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Li M, Yang J, Xiao R, Liu Y, Hu J, Li T, Wu P, Zhang M, Huang Y, Sun Y, Li C. The effect of trisomic chromosomes on spatial genome organization and global transcription in embryonic stem cells. Cell Prolif 2024; 57:e13639. [PMID: 38553796 PMCID: PMC11294443 DOI: 10.1111/cpr.13639] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2023] [Revised: 03/08/2024] [Accepted: 03/14/2024] [Indexed: 08/03/2024] Open
Abstract
Aneuploidy frequently occurs in cancer and developmental diseases such as Down syndrome, with its functional consequences implicated in dosage effects on gene expression and global perturbation of stress response and cell proliferation pathways. However, how aneuploidy affects spatial genome organization remains less understood. In this study, we addressed this question by utilizing the previously established isogenic wild-type (WT) and trisomic mouse embryonic stem cells (mESCs). We employed a combination of Hi-C, RNA-seq, chromosome painting and nascent RNA imaging technologies to compare the spatial genome structures and gene transcription among these cells. We found that trisomy has little effect on spatial genome organization at the level of A/B compartment or topologically associating domain (TAD). Inter-chromosomal interactions are associated with chromosome regions with high gene density, active histone modifications and high transcription levels, which are confirmed by imaging. Imaging also revealed contracted chromosome volume and weakened transcriptional activity for trisomic chromosomes, suggesting potential implications for the transcriptional output of these chromosomes. Our data resources and findings may contribute to a better understanding of the consequences of aneuploidy from the angle of spatial genome organization.
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Affiliation(s)
- Mengfan Li
- Center for Bioinformatics, School of Life Sciences, Center for Statistical Science, Peking‐Tsinghua Center for Life SciencesPeking UniversityBeijingChina
| | - Junsheng Yang
- State Key Laboratory of Membrane Biology, School of Life Sciences, and Biomedical Pioneering Innovation Center (BIOPIC)Peking UniversityBeijingChina
| | - Rong Xiao
- State Key Laboratory of Common Mechanism Research for Major Diseases, Department of Medical GeneticsInstitute of Basic Medical Sciences, Chinese Academy of Medical Sciences, School of Basic Medicine, Peking Union Medical CollegeBeijingChina
| | - Yunjie Liu
- Center for Bioinformatics, School of Life Sciences, Center for Statistical Science, Peking‐Tsinghua Center for Life SciencesPeking UniversityBeijingChina
| | - Jiaqi Hu
- School of Health HumanitiesPeking UniversityBeijingChina
| | - Tingting Li
- State Key Laboratory of ProteomicsInstitute of Basic Medical Sciences, National Center of Biomedical AnalysisBeijingChina
| | - Pengze Wu
- Center for Bioinformatics, School of Life Sciences, Center for Statistical Science, Peking‐Tsinghua Center for Life SciencesPeking UniversityBeijingChina
| | - Meili Zhang
- State Key Laboratory of Common Mechanism Research for Major Diseases, Department of Medical GeneticsInstitute of Basic Medical Sciences, Chinese Academy of Medical Sciences, School of Basic Medicine, Peking Union Medical CollegeBeijingChina
| | - Yue Huang
- State Key Laboratory of Common Mechanism Research for Major Diseases, Department of Medical GeneticsInstitute of Basic Medical Sciences, Chinese Academy of Medical Sciences, School of Basic Medicine, Peking Union Medical CollegeBeijingChina
| | - Yujie Sun
- State Key Laboratory of Membrane Biology, School of Life Sciences, and Biomedical Pioneering Innovation Center (BIOPIC)Peking UniversityBeijingChina
| | - Cheng Li
- Center for Bioinformatics, School of Life Sciences, Center for Statistical Science, Peking‐Tsinghua Center for Life SciencesPeking UniversityBeijingChina
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2
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Braunger JM, Cammarata LV, Sornapudi TR, Uhler C, Shivashankar GV. Transcriptional changes are tightly coupled to chromatin reorganization during cellular aging. Aging Cell 2024; 23:e14056. [PMID: 38062919 PMCID: PMC10928569 DOI: 10.1111/acel.14056] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2023] [Revised: 11/16/2023] [Accepted: 11/17/2023] [Indexed: 12/30/2023] Open
Abstract
Human life expectancy is constantly increasing and aging has become a major risk factor for many diseases, although the underlying gene regulatory mechanisms are still unclear. Using transcriptomic and chromosomal conformation capture (Hi-C) data from human skin fibroblasts from individuals across different age groups, we identified a tight coupling between the changes in co-regulation and co-localization of genes. We obtained transcription factors, cofactors, and chromatin regulators that could drive the cellular aging process by developing a time-course prize-collecting Steiner tree algorithm. In particular, by combining RNA-Seq data from different age groups and protein-protein interaction data we determined the key transcription regulators and gene regulatory changes at different life stage transitions. We then mapped these transcription regulators to the 3D reorganization of chromatin in young and old skin fibroblasts. Collectively, we identified key transcription regulators whose target genes are spatially rearranged and correlate with changes in their expression, thereby providing potential targets for reverting cellular aging.
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Affiliation(s)
- Jana M. Braunger
- Eric and Wendy Schmidt CenterBroad Institute of MIT and HarvardCambridgeMassachusettsUSA
| | - Louis V. Cammarata
- Eric and Wendy Schmidt CenterBroad Institute of MIT and HarvardCambridgeMassachusettsUSA
- Department of StatisticsHarvard UniversityCambridgeMassachusettsUSA
| | | | - Caroline Uhler
- Eric and Wendy Schmidt CenterBroad Institute of MIT and HarvardCambridgeMassachusettsUSA
- Laboratory for Information and Decision SystemsMassachusetts Institute of TechnologyCambridgeMassachusettsUSA
| | - G. V. Shivashankar
- Division of Biology and ChemistryPaul Scherrer InstituteVilligenSwitzerland
- Department of Health Sciences and TechnologyETH ZurichZurichSwitzerland
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3
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Cammarata LV, Uhler C, Shivashankar GV. Adhesome Receptor Clustering is Accompanied by the Colocalization of the Associated Genes in the Cell Nucleus. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.12.07.570697. [PMID: 38106037 PMCID: PMC10723460 DOI: 10.1101/2023.12.07.570697] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/19/2023]
Abstract
Proteins on the cell membrane cluster to respond to extracellular signals; for example, adhesion proteins cluster to enhance extracellular matrix sensing; or T-cell receptors cluster to enhance antigen sensing. Importantly, the maturation of such receptor clusters requires transcriptional control to adapt and reinforce the extracellular signal sensing. However, it has been unclear how such efficient clustering mechanisms are encoded at the level of the genes that code for these receptor proteins. Using the adhesome as an example, we show that genes that code for adhesome receptor proteins are spatially co-localized and co-regulated within the cell nucleus. Towards this, we use Hi-C maps combined with RNA-seq data of adherent cells to map the correspondence between adhesome receptor proteins and their associated genes. Interestingly, we find that the transcription factors that regulate these genes are also co-localized with the adhesome gene loci, thereby potentially facilitating a transcriptional reinforcement of the extracellular matrix sensing machinery. Collectively, our results highlight an important layer of transcriptional control of cellular signal sensing.
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Affiliation(s)
- Louis V. Cammarata
- Department of Statistics, Harvard University, Cambridge, MA 02138, USA
- Eric and Wendy Schmidt Center, Broad Institute of MIT and Harvard, Cambridge, MA 02139, USA
| | - Caroline Uhler
- Eric and Wendy Schmidt Center, Broad Institute of MIT and Harvard, Cambridge, MA 02139, USA
- Laboratory for Information and Decision Systems, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- Institute for Data, Systems, and Society, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - G. V. Shivashankar
- Department of Health Science and Technology, ETH Zurich; Zurich, Switzerland
- Paul Scherrer Institute; Villigen, Switzerland
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4
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Shivashankar GV. Mechanical forces and the 3D genome. Curr Opin Struct Biol 2023; 83:102728. [PMID: 37948897 DOI: 10.1016/j.sbi.2023.102728] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2023] [Revised: 10/09/2023] [Accepted: 10/16/2023] [Indexed: 11/12/2023]
Abstract
Traditionally, the field of genomics has been studied from a biochemical perspective. Besides chemical influences, cells are subject to a variety of mechanical signals from their surrounding tissue microenvironment. These mechanical signals can not only cause changes to a cell's physical structure but can also lead to alterations in their genomes and gene expression programs. Understanding the mechanical control of genome organization and expression may provide a new perspective on gene regulation.
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5
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Bajpai G, Safran S. Mesoscale, long-time mixing of chromosomes and its connection to polymer dynamics. PLoS Comput Biol 2023; 19:e1011142. [PMID: 37228178 DOI: 10.1371/journal.pcbi.1011142] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2022] [Accepted: 05/01/2023] [Indexed: 05/27/2023] Open
Abstract
Chromosomes are arranged in distinct territories within the nucleus of animal cells. Recent experiments have shown that these territories overlap at their edges, suggesting partial mixing during interphase. Experiments that knock-down of condensin II proteins during interphase indicate increased chromosome mixing, which demonstrates control of the mixing. In this study, we use a generic polymer simulation to quantify the dynamics of chromosome mixing over time. We introduce the chromosome mixing index, which quantifies the mixing of distinct chromosomes in the nucleus. We find that the chromosome mixing index in a small confinement volume (as a model of the nucleus), increases as a power-law of the time, with the scaling exponent varying non-monotonically with self-interaction and volume fraction. By comparing the chromosome mixing index with both monomer subdiffusion due to (non-topological) intermingling of chromosomes as well as even slower reptation, we show that for relatively large volume fractions, the scaling exponent of the chromosome mixing index is related to Rouse dynamics for relatively weak chromosome attractions and to reptation for strong attractions. In addition, we extend our model to more realistically account for the situation of the Drosophila chromosome by including the heterogeneity of the polymers and their lengths to account for microphase separation of euchromatin and heterochromatin and their interactions with the nuclear lamina. We find that the interaction with the lamina further impedes chromosome mixing.
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Affiliation(s)
- Gaurav Bajpai
- Department of Chemical and Biological Physics, Weizmann Institute of Science, Rehovot, Israel
| | - Samuel Safran
- Department of Chemical and Biological Physics, Weizmann Institute of Science, Rehovot, Israel
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6
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Shokraneh N, Arab M, Libbrecht M. Integrative chromatin domain annotation through graph embedding of Hi-C data. Bioinformatics 2022; 39:6935783. [PMID: 36534827 PMCID: PMC9848054 DOI: 10.1093/bioinformatics/btac813] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2022] [Revised: 11/02/2022] [Accepted: 12/16/2022] [Indexed: 12/24/2022] Open
Abstract
MOTIVATION The organization of the genome into domains plays a central role in gene expression and other cellular activities. Researchers identify genomic domains mainly through two views: 1D functional assays such as ChIP-seq, and chromatin conformation assays such as Hi-C. Fully understanding domains requires integrative modeling that combines these two views. However, the predominant form of integrative modeling uses segmentation and genome annotation (SAGA) along with the rigid assumption that loci in contact are more likely to share the same domain type, which is not necessarily true for epigenomic domain types and genome-wide chromatin interactions. RESULTS Here, we present an integrative approach that annotates domains using both 1D functional genomic signals and Hi-C measurements of genome-wide 3D interactions without the use of a pairwise prior. We do so by using a graph embedding to learn structural features corresponding to each genomic region, then inputting learned structural features along with functional genomic signals to a SAGA algorithm. We show that our domain types recapitulate well-known subcompartments with an additional granularity that distinguishes a combination of the spatial and functional states of the genomic regions. In particular, we identified a division of the previously identified A2 subcompartment such that the divided domain types have significantly varying expression levels. AVAILABILITY AND IMPLEMENTATION https://github.com/nedashokraneh/IChDA. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Neda Shokraneh
- Computing Science Department, Simon Fraser University, Burnaby V5A 1S6, Canada
| | - Mariam Arab
- Computing Science Department, Simon Fraser University, Burnaby V5A 1S6, Canada
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7
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Gamliel A, Meluzzi D, Oh S, Jiang N, Destici E, Rosenfeld MG, Nair SJ. Long-distance association of topological boundaries through nuclear condensates. Proc Natl Acad Sci U S A 2022; 119:e2206216119. [PMID: 35914133 PMCID: PMC9371644 DOI: 10.1073/pnas.2206216119] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2022] [Accepted: 05/24/2022] [Indexed: 01/09/2023] Open
Abstract
The eukaryotic genome is partitioned into distinct topological domains separated by boundary elements. Emerging data support the concept that several well-established nuclear compartments are ribonucleoprotein condensates assembled through the physical process of phase separation. Here, based on our demonstration that chemical disruption of nuclear condensate assembly weakens the insulation properties of a specific subset (∼20%) of topologically associated domain (TAD) boundaries, we report that the disrupted boundaries are characterized by a high level of transcription and striking spatial clustering. These topological boundary regions tend to be spatially associated, even interchromosomally, segregate with nuclear speckles, and harbor a specific subset of "housekeeping" genes widely expressed in diverse cell types. These observations reveal a previously unappreciated mode of genome organization mediated by conserved boundary elements harboring highly and widely expressed transcription units and associated transcriptional condensates.
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Affiliation(s)
- Amir Gamliel
- Department of Medicine, University of California San Diego, La Jolla, CA 92093
- HHMI, University of California San Diego, La Jolla, CA 92093
| | - Dario Meluzzi
- Department of Medicine, University of California San Diego, La Jolla, CA 92093
- HHMI, University of California San Diego, La Jolla, CA 92093
| | - Soohwan Oh
- Department of Medicine, University of California San Diego, La Jolla, CA 92093
- HHMI, University of California San Diego, La Jolla, CA 92093
| | - Nan Jiang
- Department of Neurosciences, University of California San Diego, La Jolla, CA 92093
| | - Eugin Destici
- Department of Neurosciences, University of California San Diego, La Jolla, CA 92093
| | - Michael G Rosenfeld
- Department of Medicine, University of California San Diego, La Jolla, CA 92093
- HHMI, University of California San Diego, La Jolla, CA 92093
| | - Sreejith J Nair
- Department of Medicine, University of California San Diego, La Jolla, CA 92093
- HHMI, University of California San Diego, La Jolla, CA 92093
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8
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Mora A, Huang X, Jauhari S, Jiang Q, Li X. Chromatin Hubs: A biological and computational outlook. Comput Struct Biotechnol J 2022; 20:3796-3813. [PMID: 35891791 PMCID: PMC9304431 DOI: 10.1016/j.csbj.2022.07.002] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2022] [Revised: 07/02/2022] [Accepted: 07/02/2022] [Indexed: 11/20/2022] Open
Abstract
This review discusses our current understanding of chromatin biology and bioinformatics under the unifying concept of “chromatin hubs.” The first part reviews the biology of chromatin hubs, including chromatin–chromatin interaction hubs, chromatin hubs at the nuclear periphery, hubs around macromolecules such as RNA polymerase or lncRNAs, and hubs around nuclear bodies such as the nucleolus or nuclear speckles. The second part reviews existing computational methods, including enhancer–promoter interaction prediction, network analysis, chromatin domain callers, transcription factory predictors, and multi-way interaction analysis. We introduce an integrated model that makes sense of the existing evidence. Understanding chromatin hubs may allow us (i) to explain long-unsolved biological questions such as interaction specificity and redundancy of mechanisms, (ii) to develop more realistic kinetic and functional predictions, and (iii) to explain the etiology of genomic disease.
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Affiliation(s)
- Antonio Mora
- Joint School of Life Sciences, Guangzhou Medical University and Guangzhou Institutes of Biomedicine and Health (Chinese Academy of Sciences), Guangzhou 511436, PR China
- Corresponding authors.
| | - Xiaowei Huang
- Joint School of Life Sciences, Guangzhou Medical University and Guangzhou Institutes of Biomedicine and Health (Chinese Academy of Sciences), Guangzhou 511436, PR China
| | - Shaurya Jauhari
- Joint School of Life Sciences, Guangzhou Medical University and Guangzhou Institutes of Biomedicine and Health (Chinese Academy of Sciences), Guangzhou 511436, PR China
| | - Qin Jiang
- Affiliated Eye Hospital of Nanjing Medical University, Nanjing 210000, PR China
| | - Xuri Li
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-Sen University, and Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangzhou 510060, PR China
- Corresponding authors.
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9
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Baek J, Lopez PA, Lee S, Kim TS, Kumar S, Schaffer DV. Egr1 is a 3D matrix-specific mediator of mechanosensitive stem cell lineage commitment. SCIENCE ADVANCES 2022; 8:eabm4646. [PMID: 35427160 PMCID: PMC9012469 DOI: 10.1126/sciadv.abm4646] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/20/2021] [Accepted: 02/28/2022] [Indexed: 05/31/2023]
Abstract
While extracellular matrix (ECM) mechanics strongly regulate stem cell commitment, the field's mechanistic understanding of this phenomenon largely derives from simplified two-dimensional (2D) culture substrates. Here, we found a 3D matrix-specific mechanoresponsive mechanism for neural stem cell (NSC) differentiation. NSC lineage commitment in 3D is maximally stiffness sensitive in the range of 0.1 to 1.2 kPa, a narrower and more brain-mimetic range than we had previously identified in 2D (0.75 to 75 kPa). Transcriptomics revealed stiffness-dependent up-regulation of early growth response 1 (Egr1) in 3D but not in 2D. Egr1 knockdown enhanced neurogenesis in stiff ECMs by driving β-catenin nuclear localization and activity in 3D, but not in 2D. Mechanical modeling and experimental studies under osmotic pressure indicate that stiff 3D ECMs are likely to stimulate Egr1 via increases in confining stress during cell volumetric growth. To our knowledge, Egr1 represents the first 3D-specific stem cell mechanoregulatory factor.
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Affiliation(s)
- Jieung Baek
- Department of Bioengineering, University of California, Berkeley, Berkeley, CA 94720, USA
- Department of Chemical and Biomolecular Engineering, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Paola A. Lopez
- Department of Bioengineering, University of California, Berkeley, Berkeley, CA 94720, USA
- UC Berkeley–UC San Francisco Graduate Program in Bioengineering, Berkeley, CA 94720, USA
| | - Sangmin Lee
- Department of Mechanical Engineering, KAIST, 291 Daehak-ro, Yuseong-gu, Daejeon 34141, Republic of Korea
| | - Taek-Soo Kim
- Department of Mechanical Engineering, KAIST, 291 Daehak-ro, Yuseong-gu, Daejeon 34141, Republic of Korea
| | - Sanjay Kumar
- Department of Bioengineering, University of California, Berkeley, Berkeley, CA 94720, USA
- Department of Chemical and Biomolecular Engineering, University of California, Berkeley, Berkeley, CA 94720, USA
- UC Berkeley–UC San Francisco Graduate Program in Bioengineering, Berkeley, CA 94720, USA
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, CA 94158, USA
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - David V. Schaffer
- Department of Bioengineering, University of California, Berkeley, Berkeley, CA 94720, USA
- Department of Chemical and Biomolecular Engineering, University of California, Berkeley, Berkeley, CA 94720, USA
- UC Berkeley–UC San Francisco Graduate Program in Bioengineering, Berkeley, CA 94720, USA
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
- Helen Wills Neuroscience Institute, Berkeley, CA 94720, USA
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Cytogenomic Characterization of Giant Ring or Rod Marker Chromosome in Four Cases of Well-Differentiated and Dedifferentiated Liposarcoma. Case Rep Genet 2022; 2022:6341207. [PMID: 35450197 PMCID: PMC9018199 DOI: 10.1155/2022/6341207] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2021] [Accepted: 03/31/2022] [Indexed: 12/03/2022] Open
Abstract
Chromosome and array comparative genomic hybridization (aCGH) analyses were performed on two cases of well-differentiated liposarcoma (WDLPS) and two cases of dedifferentiated liposarcoma (DDLPS). The results revealed the characteristic giant ring (GR) or giant rod marker (GRM) chromosomes in all four cases and amplification of numerous somatic copy number alterations (SCNAs) involving a core segment of 12q14.1q15 and other chromosomal regions in three cases. The levels of amplification for oncogenes OS9, CDK4, HMGA2, NUP107, MDM2, YEATS4, and FRS2 at the core segment or other SCNAs should be characterized to facilitate pathologic correlation and prognostic prediction. Further studies for the initial cellular crisis event affecting chromosome intermingling regions for cell-type specific gene regulation may reveal the underlying mutagenesis mechanism for GR and GRM in WDLPS and DDLPS.
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11
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Amar K, Wei F, Chen J, Wang N. Effects of forces on chromatin. APL Bioeng 2021; 5:041503. [PMID: 34661040 PMCID: PMC8516479 DOI: 10.1063/5.0065302] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2021] [Accepted: 09/27/2021] [Indexed: 12/29/2022] Open
Abstract
Chromatin is a unique structure of DNA and histone proteins in the cell nucleus and the site of dynamic regulation of gene expression. Soluble factors are known to affect the chromatin structure and function via activating or inhibiting specific transcription factors. Forces on chromatin come from exogenous stresses on the cell surface and/or endogenous stresses, which are regulated by substrate mechanics, geometry, and topology. Forces on chromatin involve direct (via adhesion molecules, cytoskeleton, and the linker of nucleoskeleton and cytoskeleton complexes) and indirect (via diffusion and/or translocation processes) signaling pathways to modulate levels of chromatin folding and deformation to regulate transcription, which is controlled by histone modifications and depends on magnitude, direction, rate/frequency, duration, and modes of stresses. The rapid force transmission pathway activates multiple genes simultaneously, and the force may act like a "supertranscription factor." The indirect mechanotransduction pathways and the rapid force transmission pathway together exert sustained impacts on the chromatin, the nucleus, and cell functions.
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Affiliation(s)
- Kshitij Amar
- Department of Mechanical Science and Engineering, The Grainger College of Engineering, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
| | - Fuxiang Wei
- Key Laboratory of Molecular Biophysics of the Ministry of Education, Department of Biomedical Engineering, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei 430074, China
| | - Junwei Chen
- Key Laboratory of Molecular Biophysics of the Ministry of Education, Department of Biomedical Engineering, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei 430074, China
| | - Ning Wang
- Department of Mechanical Science and Engineering, The Grainger College of Engineering, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
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12
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MacPhillamy C, Pitchford WS, Alinejad-Rokny H, Low WY. Opportunity to improve livestock traits using 3D genomics. Anim Genet 2021; 52:785-798. [PMID: 34494283 DOI: 10.1111/age.13135] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/24/2021] [Indexed: 11/30/2022]
Abstract
The advent of high-throughput chromosome conformation capture and sequencing (Hi-C) has enabled researchers to probe the 3D architecture of the mammalian genome in a genome-wide manner. Simultaneously, advances in epigenomic assays, such as chromatin immunoprecipitation and sequencing (ChIP-seq) and DNase-seq, have enabled researchers to study cis-regulatory interactions and chromatin accessibility across the same genome-wide scale. The use of these data has revealed many unique insights into gene regulation and disease pathomechanisms in several model organisms. With the advent of these high-throughput sequencing technologies, there has been an ever-increasing number of datasets available for study; however, this is often limited to model organisms. Livestock species play critical roles in the economies of developing and developed nations alike. Despite this, they are greatly underrepresented in the 3D genomics space; Hi-C and related technologies have the potential to revolutionise livestock breeding by enabling a more comprehensive understanding of how production traits are controlled. The growth in human and model organism Hi-C data has seen a surge in the availability of computational tools for use in 3D genomics, with some tools using machine learning techniques to predict features and improve dataset quality. In this review, we provide an overview of the 3D genome and discuss the status of 3D genomics in livestock before delving into advancing the field by drawing inspiration from research in human and mouse. We end by offering future directions for livestock research in the field of 3D genomics.
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Affiliation(s)
- C MacPhillamy
- Davies Livestock Research Centre, The University of Adelaide, Roseworthy Campus, Mudla Wirra Rd, Roseworthy, SA, 5371, Australia
| | - W S Pitchford
- Davies Livestock Research Centre, The University of Adelaide, Roseworthy Campus, Mudla Wirra Rd, Roseworthy, SA, 5371, Australia
| | - H Alinejad-Rokny
- Biological & Medical Machine Learning Lab, The Graduate School of Biomedical Engineering, UNSW Sydney, Sydney, NSW, 2052, Australia.,School of Computer Science and Engineering, The University of New South Wales (UNSW Sydney), Sydney, NSW, 2052, Australia
| | - W Y Low
- Davies Livestock Research Centre, The University of Adelaide, Roseworthy Campus, Mudla Wirra Rd, Roseworthy, SA, 5371, Australia
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13
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Peter M, Aschauer DF, Rose R, Sinning A, Grössl F, Kargl D, Kraitsy K, Burkard TR, Luhmann HJ, Haubensak W, Rumpel S. Rapid nucleus-scale reorganization of chromatin in neurons enables transcriptional adaptation for memory consolidation. PLoS One 2021; 16:e0244038. [PMID: 33951054 PMCID: PMC8099114 DOI: 10.1371/journal.pone.0244038] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Accepted: 03/05/2021] [Indexed: 12/27/2022] Open
Abstract
The interphase nucleus is functionally organized in active and repressed territories defining the transcriptional status of the cell. However, it remains poorly understood how the nuclear architecture of neurons adapts in response to behaviorally relevant stimuli that trigger fast alterations in gene expression patterns. Imaging of fluorescently tagged nucleosomes revealed that pharmacological manipulation of neuronal activity in vitro and auditory cued fear conditioning in vivo induce nucleus-scale restructuring of chromatin within minutes. Furthermore, the acquisition of auditory fear memory is impaired after infusion of a drug into auditory cortex which blocks chromatin reorganization in vitro. We propose that active chromatin movements at the nucleus scale act together with local gene-specific modifications to enable transcriptional adaptations at fast time scales. Introducing a transgenic mouse line for photolabeling of histones, we extend the realm of systems available for imaging of chromatin dynamics to living animals.
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Affiliation(s)
- Manuel Peter
- Research Institute of Molecular Pathology, Vienna Biocenter, Vienna, Austria
| | - Dominik F. Aschauer
- Research Institute of Molecular Pathology, Vienna Biocenter, Vienna, Austria
- Institute of Physiology, Focus Program Translational Neurosciences, University Medical Center, Johannes-Gutenberg University, Mainz, Germany
| | - Renata Rose
- Institute of Physiology, Focus Program Translational Neurosciences, University Medical Center, Johannes-Gutenberg University, Mainz, Germany
| | - Anne Sinning
- Institute of Physiology, Focus Program Translational Neurosciences, University Medical Center, Johannes-Gutenberg University, Mainz, Germany
| | - Florian Grössl
- Research Institute of Molecular Pathology, Vienna Biocenter, Vienna, Austria
| | - Dominic Kargl
- Research Institute of Molecular Pathology, Vienna Biocenter, Vienna, Austria
| | - Klaus Kraitsy
- Research Institute of Molecular Pathology, Vienna Biocenter, Vienna, Austria
- Preclinical Phenotyping, Vienna Biocenter Core Facilities, Vienna, Austria
| | - Thomas R. Burkard
- Research Institute of Molecular Pathology, Vienna Biocenter, Vienna, Austria
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences, Vienna Biocenter, Vienna, Austria
| | - Heiko J. Luhmann
- Institute of Physiology, Focus Program Translational Neurosciences, University Medical Center, Johannes-Gutenberg University, Mainz, Germany
| | - Wulf Haubensak
- Research Institute of Molecular Pathology, Vienna Biocenter, Vienna, Austria
| | - Simon Rumpel
- Institute of Physiology, Focus Program Translational Neurosciences, University Medical Center, Johannes-Gutenberg University, Mainz, Germany
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Evers TMJ, Holt LJ, Alberti S, Mashaghi A. Reciprocal regulation of cellular mechanics and metabolism. Nat Metab 2021; 3:456-468. [PMID: 33875882 PMCID: PMC8863344 DOI: 10.1038/s42255-021-00384-w] [Citation(s) in RCA: 38] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/24/2020] [Accepted: 03/12/2021] [Indexed: 12/12/2022]
Abstract
Metabolism and mechanics are intrinsically intertwined. External forces, sensed through the cytoskeleton or distortion of the cell and organelles, induce metabolic changes in the cell. The resulting changes in metabolism, in turn, feed back to regulate every level of cell biology, including the mechanical properties of cells and tissues. Here we examine the links between metabolism and mechanics, highlighting signalling pathways involved in the regulation and response to cellular mechanosensing. We consider how forces and metabolism regulate one another through nanoscale molecular sensors, micrometre-scale cytoskeletal networks, organelles and dynamic biomolecular condensates. Understanding this cross-talk will create diagnostic and therapeutic opportunities for metabolic disorders such as cancer, cardiovascular pathologies and obesity.
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Affiliation(s)
- Tom M J Evers
- Medical Systems Biophysics and Bioengineering, Leiden Academic Centre for Drug Research, Faculty of Science, Leiden University, Leiden, the Netherlands
| | - Liam J Holt
- Institute for Systems Genetics, New York University Langone Health, New York, NY, USA
| | - Simon Alberti
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
| | - Alireza Mashaghi
- Medical Systems Biophysics and Bioengineering, Leiden Academic Centre for Drug Research, Faculty of Science, Leiden University, Leiden, the Netherlands.
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15
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Lezcano ÓM, Sánchez-Polo M, Ruiz JL, Gómez-Díaz E. Chromatin Structure and Function in Mosquitoes. Front Genet 2020; 11:602949. [PMID: 33365050 PMCID: PMC7750206 DOI: 10.3389/fgene.2020.602949] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2020] [Accepted: 10/29/2020] [Indexed: 12/27/2022] Open
Abstract
The principles and function of chromatin and nuclear architecture have been extensively studied in model organisms, such as Drosophila melanogaster. However, little is known about the role of these epigenetic processes in transcriptional regulation in other insects including mosquitoes, which are major disease vectors and a worldwide threat for human health. Some of these life-threatening diseases are malaria, which is caused by protozoan parasites of the genus Plasmodium and transmitted by Anopheles mosquitoes; dengue fever, which is caused by an arbovirus mainly transmitted by Aedes aegypti; and West Nile fever, which is caused by an arbovirus transmitted by Culex spp. In this contribution, we review what is known about chromatin-associated mechanisms and the 3D genome structure in various mosquito vectors, including Anopheles, Aedes, and Culex spp. We also discuss the similarities between epigenetic mechanisms in mosquitoes and the model organism Drosophila melanogaster, and advocate that the field could benefit from the cross-application of state-of-the-art functional genomic technologies that are well-developed in the fruit fly. Uncovering the mosquito regulatory genome can lead to the discovery of unique regulatory networks associated with the parasitic life-style of these insects. It is also critical to understand the molecular interactions between the vectors and the pathogens that they transmit, which could hold the key to major breakthroughs on the fight against mosquito-borne diseases. Finally, it is clear that epigenetic mechanisms controlling mosquito environmental plasticity and evolvability are also of utmost importance, particularly in the current context of globalization and climate change.
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Affiliation(s)
| | | | - José L. Ruiz
- Instituto de Parasitología y Biomedicina López-Neyra (IPBLN), Consejo Superior de Investigaciones Científicas, Granada, Spain
| | - Elena Gómez-Díaz
- Instituto de Parasitología y Biomedicina López-Neyra (IPBLN), Consejo Superior de Investigaciones Científicas, Granada, Spain
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16
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Corvaisier M, Alvarado-Kristensson M. Non-Canonical Functions of the Gamma-Tubulin Meshwork in the Regulation of the Nuclear Architecture. Cancers (Basel) 2020; 12:cancers12113102. [PMID: 33114224 PMCID: PMC7690915 DOI: 10.3390/cancers12113102] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2020] [Revised: 10/17/2020] [Accepted: 10/21/2020] [Indexed: 12/15/2022] Open
Abstract
Simple Summary The appearance of a cell is connected to its function. For example, the fusiform of smooth muscle cells is adapted to facilitate muscle contraction, the lobed nucleus in white blood cells assists with the migratory behavior of these immune cells, and the condensed nucleus in sperm aids in their swimming efficiency. Thus, changes in appearance have been used for decades by doctors as a diagnostic method for human cancers. Here, we summarize our knowledge of how a cell maintains the shape of the nuclear compartment. Specifically, we discuss the role of a novel protein meshwork, the gamma-tubulin meshwork, in the regulation of nuclear morphology and as a therapeutic target against cancer. Abstract The nuclear architecture describes the organization of the various compartments in the nucleus of eukaryotic cells, where a plethora of processes such as nucleocytoplasmic transport, gene expression, and assembly of ribosomal subunits occur in a dynamic manner. During the different phases of the cell cycle, in post-mitotic cells and after oncogenic transformation, rearrangements of the nuclear architecture take place, and, among other things, these alterations result in reorganization of the chromatin and changes in gene expression. A member of the tubulin family, γtubulin, was first identified as part of a multiprotein complex that allows nucleation of microtubules. However, more than a decade ago, γtubulin was also characterized as a nuclear protein that modulates several crucial processes that affect the architecture of the nucleus. This review presents the latest knowledge regarding changes that arise in the nuclear architecture of healthy cells and under pathological conditions and, more specifically, considers the particular involvement of γtubulin in the modulation of the biology of the nuclear compartment.
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17
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Salem NA, Mahnke AH, Wells AB, Tseng AM, Yevtushok L, Zymak-Zakutnya N, Wertlecki W, Chambers CD, Miranda RC. Association between fetal sex and maternal plasma microRNA responses to prenatal alcohol exposure: evidence from a birth outcome-stratified cohort. Biol Sex Differ 2020; 11:51. [PMID: 32912312 PMCID: PMC7488011 DOI: 10.1186/s13293-020-00327-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/04/2020] [Accepted: 08/25/2020] [Indexed: 12/14/2022] Open
Abstract
Most persons with fetal alcohol spectrum disorders (FASDs) remain undiagnosed or are diagnosed in later life. To address the need for earlier diagnosis, we previously assessed miRNAs in the blood plasma of pregnant women who were classified as unexposed to alcohol (UE), heavily exposed with affected infants (HEa), or heavily exposed with apparently unaffected infants (HEua). We reported that maternal miRNAs predicted FASD-related growth and psychomotor deficits in infants. Here, we assessed whether fetal sex influenced alterations in maternal circulating miRNAs following prenatal alcohol exposure (PAE). To overcome the loss of statistical power due to disaggregating maternal samples by fetal sex, we adapted a strategy of iterative bootstrap resampling with replacement to assess the stability of statistical parameter estimates. Bootstrap estimates of parametric and effect size tests identified male and female fetal sex-associated maternal miRNA responses to PAE that were not observed in the aggregated sample. Additionally, we observed, in HEa mothers of female, but not male fetuses, a network of co-secreted miRNAs whose expression was linked to miRNAs encoded on the X-chromosome. Interestingly, the number of significant miRNA correlations for the HEua group mothers with female fetuses was intermediate between HEa and UE mothers at mid-pregnancy, but more similar to UE mothers by the end of pregnancy. Collectively, these data show that fetal sex predicts maternal circulating miRNA adaptations, a critical consideration when adopting maternal miRNAs as diagnostic biomarkers. Moreover, a maternal co-secretion network, predominantly in pregnancies with female fetuses, emerged as an index of risk for adverse birth outcomes due to PAE.
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Affiliation(s)
- Nihal A Salem
- Department of Neuroscience and Experimental Therapeutics, College of Medicine, Medical Research and Education Bldg., Texas A&M University Health Science Center, 8447 Riverside Parkway, Bryan, TX, 77807-3260, USA.,Texas A&M Institute for Neuroscience, Texas A&M University, College Station, TX, USA
| | - Amanda H Mahnke
- Department of Neuroscience and Experimental Therapeutics, College of Medicine, Medical Research and Education Bldg., Texas A&M University Health Science Center, 8447 Riverside Parkway, Bryan, TX, 77807-3260, USA.,Women's Health in Neuroscience Program, Texas A&M University Health Science Center, Bryan, TX, USA
| | - Alan B Wells
- Clinical and Translational Research Institute, University of California San Diego, San Diego, CA, USA.,Department of Pediatrics, University of California San Diego, 9500 Gilman Drive MC 0828, La Jolla, San Diego, CA, 92093, USA
| | - Alexander M Tseng
- Department of Neuroscience and Experimental Therapeutics, College of Medicine, Medical Research and Education Bldg., Texas A&M University Health Science Center, 8447 Riverside Parkway, Bryan, TX, 77807-3260, USA
| | - Lyubov Yevtushok
- Rivne Regional Medical Diagnostic Center, Rivne, Ukraine.,Lviv National Medical University, Lviv, Ukraine.,OMNI-Net Ukraine Birth Defects Program, Rivne, Ukraine
| | - Natalya Zymak-Zakutnya
- OMNI-Net Ukraine Birth Defects Program, Rivne, Ukraine.,Khmelnytsky Perinatal Center, Khmelnytsky, Ukraine
| | - Wladimir Wertlecki
- Department of Pediatrics, University of California San Diego, 9500 Gilman Drive MC 0828, La Jolla, San Diego, CA, 92093, USA.,OMNI-Net Ukraine Birth Defects Program, Rivne, Ukraine
| | - Christina D Chambers
- Clinical and Translational Research Institute, University of California San Diego, San Diego, CA, USA. .,Department of Pediatrics, University of California San Diego, 9500 Gilman Drive MC 0828, La Jolla, San Diego, CA, 92093, USA.
| | - Rajesh C Miranda
- Department of Neuroscience and Experimental Therapeutics, College of Medicine, Medical Research and Education Bldg., Texas A&M University Health Science Center, 8447 Riverside Parkway, Bryan, TX, 77807-3260, USA. .,Texas A&M Institute for Neuroscience, Texas A&M University, College Station, TX, USA. .,Women's Health in Neuroscience Program, Texas A&M University Health Science Center, Bryan, TX, USA.
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18
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Sandoval-Velasco M, Rodríguez JA, Perez Estrada C, Zhang G, Lieberman Aiden E, Marti-Renom MA, Gilbert MTP, Smith O. Hi-C chromosome conformation capture sequencing of avian genomes using the BGISEQ-500 platform. Gigascience 2020; 9:giaa087. [PMID: 32845983 PMCID: PMC7448675 DOI: 10.1093/gigascience/giaa087] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2020] [Revised: 06/15/2020] [Accepted: 07/23/2020] [Indexed: 01/23/2023] Open
Abstract
BACKGROUND Hi-C experiments couple DNA-DNA proximity with next-generation sequencing to yield an unbiased description of genome-wide interactions. Previous methods describing Hi-C experiments have focused on the industry-standard Illumina sequencing. With new next-generation sequencing platforms such as BGISEQ-500 becoming more widely available, protocol adaptations to fit platform-specific requirements are useful to give increased choice to researchers who routinely generate sequencing data. RESULTS We describe an in situ Hi-C protocol adapted to be compatible with the BGISEQ-500 high-throughput sequencing platform. Using zebra finch (Taeniopygia guttata) as a biological sample, we demonstrate how Hi-C libraries can be constructed to generate informative data using the BGISEQ-500 platform, following circularization and DNA nanoball generation. Our protocol is a modification of an Illumina-compatible method, based around blunt-end ligations in library construction, using un-barcoded, distally overhanging double-stranded adapters, followed by amplification using indexed primers. The resulting libraries are ready for circularization and subsequent sequencing on the BGISEQ series of platforms and yield data similar to what can be expected using Illumina-compatible approaches. CONCLUSIONS Our straightforward modification to an Illumina-compatible in situHi-C protocol enables data generation on the BGISEQ series of platforms, thus expanding the options available for researchers who wish to utilize the powerful Hi-C techniques in their research.
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Affiliation(s)
- Marcela Sandoval-Velasco
- Section for Evolutionary Genomics, The GLOBE Institute, University of Copenhagen, Øster Farimagsgade 5A, 1353 Copenhagen, Denmark
| | - Juan Antonio Rodríguez
- CNAG-CRG, Centre for Genomic Regulation, Barcelona Institute of Science and Technology, Baldiri i Reixach, 4-8, 08028 Barcelona, Spain
| | - Cynthia Perez Estrada
- Center for Genome Architecture, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Guojie Zhang
- China National GeneBank, BGI-Shenzhen, Shenzhen 518083, China
| | - Erez Lieberman Aiden
- Center for Genome Architecture, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
- Center for Theoretical Biological Physics, Rice University, Houston, TX 77005, USA
- Broad Institute of the Massachusetts Institute of Technology and Harvard University, Cambridge, MA, USA
- Department of Computer Science and Computational Applied Mathematics, Rice University, 6100 Main St, Houston, TX 77005-1827, USA
| | - Marc A Marti-Renom
- CNAG-CRG, Centre for Genomic Regulation, Barcelona Institute of Science and Technology, Baldiri i Reixach, 4-8, 08028 Barcelona, Spain
- Centre for Genomic Regulation, Barcelona Institute for Science and Technology, Doctor Aiguader 88, Barcelona 08003, Spain
- Pompeu Fabra University, Doctor Aiguader 88, Barcelona 08003, Spain
- ICREA, Pg. Lluís Companys 23, 08010 Barcelona, Spain
| | - M Thomas P Gilbert
- Section for Evolutionary Genomics, The GLOBE Institute, University of Copenhagen, Øster Farimagsgade 5A, 1353 Copenhagen, Denmark
- Norwegian University of Science and Technology, University Museum, 7491 Trondheim, Norway
| | - Oliver Smith
- Section for Evolutionary Genomics, The GLOBE Institute, University of Copenhagen, Øster Farimagsgade 5A, 1353 Copenhagen, Denmark
- Micropathology Ltd, University of Warwick Science Park, Coventry CV4 7EZ, UK
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19
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IGAP-integrative genome analysis pipeline reveals new gene regulatory model associated with nonspecific TF-DNA binding affinity. Comput Struct Biotechnol J 2020; 18:1270-1286. [PMID: 32612751 PMCID: PMC7303559 DOI: 10.1016/j.csbj.2020.05.024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2020] [Revised: 05/17/2020] [Accepted: 05/19/2020] [Indexed: 11/23/2022] Open
Abstract
The human genome is regulated in a multi-dimensional way. While biophysical factors like Non-specific Transcription factor Binding Affinity (nTBA) act at DNA sequence level, other factors act above sequence levels such as histone modifications and 3-D chromosomal interactions. This multidimensionality of regulation requires many of these factors for a proper understanding of the regulatory landscape of the human genome. Here, we propose a new biophysical model for estimating nTBA. Integration of nTBA with chromatin modifications and chromosomal interactions, using a new Integrative Genome Analysis Pipeline (IGAP), reveals additive effects of nTBA to regulatory DNA sequences and identifies three types of genomic zones in the human genome (Inactive Genomic Zones, Poised Genomic Zones, and Active Genomic Zones). It also unveils a novel long distance gene regulatory model: chromosomal interactions reduce the physical distance between the high occupancy target (HOT) regions that results in high nTBA to DNA in the area, which in turn attract TFs to such regions with higher binding potential. These findings will help to elucidate the three-dimensional diffusion process that TFs use during their search for the right targets.
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20
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Yang KD, Damodaran K, Venkatachalapathy S, Soylemezoglu AC, Shivashankar GV, Uhler C. Predicting cell lineages using autoencoders and optimal transport. PLoS Comput Biol 2020; 16:e1007828. [PMID: 32343706 PMCID: PMC7209334 DOI: 10.1371/journal.pcbi.1007828] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2019] [Revised: 05/08/2020] [Accepted: 03/27/2020] [Indexed: 12/17/2022] Open
Abstract
Lineage tracing involves the identification of all ancestors and descendants of a given cell, and is an important tool for studying biological processes such as development and disease progression. However, in many settings, controlled time-course experiments are not feasible, for example when working with tissue samples from patients. Here we present ImageAEOT, a computational pipeline based on autoencoders and optimal transport for predicting the lineages of cells using time-labeled datasets from different stages of a cellular process. Given a single-cell image from one of the stages, ImageAEOT generates an artificial lineage of this cell based on the population characteristics of the other stages. These lineages can be used to connect subpopulations of cells through the different stages and identify image-based features and biomarkers underlying the biological process. To validate our method, we apply ImageAEOT to a benchmark task based on nuclear and chromatin images during the activation of fibroblasts by tumor cells in engineered 3D tissues. We further validate ImageAEOT on chromatin images of various breast cancer cell lines and human tissue samples, thereby linking alterations in chromatin condensation patterns to different stages of tumor progression. Our results demonstrate the promise of computational methods based on autoencoding and optimal transport principles for lineage tracing in settings where existing experimental strategies cannot be used. Many key biological processes, such as development and disease progression, require analyzing lineages of cells backwards as well as forwards in time. However, current single-cell experiments tend to be destructive to cells, so that a single lineage can only be measured at one point in time. In this work, we introduce a computational framework for predicting the lineage of cells from a single snapshot in time based on measurements of other cells at other time points. The method generates these lineages by computing the most plausible path for a population of cells to transition from one time point to the next, assuming that a cell is more likely to transition to similar cells compared to dissimilar cells. We validate our computational method on imaging data of fibroblasts and cancer cells, though our method could also be applied to other modalities of single-cell data such as genomics and transcriptomics as well as multi-modal single-cell datasets.
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Affiliation(s)
- Karren Dai Yang
- Institute for Data, Systems and Society, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
- Department of Electrical Engineering & Computer Science, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
| | - Karthik Damodaran
- Mechanobiology Institute, National University of Singapore, Singapore
| | | | - Ali C. Soylemezoglu
- Institute for Data, Systems and Society, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
| | - G. V. Shivashankar
- Mechanobiology Institute, National University of Singapore, Singapore
- FIRC Institute of Molecular Oncology (IFOM), Milan, Italy
- Department of Health Sciences and Technology, ETH Zurich and Paul Scherrer Institute, Villigen, Switzerland
| | - Caroline Uhler
- Institute for Data, Systems and Society, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
- Department of Electrical Engineering & Computer Science, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
- Department of Biosystems Science and Engineering, ETH Zurich, Zurich, Switzerland
- * E-mail:
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21
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Sun J, Chen J, Mohagheghian E, Wang N. Force-induced gene up-regulation does not follow the weak power law but depends on H3K9 demethylation. SCIENCE ADVANCES 2020; 6:eaay9095. [PMID: 32270037 PMCID: PMC7112933 DOI: 10.1126/sciadv.aay9095] [Citation(s) in RCA: 40] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/28/2019] [Accepted: 01/08/2020] [Indexed: 05/25/2023]
Abstract
Mechanical forces play important roles in development, physiology, and diseases, but how force is transduced into gene transcription remains elusive. Here, we show that transcription of transgene DHFR or endogenous genes egr-1 and Cav1 is rapidly up-regulated in response to cyclic forces applied via integrins at low frequencies but not at 100 Hz. Gene up-regulation does not follow the weak power law with force frequency. Force-induced transcription up-regulation at the nuclear interior is associated with demethylation of histone H3 lysine-9 trimethylation (H3K9me3), whereas no transcription up-regulation near the nuclear periphery is associated with H3K9me3 that inhibits Pol II recruitment to the promoter site. H3K9me3 demethylation induces Pol II recruitment and increases force-induced transcription of egr-1 and Cav1 at the nuclear interior and activates mechano-nonresponsive gene FKBP5 near the nuclear periphery, whereas H3K9me3 hypermethylation has opposite effects. Our findings demonstrate that rapid up-regulation of endogenous mechanoresponsive genes depends on H3K9me3 demethylation.
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Affiliation(s)
- Jian Sun
- Department of Mechanical Science and Engineering, The Grainger College of Engineering, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Junwei Chen
- Department of Mechanical Science and Engineering, The Grainger College of Engineering, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
- Laboratory for Cellular Biomechanics and Regenerative Medicine, Department of Biomedical Engineering, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei 430074, China
| | - Erfan Mohagheghian
- Department of Mechanical Science and Engineering, The Grainger College of Engineering, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Ning Wang
- Department of Mechanical Science and Engineering, The Grainger College of Engineering, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
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22
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Venkatachalapathy S, Jokhun DS, Shivashankar GV. Multivariate analysis reveals activation-primed fibroblast geometric states in engineered 3D tumor microenvironments. Mol Biol Cell 2020; 31:803-812. [PMID: 32023167 PMCID: PMC7185960 DOI: 10.1091/mbc.e19-08-0420] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Fibroblasts are a heterogeneous group of cells comprising subpopulations that have been found to be activated in the stromal microenvironment that regulates tumor initiation and growth. The underlying mechanisms of such selective activation of fibroblasts are not understood. We propose that the intrinsic geometric heterogeneity of fibroblasts modulates the nuclear mechanotransduction of signals from the microenvironment, resulting in their selective activation. To test this, we developed an engineered 3D fibroblast tumor coculture system and used high resolution images to quantify multiple cell geometry sensitive nuclear morphological and chromatin organizational features. These features were then mapped to activation levels as measured by the nuclear abundance of transcription cofactor, megakaryoblastic leukemia, and protein levels of its target, αSMA. Importantly, our results indicate the presence of activation-“primed” cell geometries that present higher activation levels, which are further enhanced in the presence of stimuli from cancer cells. Further, we show that by enriching the population of activation-primed cell geometric states by either increasing matrix rigidity or micropatterning primed cell shapes, fibroblast activation levels can be increased. Collectively, our results reveal important cellular geometric states that select for fibroblast activation within the heterogenous tumor microenvironment.
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Affiliation(s)
- Saradha Venkatachalapathy
- Mechanobiology Institute and Department of Biological Sciences, National University of Singapore, 117411, Singapore
| | - Doorgesh Sharma Jokhun
- Mechanobiology Institute and Department of Biological Sciences, National University of Singapore, 117411, Singapore
| | - G V Shivashankar
- Mechanobiology Institute and Department of Biological Sciences, National University of Singapore, 117411, Singapore.,FIRC Institute for Molecular Oncology, Milan 20139, Italy.,Department of Health Sciences and Technology, ETH Zurich, Zurich, Switzerland.,Paul Scherrer Institut, 5232 Villigen, Switzerland
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23
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George P, Kinney NA, Liang J, Onufriev AV, Sharakhov IV. Three-dimensional Organization of Polytene Chromosomes in Somatic and Germline Tissues of Malaria Mosquitoes. Cells 2020; 9:cells9020339. [PMID: 32024176 PMCID: PMC7072178 DOI: 10.3390/cells9020339] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2019] [Revised: 01/22/2020] [Accepted: 01/28/2020] [Indexed: 12/17/2022] Open
Abstract
Spatial organization of chromosome territories and interactions between interphase chromosomes themselves, as well as with the nuclear periphery, play important roles in epigenetic regulation of the genome function. However, the interplay between inter-chromosomal contacts and chromosome-nuclear envelope attachments in an organism’s development is not well-understood. To address this question, we conducted microscopic analyses of the three-dimensional chromosome organization in malaria mosquitoes. We employed multi-colored oligonucleotide painting probes, spaced 1 Mb apart along the euchromatin, to quantitatively study chromosome territories in larval salivary gland cells and adult ovarian nurse cells of Anopheles gambiae, An. coluzzii, and An. merus. We found that the X chromosome territory has a significantly smaller volume and is more compact than the autosomal arm territories. The number of inter-chromosomal, and the percentage of the chromosome–nuclear envelope, contacts were conserved among the species within the same cell type. However, the percentage of chromosome regions located at the nuclear periphery was typically higher, while the number of inter-chromosomal contacts was lower, in salivary gland cells than in ovarian nurse cells. The inverse correlation was considerably stronger for the autosomes. Consistent with previous theoretical arguments, our data indicate that, at the genome-wide level, there is an inverse relationship between chromosome-nuclear envelope attachments and chromosome–chromosome interactions, which is a key feature of the cell type-specific nuclear architecture.
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Affiliation(s)
- Phillip George
- Department of Entomology, Virginia Tech, Blacksburg, VA 24061, USA; (P.G.); (J.L.)
| | - Nicholas A. Kinney
- Genomics, Bioinformatics and Computational Biology, Virginia Tech, Blacksburg, VA 24061, USA; (N.A.K.); (A.V.O.)
| | - Jiangtao Liang
- Department of Entomology, Virginia Tech, Blacksburg, VA 24061, USA; (P.G.); (J.L.)
| | - Alexey V. Onufriev
- Genomics, Bioinformatics and Computational Biology, Virginia Tech, Blacksburg, VA 24061, USA; (N.A.K.); (A.V.O.)
- Department of Computer Science, Virginia Tech, Blacksburg, VA 24061, USA
| | - Igor V. Sharakhov
- Department of Entomology, Virginia Tech, Blacksburg, VA 24061, USA; (P.G.); (J.L.)
- Genomics, Bioinformatics and Computational Biology, Virginia Tech, Blacksburg, VA 24061, USA; (N.A.K.); (A.V.O.)
- Department of Cytology and Genetics, Tomsk State University, 634050 Tomsk, Russian Federation
- Correspondence: ; Tel.: +1-540-231-7316
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24
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Tian D, Zhang R, Zhang Y, Zhu X, Ma J. MOCHI enables discovery of heterogeneous interactome modules in 3D nucleome. Genome Res 2020; 30:227-238. [PMID: 31907193 PMCID: PMC7050518 DOI: 10.1101/gr.250316.119] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2019] [Accepted: 01/02/2020] [Indexed: 11/24/2022]
Abstract
The composition of the cell nucleus is highly heterogeneous, with different constituents forming complex interactomes. However, the global patterns of these interwoven heterogeneous interactomes remain poorly understood. Here we focus on two different interactomes, chromatin interaction network and gene regulatory network, as a proof of principle to identify heterogeneous interactome modules (HIMs), each of which represents a cluster of gene loci that is in spatial contact more frequently than expected and that is regulated by the same group of transcription factors. HIM integrates transcription factor binding and 3D genome structure to reflect “transcriptional niche” in the nucleus. We develop a new algorithm, MOCHI, to facilitate the discovery of HIMs based on network motif clustering in heterogeneous interactomes. By applying MOCHI to five different cell types, we found that HIMs have strong spatial preference within the nucleus and show distinct functional properties. Through integrative analysis, this work shows the utility of MOCHI to identify HIMs, which may provide new perspectives on the interplay between transcriptional regulation and 3D genome organization.
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Affiliation(s)
- Dechao Tian
- Computational Biology Department, School of Computer Science, Carnegie Mellon University, Pittsburgh, Pennsylvania 15213, USA
| | - Ruochi Zhang
- Computational Biology Department, School of Computer Science, Carnegie Mellon University, Pittsburgh, Pennsylvania 15213, USA
| | - Yang Zhang
- Computational Biology Department, School of Computer Science, Carnegie Mellon University, Pittsburgh, Pennsylvania 15213, USA
| | - Xiaopeng Zhu
- Computational Biology Department, School of Computer Science, Carnegie Mellon University, Pittsburgh, Pennsylvania 15213, USA
| | - Jian Ma
- Computational Biology Department, School of Computer Science, Carnegie Mellon University, Pittsburgh, Pennsylvania 15213, USA
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25
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Zhou M, Li Y, Lin S, Chen Y, Qian Y, Zhao Z, Fan H. H3K9me3, H3K36me3, and H4K20me3 Expression Correlates with Patient Outcome in Esophageal Squamous Cell Carcinoma as Epigenetic Markers. Dig Dis Sci 2019; 64:2147-2157. [PMID: 30788686 DOI: 10.1007/s10620-019-05529-2] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/01/2018] [Accepted: 02/11/2019] [Indexed: 01/03/2023]
Abstract
BACKGROUND Histone methylation, as an essential pattern of posttranslational modifications, contributes to multiple cancer-related biological processes. Dysregulation of histone methylation is now considered a biomarker for cancer prognosis. AIMS This study investigated and evaluated the potential role of four histone lysine trimethylation markers as biomarkers for esophageal squamous cell carcinoma (ESCC) prognosis. METHODS Tissue arrays were made from 135 paraffin-embedded ESCC samples and examined for histone markers by immunohistochemistry, and 10 pairs of cancer and noncancerous mucosa tissues from ESCC patients were investigated with Western blot. Chi-squared test, Kaplan-Meier analysis with log-rank test, and Cox proportional hazard trend analyses were performed to assess the prognostic values of the markers. RESULTS Histone 3 lysine 4 trimethylation (H3K4me3), histone 3 lysine 9 trimethylation (H3K9me3), and histone 4 lysine 20 trimethylation (H4K20me3), but not histone 3 lysine 36 trimethylation (H3K36me3), showed stronger immunostaining signals in tumor tissues than in the corresponding adjacent non-neoplastic mucosa tissues. The expression patterns of H3K36me3, H3K9me3, and H4K20me3 correlated with tumor infiltrating depth, lymph node involvement, and pTNM stage. Low-scoring H3K9me3 and H4K20me3 predicted better prognosis, while H3K36me3 manifested the opposite trend. Poor prognosis occurred in ESCC patients with expression patterns of high levels of H3K9me3, high levels of H4K20me3, and low levels of H3K36me3 expression. CONCLUSIONS H3K9me3, H4K20me3, and H3K36me3 showed a close relationship with clinical features and were considered independent risk factors for survival of ESCC patients. The combination of H3K9me3, H4K20me3, and H3K36me3 expression, rather than the expression of a single histone marker, is believed to further enhance evaluations of ESCC prognosis and management.
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Affiliation(s)
- Menghan Zhou
- Department of Medical Genetics and Developmental Biology, Medical School of Southeast University, The Key Laboratory of Developmental Genes and Human Diseases, Ministry of Education, Southeast University, Nanjing, 210009, China.,Institute of Life Sciences, The Key Laboratory of Developmental Genes and Human Diseases, Southeast University, Nanjing, 210018, China
| | - Yiping Li
- Department of Pathology, Medical School, Southeast University, Nanjing, 210009, China
| | - Shaofeng Lin
- Department of Thoracic Surgery, Nanjing Medical University Affiliated Cancer Hospital & Jiangsu Cancer Hospital & Jiangsu Institute of Cancer Research, Jiangsu Key Laboratory of Molecular and Translational Cancer Research, Nanjing, 210009, China.,Department of Oncology, Fujian Provincial Cancer Hospital, Fuzhou, 350000, China
| | - Yanping Chen
- Department of Pathology, Fujian Cancer Hospital & Fujian Medical University Cancer Hospital, Fuzhou, 350014, China
| | - Yanyan Qian
- Department of Medical Genetics and Developmental Biology, Medical School of Southeast University, The Key Laboratory of Developmental Genes and Human Diseases, Ministry of Education, Southeast University, Nanjing, 210009, China
| | - Zhujiang Zhao
- Department of Medical Genetics and Developmental Biology, Medical School of Southeast University, The Key Laboratory of Developmental Genes and Human Diseases, Ministry of Education, Southeast University, Nanjing, 210009, China
| | - Hong Fan
- Department of Medical Genetics and Developmental Biology, Medical School of Southeast University, The Key Laboratory of Developmental Genes and Human Diseases, Ministry of Education, Southeast University, Nanjing, 210009, China.
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26
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Lee SH, Kim Y, Lee S, Durang X, Stenberg P, Jeon JH, Lizana L. Mapping the spectrum of 3D communities in human chromosome conformation capture data. Sci Rep 2019; 9:6859. [PMID: 31048738 PMCID: PMC6497878 DOI: 10.1038/s41598-019-42212-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2018] [Accepted: 03/22/2019] [Indexed: 11/09/2022] Open
Abstract
Several experiments show that the three dimensional (3D) organization of chromosomes affects genetic processes such as transcription and gene regulation. To better understand this connection, researchers developed the Hi-C method that is able to detect the pairwise physical contacts of all chromosomal loci. The Hi-C data show that chromosomes are composed of 3D compartments that range over a variety of scales. However, it is challenging to systematically detect these cross-scale structures. Most studies have therefore designed methods for specific scales to study foremost topologically associated domains (TADs) and A/B compartments. To go beyond this limitation, we tailor a network community detection method that finds communities in compact fractal globule polymer systems. Our method allows us to continuously scan through all scales with a single resolution parameter. We found: (i) polymer segments belonging to the same 3D community do not have to be in consecutive order along the polymer chain. In other words, several TADs may belong to the same 3D community. (ii) CTCF proteins-a loop-stabilizing protein that is ascribed a big role in TAD formation-are well correlated with community borders only at one level of organization. (iii) TADs and A/B compartments are traditionally treated as two weakly related 3D structures and detected with different algorithms. With our method, we detect both by simply adjusting the resolution parameter. We therefore argue that they represent two specific levels of a continuous spectrum 3D communities, rather than seeing them as different structural entities.
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Affiliation(s)
- Sang Hoon Lee
- Department of Liberal Arts, Gyeongnam National University of Science and Technology, Jinju, 52725, Korea.
| | - Yeonghoon Kim
- Department of Physics, Pohang University of Science and Technology, Pohang, 37673, Korea
| | - Sungmin Lee
- Department of Physics, Korea University, Seoul, 02841, Korea
| | - Xavier Durang
- Department of Physics, University of Seoul, Seoul, 02504, Korea
| | - Per Stenberg
- Department of Ecology and Environmental Science (EMG), Umeå University, Umeå, 90187, Sweden
| | - Jae-Hyung Jeon
- Department of Physics, Pohang University of Science and Technology, Pohang, 37673, Korea.
| | - Ludvig Lizana
- Integrated Science Lab, Department of Physics, Umeå University, Umeå, 90187, Sweden.
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27
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Szczepińska T, Rusek AM, Plewczynski D. Intermingling of chromosome territories. Genes Chromosomes Cancer 2019; 58:500-506. [DOI: 10.1002/gcc.22736] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2018] [Revised: 01/08/2019] [Accepted: 01/08/2019] [Indexed: 02/01/2023] Open
Affiliation(s)
| | - Anna Maria Rusek
- Centre of New TechnologiesUniversity of Warsaw Warsaw Poland
- Clinical Molecular Biology DepartmentMedical University of Bialystok Bialystok Poland
| | - Dariusz Plewczynski
- Centre of New TechnologiesUniversity of Warsaw Warsaw Poland
- Faculty of Mathematics and Information ScienceWarsaw University of Technology Warsaw Poland
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28
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Shivashankar GV. Mechanical regulation of genome architecture and cell-fate decisions. Curr Opin Cell Biol 2018; 56:115-121. [PMID: 30554028 DOI: 10.1016/j.ceb.2018.12.001] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2018] [Revised: 11/29/2018] [Accepted: 12/01/2018] [Indexed: 02/07/2023]
Abstract
Landmark experiments in vitro showed that somatic cells can be reprogrammed to stem-cells by the constitutive expression of particular transcription factors. However, in vivo cells naturally exhibit de-differentiation and trans-differentiation programs, thereby suggesting that the signals from the local mechanical microenvironment may be sufficient to induce stem-cell state transitions. In this review, we discuss recent evidence for the biophysical regulation of genome architecture and nuclear programs. We start by discussing the coupling between cellular architecture, genome organization and gene expression. We then review the role of biophysical factors in regulating genome architecture and cell-state transitions. Finally, we discuss the molecular basis of cell-state transitions during nuclear reprogramming. Collectively, we highlight the importance of the mechanical regulation of genome organization on cell-fate decisions.
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Affiliation(s)
- G V Shivashankar
- Mechanobiology Institute, National University of Singapore, Singapore & FIRC Institute of Molecular Oncology (IFOM), Milan, Italy.
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29
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Tan ZW, Guarnera E, Berezovsky IN. Exploring chromatin hierarchical organization via Markov State Modelling. PLoS Comput Biol 2018; 14:e1006686. [PMID: 30596637 PMCID: PMC6355033 DOI: 10.1371/journal.pcbi.1006686] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2018] [Revised: 01/31/2019] [Accepted: 11/27/2018] [Indexed: 01/02/2023] Open
Abstract
We propose a new computational method for exploring chromatin structural organization based on Markov State Modelling of Hi-C data represented as an interaction network between genomic loci. A Markov process describes the random walk of a traveling probe in the corresponding energy landscape, mimicking the motion of a biomolecule involved in chromatin function. By studying the metastability of the associated Markov State Model upon annealing, the hierarchical structure of individual chromosomes is observed, and corresponding set of structural partitions is identified at each level of hierarchy. Then, the notion of effective interaction between partitions is derived, delineating the overall topology and architecture of chromosomes. Mapping epigenetic data on the graphs of intra-chromosomal effective interactions helps in understanding how chromosome organization facilitates its function. A sketch of whole-genome interactions obtained from the analysis of 539 partitions from all 23 chromosomes, complemented by distributions of gene expression regulators and epigenetic factors, sheds light on the structure-function relationships in chromatin, delineating chromosomal territories, as well as structural partitions analogous to topologically associating domains and active / passive epigenomic compartments. In addition to the overall genome architecture shown by effective interactions, the affinity between partitions of different chromosomes was analyzed as an indicator of the degree of association between partitions in functionally relevant genomic interactions. The overall static picture of whole-genome interactions obtained with the method presented in this work provides a foundation for chromatin structural reconstruction, for the modelling of chromatin dynamics, and for exploring the regulation of genome function. The algorithms used in this study are implemented in a freely available Python package ChromaWalker (https://bitbucket.org/ZhenWahTan/chromawalker).
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Affiliation(s)
- Zhen Wah Tan
- Bioinformatics Institute (BII), Agency for Science, Technology and Research (A*STAR), Matrix, Singapore
| | - Enrico Guarnera
- Bioinformatics Institute (BII), Agency for Science, Technology and Research (A*STAR), Matrix, Singapore
| | - Igor N. Berezovsky
- Bioinformatics Institute (BII), Agency for Science, Technology and Research (A*STAR), Matrix, Singapore
- Department of Biological Sciences (DBS), National University of Singapore (NUS), Singapore
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30
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Pazos F, Garcia-Moreno A, Oliveros JC. Automatic detection of genomic regions with informative epigenetic patterns. BMC Genomics 2018; 19:847. [PMID: 30486775 PMCID: PMC6264639 DOI: 10.1186/s12864-018-5286-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2018] [Accepted: 11/20/2018] [Indexed: 12/14/2022] Open
Abstract
BACKGROUND Epigenetic phenomena are crucial for explaining the phenotypic plasticity seen in the cells of different tissues, developmental stages and diseases, all holding the same DNA sequence. As technology is allowing to retrieve epigenetic information in a genome-wide fashion, massive epigenomic datasets are being accumulated in public repositories. New approaches are required to mine those data to extract useful knowledge. We present here an automatic approach for detecting genomic regions with epigenetic variation patterns across samples related to a grouping of these samples, as a way of detecting regions functionally associated to the phenomenon behind the classification. RESULTS We show that the regions automatically detected by the method in the whole human genome associated to three different classifications of a set of epigenomes (cancer vs. healthy, brain vs. other organs, and fetal vs. adult tissues) are enriched in genes associated to these processes. CONCLUSIONS The method is fully automatic and can exhaustively scan the whole human genome at any resolution using large collections of epigenomes as input, although it also produces good results with small datasets. Consequently, it will be valuable for obtaining functional information from the incoming epigenomic information as it continues to accumulate.
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Affiliation(s)
- Florencio Pazos
- National Center for Biotechnology (CNB-CSIC), c/ Darwin, 3, 28049 Madrid, Spain
| | | | - Juan C. Oliveros
- National Center for Biotechnology (CNB-CSIC), c/ Darwin, 3, 28049 Madrid, Spain
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31
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Diament A, Tuller T. Modeling three-dimensional genomic organization in evolution and pathogenesis. Semin Cell Dev Biol 2018; 90:78-93. [PMID: 30030143 DOI: 10.1016/j.semcdb.2018.07.008] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2018] [Accepted: 07/08/2018] [Indexed: 12/17/2022]
Abstract
The regulation of gene expression is mediated via the complex three-dimensional (3D) conformation of the genetic material and its interactions with various intracellular factors. Various experimental and computational approaches have been developed in recent years for understating the relation between the 3D conformation of the genome and the phenotypes of cells in normal condition and diseases. In this review, we will discuss novel approaches for analyzing and modeling the 3D genomic conformation, focusing on deciphering disease-causing mutations that affect gene expression. We conclude that as this is a very challenging mission, an important direction should involve the comparative analysis of various 3D models from various organisms or cells.
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Affiliation(s)
- Alon Diament
- Dept. of Biomedical Engineering, Tel Aviv University, Tel Aviv 6997801, Israel
| | - Tamir Tuller
- Dept. of Biomedical Engineering, Tel Aviv University, Tel Aviv 6997801, Israel; The Sagol School of Neuroscience, Tel-Aviv University, Tel Aviv 6997801, Israel.
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32
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Umlauf D, Mourad R. The 3D genome: From fundamental principles to disease and cancer. Semin Cell Dev Biol 2018; 90:128-137. [PMID: 30030142 DOI: 10.1016/j.semcdb.2018.07.002] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2018] [Accepted: 07/03/2018] [Indexed: 12/18/2022]
Abstract
In higher eukaryotes, the three-dimensional (3D) organization of the genome is intimately related to numerous key biological functions including gene expression, DNA repair and DNA replication regulations. Alteration of this 3D organization is detrimental to the organism and can give rise to a broad range of diseases such as cancers. Here, we review recent advances in the field. We first describe how the genome is packed in 3D to form chromosome territories, compartments and domains. We also give an overview of the recent techniques that allow to map the genome in 3D up to the kilobase resolution. We then discuss potential mechanisms by which genome misfolding can affect proper gene expression by distal enhancers, and how the 3D genome influences the formation of genomic rearrangements.
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Affiliation(s)
- David Umlauf
- LBME, Centre de Biologie Intégrative (CBI), Université de Toulouse, CNRS, UPS, 31062 Toulouse, France.
| | - Raphaël Mourad
- LBCMCP, Centre de Biologie Intégrative (CBI), Université de Toulouse, CNRS, UPS, 31062 Toulouse, France.
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33
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Rada-Iglesias A, Grosveld FG, Papantonis A. Forces driving the three-dimensional folding of eukaryotic genomes. Mol Syst Biol 2018; 14:e8214. [PMID: 29858282 PMCID: PMC6024091 DOI: 10.15252/msb.20188214] [Citation(s) in RCA: 65] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
The last decade has radically renewed our understanding of higher order chromatin folding in the eukaryotic nucleus. As a result, most current models are in support of a mostly hierarchical and relatively stable folding of chromosomes dividing chromosomal territories into A‐ (active) and B‐ (inactive) compartments, which are then further partitioned into topologically associating domains (TADs), each of which is made up from multiple loops stabilized mainly by the CTCF and cohesin chromatin‐binding complexes. Nonetheless, the structure‐to‐function relationship of eukaryotic genomes is still not well understood. Here, we focus on recent work highlighting the biophysical and regulatory forces that contribute to the spatial organization of genomes, and we propose that the various conformations that chromatin assumes are not so much the result of a linear hierarchy, but rather of both converging and conflicting dynamic forces that act on it.
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Affiliation(s)
- Alvaro Rada-Iglesias
- Center for Molecular Medicine Cologne, University of Cologne, Cologne, Germany .,CECAD, University of Cologne, Cologne, Germany
| | - Frank G Grosveld
- Department of Cell Biology, Erasmus Medical Center, GE Rotterdam, Netherlands
| | - Argyris Papantonis
- Center for Molecular Medicine Cologne, University of Cologne, Cologne, Germany
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34
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Uhler C, Shivashankar GV. Nuclear Mechanopathology and Cancer Diagnosis. Trends Cancer 2018; 4:320-331. [PMID: 29606315 DOI: 10.1016/j.trecan.2018.02.009] [Citation(s) in RCA: 84] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2018] [Revised: 02/26/2018] [Accepted: 02/27/2018] [Indexed: 11/29/2022]
Abstract
Abnormalities in nuclear and chromatin organization are hallmarks of many diseases including cancer. In this review, we highlight our understanding of how the cellular microenvironment regulates nuclear morphology and, with it, the spatial organization of chromosomes and genes, resulting in cell type-specific genomic programs. We also discuss the molecular basis for maintaining nuclear and genomic integrity and how alterations in nuclear mechanotransduction pathways result in various diseases. Finally, we highlight the importance of digital pathology based on nuclear morphometric features combined with single-cell genomics for early cancer diagnostics.
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Affiliation(s)
- Caroline Uhler
- Department of Electrical Engineering & Computer Science, Institute for Data, Systems & 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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