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Tu K, Li X, Zhang Q, Huang W, Xie D. A data-adaptive methods in detecting exogenous methyltransferase accessible chromatin in human genome using nanopore sequencing. Bioinformatics 2024; 40:btae206. [PMID: 38613848 PMCID: PMC11256936 DOI: 10.1093/bioinformatics/btae206] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2023] [Revised: 03/15/2024] [Accepted: 04/12/2024] [Indexed: 04/15/2024] Open
Abstract
MOTIVATION Identifying chromatin accessibility is one of the key steps in studying the regulation of eukaryotic genomes. The combination of exogenous methyltransferase and nanopore sequencing provides an strategy to identify open chromatin over long genomic ranges at the single-molecule scale. However, endogenous methylation, non-open-chromatin-specific exogenous methylation and base-calling errors limit the accuracy and hinders its application to complex genomes. RESULTS We systematically evaluated the impact of these three influence factors, and developed a model-based computational method, methyltransferase accessible genome region finder (MAGNIFIER), to address the issues. By incorporating control data, MAGNIFIER attenuates the three influence factors with data-adaptive comparison strategy. We demonstrate that MAGNIFIER is not only sensitive to identify the open chromatin with much improved accuracy, but also able to detect the chromatin accessibility of repetitive regions that are missed by NGS-based methods. By incorporating long-read RNA-seq data, we revealed the association between the accessible Alu elements and non-classic gene isoforms. AVAILABILITY AND IMPLEMENTATION Freely available on web at https://github.com/Goatofmountain/MAGNIFIER.
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Affiliation(s)
- Kailing Tu
- National Frontier Center of Disease Molecular Network, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, Sichuan 610000, China
| | - Xuemei Li
- National Frontier Center of Disease Molecular Network, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, Sichuan 610000, China
| | - Qilin Zhang
- National Frontier Center of Disease Molecular Network, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, Sichuan 610000, China
| | - Wei Huang
- School of Mathematics and Statistics, Key Laboratory for Applied Statistics of the Ministry of Education, Northeast Normal University, Changchun 130024, China
| | - Dan Xie
- National Frontier Center of Disease Molecular Network, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, Sichuan 610000, China
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2
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Bhogale S, Seward C, Stubbs L, Sinha S. SEAMoD: A fully interpretable neural network for cis-regulatory analysis of differentially expressed genes. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.11.09.565900. [PMID: 38014229 PMCID: PMC10680628 DOI: 10.1101/2023.11.09.565900] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/29/2023]
Abstract
A common way to investigate gene regulatory mechanisms is to identify differentially expressed genes using transcriptomics, find their candidate enhancers using epigenomics, and search for over-represented transcription factor (TF) motifs in these enhancers using bioinformatics tools. A related follow-up task is to model gene expression as a function of enhancer sequences and rank TF motifs by their contribution to such models, thus prioritizing among regulators. We present a new computational tool called SEAMoD that performs the above tasks of motif finding and sequence-to-expression modeling simultaneously. It trains a convolutional neural network model to relate enhancer sequences to differential expression in one or more biological conditions. The model uses TF motifs to interpret the sequences, learning these motifs and their relative importance to each biological condition from data. It also utilizes epigenomic information in the form of activity scores of putative enhancers and automatically searches for the most promising enhancer for each gene. Compared to existing neural network models of non-coding sequences, SEAMoD uses far fewer parameters, requires far less training data, and emphasizes biological interpretability. We used SEAMoD to understand regulatory mechanisms underlying the differentiation of neural stem cell (NSC) derived from mouse forebrain. We profiled gene expression and histone modifications in NSC and three differentiated cell types and used SEAMoD to model differential expression of nearly 12,000 genes with an accuracy of 81%, in the process identifying the Olig2, E2f family TFs, Foxo3, and Tcf4 as key transcriptional regulators of the differentiation process.
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3
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Ouyang K, Liang Q, Miao L, Zhang Z, Li Z. Genome-wide mapping of DNase I hypersensitive sites in pineapple leaves. Front Genet 2023; 14:1086554. [PMID: 37470036 PMCID: PMC10352800 DOI: 10.3389/fgene.2023.1086554] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2022] [Accepted: 06/21/2023] [Indexed: 07/21/2023] Open
Abstract
Pineapple [Ananas comosus (L.) Merr.] is the most economically important crop possessing crassulacean acid metabolism (CAM) photosynthesis which has a higher water use efficiency by control of nocturnal opening and diurnal closure of stomata. To provide novel insights into the diel regulatory landscape in pineapple leaves, we performed genome-wide mapping of DNase I hypersensitive sites (DHSs) in pineapple leaves at day (2a.m.) and night (10a.m.) using a simplified DNase-seq method. As a result, totally 33340 and 28753 DHSs were found in green-tip tissue, and 29597 and 40068 were identified in white-base tissue at 2a.m. and 10a.m., respectively. We observed that majority of the pineapple genes occupied less than two DHSs with length shorter than 1 kb, and the promotor DHSs showed a proximal trend to the transcription start site (>77% promotor DHSs within 1 kb). In addition, more intergenic DHSs were identified around transcription factors or transcription co-regulators (TFs/TCs) than other functional genes, indicating complex regulatory contexts around TFs/TCs. Through combined analysis of tissue preferential DHSs and genes, we respectively found 839 and 888 coordinately changed genes in green-tip at 2a.m. and 10a.m. (AcG2 and AcG10). Furthermore, AcG2-specific, AcG10-specific and common accessible DHSs were dissected from the total photosynthetic preferential DHSs, and the regulatory networks indicated dynamic regulations with multiple cis-regulatory elements occurred to genes preferentially expressed in photosynthetic tissues. Interestingly, binding motifs of several cycling TFs were identified in the DHSs of key CAM genes, revealing a circadian regulation to CAM coordinately diurnal expression. Our results provide a chromatin regulatory landscape in pineapple leaves during the day and night. This will provide important information to assist with deciphering the circadian regulation of CAM photosynthesis.
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Affiliation(s)
- Kai Ouyang
- Key Laboratory of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education, Key Laboratory of Biological Breeding for Fujian and Taiwan Crops, Ministry of Agriculture and Rural Affairs, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Center for Genomics and Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Qifu Liang
- Fujian Key Laboratory of Agro-Products Quality and Safety, Institute of Quality Standards and Testing Technology for Agro-Products, Fujian Academy of Agricultural Sciences, Fuzhou, Fujian, China
| | - Li Miao
- Key Laboratory of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education, Key Laboratory of Biological Breeding for Fujian and Taiwan Crops, Ministry of Agriculture and Rural Affairs, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Center for Genomics and Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Zhiliang Zhang
- Key Laboratory of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education, Key Laboratory of Biological Breeding for Fujian and Taiwan Crops, Ministry of Agriculture and Rural Affairs, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Center for Genomics and Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, China
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Innovative Academy for Seed Design, Chinese Academy of Sciences, Beijing, China
| | - Zhanjie Li
- Key Laboratory of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education, Key Laboratory of Biological Breeding for Fujian and Taiwan Crops, Ministry of Agriculture and Rural Affairs, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Center for Genomics and Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, China
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4
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Qiu Y, Feng D, Jiang W, Zhang T, Lu Q, Zhao M. 3D genome organization and epigenetic regulation in autoimmune diseases. Front Immunol 2023; 14:1196123. [PMID: 37346038 PMCID: PMC10279977 DOI: 10.3389/fimmu.2023.1196123] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2023] [Accepted: 05/17/2023] [Indexed: 06/23/2023] Open
Abstract
Three-dimensional (3D) genomics is an emerging field of research that investigates the relationship between gene regulatory function and the spatial structure of chromatin. Chromatin folding can be studied using chromosome conformation capture (3C) technology and 3C-based derivative sequencing technologies, including chromosome conformation capture-on-chip (4C), chromosome conformation capture carbon copy (5C), and high-throughput chromosome conformation capture (Hi-C), which allow scientists to capture 3D conformations from a single site to the entire genome. A comprehensive analysis of the relationships between various regulatory components and gene function also requires the integration of multi-omics data such as genomics, transcriptomics, and epigenomics. 3D genome folding is involved in immune cell differentiation, activation, and dysfunction and participates in a wide range of diseases, including autoimmune diseases. We describe hierarchical 3D chromatin organization in this review and conclude with characteristics of C-techniques and multi-omics applications of the 3D genome. In addition, we describe the relationship between 3D genome structure and the differentiation and maturation of immune cells and address how changes in chromosome folding contribute to autoimmune diseases.
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Affiliation(s)
- Yueqi Qiu
- Institute of Dermatology, Chinese Academy of Medical Sciences and Peking Union Medical College, Nanjing, China
- Key Laboratory of Basic and Translational Research on Immune-Mediated Skin Diseases, Institute of Dermatology, Chinese Academy of Medical Sciences, Nanjing, China
| | - Delong Feng
- Department of Dermatology, The Second Xiangya Hospital of Central South University, Changsha, China
| | - Wenjuan Jiang
- Institute of Dermatology, Chinese Academy of Medical Sciences and Peking Union Medical College, Nanjing, China
- Key Laboratory of Basic and Translational Research on Immune-Mediated Skin Diseases, Institute of Dermatology, Chinese Academy of Medical Sciences, Nanjing, China
| | - Tingting Zhang
- Institute of Dermatology, Chinese Academy of Medical Sciences and Peking Union Medical College, Nanjing, China
- Key Laboratory of Basic and Translational Research on Immune-Mediated Skin Diseases, Institute of Dermatology, Chinese Academy of Medical Sciences, Nanjing, China
- State Key Laboratory of Natural Medicines, School of Basic Medicine and Clinical Pharmacy, China Pharmaceutical University, Nanjing, China
| | - Qianjin Lu
- Institute of Dermatology, Chinese Academy of Medical Sciences and Peking Union Medical College, Nanjing, China
- Key Laboratory of Basic and Translational Research on Immune-Mediated Skin Diseases, Institute of Dermatology, Chinese Academy of Medical Sciences, Nanjing, China
- Department of Dermatology, The Second Xiangya Hospital of Central South University, Changsha, China
| | - Ming Zhao
- Institute of Dermatology, Chinese Academy of Medical Sciences and Peking Union Medical College, Nanjing, China
- Key Laboratory of Basic and Translational Research on Immune-Mediated Skin Diseases, Institute of Dermatology, Chinese Academy of Medical Sciences, Nanjing, China
- Department of Dermatology, The Second Xiangya Hospital of Central South University, Changsha, China
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5
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Bina M. Defining Candidate Imprinted loci in Bos taurus. Genes (Basel) 2023; 14:1036. [PMID: 37239396 PMCID: PMC10217866 DOI: 10.3390/genes14051036] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2023] [Revised: 04/27/2023] [Accepted: 04/30/2023] [Indexed: 05/28/2023] Open
Abstract
Using a whole-genome assembly of Bos taurus, I applied my bioinformatics strategy to locate candidate imprinting control regions (ICRs) genome-wide. In mammals, genomic imprinting plays essential roles in embryogenesis. In my strategy, peaks in plots mark the locations of known, inferred, and candidate ICRs. Genes in the vicinity of candidate ICRs correspond to potential imprinted genes. By displaying my datasets on the UCSC genome browser, one could view peak positions with respect to genomic landmarks. I give two examples of candidate ICRs in loci that influence spermatogenesis in bulls: CNNM1 and CNR1. I also give examples of candidate ICRs in loci that influence muscle development: SIX1 and BCL6. By examining the ENCODE data reported for mice, I deduced regulatory clues about cattle. I focused on DNase I hypersensitive sites (DHSs). Such sites reveal accessibility of chromatin to regulators of gene expression. For inspection, I chose DHSs in chromatin from mouse embryonic stem cells (ESCs) ES-E14, mesoderm, brain, heart, and skeletal muscle. The ENCODE data revealed that the SIX1 promoter was accessible to the transcription initiation apparatus in mouse ESCs, mesoderm, and skeletal muscles. The data also revealed accessibility of BCL6 locus to regulatory proteins in mouse ESCs and examined tissues.
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Affiliation(s)
- Minou Bina
- Department of Chemistry, Purdue University, West Lafayette, IN 47907, USA
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6
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Marinov GK, Shipony Z, Kundaje A, Greenleaf WJ. Genome-Wide Mapping of Active Regulatory Elements Using ATAC-seq. Methods Mol Biol 2023; 2611:3-19. [PMID: 36807060 DOI: 10.1007/978-1-0716-2899-7_1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/23/2023]
Abstract
Active cis-regulatory elements (cREs) in eukaryotes are characterized by nucleosomal depletion and, accordingly, higher accessibility. This property has turned out to be immensely useful for identifying cREs genome-wide and tracking their dynamics across different cellular states and is the basis of numerous methods taking advantage of the preferential enzymatic cleavage/labeling of accessible DNA. ATAC-seq (Assay for Transposase-Accessible Chromatin using sequencing) has emerged as the most versatile and widely adaptable method and has been widely adopted as the standard tool for mapping open chromatin regions. Here, we discuss the current optimal practices and important considerations for carrying out ATAC-seq experiments, primarily in the context of mammalian systems.
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Affiliation(s)
| | - Zohar Shipony
- Department of Genetics, Stanford University, Stanford, CA, USA
| | - Anshul Kundaje
- Department of Genetics, Stanford University, Stanford, CA, USA.,Department of Computer Science, Stanford University, Stanford, CA, USA
| | - William J Greenleaf
- Department of Genetics, Stanford University, Stanford, CA, USA. .,Center for Personal Dynamic Regulomes, Stanford University, Stanford, CA, USA. .,Department of Applied Physics, Stanford University, Stanford, CA, USA. .,Chan Zuckerberg Biohub, San Francisco, CA, USA.
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7
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Shin B, Rothenberg EV. Multi-modular structure of the gene regulatory network for specification and commitment of murine T cells. Front Immunol 2023; 14:1108368. [PMID: 36817475 PMCID: PMC9928580 DOI: 10.3389/fimmu.2023.1108368] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2022] [Accepted: 01/11/2023] [Indexed: 02/04/2023] Open
Abstract
T cells develop from multipotent progenitors by a gradual process dependent on intrathymic Notch signaling and coupled with extensive proliferation. The stages leading them to T-cell lineage commitment are well characterized by single-cell and bulk RNA analyses of sorted populations and by direct measurements of precursor-product relationships. This process depends not only on Notch signaling but also on multiple transcription factors, some associated with stemness and multipotency, some with alternative lineages, and others associated with T-cell fate. These factors interact in opposing or semi-independent T cell gene regulatory network (GRN) subcircuits that are increasingly well defined. A newly comprehensive picture of this network has emerged. Importantly, because key factors in the GRN can bind to markedly different genomic sites at one stage than they do at other stages, the genes they significantly regulate are also stage-specific. Global transcriptome analyses of perturbations have revealed an underlying modular structure to the T-cell commitment GRN, separating decisions to lose "stem-ness" from decisions to block alternative fates. Finally, the updated network sheds light on the intimate relationship between the T-cell program, which depends on the thymus, and the innate lymphoid cell (ILC) program, which does not.
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Affiliation(s)
- Boyoung Shin
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, United States
| | - Ellen V. Rothenberg
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, United States
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8
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Genome-wide chromatin accessibility analysis unveils open chromatin convergent evolution during polyploidization in cotton. Proc Natl Acad Sci U S A 2022; 119:e2209743119. [PMID: 36279429 PMCID: PMC9636936 DOI: 10.1073/pnas.2209743119] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Allopolyploidization, resulting in divergent genomes in the same cell, is believed to trigger a “genome shock”, leading to broad genetic and epigenetic changes. However, little is understood about chromatin and gene-expression dynamics as underlying driving forces during allopolyploidization. Here, we examined the genome-wide DNase I-hypersensitive site (DHS) and its variations in domesticated allotetraploid cotton (
Gossypium hirsutum
and
Gossypium barbadense
, AADD) and its extant AA (
Gossypium arboreum
) and DD (
Gossypium raimondii
) progenitors. We observed distinct DHS distributions between
G. arboreum
and
G. raimondii
. In contrast, the DHSs of the two subgenomes of
G. hirsutum
and
G. barbadense
showed a convergent distribution. This convergent distribution of DHS was also present in the wild allotetraploids
Gossypium darwinii
and
G. hirsutum
var.
yucatanense
, but absent from a resynthesized hybrid of
G. arboreum
and
G. raimondii
, suggesting that it may be a common feature in polyploids, and not a consequence of domestication after polyploidization. We revealed that putative
cis
-regulatory elements (CREs) derived from polyploidization-related DHSs were dominated by several families, including Dof, ERF48, and BPC1. Strikingly, 56.6% of polyploidization-related DHSs were derived from transposable elements (TEs). Moreover, we observed positive correlations between DHS accessibility and the histone marks H3K4me3, H3K27me3, H3K36me3, H3K27ac, and H3K9ac, indicating that coordinated interplay among histone modifications, TEs, and CREs drives the DHS landscape dynamics under polyploidization. Collectively, these findings advance our understanding of the regulatory architecture in plants and underscore the complexity of regulome evolution during polyploidization.
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9
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Zhang X, Qiu H, Zhang F, Ding S. Advances in Single-Cell Multi-Omics and Application in Cardiovascular Research. Front Cell Dev Biol 2022; 10:883861. [PMID: 35733851 PMCID: PMC9207481 DOI: 10.3389/fcell.2022.883861] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2022] [Accepted: 05/23/2022] [Indexed: 12/30/2022] Open
Abstract
With the development of ever more powerful and versatile high-throughput sequencing techniques and innovative ways to capture single cells, mapping the multicellular tissues at the single-cell level is becoming routine practice. However, it is still challenging to depict the epigenetic landscape of a single cell, especially the genome-wide chromatin accessibility, histone modifications, and DNA methylation. We summarize the most recent methodologies to profile these epigenetic marks at the single-cell level. We also discuss the development and advancement of several multi-omics sequencing technologies from individual cells. Advantages and limitations of various methods to compare and integrate datasets obtained from different sources are also included with specific practical notes. Understanding the heart tissue at single-cell resolution and multi-modal levels will help to elucidate the cell types and states involved in physiological and pathological events during heart development and disease. The rich information produced from single-cell multi-omics studies will also promote the research of heart regeneration and precision medicine on heart diseases.
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Affiliation(s)
- Xingwu Zhang
- Center for Stem Cell Biology and Regenerative Medicine, School of Medicine, Tsinghua University, Beijing, China
- *Correspondence: Xingwu Zhang,
| | - Hui Qiu
- Center for Stem Cell Biology and Regenerative Medicine, School of Medicine, Tsinghua University, Beijing, China
- School of Life Sciences, Tsinghua University, Beijing, China
| | - Fengzhi Zhang
- First Hospital of Tsinghua University, Beijing, China
| | - Shuangyuan Ding
- Center for Stem Cell Biology and Regenerative Medicine, School of Medicine, Tsinghua University, Beijing, China
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10
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Petrusca DN, Mulcrone PL, Macar DA, Bishop RT, Berdyshev E, Suvannasankha A, Anderson JL, Sun Q, Auron PE, Galson DL, Roodman GD. GFI1-Dependent Repression of SGPP1 Increases Multiple Myeloma Cell Survival. Cancers (Basel) 2022; 14:cancers14030772. [PMID: 35159039 PMCID: PMC8833953 DOI: 10.3390/cancers14030772] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2021] [Revised: 01/27/2022] [Accepted: 01/31/2022] [Indexed: 11/16/2022] Open
Abstract
Simple Summary New therapies have greatly improved the progression-free and overall survival for patients with “standard risk” multiple myeloma (MM). However, patients with “high risk” MM, in particular patients whose MM cells harbor non-functional p53, have very short survival times because of the early relapse and rapid development of highly therapy-resistant MM. In this report, we identify a novel mechanism responsible for Growth Factor Independence-1 (GFI1) regulation of the growth and survival of MM cells through its modulation of sphingolipid metabolism, regardless of their p53 status. We identify the Sphingosine-1-Phosphate Phosphatase (SGPP1) gene as a novel direct target of GFI1 transcriptional repression in MM cells, thus increasing intracellular sphingosine-1-phosphate levels, which stabilizes c-Myc. Our results support GFI1 as an attractive therapeutic target for all types of MM, including the “high risk” patient population with non-functional p53, as well as a possible therapeutic approach for other types of cancers expressing high levels of c-Myc. Abstract Multiple myeloma (MM) remains incurable for most patients due to the emergence of drug resistant clones. Here we report a p53-independent mechanism responsible for Growth Factor Independence-1 (GFI1) support of MM cell survival by its modulation of sphingolipid metabolism to increase the sphingosine-1-phosphate (S1P) level regardless of the p53 status. We found that expression of enzymes that control S1P biosynthesis, SphK1, dephosphorylation, and SGPP1 were differentially correlated with GFI1 levels in MM cells. We detected GFI1 occupancy on the SGGP1 gene in MM cells in a predicted enhancer region at the 5’ end of intron 1, which correlated with decreased SGGP1 expression and increased S1P levels in GFI1 overexpressing cells, regardless of their p53 status. The high S1P:Ceramide intracellular ratio in MM cells protected c-Myc protein stability in a PP2A-dependent manner. The decreased MM viability by SphK1 inhibition was dependent on the induction of autophagy in both p53WT and p53mut MM. An autophagic blockade prevented GFI1 support for viability only in p53mut MM, demonstrating that GFI1 increases MM cell survival via both p53WT inhibition and upregulation of S1P independently. Therefore, GFI1 may be a key therapeutic target for all types of MM that may significantly benefit patients that are highly resistant to current therapies.
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Affiliation(s)
- Daniela N. Petrusca
- Department of Medicine, Hematology/Oncology Division, Indiana University School of Medicine, 980 Walnut St., Indianapolis, IN 46202, USA; (P.L.M.); (A.S.); (J.L.A.); (G.D.R.)
- Correspondence: ; Tel.: +1-(317)-278-5548
| | - Patrick L. Mulcrone
- Department of Medicine, Hematology/Oncology Division, Indiana University School of Medicine, 980 Walnut St., Indianapolis, IN 46202, USA; (P.L.M.); (A.S.); (J.L.A.); (G.D.R.)
| | - David A. Macar
- Department of Biological Sciences, Duquesne University, 600 Forbes Ave., Pittsburgh, PA 15219, USA; (D.A.M.); (P.E.A.)
| | - Ryan T. Bishop
- Department of Tumor Biology, H. Lee Moffitt Cancer Research Center and Institute, 12902 USF Magnolia Drive, Tampa, FL 33612, USA;
| | - Evgeny Berdyshev
- Department of Medicine, National Jewish Health, 1400 Jackson Street, Denver, CO 80206, USA;
| | - Attaya Suvannasankha
- Department of Medicine, Hematology/Oncology Division, Indiana University School of Medicine, 980 Walnut St., Indianapolis, IN 46202, USA; (P.L.M.); (A.S.); (J.L.A.); (G.D.R.)
- Richard L. Rodebush Veterans Affairs Medical Center, 1481 W 10th St., Indianapolis, IN 46202, USA
| | - Judith L. Anderson
- Department of Medicine, Hematology/Oncology Division, Indiana University School of Medicine, 980 Walnut St., Indianapolis, IN 46202, USA; (P.L.M.); (A.S.); (J.L.A.); (G.D.R.)
| | - Quanhong Sun
- Department of Medicine, Division of Hematology/Oncology, McGowan Institute for Regenerative Medicine, University of Pittsburgh, UPMC Hillman Cancer Center Research Pavilion, 5117 Centre Ave, Pittsburgh, PA 15213, USA; (Q.S.); (D.L.G.)
| | - Philip E. Auron
- Department of Biological Sciences, Duquesne University, 600 Forbes Ave., Pittsburgh, PA 15219, USA; (D.A.M.); (P.E.A.)
| | - Deborah L. Galson
- Department of Medicine, Division of Hematology/Oncology, McGowan Institute for Regenerative Medicine, University of Pittsburgh, UPMC Hillman Cancer Center Research Pavilion, 5117 Centre Ave, Pittsburgh, PA 15213, USA; (Q.S.); (D.L.G.)
| | - G. David Roodman
- Department of Medicine, Hematology/Oncology Division, Indiana University School of Medicine, 980 Walnut St., Indianapolis, IN 46202, USA; (P.L.M.); (A.S.); (J.L.A.); (G.D.R.)
- Richard L. Rodebush Veterans Affairs Medical Center, 1481 W 10th St., Indianapolis, IN 46202, USA
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11
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Marinov GK, Shipony Z, Kundaje A, Greenleaf WJ. Single-Molecule Multikilobase-Scale Profiling of Chromatin Accessibility Using m6A-SMAC-Seq and m6A-CpG-GpC-SMAC-Seq. Methods Mol Biol 2022; 2458:269-298. [PMID: 35103973 PMCID: PMC9531602 DOI: 10.1007/978-1-0716-2140-0_15] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
A hallmark feature of active cis-regulatory elements (CREs) in eukaryotes is their nucleosomal depletion and, accordingly, higher accessibility to enzymatic treatment. This property has been the basis of a number of sequencing-based assays for genome-wide identification and tracking the activity of CREs across different biological conditions, such as DNAse-seq, ATAC-seq , NOMeseq, and others. However, the fragmentation of DNA inherent to many of these assays and the limited read length of short-read sequencing platforms have so far not allowed the simultaneous measurement of the chromatin accessibility state of CREs located distally from each other. The combination of labeling accessible DNA with DNA modifications and nanopore sequencing has made it possible to develop such assays. Here, we provide a detailed protocol for carrying out the SMAC-seq assay (Single-Molecule long-read Accessible Chromatin mapping sequencing), in its m6A-SMAC-seq and m6A-CpG-GpC-SMAC-seq variants, together with methods for data processing and analysis, and discuss key experimental and analytical considerations for working with SMAC-seq datasets.
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Affiliation(s)
| | - Zohar Shipony
- Department of Genetics, Stanford University, Stanford, CA, USA.
| | - Anshul Kundaje
- Department of Genetics, Stanford University, Stanford, CA, USA
- Department of Computer Science, Stanford University, Stanford, CA, USA
| | - William J Greenleaf
- Department of Genetics, Stanford University, Stanford, CA, USA
- Center for Personal Dynamic Regulomes, Stanford University, Stanford, CA, USA
- Department of Applied Physics, Stanford University, Stanford, CA, USA
- Chan Zuckerberg Biohub, San Francisco, CA, USA
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12
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Grencewicz DJ, Romigh T, Thacker S, Abbas A, Jaini R, Luse D, Eng C. Redefining the PTEN promoter: Identification of novel upstream transcription start regions. Hum Mol Genet 2021; 30:2135-2148. [PMID: 34218272 DOI: 10.1093/hmg/ddab175] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2021] [Revised: 06/19/2021] [Accepted: 06/23/2021] [Indexed: 11/14/2022] Open
Abstract
Germline mutation of PTEN is causally observed in Cowden syndrome (CS) and is one of the most common, penetrant risk genes for autism spectrum disorder (ASD). However, the majority of individuals who present with CS-like clinical features are PTEN-mutation negative. Reassessment of PTEN promoter regulation may help explain abnormal PTEN dosage, as only the minimal promoter and coding regions are currently included in diagnostic PTEN mutation analysis. Therefore, we reanalyzed the architecture of the PTEN promoter using next-generation sequencing datasets. Specifically, run-on sequencing assays identified two additional transcription start regions (TSRs) at -2053 and - 1906 basepairs from the canonical start of PTEN, thus extending the PTEN 5'UTR and redefining the PTEN promoter. We show that these novel upstream TSRs are active in cancer cell lines, human cancer, and normal tissue. Further, these TSRs can produce novel PTEN transcripts due to the introduction of new splice donors at -2041, -1826, and - 1355, which may allow for splicing out of the PTEN 5'UTR or the first and second exon in upstream-initiated transcripts. Combining ENCODE ChIP-seq and pertinent literature, we also compile and analyze all transcription factors (TFs) binding at the redefined PTEN locus. Enrichment analyses suggest that TFs bind specifically to the upstream TSRs may be implicated in inflammatory processes. Together, these data redefine the architecture of the PTEN promoter, an important step toward a comprehensive model of PTEN transcription regulation, a basis for future investigations into the new promoters' role in disease pathogenesis.
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Affiliation(s)
- Dennis J Grencewicz
- Genomic Medicine Institute, Lerner Research Institute, Cleveland Clinic, Cleveland, OH, 44195, USA
| | - Todd Romigh
- Genomic Medicine Institute, Lerner Research Institute, Cleveland Clinic, Cleveland, OH, 44195, USA.,Department of Cardiovascular and Metabolic Sciences, Lerner Research Institute, Cleveland Clinic, Cleveland, OH 44195, USA
| | - Stetson Thacker
- Genomic Medicine Institute, Lerner Research Institute, Cleveland Clinic, Cleveland, OH, 44195, USA.,Department of Molecular Medicine, Cleveland Clinic Lerner College of Medicine, Case Western Reserve University, Cleveland, OH 44106, USA
| | - Ata Abbas
- Division of Hematology and Oncology, Department of Medicine, Case Western Reserve University, Cleveland, OH 44106, USA.,Developmental Therapeutics Program, CASE Comprehensive Cancer Center, Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA
| | - Ritika Jaini
- Genomic Medicine Institute, Lerner Research Institute, Cleveland Clinic, Cleveland, OH, 44195, USA.,Department of Molecular Medicine, Cleveland Clinic Lerner College of Medicine, Case Western Reserve University, Cleveland, OH 44106, USA.,Developmental Therapeutics Program, CASE Comprehensive Cancer Center, Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA.,Germline High Risk Focus Group, CASE Comprehensive Cancer Center, Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA
| | - Donal Luse
- Department of Cardiovascular and Metabolic Sciences, Lerner Research Institute, Cleveland Clinic, Cleveland, OH 44195, USA.,Department of Molecular Medicine, Cleveland Clinic Lerner College of Medicine, Case Western Reserve University, Cleveland, OH 44106, USA
| | - Charis Eng
- Genomic Medicine Institute, Lerner Research Institute, Cleveland Clinic, Cleveland, OH, 44195, USA.,Department of Molecular Medicine, Cleveland Clinic Lerner College of Medicine, Case Western Reserve University, Cleveland, OH 44106, USA.,Germline High Risk Focus Group, CASE Comprehensive Cancer Center, Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA.,Center for Personalized Genetic Healthcare, Cleveland Clinic Community Care and Population Health, Cleveland, OH 44195, USA.,Department of Genetics and Genome Sciences, Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA
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13
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Abstract
DNase I hypersensitive site (DHS) mapping combined with high-throughput sequencing (DNase-seq) enables the identification of cis-regulatory DNA elements (CREs) genome wide. However, despite the wide applications of DNase-seq in plants, its application to the highly repetitive genomes of plants has lagged. Here, we describe a modified DNase-seq method, making it more practical for application to plants with genomes enriched with repetitive DNA. This approach adopts a double-hit-based strategy, in which small (<250-bp) DNA fragments digested by DNase I are selected and used for sequencing library construction. Using these protocols, we have conducted DNase-seq in plants with high content of repetitive DNA, including maize, sugarcane, and tetraploid cotton. Genome-wide maps of DHS and CREs have been created using these DNase-seq datasets. © 2021 Wiley Periodicals LLC. Basic Protocol 1: Nuclei isolation Basic Protocol 2: DNase I digestion Basic Protocol 3: Target DNA isolation Basic Protocol 4: Library construction and validation.
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Affiliation(s)
- Yankun Wang
- Key Laboratory of Genetics, Breeding and Multiple Utilization of Crops (MOE), Fujian Agriculture and Forestry University, Fuzhou, China
| | - Kai Wang
- School of Life Science, Nantong University, Nantong, China.,Key Laboratory of Genetics, Breeding and Multiple Utilization of Crops (MOE), Fujian Agriculture and Forestry University, Fuzhou, China
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14
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Genomic Space of MGMT in Human Glioma Revisited: Novel Motifs, Regulatory RNAs, NRF1, 2, and CTCF Involvement in Gene Expression. Int J Mol Sci 2021; 22:ijms22052492. [PMID: 33801310 PMCID: PMC7958331 DOI: 10.3390/ijms22052492] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2021] [Revised: 02/18/2021] [Accepted: 02/25/2021] [Indexed: 01/08/2023] Open
Abstract
Background: The molecular regulation of increased MGMT expression in human brain tumors, the associated regulatory elements, and linkages of these to its epigenetic silencing are not understood. Because the heightened expression or non-expression of MGMT plays a pivotal role in glioma therapeutics, we applied bioinformatics and experimental tools to identify the regulatory elements in the MGMT and neighboring EBF3 gene loci. Results: Extensive genome database analyses showed that the MGMT genomic space was rich in and harbored many undescribed RNA regulatory sequences and recognition motifs. We extended the MGMT’s exon-1 promoter to 2019 bp to include five overlapping alternate promoters. Consensus sequences in the revised promoter for (a) the transcriptional factors CTCF, NRF1/NRF2, GAF, (b) the genetic switch MYC/MAX/MAD, and (c) two well-defined p53 response elements in MGMT intron-1, were identified. A putative protein-coding or non-coding RNA sequence was located in the extended 3′ UTR of the MGMT transcript. Eleven non-coding RNA loci coding for miRNAs, antisense RNA, and lncRNAs were identified in the MGMT-EBF3 region and six of these showed validated potential for curtailing the expression of both MGMT and EBF3 genes. ChIP analysis verified the binding site in MGMT promoter for CTCF which regulates the genomic methylation and chromatin looping. CTCF depletion by a pool of specific siRNA and shRNAs led to a significant attenuation of MGMT expression in human GBM cell lines. Computational analysis of the ChIP sequence data in ENCODE showed the presence of NRF1 in the MGMT promoter and this occurred only in MGMT-proficient cell lines. Further, an enforced NRF2 expression markedly augmented the MGMT mRNA and protein levels in glioma cells. Conclusions: We provide the first evidence for several new regulatory components in the MGMT gene locus which predict complex transcriptional and posttranscriptional controls with potential for new therapeutic avenues.
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15
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Zhou L, Huang Y, Wang Q, Guo D. Chromatin Accessibility Is Associated with Artemisinin Biosynthesis Regulation in Artemisia annua. Molecules 2021; 26:molecules26041194. [PMID: 33672342 PMCID: PMC7926469 DOI: 10.3390/molecules26041194] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2021] [Revised: 02/19/2021] [Accepted: 02/20/2021] [Indexed: 11/21/2022] Open
Abstract
Glandular trichome (GT) is the dominant site for artemisinin production in Artemisia annua. Several critical genes involved in artemisinin biosynthesis are specifically expressed in GT. However, the molecular mechanism of differential gene expression between GT and other tissue types remains elusive. Chromatin accessibility, defined as the degree to which nuclear molecules are able to interact with chromatin DNA, reflects gene expression capacity to a certain extent. Here, we investigated and compared the landscape of chromatin accessibility in Artemisia annua leaf and GT using the Assay for Transposase-Accessible Chromatin using sequencing (ATAC-seq) technique. We identified 5413 GT high accessible and 4045 GT low accessible regions, and these GT high accessible regions may contribute to GT-specific biological functions. Several GT-specific artemisinin biosynthetic genes, such as DBR2 and CYP71AV1, showed higher accessible regions in GT compared to that in leaf, implying that they might be regulated by chromatin accessibility. In addition, transcription factor binding motifs for MYB, bZIP, C2H2, and AP2 were overrepresented in the highly accessible chromatin regions associated with artemisinin biosynthetic genes in glandular trichomes. Finally, we proposed a working model illustrating the chromatin accessibility dynamics in regulating artemisinin biosynthetic gene expression. This work provided new insights into epigenetic regulation of gene expression in GT.
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Affiliation(s)
- Limeng Zhou
- State Key Laboratory of Agrobiotechnology, School of Life Science, The Chinese University of Hong Kong, Hong Kong 999077, China; (L.Z.); (Y.H.)
| | - Yingzhang Huang
- State Key Laboratory of Agrobiotechnology, School of Life Science, The Chinese University of Hong Kong, Hong Kong 999077, China; (L.Z.); (Y.H.)
| | - Qi Wang
- Artemisinin Research Center, Guangzhou University of Chinese Medicine, Guangzhou 510000, China;
| | - Dianjing Guo
- State Key Laboratory of Agrobiotechnology, School of Life Science, The Chinese University of Hong Kong, Hong Kong 999077, China; (L.Z.); (Y.H.)
- Correspondence: ; Tel.: +852-3943-6298
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16
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Abstract
The ATAC-seq assay has emerged as the most useful, versatile, and widely adaptable method for profiling accessible chromatin regions and tracking the activity of cis-regulatory elements (cREs) in eukaryotes. Thanks to its great utility, it is now being applied to map active chromatin in the context of a very wide diversity of biological systems and questions. In the course of these studies, considerable experience working with ATAC-seq data has accumulated and a standard set of computational tasks that need to be carried for most ATAC-seq analyses has emerged. Here, we review and provide examples of common such analytical procedures (including data processing, quality control, peak calling, identifying differentially accessible open chromatin regions, and variable transcription factor (TF) motif accessibility) and discuss recommended optimal practices.
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17
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Reddington JP, Garfield DA, Sigalova OM, Karabacak Calviello A, Marco-Ferreres R, Girardot C, Viales RR, Degner JF, Ohler U, Furlong EEM. Lineage-Resolved Enhancer and Promoter Usage during a Time Course of Embryogenesis. Dev Cell 2020; 55:648-664.e9. [PMID: 33171098 DOI: 10.1016/j.devcel.2020.10.009] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2020] [Revised: 08/04/2020] [Accepted: 10/09/2020] [Indexed: 02/01/2023]
Abstract
Enhancers are essential drivers of cell states, yet the relationship between accessibility, regulatory activity, and in vivo lineage commitment during embryogenesis remains poorly understood. Here, we measure chromatin accessibility in isolated neural and mesodermal lineages across a time course of Drosophila embryogenesis. Promoters, including tissue-specific genes, are often constitutively open, even in contexts where the gene is not expressed. In contrast, the majority of distal elements have dynamic, tissue-specific accessibility. Enhancer priming appears rarely within a lineage, perhaps reflecting the speed of Drosophila embryogenesis. However, many tissue-specific enhancers are accessible in other lineages early on and become progressively closed as embryogenesis proceeds. We demonstrate the usefulness of this tissue- and time-resolved resource to definitively identify single-cell clusters, to uncover predictive motifs, and to identify many regulators of tissue development. For one such predicted neural regulator, l(3)neo38, we generate a loss-of-function mutant and uncover an essential role for neuromuscular junction and brain development.
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Affiliation(s)
- James P Reddington
- European Molecular Biology Laboratory (EMBL), Genome Biology Unit, 69117 Heidelberg, Germany
| | - David A Garfield
- European Molecular Biology Laboratory (EMBL), Genome Biology Unit, 69117 Heidelberg, Germany
| | - Olga M Sigalova
- European Molecular Biology Laboratory (EMBL), Genome Biology Unit, 69117 Heidelberg, Germany
| | | | - Raquel Marco-Ferreres
- European Molecular Biology Laboratory (EMBL), Genome Biology Unit, 69117 Heidelberg, Germany
| | - Charles Girardot
- European Molecular Biology Laboratory (EMBL), Genome Biology Unit, 69117 Heidelberg, Germany
| | - Rebecca R Viales
- European Molecular Biology Laboratory (EMBL), Genome Biology Unit, 69117 Heidelberg, Germany
| | - Jacob F Degner
- European Molecular Biology Laboratory (EMBL), Genome Biology Unit, 69117 Heidelberg, Germany
| | - Uwe Ohler
- Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine, Berlin, Germany
| | - Eileen E M Furlong
- European Molecular Biology Laboratory (EMBL), Genome Biology Unit, 69117 Heidelberg, Germany.
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18
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Abstract
Spatiotemporal control of gene expression during development requires orchestrated activities of numerous enhancers, which are cis-regulatory DNA sequences that, when bound by transcription factors, support selective activation or repression of associated genes. Proper activation of enhancers is critical during embryonic development, adult tissue homeostasis, and regeneration, and inappropriate enhancer activity is often associated with pathological conditions such as cancer. Multiple consortia [e.g., the Encyclopedia of DNA Elements (ENCODE) Consortium and National Institutes of Health Roadmap Epigenomics Mapping Consortium] and independent investigators have mapped putative regulatory regions in a large number of cell types and tissues, but the sequence determinants of cell-specific enhancers are not yet fully understood. Machine learning approaches trained on large sets of these regulatory regions can identify core transcription factor binding sites and generate quantitative predictions of enhancer activity and the impact of sequence variants on activity. Here, we review these computational methods in the context of enhancer prediction and gene regulatory network models specifying cell fate.
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Affiliation(s)
- Michael A Beer
- Department of Biomedical Engineering and McKusick-Nathans Department of Genetic Medicine, Johns Hopkins University, Baltimore, Maryland 21205, USA;
| | - Dustin Shigaki
- Department of Biomedical Engineering and McKusick-Nathans Department of Genetic Medicine, Johns Hopkins University, Baltimore, Maryland 21205, USA;
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19
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Harkins KM, Schaefer NK, Troll CJ, Rao V, Kapp J, Naughton C, Shapiro B, Green RE. A novel NGS library preparation method to characterize native termini of fragmented DNA. Nucleic Acids Res 2020; 48:e47. [PMID: 32112100 PMCID: PMC7192605 DOI: 10.1093/nar/gkaa128] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2019] [Revised: 02/13/2020] [Accepted: 02/20/2020] [Indexed: 12/22/2022] Open
Abstract
Biological and chemical DNA fragmentation generates DNA molecules with a variety of termini, including blunt ends and single-stranded overhangs. We have developed a Next Generation Sequencing (NGS) assay, XACTLY, to interrogate the termini of fragmented DNA, information traditionally lost in standard NGS library preparation methods. Here we describe the XACTLY method, showcase its sensitivity and specificity, and demonstrate its utility in in vitro experiments. The XACTLY assay is able to report relative abundances of all lengths and types (5′ and 3′) of single-stranded overhangs, if present, on each DNA fragment with an overall accuracy between 80–90%. In addition, XACTLY retains the sequence of each native DNA molecule after fragmentation and can capture the genomic landscape of cleavage events at single nucleotide resolution. The XACTLY assay can be applied as a novel research and discovery tool for fragmentation analyses and in cell-free DNA.
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Affiliation(s)
| | - Nathan K Schaefer
- Department of Biomolecular Engineering, University of California Santa Cruz, Santa Cruz, CA 95064, USA
| | | | - Varsha Rao
- Claret Bioscience LLC, Santa Cruz, CA 95060, USA
| | - Joshua Kapp
- Department of Ecology and Evolutionary Biology, University of California, Santa Cruz, CA 95064, USA
| | | | - Beth Shapiro
- Department of Ecology and Evolutionary Biology, University of California, Santa Cruz, CA 95064, USA.,Howard Hughes Medical Institute, University of California, Santa Cruz, CA 95064, USA
| | - Richard E Green
- Department of Biomolecular Engineering, University of California Santa Cruz, Santa Cruz, CA 95064, USA
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20
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Liu Y, Fu L, Kaufmann K, Chen D, Chen M. A practical guide for DNase-seq data analysis: from data management to common applications. Brief Bioinform 2020; 20:1865-1877. [PMID: 30010713 DOI: 10.1093/bib/bby057] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2018] [Revised: 06/06/2018] [Accepted: 06/10/2018] [Indexed: 01/01/2023] Open
Abstract
Deoxyribonuclease I (DNase I)-hypersensitive site sequencing (DNase-seq) has been widely used to determine chromatin accessibility and its underlying regulatory lexicon. However, exploring DNase-seq data requires sophisticated downstream bioinformatics analyses. In this study, we first review computational methods for all of the major steps in DNase-seq data analysis, including experimental design, quality control, read alignment, peak calling, annotation of cis-regulatory elements, genomic footprinting and visualization. The challenges associated with each step are highlighted. Next, we provide a practical guideline and a computational pipeline for DNase-seq data analysis by integrating some of these tools. We also discuss the competing techniques and the potential applications of this pipeline for the analysis of analogous experimental data. Finally, we discuss the integration of DNase-seq with other functional genomics techniques.
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Affiliation(s)
- Yongjing Liu
- Department of Bioinformatics, College of Life Sciences, Zhejiang University, Hangzhou 310058, China
| | - Liangyu Fu
- Department for Plant Cell and Molecular Biology, Institute for Biology, Humboldt-Universität zu Berlin, Berlin 10115, Germany
| | - Kerstin Kaufmann
- Department for Plant Cell and Molecular Biology, Institute for Biology, Humboldt-Universität zu Berlin, Berlin 10115, Germany
| | - Dijun Chen
- Department of Bioinformatics, College of Life Sciences, Zhejiang University, Hangzhou 310058, China
| | - Ming Chen
- Department for Plant Cell and Molecular Biology, Institute for Biology, Humboldt-Universität zu Berlin, Berlin 10115, Germany
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21
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Kremsky I, Corces VG. Protection from DNA re-methylation by transcription factors in primordial germ cells and pre-implantation embryos can explain trans-generational epigenetic inheritance. Genome Biol 2020; 21:118. [PMID: 32423419 PMCID: PMC7236515 DOI: 10.1186/s13059-020-02036-w] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2019] [Accepted: 05/05/2020] [Indexed: 12/16/2022] Open
Abstract
Background A growing body of evidence suggests that certain epiphenotypes can be passed across generations via both the male and female germlines of mammals. These observations have been difficult to explain owing to a global loss of the majority of known epigenetic marks present in parental chromosomes during primordial germ cell development and after fertilization. Results By integrating previously published BS-seq, DNase-seq, ATAC-seq, and RNA-seq data collected during multiple stages of primordial germ cell and pre-implantation development, we find that the methylation status of the majority of CpGs genome-wide is restored after global de-methylation, despite the fact that global CpG methylation drops to 10% in primordial germ cells and 20% in the inner cell mass of the blastocyst. We estimate the proportion of such CpGs with preserved methylation status to be 78%. Further, we find that CpGs at sites bound by transcription factors during the global re-methylation phases of germline and embryonic development remain hypomethylated across all developmental stages observed. On the other hand, CpGs at sites not bound by transcription factors during the global re-methylation phase have high methylation levels prior to global de-methylation, become de-methylated during global de-methylation, and then become re-methylated. Conclusions The results suggest that transcription factors can act as carriers of epigenetic information during germ cell and pre-implantation development by ensuring that the methylation status of CpGs is maintained. These findings provide the basis for a mechanistic description of trans-generational inheritance of epigenetic information in mammals.
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Affiliation(s)
- Isaac Kremsky
- Department of Human Genetics, Emory University School of Medicine, Atlanta, GA, 30322, USA
| | - Victor G Corces
- Department of Human Genetics, Emory University School of Medicine, Atlanta, GA, 30322, USA.
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22
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Gasperini M, Tome JM, Shendure J. Towards a comprehensive catalogue of validated and target-linked human enhancers. Nat Rev Genet 2020; 21:292-310. [PMID: 31988385 PMCID: PMC7845138 DOI: 10.1038/s41576-019-0209-0] [Citation(s) in RCA: 159] [Impact Index Per Article: 39.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/13/2019] [Indexed: 12/14/2022]
Abstract
The human gene catalogue is essentially complete, but we lack an equivalently vetted inventory of bona fide human enhancers. Hundreds of thousands of candidate enhancers have been nominated via biochemical annotations; however, only a handful of these have been validated and confidently linked to their target genes. Here we review emerging technologies for discovering, characterizing and validating human enhancers at scale. We furthermore propose a new framework for operationally defining enhancers that accommodates the heterogeneous and complementary results that are emerging from reporter assays, biochemical measurements and CRISPR screens.
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Affiliation(s)
- Molly Gasperini
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | - Jacob M Tome
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | - Jay Shendure
- Department of Genome Sciences, University of Washington, Seattle, WA, USA.
- Brotman Baty Institute for Precision Medicine, Seattle, WA, USA.
- Allen Discovery Center for Cell Lineage, Seattle, WA, USA.
- Howard Hughes Medical Institute, University of Washington, Seattle, WA, USA.
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23
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Shipony Z, Marinov GK, Swaffer MP, Sinnott-Armstrong NA, Skotheim JM, Kundaje A, Greenleaf WJ. Long-range single-molecule mapping of chromatin accessibility in eukaryotes. Nat Methods 2020; 17:319-327. [PMID: 32042188 PMCID: PMC7968351 DOI: 10.1038/s41592-019-0730-2] [Citation(s) in RCA: 60] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2019] [Accepted: 12/22/2019] [Indexed: 02/06/2023]
Abstract
Mapping open chromatin regions has emerged as a widely used tool for identifying active regulatory elements in eukaryotes. However, existing approaches, limited by reliance on DNA fragmentation and short-read sequencing, cannot provide information about large-scale chromatin states or reveal coordination between the states of distal regulatory elements. We have developed a method for profiling the accessibility of individual chromatin fibers, a single-molecule long-read accessible chromatin mapping sequencing assay (SMAC-seq), enabling the simultaneous, high-resolution, single-molecule assessment of chromatin states at multikilobase length scales. Our strategy is based on combining the preferential methylation of open chromatin regions by DNA methyltransferases with low sequence specificity, in this case EcoGII, an N6-methyladenosine (m6A) methyltransferase, and the ability of nanopore sequencing to directly read DNA modifications. We demonstrate that aggregate SMAC-seq signals match bulk-level accessibility measurements, observe single-molecule nucleosome and transcription factor protection footprints, and quantify the correlation between chromatin states of distal genomic elements.
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Affiliation(s)
- Zohar Shipony
- Department of Genetics, Stanford University, Stanford, CA, USA
| | | | | | | | - Jan M Skotheim
- Department of Biology, Stanford University, Stanford, CA, USA
| | - Anshul Kundaje
- Department of Genetics, Stanford University, Stanford, CA, USA
- Department of Computer Science, Stanford University, Stanford, CA, USA
| | - William J Greenleaf
- Department of Genetics, Stanford University, Stanford, CA, USA.
- Department of Applied Physics, Stanford University, Stanford, CA, USA.
- Chan Zuckerberg Biohub, San Francisco, CA, USA.
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24
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Bhattacharya A, García-Closas M, Olshan AF, Perou CM, Troester MA, Love MI. A framework for transcriptome-wide association studies in breast cancer in diverse study populations. Genome Biol 2020; 21:42. [PMID: 32079541 PMCID: PMC7033948 DOI: 10.1186/s13059-020-1942-6] [Citation(s) in RCA: 47] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2019] [Accepted: 01/21/2020] [Indexed: 12/18/2022] Open
Abstract
BACKGROUND The relationship between germline genetic variation and breast cancer survival is largely unknown, especially in understudied minority populations who often have poorer survival. Genome-wide association studies (GWAS) have interrogated breast cancer survival but often are underpowered due to subtype heterogeneity and clinical covariates and detect loci in non-coding regions that are difficult to interpret. Transcriptome-wide association studies (TWAS) show increased power in detecting functionally relevant loci by leveraging expression quantitative trait loci (eQTLs) from external reference panels in relevant tissues. However, ancestry- or race-specific reference panels may be needed to draw correct inference in ancestrally diverse cohorts. Such panels for breast cancer are lacking. RESULTS We provide a framework for TWAS for breast cancer in diverse populations, using data from the Carolina Breast Cancer Study (CBCS), a population-based cohort that oversampled black women. We perform eQTL analysis for 406 breast cancer-related genes to train race-stratified predictive models of tumor expression from germline genotypes. Using these models, we impute expression in independent data from CBCS and TCGA, accounting for sampling variability in assessing performance. These models are not applicable across race, and their predictive performance varies across tumor subtype. Within CBCS (N = 3,828), at a false discovery-adjusted significance of 0.10 and stratifying for race, we identify associations in black women near AURKA, CAPN13, PIK3CA, and SERPINB5 via TWAS that are underpowered in GWAS. CONCLUSIONS We show that carefully implemented and thoroughly validated TWAS is an efficient approach for understanding the genetics underpinning breast cancer outcomes in diverse populations.
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Affiliation(s)
- Arjun Bhattacharya
- Department of Biostatistics, University of North Carolina-Chapel Hill, Chapel Hill, USA
| | - Montserrat García-Closas
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, USA
- Division of Genetics and Epidemiology, Institute of Cancer Research, London, UK
| | - Andrew F. Olshan
- Department of Epidemiology, University of North Carolina-Chapel Hill, Chapel Hill, USA
- Lineberger Comprehensive Cancer Center, University of North Carolina-Chapel Hill, Chapel Hill, USA
| | - Charles M. Perou
- Lineberger Comprehensive Cancer Center, University of North Carolina-Chapel Hill, Chapel Hill, USA
- Department of Genetics, University of North Carolina-Chapel Hill, Chapel Hill, USA
- Department of Pathology and Laboratory Medicine, University of North Carolina-Chapel Hill, Chapel Hill, USA
| | - Melissa A. Troester
- Department of Epidemiology, University of North Carolina-Chapel Hill, Chapel Hill, USA
- Department of Pathology and Laboratory Medicine, University of North Carolina-Chapel Hill, Chapel Hill, USA
| | - Michael I. Love
- Department of Biostatistics, University of North Carolina-Chapel Hill, Chapel Hill, USA
- Department of Genetics, University of North Carolina-Chapel Hill, Chapel Hill, USA
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25
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Zhou J, Li Y, Cao H, Yang M, Chu L, Li T, Yu Z, Yu R, Qiu B, Wang Q, Li X, Xie J. CATA: a comprehensive chromatin accessibility database for cancer. Database (Oxford) 2020; 2022:6520815. [PMID: 35134148 PMCID: PMC9246274 DOI: 10.1093/database/baab085] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2021] [Revised: 12/05/2021] [Accepted: 12/29/2021] [Indexed: 11/30/2022]
Abstract
Accessible chromatin refers to the active regions of a chromosome that are bound by many transcription factors (TFs). Changes in chromatin accessibility play a critical role in tumorigenesis. With the emergence of novel methods like Assay for Transposase-accessible Chromatin Sequencing, a sequencing method that maps chromatin-accessible regions (CARs) and enables the computational analysis of TF binding at chromatin-accessible sites, the regulatory landscape in cancer can be dissected. Herein, we developed a comprehensive cancer chromatin accessibility database named CATA, which aims to provide available resources of cancer CARs and to annotate their potential roles in the regulation of genes in a cancer type-specific manner. In this version, CATA stores 2 991 163 CARs from 23 cancer types, binding information of 1398 TFs within the CARs, and provides multiple annotations about these regions, including common single nucleotide polymorphisms (SNPs), risk SNPs, copy number variation, somatic mutations, motif changes, expression quantitative trait loci, methylation and CRISPR/Cas9 target loci. Moreover, CATA supports cancer survival analysis of the CAR-associated genes and provides detailed clinical information of the tumor samples. Database URL: CATA is available at http://www.xiejjlab.bio/cata/.
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Affiliation(s)
- Jianyuan Zhou
- Central Laboratory of Molecular Biology, Medical College of Jiaying University, 146 Huangtang Road, Meizhou 514031, China
- Shandong Provincial Key Laboratory of Radiation Oncology, Cancer Research Center, Shandong Cancer Hospital and Institute, Shandong
- First Medical University, and Shandong Academy of Medical Sciences, 440 Jiyan Road, Jinan 250000, China
| | | | | | - Min Yang
- Department of Biochemistry and Molecular Biology, Shantou University Medical College, 22 Xinling Road, Shantou 515041, China
| | - Lingyu Chu
- Department of Biochemistry and Molecular Biology, Shantou University Medical College, 22 Xinling Road, Shantou 515041, China
| | - Taisong Li
- Department of Biochemistry and Molecular Biology, Shantou University Medical College, 22 Xinling Road, Shantou 515041, China
| | - Zhengmin Yu
- School of Medical Informatics, Harbin Medical University, Daqing Campus, Daqing 163319, China
| | - Rui Yu
- School of Medical Informatics, Harbin Medical University, Daqing Campus, Daqing 163319, China
| | - Bo Qiu
- Central Laboratory of Molecular Biology, Medical College of Jiaying University, 146 Huangtang Road, Meizhou 514031, China
| | - Qiuyu Wang
- School of Medical Informatics, Harbin Medical University, Daqing Campus, Daqing 163319, China
| | - Xuecang Li
- School of Medical Informatics, Harbin Medical University, Daqing Campus, Daqing 163319, China
| | - Jianjun Xie
- Department of Biochemistry and Molecular Biology, Shantou University Medical College, 22 Xinling Road, Shantou 515041, China
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26
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Abstract
cis-regulatory DNA elements (CREs) are noncoding but functional DNA sequences. The binding of regulatory proteins into CRE regions leads to chromatin high sensitive to DNase I digestion, which are termed as DNase I hypersensitive sites (DHSs). These DHSs can be efficiently detected through DNase I digestion followed by high-throughput DNA sequencing (DNase-seq). Thus, DNase-seq has become a powerful technique for DHSs mapping at whole-genome level in both plants and animals. Here we describe a DNase-seq procedure modified and developed for crop plants. These plants usually contain large amounts of repetitive sequences and complex organic constituents. With the main improvement in nuclei isolation, this method has been successfully used in mapping DHSs in cotton and sugarcane.
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27
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Hardison RC, Zhang Y, Keller CA, Xiang G, Heuston EF, An L, Lichtenberg J, Giardine BM, Bodine D, Mahony S, Li Q, Yue F, Weiss MJ, Blobel GA, Taylor J, Hughes J, Higgs DR, Göttgens B. Systematic integration of GATA transcription factors and epigenomes via IDEAS paints the regulatory landscape of hematopoietic cells. IUBMB Life 2020; 72:27-38. [PMID: 31769130 PMCID: PMC6972633 DOI: 10.1002/iub.2195] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2019] [Accepted: 10/17/2019] [Indexed: 01/15/2023]
Abstract
Members of the GATA family of transcription factors play key roles in the differentiation of specific cell lineages by regulating the expression of target genes. Three GATA factors play distinct roles in hematopoietic differentiation. In order to better understand how these GATA factors function to regulate genes throughout the genome, we are studying the epigenomic and transcriptional landscapes of hematopoietic cells in a model-driven, integrative fashion. We have formed the collaborative multi-lab VISION project to conduct ValIdated Systematic IntegratiON of epigenomic data in mouse and human hematopoiesis. The epigenomic data included nuclease accessibility in chromatin, CTCF occupancy, and histone H3 modifications for 20 cell types covering hematopoietic stem cells, multilineage progenitor cells, and mature cells across the blood cell lineages of mouse. The analysis used the Integrative and Discriminative Epigenome Annotation System (IDEAS), which learns all common combinations of features (epigenetic states) simultaneously in two dimensions-along chromosomes and across cell types. The result is a segmentation that effectively paints the regulatory landscape in readily interpretable views, revealing constitutively active or silent loci as well as the loci specifically induced or repressed in each stage and lineage. Nuclease accessible DNA segments in active chromatin states were designated candidate cis-regulatory elements in each cell type, providing one of the most comprehensive registries of candidate hematopoietic regulatory elements to date. Applications of VISION resources are illustrated for the regulation of genes encoding GATA1, GATA2, GATA3, and Ikaros. VISION resources are freely available from our website http://usevision.org.
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Affiliation(s)
- Ross C. Hardison
- Departments of Biochemistry and Molecular Biology and of StatisticsThe Pennsylvania State University, University ParkPA
| | - Yu Zhang
- Departments of Biochemistry and Molecular Biology and of StatisticsThe Pennsylvania State University, University ParkPA
| | - Cheryl A. Keller
- Departments of Biochemistry and Molecular Biology and of StatisticsThe Pennsylvania State University, University ParkPA
| | - Guanjue Xiang
- Departments of Biochemistry and Molecular Biology and of StatisticsThe Pennsylvania State University, University ParkPA
| | - Elisabeth F. Heuston
- Genetics and Molecular Biology Branch, Hematopoiesis SectionNational Institutes of Health, NHGRIBethesdaMD
| | - Lin An
- Departments of Biochemistry and Molecular Biology and of StatisticsThe Pennsylvania State University, University ParkPA
| | - Jens Lichtenberg
- Genetics and Molecular Biology Branch, Hematopoiesis SectionNational Institutes of Health, NHGRIBethesdaMD
| | - Belinda M. Giardine
- Departments of Biochemistry and Molecular Biology and of StatisticsThe Pennsylvania State University, University ParkPA
| | - David Bodine
- Genetics and Molecular Biology Branch, Hematopoiesis SectionNational Institutes of Health, NHGRIBethesdaMD
| | - Shaun Mahony
- Departments of Biochemistry and Molecular Biology and of StatisticsThe Pennsylvania State University, University ParkPA
| | - Qunhua Li
- Departments of Biochemistry and Molecular Biology and of StatisticsThe Pennsylvania State University, University ParkPA
| | - Feng Yue
- Department of Biochemistry and Molecular BiologyThe Pennsylvania State University College of MedicineHershey, PA
| | - Mitchell J. Weiss
- Hematology DepartmentSt. Jude Children's Research HospitalMemphis, TN
| | | | - James Taylor
- Departments of Biology and of Computer ScienceJohns Hopkins UniversityBaltimore, MD
| | - Jim Hughes
- Laboratory of Gene RegulationWeatherall Institute of Molecular Medicine, Oxford UniversityOxfordUK
| | - Douglas R. Higgs
- Laboratory of Gene RegulationWeatherall Institute of Molecular Medicine, Oxford UniversityOxfordUK
| | - Berthold Göttgens
- Department of Hematology, Cambridge Institute for Medical ResearchUniversity of CambridgeCambridgeUK
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28
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Alvarez JM, Moyano TC, Zhang T, Gras DE, Herrera FJ, Araus V, O'Brien JA, Carrillo L, Medina J, Vicente-Carbajosa J, Jiang J, Gutiérrez RA. Local Changes in Chromatin Accessibility and Transcriptional Networks Underlying the Nitrate Response in Arabidopsis Roots. MOLECULAR PLANT 2019; 12:1545-1560. [PMID: 31526863 DOI: 10.1016/j.molp.2019.09.002] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/12/2019] [Revised: 08/27/2019] [Accepted: 09/05/2019] [Indexed: 05/13/2023]
Abstract
Transcriptional regulation, determined by the chromatin structure and regulatory elements interacting at promoter regions, is a key step in plant responses to environmental cues. Nitrate (NO3-) is a nutrient signal that regulates the expression of hundreds of genes in Arabidopsis thaliana. Here, we integrate mRNA sequencing, genome-wide RNA polymerase II (RNPII), chromatin immunoprecipitation sequencing, and DNase sequencing datasets to establish the relationship between RNPII occupancy and chromatin accessibility in response to NO3- treatments in Arabidopsis roots. Genomic footprinting allowed us to identify in vivo regulatory elements controlling gene expression in response to NO3- treatments. NO3--modulated transcription factor (TF) footprints are important for a rapid increase in RNPII occupancy and transcript accumulation over time. We mapped key TF regulatory interactions and functionally validated the role of NAP, an NAC-domain containing TF, as a new regulatory factor in NO3- transport. Taken together, our study provides a comprehensive view of transcriptional networks in response to a nutrient signal in Arabidopsis roots.
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Affiliation(s)
- José M Alvarez
- Pontificia Universidad Catolica de Chile, Santiago, Chile
| | - Tomás C Moyano
- Pontificia Universidad Catolica de Chile, Santiago, Chile
| | - Tao Zhang
- Yangzhou University, Yangzhou, China
| | - Diana E Gras
- Instituto de Agrobiotecnologia del Litoral, CONICET, Santa Fe, Argentina
| | - Francisco J Herrera
- University of California, Berkeley, CA, USA; Trancura Biosciences, Inc., San Francisco, CA 94158, USA
| | - Viviana Araus
- Pontificia Universidad Catolica de Chile, Santiago, Chile
| | - José A O'Brien
- Pontificia Universidad Catolica de Chile, Santiago, Chile
| | - Laura Carrillo
- Centro de Biotecnología y Genómica de Plantas (CBGP, UPM-INIA), Universidad Politécnica de Madrid (UPM), Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA), Campus de Montegancedo, 28223-Pozuelo de Alarcón, Madrid, Spain
| | - Joaquín Medina
- Centro de Biotecnología y Genómica de Plantas (CBGP, UPM-INIA), Universidad Politécnica de Madrid (UPM), Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA), Campus de Montegancedo, 28223-Pozuelo de Alarcón, Madrid, Spain
| | - Jesús Vicente-Carbajosa
- Centro de Biotecnología y Genómica de Plantas (CBGP, UPM-INIA), Universidad Politécnica de Madrid (UPM), Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA), Campus de Montegancedo, 28223-Pozuelo de Alarcón, Madrid, Spain
| | - Jiming Jiang
- Department of Horticulture, University of Wisconsin-Madison, Madison, WI 53706, USA; Department of Plant Biology and Horticulture, Michigan State University, MI 48824, USA
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29
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Klein DC, Hainer SJ. Genomic methods in profiling DNA accessibility and factor localization. Chromosome Res 2019; 28:69-85. [PMID: 31776829 PMCID: PMC7125251 DOI: 10.1007/s10577-019-09619-9] [Citation(s) in RCA: 54] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2019] [Revised: 10/10/2019] [Accepted: 10/15/2019] [Indexed: 12/24/2022]
Abstract
Recent advancements in next-generation sequencing technologies and accompanying reductions in cost have led to an explosion of techniques to examine DNA accessibility and protein localization on chromatin genome-wide. Generally, accessible regions of chromatin are permissive for factor binding and are therefore hotspots for regulation of gene expression; conversely, genomic regions that are highly occupied by histone proteins are not permissive for factor binding and are less likely to be active regulatory regions. Identifying regions of differential accessibility can be useful to uncover putative gene regulatory regions, such as enhancers, promoters, and insulators. In addition, DNA-binding proteins, such as transcription factors that preferentially bind certain DNA sequences and histone proteins that form the core of the nucleosome, play essential roles in all DNA-templated processes. Determining the genomic localization of chromatin-bound proteins is therefore essential in determining functional roles, sequence motifs important for factor binding, and regulatory networks controlling gene expression. In this review, we discuss techniques for determining DNA accessibility and nucleosome positioning (DNase-seq, FAIRE-seq, MNase-seq, and ATAC-seq) and techniques for detecting and functionally characterizing chromatin-bound proteins (ChIP-seq, DamID, and CUT&RUN). These methods have been optimized to varying degrees of resolution, specificity, and ease of use. Here, we outline some advantages and disadvantages of these techniques, their general protocols, and a brief discussion of their development. Together, these complimentary approaches have provided an unparalleled view of chromatin architecture and functional gene regulation.
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Affiliation(s)
- David C Klein
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA, 15260, USA
| | - Sarah J Hainer
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA, 15260, USA.
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30
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Abstract
Every microarray experiment is based on a common format. First, a large number of nucleotide "spots" are arrayed onto a substrate, typically a glass slide, a silicon chip, or microbeads. Second, a complex population of nucleic acids (isolated from cells, selected from in vitro-synthesized libraries, or obtained from another source) is labeled, typically with fluorescent dyes. Third, the labeled nucleic acids are allowed to hybridize to their complementary spot(s) on the microarray. Fourth, the hybridized microarray is washed, allowing the amount of hybridized label to then be quantified. Analysis of the raw data generates a readout of the levels of each species of RNA in the original complex population. This introduction includes several examples of microarray applications and provides a discussion of the basic steps of most microarray experiments.
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31
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Abstract
Physical access to DNA is a highly dynamic property of chromatin that plays an essential role in establishing and maintaining cellular identity. The organization of accessible chromatin across the genome reflects a network of permissible physical interactions through which enhancers, promoters, insulators and chromatin-binding factors cooperatively regulate gene expression. This landscape of accessibility changes dynamically in response to both external stimuli and developmental cues, and emerging evidence suggests that homeostatic maintenance of accessibility is itself dynamically regulated through a competitive interplay between chromatin-binding factors and nucleosomes. In this Review, we examine how the accessible genome is measured and explore the role of transcription factors in initiating accessibility remodelling; our goal is to illustrate how chromatin accessibility defines regulatory elements within the genome and how these epigenetic features are dynamically established to control gene expression.
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Affiliation(s)
- Sandy L Klemm
- Department of Genetics, Stanford University, Stanford, CA, USA
| | - Zohar Shipony
- Department of Genetics, Stanford University, Stanford, CA, USA
| | - William J Greenleaf
- Department of Genetics, Stanford University, Stanford, CA, USA. .,Department of Applied Physics, Stanford University, Stanford, CA, USA. .,Chan Zuckerberg BioHub, San Francisco, CA, USA.
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32
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Larsen S, Davidsen J, Dahlgaard K, Pedersen OB, Troelsen JT. HNF4α and CDX2 Regulate Intestinal YAP1 Promoter Activity. Int J Mol Sci 2019; 20:ijms20122981. [PMID: 31216773 PMCID: PMC6627140 DOI: 10.3390/ijms20122981] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2019] [Revised: 06/10/2019] [Accepted: 06/16/2019] [Indexed: 01/06/2023] Open
Abstract
The Hippo pathway is important for tissue homeostasis, regulation of organ size and growth in most tissues. The co-transcription factor yes-associated protein 1 (YAP1) serves as a main downstream effector of the Hippo pathway and its dysregulation increases cancer development and blocks colonic tissue repair. Nevertheless, little is known about the transcriptional regulation of YAP1 in intestinal cells. The aim of this study to identify gene control regions in the YAP1 gene and transcription factors important for intestinal expression. Bioinformatic analysis of caudal type homeobox 2 (CDX2) and hepatocyte nuclear factor 4 alpha (HNF4α) chromatin immunoprecipitated DNA from differentiated Caco-2 cells revealed potential intragenic enhancers in the YAP1 gene. Transfection of luciferase-expressing YAP1 promoter-reporter constructs containing the potential enhancer regions validated one potent enhancer of the YAP1 promoter activity in Caco-2 and T84 cells. Two potential CDX2 and one HNF4α binding sites were identified in the enhancer by in silico transcription factor binding site analysis and protein-DNA binding was confirmed in vitro using electrophoretic mobility shift assay. It was found by chromatin immunoprecipitation experiments that CDX2 and HNF4α bind to the YAP1 enhancer in Caco-2 cells. These results reveal a previously unknown enhancer of the YAP1 promoter activity in the YAP1 gene, with importance for high expression levels in intestinal epithelial cells. Additionally, CDX2 and HNF4α binding are important for the YAP1 enhancer activity in intestinal epithelial cells.
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Affiliation(s)
- Sylvester Larsen
- Department of Science and Environment, Roskilde University, Universitetsvej 1, 4000 Roskilde, Denmark.
- Department of Clinical Immunology, Næstved Hospital, Ringstedgade 77B, 4700 Næstved, Denmark.
| | - Johanne Davidsen
- Department of Science and Environment, Roskilde University, Universitetsvej 1, 4000 Roskilde, Denmark.
- Department of Surgery, Center for Surgical Science, Enhanced Perioperative Oncology (EPEONC) Consortium, Zealand University Hospital, Lykkebækvej 1, 4600 Køge, Denmark.
| | - Katja Dahlgaard
- Department of Science and Environment, Roskilde University, Universitetsvej 1, 4000 Roskilde, Denmark.
| | - Ole B Pedersen
- Department of Clinical Immunology, Næstved Hospital, Ringstedgade 77B, 4700 Næstved, Denmark.
| | - Jesper T Troelsen
- Department of Science and Environment, Roskilde University, Universitetsvej 1, 4000 Roskilde, Denmark.
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33
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Alexandre CM, Urton JR, Jean-Baptiste K, Huddleston J, Dorrity MW, Cuperus JT, Sullivan AM, Bemm F, Jolic D, Arsovski AA, Thompson A, Nemhauser JL, Fields S, Weigel D, Bubb KL, Queitsch C. Complex Relationships between Chromatin Accessibility, Sequence Divergence, and Gene Expression in Arabidopsis thaliana. Mol Biol Evol 2019; 35:837-854. [PMID: 29272536 DOI: 10.1093/molbev/msx326] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Variation in regulatory DNA is thought to drive phenotypic variation, evolution, and disease. Prior studies of regulatory DNA and transcription factors across animal species highlighted a fundamental conundrum: Transcription factor binding domains and cognate binding sites are conserved, while regulatory DNA sequences are not. It remains unclear how conserved transcription factors and dynamic regulatory sites produce conserved expression patterns across species. Here, we explore regulatory DNA variation and its functional consequences within Arabidopsis thaliana, using chromatin accessibility to delineate regulatory DNA genome-wide. Unlike in previous cross-species comparisons, the positional homology of regulatory DNA is maintained among A. thaliana ecotypes and less nucleotide divergence has occurred. Of the ∼50,000 regulatory sites in A. thaliana, we found that 15% varied in accessibility among ecotypes. Some of these accessibility differences were associated with extensive, previously unannotated sequence variation, encompassing many deletions and ancient hypervariable alleles. Unexpectedly, for the majority of such regulatory sites, nearby gene expression was unaffected. Nevertheless, regulatory sites with high levels of sequence variation and differential chromatin accessibility were the most likely to be associated with differential gene expression. Finally, and most surprising, we found that the vast majority of differentially accessible sites show no underlying sequence variation. We argue that these surprising results highlight the necessity to consider higher-order regulatory context in evaluating regulatory variation and predicting its phenotypic consequences.
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Affiliation(s)
| | - James R Urton
- Department of Genome Sciences, University of Washington, Seattle, WA
| | - Ken Jean-Baptiste
- Department of Genome Sciences, University of Washington, Seattle, WA
| | - John Huddleston
- Department of Genome Sciences, University of Washington, Seattle, WA.,Molecular and Cellular Biology Graduate Program, University of Washington, Seattle, WA
| | - Michael W Dorrity
- Department of Genome Sciences, University of Washington, Seattle, WA
| | - Josh T Cuperus
- Department of Genome Sciences, University of Washington, Seattle, WA
| | | | - Felix Bemm
- Department of Molecular Biology, Max Planck Institute for Developmental Biology, Tübingen, Germany
| | - Dino Jolic
- Department of Molecular Biology, Max Planck Institute for Developmental Biology, Tübingen, Germany
| | | | | | | | - Stan Fields
- Department of Genome Sciences, University of Washington, Seattle, WA.,Howard Hughes Medical Institute, University of Washington, Seattle, WA
| | - Detlef Weigel
- Department of Molecular Biology, Max Planck Institute for Developmental Biology, Tübingen, Germany
| | - Kerry L Bubb
- Department of Genome Sciences, University of Washington, Seattle, WA
| | - Christin Queitsch
- Department of Genome Sciences, University of Washington, Seattle, WA
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34
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Lu Y, Wang X, Yu H, Li J, Jiang Z, Chen B, Lu Y, Wang W, Han C, Ouyang Y, Huang L, Chen C, Tian W, Ling F. Evolution and Comprehensive Analysis of DNaseI Hypersensitive Sites in Regulatory Regions of Primate Brain-Related Genes. Front Genet 2019; 10:152. [PMID: 30930929 PMCID: PMC6423895 DOI: 10.3389/fgene.2019.00152] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2018] [Accepted: 02/13/2019] [Indexed: 11/23/2022] Open
Abstract
How the human brain differs from those of non-human primates is largely unknown and the complex drivers underlying such differences at the genomic level remain unclear. In this study, we selected 243 brain-related genes, based on Gene Ontology, and identified 184,113 DNaseI hypersensitive sites (DHSs) within their regulatory regions. To performed comprehensive evolutionary analyses, we set strict filtering criteria for alignment quality and filtered 39,132 DHSs for inclusion in the investigation and found that 2,397 (~6%) exhibited evidence of accelerated evolution (aceDHSs), which was a much higher proportion that DHSs genome-wide. Target genes predicted to be regulated by brain-aceDHSs were functionally enriched for brain development and exhibited differential expression between human and chimpanzee. Alignments indicated 61 potential human-specific transcription factor binding sites in brain-aceDHSs, including for CTCF, FOXH1, and FOXQ1. Furthermore, based on GWAS, Hi-C, and eQTL data, 16 GWAS SNPs, and 82 eQTL SNPs were in brain-aceDHSs that regulate genes related to brain development or disease. Among these brain-aceDHSs, we confirmed that one enhanced the expression of GPR133, using CRISPR-Cas9 and western blotting. The GPR133 gene is associated with glioblastoma, indicating that SNPs within DHSs could be related to brain disorders. These findings suggest that brain-related gene regulatory regions are under adaptive evolution and contribute to the differential expression profiles among primates, providing new insights into the genetic basis of brain phenotypes or disorders between humans and other primates.
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Affiliation(s)
- Yueer Lu
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou, China
| | - Xiao Wang
- State Key Laboratory of Genetic Engineering, Department of Biostatistics and Computational Biology, Collaborative Innovation Center of Genetics and Development, School of Life Sciences, Fudan University, Shanghai, China
| | - Hang Yu
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou, China
| | - Jianlin Li
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou, China
| | - Zhiqiang Jiang
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou, China
| | - Bangwei Chen
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou, China
| | - Yueqi Lu
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou, China
| | - Wei Wang
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou, China
| | - Chongyin Han
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou, China
| | - Ying Ouyang
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou, China
| | - Lizhen Huang
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou, China
| | - Chunbo Chen
- Department of Critical Care Medicine, Guangdong General Hospital, Guangdong Academy of Medical Sciences, Guangzhou, China
| | - Weidong Tian
- State Key Laboratory of Genetic Engineering, Department of Biostatistics and Computational Biology, Collaborative Innovation Center of Genetics and Development, School of Life Sciences, Fudan University, Shanghai, China
| | - Fei Ling
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou, China
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35
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Michael DG, Pranzatelli TJF, Warner BM, Yin H, Chiorini JA. Integrated Epigenetic Mapping of Human and Mouse Salivary Gene Regulation. J Dent Res 2018; 98:209-217. [PMID: 30392435 DOI: 10.1177/0022034518806518] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Significant effort has been applied to identify the genome-wide gene expression profiles associated with salivary gland development and pathophysiology. However, relatively little is known about the regulators that control salivary gland gene expression. We integrated data from DNase1 digital genomic footprinting, RNA-seq, and gene expression microarrays to comprehensively characterize the cis- and trans-regulatory components controlling gene expression of the healthy submandibular salivary gland. Analysis of 32 human tissues and 87 mouse tissues was performed to identify the highly expressed and tissue-enriched transcription factors driving salivary gland gene expression. Following RNA analysis, protein expression levels and subcellular localization of 39 salivary transcription factors were confirmed by immunohistochemistry. These expression analyses revealed that the salivary gland highly expresses transcription factors associated with endoplasmic reticulum stress, human T-cell lymphotrophic virus 1 expression, and Epstein-Barr virus reactivation. DNase1 digital genomic footprinting to a depth of 333,426,353 reads was performed and utilized to generate a salivary gland gene regulatory network describing the genome-wide chromatin accessibility and transcription factor binding of the salivary gland at a single-nucleotide resolution. Analysis of the DNase1 gene regulatory network identified dense interconnectivity among PLAG1, MYB, and 13 other transcription factors associated with balanced chromosomal translocations and salivary gland tumors. Collectively, these analyses provide a comprehensive atlas of the cis- and trans-regulators of the salivary gland and highlight known aberrantly regulated pathways of diseases affecting the salivary glands.
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Affiliation(s)
- D G Michael
- 1 Adeno-Associated Virus Biology Section, National Institute of Dental and Craniofacial Research, National Institutes of Health, Bethesda, MD, USA
| | - T J F Pranzatelli
- 1 Adeno-Associated Virus Biology Section, National Institute of Dental and Craniofacial Research, National Institutes of Health, Bethesda, MD, USA
| | - B M Warner
- 1 Adeno-Associated Virus Biology Section, National Institute of Dental and Craniofacial Research, National Institutes of Health, Bethesda, MD, USA
| | - H Yin
- 1 Adeno-Associated Virus Biology Section, National Institute of Dental and Craniofacial Research, National Institutes of Health, Bethesda, MD, USA
| | - J A Chiorini
- 1 Adeno-Associated Virus Biology Section, National Institute of Dental and Craniofacial Research, National Institutes of Health, Bethesda, MD, USA
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36
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Jänes J, Dong Y, Schoof M, Serizay J, Appert A, Cerrato C, Woodbury C, Chen R, Gemma C, Huang N, Kissiov D, Stempor P, Steward A, Zeiser E, Sauer S, Ahringer J. Chromatin accessibility dynamics across C. elegans development and ageing. eLife 2018; 7:37344. [PMID: 30362940 PMCID: PMC6231769 DOI: 10.7554/elife.37344] [Citation(s) in RCA: 46] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2018] [Accepted: 10/25/2018] [Indexed: 12/21/2022] Open
Abstract
An essential step for understanding the transcriptional circuits that control development and physiology is the global identification and characterization of regulatory elements. Here, we present the first map of regulatory elements across the development and ageing of an animal, identifying 42,245 elements accessible in at least one Caenorhabditis elegans stage. Based on nuclear transcription profiles, we define 15,714 protein-coding promoters and 19,231 putative enhancers, and find that both types of element can drive orientation-independent transcription. Additionally, more than 1000 promoters produce transcripts antisense to protein coding genes, suggesting involvement in a widespread regulatory mechanism. We find that the accessibility of most elements changes during development and/or ageing and that patterns of accessibility change are linked to specific developmental or physiological processes. The map and characterization of regulatory elements across C. elegans life provides a platform for understanding how transcription controls development and ageing.
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Affiliation(s)
- Jürgen Jänes
- Department of Genetics, University of Cambridge, Cambridge, United Kingdom.,The Gurdon Institute, University of Cambridge, Cambridge, United Kingdom
| | - Yan Dong
- Department of Genetics, University of Cambridge, Cambridge, United Kingdom.,The Gurdon Institute, University of Cambridge, Cambridge, United Kingdom
| | - Michael Schoof
- Department of Genetics, University of Cambridge, Cambridge, United Kingdom.,The Gurdon Institute, University of Cambridge, Cambridge, United Kingdom
| | - Jacques Serizay
- Department of Genetics, University of Cambridge, Cambridge, United Kingdom.,The Gurdon Institute, University of Cambridge, Cambridge, United Kingdom
| | - Alex Appert
- Department of Genetics, University of Cambridge, Cambridge, United Kingdom.,The Gurdon Institute, University of Cambridge, Cambridge, United Kingdom
| | - Chiara Cerrato
- Department of Genetics, University of Cambridge, Cambridge, United Kingdom.,The Gurdon Institute, University of Cambridge, Cambridge, United Kingdom
| | - Carson Woodbury
- Department of Genetics, University of Cambridge, Cambridge, United Kingdom.,The Gurdon Institute, University of Cambridge, Cambridge, United Kingdom
| | - Ron Chen
- Department of Genetics, University of Cambridge, Cambridge, United Kingdom.,The Gurdon Institute, University of Cambridge, Cambridge, United Kingdom
| | - Carolina Gemma
- Department of Genetics, University of Cambridge, Cambridge, United Kingdom.,The Gurdon Institute, University of Cambridge, Cambridge, United Kingdom
| | - Ni Huang
- Department of Genetics, University of Cambridge, Cambridge, United Kingdom.,The Gurdon Institute, University of Cambridge, Cambridge, United Kingdom
| | - Djem Kissiov
- Department of Genetics, University of Cambridge, Cambridge, United Kingdom.,The Gurdon Institute, University of Cambridge, Cambridge, United Kingdom
| | - Przemyslaw Stempor
- Department of Genetics, University of Cambridge, Cambridge, United Kingdom.,The Gurdon Institute, University of Cambridge, Cambridge, United Kingdom
| | - Annette Steward
- Department of Genetics, University of Cambridge, Cambridge, United Kingdom.,The Gurdon Institute, University of Cambridge, Cambridge, United Kingdom
| | - Eva Zeiser
- Department of Genetics, University of Cambridge, Cambridge, United Kingdom.,The Gurdon Institute, University of Cambridge, Cambridge, United Kingdom
| | - Sascha Sauer
- Max Delbrück Center for Molecular Medicine, Berlin, Germany.,Max Planck Institute for Molecular Genetics, Otto-Warburg Laboratories, Berlin, Germany
| | - Julie Ahringer
- Department of Genetics, University of Cambridge, Cambridge, United Kingdom.,The Gurdon Institute, University of Cambridge, Cambridge, United Kingdom
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37
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Levings DC, Wang X, Kohlhase D, Bell DA, Slattery M. A distinct class of antioxidant response elements is consistently activated in tumors with NRF2 mutations. Redox Biol 2018; 19:235-249. [PMID: 30195190 PMCID: PMC6128101 DOI: 10.1016/j.redox.2018.07.026] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2018] [Revised: 07/23/2018] [Accepted: 07/31/2018] [Indexed: 12/17/2022] Open
Abstract
NRF2 is a redox-responsive transcription factor that regulates expression of cytoprotective genes via its interaction with DNA sequences known as antioxidant response elements (AREs). NRF2 activity is induced by oxidative stress, but oxidative stress is not the only context in which NRF2 can be activated. Mutations that disrupt the interaction between NRF2 and KEAP1, an inhibitor of NRF2, lead to NRF2 hyperactivation and promote oncogenesis. The mechanisms underlying NRF2's oncogenic properties remain unclear, but likely involve aberrant expression of select NRF2 target genes. We tested this possibility using an integrative genomics approach to get a precise view of the direct NRF2 target genes dysregulated in tumors with NRF2 hyperactivating mutations. This approach revealed a core set of 32 direct NRF2 targets that are consistently upregulated in NRF2 hyperactivated tumors. This set of NRF2 "cancer target genes" includes canonical redox-related NRF2 targets, as well as target genes that have not been previously linked to NRF2 activation. Importantly, NRF2-driven upregulation of this gene set is largely independent of the organ system where the tumor developed. One key distinguishing feature of these NRF2 cancer target genes is that they are regulated by high affinity AREs that fall within genomic regions possessing a ubiquitously permissive chromatin signature. This implies that these NRF2 cancer target genes are responsive to oncogenic NRF2 in most tissues because they lack the regulatory constraints that restrict expression of most other NRF2 target genes. This NRF2 cancer target gene set also serves as a reliable proxy for NRF2 activity, and high NRF2 activity is associated with significant decreases in survival in multiple cancer types. Overall, the pervasive upregulation of these NRF2 cancer targets across multiple cancers, and their association with negative outcomes, suggests that these will be central to dissecting the functional implications of NRF2 hyperactivation in several cancer contexts.
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Affiliation(s)
- Daniel C Levings
- Department of Biomedical Sciences, University of Minnesota Medical School, Duluth, MN 55812, USA
| | - Xuting Wang
- Environmental Epigenomics and Disease Group, Immunity, Inflammation and Disease Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC 27709, USA
| | - Derek Kohlhase
- Department of Biomedical Sciences, University of Minnesota Medical School, Duluth, MN 55812, USA
| | - Douglas A Bell
- Environmental Epigenomics and Disease Group, Immunity, Inflammation and Disease Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC 27709, USA
| | - Matthew Slattery
- Department of Biomedical Sciences, University of Minnesota Medical School, Duluth, MN 55812, USA.
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Evolution of DNAase I Hypersensitive Sites in MHC Regulatory Regions of Primates. Genetics 2018; 209:579-589. [PMID: 29669733 DOI: 10.1534/genetics.118.301028] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2018] [Accepted: 04/16/2018] [Indexed: 01/08/2023] Open
Abstract
It has been challenging to determine the disease-causing variant(s) for most major histocompatibility complex (MHC)-associated diseases. However, it is becoming increasingly clear that regulatory variation is pervasive and a fundamentally important mechanism governing phenotypic diversity and disease susceptibility. We gathered DNase I data from 136 human cells to characterize the regulatory landscape of the MHC region, including 4867 DNase I hypersensitive sites (DHSs). We identified thousands of regulatory elements that have been gained or lost in the human or chimpanzee genomes since their evolutionary divergence. We compared alignments of the DHS across six primates and found 149 DHSs with convincing evidence of positive and/or purifying selection. Of these DHSs, compared to neutral sequences, 24 evolved rapidly in the human lineage. We identified 15 instances of transcription-factor-binding motif gains, such as USF, MYC, MAX, MAFK, STAT1, PBX3, etc, and observed 16 GWAS (genome-wide association study) SNPs associated with diseases within these 24 DHSs using FIMO (Find Individual Motif Occurrences) and UCSC (University of California, Santa Cruz) ChIP-seq data. Combining eQTL and Hi-C data, our results indicated that there were five SNPs located in human gains motifs affecting the corresponding gene's expression, two of which closely matched DHS target genes. In addition, a significant SNP, rs7756521, at genome-wide significant level likely affects DDR expression and represents a causal genetic variant for HIV-1 control. These results indicated that species-specific motif gains or losses of rapidly evolving DHSs in the primate genomes might play a role during adaptation evolution and provided some new evidence for a potentially causal role for these GWAS SNPs.
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Boone M, De Koker A, Callewaert N. Capturing the 'ome': the expanding molecular toolbox for RNA and DNA library construction. Nucleic Acids Res 2018; 46:2701-2721. [PMID: 29514322 PMCID: PMC5888575 DOI: 10.1093/nar/gky167] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2017] [Revised: 02/05/2018] [Accepted: 02/23/2018] [Indexed: 12/14/2022] Open
Abstract
All sequencing experiments and most functional genomics screens rely on the generation of libraries to comprehensively capture pools of targeted sequences. In the past decade especially, driven by the progress in the field of massively parallel sequencing, numerous studies have comprehensively assessed the impact of particular manipulations on library complexity and quality, and characterized the activities and specificities of several key enzymes used in library construction. Fortunately, careful protocol design and reagent choice can substantially mitigate many of these biases, and enable reliable representation of sequences in libraries. This review aims to guide the reader through the vast expanse of literature on the subject to promote informed library generation, independent of the application.
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Affiliation(s)
- Morgane Boone
- Center for Medical Biotechnology, VIB, Zwijnaarde 9052, Belgium
- Department of Biochemistry and Microbiology, Ghent University, Ghent 9000, Belgium
| | - Andries De Koker
- Center for Medical Biotechnology, VIB, Zwijnaarde 9052, Belgium
- Department of Biochemistry and Microbiology, Ghent University, Ghent 9000, Belgium
| | - Nico Callewaert
- Center for Medical Biotechnology, VIB, Zwijnaarde 9052, Belgium
- Department of Biochemistry and Microbiology, Ghent University, Ghent 9000, Belgium
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Hypomethylated domain-enriched DNA motifs prepattern the accessible nucleosome organization in teleosts. Epigenetics Chromatin 2017; 10:44. [PMID: 28931432 PMCID: PMC5607494 DOI: 10.1186/s13072-017-0152-2] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2017] [Accepted: 09/13/2017] [Indexed: 12/22/2022] Open
Abstract
Background Gene promoters in vertebrate genomes show distinct chromatin features such as stably positioned nucleosome array and DNA hypomethylation. The nucleosomes are known to have certain sequence preferences, and the prediction of nucleosome positioning from DNA sequence has been successful in some organisms such as yeast. However, at gene promoters where nucleosomes are much more stably positioned than in other regions, the sequence-based model has failed to work well, and sequence-independent mechanisms have been proposed. Results Using DNase I-seq in medaka embryos, we demonstrated that hypomethylated domains (HMDs) specifically possess accessible nucleosome organization with longer linkers, and we reassessed the DNA sequence preference for nucleosome positioning in these specific regions. Remarkably, we found with a supervised machine learning algorithm, k-mer SVM, that nucleosome positioning in HMDs is accurately predictable from DNA sequence alone. Specific short sequences (6-mers) that contribute to the prediction are specifically enriched in HMDs and distribute periodically with approximately 200-bp intervals which prepattern the position of accessible linkers. Surprisingly, the sequence preference of the nucleosome and linker in HMDs is opposite from that reported previously. Furthermore, the periodicity of specific motifs at hypomethylated promoters was conserved in zebrafish. Conclusion This study reveals strong link between nucleosome positioning and DNA sequence at vertebrate promoters, and we propose hypomethylated DNA-specific regulation of nucleosome positioning. Electronic supplementary material The online version of this article (doi:10.1186/s13072-017-0152-2) contains supplementary material, which is available to authorized users.
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Bina M. Imprinted control regions include composite DNA elements consisting of the ZFP57 binding site overlapping MLL1 morphemes. Genomics 2017; 109:265-273. [PMID: 28476430 DOI: 10.1016/j.ygeno.2017.04.008] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2017] [Revised: 04/25/2017] [Accepted: 04/30/2017] [Indexed: 12/16/2022]
Abstract
Mammalian genomes include DNA segments that are imprinted (CpG-methylated) only on one of the two parental chromosomes, leading to parent-of-origin-specific gene expression. The process is regulated by Imprinting Control Regions (ICRs) and germline Differentially Methylated Regions (gDMRs). Previously, ZFP57 was shown to recognize a methylated hexanucleotide in ICRs to maintain allele-specific gene repression. In Bioinformatics analyses, I found that the hexamer occurred frequently in mouse chromosomal DNA, suggesting that beside the ZFP57 binding site (ZFBS), ICRs contained sequence features with unknown characteristics. To identify such features, I examined chromosomal abundance of motifs in which the length of the hexamer was extended by one or several nucleotides. Results led to the discovery of a group of functionally significant composite DNA elements (ZFBS-Morph overlaps) that may play dual roles in the regulation of allele-specific gene expression. Importantly, results of genome-wide evaluations revealed that nearly 90% of the gDMRs included closely-spaced ZFBS-Morph overlaps.
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Affiliation(s)
- Minou Bina
- Department of Chemistry, Purdue University, West Lafayette, IN 47907, USA.
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CRISPR-Cas9 epigenome editing enables high-throughput screening for functional regulatory elements in the human genome. Nat Biotechnol 2017; 35:561-568. [PMID: 28369033 PMCID: PMC5462860 DOI: 10.1038/nbt.3853] [Citation(s) in RCA: 279] [Impact Index Per Article: 39.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2016] [Accepted: 03/17/2017] [Indexed: 12/27/2022]
Abstract
Large genome-mapping consortia and thousands of genome-wide association studies have identified non-protein coding elements in the genome as a having a central role in various biological processes. However, decoding the function of the millions of putative regulatory elements discovered in these studies remains challenging. CRISPR–Cas9-based epigenome editing technologies have enabled precise perturbation of the activity of specific regulatory elements. Here we describe CRISPR–Cas9-based epigenomic regulatory element screening (CERES) for improved high-throughput screening of regulatory element activity within the native genomic context. Using dCas9KRAB repressor and dCas9p300 activator constructs and lentiviral sgRNA libraries targeting DNase I hypersensitive sites surrounding a gene of interest, we perform both loss- and gain-of-function screens to identify regulatory elements for the β-globin and the HER2 loci in human cells. CERES readily identified known and novel regulatory elements, some of which were dependent on cell type or direction of perturbation. This technology allows the high-throughput functional annotation of putative regulatory elements in their native chromosomal context.
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Salzberg AC, Harris-Becker A, Popova EY, Keasey N, Loughran TP, Claxton DF, Grigoryev SA. Genome-wide mapping of histone H3K9me2 in acute myeloid leukemia reveals large chromosomal domains associated with massive gene silencing and sites of genome instability. PLoS One 2017; 12:e0173723. [PMID: 28301528 PMCID: PMC5354391 DOI: 10.1371/journal.pone.0173723] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2016] [Accepted: 02/24/2017] [Indexed: 01/05/2023] Open
Abstract
A facultative heterochromatin mark, histone H3 lysine 9 dimethylation (H3K9me2), which is mediated by histone methyltransferases G9a/GLP (EHMT2/1), undergoes dramatic rearrangements during myeloid cell differentiation as observed by chromatin imaging. To determine whether these structural transitions also involve genomic repositioning of H3K9me2, we used ChIP-sequencing to map genome-wide topography of H3K9me2 in normal human granulocytes, normal CD34+ hematopoietic progenitors, primary myeloblasts from acute myeloid leukemia (AML) patients, and a model leukemia cell line K562. We observe that H3K9me2 naturally repositions from the previously designated “repressed” chromatin state in hematopoietic progenitors to predominant association with heterochromatin regions in granulocytes. In contrast, AML cells accumulate H3K9me2 on previously undefined large (> 100 Kb) genomic blocks that are enriched with AML-specific single nucleotide variants, sites of chromosomal translocations, and genes downregulated in AML. Specifically, the AML-specific H3K9me2 blocks are enriched with genes regulated by the proto-oncogene ERG that promotes stem cell characteristics. The AML-enriched H3K9me2 blocks (in contrast to the heterochromatin-associated H3K9me2 blocks enriched in granulocytes) are reduced by pharmacological inhibition of the histone methyltransferase G9a/GLP in K562 cells concomitantly with transcriptional activation of ERG and ETS1 oncogenes. Our data suggest that G9a/GLP mediate formation of transient H3K9me2 blocks that are preserved in AML myeloblasts and may lead to an increased rate of AML-specific mutagenesis and chromosomal translocations.
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Affiliation(s)
- Anna C. Salzberg
- Division of Biostatistics and Bioinformatics and Penn State Institute for Personalized Medicine, Hershey, Pennsylvania, United States of America
| | - Abigail Harris-Becker
- Penn State College of Medicine, Dept. Biochemistry & Molecular Biology, H171, Hershey, Pennsylvania, United States of America
| | - Evgenya Y. Popova
- Penn State College of Medicine, Department of Neural and Behavioral Sciences, Hershey, Pennsylvania, United States of America
| | - Nikki Keasey
- Penn State Cancer Institute; Milton S. Hershey Medical Center, 500 University Drive, Hershey, Pennsylvania, United States of America
| | - Thomas P. Loughran
- University of Virginia Cancer Center, Charlottesville, Virginia, United States of America
| | - David F. Claxton
- Penn State Cancer Institute; Milton S. Hershey Medical Center, 500 University Drive, Hershey, Pennsylvania, United States of America
- * E-mail: (SAG); (DFC)
| | - Sergei A. Grigoryev
- Penn State College of Medicine, Dept. Biochemistry & Molecular Biology, H171, Hershey, Pennsylvania, United States of America
- * E-mail: (SAG); (DFC)
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Genome-wide analysis of p53-regulated transcription in Myc-driven lymphomas. Oncogene 2017; 36:2921-2929. [PMID: 28092679 PMCID: PMC5454316 DOI: 10.1038/onc.2016.443] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2016] [Revised: 09/16/2016] [Accepted: 10/14/2016] [Indexed: 01/20/2023]
Abstract
The tumour suppressor p53 is a transcription factor that controls cellular stress responses. Here, we dissected the transcriptional programmes triggered upon restoration of p53 in Myc-driven lymphomas, based on the integrated analysis of p53 genomic occupancy and gene regulation. p53 binding sites were identified at promoters and enhancers, both characterized by the pre-existence of active chromatin marks. Only a small fraction of these sites showed the 20 base-pair p53 consensus motif, suggesting that p53 recruitment to genomic DNA was primarily mediated through protein-protein interactions in a chromatin context. p53 also targeted distal sites devoid of activation marks, at which binding was prevalently driven by sequence recognition. In all instances, the relevant motif was the canonical unsplit consensus element, with no clear evidence for p53 recruitment by split motifs. At promoters, p53 binding to the consensus motif was associated with gene induction, but not repression, indicating that the latter was most likely indirect. Altogether, our data highlight key features of genome recognition by p53 and provide unprecedented insight into the pathways associated with p53 reactivation and tumour regression, paving the way for their therapeutic application.
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45
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Zhang J, Han B, Li X, Bies J, Jiang P, Koller RP, Wolff L. Distal regulation of c-myb expression during IL-6-induced differentiation in murine myeloid progenitor M1 cells. Cell Death Dis 2016; 7:e2364. [PMID: 27607579 PMCID: PMC5059869 DOI: 10.1038/cddis.2016.267] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2016] [Revised: 07/25/2016] [Accepted: 07/29/2016] [Indexed: 12/31/2022]
Abstract
The c-Myb transcription factor is a major regulator that controls differentiation and proliferation of hematopoietic progenitor cells, which is frequently deregulated in hematological diseases, such as lymphoma and leukemia. Understanding of the mechanisms regulating the transcription of c-myb gene is challenging as it lacks a typical promoter and multiple factors are involved. Our previous studies identified some distal regulatory elements in the upstream regions of c-myb gene in murine myeloid progenitor M1 cells, but the detailed mechanisms still remain unclear. In the present study, we found that a cell differentiation-related DNase1 hypersensitive site is located at a -28k region upstream of c-myb gene and that transcription factors Hoxa9, Meis1 and PU.1 bind to the -28k region. Circular chromosome conformation capture (4C) assay confirmed the interaction between the -28k region and the c-myb promoter, which is supported by the enrichment of CTCF and Cohesin. Our analysis also points to a critical role for Hoxa9 and PU.1 in distal regulation of c-myb expression in murine myeloid cells and cell differentiation. Overexpression of Hoxa9 disrupted the IL-6-induced differentiation of M1 cells and upregulated c-myb expression through binding of the -28k region. Taken together, our results provide an evidence for critical role of the -28k region in distal regulatory mechanism for c-myb gene expression during differentiation of myeloid progenitor M1 cells.
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Affiliation(s)
- Junfang Zhang
- Key Laboratory of Aquacultural Resources and Utilization, Ministry of Education, College of Fishery and Life Science, Shanghai Ocean University, No.999 Huchenghuan Road, Pudong New District, Shanghai 201306, China
| | - Bingshe Han
- Key Laboratory of Aquacultural Resources and Utilization, Ministry of Education, College of Fishery and Life Science, Shanghai Ocean University, No.999 Huchenghuan Road, Pudong New District, Shanghai 201306, China
| | - Xiaoxia Li
- Key Laboratory of Aquacultural Resources and Utilization, Ministry of Education, College of Fishery and Life Science, Shanghai Ocean University, No.999 Huchenghuan Road, Pudong New District, Shanghai 201306, China
| | - Juraj Bies
- Laboratory of Cellular Oncology, Center for Cancer Research, National Cancer Institute, Bethesda, MD 20892, USA
| | - Penglei Jiang
- Key Laboratory of Aquacultural Resources and Utilization, Ministry of Education, College of Fishery and Life Science, Shanghai Ocean University, No.999 Huchenghuan Road, Pudong New District, Shanghai 201306, China
| | - Richard P Koller
- Laboratory of Cellular Oncology, Center for Cancer Research, National Cancer Institute, Bethesda, MD 20892, USA
| | - Linda Wolff
- Laboratory of Cellular Oncology, Center for Cancer Research, National Cancer Institute, Bethesda, MD 20892, USA
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46
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Yu M, Al-Dallal S, Al-Haj L, Panjwani S, McCartney AS, Edwards SM, Manjunath P, Walker C, Awgulewitsch A, Hentges KE. Transcriptional regulation of the proto-oncogene Zfp521 by SPI1 (PU.1) and HOXC13. Genesis 2016; 54:519-533. [PMID: 27506447 PMCID: PMC5073027 DOI: 10.1002/dvg.22963] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2016] [Revised: 08/08/2016] [Accepted: 08/08/2016] [Indexed: 12/19/2022]
Abstract
The mouse zinc‐finger gene Zfp521 (also known as ecotropic viral insertion site 3; Evi3; and ZNF521 in humans) has been identified as a B‐cell proto‐oncogene, causing leukemia in mice following retroviral insertions in its promoter region that drive Zfp521 over‐expression. Furthermore, ZNF521 is expressed in human hematopoietic cells, and translocations between ZNF521 and PAX5 are associated with pediatric acute lymphoblastic leukemia. However, the regulatory factors that control Zfp521 expression directly have not been characterized. Here we demonstrate that the transcription factors SPI1 (PU.1) and HOXC13 synergistically regulate Zfp521 expression, and identify the regions of the Zfp521 promoter required for this transcriptional activity. We also show that SPI1 and HOXC13 activate Zfp521 in a dose‐dependent manner. Our data support a role for this regulatory mechanism in vivo, as transgenic mice over‐expressing Hoxc13 in the fetal liver show a strong correlation between Hoxc13 expression levels and Zfp521 expression. Overall these experiments provide insights into the regulation of Zfp521 expression in a nononcogenic context. The identification of transcription factors capable of activating Zfp521 provides a foundation for further investigation of the regulatory mechanisms involved in ZFP521‐driven cell differentiation processes and diseases linked to Zfp521 mis‐expression.
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Affiliation(s)
- Ming Yu
- Faculty of Life Sciences, University of Manchester, Manchester, M13 9PT, UK.,The Key Laboratory of Stem Cell and Regenerative Medicine, Institute of Molecular and Clinical Medicine, Kunming Medical University, Kunming, Yunnan Province, 650500, People's Republic of China
| | - Salma Al-Dallal
- Faculty of Life Sciences, University of Manchester, Manchester, M13 9PT, UK
| | - Latifa Al-Haj
- Faculty of Life Sciences, University of Manchester, Manchester, M13 9PT, UK.,Molecular Biomedicine Program, Program in Biomolecular Research, King Faisal Specialist Hospital and Research Center, Riyadh, 11211, Saudi Arabia
| | - Shiraj Panjwani
- Faculty of Life Sciences, University of Manchester, Manchester, M13 9PT, UK
| | - Akina S McCartney
- Faculty of Life Sciences, University of Manchester, Manchester, M13 9PT, UK
| | - Sarah M Edwards
- Faculty of Life Sciences, University of Manchester, Manchester, M13 9PT, UK
| | - Pooja Manjunath
- Faculty of Life Sciences, University of Manchester, Manchester, M13 9PT, UK
| | - Catherine Walker
- Faculty of Life Sciences, University of Manchester, Manchester, M13 9PT, UK
| | | | - Kathryn E Hentges
- Faculty of Life Sciences, University of Manchester, Manchester, M13 9PT, UK.
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García-González E, Escamilla-Del-Arenal M, Arzate-Mejía R, Recillas-Targa F. Chromatin remodeling effects on enhancer activity. Cell Mol Life Sci 2016; 73:2897-910. [PMID: 27026300 PMCID: PMC11108574 DOI: 10.1007/s00018-016-2184-3] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2015] [Revised: 03/04/2016] [Accepted: 03/14/2016] [Indexed: 01/02/2023]
Abstract
During organism development, a diversity of cell types emerges with disparate, yet stable profiles of gene expression with distinctive cellular functions. In addition to gene promoters, the genome contains enhancer regulatory sequences, which are implicated in cellular specialization by facilitating cell-type and tissue-specific gene expression. Enhancers are DNA binding elements characterized by highly sophisticated and various mechanisms of action allowing for the specific interaction of general and tissue-specific transcription factors (TFs). However, eukaryotic organisms package their genetic material into chromatin, generating a physical barrier for TFs to interact with their cognate sequences. The ability of TFs to bind DNA regulatory elements is also modulated by changes in the chromatin structure, including histone modifications, histone variants, ATP-dependent chromatin remodeling, and the methylation status of DNA. Furthermore, it has recently been revealed that enhancer sequences are also transcribed into a set of enhancer RNAs with regulatory potential. These interdependent processes act in the context of a complex network of chromatin interactions, which together contributes to a renewed vision of how gene activation is coordinated in a cell-type-dependent manner. In this review, we describe the interplay between genetic and epigenetic aspects associated with enhancers and discuss their possible roles on enhancer function.
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Affiliation(s)
- Estela García-González
- Departamento de Genética Molecular, Instituto de Fisiología Celular, Universidad Nacional Autónoma de México, Circuito Exterior S/N, Ciudad Universitaria, C.P. 04510, Mexico City, México
| | - Martín Escamilla-Del-Arenal
- Department of Biochemistry and Molecular Biophysics, Mortimer B. Zuckerman Mind Brain and Behavior Institute, Columbia University, New York City, NY, 10027, USA
| | - Rodrigo Arzate-Mejía
- Departamento de Genética Molecular, Instituto de Fisiología Celular, Universidad Nacional Autónoma de México, Circuito Exterior S/N, Ciudad Universitaria, C.P. 04510, Mexico City, México
| | - Félix Recillas-Targa
- Departamento de Genética Molecular, Instituto de Fisiología Celular, Universidad Nacional Autónoma de México, Circuito Exterior S/N, Ciudad Universitaria, C.P. 04510, Mexico City, México.
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48
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Drillon G, Audit B, Argoul F, Arneodo A. Evidence of selection for an accessible nucleosomal array in human. BMC Genomics 2016; 17:526. [PMID: 27472913 PMCID: PMC4966569 DOI: 10.1186/s12864-016-2880-2] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2015] [Accepted: 07/04/2016] [Indexed: 11/13/2022] Open
Abstract
BACKGROUND Recently, a physical model of nucleosome formation based on sequence-dependent bending properties of the DNA double-helix has been used to reveal some enrichment of nucleosome-inhibiting energy barriers (NIEBs) nearby ubiquitous human "master" replication origins. Here we use this model to predict the existence of about 1.6 millions NIEBs over the 22 human autosomes. RESULTS We show that these high energy barriers of mean size 153 bp correspond to nucleosome-depleted regions (NDRs) in vitro, as expected, but also in vivo. On either side of these NIEBs, we observe, in vivo and in vitro, a similar compacted nucleosome ordering, suggesting an absence of chromatin remodeling. This nucleosomal ordering strongly correlates with oscillations of the GC content as well as with the interspecies and intraspecies mutation profiles along these regions. Comparison of these divergence rates reveals the existence of both positive and negative selections linked to nucleosome positioning around these intrinsic NDRs. Overall, these NIEBs and neighboring nucleosomes cover 37.5 % of the human genome where nucleosome occupancy is stably encoded in the DNA sequence. These 1 kb-sized regions of intrinsic nucleosome positioning are equally found in GC-rich and GC-poor isochores, in early and late replicating regions, in intergenic and genic regions but not at gene promoters. CONCLUSION The source of selection pressure on the NIEBs has yet to be resolved in future work. One possible scenario is that these widely distributed chromatin patterns have been selected in human to impair the condensation of the nucleosomal array into the 30 nm chromatin fiber, so as to facilitate the epigenetic regulation of nuclear functions in a cell-type-specific manner.
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Affiliation(s)
- Guénola Drillon
- Univ Lyon, Ens de Lyon, Univ Claude Bernard Lyon 1, CNRS, Laboratoire de Physique, Lyon, F-69342 France
| | - Benjamin Audit
- Univ Lyon, Ens de Lyon, Univ Claude Bernard Lyon 1, CNRS, Laboratoire de Physique, Lyon, F-69342 France
| | - Françoise Argoul
- Univ Lyon, Ens de Lyon, Univ Claude Bernard Lyon 1, CNRS, Laboratoire de Physique, Lyon, F-69342 France
- LOMA, Université de Bordeaux, CNRS, UMR 5798, 51 Cours de le Libération, Talence, F-33405 France
| | - Alain Arneodo
- Univ Lyon, Ens de Lyon, Univ Claude Bernard Lyon 1, CNRS, Laboratoire de Physique, Lyon, F-69342 France
- LOMA, Université de Bordeaux, CNRS, UMR 5798, 51 Cours de le Libération, Talence, F-33405 France
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Tonelli C, Morelli MJ, Bianchi S, Rotta L, Capra T, Sabò A, Campaner S, Amati B. Genome-wide analysis of p53 transcriptional programs in B cells upon exposure to genotoxic stress in vivo. Oncotarget 2016; 6:24611-26. [PMID: 26372730 PMCID: PMC4694782 DOI: 10.18632/oncotarget.5232] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2015] [Accepted: 08/13/2015] [Indexed: 12/26/2022] Open
Abstract
The tumor suppressor p53 is a transcription factor that coordinates the cellular response to DNA damage. Here we provide an integrated analysis of p53 genomic occupancy and p53-dependent gene regulation in the splenic B and non-B cell compartments of mice exposed to whole-body ionizing radiation, providing insight into general principles of p53 activity in vivo. In unstressed conditions, p53 bound few genomic targets; induction of p53 by ionizing radiation increased the number of p53 bound sites, leading to highly overlapping profiles in the different cell types. Comparison of these profiles with chromatin features in unstressed B cells revealed that, upon activation, p53 localized at active promoters, distal enhancers, and a smaller set of unmarked distal regions. At promoters, recognition of the canonical p53 motif as well as binding strength were associated with p53-dependent transcriptional activation, but not repression, indicating that the latter was most likely indirect. p53-activated targets constituted the core of a cell type-independent response, superimposed onto a cell type-specific program. Core response genes included most of the known p53-regulated genes, as well as many new ones. Our data represent a unique characterization of the p53-regulated response to ionizing radiation in vivo.
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Affiliation(s)
- Claudia Tonelli
- Department of Experimental Oncology, European Institute of Oncology (IEO), Milan, Italy
| | - Marco J Morelli
- Center for Genomic Science of IIT@SEMM, Fondazione Istituto Italiano di Tecnologia (IIT), Milan, Italy
| | - Salvatore Bianchi
- Center for Genomic Science of IIT@SEMM, Fondazione Istituto Italiano di Tecnologia (IIT), Milan, Italy
| | - Luca Rotta
- Department of Experimental Oncology, European Institute of Oncology (IEO), Milan, Italy
| | - Thelma Capra
- Department of Experimental Oncology, European Institute of Oncology (IEO), Milan, Italy
| | - Arianna Sabò
- Center for Genomic Science of IIT@SEMM, Fondazione Istituto Italiano di Tecnologia (IIT), Milan, Italy
| | - Stefano Campaner
- Center for Genomic Science of IIT@SEMM, Fondazione Istituto Italiano di Tecnologia (IIT), Milan, Italy
| | - Bruno Amati
- Department of Experimental Oncology, European Institute of Oncology (IEO), Milan, Italy.,Center for Genomic Science of IIT@SEMM, Fondazione Istituto Italiano di Tecnologia (IIT), Milan, Italy
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Abstract
Background Peak calling is a fundamental step in the analysis of data generated by ChIP-seq or similar techniques to acquire epigenetics information. Current peak callers are often hard to parameterise and may therefore be difficult to use for non-bioinformaticians. In this paper, we present the ChIP-seq analysis tool available in CLC Genomics Workbench and CLC Genomics Server (version 7.5 and up), a user-friendly peak-caller designed to be not specific to a particular *-seq protocol. Results We illustrate the advantages of a shape-based approach and describe the algorithmic principles underlying the implementation. Thanks to the generality of the idea and the fact the algorithm is able to learn the peak shape from the data, the implementation requires only minimal user input, while still being applicable to a range of *-seq protocols. Using independently validated benchmark datasets, we compare our implementation to other state-of-the-art algorithms explicitly designed to analyse ChIP-seq data and provide an evaluation in terms of receiver-operator characteristic (ROC) plots. In order to show the applicability of the method to similar *-seq protocols, we also investigate algorithmic performances on DNase-seq data. Conclusions The results show that CLC shape-based peak caller ranks well among popular state-of-the-art peak callers while providing flexibility and ease-of-use.
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Affiliation(s)
| | - Michael Lappe
- Qiagen Aarhus, Silkeborgvej 2, Aarhus, 8000, DK, Denmark.
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