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Singh H. Role of gene therapy in treatment of cancer with craniofacial regeneration-current molecular strategies, future perspectives, and challenges: a narrative review. JOURNAL OF YEUNGNAM MEDICAL SCIENCE 2024; 41:13-21. [PMID: 37218144 PMCID: PMC10834268 DOI: 10.12701/jyms.2023.00073] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/26/2023] [Accepted: 03/30/2023] [Indexed: 05/24/2023]
Abstract
Gene therapy involves the introduction of foreign genetic material into host tissue to alter the expression of genetic products. Gene therapy represents an opportunity to alter the course of various diseases. Hence, genetic products utilizing safe and reliable vectors with improved biotechnology will play a critical role in the treatment of various diseases in the future. This review summarizes various important vectors for gene therapy along with modern techniques for potential craniofacial regeneration using gene therapy. This review also explains current molecular approaches for the management and treatment of cancer using gene therapy. The existing literature was searched to find studies related to gene therapy and its role in craniofacial regeneration and cancer treatment. Various databases such as PubMed, Science Direct, Scopus, Web of Science, and Google Scholar were searched for English language articles using the keywords "gene therapy," "gene therapy in present scenario," "gene therapy in cancer," "gene therapy and vector," "gene therapy in diseases," and "gene therapy and molecular strategies."
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Affiliation(s)
- Himanshu Singh
- Department of Oral and Maxillofacial Pathology and Oral Microbiology, Index Institute of Dental Sciences, Indore, India
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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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Hui-Yuen J, Jiang K, Malkiel S, Eberhard BA, Walters H, Diamond B, Jarvis J. B lymphocytes in treatment-naive paediatric patients with lupus are epigenetically distinct from healthy children. Lupus Sci Med 2023; 10:10/1/e000921. [PMID: 37202122 DOI: 10.1136/lupus-2023-000921] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2023] [Accepted: 05/04/2023] [Indexed: 05/20/2023]
Abstract
BACKGROUND SLE is likely triggered by gene-environment interactions. We have shown that most SLE-associated haplotypes encompass genomic regions enriched for epigenetic marks associated with enhancer function in lymphocytes, suggesting genetic risk is exerted through altered gene regulation. Data remain scarce on how epigenetic variance contributes to disease risk in paediatric SLE (pSLE). We aim to identify differences in epigenetically regulated chromatin architecture in treatment-naive patients with pSLE compared with healthy children. METHODS Using the assay for transposase-accessible chromatin with sequencing (ATACseq), we surveyed open chromatin in 10 treatment-naive patients with pSLE, with at least moderate disease severity, and 5 healthy children. We investigated whether regions of open chromatin unique to patients with pSLE demonstrate enrichment for specific transcriptional regulators, using standard computational approaches to identify unique peaks and a false discovery rate of <0.05. Further analyses for histone modification enrichment and variant calling were performed using bioinformatics packages in R and Linux. RESULTS We identified 30 139 differentially accessible regions (DAR) unique to pSLE B cells; 64.3% are more accessible in pSLE than healthy children. Many DAR are found in distal, intergenic regions and enriched for enhancer histone marks (p=0.027). B cells from adult patients with SLE contain more regions of inaccessible chromatin than those in pSLE. In pSLE B cells, 65.2% of the DAR are located within or near known SLE haplotypes. Further analysis revealed enrichment of transcription factor binding motifs within these DAR that may regulate genes involved in pro-inflammatory responses and cellular adhesion. CONCLUSIONS We demonstrate an epigenetically distinct profile in pSLE B cells when compared with healthy children and adults with lupus, indicating that pSLE B cells are predisposed for disease onset/development. Increased chromatin accessibility in non-coding genomic regions controlling activation of inflammation suggest that transcriptional dysregulation by regulatory elements controlling B cell activation plays an important role in pSLE pathogenesis.
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Affiliation(s)
- Joyce Hui-Yuen
- Pediatric Rheumatology, Northwell Health, Lake Success, New York, USA
- Pediatrics, Hofstra Northwell School of Medicine at Hofstra University, Hempstead, New York, USA
- Center for Autoimmune, Musculoskeletal, and Hematopoietic Diseases Research, The Feinstein Institutes for Medical Research, Manhasset, New York, USA
| | - Kaiyu Jiang
- Pediatrics, University at Buffalo School of Medicine and Biomedical Sciences, Buffalo, New York, USA
| | - Susan Malkiel
- Center for Autoimmune, Musculoskeletal, and Hematopoietic Diseases Research, The Feinstein Institutes for Medical Research, Manhasset, New York, USA
| | - Barbara Anne Eberhard
- Pediatric Rheumatology, Northwell Health, Lake Success, New York, USA
- Pediatrics, Hofstra Northwell School of Medicine at Hofstra University, Hempstead, New York, USA
| | - Heather Walters
- Pediatric Rheumatology, Northwell Health, Lake Success, New York, USA
- Pediatrics, Hofstra Northwell School of Medicine at Hofstra University, Hempstead, New York, USA
| | - Betty Diamond
- Center for Autoimmune, Musculoskeletal, and Hematopoietic Diseases Research, The Feinstein Institutes for Medical Research, Manhasset, New York, USA
| | - James Jarvis
- Pediatrics, University at Buffalo School of Medicine and Biomedical Sciences, Buffalo, New York, USA
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Di Benedetto C, Khan T, Serrano-Saenz S, Rodriguez-Lemus A, Klomsiri C, Beutel TM, Thach A, Walczak H, Betancur P. Enhancer Clusters Drive Type I Interferon-Induced TRAIL Overexpression in Cancer, and Its Intracellular Protein Accumulation Fails to Induce Apoptosis. Cancers (Basel) 2023; 15:967. [PMID: 36765925 PMCID: PMC9913803 DOI: 10.3390/cancers15030967] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2022] [Revised: 01/14/2023] [Accepted: 01/29/2023] [Indexed: 02/05/2023] Open
Abstract
Tumor necrosis factor-related apoptosis-inducing ligand (TRAIL) is a cytokine produced and secreted by immune cells in response to an infection, often in response to interferon (IFN) stimulation. In cancer, it has also been shown that IFN stimulates the production of TRAIL, and it has been proposed that this TRAIL can induce apoptosis in an autocrine or paracrine manner in different cancer cells. Yet, the mechanism mediating TRAIL upregulation and the implications of TRAIL as an apoptotic molecule in cancer cells are still poorly understood. We show here that in certain cancer cells, TRAIL is upregulated by enhancer clusters, potent genomic regulatory regions containing densely packed enhancers that have combinatorial and additive activity and that are usually found to be associated with cancer-promoting genes. Moreover, we found that TRAIL upregulation by IFNα is mediated by these enhancer clusters in breast and lung cancer cells. Surprisingly, IFNα stimulation leads to the intracellular accumulation of TRAIL protein in these cancer cells. Consequently, this TRAIL is not capable of inducing apoptosis. Our study provides novel insights into the mechanism behind the interferon-mediated upregulation of TRAIL and its protein accumulation in cancer cells. Further investigation is required to understand the role of intracellular TRAIL or depict the mechanisms mediating its apoptosis impairment in cancer cells.
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Affiliation(s)
- Carolina Di Benedetto
- Department of Radiation Oncology, University of California, San Francisco (UCSF), San Francisco, CA 94143, USA
| | - Taimoor Khan
- Department of Radiation Oncology, University of California, San Francisco (UCSF), San Francisco, CA 94143, USA
| | - Santiago Serrano-Saenz
- CECAD Cluster of Excellence, University of Cologne, 50931 Cologne, Germany
- Center for Biochemistry, Medical Faculty, University of Cologne, 50931 Cologne, Germany
| | - Anthony Rodriguez-Lemus
- Department of Radiation Oncology, University of California, San Francisco (UCSF), San Francisco, CA 94143, USA
| | - Chananat Klomsiri
- Department of Radiation Oncology, University of California, San Francisco (UCSF), San Francisco, CA 94143, USA
| | - Tim-Mathis Beutel
- CECAD Cluster of Excellence, University of Cologne, 50931 Cologne, Germany
- Center for Biochemistry, Medical Faculty, University of Cologne, 50931 Cologne, Germany
| | - Alysia Thach
- Department of Radiation Oncology, University of California, San Francisco (UCSF), San Francisco, CA 94143, USA
| | - Henning Walczak
- CECAD Cluster of Excellence, University of Cologne, 50931 Cologne, Germany
- Center for Biochemistry, Medical Faculty, University of Cologne, 50931 Cologne, Germany
- Centre for Cell Death, Cancer, and Inflammation (CCCI), UCL Cancer Institute, University College London, London WC1E 6DD, UK
| | - Paola Betancur
- Department of Radiation Oncology, University of California, San Francisco (UCSF), San Francisco, CA 94143, USA
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Tang X, Zheng P, Liu Y, Yao Y, Huang G. LangMoDHS: A deep learning language model for predicting DNase I hypersensitive sites in mouse genome. MATHEMATICAL BIOSCIENCES AND ENGINEERING : MBE 2023; 20:1037-1057. [PMID: 36650801 DOI: 10.3934/mbe.2023048] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/17/2023]
Abstract
DNase I hypersensitive sites (DHSs) are a specific genomic region, which is critical to detect or understand cis-regulatory elements. Although there are many methods developed to detect DHSs, there is a big gap in practice. We presented a deep learning-based language model for predicting DHSs, named LangMoDHS. The LangMoDHS mainly comprised the convolutional neural network (CNN), the bi-directional long short-term memory (Bi-LSTM) and the feed-forward attention. The CNN and the Bi-LSTM were stacked in a parallel manner, which was helpful to accumulate multiple-view representations from primary DNA sequences. We conducted 5-fold cross-validations and independent tests over 14 tissues and 4 developmental stages. The empirical experiments showed that the LangMoDHS is competitive with or slightly better than the iDHS-Deep, which is the latest method for predicting DHSs. The empirical experiments also implied substantial contribution of the CNN, Bi-LSTM, and attention to DHSs prediction. We implemented the LangMoDHS as a user-friendly web server which is accessible at http:/www.biolscience.cn/LangMoDHS/. We used indices related to information entropy to explore the sequence motif of DHSs. The analysis provided a certain insight into the DHSs.
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Affiliation(s)
- Xingyu Tang
- School of Electrical Engineering, Shaoyang University, Shaoyang 422000, China
| | - Peijie Zheng
- School of Electrical Engineering, Shaoyang University, Shaoyang 422000, China
| | - Yuewu Liu
- College of Information and Intelligence, Hunan Agricultural University, Changsha 410128, China
| | - Yuhua Yao
- School of Mathematics and Statistics, Hainan Normal University, Haikou 571158, China
| | - Guohua Huang
- School of Electrical Engineering, Shaoyang University, Shaoyang 422000, China
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Jain M, Garg R. Enhancers as potential targets for engineering salinity stress tolerance in crop plants. PHYSIOLOGIA PLANTARUM 2021; 173:1382-1391. [PMID: 33837536 DOI: 10.1111/ppl.13421] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/08/2021] [Revised: 03/19/2021] [Accepted: 04/06/2021] [Indexed: 06/12/2023]
Abstract
Enhancers represent noncoding regulatory regions of the genome located distantly from their target genes. They regulate gene expression programs in a context-specific manner via interacting with promoters of one or more target genes and are generally associated with transcription factor binding sites and epi(genomic)/chromatin features, such as regions of chromatin accessibility and histone modifications. The enhancers are difficult to identify due to the modularity of their associated features. Although enhancers have been studied extensively in human and animals, only a handful of them has been identified in few plant species till date due to nonavailability of plant-specific experimental and computational approaches for their discovery. Being an important regulatory component of the genome, enhancers represent potential targets for engineering agronomic traits, including salinity stress tolerance in plants. Here, we provide a review of the available experimental and computational approaches along with the associated sequence and chromatin/epigenetic features for the discovery of enhancers in plants. In addition, we provide insights into the challenges and future prospects of enhancer research in plant biology with emphasis on potential applications in engineering salinity stress tolerance in crop plants.
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Affiliation(s)
- Mukesh Jain
- School of Computational and Integrative Sciences, Jawaharlal Nehru University, New Delhi, India
| | - Rohini Garg
- Department of Life Sciences, School of Natural Sciences, Shiv Nadar University, Gautam Buddha Nagar, Uttar Pradesh, India
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Sheikh A, Md S, Kesharwani P. RGD engineered dendrimer nanotherapeutic as an emerging targeted approach in cancer therapy. J Control Release 2021; 340:221-242. [PMID: 34757195 DOI: 10.1016/j.jconrel.2021.10.028] [Citation(s) in RCA: 47] [Impact Index Per Article: 15.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2021] [Revised: 10/24/2021] [Accepted: 10/28/2021] [Indexed: 12/15/2022]
Abstract
A bird's eye view is now demanded in the area of cancer research to suppress the suffering of cancer patient and mediate the lack of treatment related to chemotherapy. Chemotherapy is always preferred over surgery or radiation therapy, but they never met the patient's demand of safe medication. Targeted therapy has now been in research that could hinder the unnecessary effect of drug on normal cells but could affect the tumor cells in much efficient manner. Angiogenesis is process involved in development of new blood vessel that nourishes tumor growth. Integrin receptors are over expressed on cancer cells that play vital role in angiogenesis for growth and metastasis of tumor cell. A delivery of RGD based peptide to integrin targeted site could help in its successful binding and liberation of drug in tumor vasculature. Dendrimers, in addition to its excellent pharmacokinetic properties also helps to carry targeting ligand to site of tumor by successfully conjugating with them. The aim of this review is to bring light upon the role of integrin in cancer progression, interaction of RGD to integrin receptor and more importantly the RGD-dendrimer based targeted therapy for the treatment of various cancers.
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Affiliation(s)
- Afsana Sheikh
- Department of Pharmaceutics, School of Pharmaceutical Education and Research, Jamia Hamdard, New Delhi 110062, India
| | - Shadab Md
- Department of Pharmaceutics, Faculty of Pharmacy, King Abdulaziz University, Jeddah 21589, Saudi Arabia; Center of Excellence for Drug Research & Pharmaceutical Industries, King Abdulaziz University, Jeddah 21589, Saudi Arabia
| | - Prashant Kesharwani
- Department of Pharmaceutics, School of Pharmaceutical Education and Research, Jamia Hamdard, New Delhi 110062, India.
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Schwope R, Magris G, Miculan M, Paparelli E, Celii M, Tocci A, Marroni F, Fornasiero A, De Paoli E, Morgante M. Open chromatin in grapevine marks candidate CREs and with other chromatin features correlates with gene expression. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2021; 107:1631-1647. [PMID: 34219317 PMCID: PMC8518642 DOI: 10.1111/tpj.15404] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/07/2020] [Revised: 06/24/2021] [Accepted: 06/25/2021] [Indexed: 05/14/2023]
Abstract
Vitis vinifera is an economically important crop and a useful model in which to study chromatin dynamics. In contrast to the small and relatively simple genome of Arabidopsis thaliana, grapevine contains a complex genome of 487 Mb that exhibits extensive colonization by transposable elements. We used Hi-C, ChIP-seq and ATAC-seq to measure how chromatin features correlate to the expression of 31 845 grapevine genes. ATAC-seq revealed the presence of more than 16 000 open chromatin regions, of which we characterize nearly 5000 as possible distal enhancer candidates that occur in intergenic space > 2 kb from the nearest transcription start site (TSS). A motif search identified more than 480 transcription factor (TF) binding sites in these regions, with those for TCP family proteins in greatest abundance. These open chromatin regions are typically within 15 kb from their nearest promoter, and a gene ontology analysis indicated that their nearest genes are significantly enriched for TF activity. The presence of a candidate cis-regulatory element (cCRE) > 2 kb upstream of the TSS, location in the active nuclear compartment as determined by Hi-C, and the enrichment of H3K4me3, H3K4me1 and H3K27ac at the gene are correlated with gene expression. Taken together, these results suggest that regions of intergenic open chromatin identified by ATAC-seq can be considered potential candidates for cis-regulatory regions in V. vinifera. Our findings enhance the characterization of a valuable agricultural crop, and help to clarify the understanding of unique plant biology.
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Affiliation(s)
- Rachel Schwope
- Dipartimento di Scienze AgroalimentariAmbientali e Animali (DI4A)UdineI‐33100Italy
- Istituto di Genomica ApplicataUdineI‐33100Italy
| | - Gabriele Magris
- Dipartimento di Scienze AgroalimentariAmbientali e Animali (DI4A)UdineI‐33100Italy
- Istituto di Genomica ApplicataUdineI‐33100Italy
| | - Mara Miculan
- Dipartimento di Scienze AgroalimentariAmbientali e Animali (DI4A)UdineI‐33100Italy
- Istituto di Genomica ApplicataUdineI‐33100Italy
- Present address:
Institute of Life SciencesScuola Superiore Sant'Anna PisaPisa56127Italy
| | - Eleonora Paparelli
- Dipartimento di Scienze AgroalimentariAmbientali e Animali (DI4A)UdineI‐33100Italy
- Istituto di Genomica ApplicataUdineI‐33100Italy
- Present address:
IGA Technology ServicesUdineI‐33100Italy
| | - Mirko Celii
- Dipartimento di Scienze AgroalimentariAmbientali e Animali (DI4A)UdineI‐33100Italy
- Istituto di Genomica ApplicataUdineI‐33100Italy
- Present address:
Center for Desert Agriculture, Biological and Environmental Sciences & Engineering Division (BESE)KAUSTThuwalMakkahSaudi Arabia
| | - Aldo Tocci
- Dipartimento di Scienze AgroalimentariAmbientali e Animali (DI4A)UdineI‐33100Italy
- Istituto di Genomica ApplicataUdineI‐33100Italy
- Scuola Internazionale Superiore di Studi AvanzatiTriesteFriuli‐Venezia GiuliaItaly
| | - Fabio Marroni
- Dipartimento di Scienze AgroalimentariAmbientali e Animali (DI4A)UdineI‐33100Italy
- Istituto di Genomica ApplicataUdineI‐33100Italy
| | - Alice Fornasiero
- Dipartimento di Scienze AgroalimentariAmbientali e Animali (DI4A)UdineI‐33100Italy
- Istituto di Genomica ApplicataUdineI‐33100Italy
- Present address:
Center for Desert Agriculture, Biological and Environmental Sciences & Engineering Division (BESE)KAUSTThuwalMakkahSaudi Arabia
| | - Emanuele De Paoli
- Dipartimento di Scienze AgroalimentariAmbientali e Animali (DI4A)UdineI‐33100Italy
| | - Michele Morgante
- Dipartimento di Scienze AgroalimentariAmbientali e Animali (DI4A)UdineI‐33100Italy
- Istituto di Genomica ApplicataUdineI‐33100Italy
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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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Henikoff S, Henikoff JG, Ahmad K. Simplified Epigenome Profiling Using Antibody-tethered Tagmentation. Bio Protoc 2021; 11:e4043. [PMID: 34250209 PMCID: PMC8250384 DOI: 10.21769/bioprotoc.4043] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2021] [Revised: 03/24/2021] [Accepted: 04/29/2021] [Indexed: 12/02/2022] Open
Abstract
We previously introduced Cleavage Under Targets & Tagmentation (CUT&Tag), an epigenomic profiling method in which antibody tethering of the Tn5 transposase to a chromatin epitope of interest maps specific chromatin features in small samples and single cells. With CUT&Tag, intact cells or nuclei are permeabilized, followed by successive addition of a primary antibody, a secondary antibody, and a chimeric Protein A-Transposase fusion protein that binds to the antibody. Addition of Mg++ activates the transposase and inserts sequencing adapters into adjacent DNA in situ. We have since adapted CUT&Tag to also map chromatin accessibility by simply modifying the transposase activation conditions when using histone H3K4me2, H3K4me3, or Serine-5-phosphorylated RNA Polymerase II antibodies. Using these antibodies, we redirect the tagmentation of accessible DNA sites to produce chromatin accessibility maps with exceptionally high signal-to-noise and resolution. All steps from nuclei to amplified sequencing-ready libraries are performed in single PCR tubes using non-toxic reagents and inexpensive equipment, making our simplified strategy for simultaneous chromatin profiling and accessibility mapping suitable for the lab, home workbench, or classroom.
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Affiliation(s)
- Steven Henikoff
- Basic Sciences Division, Fred Hutchinson Cancer Research Center, 1100 Fairview Ave N, Seattle, Washington 98109, USA.,Howard Hughes Medical Institute, Seattle WA, USA
| | - Jorja G Henikoff
- Basic Sciences Division, Fred Hutchinson Cancer Research Center, 1100 Fairview Ave N, Seattle, Washington 98109, USA
| | - Kami Ahmad
- Basic Sciences Division, Fred Hutchinson Cancer Research Center, 1100 Fairview Ave N, Seattle, Washington 98109, USA
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Alhakamy NA, Curiel DT, Berkland CJ. The era of gene therapy: From preclinical development to clinical application. Drug Discov Today 2021; 26:1602-1619. [PMID: 33781953 DOI: 10.1016/j.drudis.2021.03.021] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2020] [Revised: 12/09/2020] [Accepted: 03/21/2021] [Indexed: 12/16/2022]
Abstract
Three decades of promise have culminated in the development of gene therapies that can be applied to a broad range of human diseases. After a brief history, we provide an overview of gene therapy types and delivery methods, gene editing technologies, regulatory affairs, clinical trials, approved products, ongoing challenges, and future goals. Information on clinical trials of candidates and on approved products for gene therapy developed between 1988 and 2020 is systematically collated. To obtain this global information, we scanned and reviewed more than 46,000 records of clinical trials from 17 clinical trial database providers. The medical benefits of transformative gene therapies are gradually being accepted by payors, and a significant increase in the number of gene therapy clinical trials and approved gene therapy products has resulted.
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Affiliation(s)
- Nabil A Alhakamy
- Department of Pharmaceutics, Faculty of Pharmacy, King Abdulaziz University, Jeddah, Saudi Arabia; Center of Excellence for Drug Research and Pharmaceutical Industries, King Abdulaziz University, Jeddah 21589, Saudi Arabia; Mohamed Saeed Tamer Chair for Pharmaceutical Industries, King Abdulaziz University, Jeddah 21589, Saudi Arabia; Department of Pharmaceutical Chemistry, University of Kansas, Lawrence, KS 66047, USA
| | - David T Curiel
- Department of Radiation Oncology, School of Medicine, Washington University, St. Louis, MO 63108, USA
| | - Cory J Berkland
- Department of Pharmaceutical Chemistry, University of Kansas, Lawrence, KS 66047, USA; Department of Chemical & Petroleum Engineering, University of Kansas, Lawrence, KS 66047, USA.
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Fernando N, Sciumè G, O'Shea JJ, Shih HY. Multi-Dimensional Gene Regulation in Innate and Adaptive Lymphocytes: A View From Regulomes. Front Immunol 2021; 12:655590. [PMID: 33841440 PMCID: PMC8034253 DOI: 10.3389/fimmu.2021.655590] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2021] [Accepted: 03/09/2021] [Indexed: 12/24/2022] Open
Abstract
The precise control of cytokine production by innate lymphoid cells (ILCs) and their T cell adaptive system counterparts is critical to mounting a proper host defense immune response without inducing collateral damage and autoimmunity. Unlike T cells that differentiate into functionally divergent subsets upon antigen recognition, ILCs are developmentally programmed to rapidly respond to environmental signals in a polarized manner, without the need of T cell receptor (TCR) signaling. The specification of cytokine production relies on dynamic regulation of cis-regulatory elements that involve multi-dimensional epigenetic mechanisms, including DNA methylation, transcription factor binding, histone modification and DNA-DNA interactions that form chromatin loops. How these different layers of gene regulation coordinate with each other to fine tune cytokine production, and whether ILCs and their T cell analogs utilize the same regulatory strategy, remain largely unknown. Herein, we review the molecular mechanisms that underlie cell identity and functionality of helper T cells and ILCs, focusing on networks of transcription factors and cis-regulatory elements. We discuss how higher-order chromatin architecture orchestrates these components to construct lineage- and state-specific regulomes that support ordered immunoregulation.
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Affiliation(s)
- Nilisha Fernando
- Neuro-Immune Regulome Unit, National Eye Institute, National Institutes of Health, Bethesda, MD, United States
| | - Giuseppe Sciumè
- Laboratory Affiliated to Istituto Pasteur Italia - Fondazione Cenci-Bolognetti, Department of Molecular Medicine, Sapienza University of Rome, Rome, Italy
| | - John J O'Shea
- Lymphocyte Cell Biology Section, Molecular Immunology and Inflammation Branch, National Institute of Arthritis, Musculoskeletal and Skin Diseases, National Institutes of Health, Bethesda, MD, United States
| | - Han-Yu Shih
- Neuro-Immune Regulome Unit, National Eye Institute, National Institutes of Health, Bethesda, MD, United States.,National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, United States
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13
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Dao FY, Lv H, Su W, Sun ZJ, Huang QL, Lin H. iDHS-Deep: an integrated tool for predicting DNase I hypersensitive sites by deep neural network. Brief Bioinform 2021; 22:6158360. [PMID: 33751027 DOI: 10.1093/bib/bbab047] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2020] [Revised: 01/28/2021] [Accepted: 01/29/2021] [Indexed: 01/09/2023] Open
Abstract
DNase I hypersensitive site (DHS) refers to the hypersensitive region of chromatin for the DNase I enzyme. It is an important part of the noncoding region and contains a variety of regulatory elements, such as promoter, enhancer, and transcription factor-binding site, etc. Moreover, the related locus of disease (or trait) are usually enriched in the DHS regions. Therefore, the detection of DHS region is of great significance. In this study, we develop a deep learning-based algorithm to identify whether an unknown sequence region would be potential DHS. The proposed method showed high prediction performance on both training datasets and independent datasets in different cell types and developmental stages, demonstrating that the method has excellent superiority in the identification of DHSs. Furthermore, for the convenience of related wet-experimental researchers, the user-friendly web-server iDHS-Deep was established at http://lin-group.cn/server/iDHS-Deep/, by which users can easily distinguish DHS and non-DHS and obtain the corresponding developmental stage ofDHS.
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Affiliation(s)
- Fu-Ying Dao
- Informational Biology at University of Electronic Science and Technology of China, China
| | - Hao Lv
- Informational Biology at University of Electronic Science and Technology of China, China
| | - Wei Su
- Informational Biology at University of Electronic Science and Technology of China, China
| | - Zi-Jie Sun
- Informational Biology at University of Electronic Science and Technology of China, China
| | - Qin-Lai Huang
- Informational Biology at University of Electronic Science and Technology of China, China
| | - Hao Lin
- Informational Biology at University of Electronic Science and Technology of China, China
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14
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Henikoff S, Henikoff JG, Kaya-Okur HS, Ahmad K. Efficient chromatin accessibility mapping in situ by nucleosome-tethered tagmentation. eLife 2020; 9:e63274. [PMID: 33191916 PMCID: PMC7721439 DOI: 10.7554/elife.63274] [Citation(s) in RCA: 59] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2020] [Accepted: 11/13/2020] [Indexed: 12/27/2022] Open
Abstract
Chromatin accessibility mapping is a powerful approach to identify potential regulatory elements. A popular example is ATAC-seq, whereby Tn5 transposase inserts sequencing adapters into accessible DNA ('tagmentation'). CUT&Tag is a tagmentation-based epigenomic profiling method in which antibody tethering of Tn5 to a chromatin epitope of interest profiles specific chromatin features in small samples and single cells. Here, we show that by simply modifying the tagmentation conditions for histone H3K4me2 or H3K4me3 CUT&Tag, antibody-tethered tagmentation of accessible DNA sites is redirected to produce chromatin accessibility maps that are indistinguishable from the best ATAC-seq maps. Thus, chromatin accessibility maps can be produced in parallel with CUT&Tag maps of other epitopes with all steps from nuclei to amplified sequencing-ready libraries performed in single PCR tubes in the laboratory or on a home workbench. As H3K4 methylation is produced by transcription at promoters and enhancers, our method identifies transcription-coupled accessible regulatory sites.
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Affiliation(s)
- Steven Henikoff
- Basic Sciences Division Fred Hutchinson Cancer Research CenterSeattleUnited States
- Howard Hughes Medical InstituteSeattleUnited States
| | - Jorja G Henikoff
- Basic Sciences Division Fred Hutchinson Cancer Research CenterSeattleUnited States
| | - Hatice S Kaya-Okur
- Basic Sciences Division Fred Hutchinson Cancer Research CenterSeattleUnited States
| | - Kami Ahmad
- Basic Sciences Division Fred Hutchinson Cancer Research CenterSeattleUnited States
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15
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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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16
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Raxwal VK, Ghosh S, Singh S, Katiyar-Agarwal S, Goel S, Jagannath A, Kumar A, Scaria V, Agarwal M. Abiotic stress-mediated modulation of the chromatin landscape in Arabidopsis thaliana. JOURNAL OF EXPERIMENTAL BOTANY 2020; 71:5280-5293. [PMID: 32526034 DOI: 10.1093/jxb/eraa286] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/23/2020] [Accepted: 06/10/2020] [Indexed: 05/18/2023]
Abstract
Limited information is available on abiotic stress-mediated alterations of chromatin conformation influencing gene expression in plants. In order to characterize the effect of abiotic stresses on changes in chromatin conformation, we employed FAIRE-seq (formaldehyde-assisted isolation of regulatory element sequencing) and DNase-seq to isolate accessible regions of chromatin from Arabidopsis thaliana seedlings exposed to either heat, cold, salt, or drought stress. Approximately 25% of regions in the Arabidopsis genome were captured as open chromatin, the majority of which included promoters and exons. A large proportion of chromatin regions apparently did not change their conformation in response to any of the four stresses. Digital footprints present within these regions had differential enrichment of motifs for binding of 43 different transcription factors. Further, in contrast to drought and salt stress, both high and low temperature treatments resulted in increased accessibility of the chromatin. Also, pseudogenes attained increased chromatin accessibility in response to cold and drought stresses. The highly accessible and inaccessible chromatin regions of seedlings exposed to drought stress correlated with the Ser/Thr protein kinases (MLK1 and MLK2)-mediated reduction and increase in H3 phosphorylation (H3T3Ph), respectively. The presented results provide a deeper understanding of abiotic stress-mediated chromatin modulation in plants.
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Affiliation(s)
- Vivek Kumar Raxwal
- Department of Botany, University of Delhi, Delhi, India
- Central European Institute of Technology (CEITEC), Masaryk University, Brno, Czech Republic
| | - Sourav Ghosh
- Academy of Scientific and Innovative Research, CSIR-IGIB South Campus, New Delhi, India
- GN Ramachandran Knowledge Center for Genome Informatics, CSIR Institute of Genomics and Integrative Biology, New Delhi, India
| | - Somya Singh
- Department of Botany, University of Delhi, Delhi, India
| | | | | | | | - Amar Kumar
- Department of Botany, University of Delhi, Delhi, India
| | - Vinod Scaria
- Academy of Scientific and Innovative Research, CSIR-IGIB South Campus, New Delhi, India
- GN Ramachandran Knowledge Center for Genome Informatics, CSIR Institute of Genomics and Integrative Biology, New Delhi, India
| | - Manu Agarwal
- Department of Botany, University of Delhi, Delhi, India
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17
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Gordon MG, Inoue F, Martin B, Schubach M, Agarwal V, Whalen S, Feng S, Zhao J, Ashuach T, Ziffra R, Kreimer A, Georgakopoulos-Soares I, Yosef N, Ye CJ, Pollard KS, Shendure J, Kircher M, Ahituv N. lentiMPRA and MPRAflow for high-throughput functional characterization of gene regulatory elements. Nat Protoc 2020; 15:2387-2412. [PMID: 32641802 PMCID: PMC7550205 DOI: 10.1038/s41596-020-0333-5] [Citation(s) in RCA: 52] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2020] [Accepted: 04/17/2020] [Indexed: 12/22/2022]
Abstract
Massively parallel reporter assays (MPRAs) can simultaneously measure the function of thousands of candidate regulatory sequences (CRSs) in a quantitative manner. In this method, CRSs are cloned upstream of a minimal promoter and reporter gene, alongside a unique barcode, and introduced into cells. If the CRS is a functional regulatory element, it will lead to the transcription of the barcode sequence, which is measured via RNA sequencing and normalized for cellular integration via DNA sequencing of the barcode. This technology has been used to test thousands of sequences and their variants for regulatory activity, to decipher the regulatory code and its evolution, and to develop genetic switches. Lentivirus-based MPRA (lentiMPRA) produces 'in-genome' readouts and enables the use of this technique in hard-to-transfect cells. Here, we provide a detailed protocol for lentiMPRA, along with a user-friendly Nextflow-based computational pipeline-MPRAflow-for quantifying CRS activity from different MPRA designs. The lentiMPRA protocol takes ~2 months, which includes sequencing turnaround time and data processing with MPRAflow.
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Affiliation(s)
- M Grace Gordon
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, CA, USA
- Institute for Human Genetics, University of California, San Francisco, San Francisco, CA, USA
- Biological and Medical Informatics Graduate Program, University of California, San Francisco, San Francisco, CA, USA
| | - Fumitaka Inoue
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, CA, USA.
- Institute for Human Genetics, University of California, San Francisco, San Francisco, CA, USA.
| | - Beth Martin
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | - Max Schubach
- Berlin Institute of Health (BIH), Berlin, Germany
- Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Vikram Agarwal
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
- Calico Life Sciences LLC, South San Francisco, CA, USA
| | - Sean Whalen
- Gladstone Institutes, San Francisco, CA, USA
| | - Shiyun Feng
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, CA, USA
- Institute for Human Genetics, University of California, San Francisco, San Francisco, CA, USA
| | - Jingjing Zhao
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, CA, USA
- Institute for Human Genetics, University of California, San Francisco, San Francisco, CA, USA
| | - Tal Ashuach
- Department of Electrical Engineering and Computer Sciences and Center for Computational Biology, University of California, Berkeley, Berkeley, CA, USA
| | - Ryan Ziffra
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, CA, USA
- Institute for Human Genetics, University of California, San Francisco, San Francisco, CA, USA
| | - Anat Kreimer
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, CA, USA
- Institute for Human Genetics, University of California, San Francisco, San Francisco, CA, USA
- Department of Electrical Engineering and Computer Sciences and Center for Computational Biology, University of California, Berkeley, Berkeley, CA, USA
| | - Ilias Georgakopoulos-Soares
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, CA, USA
- Institute for Human Genetics, University of California, San Francisco, San Francisco, CA, USA
| | - Nir Yosef
- Department of Electrical Engineering and Computer Sciences and Center for Computational Biology, University of California, Berkeley, Berkeley, CA, USA
- Chan-Zuckerberg Biohub, San Francisco, CA, USA
| | - Chun Jimmie Ye
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, CA, USA
- Institute for Human Genetics, University of California, San Francisco, San Francisco, CA, USA
- Chan-Zuckerberg Biohub, San Francisco, CA, USA
- Division of Rheumatology, Department of Medicine, University of California, San Francisco, San Francisco, CA, USA
- Institute for Computational Health Sciences, University of California, San Francisco, San Francisco, California, USA
| | - Katherine S Pollard
- Institute for Human Genetics, University of California, San Francisco, San Francisco, CA, USA
- Gladstone Institutes, San Francisco, CA, USA
- Chan-Zuckerberg Biohub, San Francisco, CA, USA
- Department of Epidemiology and Biostatistics and Institute of Computational Health Sciences, University of California, San Francisco, San Francisco, CA, USA
| | - Jay Shendure
- Department of Genome Sciences, University of Washington, Seattle, WA, USA.
- Howard Hughes Medical Institute, Seattle, WA, USA.
- Brotman Baty Institute for Precision Medicine, University of Washington, Seattle, WA, USA.
| | - Martin Kircher
- Berlin Institute of Health (BIH), Berlin, Germany.
- Charité-Universitätsmedizin Berlin, Berlin, Germany.
| | - Nadav Ahituv
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, CA, USA.
- Institute for Human Genetics, University of California, San Francisco, San Francisco, CA, USA.
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18
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Meuleman W, Muratov A, Rynes E, Halow J, Lee K, Bates D, Diegel M, Dunn D, Neri F, Teodosiadis A, Reynolds A, Haugen E, Nelson J, Johnson A, Frerker M, Buckley M, Sandstrom R, Vierstra J, Kaul R, Stamatoyannopoulos J. Index and biological spectrum of human DNase I hypersensitive sites. Nature 2020; 584:244-251. [PMID: 32728217 PMCID: PMC7422677 DOI: 10.1038/s41586-020-2559-3] [Citation(s) in RCA: 148] [Impact Index Per Article: 37.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2019] [Accepted: 07/01/2020] [Indexed: 01/08/2023]
Abstract
DNase I hypersensitive sites (DHSs) are generic markers of regulatory DNA1–5 and contain genetic variations associated with diseases and phenotypic traits6–8. We created high-resolution maps of DHSs from 733 human biosamples encompassing 438 cell and tissue types and states, and integrated these to delineate and numerically index approximately 3.6 million DHSs within the human genome sequence, providing a common coordinate system for regulatory DNA. Here we show that these maps highly resolve the cis-regulatory compartment of the human genome, which encodes unexpectedly diverse cell- and tissue-selective regulatory programs at very high density. These programs can be captured comprehensively by a simple vocabulary that enables the assignment to each DHS of a regulatory barcode that encapsulates its tissue manifestations, and global annotation of protein-coding and non-coding RNA genes in a manner orthogonal to gene expression. Finally, we show that sharply resolved DHSs markedly enhance the genetic association and heritability signals of diseases and traits. Rather than being confined to a small number of distal elements or promoters, we find that genetic signals converge on congruently regulated sets of DHSs that decorate entire gene bodies. Together, our results create a universal, extensible coordinate system and vocabulary for human regulatory DNA marked by DHSs, and provide a new global perspective on the architecture of human gene regulation. High-resolution maps of DNase I hypersensitive sites from 733 human biosamples are used to identify and index regulatory DNA within the human genome.
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Affiliation(s)
| | | | - Eric Rynes
- Altius Institute for Biomedical Sciences, Seattle, WA, USA
| | - Jessica Halow
- Altius Institute for Biomedical Sciences, Seattle, WA, USA
| | - Kristen Lee
- Altius Institute for Biomedical Sciences, Seattle, WA, USA
| | - Daniel Bates
- Altius Institute for Biomedical Sciences, Seattle, WA, USA
| | - Morgan Diegel
- Altius Institute for Biomedical Sciences, Seattle, WA, USA
| | - Douglas Dunn
- Altius Institute for Biomedical Sciences, Seattle, WA, USA
| | - Fidencio Neri
- Altius Institute for Biomedical Sciences, Seattle, WA, USA
| | | | - Alex Reynolds
- Altius Institute for Biomedical Sciences, Seattle, WA, USA
| | - Eric Haugen
- Altius Institute for Biomedical Sciences, Seattle, WA, USA
| | - Jemma Nelson
- Altius Institute for Biomedical Sciences, Seattle, WA, USA
| | - Audra Johnson
- Altius Institute for Biomedical Sciences, Seattle, WA, USA
| | - Mark Frerker
- Altius Institute for Biomedical Sciences, Seattle, WA, USA
| | | | | | - Jeff Vierstra
- Altius Institute for Biomedical Sciences, Seattle, WA, USA
| | - Rajinder Kaul
- Altius Institute for Biomedical Sciences, Seattle, WA, USA
| | - John Stamatoyannopoulos
- Altius Institute for Biomedical Sciences, Seattle, WA, USA. .,Department of Genome Sciences, University of Washington, Seattle, WA, USA. .,Division of Oncology, Department of Medicine, University of Washington, Seattle, WA, USA.
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19
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Zhang Y, Shen Y, Yin L, Qi T, Jia X, Lu H, Zhang L. Plasma Membrane Proteomic Profile Discovers Macrophage-capping Protein Related to Latent HIV-1. Curr HIV Res 2020; 17:42-52. [PMID: 31057110 DOI: 10.2174/1570162x17666190506155222] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2019] [Revised: 04/24/2019] [Accepted: 04/25/2019] [Indexed: 02/03/2023]
Abstract
BACKGROUND Due to the persistence of latent HIV-infected cellular reservoirs, HIV virus can not be eradicated completely. OBJECTIVE To identify proteins related to HIV latency, we performed a subcellular proteomic study in HIV latent cell lines. METHODS An established HIV-1 latent cell model (J-Lat Tat-GFP Clone A7 cells, A7 cells) and its parental cell line (Jurkat cells) were used. The plasma membrane (PM) fraction from cultured cells was enriched through aqueous two-phase partition. PM proteins were extracted and then separated using two-dimensional electrophoresis (2DE). Differentially expressed proteins were identified by mass spectrometry, and verified by western blotting. RESULTS Thirteen non-redundant proteins were identified to be differentially expressed in the A7 PM fraction compared to those in the Jurkat PM. Eight had a PM location through Gene Ontology (GO) analysis. A differential protein network of CAPG-ACTR3-CD3D was detected to have interactions with HIV Vpr, Tat, gp160, etc. through STRING software analysis. One of the differential proteins (Macrophage-capping protein (CAPG)) was verified by western blotting to be down- regulated in two cell lines and HIV resting CD4+ T cells negatively selected from patients. CONCLUSION We identified 13 proteins in A7 compared to Jurkat cells. CAPG may be a potential biomarker related to HIV latency.
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Affiliation(s)
- Yujiao Zhang
- Shanghai Public Health Clinical Center, Fudan University, Shanghai 201508, China
| | - Yinzhong Shen
- Shanghai Public Health Clinical Center, Fudan University, Shanghai 201508, China
| | - Lin Yin
- Shanghai Public Health Clinical Center, Fudan University, Shanghai 201508, China
| | - Tangkai Qi
- Shanghai Public Health Clinical Center, Fudan University, Shanghai 201508, China
| | - Xiaofang Jia
- Shanghai Public Health Clinical Center, Fudan University, Shanghai 201508, China
| | - Hongzhou Lu
- Shanghai Public Health Clinical Center, Fudan University, Shanghai 201508, China
| | - Lijun Zhang
- Shanghai Public Health Clinical Center, Fudan University, Shanghai 201508, China
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20
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Mangum KD, Farber MA. Genetic and epigenetic regulation of abdominal aortic aneurysms. Clin Genet 2020; 97:815-826. [PMID: 31957007 DOI: 10.1111/cge.13705] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2019] [Revised: 12/22/2019] [Accepted: 01/11/2020] [Indexed: 12/11/2022]
Abstract
Abdominal aortic aneurysms (AAAs) are focal dilations of the aorta that develop from degenerative changes in the media and adventitia of the vessel. Ruptured AAAs have a mortality of up to 85%, thus it is important to identify patients with AAA at increased risk for rupture who would benefit from increased surveillance and/or surgical repair. Although the exact genetic and epigenetic mechanisms regulating AAA formation are not completely understood, Mendelian cases of AAA, which result from pathologic variants in a single gene, have helped provide a basic understanding of AAA pathophysiology. More recently, genome wide associated studies (GWAS) have identified additional variants, termed single nucleotide polymorphisms, in humans that may be associated with AAAs. While some variants may be associated with AAAs and play causal roles in aneurysm pathogenesis, it should be emphasized that the majority of SNPs do not actually cause disease. In addition to GWAS, other studies have uncovered epigenetic causes of disease that regulate expression of genes known to be important in AAA pathogenesis. This review describes many of these genetic and epigenetic contributors of AAAs, which altogether provide a deeper insight into AAA pathogenesis.
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Affiliation(s)
- Kevin D Mangum
- Section of Vascular Surgery, Department of Surgery, University of Michigan, Ann Arbor, Michigan
| | - Mark A Farber
- Division of Vascular Surgery, UNC Department of Surgery, Chapel Hill, North Carolina
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21
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Wong D, Turner AW, Miller CL. Genetic Insights Into Smooth Muscle Cell Contributions to Coronary Artery Disease. Arterioscler Thromb Vasc Biol 2020; 39:1006-1017. [PMID: 31043074 DOI: 10.1161/atvbaha.119.312141] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Coronary artery disease is a complex cardiovascular disease involving an interplay of genetic and environmental influences over a lifetime. Although considerable progress has been made in understanding lifestyle risk factors, genetic factors identified from genome-wide association studies may capture additional hidden risk undetected by traditional clinical tests. These genetic discoveries have highlighted many candidate genes and pathways dysregulated in the vessel wall, including those involving smooth muscle cell phenotypic modulation and injury responses. Here, we summarize experimental evidence for a few genome-wide significant loci supporting their roles in smooth muscle cell biology and disease. We also discuss molecular quantitative trait locus mapping as a powerful discovery and fine-mapping approach applied to smooth muscle cell and coronary artery disease-relevant tissues. We emphasize the critical need for alternative genetic strategies, including cis/trans-regulatory network analysis, genome editing, and perturbations, as well as single-cell sequencing in smooth muscle cell tissues and model organisms, under both normal and disease states. By integrating multiple experimental and analytical modalities, these multidimensional datasets should improve the interpretation of coronary artery disease genome-wide association studies and molecular quantitative trait locus signals and inform candidate targets for therapeutic intervention or risk prediction.
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Affiliation(s)
- Doris Wong
- From the Center for Public Health Genomics (D.W., A.W.T., C.L.M.), University of Virginia, Charlottesville.,Department of Biochemistry and Molecular Genetics (D.W., C.L.M.), University of Virginia, Charlottesville
| | - Adam W Turner
- From the Center for Public Health Genomics (D.W., A.W.T., C.L.M.), University of Virginia, Charlottesville
| | - Clint L Miller
- From the Center for Public Health Genomics (D.W., A.W.T., C.L.M.), University of Virginia, Charlottesville.,Department of Biochemistry and Molecular Genetics (D.W., C.L.M.), University of Virginia, Charlottesville.,Department of Biomedical Engineering (C.L.M.), University of Virginia, Charlottesville.,Department of Public Health Sciences (C.L.M.), University of Virginia, Charlottesville
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22
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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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23
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Chen Y, Chen A. Unveiling the gene regulatory landscape in diseases through the identification of DNase I-hypersensitive sites. Biomed Rep 2019; 11:87-97. [PMID: 31423302 PMCID: PMC6684942 DOI: 10.3892/br.2019.1233] [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: 12/11/2018] [Accepted: 07/03/2019] [Indexed: 01/18/2023] Open
Abstract
DNase I-hypersensitive sites (DHSs) serve key roles in the regulation of gene transcription as markers of cis-regulatory elements (CREs). Recent advances in next-generation sequencing have enabled the genome-wide location and annotation of DHSs in a variety of cells. Numerous studies have confirmed that DHSs are involved in several processes in cell fate decision and development. DHSs have also been indicated in cancer and inherited diseases as driver distal regulatory elements. Here, the definition of DHSs is reviewed, in addition to high-throughput methods of DHS identification. Furthermore, the function of DHSs in gene expression is probed. The roles of DHSs in disease occurrence are also reviewed and discussed. Concomitant advances in the identification of essential roles of DHSs will assist in disclosing the underlying molecular mechanisms, supplementing gene transcription and enlarging the molecular basis of DHS-related bioprocesses, phenotypes, distinct traits and diseases.
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Affiliation(s)
- Ying Chen
- Central Laboratory, The Affiliated Wuxi Maternity and Child Health Care Hospital of Nanjing Medical University, Wuxi, Jiangsu 214002, P.R. China
| | - Ailing Chen
- Central Laboratory, The Affiliated Wuxi Maternity and Child Health Care Hospital of Nanjing Medical University, Wuxi, Jiangsu 214002, P.R. China
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24
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Placek K, Schultze JL, Aschenbrenner AC. Epigenetic reprogramming of immune cells in injury, repair, and resolution. J Clin Invest 2019; 129:2994-3005. [PMID: 31329166 DOI: 10.1172/jci124619] [Citation(s) in RCA: 46] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Immune cells are pivotal in the reaction to injury, whereupon, under ideal conditions, repair and resolution phases restore homeostasis following initial acute inflammation. Immune cell activation and reprogramming require transcriptional changes that can only be initiated if epigenetic alterations occur. Recently, accelerated deciphering of epigenetic mechanisms has extended knowledge of epigenetic regulation, including long-distance chromatin remodeling, DNA methylation, posttranslational histone modifications, and involvement of small and long noncoding RNAs. Epigenetic changes have been linked to aspects of immune cell development, activation, and differentiation. Furthermore, genome-wide epigenetic landscapes have been established for some immune cells, including tissue-resident macrophages, and blood-derived cells including T cells. The epigenetic mechanisms underlying developmental steps from hematopoietic stem cells to fully differentiated immune cells led to development of epigenetic technologies and insights into general rules of epigenetic regulation. Compared with more advanced research areas, epigenetic reprogramming of immune cells in injury remains in its infancy. While the early epigenetic mechanisms supporting activation of the immune response to injury have been studied, less is known about resolution and repair phases and cell type-specific changes. We review prominent recent findings concerning injury-mediated epigenetic reprogramming, particularly in stroke and myocardial infarction. Lastly, we illustrate how single-cell technologies will be crucial to understanding epigenetic reprogramming in the complex sequential processes following injury.
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Affiliation(s)
- Katarzyna Placek
- Immunology and Metabolism, LIMES Institute, University of Bonn, Bonn, Germany
| | - Joachim L Schultze
- Platform for Single Cell Genomics and Epigenomics at the German Center for Neurodegenerative Diseases and the University of Bonn, Bonn, Germany.,Genomics and Immunoregulation, LIMES Institute, University of Bonn, Bonn, Germany
| | - Anna C Aschenbrenner
- Genomics and Immunoregulation, LIMES Institute, University of Bonn, Bonn, Germany
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25
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Chahal G, Tyagi S, Ramialison M. Navigating the non-coding genome in heart development and Congenital Heart Disease. Differentiation 2019; 107:11-23. [PMID: 31102825 DOI: 10.1016/j.diff.2019.05.001] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2018] [Revised: 01/14/2019] [Accepted: 05/06/2019] [Indexed: 12/12/2022]
Abstract
Congenital Heart Disease (CHD) is characterised by a wide range of cardiac defects, from mild to life-threatening, which occur in babies worldwide. To date, there is no cure to CHD, however, progress in surgery has reduced its mortality allowing children affected by CHD to reach adulthood. In an effort to understand its genetic basis, several studies involving whole-genome sequencing (WGS) of patients with CHD have been undertaken and generated a great wealth of information. The majority of putative causative mutations identified in WGS studies fall into the non-coding part of the genome. Unfortunately, due to the lack of understanding of the function of these non-coding mutations, it is challenging to establish a causal link between the non-coding mutation and the disease. Thus, here we review the state-of-the-art approaches to interpret non-coding mutations in the context of CHD and address the following questions: What are the non-coding sequences important for cardiac function? Which technologies are used to identify them? Which resources are available to analyse them? What mutations are expected in these non-coding sequences? Learning from developmental process, what is their expected role in CHD?
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Affiliation(s)
- Gulrez Chahal
- Australian Regenerative Medicine Institute (ARMI), 15 Innovation Walk, Monash University, Wellington Road, Clayton, 3800, VIC, Australia; Systems Biology Institute (SBI), Wellington Road, Clayton, 3800, VIC, Australia
| | - Sonika Tyagi
- School of Biological Sciences, Monash University, Wellington Road, Clayton, 3800, VIC, Australia; Australian Genome Research Facility, 305 Grattan Street, Melbourne, VIC, 3000, Australia.
| | - Mirana Ramialison
- Australian Regenerative Medicine Institute (ARMI), 15 Innovation Walk, Monash University, Wellington Road, Clayton, 3800, VIC, Australia; Systems Biology Institute (SBI), Wellington Road, Clayton, 3800, VIC, Australia.
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26
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Goswami R, Subramanian G, Silayeva L, Newkirk I, Doctor D, Chawla K, Chattopadhyay S, Chandra D, Chilukuri N, Betapudi V. Gene Therapy Leaves a Vicious Cycle. Front Oncol 2019; 9:297. [PMID: 31069169 PMCID: PMC6491712 DOI: 10.3389/fonc.2019.00297] [Citation(s) in RCA: 170] [Impact Index Per Article: 34.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2019] [Accepted: 04/01/2019] [Indexed: 12/14/2022] Open
Abstract
The human genetic code encrypted in thousands of genes holds the secret for synthesis of proteins that drive all biological processes necessary for normal life and death. Though the genetic ciphering remains unchanged through generations, some genes get disrupted, deleted and or mutated, manifesting diseases, and or disorders. Current treatment options—chemotherapy, protein therapy, radiotherapy, and surgery available for no more than 500 diseases—neither cure nor prevent genetic errors but often cause many side effects. However, gene therapy, colloquially called “living drug,” provides a one-time treatment option by rewriting or fixing errors in the natural genetic ciphering. Since gene therapy is predominantly a viral vector-based medicine, it has met with a fair bit of skepticism from both the science fraternity and patients. Now, thanks to advancements in gene editing and recombinant viral vector development, the interest of clinicians and pharmaceutical industries has been rekindled. With the advent of more than 12 different gene therapy drugs for curing cancer, blindness, immune, and neuronal disorders, this emerging experimental medicine has yet again come in the limelight. The present review article delves into the popular viral vectors used in gene therapy, advances, challenges, and perspectives.
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Affiliation(s)
- Reena Goswami
- Neuroscience Branch, Research Division, United States Army Medical Research Institute of Chemical Defense, Aberdeen, MD, United States
| | - Gayatri Subramanian
- Department of Medical Microbiology and Immunology, University of Toledo College of Medicine and Life Sciences, Toledo, OH, United States
| | - Liliya Silayeva
- Neuroscience Branch, Research Division, United States Army Medical Research Institute of Chemical Defense, Aberdeen, MD, United States
| | - Isabelle Newkirk
- Neuroscience Branch, Research Division, United States Army Medical Research Institute of Chemical Defense, Aberdeen, MD, United States
| | - Deborah Doctor
- Neuroscience Branch, Research Division, United States Army Medical Research Institute of Chemical Defense, Aberdeen, MD, United States
| | - Karan Chawla
- Department of Medical Microbiology and Immunology, University of Toledo College of Medicine and Life Sciences, Toledo, OH, United States
| | - Saurabh Chattopadhyay
- Department of Medical Microbiology and Immunology, University of Toledo College of Medicine and Life Sciences, Toledo, OH, United States
| | - Dhyan Chandra
- Roswell Park Comprehensive Cancer Center, Buffalo, NY, United States
| | - Nageswararao Chilukuri
- Neuroscience Branch, Research Division, United States Army Medical Research Institute of Chemical Defense, Aberdeen, MD, United States
| | - Venkaiah Betapudi
- Neuroscience Branch, Research Division, United States Army Medical Research Institute of Chemical Defense, Aberdeen, MD, United States.,Department of Physiology and Biophysics, Case Western Reserve University, Cleveland, OH, United States
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27
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Hainer SJ, Bošković A, McCannell KN, Rando OJ, Fazzio TG. Profiling of Pluripotency Factors in Single Cells and Early Embryos. Cell 2019; 177:1319-1329.e11. [PMID: 30955888 DOI: 10.1016/j.cell.2019.03.014] [Citation(s) in RCA: 118] [Impact Index Per Article: 23.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2018] [Revised: 02/13/2019] [Accepted: 03/05/2019] [Indexed: 02/09/2023]
Abstract
Cell fate decisions are governed by sequence-specific transcription factors (TFs) that act in small populations of cells within developing embryos. To understand their functions in vivo, it is important to identify TF binding sites in these cells. However, current methods cannot profile TFs genome-wide at or near the single-cell level. Here we adapt the cleavage under targets and release using nuclease (CUT&RUN) method to profile TFs in low cell numbers, including single cells and individual pre-implantation embryos. Single-cell experiments suggest that only a fraction of TF binding sites are occupied in most cells, in a manner broadly consistent with measurements of peak intensity from multi-cell studies. We further show that chromatin binding by the pluripotency TF NANOG is highly dependent on the SWI/SNF chromatin remodeling complex in individual blastocysts but not in cultured cells. Ultra-low input CUT&RUN (uliCUT&RUN) therefore enables interrogation of TF binding from rare cell populations of particular importance in development or disease.
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Affiliation(s)
- Sarah J Hainer
- Department of Molecular, Cell, and Cancer Biology, University of Massachusetts Medical School, Worcester, MA 01605, USA; Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA 15260, USA.
| | - Ana Bošković
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Kurtis N McCannell
- Department of Molecular, Cell, and Cancer Biology, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Oliver J Rando
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Thomas G Fazzio
- Department of Molecular, Cell, and Cancer Biology, University of Massachusetts Medical School, Worcester, MA 01605, USA.
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28
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Sanjana NE, Wright J, Zheng K, Shalem O, Fontanillas P, Joung J, Cheng C, Regev A, Zhang F. High-resolution interrogation of functional elements in the noncoding genome. Science 2016; 353:1545-1549. [PMID: 27708104 PMCID: PMC5144102 DOI: 10.1126/science.aaf7613] [Citation(s) in RCA: 205] [Impact Index Per Article: 25.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2016] [Accepted: 08/16/2016] [Indexed: 12/19/2022]
Abstract
The noncoding genome affects gene regulation and disease, yet we lack tools for rapid identification and manipulation of noncoding elements. We developed a CRISPR screen using ~18,000 single guide RNAs targeting >700 kilobases surrounding the genes NF1, NF2, and CUL3, which are involved in BRAF inhibitor resistance in melanoma. We find that noncoding locations that modulate drug resistance also harbor predictive hallmarks of noncoding function. With a subset of regions at the CUL3 locus, we demonstrate that engineered mutations alter transcription factor occupancy and long-range and local epigenetic environments, implicating these sites in gene regulation and chemotherapeutic resistance. Through our expansion of the potential of pooled CRISPR screens, we provide tools for genomic discovery and for elucidating biologically relevant mechanisms of gene regulation.
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Affiliation(s)
- Neville E Sanjana
- Broad Institute of MIT and Harvard, 7 Cambridge Center, Cambridge, MA 02142, USA. McGovern Institute for Brain Research, Department of Brain and Cognitive Sciences, Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.
| | - Jason Wright
- Broad Institute of MIT and Harvard, 7 Cambridge Center, Cambridge, MA 02142, USA. McGovern Institute for Brain Research, Department of Brain and Cognitive Sciences, Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Kaijie Zheng
- Broad Institute of MIT and Harvard, 7 Cambridge Center, Cambridge, MA 02142, USA. McGovern Institute for Brain Research, Department of Brain and Cognitive Sciences, Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Ophir Shalem
- Broad Institute of MIT and Harvard, 7 Cambridge Center, Cambridge, MA 02142, USA. McGovern Institute for Brain Research, Department of Brain and Cognitive Sciences, Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Pierre Fontanillas
- Broad Institute of MIT and Harvard, 7 Cambridge Center, Cambridge, MA 02142, USA
| | - Julia Joung
- Broad Institute of MIT and Harvard, 7 Cambridge Center, Cambridge, MA 02142, USA. McGovern Institute for Brain Research, Department of Brain and Cognitive Sciences, Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Christine Cheng
- Broad Institute of MIT and Harvard, 7 Cambridge Center, Cambridge, MA 02142, USA. Howard Hughes Medical Institute, David H. Koch Institute of Integrative Cancer Biology, Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02142, USA
| | - Aviv Regev
- Broad Institute of MIT and Harvard, 7 Cambridge Center, Cambridge, MA 02142, USA. Howard Hughes Medical Institute, David H. Koch Institute of Integrative Cancer Biology, Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02142, USA
| | - Feng Zhang
- Broad Institute of MIT and Harvard, 7 Cambridge Center, Cambridge, MA 02142, USA. McGovern Institute for Brain Research, Department of Brain and Cognitive Sciences, Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.
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29
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Sullivan LL, Maloney KA, Towers AJ, Gregory SG, Sullivan BA. Human centromere repositioning within euchromatin after partial chromosome deletion. Chromosome Res 2016; 24:451-466. [PMID: 27581771 DOI: 10.1007/s10577-016-9536-6] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2016] [Revised: 08/18/2016] [Accepted: 08/22/2016] [Indexed: 10/21/2022]
Abstract
Centromeres are defined by a specialized chromatin organization that includes nucleosomes that contain the centromeric histone variant centromere protein A (CENP-A) instead of canonical histone H3. Studies in various organisms have shown that centromeric chromatin (i.e., CENP-A chromatin or centrochromatin) exhibits plasticity, in that it can assemble on different types of DNA sequences. However, once established on a chromosome, the centromere is maintained at the same position. In humans, this location is the highly homogeneous repetitive DNA alpha satellite. Mislocalization of centromeric chromatin to atypical locations can lead to genome instability, indicating that restriction of centromeres to a distinct genomic position is important for cell and organism viability. Here, we describe a rearrangement of Homo sapiens chromosome 17 (HSA17) that has placed alpha satellite DNA next to euchromatin. We show that on this mutant chromosome, CENP-A chromatin has spread from the alpha satellite into the short arm of HSA17, establishing a ∼700 kb hybrid centromeric domain that spans both repetitive and unique sequences and changes the expression of at least one gene over which it spreads. Our results illustrate the plasticity of human centromeric chromatin and suggest that heterochromatin normally constrains CENP-A chromatin onto alpha satellite DNA. This work highlights that chromosome rearrangements, particularly those that remove the pericentromere, create opportunities for centromeric nucleosomes to move into non-traditional genomic locations, potentially changing the surrounding chromatin environment and altering gene expression.
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Affiliation(s)
- Lori L Sullivan
- Department of Molecular Genetics and Microbiology, Duke University School of Medicine, DUMC 3054, Durham, NC, 27710, USA
| | - Kristin A Maloney
- Department of Molecular Genetics and Microbiology, Duke University School of Medicine, DUMC 3054, Durham, NC, 27710, USA.,Department of Medicine, Division of Endocrinology, Diabetes, and Nutrition, University of Maryland School of Medicine, Baltimore, MD, 21201, USA
| | - Aaron J Towers
- University Program in Genetics and Genomics, Duke University School of Medicine, Durham, NC, 27710, USA.,Quintiles, 4820 Emperor Blvd., Durham, NC, 27703, USA
| | - Simon G Gregory
- Department of Medicine, Duke Molecular Physiology Institute, 300 N. Duke Street, Durham, NC, 27701, USA.,Division of Human Genetics, Duke University School of Medicine, Durham, NC, 27710, USA
| | - Beth A Sullivan
- Department of Molecular Genetics and Microbiology, Duke University School of Medicine, DUMC 3054, Durham, NC, 27710, USA. .,Quintiles, 4820 Emperor Blvd., Durham, NC, 27703, USA.
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30
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Marand AP, Zhang T, Zhu B, Jiang J. Towards genome-wide prediction and characterization of enhancers in plants. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2016; 1860:131-139. [PMID: 27321818 DOI: 10.1016/j.bbagrm.2016.06.006] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/12/2016] [Revised: 06/13/2016] [Accepted: 06/14/2016] [Indexed: 11/19/2022]
Abstract
Enhancers are important cis-regulatory DNA elements that regulate transcription programs by recruiting transcription factors and directing them to the promoters of target genes in a cell-type/tissue-specific manner. The expression of a gene can be regulated by one or multiple enhancers at different developmental stages and/or in different tissues. Enhancers are difficult to identify because of their unpredictable positions relative to their cognate promoters. Remarkably, only a handful of enhancers have been identified in plant species largely due to the lack of general approaches for enhancer identification. Extensive genomic and epigenomic research in mammalian species has revealed that the genomic locations of enhancers can be predicted based on the binding sites of transcriptional co-factors and several distinct features associated with open chromatin. Here we review the methodologies used in enhancer prediction in mammalian species. We also review the recent applications of these methodologies in Arabidopsis thaliana and discuss the future directions of enhancer identification in plants. This article is part of a Special Issue entitled: Plant Gene Regulatory Mechanisms and Networks, edited by Dr. Erich Grotewold and Dr. Nathan Springer.
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Affiliation(s)
- Alexandre P Marand
- Department of Horticulture, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Tao Zhang
- Department of Horticulture, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Bo Zhu
- Department of Horticulture, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Jiming Jiang
- Department of Horticulture, University of Wisconsin-Madison, Madison, WI 53706, USA.
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31
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Johnson GD, Jodar M, Pique-Regi R, Krawetz SA. Nuclease Footprints in Sperm Project Past and Future Chromatin Regulatory Events. Sci Rep 2016; 6:25864. [PMID: 27184706 PMCID: PMC4869110 DOI: 10.1038/srep25864] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2015] [Accepted: 04/22/2016] [Indexed: 01/08/2023] Open
Abstract
Nuclear remodeling to a condensed state is a hallmark of spermatogenesis. This is achieved by replacement of histones with protamines. Regions retaining nucleosomes may be of functional significance. To determine their potential roles, sperm from wild type and transgenic mice harboring a single copy insert of the human protamine cluster were subjected to Micrococcal Nuclease-seq. CENTIPEDE, a hierarchical Bayesian model, was used to identify multiple spatial patterns, "footprints", of MNase-seq reads along the sperm genome. Regions predicted by CENTIPEDE analysis to be bound by a regulatory factor in sperm were correlated with genomic landmarks and higher order chromatin structure datasets to identify potential roles for these factors in regulating either prior or post spermatogenic, i.e., early embryonic events. This approach linked robust endogenous protamine transcription and transgene suppression to its chromatin environment within topologically associated domains. Of the candidate enhancer-bound regulatory proteins, Ctcf, was associated with chromatin domain boundaries in testes and embryonic stem cells. The continuity of Ctcf binding through the murine germline may permit rapid reconstitution of chromatin organization following fertilization. This likely reflects its preparation for early zygotic genome activation and comparatively accelerated preimplantation embryonic development program observed in mouse as compared to human and bull.
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Affiliation(s)
- Graham D Johnson
- Center for Molecular Medicine and Genetics, Wayne State University School of Medicine, Detroit, MI, 48201, USA
| | - Meritxell Jodar
- Center for Molecular Medicine and Genetics, Wayne State University School of Medicine, Detroit, MI, 48201, USA.,Department of Obstetrics and Gynecology, Wayne State University School of Medicine, Detroit, MI, 48201, USA
| | - Roger Pique-Regi
- Center for Molecular Medicine and Genetics, Wayne State University School of Medicine, Detroit, MI, 48201, USA.,Department of Obstetrics and Gynecology, Wayne State University School of Medicine, Detroit, MI, 48201, USA
| | - Stephen A Krawetz
- Center for Molecular Medicine and Genetics, Wayne State University School of Medicine, Detroit, MI, 48201, USA.,Department of Obstetrics and Gynecology, Wayne State University School of Medicine, Detroit, MI, 48201, USA
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32
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Lu Q, Powles RL, Wang Q, He BJ, Zhao H. Integrative Tissue-Specific Functional Annotations in the Human Genome Provide Novel Insights on Many Complex Traits and Improve Signal Prioritization in Genome Wide Association Studies. PLoS Genet 2016; 12:e1005947. [PMID: 27058395 PMCID: PMC4825932 DOI: 10.1371/journal.pgen.1005947] [Citation(s) in RCA: 63] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2015] [Accepted: 03/01/2016] [Indexed: 12/20/2022] Open
Abstract
Extensive efforts have been made to understand genomic function through both experimental and computational approaches, yet proper annotation still remains challenging, especially in non-coding regions. In this manuscript, we introduce GenoSkyline, an unsupervised learning framework to predict tissue-specific functional regions through integrating high-throughput epigenetic annotations. GenoSkyline successfully identified a variety of non-coding regulatory machinery including enhancers, regulatory miRNA, and hypomethylated transposable elements in extensive case studies. Integrative analysis of GenoSkyline annotations and results from genome-wide association studies (GWAS) led to novel biological insights on the etiologies of a number of human complex traits. We also explored using tissue-specific functional annotations to prioritize GWAS signals and predict relevant tissue types for each risk locus. Brain and blood-specific annotations led to better prioritization performance for schizophrenia than standard GWAS p-values and non-tissue-specific annotations. As for coronary artery disease, heart-specific functional regions was highly enriched of GWAS signals, but previously identified risk loci were found to be most functional in other tissues, suggesting a substantial proportion of still undetected heart-related loci. In summary, GenoSkyline annotations can guide genetic studies at multiple resolutions and provide valuable insights in understanding complex diseases. GenoSkyline is available at http://genocanyon.med.yale.edu/GenoSkyline.
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Affiliation(s)
- Qiongshi Lu
- Department of Biostatistics, Yale School of Public Health, New Haven, Connecticut, United States of America
| | - Ryan Lee Powles
- Program of Computational Biology and Bioinformatics, Yale University, New Haven, Connecticut, United States of America
| | - Qian Wang
- Program of Computational Biology and Bioinformatics, Yale University, New Haven, Connecticut, United States of America
| | - Beixin Julie He
- Division of Cardiovascular Medicine, Department of Internal Medicine, Yale School of Medicine, New Haven, Connecticut, United States of America
| | - Hongyu Zhao
- Department of Biostatistics, Yale School of Public Health, New Haven, Connecticut, United States of America
- Program of Computational Biology and Bioinformatics, Yale University, New Haven, Connecticut, United States of America
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Lennartsson A, Arner E, Fagiolini M, Saxena A, Andersson R, Takahashi H, Noro Y, Sng J, Sandelin A, Hensch TK, Carninci P. Remodeling of retrotransposon elements during epigenetic induction of adult visual cortical plasticity by HDAC inhibitors. Epigenetics Chromatin 2015; 8:55. [PMID: 26673794 PMCID: PMC4678690 DOI: 10.1186/s13072-015-0043-3] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2015] [Accepted: 11/09/2015] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND The capacity for plasticity in the adult brain is limited by the anatomical traces laid down during early postnatal life. Removing certain molecular brakes, such as histone deacetylases (HDACs), has proven to be effective in recapitulating juvenile plasticity in the mature visual cortex (V1). We investigated the chromatin structure and transcriptional control by genome-wide sequencing of DNase I hypersensitive sites (DHSS) and cap analysis of gene expression (CAGE) libraries after HDAC inhibition by valproic acid (VPA) in adult V1. RESULTS We found that VPA reliably reactivates the critical period plasticity and induces a dramatic change of chromatin organization in V1 yielding significantly greater accessibility distant from promoters, including at enhancer regions. VPA also induces nucleosome eviction specifically from retrotransposon (in particular SINE) elements. The transiently accessible SINE elements overlap with transcription factor-binding sites of the Fox family. Mapping of transcription start site activity using CAGE revealed transcription of epigenetic and neural plasticity-regulating genes following VPA treatment, which may help to re-program the genomic landscape and reactivate plasticity in the adult cortex. CONCLUSIONS Treatment with HDAC inhibitors increases accessibility to enhancers and repetitive elements underlying brain-specific gene expression and reactivation of visual cortical plasticity.
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Affiliation(s)
- Andreas Lennartsson
- />Department of Biosciences and Nutrition, NOVUM, Karolinska Institutet, Stockholm, Sweden
- />Genome Science Lab, RIKEN, Hirosawa, Wako-shi, Saitama 351-0198 Japan
| | - Erik Arner
- />Division of Genomic Technologies, RIKEN Center for Life Science Technologies, RIKEN Yokohama Institute, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045 Japan
| | - Michela Fagiolini
- />Lab for Neuronal Circuit Development, RIKEN Brain Science Institute, 2-1 Hirosawa, Wako-shi, Saitama, 351-0198 Japan
- />F. M. Kirby Neurobiology Center, Boston Children’s Hospital, Harvard Medical School, Boston, MA 02115 USA
| | - Alka Saxena
- />Division of Genomic Technologies, RIKEN Center for Life Science Technologies, RIKEN Yokohama Institute, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045 Japan
| | - Robin Andersson
- />Department of Biology and BRIC, The Bioinformatics Centre, University of Copenhagen, Copenhagen, Denmark
| | - Hazuki Takahashi
- />Division of Genomic Technologies, RIKEN Center for Life Science Technologies, RIKEN Yokohama Institute, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045 Japan
| | - Yukihiko Noro
- />Division of Genomic Technologies, RIKEN Center for Life Science Technologies, RIKEN Yokohama Institute, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045 Japan
| | - Judy Sng
- />Lab for Neuronal Circuit Development, RIKEN Brain Science Institute, 2-1 Hirosawa, Wako-shi, Saitama, 351-0198 Japan
- />F. M. Kirby Neurobiology Center, Boston Children’s Hospital, Harvard Medical School, Boston, MA 02115 USA
- />Department of Pharmacology, National University of Singapore, 10 Medical Drive 05-34, Singapore, Singapore
| | - Albin Sandelin
- />Department of Biology and BRIC, The Bioinformatics Centre, University of Copenhagen, Copenhagen, Denmark
| | - Takao K. Hensch
- />Lab for Neuronal Circuit Development, RIKEN Brain Science Institute, 2-1 Hirosawa, Wako-shi, Saitama, 351-0198 Japan
- />F. M. Kirby Neurobiology Center, Boston Children’s Hospital, Harvard Medical School, Boston, MA 02115 USA
- />Department of Molecular and Cellular Biology, Center for Brain Science, Harvard University, 52 Oxford Street, Cambridge, MA 02138 USA
| | - Piero Carninci
- />Division of Genomic Technologies, RIKEN Center for Life Science Technologies, RIKEN Yokohama Institute, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045 Japan
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34
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Taher L, Narlikar L, Ovcharenko I. Identification and computational analysis of gene regulatory elements. Cold Spring Harb Protoc 2015; 2015:pdb.top083642. [PMID: 25561628 PMCID: PMC5885252 DOI: 10.1101/pdb.top083642] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Over the last two decades, advances in experimental and computational technologies have greatly facilitated genomic research. Next-generation sequencing technologies have made de novo sequencing of large genomes affordable, and powerful computational approaches have enabled accurate annotations of genomic DNA sequences. Charting functional regions in genomes must account for not only the coding sequences, but also noncoding RNAs, repetitive elements, chromatin states, epigenetic modifications, and gene regulatory elements. A mix of comparative genomics, high-throughput biological experiments, and machine learning approaches has played a major role in this truly global effort. Here we describe some of these approaches and provide an account of our current understanding of the complex landscape of the human genome. We also present overviews of different publicly available, large-scale experimental data sets and computational tools, which we hope will prove beneficial for researchers working with large and complex genomes.
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Affiliation(s)
- Leila Taher
- Computational Biology Branch, National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland 20894
- Institute for Biostatistics and Informatics in Medicine and Ageing Research, University of Rostock, 18051 Rostock, Germany
| | - Leelavati Narlikar
- Chemical Engineering and Process Development Division, National Chemical Laboratory, CSIR, Pune 411008, India
| | - Ivan Ovcharenko
- Computational Biology Branch, National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland 20894
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35
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Abstract
Genomic regions associated with regulatory proteins are known to be highly sensitive to DNase I digestion and are termed DNase I hypersensitive sites (DHSs). DHSs can be identified by DNase I digestion followed by high-throughput DNA sequencing (DNase-seq). DNase-seq has become a powerful technique for genome-wide mapping of chromatin accessibility in eukaryotes with a sequenced genome. We have developed a DNase-seq procedure in plants. This procedure was adapted from the protocol originally developed for mammalian cell lines. It includes plant nuclei isolation, digestion of purified nuclei with DNase I, recovery of DNase-trimmed DNA fragments, DNase-seq library development, Illumina sequencing and data analysis. We also introduce a barcoding system for library preparation. We have conducted DNase-seq in both Arabidopsis thaliana and rice, and developed genome-wide open chromatin maps in both species. These DHS datasets have been used to detect footprints from regulatory protein binding and to reveal genome-wide nucleosome positioning patterns.
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Affiliation(s)
- Wenli Zhang
- Department of Horticulture, University of Wisconsin-Madison, 1575 Linden Drive, Madison, WI, 53706-1580, USA
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36
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Tsompana M, Buck MJ. Chromatin accessibility: a window into the genome. Epigenetics Chromatin 2014; 7:33. [PMID: 25473421 PMCID: PMC4253006 DOI: 10.1186/1756-8935-7-33] [Citation(s) in RCA: 251] [Impact Index Per Article: 25.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2014] [Accepted: 11/05/2014] [Indexed: 01/09/2023] Open
Abstract
Transcriptional activation throughout the eukaryotic lineage has been tightly linked with disruption of nucleosome organization at promoters, enhancers, silencers, insulators and locus control regions due to transcription factor binding. Regulatory DNA thus coincides with open or accessible genomic sites of remodeled chromatin. Current chromatin accessibility assays are used to separate the genome by enzymatic or chemical means and isolate either the accessible or protected locations. The isolated DNA is then quantified using a next-generation sequencing platform. Wide application of these assays has recently focused on the identification of the instrumental epigenetic changes responsible for differential gene expression, cell proliferation, functional diversification and disease development. Here we discuss the limitations and advantages of current genome-wide chromatin accessibility assays with especial attention on experimental precautions and sequence data analysis. We conclude with our perspective on future improvements necessary for moving the field of chromatin profiling forward.
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Affiliation(s)
- Maria Tsompana
- New York State Center of Excellence in Bioinformatics and Life Sciences, State University of New York at Buffalo, 701 Ellicott St, Buffalo, NY 14203 USA
| | - Michael J Buck
- New York State Center of Excellence in Bioinformatics and Life Sciences, State University of New York at Buffalo, 701 Ellicott St, Buffalo, NY 14203 USA ; Department of Biochemistry, State University of New York at Buffalo, Buffalo, NY USA
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37
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Yardımcı GG, Frank CL, Crawford GE, Ohler U. Explicit DNase sequence bias modeling enables high-resolution transcription factor footprint detection. Nucleic Acids Res 2014; 42:11865-78. [PMID: 25294828 PMCID: PMC4231734 DOI: 10.1093/nar/gku810] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2014] [Revised: 08/22/2014] [Accepted: 08/27/2014] [Indexed: 12/31/2022] Open
Abstract
DNaseI footprinting is an established assay for identifying transcription factor (TF)-DNA interactions with single base pair resolution. High-throughput DNase-seq assays have recently been used to detect in vivo DNase footprints across the genome. Multiple computational approaches have been developed to identify DNase-seq footprints as predictors of TF binding. However, recent studies have pointed to a substantial cleavage bias of DNase and its negative impact on predictive performance of footprinting. To assess the potential for using DNase-seq to identify individual binding sites, we performed DNase-seq on deproteinized genomic DNA and determined sequence cleavage bias. This allowed us to build bias corrected and TF-specific footprint models. The predictive performance of these models demonstrated that predicted footprints corresponded to high-confidence TF-DNA interactions. DNase-seq footprints were absent under a fraction of ChIP-seq peaks, which we show to be indicative of weaker binding, indirect TF-DNA interactions or possible ChIP artifacts. The modeling approach was also able to detect variation in the consensus motifs that TFs bind to. Finally, cell type specific footprints were detected within DNase hypersensitive sites that are present in multiple cell types, further supporting that footprints can identify changes in TF binding that are not detectable using other strategies.
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Affiliation(s)
- Galip Gürkan Yardımcı
- Computational Biology and Bioinformatics Program, Duke University, Durham, NC 27708, USA Center for Genomic and Computational Biology, Duke University, Durham, NC 27708, USA
| | - Christopher L Frank
- Center for Genomic and Computational Biology, Duke University, Durham, NC 27708, USA Department of Molecular Genetics and Microbiology, Duke University, Durham, NC 27708, USA
| | - Gregory E Crawford
- Center for Genomic and Computational Biology, Duke University, Durham, NC 27708, USA Department of Pediatrics, Division of Medical Genetics, Duke University, Durham, NC 27708, USA
| | - Uwe Ohler
- Department of Biostatistics and Bioinformatics, Duke University, Durham, NC 27708, USA Max Delbruck Center for Molecular Medicine, 13125 Berlin, Germany
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Wortham M, Guo C, Zhang M, Song L, Lee BK, Iyer VR, Furey TS, Crawford GE, Yan H, He Y. Chromatin accessibility mapping identifies mediators of basal transcription and retinoid-induced repression of OTX2 in medulloblastoma. PLoS One 2014; 9:e107156. [PMID: 25198066 PMCID: PMC4157845 DOI: 10.1371/journal.pone.0107156] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2014] [Accepted: 08/06/2014] [Indexed: 12/01/2022] Open
Abstract
Despite an emerging understanding of the genetic alterations giving rise to various tumors, the mechanisms whereby most oncogenes are overexpressed remain unclear. Here we have utilized an integrated approach of genomewide regulatory element mapping via DNase-seq followed by conventional reporter assays and transcription factor binding site discovery to characterize the transcriptional regulation of the medulloblastoma oncogene Orthodenticle Homeobox 2 (OTX2). Through these studies we have revealed that OTX2 is differentially regulated in medulloblastoma at the level of chromatin accessibility, which is in part mediated by DNA methylation. In cell lines exhibiting chromatin accessibility of OTX2 regulatory regions, we found that autoregulation maintains OTX2 expression. Comparison of medulloblastoma regulatory elements with those of the developing brain reveals that these tumors engage a developmental regulatory program to drive OTX2 transcription. Finally, we have identified a transcriptional regulatory element mediating retinoid-induced OTX2 repression in these tumors. This work characterizes for the first time the mechanisms of OTX2 overexpression in medulloblastoma. Furthermore, this study establishes proof of principle for applying ENCODE datasets towards the characterization of upstream trans-acting factors mediating expression of individual genes.
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Affiliation(s)
- Matthew Wortham
- Department of Pathology, The Pediatric Brain Tumor Foundation Institute, and The Preston Robert Tisch Brain Tumor Center at Duke, Duke University Medical Center, Durham, North Carolina, United States of America
| | - Changcun Guo
- Department of Pathology, The Pediatric Brain Tumor Foundation Institute, and The Preston Robert Tisch Brain Tumor Center at Duke, Duke University Medical Center, Durham, North Carolina, United States of America
| | - Monica Zhang
- Department of Pathology, The Pediatric Brain Tumor Foundation Institute, and The Preston Robert Tisch Brain Tumor Center at Duke, Duke University Medical Center, Durham, North Carolina, United States of America
| | - Lingyun Song
- Duke Center for Genomic and Computational Biology, Duke University, Durham, North Carolina, United States of America
| | - Bum-Kyu Lee
- Department of Molecular Biosciences, University of Texas at Austin, Austin, Texas, United States of America
| | - Vishwanath R. Iyer
- Department of Molecular Biosciences, University of Texas at Austin, Austin, Texas, United States of America
| | - Terrence S. Furey
- Department of Genetics, Department of Biology, Carolina Center for Genome Sciences, and Lineberger Comprehensive Cancer Center, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - Gregory E. Crawford
- Duke Center for Genomic and Computational Biology, Duke University, Durham, North Carolina, United States of America
- Department of Pediatrics, Division of Medical Genetics, Duke University Medical Center, Durham, North Carolina, United States of America
| | - Hai Yan
- Department of Pathology, The Pediatric Brain Tumor Foundation Institute, and The Preston Robert Tisch Brain Tumor Center at Duke, Duke University Medical Center, Durham, North Carolina, United States of America
- * E-mail: (YH); (HY)
| | - Yiping He
- Department of Pathology, The Pediatric Brain Tumor Foundation Institute, and The Preston Robert Tisch Brain Tumor Center at Duke, Duke University Medical Center, Durham, North Carolina, United States of America
- * E-mail: (YH); (HY)
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39
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Brooks AN, Reiss DJ, Allard A, Wu WJ, Salvanha DM, Plaisier CL, Chandrasekaran S, Pan M, Kaur A, Baliga NS. A system-level model for the microbial regulatory genome. Mol Syst Biol 2014; 10:740. [PMID: 25028489 PMCID: PMC4299497 DOI: 10.15252/msb.20145160] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Microbes can tailor transcriptional responses to diverse environmental challenges despite having streamlined genomes and a limited number of regulators. Here, we present data-driven models that capture the dynamic interplay of the environment and genome-encoded regulatory programs of two types of prokaryotes: Escherichia coli (a bacterium) and Halobacterium salinarum (an archaeon). The models reveal how the genome-wide distributions of cis-acting gene regulatory elements and the conditional influences of transcription factors at each of those elements encode programs for eliciting a wide array of environment-specific responses. We demonstrate how these programs partition transcriptional regulation of genes within regulons and operons to re-organize gene-gene functional associations in each environment. The models capture fitness-relevant co-regulation by different transcriptional control mechanisms acting across the entire genome, to define a generalized, system-level organizing principle for prokaryotic gene regulatory networks that goes well beyond existing paradigms of gene regulation. An online resource (http://egrin2.systemsbiology.net) has been developed to facilitate multiscale exploration of conditional gene regulation in the two prokaryotes.
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Affiliation(s)
- Aaron N Brooks
- Institute for Systems Biology, Seattle, WA, USA Molecular and Cellular Biology Program, University of Washington, Seattle, WA, USA
| | | | - Antoine Allard
- Département de Physique, de Génie Physique et d'Optique, Université Laval, Québec, QC, Canada
| | - Wei-Ju Wu
- Institute for Systems Biology, Seattle, WA, USA
| | - Diego M Salvanha
- Institute for Systems Biology, Seattle, WA, USA LabPIB, Department of Computing and Mathematics FFCLRP-USP, University of Sao Paulo, Ribeirao Preto, Brazil
| | | | | | - Min Pan
- Institute for Systems Biology, Seattle, WA, USA
| | | | - Nitin S Baliga
- Institute for Systems Biology, Seattle, WA, USA Molecular and Cellular Biology Program, University of Washington, Seattle, WA, USA Departments of Microbiology and Biology, University of Washington, Seattle, WA, USA Lawrence Berkeley National Laboratories, Berkeley, CA, USA
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40
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Zhang W, Zhang T, Wu Y, Jiang J. Open Chromatin in Plant Genomes. Cytogenet Genome Res 2014; 143:18-27. [DOI: 10.1159/000362827] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
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41
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Genome-wide analysis of the chromatin composition of histone H2A and H3 variants in mouse embryonic stem cells. PLoS One 2014; 9:e92689. [PMID: 24658136 PMCID: PMC3962432 DOI: 10.1371/journal.pone.0092689] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2013] [Accepted: 02/24/2014] [Indexed: 12/31/2022] Open
Abstract
Genome-wide distribution of the majority of H2A and H3 variants (H2A, H2AX, H2AZ, macroH2A, H3.1, H3.2 and H3.3) was simultaneously investigated in mouse embryonic stem cells by chromatin immunoprecipitation sequencing. Around the transcription start site, histone variant distribution differed between genes possessing promoters of high and low CpG density, regardless of their expression levels. In the intergenic regions, regulatory elements were enriched in H2A.Z and H3.3, whereas repeat elements were abundant in H2A and macroH2A, and H3.1, respectively. Analysis of H2A and H3 variant combinations composing nucleosomes revealed that the H2A.Z and H3.3 combinations were present at a higher frequency throughout the genome than the other combinations, suggesting that H2A.Z and H3.3 associate preferentially with each other to comprise the nucleosomes independently of genome region. Finally, we found that chromatin was unstable only in regions where it was enriched in both H2A.Z and H3.3, but strongly quantified stable in regions in which only H3.3 was abundant. Therefore, histone variant composition is an important determinant of chromatin structure, which is associated with specific genomic functions.
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42
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Rani A, Greenlaw R, Runglall M, Jurcevic S, John S. FRA2 is a STAT5 target gene regulated by IL-2 in human CD4 T cells. PLoS One 2014; 9:e90370. [PMID: 24587342 PMCID: PMC3938719 DOI: 10.1371/journal.pone.0090370] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2013] [Accepted: 01/29/2014] [Indexed: 01/05/2023] Open
Abstract
Signal transducers and activators of transcription 5(STAT5) are cytokine induced signaling proteins, which regulate key immunological processes, such as tolerance induction, maintenance of homeostasis, and CD4 T-effector cell differentiation. In this study, transcriptional targets of STAT5 in CD4 T cells were studied by Chromatin Immunoprecipitation (ChIP). Genomic mapping of the sites cloned and identified in this study revealed the striking observation that the majority of STAT5-binding sites mapped to intergenic (>50 kb upstream) or intronic, rather than promoter proximal regions. Of the 105 STAT5 responsive binding sites identified, 94% contained the canonical (IFN-γ activation site) GAS motifs. A number of putative target genes identified here are associated with tumor biology. Here, we identified Fos-related antigen 2 (FRA2) as a transcriptional target of IL-2 regulated STAT5. FRA2 is a basic -leucine zipper (bZIP) motif ‘Fos’ family transcription factor that is part of the AP-1 transcription factor complex and is also known to play a critical role in the progression of human tumours and more recently as a determinant of T cell plasticity. The binding site mapped to an internal intron within the FRA2 gene. The epigenetic architecture of FRA2, characterizes a transcriptionally active promoter as indicated by enrichment for histone methylation marks H3K4me1, H3K4me2, H3K4me3, and transcription/elongation associated marks H2BK5me1 and H4K20me1. FRA2 is regulated by IL-2 in activated CD4 T cells. Consistently, STAT5 bound to GAS sequence in the internal intron of FRA2 and reporter gene assays confirmed IL-2 induced STAT5 binding and transcriptional activation. Furthermore, addition of JAK3 inhibitor (R333) or Daclizumab inhibited the induction in TCR stimulated cells. Taken together, our data suggest that FRA2 is a novel STAT5 target gene, regulated by IL-2 in activated CD4 T cells.
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Affiliation(s)
- Aradhana Rani
- Division of Transplantation Immunology and Mucosal Biology, King's College London, London, United Kingdom
| | - Roseanna Greenlaw
- Division of Transplantation Immunology and Mucosal Biology, King's College London, London, United Kingdom
| | - Manohursingh Runglall
- Division of Transplantation Immunology and Mucosal Biology, King's College London, London, United Kingdom
| | - Stipo Jurcevic
- Division of Transplantation Immunology and Mucosal Biology, King's College London, London, United Kingdom
- * E-mail: (SJurcevic); (SJohn)
| | - Susan John
- Department of Immunobiology, King's College London, London, United Kingdom
- * E-mail: (SJurcevic); (SJohn)
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43
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Burger L, Gaidatzis D, Schübeler D, Stadler MB. Identification of active regulatory regions from DNA methylation data. Nucleic Acids Res 2013; 41:e155. [PMID: 23828043 PMCID: PMC3763559 DOI: 10.1093/nar/gkt599] [Citation(s) in RCA: 142] [Impact Index Per Article: 12.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2013] [Revised: 05/23/2013] [Accepted: 06/15/2013] [Indexed: 12/21/2022] Open
Abstract
We have recently shown that transcription factor binding leads to defined reduction in DNA methylation, allowing for the identification of active regulatory regions from high-resolution methylomes. Here, we present MethylSeekR, a computational tool to accurately identify such footprints from bisulfite-sequencing data. Applying our method to a large number of published human methylomes, we demonstrate its broad applicability and generalize our previous findings from a neuronal differentiation system to many cell types and tissues. MethylSeekR is available as an R package at www.bioconductor.org.
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Affiliation(s)
- Lukas Burger
- Friedrich Miescher Institute for Biomedical Research, Maulbeerstrasse 66, 4058 Basel, Switzerland, Swiss Institute of Bioinformatics, Maulbeerstrasse 66, 4058 Basel, Switzerland and University of Basel, Petersplatz 1, 4003 Basel, Switzerland
| | - Dimos Gaidatzis
- Friedrich Miescher Institute for Biomedical Research, Maulbeerstrasse 66, 4058 Basel, Switzerland, Swiss Institute of Bioinformatics, Maulbeerstrasse 66, 4058 Basel, Switzerland and University of Basel, Petersplatz 1, 4003 Basel, Switzerland
| | - Dirk Schübeler
- Friedrich Miescher Institute for Biomedical Research, Maulbeerstrasse 66, 4058 Basel, Switzerland, Swiss Institute of Bioinformatics, Maulbeerstrasse 66, 4058 Basel, Switzerland and University of Basel, Petersplatz 1, 4003 Basel, Switzerland
| | - Michael B. Stadler
- Friedrich Miescher Institute for Biomedical Research, Maulbeerstrasse 66, 4058 Basel, Switzerland, Swiss Institute of Bioinformatics, Maulbeerstrasse 66, 4058 Basel, Switzerland and University of Basel, Petersplatz 1, 4003 Basel, Switzerland
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44
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Shu H, Gruissem W, Hennig L. Measuring Arabidopsis chromatin accessibility using DNase I-polymerase chain reaction and DNase I-chip assays. PLANT PHYSIOLOGY 2013; 162:1794-801. [PMID: 23739687 PMCID: PMC3729761 DOI: 10.1104/pp.113.220400] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
DNA accessibility is an important layer of regulation of DNA-dependent processes. Methods that measure DNA accessibility at local and genome-wide scales have facilitated a rapid increase in the knowledge of chromatin architecture in animal and yeast systems. In contrast, much less is known about chromatin organization in plants. We developed a robust DNase I-polymerase chain reaction (PCR) protocol for the model plant Arabidopsis (Arabidopsis thaliana). DNA accessibility is probed by digesting nuclei with a gradient of DNase I followed by locus-specific PCR. The reduction in PCR product formation along the gradient of increasing DNase I concentrations is used to determine the accessibility of the chromatin DNA. We explain a strategy to calculate the decay constant of such signal reduction as a function of increasing DNase I concentration. This allows describing DNA accessibility using a single variable: the decay constant. We also used the protocol together with AGRONOMICS1 DNA tiling microarrays to establish genome-wide DNase I sensitivity landscapes.
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45
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Yoo EJ, Cooke NE, Liebhaber SA. Identification of a secondary promoter within the human B cell receptor component gene hCD79b. J Biol Chem 2013; 288:18353-65. [PMID: 23649625 DOI: 10.1074/jbc.m113.461988] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023] Open
Abstract
The human B cell-specific protein, CD79b (also known as Igβ and B29) constitutes an essential signal transduction component of the B cell receptor. Although its function is central to the triggering of B cell terminal differentiation in response to antigen stimulation, the transcriptional determinants that control CD79b gene expression remain poorly defined. In the present study, we explored these determinants using a series of hCD79b transgenic mouse models. Remarkably, we observed that the previously described hCD79b promoter along with its associated enhancer elements and first exon could be deleted without appreciable loss of hCD79b transcriptional activity or tissue specificity. In this deletion setting, a secondary promoter located within exon 2 maintained full levels and specificity of hCD79b transcription. Of note, this secondary promoter was also active, albeit at lower levels, in the wild-type hCD79b locus. The activity of the secondary promoter was dependent on the action(s) of a conserved sequence element mapping to a chromatin DNase I hypersensitive site located within intron 1. mRNA generated from this secondary promoter is predicted to encode an Igβ protein lacking a signal sequence and thus unable to serve normal B cell receptor function. Although the physiologic role of the hCD79b secondary promoter and its encoded protein remain unclear, the current data suggest that it has the capacity to play a role in normal as well as pathologic states in B cell proliferation and function.
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Affiliation(s)
- Eung Jae Yoo
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
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46
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Shin H, Liu T, Duan X, Zhang Y, Liu XS. Computational methodology for ChIP-seq analysis. QUANTITATIVE BIOLOGY 2013; 1:54-70. [PMID: 25741452 DOI: 10.1007/s40484-013-0006-2] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Chromatin immunoprecipitation coupled with massive parallel sequencing (ChIP-seq) is a powerful technology to identify the genome-wide locations of DNA binding proteins such as transcription factors or modified histones. As more and more experimental laboratories are adopting ChIP-seq to unravel the transcriptional and epigenetic regulatory mechanisms, computational analyses of ChIP-seq also become increasingly comprehensive and sophisticated. In this article, we review current computational methodology for ChIP-seq analysis, recommend useful algorithms and workflows, and introduce quality control measures at different analytical steps. We also discuss how ChIP-seq could be integrated with other types of genomic assays, such as gene expression profiling and genome-wide association studies, to provide a more comprehensive view of gene regulatory mechanisms in important physiological and pathological processes.
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Affiliation(s)
- Hyunjin Shin
- Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute/Harvard School of Public Health, Boston, MA 02115, USA
| | - Tao Liu
- Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute/Harvard School of Public Health, Boston, MA 02115, USA
| | - Xikun Duan
- Department of Bioinformatics, School of Life Science and Technology, Tongji University, Shanghai 200092, China
| | - Yong Zhang
- Department of Bioinformatics, School of Life Science and Technology, Tongji University, Shanghai 200092, China
| | - X Shirley Liu
- Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute/Harvard School of Public Health, Boston, MA 02115, USA
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47
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Lafon-Placette C, Faivre-Rampant P, Delaunay A, Street N, Brignolas F, Maury S. Methylome of DNase I sensitive chromatin in Populus trichocarpa shoot apical meristematic cells: a simplified approach revealing characteristics of gene-body DNA methylation in open chromatin state. THE NEW PHYTOLOGIST 2013; 197:416-430. [PMID: 23253333 DOI: 10.1111/nph.12026] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/07/2012] [Accepted: 10/02/2012] [Indexed: 05/17/2023]
Abstract
DNA methylation is involved in the control of plant development and adaptation to the environment through modifications of chromatin compaction and gene expression. In poplar (Populus trichocarpa), a perennial plant, variations in DNA methylation have been reported between genotypes and tissues or in response to drought. Nevertheless, the relationships between gene-body DNA methylation, gene expression and chromatin compaction still need clarification. Here, DNA methylation was mapped in the noncondensed chromatin fraction from P. trichocarpa shoot apical meristematic cells, the center of plant morphogenesis, where DNA methylation variations could influence the developmental trajectory. DNase I was used to isolate the noncondensed chromatin fraction. Methylated sequences were immunoprecipitated, sequenced using Illumina/Solexa technology and mapped on the v2.0 poplar genome. Bisulfite sequencing of candidate sequences was used to confirm mapping data and to assess cytosine contexts and methylation levels. While the methylated DNase I hypersensitive site fraction covered 1.9% of the poplar genome, it contained sequences corresponding to 74% of poplar gene models, mostly exons. The level and cytosine context of gene-body DNA methylation varied with the structural characteristics of the genes. Taken together, our data show that DNA methylation is widespread and variable among genes in open chromatin of meristematic cells, in agreement with a role in their developmental trajectory.
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Affiliation(s)
- Clément Lafon-Placette
- Université d'Orléans, Faculté des Sciences, Laboratoire de Biologie des Ligneux et des Grandes Cultures (LBLGC), UPRES EA 1207, Orléans, 45067, France
- INRA, USC1328 Arbres et Réponses aux Contraintes Hydriques et Environnementales (ARCHE), Orléans, 45067, France
| | - Patricia Faivre-Rampant
- INRA, UMR1165, UMR INRA / Université d'Evry, Unité de Recherche en Génomique Végétale, Centre de Recherche de Versailles-Grignon, Evry, 91057, France
| | - Alain Delaunay
- Université d'Orléans, Faculté des Sciences, Laboratoire de Biologie des Ligneux et des Grandes Cultures (LBLGC), UPRES EA 1207, Orléans, 45067, France
- INRA, USC1328 Arbres et Réponses aux Contraintes Hydriques et Environnementales (ARCHE), Orléans, 45067, France
| | - Nathaniel Street
- Department of Plant Physiology, Umeå Plant Science Centre, Umeå University, Umeå, 901 87, Sweden
| | - Franck Brignolas
- Université d'Orléans, Faculté des Sciences, Laboratoire de Biologie des Ligneux et des Grandes Cultures (LBLGC), UPRES EA 1207, Orléans, 45067, France
- INRA, USC1328 Arbres et Réponses aux Contraintes Hydriques et Environnementales (ARCHE), Orléans, 45067, France
| | - Stéphane Maury
- Université d'Orléans, Faculté des Sciences, Laboratoire de Biologie des Ligneux et des Grandes Cultures (LBLGC), UPRES EA 1207, Orléans, 45067, France
- INRA, USC1328 Arbres et Réponses aux Contraintes Hydriques et Environnementales (ARCHE), Orléans, 45067, France
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48
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Wang YM, Zhou P, Wang LY, Li ZH, Zhang YN, Zhang YX. Correlation between DNase I hypersensitive site distribution and gene expression in HeLa S3 cells. PLoS One 2012; 7:e42414. [PMID: 22900019 PMCID: PMC3416863 DOI: 10.1371/journal.pone.0042414] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2012] [Accepted: 07/05/2012] [Indexed: 01/23/2023] Open
Abstract
Mapping DNase I hypersensitive sites (DHSs) within nuclear chromatin is a traditional and powerful method of identifying genetic regulatory elements. DHSs have been mapped by capturing the ends of long DNase I-cut fragments (>100,000 bp), or 100-1200 bp DNase I-double cleavage fragments (also called double-hit fragments). But next generation sequencing requires a DNA library containing DNA fragments of 100-500 bp. Therefore, we used short DNA fragments released by DNase I digestion to generate DNA libraries for next generation sequencing. The short segments are 100-300 bp and can be directly cloned and used for high-throughput sequencing. We identified 83,897 DHSs in 2,343,479 tags across the human genome. Our results indicate that the DHSs identified by this DHS assay are consistent with those identified by longer fragments in previous studies. We also found: (1) the distribution of DHSs in promoter and other gene regions of similarly expressed genes differs among different chromosomes; (2) silenced genes had a more open chromatin structure than previously thought; (3) DHSs in 3'untranslated regions (3'UTRs) are negatively correlated with level of gene expression.
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Affiliation(s)
- Ya-Mei Wang
- Department of Biochemistry and Molecular Biology, Cancer Institute, Capital Medical University, Beijing, China
| | - Ping Zhou
- Department of Bioinformatics and Computer Science, School of Biomedical Engineering, Capital Medical University, Beijing, China
| | - Li-Yong Wang
- Microarray Core Facility, Capital Medical University, Beijing, China
| | - Zhen-Hua Li
- Department of Biochemistry and Molecular Biology, Cancer Institute, Capital Medical University, Beijing, China
| | - Yao-Nan Zhang
- Department of Biochemistry and Molecular Biology, Cancer Institute, Capital Medical University, Beijing, China
| | - Yu-Xiang Zhang
- Department of Biochemistry and Molecular Biology, Cancer Institute, Capital Medical University, Beijing, China
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Kanno Y, Vahedi G, Hirahara K, Singleton K, O'Shea JJ. Transcriptional and epigenetic control of T helper cell specification: molecular mechanisms underlying commitment and plasticity. Annu Rev Immunol 2012; 30:707-31. [PMID: 22224760 PMCID: PMC3314163 DOI: 10.1146/annurev-immunol-020711-075058] [Citation(s) in RCA: 266] [Impact Index Per Article: 22.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
T helper cell differentiation occurs in the context of the extracellular cytokine milieu evoked by diverse microbes and other pathogenic stimuli along with T cell receptor stimulation. The culmination of these signals results in specification of T helper lineages, which occurs through the combinatorial action of multiple transcription factors that establish distinctive transcriptomes. In this manner, inducible, but constitutively active, master regulators work in conjunction with factors such as the signal transducer and activator of transcriptions (STATs) that sense the extracellular environment. The acquisition of a distinctive transcriptome also depends on chromatin modifications that impact key cis elements as well as the changes in global genomic organization. Thus, signal transduction and epigenetics are linked in these processes of differentiation. In this review, recent advances in understanding T helper lineage specification and deciphering the action of transcription factors are summarized with emphasis on comprehensive views of the dynamic T cell epigenome.
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Affiliation(s)
- Yuka Kanno
- Molecular Immunology and Inflammation Branch, National Institutes of Arthritis, and Musculoskeletal and Skin Diseases, National Institutes of Health, Bethesda, Maryland 20892, USA.
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Abstract
Salt fractionation of nucleosomes, a classical method for defining "active" chromatin based on nucleosome solubility, has recently been adapted for genome-scale profiling. This method has several advantages for profiling chromatin dynamics, including general applicability to cell lines and tissues, quantitative recovery of chromatin, base-pair resolution of nucleosomes, and overall simplicity both in concept and execution. This chapter provides detailed protocols for nuclear isolation, chromatin fragmentation by micrococcal nuclease digestion, successive solubilization of chromatin fractions by addition of increasing concentrations of salt, and genome-wide analyses through microarray hybridization and next-generation sequencing.
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Affiliation(s)
- Sheila S Teves
- Division of Basic Sciences, Fred Hutchinson Cancer Research Center and Molecular and Cellular Biology Program, University of Washington, Seattle, WA, USA
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