriuretic peptide and brain natriuretic peptide promoter activation.
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180
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Arnes L, Akerman I, Balderes DA, Ferrer J, Sussel L. βlinc1 encodes a long noncoding RNA that regulates islet β-cell formation and function. Genes Dev 2016; 30:502-7. [PMID: 26944677 PMCID: PMC4782045 DOI: 10.1101/gad.273821.115] [Citation(s) in RCA: 96] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Pancreatic β cells are responsible for maintaining glucose homeostasis; their absence or malfunction results in diabetes mellitus. Although there is evidence that long noncoding RNAs (lncRNAs) play important roles in development and disease, none have been investigated in vivo in the context of pancreas development. In this study, we demonstrate that βlinc1 (β-cell long intergenic noncoding RNA 1), a conserved lncRNA, is necessary for the specification and function of insulin-producing β cells through the coordinated regulation of a number of islet-specific transcription factors located in the genomic vicinity of βlinc1. Furthermore, deletion of βlinc1 results in defective islet development and disruption of glucose homeostasis in adult mice.
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Affiliation(s)
- Luis Arnes
- Department of Genetics and Development, Columbia University, New York, New York 10032, USA
| | - Ildem Akerman
- Genomic Programming of Β-Cells Laboratory, Institut d'Investigacions August Pi I Sunyer (IDIBAPS), Barcelona 08036, Spain; Department of Medicine, Imperial College London, London W12 0NN, United Kingdom
| | - Dina A Balderes
- Department of Genetics and Development, Columbia University, New York, New York 10032, USA
| | - Jorge Ferrer
- Genomic Programming of Β-Cells Laboratory, Institut d'Investigacions August Pi I Sunyer (IDIBAPS), Barcelona 08036, Spain; Department of Medicine, Imperial College London, London W12 0NN, United Kingdom
| | - Lori Sussel
- Department of Genetics and Development, Columbia University, New York, New York 10032, USA
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181
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A novel single cell method to identify the genetic composition at a single nuclear body. Sci Rep 2016; 6:29191. [PMID: 27389808 PMCID: PMC4937434 DOI: 10.1038/srep29191] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2015] [Accepted: 06/14/2016] [Indexed: 11/24/2022] Open
Abstract
Gene loci make specific associations with compartments of the nucleus (e.g. the nuclear envelope, nucleolus, and transcription factories) and this association may determine or reflect a mechanism of genetic control. With current methods, it is not possible to identify sets of genes that converge to form a “gene hub” as there is a reliance on loci-specific probes, or immunoprecipitation of a particular protein from bulk cells. We introduce a method that will allow for the identification of loci contained within the vicinity of a single nuclear body in a single cell. For the first time, we demonstrate that the DNA sequences originating from a single sub-nuclear structure in a single cell targeted by two-photon irradiation can be determined, and mapped to a particular locus. Its application to single PML nuclear bodies reveals ontologically related loci that frequently associate with each other and with PML bodies in a population of cells, and a possible nuclear body targeting role for specific transcription factor binding sites.
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182
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Uhler C, Shivashankar G. Geometric control and modeling of genome reprogramming. BIOARCHITECTURE 2016; 6:76-84. [PMID: 27434579 PMCID: PMC6085119 DOI: 10.1080/19490992.2016.1201620] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/31/2016] [Revised: 06/08/2016] [Accepted: 06/08/2016] [Indexed: 12/29/2022]
Abstract
Cell geometry is tightly coupled to gene expression patterns within the tissue microenvironment. This perspective synthesizes evidence that the 3D organization of chromosomes is a critical intermediate for geometric control of genomic programs. Using a combination of experiments and modeling we outline approaches to decipher the mechano-genomic code that governs cellular homeostasis and reprogramming.
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Affiliation(s)
- Caroline Uhler
- Department of Electrical Engineering & Computer Science, and Institute for Data, Systems and Society, MIT, Cambridge, MA, USA
| | - G.V. Shivashankar
- Mechanobiology Institute National University of Singapore, Singapore
- FIRC Institute of Molecular Oncology (IFOM), Milan, Italy
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183
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3D genomics imposes evolution of the domain model of eukaryotic genome organization. Chromosoma 2016; 126:59-69. [DOI: 10.1007/s00412-016-0604-7] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2016] [Revised: 05/11/2016] [Accepted: 06/06/2016] [Indexed: 10/21/2022]
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184
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Proudhon C, Snetkova V, Raviram R, Lobry C, Badri S, Jiang T, Hao B, Trimarchi T, Kluger Y, Aifantis I, Bonneau R, Skok JA. Active and Inactive Enhancers Cooperate to Exert Localized and Long-Range Control of Gene Regulation. Cell Rep 2016; 15:2159-2169. [PMID: 27239026 PMCID: PMC4899175 DOI: 10.1016/j.celrep.2016.04.087] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2015] [Revised: 04/06/2016] [Accepted: 04/20/2016] [Indexed: 01/24/2023] Open
Abstract
V(D)J recombination relies on the presence of proximal enhancers that activate the antigen receptor (AgR) loci in a lineage- and stage-specific manner. Unexpectedly, we find that both active and inactive AgR enhancers cooperate to disseminate their effects in a localized and long-range manner. Here, we demonstrate the importance of short-range contacts between active enhancers that constitute an Igk super-enhancer in B cells. Deletion of one element reduces the interaction frequency between other enhancers in the hub, which compromises the transcriptional output of each component. Furthermore, we establish that, in T cells, long-range contact and cooperation between the inactive Igk enhancer MiEκ and the active Tcrb enhancer Eβ alters enrichment of CBFβ binding in a manner that impacts Tcrb recombination. These findings underline the complexities of enhancer regulation and point to a role for localized and long-range enhancer-sharing between active and inactive elements in lineage- and stage-specific control.
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MESH Headings
- Animals
- Enhancer Elements, Genetic
- Gene Expression Regulation
- Gene Rearrangement, beta-Chain T-Cell Antigen Receptor
- Mice, Inbred C57BL
- Protein Binding/genetics
- RNA, Messenger/genetics
- RNA, Messenger/metabolism
- Receptors, Antigen, T-Cell, alpha-beta/genetics
- Receptors, Antigen, T-Cell, alpha-beta/metabolism
- T-Lymphocytes/immunology
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Affiliation(s)
- Charlotte Proudhon
- Department of Pathology, NYU School of Medicine, New York, NY 10016, USA
| | - Valentina Snetkova
- Department of Pathology, NYU School of Medicine, New York, NY 10016, USA
| | - Ramya Raviram
- Department of Pathology, NYU School of Medicine, New York, NY 10016, USA; Department of Biology, NYU, New York, NY 10003, USA
| | - Camille Lobry
- Department of Pathology, NYU School of Medicine, New York, NY 10016, USA
| | - Sana Badri
- Department of Pathology, NYU School of Medicine, New York, NY 10016, USA; Department of Biology, NYU, New York, NY 10003, USA; Center for Health Informatics and Bioinformatics, NYU School of Medicine, New York, NY 10016, USA
| | - Tingting Jiang
- Department of Pathology, Yale University, New Haven, CT 06510, USA
| | - Bingtao Hao
- Department of Pathology, NYU School of Medicine, New York, NY 10016, USA
| | - Thomas Trimarchi
- Department of Pathology, NYU School of Medicine, New York, NY 10016, USA
| | - Yuval Kluger
- Department of Pathology, Yale University, New Haven, CT 06510, USA
| | - Iannis Aifantis
- Department of Pathology, NYU School of Medicine, New York, NY 10016, USA
| | - Richard Bonneau
- Department of Biology, NYU, New York, NY 10003, USA; Department of Computer Science, Courant Institute of Mathematical Sciences, NYU, New York, NY 10003, USA; Simons Center for Data Analysis, New York, NY 10010, USA
| | - Jane A Skok
- Department of Pathology, NYU School of Medicine, New York, NY 10016, USA.
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185
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Dai C, Li W, Tjong H, Hao S, Zhou Y, Li Q, Chen L, Zhu B, Alber F, Jasmine Zhou X. Mining 3D genome structure populations identifies major factors governing the stability of regulatory communities. Nat Commun 2016; 7:11549. [PMID: 27240697 PMCID: PMC4895025 DOI: 10.1038/ncomms11549] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2015] [Accepted: 04/08/2016] [Indexed: 11/25/2022] Open
Abstract
Three-dimensional (3D) genome structures vary from cell to cell even in an isogenic sample. Unlike protein structures, genome structures are highly plastic, posing a significant challenge for structure-function mapping. Here we report an approach to comprehensively identify 3D chromatin clusters that each occurs frequently across a population of genome structures, either deconvoluted from ensemble-averaged Hi-C data or from a collection of single-cell Hi-C data. Applying our method to a population of genome structures (at the macrodomain resolution) of lymphoblastoid cells, we identify an atlas of stable inter-chromosomal chromatin clusters. A large number of these clusters are enriched in binding of specific regulatory factors and are therefore defined as ‘Regulatory Communities.' We reveal two major factors, centromere clustering and transcription factor binding, which significantly stabilize such communities. Finally, we show that the regulatory communities differ substantially from cell to cell, indicating that expression variability could be impacted by genome structures. 3D genome structures are plastic and vary from cell to cell even in an isogenic sample. Here, the authors present an approach to identify frequent 3D chromatin clusters across a population of genome structures, either deconvoluted from ensemble-averaged Hi-C data or from a collection of single-cell Hi-C data.
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Affiliation(s)
- Chao Dai
- Molecular and Computational Biology, Department of Biological Sciences, University of Southern California, 1050 Childs Way, Los Angeles, California 90089, USA
| | - Wenyuan Li
- Molecular and Computational Biology, Department of Biological Sciences, University of Southern California, 1050 Childs Way, Los Angeles, California 90089, USA
| | - Harianto Tjong
- Molecular and Computational Biology, Department of Biological Sciences, University of Southern California, 1050 Childs Way, Los Angeles, California 90089, USA
| | - Shengli Hao
- Molecular and Computational Biology, Department of Biological Sciences, University of Southern California, 1050 Childs Way, Los Angeles, California 90089, USA
| | - Yonggang Zhou
- Molecular and Computational Biology, Department of Biological Sciences, University of Southern California, 1050 Childs Way, Los Angeles, California 90089, USA
| | - Qingjiao Li
- Molecular and Computational Biology, Department of Biological Sciences, University of Southern California, 1050 Childs Way, Los Angeles, California 90089, USA
| | - Lin Chen
- Molecular and Computational Biology, Department of Biological Sciences, University of Southern California, 1050 Childs Way, Los Angeles, California 90089, USA
| | - Bing Zhu
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Frank Alber
- Molecular and Computational Biology, Department of Biological Sciences, University of Southern California, 1050 Childs Way, Los Angeles, California 90089, USA
| | - Xianghong Jasmine Zhou
- Molecular and Computational Biology, Department of Biological Sciences, University of Southern California, 1050 Childs Way, Los Angeles, California 90089, USA
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186
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Fotuhi Siahpirani A, Ay F, Roy S. A multi-task graph-clustering approach for chromosome conformation capture data sets identifies conserved modules of chromosomal interactions. Genome Biol 2016; 17:114. [PMID: 27233632 PMCID: PMC4882777 DOI: 10.1186/s13059-016-0962-8] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2016] [Accepted: 04/22/2016] [Indexed: 01/13/2023] Open
Abstract
Chromosome conformation capture methods are being increasingly used to study three-dimensional genome architecture in multiple cell types and species. An important challenge is to examine changes in three-dimensional architecture across cell types and species. We present Arboretum-Hi-C, a multi-task spectral clustering method, to identify common and context-specific aspects of genome architecture. Compared to standard clustering, Arboretum-Hi-C produced more biologically consistent patterns of conservation. Most clusters are conserved and enriched for either high- or low-activity genomic signals. Most genomic regions diverge between clusters with similar chromatin state except for a few that are associated with lamina-associated domains and open chromatin.
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Affiliation(s)
| | - Ferhat Ay
- La Jolla Institute for Allergy and Immunology, 9420 Athena Circle, La Jolla, 92037, CA, USA
| | - Sushmita Roy
- Wisconsin Institute for Discovery, University of Wisconsin, Madison, 53717, WI, USA. .,Department of Biostatistics and Medical Informatics, University of Wisconsin, Madison, 53717, WI, USA.
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187
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Engel KL, Mackiewicz M, Hardigan AA, Myers RM, Savic D. Decoding transcriptional enhancers: Evolving from annotation to functional interpretation. Semin Cell Dev Biol 2016; 57:40-50. [PMID: 27224938 DOI: 10.1016/j.semcdb.2016.05.014] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2016] [Revised: 05/06/2016] [Accepted: 05/18/2016] [Indexed: 12/18/2022]
Abstract
Deciphering the intricate molecular processes that orchestrate the spatial and temporal regulation of genes has become an increasingly major focus of biological research. The differential expression of genes by diverse cell types with a common genome is a hallmark of complex cellular functions, as well as the basis for multicellular life. Importantly, a more coherent understanding of gene regulation is critical for defining developmental processes, evolutionary principles and disease etiologies. Here we present our current understanding of gene regulation by focusing on the role of enhancer elements in these complex processes. Although functional genomic methods have provided considerable advances to our understanding of gene regulation, these assays, which are usually performed on a genome-wide scale, typically provide correlative observations that lack functional interpretation. Recent innovations in genome editing technologies have placed gene regulatory studies at an exciting crossroads, as systematic, functional evaluation of enhancers and other transcriptional regulatory elements can now be performed in a coordinated, high-throughput manner across the entire genome. This review provides insights on transcriptional enhancer function, their role in development and disease, and catalogues experimental tools commonly used to study these elements. Additionally, we discuss the crucial role of novel techniques in deciphering the complex gene regulatory landscape and how these studies will shape future research.
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Affiliation(s)
- Krysta L Engel
- HudsonAlpha Institute for Biotechnology, Huntsville, AL 35806, United States
| | - Mark Mackiewicz
- HudsonAlpha Institute for Biotechnology, Huntsville, AL 35806, United States
| | - Andrew A Hardigan
- HudsonAlpha Institute for Biotechnology, Huntsville, AL 35806, United States; Department of Genetics, University of Alabama at Birmingham, Birmingham, AL 35294, United States
| | - Richard M Myers
- HudsonAlpha Institute for Biotechnology, Huntsville, AL 35806, United States
| | - Daniel Savic
- HudsonAlpha Institute for Biotechnology, Huntsville, AL 35806, United States.
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188
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Brackley CA, Johnson J, Kelly S, Cook PR, Marenduzzo D. Simulated binding of transcription factors to active and inactive regions folds human chromosomes into loops, rosettes and topological domains. Nucleic Acids Res 2016; 44:3503-12. [PMID: 27060145 PMCID: PMC4856988 DOI: 10.1093/nar/gkw135] [Citation(s) in RCA: 110] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2015] [Revised: 02/22/2016] [Accepted: 02/24/2016] [Indexed: 01/12/2023] Open
Abstract
Biophysicists are modeling conformations of interphase chromosomes, often basing the strengths of interactions between segments distant on the genetic map on contact frequencies determined experimentally. Here, instead, we develop a fitting-free, minimal model: bivalent or multivalent red and green 'transcription factors' bind to cognate sites in strings of beads ('chromatin') to form molecular bridges stabilizing loops. In the absence of additional explicit forces, molecular dynamic simulations reveal that bound factors spontaneously cluster-red with red, green with green, but rarely red with green-to give structures reminiscent of transcription factories. Binding of just two transcription factors (or proteins) to active and inactive regions of human chromosomes yields rosettes, topological domains and contact maps much like those seen experimentally. This emergent 'bridging-induced attraction' proves to be a robust, simple and generic force able to organize interphase chromosomes at all scales.
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Affiliation(s)
- Chris A Brackley
- SUPA, School of Physics & Astronomy, University of Edinburgh, Peter Guthrie Tait Road, Edinburgh, EH9 3FD, UK
| | - James Johnson
- SUPA, School of Physics & Astronomy, University of Edinburgh, Peter Guthrie Tait Road, Edinburgh, EH9 3FD, UK
| | - Steven Kelly
- Department of Plant Sciences, University of Oxford, South Parks Road, Oxford OX1 3RB, UK
| | - Peter R Cook
- Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford, OX1 3RE, UK
| | - Davide Marenduzzo
- SUPA, School of Physics & Astronomy, University of Edinburgh, Peter Guthrie Tait Road, Edinburgh, EH9 3FD, UK
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189
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Iwasaki O, Corcoran CJ, Noma KI. Involvement of condensin-directed gene associations in the organization and regulation of chromosome territories during the cell cycle. Nucleic Acids Res 2016; 44:3618-28. [PMID: 26704981 PMCID: PMC4856965 DOI: 10.1093/nar/gkv1502] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2015] [Revised: 12/11/2014] [Accepted: 12/14/2015] [Indexed: 11/14/2022] Open
Abstract
Chromosomes are not randomly disposed in the nucleus but instead occupy discrete sub-nuclear domains, referred to as chromosome territories. The molecular mechanisms that underlie the formation of chromosome territories and how they are regulated during the cell cycle remain largely unknown. Here, we have developed two different chromosome-painting approaches to address how chromosome territories are organized in the fission yeast model organism. We show that condensin frequently associates RNA polymerase III-transcribed genes (tRNA and 5S rRNA) that are present on the same chromosomes, and that the disruption of these associations by condensin mutations significantly compromises the chromosome territory arrangement. We also find that condensin-dependent intra-chromosomal gene associations and chromosome territories are co-regulated during the cell cycle. For example, condensin-directed gene associations occur to the least degree during S phase, with the chromosomal overlap becoming largest. In clear contrast, condensin-directed gene associations become tighter in other cell-cycle phases, especially during mitosis, with the overlap between the different chromosomes being smaller. This study suggests that condensin-driven intra-chromosomal gene associations contribute to the organization and regulation of chromosome territories during the cell cycle.
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190
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Chromosome conformation capture technologies and their impact in understanding genome function. Chromosoma 2016; 126:33-44. [DOI: 10.1007/s00412-016-0593-6] [Citation(s) in RCA: 92] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2015] [Revised: 04/10/2016] [Accepted: 04/12/2016] [Indexed: 12/17/2022]
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191
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Vaquerizas JM, Akhtar A, Luscombe NM. Large-scale nuclear architecture and transcriptional control. Subcell Biochem 2016; 52:279-95. [PMID: 21557088 DOI: 10.1007/978-90-481-9069-0_13] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
Transcriptional regulation is one the most basic mechanisms for controlling gene expression. Over the past few years, much research has been devoted to understanding the interplay between transcription factors, histone modifications and associated enzymes required to achieve this control. However, it is becoming increasingly apparent that the three-dimensional conformation of chromatin in the interphase nucleus also plays a critical role in regulating transcription. Chromatin localisation in the nucleus is highly organised, and early studies described strong interactions between chromatin and sub-nuclear components. Single-gene studies have shed light on how chromosomal architecture affects gene expression. Lately, this has been complemented by whole-genome studies that have determined the global chromatin conformation of living cells in interphase. These studies have greatly expanded our understanding of nuclear architecture and its interplay with different physiological processes. Despite these advances, however, most of the mechanisms used to impose the three-dimensional chromatin structure remain unknown. Here, we summarise the different levels of chromatin organisation in the nucleus and discuss current efforts into characterising the mechanisms that govern it.
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192
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Joyce EF, Erceg J, Wu CT. Pairing and anti-pairing: a balancing act in the diploid genome. Curr Opin Genet Dev 2016; 37:119-128. [PMID: 27065367 DOI: 10.1016/j.gde.2016.03.002] [Citation(s) in RCA: 62] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2015] [Revised: 03/02/2016] [Accepted: 03/05/2016] [Indexed: 12/22/2022]
Abstract
The presence of maternal and paternal homologs appears to be much more than just a doubling of genetic material. We know this because genomes have evolved elaborate mechanisms that permit homologous regions to sense and then respond to each other. One way in which homologs communicate is to come into contact and, in fact, Dipteran insects such as Drosophila excel at this task, aligning all pairs of maternal and paternal chromosomes, end-to-end, in essentially all somatic tissues throughout development. Here, we reexamine the widely held tenet that extensive somatic pairing of homologous sequences cannot occur in mammals and suggest, instead, that pairing may be a widespread and significant potential that has gone unnoticed in mammals because they expend considerable effort to prevent it. We then extend this discussion to interchromosomal interactions, in general, and speculate about the potential of nuclear organization and pairing to impact inheritance.
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Affiliation(s)
- Eric F Joyce
- Department of Genetics, Harvard Medical School, Boston, MA 02115, United States.
| | - Jelena Erceg
- Department of Genetics, Harvard Medical School, Boston, MA 02115, United States
| | - C-Ting Wu
- Department of Genetics, Harvard Medical School, Boston, MA 02115, United States.
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193
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Ito K, Sanosaka T, Igarashi K, Ideta-Otsuka M, Aizawa A, Uosaki Y, Noguchi A, Arakawa H, Nakashima K, Takizawa T. Identification of genes associated with the astrocyte-specific gene Gfap during astrocyte differentiation. Sci Rep 2016; 6:23903. [PMID: 27041678 PMCID: PMC4819225 DOI: 10.1038/srep23903] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2015] [Accepted: 03/16/2016] [Indexed: 01/15/2023] Open
Abstract
Chromosomes and genes are non-randomly arranged within the mammalian cell nucleus, and gene clustering is of great significance in transcriptional regulation. However, the relevance of gene clustering and their expression during the differentiation of neural precursor cells (NPCs) into astrocytes remains unclear. We performed a genome-wide enhanced circular chromosomal conformation capture (e4C) to screen for genes associated with the astrocyte-specific gene glial fibrillary acidic protein (Gfap) during astrocyte differentiation. We identified 18 genes that were specifically associated with Gfap and expressed in NPC-derived astrocytes. Our results provide additional evidence for the functional significance of gene clustering in transcriptional regulation during NPC differentiation.
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Affiliation(s)
- Kenji Ito
- Department of Pediatrics, Graduate School of Medicine, Gunma University, 3-39-22 Showa-machi, Maebashi, Gunma 371-8511, Japan
| | - Tsukasa Sanosaka
- Stem Cell Biology and Medicine, Department of Stem cell Biology and Medicine, Graduate School of Medical Sciences, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka, 812-8582, Japan
| | - Katsuhide Igarashi
- Life Science Tokyo Advanced Research Center (L-StaR), Pharmacy and Pharmaceutical Science, Hoshi University, 2-4-41 Ebara, Shinagawa-ku, Tokyo 142-5801, Japan
| | - Maky Ideta-Otsuka
- Life Science Tokyo Advanced Research Center (L-StaR), Pharmacy and Pharmaceutical Science, Hoshi University, 2-4-41 Ebara, Shinagawa-ku, Tokyo 142-5801, Japan
| | - Akira Aizawa
- Department of Pediatrics, Graduate School of Medicine, Gunma University, 3-39-22 Showa-machi, Maebashi, Gunma 371-8511, Japan
| | - Yuichi Uosaki
- Department of Pediatrics, Graduate School of Medicine, Gunma University, 3-39-22 Showa-machi, Maebashi, Gunma 371-8511, Japan
| | - Azumi Noguchi
- Department of Pediatrics, Graduate School of Medicine, Gunma University, 3-39-22 Showa-machi, Maebashi, Gunma 371-8511, Japan
| | - Hirokazu Arakawa
- Department of Pediatrics, Graduate School of Medicine, Gunma University, 3-39-22 Showa-machi, Maebashi, Gunma 371-8511, Japan
| | - Kinichi Nakashima
- Stem Cell Biology and Medicine, Department of Stem cell Biology and Medicine, Graduate School of Medical Sciences, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka, 812-8582, Japan
| | - Takumi Takizawa
- Department of Pediatrics, Graduate School of Medicine, Gunma University, 3-39-22 Showa-machi, Maebashi, Gunma 371-8511, Japan
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194
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Abstract
InDrosophila, homologous chromosome pairing leads to "transvection," in which the enhancer of a gene can regulate the allelic transcription intrans.Interallelic interactions were also observed in vegetative diploid budding yeast, but their functional significance is unknown. Here, we show that aGAL1reporter can interact with its homologous allele and affect its expression. By ectopically inserting two allelic reporters, one driven by wild-typeGAL1promoter (WTGAL1pr) and the other by a mutant promoter with delayed response to galactose induction, we found that the two reporters physically associate, and the WTGAL1prtriggers synchronized firing of the defective promoter and accelerates its activation without affecting its steady-state expression level. This interaction and the transregulatory effect disappear when the same reporters are located at nonallelic sites. We further demonstrated that the activator Gal4 is essential for the interallelic interaction, and the transregulation requires fully activated WTGAL1prtranscription. The mechanism of this phenomenon was further discussed. Taken together, our data revealed the existence of interallelic gene regulation in yeast, which serves as a starting point for understanding long-distance gene regulation in this genetically tractable system.
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195
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Xu Y, Zhang M, Li W, Zhu X, Bao X, Qin B, Hutchins AP, Esteban MA. Transcriptional Control of Somatic Cell Reprogramming. Trends Cell Biol 2016; 26:272-288. [DOI: 10.1016/j.tcb.2015.12.003] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2015] [Revised: 12/07/2015] [Accepted: 12/16/2015] [Indexed: 01/26/2023]
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196
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Topologically associated domains enriched for lineage-specific genes reveal expression-dependent nuclear topologies during myogenesis. Proc Natl Acad Sci U S A 2016; 113:E1691-700. [PMID: 26957603 DOI: 10.1073/pnas.1521826113] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
The linear distribution of genes across chromosomes and the spatial localization of genes within the nucleus are related to their transcriptional regulation. The mechanistic consequences of linear gene order, and how it may relate to the functional output of genome organization, remain to be fully resolved, however. Here we tested the relationship between linear and 3D organization of gene regulation during myogenesis. Our analysis has identified a subset of topologically associated domains (TADs) that are significantly enriched for muscle-specific genes. These lineage-enriched TADs demonstrate an expression-dependent pattern of nuclear organization that influences the positioning of adjacent nonenriched TADs. Therefore, lineage-enriched TADs inform cell-specific genome organization during myogenesis. The reduction of allelic spatial distance of one of these domains, which contains Myogenin, correlates with reduced transcriptional variability, identifying a potential role for lineage-specific nuclear topology. Using a fusion-based strategy to decouple mitosis and myotube formation, we demonstrate that the cell-specific topology of syncytial nuclei is dependent on cell division. We propose that the effects of linear and spatial organization of gene loci on gene regulation are linked through TAD architecture, and that mitosis is critical for establishing nuclear topologies during cellular differentiation.
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197
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Randise-Hinchliff C, Coukos R, Sood V, Sumner MC, Zdraljevic S, Meldi Sholl L, Garvey Brickner D, Ahmed S, Watchmaker L, Brickner JH. Strategies to regulate transcription factor-mediated gene positioning and interchromosomal clustering at the nuclear periphery. J Cell Biol 2016; 212:633-46. [PMID: 26953353 PMCID: PMC4792077 DOI: 10.1083/jcb.201508068] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2015] [Accepted: 02/02/2016] [Indexed: 11/23/2022] Open
Abstract
In yeast, transcription factors mediate gene positioning at the nuclear periphery and interchromosomal clustering. These phenomena are regulated by several different strategies that lead to dynamic changes in the spatial arrangement of genes over different time scales. In budding yeast, targeting of active genes to the nuclear pore complex (NPC) and interchromosomal clustering is mediated by transcription factor (TF) binding sites in the gene promoters. For example, the binding sites for the TFs Put3, Ste12, and Gcn4 are necessary and sufficient to promote positioning at the nuclear periphery and interchromosomal clustering. However, in all three cases, gene positioning and interchromosomal clustering are regulated. Under uninducing conditions, local recruitment of the Rpd3(L) histone deacetylase by transcriptional repressors blocks Put3 DNA binding. This is a general function of yeast repressors: 16 of 21 repressors blocked Put3-mediated subnuclear positioning; 11 of these required Rpd3. In contrast, Ste12-mediated gene positioning is regulated independently of DNA binding by mitogen-activated protein kinase phosphorylation of the Dig2 inhibitor, and Gcn4-dependent targeting is up-regulated by increasing Gcn4 protein levels. These different regulatory strategies provide either qualitative switch-like control or quantitative control of gene positioning over different time scales.
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Affiliation(s)
| | - Robert Coukos
- Department of Molecular Biosciences, Northwestern University, Evanston, IL 60201
| | - Varun Sood
- Department of Molecular Biosciences, Northwestern University, Evanston, IL 60201
| | - Michael Chas Sumner
- Department of Molecular Biosciences, Northwestern University, Evanston, IL 60201
| | - Stefan Zdraljevic
- Department of Molecular Biosciences, Northwestern University, Evanston, IL 60201
| | - Lauren Meldi Sholl
- Department of Molecular Biosciences, Northwestern University, Evanston, IL 60201
| | | | - Sara Ahmed
- Department of Molecular Biosciences, Northwestern University, Evanston, IL 60201
| | - Lauren Watchmaker
- Department of Molecular Biosciences, Northwestern University, Evanston, IL 60201
| | - Jason H Brickner
- Department of Molecular Biosciences, Northwestern University, Evanston, IL 60201
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198
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Raviram R, Rocha PP, Müller CL, Miraldi ER, Badri S, Fu Y, Swanzey E, Proudhon C, Snetkova V, Bonneau R, Skok JA. 4C-ker: A Method to Reproducibly Identify Genome-Wide Interactions Captured by 4C-Seq Experiments. PLoS Comput Biol 2016; 12:e1004780. [PMID: 26938081 PMCID: PMC4777514 DOI: 10.1371/journal.pcbi.1004780] [Citation(s) in RCA: 64] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2015] [Accepted: 01/29/2016] [Indexed: 01/17/2023] Open
Abstract
4C-Seq has proven to be a powerful technique to identify genome-wide interactions with a single locus of interest (or "bait") that can be important for gene regulation. However, analysis of 4C-Seq data is complicated by the many biases inherent to the technique. An important consideration when dealing with 4C-Seq data is the differences in resolution of signal across the genome that result from differences in 3D distance separation from the bait. This leads to the highest signal in the region immediately surrounding the bait and increasingly lower signals in far-cis and trans. Another important aspect of 4C-Seq experiments is the resolution, which is greatly influenced by the choice of restriction enzyme and the frequency at which it can cut the genome. Thus, it is important that a 4C-Seq analysis method is flexible enough to analyze data generated using different enzymes and to identify interactions across the entire genome. Current methods for 4C-Seq analysis only identify interactions in regions near the bait or in regions located in far-cis and trans, but no method comprehensively analyzes 4C signals of different length scales. In addition, some methods also fail in experiments where chromatin fragments are generated using frequent cutter restriction enzymes. Here, we describe 4C-ker, a Hidden-Markov Model based pipeline that identifies regions throughout the genome that interact with the 4C bait locus. In addition, we incorporate methods for the identification of differential interactions in multiple 4C-seq datasets collected from different genotypes or experimental conditions. Adaptive window sizes are used to correct for differences in signal coverage in near-bait regions, far-cis and trans chromosomes. Using several datasets, we demonstrate that 4C-ker outperforms all existing 4C-Seq pipelines in its ability to reproducibly identify interaction domains at all genomic ranges with different resolution enzymes.
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Affiliation(s)
- Ramya Raviram
- Department of Pathology, New York University School of Medicine, New York, New York, United States of America.,Department of Biology, New York University, New York, New York, United States of America
| | - Pedro P Rocha
- Department of Pathology, New York University School of Medicine, New York, New York, United States of America
| | - Christian L Müller
- Department of Biology, New York University, New York, New York, United States of America.,Department of Computer Science, Courant Institute of Mathematical Sciences, New York, New York, United States of America.,Simons Center for Data Analysis, New York, New York, United States of America
| | - Emily R Miraldi
- Department of Biology, New York University, New York, New York, United States of America.,Department of Computer Science, Courant Institute of Mathematical Sciences, New York, New York, United States of America.,Simons Center for Data Analysis, New York, New York, United States of America
| | - Sana Badri
- Department of Pathology, New York University School of Medicine, New York, New York, United States of America
| | - Yi Fu
- Department of Pathology, New York University School of Medicine, New York, New York, United States of America.,Department of Biology, New York University, New York, New York, United States of America
| | - Emily Swanzey
- Skirball Institute, New York University School of Medicine, New York, New York, United States of America
| | - Charlotte Proudhon
- Department of Pathology, New York University School of Medicine, New York, New York, United States of America
| | - Valentina Snetkova
- Department of Pathology, New York University School of Medicine, New York, New York, United States of America
| | - Richard Bonneau
- Department of Biology, New York University, New York, New York, United States of America.,Department of Computer Science, Courant Institute of Mathematical Sciences, New York, New York, United States of America.,Simons Center for Data Analysis, New York, New York, United States of America
| | - Jane A Skok
- Department of Pathology, New York University School of Medicine, New York, New York, United States of America
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199
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Maharana S, Iyer KV, Jain N, Nagarajan M, Wang Y, Shivashankar GV. Chromosome intermingling-the physical basis of chromosome organization in differentiated cells. Nucleic Acids Res 2016; 44:5148-60. [PMID: 26939888 PMCID: PMC5603959 DOI: 10.1093/nar/gkw131] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2016] [Accepted: 02/19/2016] [Indexed: 12/16/2022] Open
Abstract
Chromosome territories (CTs) in higher eukaryotes occupy tissue-specific non-random three-dimensional positions in the interphase nucleus. To understand the mechanisms underlying CT organization, we mapped CT position and transcriptional changes in undifferentiated embryonic stem (ES) cells, during early onset of mouse ES cell differentiation and in terminally differentiated NIH3T3 cells. We found chromosome intermingling volume to be a reliable CT surface property, which can be used to define CT organization. Our results show a correlation between the transcriptional activity of chromosomes and heterologous chromosome intermingling volumes during differentiation. Furthermore, these regions were enriched in active RNA polymerase and other histone modifications in the differentiated states. These findings suggest a correlation between the evolution of transcription program in modifying CT architecture in undifferentiated stem cells. This leads to the formation of functional CT surfaces, which then interact to define the three-dimensional CT organization during differentiation.
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Affiliation(s)
| | - K Venkatesan Iyer
- Mechanobiology Institute, National University of Singapore, Singapore
| | - Nikhil Jain
- Mechanobiology Institute, National University of Singapore, Singapore Department of Biological Sciences, National University of Singapore, Singapore
| | - Mallika Nagarajan
- Mechanobiology Institute, National University of Singapore, Singapore
| | - Yejun Wang
- Mechanobiology Institute, National University of Singapore, Singapore
| | - G V Shivashankar
- Mechanobiology Institute, National University of Singapore, Singapore Department of Biological Sciences, National University of Singapore, Singapore
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200
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Singh A, Bagadia M, Sandhu KS. Spatially coordinated replication and minimization of expression noise constrain three-dimensional organization of yeast genome. DNA Res 2016; 23:155-69. [PMID: 26932984 PMCID: PMC4833423 DOI: 10.1093/dnares/dsw005] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2015] [Accepted: 01/31/2016] [Indexed: 01/01/2023] Open
Abstract
Despite recent advances, the underlying functional constraints that shape the three-dimensional organization of eukaryotic genome are not entirely clear. Through comprehensive multivariate analyses of genome-wide datasets, we show that cis and trans interactions in yeast genome have significantly distinct functional associations. In particular, (i) the trans interactions are constrained by coordinated replication and co-varying mutation rates of early replicating domains through interactions among early origins, while cis interactions are constrained by coordination of late replication through interactions among late origins; (ii)cis and trans interactions exhibit differential preference for nucleosome occupancy; (iii)cis interactions are also constrained by the essentiality and co-fitness of interacting genes. Essential gene clusters associate with high average interaction frequency, relatively short-range interactions of low variance, and exhibit less fluctuations in chromatin conformation, marking a physically restrained state of engaged loci that, we suggest, is important to mitigate the epigenetic errors by restricting the spatial mobility of loci. Indeed, the genes with lower expression noise associate with relatively short-range interactions of lower variance and exhibit relatively higher average interaction frequency, a property that is conserved across Escherichia coli,yeast, and mESCs. Altogether, our observations highlight the coordination of replication and the minimization of expression noise, not necessarily co-expression of genes, as potent evolutionary constraints shaping the spatial organization of yeast genome.
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Affiliation(s)
- Arashdeep Singh
- Department of Biological Sciences, Indian Institute of Science Education and Research (IISER)-Mohali, SAS Nagar 140306, India
| | - Meenakshi Bagadia
- Department of Biological Sciences, Indian Institute of Science Education and Research (IISER)-Mohali, SAS Nagar 140306, India
| | - Kuljeet Singh Sandhu
- Department of Biological Sciences, Indian Institute of Science Education and Research (IISER)-Mohali, SAS Nagar 140306, India
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