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Anderson EM, Anderson SK. Economy of Effort or Sophisticated Programming? The Prevalence of Bidirectional Promoter Complexes in the Human Genome. Genes (Basel) 2024; 15:252. [PMID: 38397241 PMCID: PMC10887517 DOI: 10.3390/genes15020252] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2024] [Revised: 02/16/2024] [Accepted: 02/16/2024] [Indexed: 02/25/2024] Open
Abstract
An abundance of antisense promoters in the vicinity of the transcriptional start site of coding genes suggests that they play an important role in gene regulation. The divergent transcription of housekeeping genes by a common central promoter region allows for coordinated regulation of genes in related pathways and is also linked to higher promoter activity. However, closely positioned transcription start sites can also result in competition between overlapping promoter elements and generate a binary switch element. Furthermore, the direct competition resulting from the presence of an antisense promoter immediately downstream of the transcription start site of the gene produces an element that can exist in only one of two stable transcriptional states: sense or antisense. In this review, we summarize analyses of the prevalence of antisense transcription in higher eukaryotes and viruses, with a focus on the antisense promoters competing with the promoters of coding genes. The structures of bidirectional promoters driving the simultaneous expression of housekeeping genes are compared with examples of human bidirectional elements that have been shown to act as switches. Since many bidirectional elements contain a noncoding RNA as the divergent transcript, we describe examples of functional noncoding antisense transcripts that affect the epigenetic landscape and alter the expression of their host gene. Finally, we discuss opportunities for additional research on competing sense/antisense promoters, uncovering their potential role in programming cell differentiation.
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Affiliation(s)
- Erik M. Anderson
- Cancer Innovation Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, MD 21702, USA;
| | - Stephen K. Anderson
- Cancer Innovation Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, MD 21702, USA;
- Basic Science Program, Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA
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Peng Y, Song W, Teif VB, Ovcharenko I, Landsman D, Panchenko AR. Detection of new pioneer transcription factors as cell-type-specific nucleosome binders. eLife 2024; 12:RP88936. [PMID: 38293962 PMCID: PMC10945518 DOI: 10.7554/elife.88936] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2024] Open
Abstract
Wrapping of DNA into nucleosomes restricts accessibility to DNA and may affect the recognition of binding motifs by transcription factors. A certain class of transcription factors, the pioneer transcription factors, can specifically recognize their DNA binding sites on nucleosomes, initiate local chromatin opening, and facilitate the binding of co-factors in a cell-type-specific manner. For the majority of human pioneer transcription factors, the locations of their binding sites, mechanisms of binding, and regulation remain unknown. We have developed a computational method to predict the cell-type-specific ability of transcription factors to bind nucleosomes by integrating ChIP-seq, MNase-seq, and DNase-seq data with details of nucleosome structure. We have demonstrated the ability of our approach in discriminating pioneer from canonical transcription factors and predicted new potential pioneer transcription factors in H1, K562, HepG2, and HeLa-S3 cell lines. Last, we systematically analyzed the interaction modes between various pioneer transcription factors and detected several clusters of distinctive binding sites on nucleosomal DNA.
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Affiliation(s)
- Yunhui Peng
- Institute of Biophysics and Department of Physics, Central China Normal UniversityWuhanChina
- National Library of Medicine, National Institutes of HealthBethesdaUnited States
| | - Wei Song
- National Library of Medicine, National Institutes of HealthBethesdaUnited States
| | - Vladimir B Teif
- School of Life Sciences, University of Essex, Wivenhoe ParkColchesterUnited Kingdom
| | - Ivan Ovcharenko
- National Library of Medicine, National Institutes of HealthBethesdaUnited States
| | - David Landsman
- National Library of Medicine, National Institutes of HealthBethesdaUnited States
| | - Anna R Panchenko
- Department of Pathology and Molecular Medicine, Queen’s UniversityKingstonCanada
- Department of Biology and Molecular Sciences, Queen’s UniversityKingstonCanada
- School of Computing, Queen’s UniversityKingstonCanada
- Ontario Institute of Cancer ResearchTorontoCanada
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Peng Y, Song W, Teif VB, Ovcharenko I, Landsman D, Panchenko AR. Detection of new pioneer transcription factors as cell-type specific nucleosome binders. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.05.10.540098. [PMID: 37425841 PMCID: PMC10327179 DOI: 10.1101/2023.05.10.540098] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/11/2023]
Abstract
Wrapping of DNA into nucleosomes restricts accessibility to the DNA and may affect the recognition of binding motifs by transcription factors. A certain class of transcription factors, the pioneer transcription factors, can specifically recognize their DNA binding sites on nucleosomes, may initiate local chromatin opening and facilitate the binding of co-factors in a cell-type-specific manner. For the majority of human pioneer transcription factors, the locations of their binding sites, mechanisms of binding and regulation remain unknown. We have developed a computational method to predict the cell-type-specific ability of transcription factors to bind nucleosomes by integrating ChIP-seq, MNase-seq and DNase-seq data with details of nucleosome structure. We have demonstrated the ability of our approach in discriminating pioneer from canonical transcription factors and predicted new potential pioneer transcription factors in H1, K562, HepG2 and HeLa cell lines. Lastly, we systemically analyzed the interaction modes between various pioneer transcription factors and detected several clusters of distinctive binding sites on nucleosomal DNA.
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Affiliation(s)
- Yunhui Peng
- current address: Institute of Biophysics and Department of Physics, Central China Normal University, Wuhan 430079, China
- National Library of Medicine, National Institutes of Health, Bethesda, MD, USA
| | - Wei Song
- National Library of Medicine, National Institutes of Health, Bethesda, MD, USA
| | - Vladimir B. Teif
- School of Life Sciences, University of Essex, Wivenhoe Park, Colchester, CO4 3SQ, UK
| | - Ivan Ovcharenko
- National Library of Medicine, National Institutes of Health, Bethesda, MD, USA
| | - David Landsman
- National Library of Medicine, National Institutes of Health, Bethesda, MD, USA
| | - Anna R. Panchenko
- Department of Pathology and Molecular Medicine, Queen’s University, ON, Canada
- Department of Biology and Molecular Sciences, Queen’s University, ON, Canada
- School of Computing, Queen’s University, ON, Canada
- Ontario Institute of Cancer Research, Toronto, ON, Canada
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Heuts BMH, Martens JHA. Understanding blood development and leukemia using sequencing-based technologies and human cell systems. Front Mol Biosci 2023; 10:1266697. [PMID: 37886034 PMCID: PMC10598665 DOI: 10.3389/fmolb.2023.1266697] [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: 07/25/2023] [Accepted: 09/06/2023] [Indexed: 10/28/2023] Open
Abstract
Our current understanding of human hematopoiesis has undergone significant transformation throughout the years, challenging conventional views. The evolution of high-throughput technologies has enabled the accumulation of diverse data types, offering new avenues for investigating key regulatory processes in blood cell production and disease. In this review, we will explore the opportunities presented by these advancements for unraveling the molecular mechanisms underlying normal and abnormal hematopoiesis. Specifically, we will focus on the importance of enhancer-associated regulatory networks and highlight the crucial role of enhancer-derived transcription regulation. Additionally, we will discuss the unprecedented power of single-cell methods and the progression in using in vitro human blood differentiation system, in particular induced pluripotent stem cell models, in dissecting hematopoietic processes. Furthermore, we will explore the potential of ever more nuanced patient profiling to allow precision medicine approaches. Ultimately, we advocate for a multiparameter, regulatory network-based approach for providing a more holistic understanding of normal hematopoiesis and blood disorders.
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Affiliation(s)
- Branco M H Heuts
- Department of Molecular Biology, Faculty of Science, Radboud University, Nijmegen, Netherlands
| | - Joost H A Martens
- Department of Molecular Biology, Faculty of Science, Radboud University, Nijmegen, Netherlands
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