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Heskett MB, Vouzas AE, Smith LG, Yates PA, Boniface C, Bouhassira EE, Spellman PT, Gilbert DM, Thayer MJ. Epigenetic control of chromosome-associated lncRNA genes essential for replication and stability. Nat Commun 2022; 13:6301. [PMID: 36273230 PMCID: PMC9588035 DOI: 10.1038/s41467-022-34099-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2022] [Accepted: 10/13/2022] [Indexed: 01/18/2023] Open
Abstract
ASARs are long noncoding RNA genes that control replication timing of entire human chromosomes in cis. The three known ASAR genes are located on human chromosomes 6 and 15, and are essential for chromosome integrity. To identify ASARs on all human chromosomes we utilize a set of distinctive ASAR characteristics that allow for the identification of hundreds of autosomal loci with epigenetically controlled, allele-restricted behavior in expression and replication timing of coding and noncoding genes, and is distinct from genomic imprinting. Disruption of noncoding RNA genes at five of five tested loci result in chromosome-wide delayed replication and chromosomal instability, validating their ASAR activity. In addition to the three known essential cis-acting chromosomal loci, origins, centromeres, and telomeres, we propose that all mammalian chromosomes also contain "Inactivation/Stability Centers" that display allele-restricted epigenetic regulation of protein coding and noncoding ASAR genes that are essential for replication and stability of each chromosome.
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Affiliation(s)
- Michael B Heskett
- Stanford Cancer Institute, Stanford University School of Medicine, Stanford, CA, 94305, USA
- Department of Molecular and Medical Genetics Oregon Health & Science University, Portland, OR, 97239, USA
| | - Athanasios E Vouzas
- Department of Biological Science, Florida State University, Tallahassee, FL, 32306, USA
| | - Leslie G Smith
- Department of Chemical Physiology and Biochemistry Oregon Health & Science University, Portland, OR, 97239, USA
| | - Phillip A Yates
- Department of Chemical Physiology and Biochemistry Oregon Health & Science University, Portland, OR, 97239, USA
| | - Christopher Boniface
- Cancer Early Detection Advanced Research Center, Knight Cancer Institute Oregon Health & Science University, Portland, OR, 97239, USA
| | - Eric E Bouhassira
- Department of Cell Biology and Department of Medicine, Albert Einstein College of Medicine, Bronx, NY, 10461, USA
| | - Paul T Spellman
- Department of Molecular and Medical Genetics Oregon Health & Science University, Portland, OR, 97239, USA
- Cancer Early Detection Advanced Research Center, Knight Cancer Institute Oregon Health & Science University, Portland, OR, 97239, USA
| | - David M Gilbert
- San Diego Biomedical Research Institute, San Diego, CA, 92121, USA
| | - Mathew J Thayer
- Department of Chemical Physiology and Biochemistry Oregon Health & Science University, Portland, OR, 97239, USA.
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2
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Nascimben M, Rimondini L, Corà D, Venturin M. Polygenic risk modeling of tumor stage and survival in bladder cancer. BioData Min 2022; 15:23. [PMID: 36175974 PMCID: PMC9523990 DOI: 10.1186/s13040-022-00306-w] [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: 11/19/2021] [Accepted: 09/18/2022] [Indexed: 11/26/2022] Open
Abstract
Introduction Bladder cancer assessment with non-invasive gene expression signatures facilitates the detection of patients at risk and surveillance of their status, bypassing the discomforts given by cystoscopy. To achieve accurate cancer estimation, analysis pipelines for gene expression data (GED) may integrate a sequence of several machine learning and bio-statistical techniques to model complex characteristics of pathological patterns. Methods Numerical experiments tested the combination of GED preprocessing by discretization with tree ensemble embeddings and nonlinear dimensionality reductions to categorize oncological patients comprehensively. Modeling aimed to identify tumor stage and distinguish survival outcomes in two situations: complete and partial data embedding. This latter experimental condition simulates the addition of new patients to an existing model for rapid monitoring of disease progression. Machine learning procedures were employed to identify the most relevant genes involved in patient prognosis and test the performance of preprocessed GED compared to untransformed data in predicting patient conditions. Results Data embedding paired with dimensionality reduction produced prognostic maps with well-defined clusters of patients, suitable for medical decision support. A second experiment simulated the addition of new patients to an existing model (partial data embedding): Uniform Manifold Approximation and Projection (UMAP) methodology with uniform data discretization led to better outcomes than other analyzed pipelines. Further exploration of parameter space for UMAP and t-distributed stochastic neighbor embedding (t-SNE) underlined the importance of tuning a higher number of parameters for UMAP rather than t-SNE. Moreover, two different machine learning experiments identified a group of genes valuable for partitioning patients (gene relevance analysis) and showed the higher precision obtained by preprocessed data in predicting tumor outcomes for cancer stage and survival rate (six classes prediction). Conclusions The present investigation proposed new analysis pipelines for disease outcome modeling from bladder cancer-related biomarkers. Complete and partial data embedding experiments suggested that pipelines employing UMAP had a more accurate predictive ability, supporting the recent literature trends on this methodology. However, it was also found that several UMAP parameters influence experimental results, therefore deriving a recommendation for researchers to pay attention to this aspect of the UMAP technique. Machine learning procedures further demonstrated the effectiveness of the proposed preprocessing in predicting patients’ conditions and determined a sub-group of biomarkers significant for forecasting bladder cancer prognosis.
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Affiliation(s)
- Mauro Nascimben
- Department of Health Sciences, Università del Piemonte Orientale, Via Solaroli 17, 28100, Novara, Italy. .,Enginsoft SpA, Via Giambellino 7, 35129, Padova, Italy.
| | - Lia Rimondini
- Department of Health Sciences, Università del Piemonte Orientale, Via Solaroli 17, 28100, Novara, Italy
| | - Davide Corà
- Department of Health Sciences, Università del Piemonte Orientale, Via Solaroli 17, 28100, Novara, Italy.,Department of Translational Medicine, Università del Piemonte Orientale, Via Solaroli 17, 28100, Novara, Italy
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3
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Kubasova N, Alves-Pereira CF, Gupta S, Vinogradova S, Gimelbrant A, Barreto VM. In Vivo Clonal Analysis Reveals Random Monoallelic Expression in Lymphocytes That Traces Back to Hematopoietic Stem Cells. Front Cell Dev Biol 2022; 10:827774. [PMID: 36003148 PMCID: PMC9393635 DOI: 10.3389/fcell.2022.827774] [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: 12/02/2021] [Accepted: 05/16/2022] [Indexed: 11/24/2022] Open
Abstract
Evaluating the epigenetic landscape in the stem cell compartment at the single-cell level is essential to assess the cells’ heterogeneity and predict their fate. Here, using a genome-wide transcriptomics approach in vivo, we evaluated the allelic expression imbalance in the progeny of single hematopoietic cells (HSCs) as a read-out of epigenetic marking. After 4 months of extensive proliferation and differentiation, we found that X-chromosome inactivation (XCI) is tightly maintained in all single-HSC derived hematopoietic cells. In contrast, the vast majority of the autosomal genes did not show clonal patterns of random monoallelic expression (RME). However, a persistent allele-specific autosomal transcription in HSCs and their progeny was found in a rare number of cases, none of which has been previously reported. These data show that: 1) XCI and RME in the autosomal chromosomes are driven by different mechanisms; 2) the previously reported high frequency of genes under RME in clones expanded in vitro (up to 15%) is not found in clones undergoing multiple differentiation steps in vivo; 3) prior to differentiation, HSCs have stable patterns of autosomal RME. We propose that most RME patterns in autosomal chromosomes are erased and established de novo during cell lineage differentiation.
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Affiliation(s)
- Nadiya Kubasova
- Chronic Diseases Research Centre, Nova Medical School, CEDOC, Lisbon, Portugal
- Genetagus, Egas Moniz – Cooperativa de Ensino Superior, CRL, Monte de Caparica, Portugal
| | - Clara F. Alves-Pereira
- Center of Cancer Systems Biology, Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, United States
- Department of Genetics, Harvard Medical School, Boston, MA, United States
- Broad Institute of MIT and Harvard, Cambridge, MA, United States
- Department of Genetics, Smurfit Institute of Genetics, Trinity College Dublin, University of Dublin, Dublin, Ireland
| | - Saumya Gupta
- Center of Cancer Systems Biology, Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, United States
- Department of Genetics, Harvard Medical School, Boston, MA, United States
- Broad Institute of MIT and Harvard, Cambridge, MA, United States
| | - Svetlana Vinogradova
- Center of Cancer Systems Biology, Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, United States
- Department of Genetics, Harvard Medical School, Boston, MA, United States
- Broad Institute of MIT and Harvard, Cambridge, MA, United States
| | - Alexander Gimelbrant
- Center of Cancer Systems Biology, Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, United States
- Department of Genetics, Harvard Medical School, Boston, MA, United States
- Broad Institute of MIT and Harvard, Cambridge, MA, United States
- *Correspondence: Vasco M. Barreto, ; Alexander Gimelbrant,
| | - Vasco M. Barreto
- Chronic Diseases Research Centre, Nova Medical School, CEDOC, Lisbon, Portugal
- UCIBIO, Departamento de Ciências da Vida, Faculdade de Ciências e Tecnologia, Universidade NOVA de Lisboa, Costa da Caparica, Portugal
- *Correspondence: Vasco M. Barreto, ; Alexander Gimelbrant,
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4
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Heskett MB, Spellman PT, Thayer MJ. Differential Allelic Expression among Long Non-Coding RNAs. Noncoding RNA 2021; 7:ncrna7040066. [PMID: 34698262 PMCID: PMC8544735 DOI: 10.3390/ncrna7040066] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2021] [Revised: 10/11/2021] [Accepted: 10/20/2021] [Indexed: 12/23/2022] Open
Abstract
Long non-coding RNAs (lncRNA) comprise a diverse group of non-protein-coding RNAs >200 bp in length that are involved in various normal cellular processes and disease states, and can affect coding gene expression through mechanisms in cis or in trans. Since the discovery of the first functional lncRNAs transcribed by RNA Polymerase II, H19 and Xist, many others have been identified and noted for their unusual transcriptional pattern, whereby expression from one chromosome homolog is strongly favored over the other, also known as mono-allelic or differential allelic expression. lncRNAs with differential allelic expression have been observed to play critical roles in developmental gene regulation, chromosome structure, and disease. Here, we will focus on known examples of differential allelic expression of lncRNAs and highlight recent research describing functional lncRNAs expressed from both imprinted and random mono-allelic expression domains.
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Affiliation(s)
- Michael B. Heskett
- Department of Genetics, Oregon Health & Science University, Portland, OR 97239, USA; (M.B.H.); (P.T.S.)
| | - Paul T. Spellman
- Department of Genetics, Oregon Health & Science University, Portland, OR 97239, USA; (M.B.H.); (P.T.S.)
| | - Mathew J. Thayer
- Department of Chemical Physiology and Biochemistry, Oregon Health & Science University, Portland, OR 97239, USA
- Correspondence:
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Nicolet A, Assouline D, Le Pogam MA, Perraudin C, Bagnoud C, Wagner J, Marti J, Peytremann-Bridevaux I. Exploring patient multimorbidity and complexity using health insurance claims data: a cluster analysis approach (Preprint). JMIR Med Inform 2021; 10:e34274. [PMID: 35377334 PMCID: PMC9016510 DOI: 10.2196/34274] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2021] [Revised: 02/04/2022] [Accepted: 02/06/2022] [Indexed: 11/23/2022] Open
Abstract
Background Although the trend of progressing morbidity is widely recognized, there are numerous challenges when studying multimorbidity and patient complexity. For multimorbid or complex patients, prone to fragmented care and high health care use, novel estimation approaches need to be developed. Objective This study aims to investigate the patient multimorbidity and complexity of Swiss residents aged ≥50 years using clustering methodology in claims data. Methods We adopted a clustering methodology based on random forests and used 34 pharmacy-based cost groups as the only input feature for the procedure. To detect clusters, we applied hierarchical density-based spatial clustering of applications with noise. The reasonable hyperparameters were chosen based on various metrics embedded in the algorithms (out-of-bag misclassification error, normalized stress, and cluster persistence) and the clinical relevance of the obtained clusters. Results Based on cluster analysis output for 18,732 individuals, we identified an outlier group and 7 clusters: individuals without diseases, patients with only hypertension-related diseases, patients with only mental diseases, complex high-cost high-need patients, slightly complex patients with inexpensive low-severity pharmacy-based cost groups, patients with 1 costly disease, and older high-risk patients. Conclusions Our study demonstrated that cluster analysis based on pharmacy-based cost group information from claims-based data is feasible and highlights clinically relevant clusters. Such an approach allows expanding the understanding of multimorbidity beyond simple disease counts and can identify the population profiles with increased health care use and costs. This study may foster the development of integrated and coordinated care, which is high on the agenda in policy making, care planning, and delivery.
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Affiliation(s)
- Anna Nicolet
- Center for Primary Care and Public Health (Unisanté), University of Lausanne, Lausanne, Switzerland
| | - Dan Assouline
- Center for Primary Care and Public Health (Unisanté), University of Lausanne, Lausanne, Switzerland
| | - Marie-Annick Le Pogam
- Center for Primary Care and Public Health (Unisanté), University of Lausanne, Lausanne, Switzerland
| | - Clémence Perraudin
- Center for Primary Care and Public Health (Unisanté), University of Lausanne, Lausanne, Switzerland
| | | | - Joël Wagner
- Department of Actuarial Science, Faculty of Business and Economics, and Swiss Finance Institute, University of Lausanne, Lausanne, Switzerland
| | - Joachim Marti
- Center for Primary Care and Public Health (Unisanté), University of Lausanne, Lausanne, Switzerland
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6
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Barreto VM, Kubasova N, Alves-Pereira CF, Gendrel AV. X-Chromosome Inactivation and Autosomal Random Monoallelic Expression as "Faux Amis". Front Cell Dev Biol 2021; 9:740937. [PMID: 34631717 PMCID: PMC8495168 DOI: 10.3389/fcell.2021.740937] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2021] [Accepted: 08/30/2021] [Indexed: 12/23/2022] Open
Abstract
X-chromosome inactivation (XCI) and random monoallelic expression of autosomal genes (RMAE) are two paradigms of gene expression regulation where, at the single cell level, genes can be expressed from either the maternal or paternal alleles. X-chromosome inactivation takes place in female marsupial and placental mammals, while RMAE has been described in mammals and also other species. Although the outcome of both processes results in random monoallelic expression and mosaicism at the cellular level, there are many important differences. We provide here a brief sketch of the history behind the discovery of XCI and RMAE. Moreover, we review some of the distinctive features of these two phenomena, with respect to when in development they are established, their roles in dosage compensation and cellular phenotypic diversity, and the molecular mechanisms underlying their initiation and stability.
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Affiliation(s)
- Vasco M Barreto
- Chronic Diseases Research Centre, CEDOC, Nova Medical School, Lisbon, Portugal
| | - Nadiya Kubasova
- Chronic Diseases Research Centre, CEDOC, Nova Medical School, Lisbon, Portugal
| | - Clara F Alves-Pereira
- Department of Genetics, Smurfit Institute of Genetics, Trinity College Dublin, University of Dublin, Dublin, Ireland
| | - Anne-Valerie Gendrel
- Instituto de Medicina Molecular João Lobo Antunes, Faculdade de Medicina da Universidade de Lisboa, Lisbon, Portugal
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7
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Ramos KS, Bojang P, Bowers E. Role of long interspersed nuclear element-1 in the regulation of chromatin landscapes and genome dynamics. Exp Biol Med (Maywood) 2021; 246:2082-2097. [PMID: 34304633 DOI: 10.1177/15353702211031247] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
LINE-1 retrotransposon, the most active mobile element of the human genome, is subject to tight regulatory control. Stressful environments and disease modify the recruitment of regulatory proteins leading to unregulated activation of LINE-1. The activation of LINE-1 influences genome dynamics through altered chromatin landscapes, insertion mutations, deletions, and modulation of cellular plasticity. To date, LINE-1 retrotransposition has been linked to various cancer types and may in fact underwrite the genetic basis of various other forms of chronic human illness. The occurrence of LINE-1 polymorphisms in the human population may define inter-individual differences in susceptibility to disease. This review is written in honor of Dr Peter Stambrook, a friend and colleague who carried out highly impactful cancer research over many years of professional practice. Dr Stambrook devoted considerable energy to helping others live up to their full potential and to navigate the complexities of professional life. He was an inspirational leader, a strong advocate, a kind mentor, a vocal supporter and cheerleader, and yes, a hard critic and tough friend when needed. His passionate stand on issues, his witty sense of humor, and his love for humanity have left a huge mark in our lives. We hope that that the knowledge summarized here will advance our understanding of the role of LINE-1 in cancer biology and expedite the development of innovative cancer diagnostics and treatments in the ways that Dr Stambrook himself had so passionately envisioned.
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Affiliation(s)
- Kenneth S Ramos
- Institute of Biosciences and Technology, Texas A&M Health, Houston, TX 77030, USA
| | - Pasano Bojang
- University of Kentucky College of Medicine, Lexington, KY 40506, USA
| | - Emma Bowers
- Institute of Biosciences and Technology, Texas A&M Health, Houston, TX 77030, USA
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8
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Patel H, Vock DM, Marai GE, Fuller CD, Mohamed ASR, Canahuate G. Oropharyngeal cancer patient stratification using random forest based-learning over high-dimensional radiomic features. Sci Rep 2021; 11:14057. [PMID: 34234160 PMCID: PMC8263609 DOI: 10.1038/s41598-021-92072-8] [Citation(s) in RCA: 3] [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: 12/23/2020] [Accepted: 05/10/2021] [Indexed: 11/27/2022] Open
Abstract
To improve risk prediction for oropharyngeal cancer (OPC) patients using cluster analysis on the radiomic features extracted from pre-treatment Computed Tomography (CT) scans. 553 OPC Patients randomly split into training (80%) and validation (20%), were classified into 2 or 3 risk groups by applying hierarchical clustering over the co-occurrence matrix obtained from a random survival forest (RSF) trained over 301 radiomic features. The cluster label was included together with other clinical data to train an ensemble model using five predictive models (Cox, random forest, RSF, logistic regression, and logistic-elastic net). Ensemble performance was evaluated over the independent test set for both recurrence free survival (RFS) and overall survival (OS). The Kaplan-Meier curves for OS stratified by cluster label show significant differences for both training and testing (p val < 0.0001). When compared to the models trained using clinical data only, the inclusion of the cluster label improves AUC test performance from .62 to .79 and from .66 to .80 for OS and RFS, respectively. The extraction of a single feature, namely a cluster label, to represent the high-dimensional radiomic feature space reduces the dimensionality and sparsity of the data. Moreover, inclusion of the cluster label improves model performance compared to clinical data only and offers comparable performance to the models including raw radiomic features.
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Affiliation(s)
- Harsh Patel
- Department of Electrical and Computer Engineering, University of Iowa, Iowa City, 52242, USA
| | - David M Vock
- Division of Biostatistics, University of Minnesota, Minneapolis, 55455, USA
| | - G Elisabeta Marai
- Department of Department of Computer Science, University of Illinois at Chicago, Chicago, 60607, USA
| | - Clifton D Fuller
- Department of Radiation Oncology, MD Anderson Cancer Center, Houston, 77030, USA
| | - Abdallah S R Mohamed
- Department of Radiation Oncology, MD Anderson Cancer Center, Houston, 77030, USA
| | - Guadalupe Canahuate
- Department of Electrical and Computer Engineering, University of Iowa, Iowa City, 52242, USA.
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9
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A Data-driven project categorization process for portfolio selection. JOURNAL OF MODELLING IN MANAGEMENT 2021. [DOI: 10.1108/jm2-10-2020-0257] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Purpose
Categorizing projects allows for better alignment of a portfolio with the organizational strategy and goals. An appropriate project categorization helps understand portfolio’s structure and enables proper project portfolio selection (PPS). In practice, project categorization is, however, conducted in intuitive approaches. Furthermore, little attention has been given to project categorization methods in the project management literature. The purpose of this paper is to provide researchers and practitioners with a data-driven project categorization process designed for PPS.
Design/methodology/approach
The suggested process was modeled considering the main characteristics of project categorization systems revealed from the literature. The clustering analysis is used as the core-computing technology, allowing for an empirically based categorization. This study also presents a real-world case study in the automotive industry to illustrate the proposed approach.
Findings
This study confirmed the potential of clustering analysis for a consistent project categorization. The most important attributes that influenced the project grouping have been identified including strategic and intrinsic features. The proposed approach helps increase the visibility of the portfolio’s structure and the comparability of its components.
Originality/value
There is a lack of research regarding project categorization methods, particularly for the purpose of PPS. A novel data-driven process is proposed to help mitigate the issues raised by prior researchers including the inconsistencies, ambiguities and multiple interpretations related to the taken-for-granted categories. The suggested approach is also expected to facilitate projects evaluation and prioritization within appropriate categories and contribute in PPS effectiveness.
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10
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Zhang X, Zhang R, Yu J. New Understanding of the Relevant Role of LINE-1 Retrotransposition in Human Disease and Immune Modulation. Front Cell Dev Biol 2020; 8:657. [PMID: 32850797 PMCID: PMC7426637 DOI: 10.3389/fcell.2020.00657] [Citation(s) in RCA: 47] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2020] [Accepted: 07/01/2020] [Indexed: 12/21/2022] Open
Abstract
Long interspersed nuclear element-1 (LINE-1) retrotransposition is a major hallmark of cancer accompanied by global chromosomal instability, genomic instability, and genetic heterogeneity and has become one indicator for the occurrence, development, and poor prognosis of many diseases. LINE-1 also modulates the immune system and affects the immune microenvironment in a variety of ways. Aberrant expression of LINE-1 retrotransposon can provide strong stimuli for an innate immune response, activate the immune system, and induce autoimmunity and inflammation. Therefore, inhibition the activity of LINE-1 has become a potential treatment strategy for various diseases. In this review, we discussed the components and regulatory mechanisms involved with LINE-1, its correlations with disease and immunity, and multiple inhibitors of LINE-1, providing a new understanding of LINE-1.
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Affiliation(s)
- Xiao Zhang
- Cancer Molecular Diagnostics Core, Tianjin Medical University Cancer Institute & Hospital, National Clinical Research Center of Caner, Key Laboratory of Cancer Prevention and Therapy, Key Laboratory of Cancer Immunology and Biotherapy, Tianjin, China.,Tianjin's Clinical Research Center for Cancer, Tianjin, China
| | - Rui Zhang
- Cancer Molecular Diagnostics Core, Tianjin Medical University Cancer Institute & Hospital, National Clinical Research Center of Caner, Key Laboratory of Cancer Prevention and Therapy, Key Laboratory of Cancer Immunology and Biotherapy, Tianjin, China.,Tianjin's Clinical Research Center for Cancer, Tianjin, China
| | - Jinpu Yu
- Cancer Molecular Diagnostics Core, Tianjin Medical University Cancer Institute & Hospital, National Clinical Research Center of Caner, Key Laboratory of Cancer Prevention and Therapy, Key Laboratory of Cancer Immunology and Biotherapy, Tianjin, China.,Tianjin's Clinical Research Center for Cancer, Tianjin, China
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Heskett MB, Smith LG, Spellman P, Thayer MJ. Reciprocal monoallelic expression of ASAR lncRNA genes controls replication timing of human chromosome 6. RNA (NEW YORK, N.Y.) 2020; 26:724-738. [PMID: 32144193 PMCID: PMC7266157 DOI: 10.1261/rna.073114.119] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/26/2019] [Accepted: 02/22/2020] [Indexed: 06/10/2023]
Abstract
DNA replication occurs on mammalian chromosomes in a cell-type distinctive temporal order known as the replication timing program. We previously found that disruption of the noncanonical lncRNA genes ASAR6 and ASAR15 results in delayed replication timing and delayed mitotic chromosome condensation of human chromosomes 6 and 15, respectively. ASAR6 and ASAR15 display random monoallelic expression and display asynchronous replication between alleles that is coordinated with other random monoallelic genes on their respective chromosomes. Disruption of the expressed allele, but not the silent allele, of ASAR6 leads to delayed replication, activation of the previously silent alleles of linked monoallelic genes, and structural instability of human chromosome 6. In this report, we describe a second lncRNA gene (ASAR6-141) on human chromosome 6 that when disrupted results in delayed replication timing in cisASAR6-141 is subject to random monoallelic expression and asynchronous replication and is expressed from the opposite chromosome 6 homolog as ASAR6 ASAR6-141 RNA, like ASAR6 and ASAR15 RNAs, contains a high L1 content and remains associated with the chromosome territory where it is transcribed. Three classes of cis-acting elements control proper chromosome function in mammals: origins of replication, centromeres, and telomeres, which are responsible for replication, segregation, and stability of all chromosomes. Our work supports a fourth type of essential chromosomal element, the "Inactivation/Stability Center," which expresses ASAR lncRNAs responsible for proper replication timing, monoallelic expression, and structural stability of each chromosome.
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Affiliation(s)
- Michael B Heskett
- Department of Molecular and Medical Genetics, Oregon Health & Science University, Portland, Oregon 97239, USA
| | - Leslie G Smith
- Department of Chemical Physiology and Biochemistry, Oregon Health & Science University, Portland, Oregon 97239, USA
| | - Paul Spellman
- Department of Molecular and Medical Genetics, Oregon Health & Science University, Portland, Oregon 97239, USA
| | - Mathew J Thayer
- Department of Chemical Physiology and Biochemistry, Oregon Health & Science University, Portland, Oregon 97239, USA
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12
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LINE-1 specific nuclear organization in mice olfactory sensory neurons. Mol Cell Neurosci 2020; 105:103494. [PMID: 32387751 DOI: 10.1016/j.mcn.2020.103494] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2020] [Revised: 03/31/2020] [Accepted: 04/05/2020] [Indexed: 12/21/2022] Open
Abstract
Long interspersed nuclear elements-1 (LINE-1) are mobile DNA elements that comprise the majority of interspersed repeats in the mammalian genome. During the last decade, these transposable sequences have been described as controlling elements involved in transcriptional regulation and genome plasticity. Recently, LINE-1 have been implicated in neurogenesis, but to date little is known about their nuclear organization in neurons. The olfactory epithelium is a site of continuous neurogenesis, and loci of olfactory receptor genes are enriched in LINE-1 copies. Olfactory neurons have a unique inverted nuclear architecture and constitutive heterochromatin forms a block in the center of the nuclei. Our DNA FISH images show that, even though LINE-1 copies are dispersed throughout the mice genome, they are clustered forming a cap around the central heterochromatin block and frequently occupy the same position as facultative heterochromatin in olfactory neurons nuclei. This specific LINE-1 organization could not be observed in other olfactory epithelium cell types. Analyses of H3K27me3 and H3K9me3 ChIP-seq data from olfactory epithelium revealed that LINE-1 copies located at OR gene loci show different enrichment for these heterochromatin marks. We also found that LINE-1 are transcribed in mouse olfactory epithelium. These results suggest that LINE-1 play a role in the olfactory neurons' nuclear architecture. SIGNIFICANCE STATEMENT: LINE-1 are mobile DNA elements and comprise almost 20% of mice and human genomes. These retrotransposons have been implicated in neurogenesis. We show for the first time that LINE-1 retrotransposons have a specific nuclear organization in olfactory neurons, forming aggregates concentric to the heterochromatin block and frequently occupying the same region as facultative heterochromatin. We found that LINE-1 at olfactory receptor gene loci are differently enriched for H3K9me3 and H3K27me3, but LINE-1 transcripts could be detected in the olfactory epithelium. We speculate that these retrotransposons play an active role in olfactory neurons' nuclear architecture.
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13
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Broad Heterochromatic Domains Open in Gonocyte Development Prior to De Novo DNA Methylation. Dev Cell 2019; 51:21-34.e5. [PMID: 31474564 DOI: 10.1016/j.devcel.2019.07.023] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2018] [Revised: 03/28/2019] [Accepted: 07/24/2019] [Indexed: 02/03/2023]
Abstract
Facultative heterochromatin forms and reorganizes in response to external stimuli. However, how the initial establishment of such a chromatin state is regulated in cell-cycle-arrested cells remains unexplored. Mouse gonocytes are arrested male germ cells, at which stage the genome-wide DNA methylome forms. Here, we discovered transiently accessible heterochromatin domains of several megabases in size in gonocytes and named them differentially accessible domains (DADs). Open DADs formed in gene desert and gene cluster regions, primarily at transposons, with the reprogramming of histone marks, suggesting DADs as facultative heterochromatin. De novo DNA methylation took place with two waves in gonocytes: the first region specific and the second genome-wide. DADs were resistant to the first wave and their opening preceded the second wave. In addition, the higher-order chromosome architecture was reorganized with less defined chromosome compartments in gonocytes. These findings suggest that multiple layers of chromatin reprogramming facilitate de novo DNA methylation.
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14
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Karami K, Zerehdaran S, Javadmanesh A, Shariati MM, Fallahi H. Characterization of bovine (Bos taurus) imprinted genes from genomic to amino acid attributes by data mining approaches. PLoS One 2019; 14:e0217813. [PMID: 31170205 PMCID: PMC6553745 DOI: 10.1371/journal.pone.0217813] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2018] [Accepted: 05/21/2019] [Indexed: 01/05/2023] Open
Abstract
Genomic imprinting results in monoallelic expression of genes in mammals and flowering plants. Understanding the function of imprinted genes improves our knowledge of the regulatory processes in the genome. In this study, we have employed classification and clustering algorithms with attribute weighting to specify the unique attributes of both imprinted (monoallelic) and biallelic expressed genes. We have obtained characteristics of 22 known monoallelically expressed (imprinted) and 8 biallelic expressed genes that have been experimentally validated alongside 208 randomly selected genes in bovine (Bos taurus). Attribute weighting methods and various supervised and unsupervised algorithms in machine learning were applied. Unique characteristics were discovered and used to distinguish mono and biallelic expressed genes from each other in bovine. To obtain the accuracy of classification, 10-fold cross-validation with concerning each combination of attribute weighting (feature selection) and machine learning algorithms, was used. Our approach was able to accurately predict mono and biallelic genes using the genomics and proteomics attributes.
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Affiliation(s)
- Keyvan Karami
- Department of Animal Science, Faculty of Agriculture, Ferdowsi University of Mashhad, Mashhad, Iran
| | - Saeed Zerehdaran
- Department of Animal Science, Faculty of Agriculture, Ferdowsi University of Mashhad, Mashhad, Iran
- * E-mail:
| | - Ali Javadmanesh
- Department of Animal Science, Faculty of Agriculture, Ferdowsi University of Mashhad, Mashhad, Iran
| | - Mohammad Mahdi Shariati
- Department of Animal Science, Faculty of Agriculture, Ferdowsi University of Mashhad, Mashhad, Iran
| | - Hossein Fallahi
- Department of Biology, School of Sciences, Razi University, Kermanshah, Iran
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15
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Soares ML, Edwards CA, Dearden FL, Ferrón SR, Curran S, Corish JA, Rancourt RC, Allen SE, Charalambous M, Ferguson-Smith MA, Rens W, Adams DJ, Ferguson-Smith AC. Targeted deletion of a 170-kb cluster of LINE-1 repeats and implications for regional control. Genome Res 2018; 28:gr.221366.117. [PMID: 29367313 PMCID: PMC5848613 DOI: 10.1101/gr.221366.117] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2017] [Accepted: 01/10/2018] [Indexed: 12/31/2022]
Abstract
Approximately half the mammalian genome is composed of repetitive sequences, and accumulating evidence suggests that some may have an impact on genome function. Here, we characterized a large array class of repeats of long-interspersed elements (LINE-1). Although widely distributed in mammals, locations of such arrays are species specific. Using targeted deletion, we asked whether a 170-kb LINE-1 array located at a mouse imprinted domain might function as a modulator of local transcriptional control. The LINE-1 array is lamina associated in differentiated ES cells consistent with its AT-richness, and although imprinting occurs both proximally and distally to the array, active LINE-1 transcripts within the tract are biallelically expressed. Upon deletion of the array, no perturbation of imprinting was observed, and abnormal phenotypes were not detected in maternal or paternal heterozygous or homozygous mutant mice. The array does not shield nonimprinted genes in the vicinity from local imprinting control. Reduced neural expression of protein-coding genes observed upon paternal transmission of the deletion is likely due to the removal of a brain-specific enhancer embedded within the LINE array. Our findings suggest that presence of a 170-kb LINE-1 array reflects the tolerance of the site for repeat insertion rather than an important genomic function in normal development.
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Affiliation(s)
- Miguel L Soares
- Department of Genetics, University of Cambridge, Cambridge CB2 3EH, United Kingdom
- Departamento de Biomedicina, Unidade de Biologia Experimental, Faculdade de Medicina da Universidade do Porto, Porto; and i3S-Instituto de Investigação e Inovação em Saúde, Universidade do Porto, 4200-319 Porto, Portugal
| | - Carol A Edwards
- Department of Genetics, University of Cambridge, Cambridge CB2 3EH, United Kingdom
| | - Frances L Dearden
- Department of Genetics, University of Cambridge, Cambridge CB2 3EH, United Kingdom
| | - Sacri R Ferrón
- Department of Genetics, University of Cambridge, Cambridge CB2 3EH, United Kingdom
| | - Scott Curran
- Department of Genetics, University of Cambridge, Cambridge CB2 3EH, United Kingdom
| | - Jennifer A Corish
- Department of Genetics, University of Cambridge, Cambridge CB2 3EH, United Kingdom
| | - Rebecca C Rancourt
- Department of Genetics, University of Cambridge, Cambridge CB2 3EH, United Kingdom
| | - Sarah E Allen
- Department of Genetics, University of Cambridge, Cambridge CB2 3EH, United Kingdom
| | - Marika Charalambous
- Department of Genetics, University of Cambridge, Cambridge CB2 3EH, United Kingdom
| | | | - Willem Rens
- Department of Veterinary Medicine, University of Cambridge, Cambridge CB3 0ES, United Kingdom
| | - David J Adams
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, United Kingdom
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16
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Platt EJ, Smith L, Thayer MJ. L1 retrotransposon antisense RNA within ASAR lncRNAs controls chromosome-wide replication timing. J Cell Biol 2017; 217:541-553. [PMID: 29288153 PMCID: PMC5800813 DOI: 10.1083/jcb.201707082] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2017] [Revised: 09/19/2017] [Accepted: 11/27/2017] [Indexed: 12/11/2022] Open
Abstract
Proper chromosome duplication is critical for genome integrity and normal cellular function. Platt et al. show that the lncRNA genes ASAR6 and ASAR15 control chromosome-wide replication timing via the antisense strand of L1 retrotransposons located within ASAR6 and ASAR15 RNAs. Mammalian cells replicate their chromosomes via a temporal replication program. The ASAR6 and ASAR15 genes were identified as loci that when disrupted result in delayed replication and condensation of entire human chromosomes. ASAR6 and ASAR15 are monoallelically expressed long noncoding RNAs that remain associated with the chromosome from which they are transcribed. The chromosome-wide effects of ASAR6 map to the antisense strand of an L1 retrotransposon within ASAR6 RNA, deletion or inversion of which delayed replication of human chromosome 6. Furthermore, ectopic integration of ASAR6 or ASAR15 transgenes into mouse chromosomes resulted in delayed replication and condensation, an increase in H3K27me3, coating of the mouse chromosome with ASAR RNA, and a loss of mouse Cot-1 RNA expression in cis. Targeting the antisense strand of the L1 within ectopically expressed ASAR6 RNA restored normal replication timing. Our results provide direct evidence that L1 antisense RNA plays a functional role in chromosome-wide replication timing of mammalian chromosomes.
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Affiliation(s)
- Emily J Platt
- Department of Biochemistry and Molecular Biology, Oregon Health & Science University, Portland, OR
| | - Leslie Smith
- Department of Biochemistry and Molecular Biology, Oregon Health & Science University, Portland, OR
| | - Mathew J Thayer
- Department of Biochemistry and Molecular Biology, Oregon Health & Science University, Portland, OR
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17
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De Donato M, Hussain T, Rodulfo H, Peters SO, Imumorin IG, Thomas BN. Conservation of Repeats at the Mammalian KCNQ1OT1-CDKN1C Region Suggests a Role in Genomic Imprinting. Evol Bioinform Online 2017; 13:1176934317715238. [PMID: 28659711 PMCID: PMC5476424 DOI: 10.1177/1176934317715238] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2017] [Accepted: 05/23/2017] [Indexed: 12/19/2022] Open
Abstract
KCNQ1OT1 is located in the region with the highest number of genes showing genomic imprinting, but the mechanisms controlling the genes under its influence have not been fully elucidated. Therefore, we conducted a comparative analysis of the KCNQ1/KCNQ1OT1-CDKN1C region to study its conservation across the best assembled eutherian mammalian genomes sequenced to date and analyzed potential elements that may be implicated in the control of genomic imprinting in this region. The genomic features in these regions from human, mouse, cattle, and dog show a higher number of genes and CpG islands (detected using cpgplot from EMBOSS), but lower number of repetitive elements (including short interspersed nuclear elements and long interspersed nuclear elements), compared with their whole chromosomes (detected by RepeatMasker). The KCNQ1OT1-CDKN1C region contains the highest number of conserved noncoding sequences (CNS) among mammals, where we found 16 regions containing about 38 different highly conserved repetitive elements (using mVista), such as LINE1 elements: L1M4, L1MB7, HAL1, L1M4a, L1Med, and an LTR element: MLT1H. From these elements, we found 74 CNS showing high sequence identity (>70%) between human, cattle, and mouse, from which we identified 13 motifs (using Multiple Em for Motif Elicitation/Motif Alignment and Search Tool) with a significant probability of occurrence, 3 of which were the most frequent and were used to find transcription factor-binding sites. We detected several transcription factors (using JASPAR suite) from the families SOX, FOX, and GATA. A phylogenetic analysis of these CNS from human, marmoset, mouse, rat, cattle, dog, horse, and elephant shows branches with high levels of support and very similar phylogenetic relationships among these groups, confirming previous reports. Our results suggest that functional DNA elements identified by comparative genomics in a region densely populated with imprinted mammalian genes may be related to the regulation of imprinted gene expression.
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Affiliation(s)
- Marcos De Donato
- Animal Genetics and Genomics Laboratory, Office of International Programs, College of Agriculture and Life Sciences, Cornell University, Ithaca, NY, USA.,Escuela de Bioingenierias, Tecnologico de Monterrey, Campus Querétaro, Santiago de Querétaro, Mexico
| | - Tanveer Hussain
- Animal Genetics and Genomics Laboratory, Office of International Programs, College of Agriculture and Life Sciences, Cornell University, Ithaca, NY, USA.,Department Molecular Biology, Virtual University of Pakistan, Lahore, Pakistan
| | - Hectorina Rodulfo
- Escuela de Bioingenierias, Tecnologico de Monterrey, Campus Querétaro, Santiago de Querétaro, Mexico
| | - Sunday O Peters
- Department of Animal Science, Berry College, Mount Berry, GA, USA
| | - Ikhide G Imumorin
- Animal Genetics and Genomics Laboratory, Office of International Programs, College of Agriculture and Life Sciences, Cornell University, Ithaca, NY, USA.,African Institute for Biosciences Research and Training, Ibadan, Nigeria.,School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, USA
| | - Bolaji N Thomas
- Department of Biomedical Sciences, Rochester Institute of Technology, Rochester, NY, USA
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18
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Vasilyev SA, Tolmacheva EN, Lebedev IN. Epigenetic regulation and role of LINE-1 retrotransposon in embryogenesis. RUSS J GENET+ 2016. [DOI: 10.1134/s1022795416120152] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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19
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Shapiro JA. Exploring the read-write genome: mobile DNA and mammalian adaptation. Crit Rev Biochem Mol Biol 2016; 52:1-17. [DOI: 10.1080/10409238.2016.1226748] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Affiliation(s)
- James A. Shapiro
- Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, IL, USA
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20
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Uriarte RB, Tiezzi F, Tsaftaris SA. Supporting Autonomic Management of Clouds: Service Clustering With Random Forest. IEEE TRANSACTIONS ON NETWORK AND SERVICE MANAGEMENT 2016. [DOI: 10.1109/tnsm.2016.2569000] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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21
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Gendrel AV, Marion-Poll L, Katoh K, Heard E. Random monoallelic expression of genes on autosomes: Parallels with X-chromosome inactivation. Semin Cell Dev Biol 2016; 56:100-110. [PMID: 27101886 DOI: 10.1016/j.semcdb.2016.04.007] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2016] [Revised: 04/08/2016] [Accepted: 04/15/2016] [Indexed: 01/04/2023]
Abstract
Genes are generally expressed from their two alleles, except in some particular cases such as random inactivation of one of the two X chromosomes in female mammals or imprinted genes which are expressed only from the maternal or the paternal allele. A lesser-known phenomenon is random monoallelic expression (RME) of autosomal genes, where genes can be stably expressed in a monoallelic manner, from either one of the parental alleles. Studies on autosomal RME face several challenges. First, RME that is based on epigenetic mechanisms has to be distinguished from biased expression of one allele caused by a DNA sequence polymorphism in a regulatory element. Second, RME should not be confused with transient monoallelic expression often observed in single cell analyses, and that often corresponds to dynamic bursting of expression. Thanks to analyses on clonal cell populations, the existence of RME in cultured cells is now well established. Future studies of RME in vivo will have to overcome tissue heterogeneity and certain technical limitations. Here, we discuss current knowledge on autosomal RME, as well as possible mechanisms controlling these expression patterns and potential implications for development and disease, drawing parallels with what is known for X-chromosome inactivation, a paradigm of random monoallelic expression.
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Affiliation(s)
- Anne-Valerie Gendrel
- Institut Curie, PSL Research University, CNRS UMR 3215, INSERM U934, Mammalian Developmental Epigenetics group, F-75005 Paris, France; Sorbonne Universités, UPMC Univ Paris 6, F-75005 Paris, France.
| | - Lucile Marion-Poll
- Institut Curie, PSL Research University, CNRS UMR 3215, INSERM U934, Mammalian Developmental Epigenetics group, F-75005 Paris, France; Sorbonne Universités, UPMC Univ Paris 6, F-75005 Paris, France
| | - Kimiko Katoh
- Institut Curie, PSL Research University, CNRS UMR 3215, INSERM U934, Mammalian Developmental Epigenetics group, F-75005 Paris, France; Sorbonne Universités, UPMC Univ Paris 6, F-75005 Paris, France
| | - Edith Heard
- Institut Curie, PSL Research University, CNRS UMR 3215, INSERM U934, Mammalian Developmental Epigenetics group, F-75005 Paris, France; Sorbonne Universités, UPMC Univ Paris 6, F-75005 Paris, France.
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22
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Habibi L, Pedram M, AmirPhirozy A, Bonyadi K. Mobile DNA Elements: The Seeds of Organic Complexity on Earth. DNA Cell Biol 2015. [DOI: 10.1089/dna.2015.2938] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Affiliation(s)
- Laleh Habibi
- Department of Pharmaceutics, School of Pharmacy, Tehran University of Medical Sciences, Tehran, Iran
- Cellular and Molecular Nutrition Department, School of Nutritional Science and Dietetics, Tehran University of Medical Sciences, Tehran, Iran
| | - Mehrdad Pedram
- Department of Genetics and Molecular Medicine, School of Medicine, Zanjan University of Medical Sciences, Zanjan, Iran
| | - Akbar AmirPhirozy
- Department of Medical Genetics, School of Medicine, Tehran University of Medical Sciences, Tehran, Iran
| | - Khadijeh Bonyadi
- Department of Medical Genetics, School of Medicine, Tehran University of Medical Sciences, Tehran, Iran
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23
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Grandi FC, Rosser JM, Newkirk SJ, Yin J, Jiang X, Xing Z, Whitmore L, Bashir S, Ivics Z, Izsvák Z, Ye P, Yu YE, An W. Retrotransposition creates sloping shores: a graded influence of hypomethylated CpG islands on flanking CpG sites. Genome Res 2015; 25:1135-46. [PMID: 25995269 PMCID: PMC4509998 DOI: 10.1101/gr.185132.114] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2014] [Accepted: 05/19/2015] [Indexed: 11/25/2022]
Abstract
Long interspersed elements (LINEs), through both self-mobilization and trans-mobilization of short interspersed elements and processed pseudogenes, have made an indelible impact on the structure and function of the human genome. One consequence is the creation of new CpG islands (CGIs). In fact, more than half of all CGIs in the genome are associated with repetitive DNA, three-quarters of which are derived from retrotransposons. However, little is known about the epigenetic impact of newly inserted CGIs. We utilized a transgenic LINE-1 mouse model and tracked DNA methylation dynamics of individual germline insertions during mouse development. The retrotransposed GFP marker sequence, a strong CGI, is hypomethylated in male germ cells but hypermethylated in somatic tissues, regardless of genomic location. The GFP marker is similarly methylated when delivered into the genome via the Sleeping Beauty DNA transposon, suggesting that the observed methylation pattern may be independent of the mode of insertion. Comparative analyses between insertion- and non-insertion-containing alleles further reveal a graded influence of the retrotransposed CGI on flanking CpG sites, a phenomenon that we described as "sloping shores." Computational analyses of human and mouse methylomic data at single-base resolution confirm that sloping shores are universal for hypomethylated CGIs in sperm and somatic tissues. Additionally, the slope of a hypomethylated CGI can be affected by closely positioned CGI neighbors. Finally, by tracing sloping shore dynamics through embryonic and germ cell reprogramming, we found evidence of bookmarking, a mechanism that likely determines which CGIs will be eventually hyper- or hypomethylated.
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Affiliation(s)
- Fiorella C Grandi
- School of Molecular Biosciences, Washington State University, Pullman, Washington 99164, USA
| | - James M Rosser
- School of Molecular Biosciences, Washington State University, Pullman, Washington 99164, USA
| | - Simon J Newkirk
- School of Molecular Biosciences, Washington State University, Pullman, Washington 99164, USA; Department of Pharmaceutical Sciences, South Dakota State University, Brookings, South Dakota 57007, USA
| | - Jun Yin
- School of Molecular Biosciences, Washington State University, Pullman, Washington 99164, USA
| | - Xiaoling Jiang
- The Children's Guild Foundation Down Syndrome Research Program, Department of Cancer Genetics and Genetics Program, Roswell Park Cancer Institute, Buffalo, New York 14263, USA
| | - Zhuo Xing
- The Children's Guild Foundation Down Syndrome Research Program, Department of Cancer Genetics and Genetics Program, Roswell Park Cancer Institute, Buffalo, New York 14263, USA
| | - Leanne Whitmore
- School of Molecular Biosciences, Washington State University, Pullman, Washington 99164, USA
| | - Sanum Bashir
- Max Delbrück Center for Molecular Medicine, 13092 Berlin, Germany
| | - Zoltán Ivics
- Division of Medical Biotechnology, Paul Ehrlich Institute, 63225 Langen, Germany
| | - Zsuzsanna Izsvák
- Max Delbrück Center for Molecular Medicine, 13092 Berlin, Germany
| | - Ping Ye
- School of Molecular Biosciences, Washington State University, Pullman, Washington 99164, USA
| | - Y Eugene Yu
- The Children's Guild Foundation Down Syndrome Research Program, Department of Cancer Genetics and Genetics Program, Roswell Park Cancer Institute, Buffalo, New York 14263, USA
| | - Wenfeng An
- Department of Pharmaceutical Sciences, South Dakota State University, Brookings, South Dakota 57007, USA
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24
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Jachowicz JW, Torres-Padilla ME. LINEs in mice: features, families, and potential roles in early development. Chromosoma 2015; 125:29-39. [PMID: 25975894 DOI: 10.1007/s00412-015-0520-2] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2014] [Revised: 04/27/2015] [Accepted: 05/05/2015] [Indexed: 01/08/2023]
Abstract
Approximately half of the mammalian genome is composed of repetitive elements, including LINE-1 (L1) elements. Because of their potential ability to transpose and integrate into other regions of the genome, their activation represents a threat to genome stability. Molecular pathways have emerged to tightly regulate and repress their transcriptional activity, including DNA methylation, histone modifications, and RNA pathways. It has become evident that Line-L1 elements are evolutionary diverse and dedicated repression pathways have been recently uncovered that discriminate between evolutionary old and young elements, with RNA-directed silencing mechanisms playing a prominent role. During periods of epigenetic reprogramming in development, specific classes of repetitive elements are upregulated, presumably due to the loss of most heterochromatic marks in this process. While we have learnt a lot on the molecular mechanisms that regulate Line-L1 expression over the last years, it is still unclear whether reactivation of Line-L1 after fertilization serves a functional purpose or it is a simple side effect of reprogramming.
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Affiliation(s)
- Joanna W Jachowicz
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, CNRS/INSERM U964, Université de Strasbourg, 67404, Illkirch, France
| | - Maria-Elena Torres-Padilla
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, CNRS/INSERM U964, Université de Strasbourg, 67404, Illkirch, France.
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25
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Brečević L, Rinčić M, Krsnik Ž, Sedmak G, Hamid AB, Kosyakova N, Galić I, Liehr T, Borovečki F. Association of new deletion/duplication region at chromosome 1p21 with intellectual disability, severe speech deficit and autism spectrum disorder-like behavior: an all-in approach to solving the DPYD enigma. Transl Neurosci 2015; 6:59-86. [PMID: 28123791 PMCID: PMC4936614 DOI: 10.1515/tnsci-2015-0007] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2014] [Accepted: 12/29/2014] [Indexed: 12/14/2022] Open
Abstract
We describe an as yet unreported neocentric small supernumerary marker chromosome (sSMC) derived from chromosome 1p21.3p21.2. It was present in 80% of the lymphocytes in a male patient with intellectual disability, severe speech deficit, mild dysmorphic features, and hyperactivity with elements of autism spectrum disorder (ASD). Several important neurodevelopmental genes are affected by the 3.56 Mb copy number gain of 1p21.3p21.2, which may be considered reciprocal in gene content to the recently recognized 1p21.3 microdeletion syndrome. Both 1p21.3 deletions and the presented duplication display overlapping symptoms, fitting the same disorder category. Contribution of coding and non-coding genes to the phenotype is discussed in the light of cellular and intercellular homeostasis disequilibrium. In line with this the presented 1p21.3p21.2 copy number gain correlated to 1p21.3 microdeletion syndrome verifies the hypothesis of a cumulative effect of the number of deregulated genes - homeostasis disequilibrium leading to overlapping phenotypes between microdeletion and microduplication syndromes. Although miR-137 appears to be the major player in the 1p21.3p21.2 region, deregulation of the DPYD (dihydropyrimidine dehydrogenase) gene may potentially affect neighboring genes underlying the overlapping symptoms present in both the copy number loss and copy number gain of 1p21. Namely, the all-in approach revealed that DPYD is a complex gene whose expression is epigenetically regulated by long non-coding RNAs (lncRNAs) within the locus. Furthermore, the long interspersed nuclear element-1 (LINE-1) L1MC1 transposon inserted in DPYD intronic transcript 1 (DPYD-IT1) lncRNA with its parasites, TcMAR-Tigger5b and pair of Alu repeats appears to be the “weakest link” within the DPYD gene liable to break. Identification of the precise mechanism through which DPYD is epigenetically regulated, and underlying reasons why exactly the break (FRA1E) happens, will consequently pave the way toward preventing severe toxicity to the antineoplastic drug 5-fluorouracil (5-FU) and development of the causative therapy for the dihydropyrimidine dehydrogenase deficiency.
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Affiliation(s)
- Lukrecija Brečević
- Croatian Institute for Brain Research, University of Zagreb Medical School, Šalata 12, 10000 Zagreb, Croatia
- Department for Functional Genomics, Center for Translational and Clinical Research, University of Zagreb Medical School, University Hospital Center Zagreb, Šalata 2, 10000 Zagreb, Croatia
- E-mail: ;
| | - Martina Rinčić
- Croatian Institute for Brain Research, University of Zagreb Medical School, Šalata 12, 10000 Zagreb, Croatia
- Department for Functional Genomics, Center for Translational and Clinical Research, University of Zagreb Medical School, University Hospital Center Zagreb, Šalata 2, 10000 Zagreb, Croatia
- Jena University Hospital, Friedrich Schiller University, Institute of Human Genetics, Kollegiengasse 10, 07743 Jena, Germany
| | - Željka Krsnik
- Croatian Institute for Brain Research, University of Zagreb Medical School, Šalata 12, 10000 Zagreb, Croatia
| | - Goran Sedmak
- Croatian Institute for Brain Research, University of Zagreb Medical School, Šalata 12, 10000 Zagreb, Croatia
| | - Ahmed B. Hamid
- Jena University Hospital, Friedrich Schiller University, Institute of Human Genetics, Kollegiengasse 10, 07743 Jena, Germany
| | - Nadezda Kosyakova
- Jena University Hospital, Friedrich Schiller University, Institute of Human Genetics, Kollegiengasse 10, 07743 Jena, Germany
| | - Ivan Galić
- Center for Rehabilitation Stančić, Stančić bb, 10370 Stančić, Croatia
| | - Thomas Liehr
- Jena University Hospital, Friedrich Schiller University, Institute of Human Genetics, Kollegiengasse 10, 07743 Jena, Germany
| | - Fran Borovečki
- Department for Functional Genomics, Center for Translational and Clinical Research, University of Zagreb Medical School, University Hospital Center Zagreb, Šalata 2, 10000 Zagreb, Croatia
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26
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Donley N, Smith L, Thayer MJ. ASAR15, A cis-acting locus that controls chromosome-wide replication timing and stability of human chromosome 15. PLoS Genet 2015; 11:e1004923. [PMID: 25569254 PMCID: PMC4287527 DOI: 10.1371/journal.pgen.1004923] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2014] [Accepted: 11/25/2014] [Indexed: 01/01/2023] Open
Abstract
DNA replication initiates at multiple sites along each mammalian chromosome at different times during each S phase, following a temporal replication program. We have used a Cre/loxP-based strategy to identify cis-acting elements that control this replication-timing program on individual human chromosomes. In this report, we show that rearrangements at a complex locus at chromosome 15q24.3 result in delayed replication and structural instability of human chromosome 15. Characterization of this locus identified long, RNA transcripts that are retained in the nucleus and form a “cloud” on one homolog of chromosome 15. We also found that this locus displays asynchronous replication that is coordinated with other random monoallelic genes on chromosome 15. We have named this locus ASynchronous replication and Autosomal RNA on chromosome 15, or ASAR15. Previously, we found that disruption of the ASAR6 lincRNA gene results in delayed replication, delayed mitotic condensation and structural instability of human chromosome 6. Previous studies in the mouse found that deletion of the Xist gene, from the X chromosome in adult somatic cells, results in a delayed replication and instability phenotype that is indistinguishable from the phenotype caused by disruption of either ASAR6 or ASAR15. In addition, delayed replication and chromosome instability were detected following structural rearrangement of many different human or mouse chromosomes. These observations suggest that all mammalian chromosomes contain similar cis-acting loci. Thus, under this scenario, all mammalian chromosomes contain four distinct types of essential cis-acting elements: origins, telomeres, centromeres and “inactivation/stability centers”, all functioning to promote proper replication, segregation and structural stability of each chromosome. Mammalian cells replicate their DNA along each chromosome during a precise temporal replication program. In this report, we used a novel “chromosome-engineering” strategy to identify a DNA element that controls this replication-timing program of human chromosome 15. Characterization of this element indicated that it encodes large non-protein-coding RNAs that are retained in the nucleus and form a “cloud” on one copy of chromosome 15. Previously, we found that structural rearrangements of a similar element on human chromosome 6 causes delayed replication and structural instability of chromosome 6. Mammalian chromosomes are known to contain three distinct types of essential DNA elements that promote proper chromosome function. Thus, every chromosome contains: 1) origins of replication, which are responsible for proper initiation of DNA synthesis; 2) centromeres, which are responsible for proper chromosome separation during cell division; and 3) telomeres, which are responsible for replication and protection of the ends of linear chromosomes. Our work supports a model in which all mammalian chromosomes contain a fourth type of essential DNA element, the “inactivation/stability center”, which is responsible for proper DNA replication timing and structural stability of each chromosome.
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Affiliation(s)
- Nathan Donley
- Department of Biochemistry and Molecular Biology, Oregon Health & Science University, Portland, Oregon, United States of America
| | - Leslie Smith
- Department of Biochemistry and Molecular Biology, Oregon Health & Science University, Portland, Oregon, United States of America
| | - Mathew J. Thayer
- Department of Biochemistry and Molecular Biology, Oregon Health & Science University, Portland, Oregon, United States of America
- * E-mail:
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Alves-Pereira CF, de Freitas R, Lopes T, Gardner R, Marta F, Vieira P, Barreto VM. Independent recruitment of Igh alleles in V(D)J recombination. Nat Commun 2014; 5:5623. [PMID: 25517887 PMCID: PMC4351640 DOI: 10.1038/ncomms6623] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2014] [Accepted: 10/20/2014] [Indexed: 01/05/2023] Open
Abstract
How the vast majority of B cells express only one of the two alleles at their immunoglobulin loci remains a biological puzzle. Here, in mice reconstituted with a single haematopoietic stem cell, we demonstrate that each of the two immunoglobulin heavy chain (Igh) alleles has a similar probability to be the first to undergo V(H) to DJ(H) rearrangement. We also observe this similar probability in clones from multipotent and common lymphoid precursors. The extreme biases in the expression of the alleles that we find in more differentiated subsets are mostly due to constraints imposed by early rearrangements. Our data demonstrate that each of the two Igh alleles in a B cell behaves independently of the other, up to the moment when a successful rearrangement in one allele triggers a feedback mechanism that prevents further recombination.
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Affiliation(s)
- Clara F. Alves-Pereira
- Epigenetics and Soma Laboratory, Instituto Gulbenkian de Ciência, Rua da Quinta Grande, n° 6, 2780-156 Oeiras, Portugal
| | - Raquel de Freitas
- Epigenetics and Soma Laboratory, Instituto Gulbenkian de Ciência, Rua da Quinta Grande, n° 6, 2780-156 Oeiras, Portugal
| | - Telma Lopes
- Flow Cytometry Laboratory UIC, Instituto Gulbenkian de Ciência, Rua da Quinta Grande, n° 6, 2780-156 Oeiras, Portugal
| | - Rui Gardner
- Flow Cytometry Laboratory UIC, Instituto Gulbenkian de Ciência, Rua da Quinta Grande, n° 6, 2780-156 Oeiras, Portugal
| | - Filipa Marta
- Epigenetics and Soma Laboratory, Instituto Gulbenkian de Ciência, Rua da Quinta Grande, n° 6, 2780-156 Oeiras, Portugal
| | - Paulo Vieira
- Unité Lymphopoïèse, Institut Pasteur, 25, Rue du Dr Roux, 75724 Paris, France
- INSERM U668, F-75015 Paris, France
| | - Vasco M. Barreto
- Epigenetics and Soma Laboratory, Instituto Gulbenkian de Ciência, Rua da Quinta Grande, n° 6, 2780-156 Oeiras, Portugal
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Genome-wide detection of allelic gene expression in hepatocellular carcinoma cells using a human exome SNP chip. Gene 2014; 551:236-42. [DOI: 10.1016/j.gene.2014.09.001] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2014] [Revised: 08/19/2014] [Accepted: 09/01/2014] [Indexed: 11/22/2022]
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LINE-1 retrotransposons: from 'parasite' sequences to functional elements. J Appl Genet 2014; 56:133-45. [PMID: 25106509 DOI: 10.1007/s13353-014-0241-x] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2014] [Revised: 07/24/2014] [Accepted: 07/25/2014] [Indexed: 10/24/2022]
Abstract
Long interspersed nuclear elements-1 (LINE-1) are the most abundant and active retrotransposons in the mammalian genomes. Traditionally, the occurrence of LINE-1 sequences in the genome of mammals has been explained by the selfish DNA hypothesis. Nevertheless, recently, it has also been argued that these sequences could play important roles in these genomes, as in the regulation of gene expression, genome modelling and X-chromosome inactivation. The non-random chromosomal distribution is a striking feature of these retroelements that somehow reflects its functionality. In the present study, we have isolated and analysed a fraction of the open reading frame 2 (ORF2) LINE-1 sequence from three rodent species, Cricetus cricetus, Peromyscus eremicus and Praomys tullbergi. Physical mapping of the isolated sequences revealed an interspersed longitudinal AT pattern of distribution along all the chromosomes of the complement in the three genomes. A detailed analysis shows that these sequences are preferentially located in the euchromatic regions, although some signals could be detected in the heterochromatin. In addition, a coincidence between the location of imprinted gene regions (as Xist and Tsix gene regions) and the LINE-1 retroelements was also observed. According to these results, we propose an involvement of LINE-1 sequences in different genomic events as gene imprinting, X-chromosome inactivation and evolution of repetitive sequences located at the heterochromatic regions (e.g. satellite DNA sequences) of the rodents' genomes analysed.
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Gendrel AV, Attia M, Chen CJ, Diabangouaya P, Servant N, Barillot E, Heard E. Developmental dynamics and disease potential of random monoallelic gene expression. Dev Cell 2014; 28:366-80. [PMID: 24576422 DOI: 10.1016/j.devcel.2014.01.016] [Citation(s) in RCA: 100] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2013] [Revised: 12/23/2013] [Accepted: 01/21/2014] [Indexed: 11/19/2022]
Abstract
X chromosome inactivation (XCI) and allelic exclusion of olfactory receptors or immunoglobulin loci represent classic examples of random monoallelic expression (RME). RME of some single copy genes has also been reported, but the in vivo relevance of this remains unclear. Here we identify several hundred RME genes in clonal neural progenitor cell lines derived from embryonic stem cells. RME occurs during differentiation, and, once established, the monoallelic state can be highly stable. We show that monoallelic expression also occurs in vivo, in the absence of DNA sequence polymorphism. Several of the RME genes identified play important roles in development and have been implicated in human autosomal-dominant disorders. We propose that monoallelic expression of such genes contributes to the fine-tuning of the developmental regulatory pathways they control, and, in the context of a mutation, RME can predispose to loss of function in a proportion of cells and thus contribute to disease.
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Affiliation(s)
- Anne-Valerie Gendrel
- Institut Curie, 26 rue d'Ulm, Paris 75248, France; Genetics and Developmental Biology Unit, INSERM U934/CNRS UMR3215, Paris 75248, France
| | - Mikael Attia
- Institut Curie, 26 rue d'Ulm, Paris 75248, France; Genetics and Developmental Biology Unit, INSERM U934/CNRS UMR3215, Paris 75248, France
| | - Chong-Jian Chen
- Institut Curie, 26 rue d'Ulm, Paris 75248, France; Genetics and Developmental Biology Unit, INSERM U934/CNRS UMR3215, Paris 75248, France; Bioinformatics and Computational Systems Biology of Cancer, INSERM U900, Paris 75248, France; Mines ParisTech, Fontainebleau 77300, France
| | - Patricia Diabangouaya
- Institut Curie, 26 rue d'Ulm, Paris 75248, France; Genetics and Developmental Biology Unit, INSERM U934/CNRS UMR3215, Paris 75248, France
| | - Nicolas Servant
- Institut Curie, 26 rue d'Ulm, Paris 75248, France; Bioinformatics and Computational Systems Biology of Cancer, INSERM U900, Paris 75248, France; Mines ParisTech, Fontainebleau 77300, France
| | - Emmanuel Barillot
- Institut Curie, 26 rue d'Ulm, Paris 75248, France; Bioinformatics and Computational Systems Biology of Cancer, INSERM U900, Paris 75248, France; Mines ParisTech, Fontainebleau 77300, France
| | - Edith Heard
- Institut Curie, 26 rue d'Ulm, Paris 75248, France; Genetics and Developmental Biology Unit, INSERM U934/CNRS UMR3215, Paris 75248, France.
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Bala Tannan N, Brahmachary M, Garg P, Borel C, Alnefaie R, Watson CT, Thomas NS, Sharp AJ. DNA methylation profiling in X;autosome translocations supports a role for L1 repeats in the spread of X chromosome inactivation. Hum Mol Genet 2013; 23:1224-36. [PMID: 24186870 DOI: 10.1093/hmg/ddt553] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
X chromosome inactivation (XCI) is an epigenetic mechanism that silences the majority of genes on one X chromosome in females. Previous studies have suggested that the spread of XCI might be facilitated in part by common repeats such as long interspersed nuclear elements (LINEs). However, owing to the unusual sequence content of the X and the nonrandom distribution of genes that escape XCI, it has been unclear whether the correlation between repeat elements and XCI is a functional one. To test the hypothesis that the spread of XCI shows sequence specificity, we have analyzed the pattern of XCI in autosomal chromatin by performing DNA methylation profiling in six unbalanced X;autosome translocations. Using promoter hypermethylation as an epigenetic signature of XCI, we have determined the inactivation status of 1050 autosomal genes after translocation onto an inactive derivative X. By performing a comparative sequence analysis of autosomal genes that are either subject to or escape the X inactivation signal, we identified a number of common repetitive elements, including L1 and L2 LINEs, and DNA motifs that are significantly enriched around inactive autosomal genes. We show that these same motifs predominantly map to L1P repeat elements, are significantly enriched on the X chromosome versus the autosomes and also occur at higher densities around X-linked genes that are subject to X inactivation compared with those that escape X inactivation. These results are consistent with a potential causal relationship between DNA sequence features such as L1s and the spread of XCI, lending strong support to Mary Lyon's 'repeat hypothesis'.
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Affiliation(s)
- Neeta Bala Tannan
- Department of Genetics and Genomic Sciences, Mount Sinai School of Medicine, New York, USA
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32
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Genes associated with the cis-regulatory functions of intragenic LINE-1 elements. BMC Genomics 2013; 14:205. [PMID: 23530910 PMCID: PMC3643820 DOI: 10.1186/1471-2164-14-205] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2012] [Accepted: 03/19/2013] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Thousands of intragenic long interspersed element 1 sequences (LINE-1 elements or L1s) reside within genes. These intragenic L1 sequences are conserved and regulate the expression of their host genes. When L1 methylation is decreased, either through chemical induction or in cancer, the intragenic L1 transcription is increased. The resulting L1 mRNAs form RISC complexes with pre-mRNA to degrade the complementary mRNA. In this study, we screened for genes that are involved in intragenic L1 regulation networks. RESULTS Genes containing L1s were obtained from L1Base (http://l1base.molgen.mpg.de). The expression profiles of 205 genes in 516 gene knockdown experiments were obtained from the Gene Expression Omnibus (GEO) (http://www.ncbi.nlm.nih.gov/geo). The expression levels of the genes with and without L1s were compared using Pearson's chi-squared test. After a permutation based statistical analysis and a multiple hypothesis testing, 73 genes were found to induce significant regulatory changes (upregulation and/or downregulation) in genes with L1s. In detail, 5 genes were found to induce both the upregulation and downregulation of genes with L1s, whereas 27 and 37 genes induced the downregulation and upregulation, respectively, of genes with L1s. These regulations sometimes differed depending on the cell type and the orientation of the intragenic L1s. Moreover, the siRNA-regulating genes containing L1s possess a variety of molecular functions, are responsible for many cellular phenotypes and are associated with a number of diseases. CONCLUSIONS Cells use intragenic L1s as cis-regulatory elements within gene bodies to modulate gene expression. There may be several mechanisms by which L1s mediate gene expression. Intragenic L1s may be involved in the regulation of several biological processes, including DNA damage and repair, inflammation, immune function, embryogenesis, cell differentiation, cellular response to external stimuli and hormonal responses. Furthermore, in addition to cancer, intragenic L1s may alter gene expression in a variety of diseases and abnormalities.
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Jeffries AR, Perfect LW, Ledderose J, Schalkwyk LC, Bray NJ, Mill J, Price J. Stochastic choice of allelic expression in human neural stem cells. Stem Cells 2013; 30:1938-47. [PMID: 22714879 DOI: 10.1002/stem.1155] [Citation(s) in RCA: 51] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
Monoallelic gene expression, such as genomic imprinting, is well described. Less well-characterized are genes undergoing stochastic monoallelic expression (MA), where specific clones of cells express just one allele at a given locus. We performed genome-wide allelic expression assessment of human clonal neural stem cells derived from cerebral cortex, striatum, and spinal cord, each with differing genotypes. We assayed three separate clonal lines from each donor, distinguishing stochastic MA from genotypic effects. Roughly 2% of genes showed evidence for autosomal MA, and in about half of these, allelic expression was stochastic between different clones. Many of these loci were known neurodevelopmental genes, such as OTX2 and OLIG2. Monoallelic genes also showed increased levels of DNA methylation compared to hypomethylated biallelic loci. Identified monoallelic gene loci showed altered chromatin signatures in fetal brain, suggesting an in vivo correlate of this phenomenon. We conclude that stochastic allelic expression is prevalent in neural stem cells, providing clonal diversity to developing tissues such as the human brain.
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Affiliation(s)
- Aaron R Jeffries
- King's College London, Institute of Psychiatry, Centre for the Cellular Basis of Behaviour, Department of Neuroscience, London, United Kingdom.
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Del Giudice M. Fetal programming by maternal stress: Insights from a conflict perspective. Psychoneuroendocrinology 2012; 37:1614-29. [PMID: 22694951 DOI: 10.1016/j.psyneuen.2012.05.014] [Citation(s) in RCA: 69] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/17/2012] [Revised: 05/21/2012] [Accepted: 05/22/2012] [Indexed: 02/07/2023]
Abstract
Maternal stress during pregnancy has pervasive effects on the offspring's physiology and behavior, including the development of anxious, reactive temperament and increased stress responsivity. These outcomes can be seen as the result of adaptive developmental plasticity: maternal stress hormones carry useful information about the state of the external world, which can be used by the developing fetus to match its phenotype to the predicted environment. This account, however, neglects the inherent conflict of interest between mother and fetus about the outcomes of fetal programming. The aim of this paper is to extend the adaptive model of prenatal stress by framing mother-fetus interactions in an evolutionary conflict perspective. In the paper, I show how a conflict perspective provides many new insights in the functions and mechanisms of fetal programming, with particular emphasis on human pregnancy. I then take advantage of those insights to make sense of some puzzling features of maternal and fetal physiology and generate novel empirical predictions.
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Affiliation(s)
- Marco Del Giudice
- Department of Psychology, University of Turin, Via Po 14, 10123 Torino, Italy.
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35
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Wang J, Lunyak VV, Jordan IK. Chromatin signature discovery via histone modification profile alignments. Nucleic Acids Res 2012; 40:10642-56. [PMID: 22989711 PMCID: PMC3505981 DOI: 10.1093/nar/gks848] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
We report on the development of an unsupervised algorithm for the genome-wide discovery and analysis of chromatin signatures. Our Chromatin-profile Alignment followed by Tree-clustering algorithm (ChAT) employs dynamic programming of combinatorial histone modification profiles to identify locally similar chromatin sub-regions and provides complementary utility with respect to existing methods. We applied ChAT to genomic maps of 39 histone modifications in human CD4+ T cells to identify both known and novel chromatin signatures. ChAT was able to detect chromatin signatures previously associated with transcription start sites and enhancers as well as novel signatures associated with a variety of regulatory elements. Promoter-associated signatures discovered with ChAT indicate that complex chromatin signatures, made up of numerous co-located histone modifications, facilitate cell-type specific gene expression. The discovery of novel L1 retrotransposon-associated bivalent chromatin signatures suggests that these elements influence the mono-allelic expression of human genes by shaping the chromatin environment of imprinted genomic regions. Analysis of long gene-associated chromatin signatures point to a role for the H4K20me1 and H3K79me3 histone modifications in transcriptional pause release. The novel chromatin signatures and functional associations uncovered by ChAT underscore the ability of the algorithm to yield novel insight on chromatin-based regulatory mechanisms.
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Affiliation(s)
- Jianrong Wang
- School of Biology, Georgia Institute of Technology, Atlanta, GA 30332, USA
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36
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Abstract
Repetitive sequences, especially transposon-derived interspersed repetitive elements, account for a large fraction of the genome in most eukaryotes. Despite the repetitive nature, these transposable elements display quantitative and qualitative differences even among species of the same lineage. Although transposable elements contribute greatly as a driving force to the biological diversity during evolution, they can induce embryonic lethality and genetic disorders as a result of insertional mutagenesis and genomic rearrangement. Temporary relaxation of the epigenetic control of retrotransposons during early germline development opens a risky window that can allow retrotransposons to escape from host constraints and to propagate abundantly in the host genome. Because germline mutations caused by retrotransposon activation are heritable and thus can be deleterious to the offspring, an adaptive strategy has evolved in host cells, especially in the germline. In this review, we will attempt to summarize general defense mechanisms deployed by the eukaryotic genome, with an emphasis on pathways utilized by the male germline to confer retrotransposon silencing.
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Affiliation(s)
- Jianqiang Bao
- Department of Physiology and Cell Biology, University of Nevada School of Medicine, Reno, Nevada, USA
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37
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Affiliation(s)
- Tao Shi
- Please E-mail correspondence to . Steve Horvath is an Assistant Professor in the Departments of Human Genetics and Biostatistics, Gonda Center, University of California, Los Angeles,CA90095-7088. Tao Shi is a Senior Bioinformatics Scientist, Ortho-Clinical Diagnostics, a Johnson & Johnson Company, 3210 Merryfield Row, San Diego, CA 92121, and graduated with a Ph.D. in Human Genetics from UCLA
| | - Steve Horvath
- Please E-mail correspondence to . Steve Horvath is an Assistant Professor in the Departments of Human Genetics and Biostatistics, Gonda Center, University of California, Los Angeles,CA90095-7088. Tao Shi is a Senior Bioinformatics Scientist, Ortho-Clinical Diagnostics, a Johnson & Johnson Company, 3210 Merryfield Row, San Diego, CA 92121, and graduated with a Ph.D. in Human Genetics from UCLA
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Kines KJ, Belancio VP. Expressing genes do not forget their LINEs: transposable elements and gene expression. FRONT BIOSCI-LANDMRK 2012; 17:1329-44. [PMID: 22201807 DOI: 10.2741/3990] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Historically the accumulated mass of mammalian transposable elements (TEs), particularly those located within gene boundaries, was viewed as a genetic burden potentially detrimental to the genomic landscape. This notion has been strengthened by the discovery that transposable sequences can alter the architecture of the transcriptome, not only through insertion, but also long after the integration process is completed. Insertions previously considered harmless are now known to impact the expression of host genes via modification of the transcript quality or quantity, transcriptional interference, or by the control of pathways that affect the mRNA life-cycle. Conversely, several examples of the evolutionary advantageous impact of TEs on the host gene structure that diversified the cellular transcriptome are reported. TE-induced changes in gene expression can be tissue- or disease-specific, raising the possibility that the impact of TE sequences may vary during development, among normal cell types, and between normal and disease-affected tissues. The understanding of the rules and abundance of TE-interference with gene expression is in its infancy, and its contribution to human disease and/or evolution remains largely unexplored.
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Affiliation(s)
- Kristine J Kines
- Department of Structural and Cellular Biology, Tulane University School of Medicine, Tulane University Cancer Center and Tulane Center for Aging
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39
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Wolf C, Linden DEJ. Biological pathways to adaptability - interactions between genome, epigenome, nervous system and environment for adaptive behavior. GENES BRAIN AND BEHAVIOR 2011; 11:3-28. [DOI: 10.1111/j.1601-183x.2011.00752.x] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
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40
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Wang X, Morgan DM, Wang G, Mozier NM. Residual DNA analysis in biologics development: Review of measurement and quantitation technologies and future directions. Biotechnol Bioeng 2011; 109:307-17. [DOI: 10.1002/bit.23343] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2011] [Revised: 08/09/2011] [Accepted: 09/19/2011] [Indexed: 01/09/2023]
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41
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Baysal BE, McKay SE, Kim YJ, Zhang Z, Alila L, Willett-Brozick JE, Pacak K, Kim TH, Shadel GS. Genomic imprinting at a boundary element flanking the SDHD locus. Hum Mol Genet 2011; 20:4452-61. [PMID: 21862453 DOI: 10.1093/hmg/ddr376] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Germline mutations in SDHD, a mitochondrial complex II (succinate dehydrogenase) subunit gene at chromosome band 11q23, cause highly penetrant paraganglioma (PGL) tumors when transmitted through fathers. In contrast, maternal transmission rarely, if ever, leads to tumor development. The mechanism underlying this unusual monogenic tumor predisposition pattern is poorly understood. Here, we describe identification of imprinted methylation within an alternative promoter for a large intergenic non-coding RNA located at a distant gene desert boundary flanking SDHD. Methylation at this site primarily occurs within two consecutive HpaII restriction enzyme sites in a tissue-specific manner, most commonly in the adrenal gland. Informative fetal tissues and PGL tumors demonstrate maternal allelic hypermethylation. While a strong binding site for the enhancer-blocking protein CTCF within the alternative promoter shows no evidence of methylation, hyper-methylated adrenal tissues show increased binding of the chromatin-looping factor cohesin relative to the hypo-methylated tissues. These results suggest that the differential allelic methylation we observe at this locus is associated with altered chromatin architectures. These results provide molecular evidence for imprinting at a boundary element flanking the SDHD locus and suggest that epigenetic suppression of the maternal allele is the underlying mechanism of the imprinted penetrance of SDHD mutations.
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Affiliation(s)
- Bora E Baysal
- Department of Pathology, Yale University School of Medicine, New Haven, CT 06510, USA.
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Cowley M, de Burca A, McCole RB, Chahal M, Saadat G, Oakey RJ, Schulz R. Short interspersed element (SINE) depletion and long interspersed element (LINE) abundance are not features universally required for imprinting. PLoS One 2011; 6:e18953. [PMID: 21533089 PMCID: PMC3080381 DOI: 10.1371/journal.pone.0018953] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2010] [Accepted: 03/18/2011] [Indexed: 01/22/2023] Open
Abstract
Genomic imprinting is a form of gene dosage regulation in which a gene is expressed from only one of the alleles, in a manner dependent on the parent of origin. The mechanisms governing imprinted gene expression have been investigated in detail and have greatly contributed to our understanding of genome regulation in general. Both DNA sequence features, such as CpG islands, and epigenetic features, such as DNA methylation and non-coding RNAs, play important roles in achieving imprinted expression. However, the relative importance of these factors varies depending on the locus in question. Defining the minimal features that are absolutely required for imprinting would help us to understand how imprinting has evolved mechanistically. Imprinted retrogenes are a subset of imprinted loci that are relatively simple in their genomic organisation, being distinct from large imprinting clusters, and have the potential to be used as tools to address this question. Here, we compare the repeat element content of imprinted retrogene loci with non-imprinted controls that have a similar locus organisation. We observe no significant differences that are conserved between mouse and human, suggesting that the paucity of SINEs and relative abundance of LINEs at imprinted loci reported by others is not a sequence feature universally required for imprinting.
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Affiliation(s)
- Michael Cowley
- Department of Medical & Molecular Genetics, King's College London, Guy's Hospital, London, United Kingdom
| | - Anna de Burca
- Department of Medical & Molecular Genetics, King's College London, Guy's Hospital, London, United Kingdom
| | - Ruth B. McCole
- Department of Medical & Molecular Genetics, King's College London, Guy's Hospital, London, United Kingdom
| | - Mandeep Chahal
- Department of Medical & Molecular Genetics, King's College London, Guy's Hospital, London, United Kingdom
| | - Ghazal Saadat
- Department of Medical & Molecular Genetics, King's College London, Guy's Hospital, London, United Kingdom
| | - Rebecca J. Oakey
- Department of Medical & Molecular Genetics, King's College London, Guy's Hospital, London, United Kingdom
| | - Reiner Schulz
- Department of Medical & Molecular Genetics, King's College London, Guy's Hospital, London, United Kingdom
- * E-mail:
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44
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Stoffregen EP, Donley N, Stauffer D, Smith L, Thayer MJ. An autosomal locus that controls chromosome-wide replication timing and mono-allelic expression. Hum Mol Genet 2011; 20:2366-78. [PMID: 21459774 DOI: 10.1093/hmg/ddr138] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Mammalian DNA replication initiates at multiple sites along chromosomes at different times, following a temporal replication program. Homologous alleles typically replicate synchronously; however, mono-allelically expressed genes such as imprinted genes, allelically excluded genes and genes on the female X chromosome replicate asynchronously. We have used a chromosome engineering strategy to identify a human autosomal locus that controls this replication timing program in cis. We show that Cre/loxP-mediated rearrangements at a discrete locus at 6q16.1 result in delayed replication of the entire chromosome. This locus displays asynchronous replication timing that is coordinated with other mono-allelically expressed genes on chromosome 6. Characterization of this locus revealed mono-allelic expression of a large intergenic non-coding RNA, which we have named asynchronous replication and autosomal RNA on chromosome 6, ASAR6. Finally, disruption of this locus results in the activation of the previously silent alleles of linked mono-allelically expressed genes. We previously found that chromosome rearrangements involving eight different autosomes display delayed replication timing, and that cells containing chromosomes with delayed replication timing have a 30-80-fold increase in the rate at which new gross chromosomal rearrangements occurred. Taken together, these observations indicate that human autosomes contain discrete cis-acting loci that control chromosome-wide replication timing, mono-allelic expression and the stability of entire chromosomes.
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Affiliation(s)
- Eric P Stoffregen
- Department of Biochemistry and Molecular Biology, Oregon Health & Science University, 3181 S W Sam Jackson Park Road, Portland, OR 97239, USA
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Hutter B, Bieg M, Helms V, Paulsen M. Imprinted genes show unique patterns of sequence conservation. BMC Genomics 2010; 11:649. [PMID: 21092170 PMCID: PMC3091771 DOI: 10.1186/1471-2164-11-649] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2010] [Accepted: 11/22/2010] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Genomic imprinting is an evolutionary conserved mechanism of epigenetic gene regulation in placental mammals that results in silencing of one of the parental alleles. In order to decipher interactions between allele-specific DNA methylation of imprinted genes and evolutionary conservation, we performed a genome-wide comparative investigation of genomic sequences and highly conserved elements of imprinted genes in human and mouse. RESULTS Evolutionarily conserved elements in imprinted regions differ from those associated with autosomal genes in various ways. Whereas for maternally expressed genes strong divergence of protein-encoding sequences is most prominent, paternally expressed genes exhibit substantial conservation of coding and noncoding sequences. Conserved elements in imprinted regions are marked by enrichment of CpG dinucleotides and low (TpG+CpA)/(2·CpG) ratios indicate reduced CpG deamination. Interestingly, paternally and maternally expressed genes can be distinguished by differences in G+C and CpG contents that might be associated with unusual epigenetic features. Especially noncoding conserved elements of paternally expressed genes are exceptionally G+C and CpG rich. In addition, we confirmed a frequent occurrence of intronic CpG islands and observed a decelerated degeneration of ancient LINE-1 repeats. We also found a moderate enrichment of YY1 and CTCF binding sites in imprinted regions and identified several short sequence motifs in highly conserved elements that might act as additional regulatory elements. CONCLUSIONS We discovered several novel conserved DNA features that might be related to allele-specific DNA methylation. Our results hint at reduced CpG deamination rates in imprinted regions, which affects mostly noncoding conserved elements of paternally expressed genes. Pronounced differences between maternally and paternally expressed genes imply specific modes of evolution as a result of differences in epigenetic features and a special response to selective pressure. In addition, our data support the potential role of intronic CpG islands as epigenetic key regulatory elements and suggest that evolutionary conserved LINE-1 elements fulfill regulatory functions in imprinted regions.
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Affiliation(s)
- Barbara Hutter
- Lehrstuhl für Computational Biology, Universität des Saarlandes, Postfach 151150, D-66041 Saarbrücken, Germany
- Theoretische Bioinformatik (B080), Deutsches Krebsforschungszentrum, Im Neuenheimer Feld 580, D-69120 Heidelberg, Germany
| | - Matthias Bieg
- Lehrstuhl für Computational Biology, Universität des Saarlandes, Postfach 151150, D-66041 Saarbrücken, Germany
| | - Volkhard Helms
- Lehrstuhl für Computational Biology, Universität des Saarlandes, Postfach 151150, D-66041 Saarbrücken, Germany
| | - Martina Paulsen
- Lehrstuhl für Genetik/Epigenetik, Universität des Saarlandes, Postfach 151150, D-66041 Saarbrücken, Germany
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Abstract
Patterns and risks of human disease have evolved. In this article, I review evidence regarding the importance of recent adaptive evolution, positive selection, and genomic conflicts in shaping the genetic and phenotypic architectures of polygenic human diseases. Strong recent selection in human populations can create and maintain genetically based disease risk primarily through three processes: increased scope for dysregulation from recent human adaptations, divergent optima generated by intraspecific genomic conflicts, and transient or stable deleterious by-products of positive selection caused by antagonistic pleiotropy, ultimately due to trade-offs at the levels of molecular genetics, development, and physiology. Human disease due to these processes appears to be concentrated in three sets of phenotypes: cognition and emotion, reproductive traits, and life-history traits related to long life-span. Diverse, convergent lines of evidence suggest that a small set of tissues whose pleiotropic patterns of gene function and expression are under especially strong selection-brain, placenta, testis, prostate, breast, and ovary-has mediated a considerable proportion of disease risk in modern humans.
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Affiliation(s)
- Bernard J Crespi
- Department of Biosciences, Simon Fraser University, Burnaby, B. C., Canada V5A 1S6.
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Estécio MR, Gallegos J, Vallot C, Castoro RJ, Chung W, Maegawa S, Oki Y, Kondo Y, Jelinek J, Shen L, Hartung H, Aplan PD, Czerniak BA, Liang S, Issa JPJ. Genome architecture marked by retrotransposons modulates predisposition to DNA methylation in cancer. Genome Res 2010; 20:1369-82. [DOI: 10.1101/gr.107318.110] [Citation(s) in RCA: 71] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Epigenetic silencing plays an important role in cancer development. An attractive hypothesis is that local DNA features may participate in differential predisposition to gene hypermethylation. We found that, compared with methylation-resistant genes, methylation-prone genes have a lower frequency of SINE and LINE retrotransposons near their transcription start site. In several large testing sets, this distribution was highly predictive of promoter methylation. Genome-wide analysis showed that 22% of human genes were predicted to be methylation-prone in cancer; these tended to be genes that are down-regulated in cancer and that function in developmental processes. Moreover, retrotransposon distribution marks a larger fraction of methylation-prone genes compared to Polycomb group protein (PcG) marking in embryonic stem cells; indeed, PcG marking and our predictive model based on retrotransposon frequency appear to be correlated but also complementary. In summary, our data indicate that retrotransposon elements, which are widespread in our genome, are strongly associated with gene promoter DNA methylation in cancer and may in fact play a role in influencing epigenetic regulation in normal and abnormal physiological states.
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Muramoto H, Yagi S, Hirabayashi K, Sato S, Ohgane J, Tanaka S, Shiota K. Enrichment of short interspersed transposable elements to embryonic stem cell-specific hypomethylated gene regions. Genes Cells 2010; 15:855-65. [DOI: 10.1111/j.1365-2443.2010.01423.x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
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Lee SH, Cho SY, Shannon MF, Fan J, Rangasamy D. The impact of CpG island on defining transcriptional activation of the mouse L1 retrotransposable elements. PLoS One 2010; 5:e11353. [PMID: 20613872 PMCID: PMC2894050 DOI: 10.1371/journal.pone.0011353] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2010] [Accepted: 05/20/2010] [Indexed: 12/31/2022] Open
Abstract
Background L1 retrotransposable elements are potent insertional mutagens responsible for the generation of genomic variation and diversification of mammalian genomes, but reliable estimates of the numbers of actively transposing L1 elements are mostly nonexistent. While the human and mouse genomes contain comparable numbers of L1 elements, several phylogenetic and L1Xplore analyses in the mouse genome suggest that 1,500–3,000 active L1 elements currently exist and that they are still expanding in the genome. Conversely, the human genome contains only 150 active L1 elements. In addition, there is a discrepancy among the nature and number of mouse L1 elements in L1Xplore and the mouse genome browser at the UCSC and in the literature. To date, the reason why a high copy number of active L1 elements exist in the mouse genome but not in the human genome is unknown, as are the potential mechanisms that are responsible for transcriptional activation of mouse L1 elements. Methodology/Principal Findings We analyzed the promoter sequences of the 1,501 potentially active mouse L1 elements retrieved from the GenBank and L1Xplore databases and evaluated their transcription factors binding sites and CpG content. To this end, we found that a substantial number of mouse L1 elements contain altered transcription factor YY1 binding sites on their promoter sequences that are required for transcriptional initiation, suggesting that only a half of L1 elements are capable of being transcriptionally active. Furthermore, we present experimental evidence that previously unreported CpG islands exist in the promoters of the most active TF family of mouse L1 elements. The presence of sequence variations and polymorphisms in CpG islands of L1 promoters that arise from transition mutations indicates that CpG methylation could play a significant role in determining the activity of L1 elements in the mouse genome. Conclusions A comprehensive analysis of mouse L1 promoters suggests that the number of transcriptionally active elements is significantly lower than the total number of full-length copies from the three active mouse L1 families. Like human L1 elements, the CpG islands and potentially the transcription factor YY1 binding sites are likely to be required for transcriptional initiation of mouse L1 elements.
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Affiliation(s)
- Sung-Hun Lee
- The John Curtin School of Medical Research, Australian National University, Canberra, Australia
| | - Soo-Young Cho
- Division of Molecular and Life Sciences, Hanyang University, Ansan, Republic of Korea
| | - M. Frances Shannon
- The John Curtin School of Medical Research, Australian National University, Canberra, Australia
| | - Jun Fan
- The John Curtin School of Medical Research, Australian National University, Canberra, Australia
| | - Danny Rangasamy
- The John Curtin School of Medical Research, Australian National University, Canberra, Australia
- * E-mail:
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Abstract
There is longstanding evidence that X-chromosome inactivation
(XCI) travels less successfully in autosomal than in X-chromosomal chromatin. The interspersed repeat elements LINE1s (L1s) have been suggested as candidates for “boosters” which promote the spread of XCI in the X-chromosome. The present paper reviews the current evidence concerning the possible role of L1s in XCI. Recent evidence, accruing from the human genome sequencing project and other sources, confirms that mammalian X-chromosomes are indeed rich in L1s, except in regions where there are many genes escaping XCI. The density of L1s is the highest in the evolutionarily oldest regions. Recent work on X; autosome translocations in human and mouse suggested failure of stabilization of XCI in autosomal material, so that genes are reactivated, but resistance of autosomal genes to the original silencing is not excluded. The accumulation of L1s on the X-chromosome may have resulted from reduced recombination or late replication. Whether L1s are part of the mechanism of XCI or a
result of it remains enigmatic.
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Affiliation(s)
- Mary F. Lyon
- Mammalian Genetics Unit, Medical Research Council (MRC), Harwell, Oxfordshire OX11 0RD, UK
- *Mary F. Lyon:
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