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Kyrchanova O, Ibragimov A, Postika N, Georgiev P, Schedl P. Boundary bypass activity in the abdominal-B region of the Drosophila bithorax complex is position dependent and regulated. Open Biol 2023; 13:230035. [PMID: 37582404 PMCID: PMC10427195 DOI: 10.1098/rsob.230035] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2023] [Accepted: 07/17/2023] [Indexed: 08/17/2023] Open
Abstract
Expression of Abdominal-B (Abd-B) in abdominal segments A5-A8 is controlled by four regulatory domains, iab-5-iab-8. Each domain has an initiator element (which sets the activity state), elements that maintain this state and tissue-specific enhancers. To ensure their functional autonomy, each domain is bracketed by boundary elements (Mcp, Fab-7, Fab-7 and Fab-8). In addition to blocking crosstalk between adjacent regulatory domains, the Fab boundaries must also have bypass activity so the relevant regulatory domains can 'jump over' intervening boundaries and activate the Abd-B promoter. In the studies reported here we have investigated the parameters governing bypass activity. We find that the bypass elements in the Fab-7 and Fab-8 boundaries must be located in the regulatory domain that is responsible for driving Abd-B expression. We suggest that bypass activity may also be subject to regulation.
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Affiliation(s)
- Olga Kyrchanova
- Department of the Control of Genetic Processes, Institute of Gene Biology Russian Academy of Sciences, 34/5 Vavilov St., Moscow 119334, Russia
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Institute of Gene Biology, Russian Academy of Sciences, 34/5 Vavilov St., Moscow 119334, Russia
| | - Airat Ibragimov
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Institute of Gene Biology, Russian Academy of Sciences, 34/5 Vavilov St., Moscow 119334, Russia
- Laboratory of Gene Expression Regulation in Development, Institute of Gene Biology, Russian Academy of Sciences, 34/5 Vavilov St., Moscow 119334, Russia
| | - Nikolay Postika
- Department of the Control of Genetic Processes, Institute of Gene Biology Russian Academy of Sciences, 34/5 Vavilov St., Moscow 119334, Russia
| | - Pavel Georgiev
- Department of the Control of Genetic Processes, Institute of Gene Biology Russian Academy of Sciences, 34/5 Vavilov St., Moscow 119334, Russia
| | - Paul Schedl
- Laboratory of Gene Expression Regulation in Development, Institute of Gene Biology, Russian Academy of Sciences, 34/5 Vavilov St., Moscow 119334, Russia
- Department of Molecular Biology, Princeton University, Princeton, NJ 08544, USA
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Hao X, Wang C, Zhang R. Chromatin basis of the senescence-associated secretory phenotype. Trends Cell Biol 2022:S0962-8924(21)00250-6. [PMID: 35012849 DOI: 10.1016/j.tcb.2021.12.003] [Citation(s) in RCA: 24] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2021] [Revised: 12/12/2021] [Accepted: 12/14/2021] [Indexed: 01/07/2023]
Abstract
Cellular senescence is a stable cell growth arrest. Senescent cells are metabolically active, as exemplified by the secretion of inflammatory cytokines, chemokines, and growth factors, which is termed senescence-associated secretory phenotype (SASP). The SASP exerts a range of functions in both normal health and pathology, which is possibly best characterized in cancers and physical aging. Recent studies demonstrated that chromatin is instrumental in regulating the SASP both through nuclear transcription and via the innate immune cyclic GMP-AMP synthase (cGAS)-stimulator of interferon genes (STING) pathway in the cytoplasm. Here, we will review these regulatory mechanisms, with an emphasis on most recent developments in the field. We will highlight the challenges and opportunities in developing intervention approaches, such as targeting chromatin regulatory mechanisms, to alter the SASP as an emerging approach to combat cancers and achieve healthy aging.
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Dao FY, Lv H, Zhang D, Zhang ZM, Liu L, Lin H. DeepYY1: a deep learning approach to identify YY1-mediated chromatin loops. Brief Bioinform 2020; 22:6024741. [PMID: 33279983 DOI: 10.1093/bib/bbaa356] [Citation(s) in RCA: 56] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2020] [Revised: 10/19/2020] [Accepted: 11/04/2020] [Indexed: 12/29/2022] Open
Abstract
The protein Yin Yang 1 (YY1) could form dimers that facilitate the interaction between active enhancers and promoter-proximal elements. YY1-mediated enhancer-promoter interaction is the general feature of mammalian gene control. Recently, some computational methods have been developed to characterize the interactions between DNA elements by elucidating important features of chromatin folding; however, no computational methods have been developed for identifying the YY1-mediated chromatin loops. In this study, we developed a deep learning algorithm named DeepYY1 based on word2vec to determine whether a pair of YY1 motifs would form a loop. The proposed models showed a high prediction performance (AUCs$\ge$0.93) on both training datasets and testing datasets in different cell types, demonstrating that DeepYY1 has an excellent performance in the identification of the YY1-mediated chromatin loops. Our study also suggested that sequences play an important role in the formation of YY1-mediated chromatin loops. Furthermore, we briefly discussed the distribution of the replication origin site in the loops. Finally, a user-friendly web server was established, and it can be freely accessed at http://lin-group.cn/server/DeepYY1.
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Affiliation(s)
- Fu-Ying Dao
- Center for Informational Biology at the University of Electronic Science and Technology of China
| | - Hao Lv
- Center for Informational Biology at the University of Electronic Science and Technology of China
| | - Dan Zhang
- Center for Informational Biology at the University of Electronic Science and Technology of China
| | - Zi-Mei Zhang
- Center for Informational Biology at the University of Electronic Science and Technology of China
| | - Li Liu
- Laboratory of Theoretical Biophysics at the Inner Mongolia University
| | - Hao Lin
- Center for Informational Biology at the University of Electronic Science and Technology of China
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Abstract
More than 98% of the human genome does not encode proteins, and the vast majority of the noncoding regions have not been well studied. Some of these regions contain enhancers and functional non-coding RNAs. Previous research suggested that enhancer transcripts could be potent independent indicators of enhancer activity, and some enhancer lncRNAs (elncRNAs) have been proven to play critical roles in gene regulation. Here, we identified enhancer–promoter interactions from high-throughput chromosome conformation capture (Hi-C) data. We found that elncRNAs were highly enriched surrounding chromatin loop anchors. Additionally, the interaction frequency of elncRNA-associated enhancer–promoter pairs was significantly higher than the interaction frequency of other enhancer–promoter pairs, suggesting that elncRNAs may reinforce the interactions between enhancers and promoters. We also found that elncRNA expression levels were positively correlated with the interaction frequency of enhancer–promoter pairs. The promoters interacting with elncRNA-associated enhancers were rich in RNA polymerase II and YY1 transcription factor binding sites. We clustered enhancer–promoter pairs into different groups to reflect the different ways in which elncRNAs could influence enhancer–promoter pairs. Interestingly, G-quadruplexes were found to potentially mediate some enhancer–promoter interaction pairs, and the interaction frequency of these pairs was significantly higher than that of other enhancer–promoter pairs. We also found that the G-quadruplexes on enhancers were highly related to the expression of elncRNAs. G-quadruplexes located in the promoters of elncRNAs led to high expression of elncRNAs, whereas G-quadruplexes located in the gene bodies of elncRNAs generally resulted in low expression of elncRNAs.
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Affiliation(s)
- Yue Hou
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing, China
| | - Rongxin Zhang
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing, China
| | - Xiao Sun
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing, China
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Gonzalez-Sandoval A, Gasser SM. On TADs and LADs: Spatial Control Over Gene Expression. Trends Genet 2016; 32:485-495. [PMID: 27312344 DOI: 10.1016/j.tig.2016.05.004] [Citation(s) in RCA: 114] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2016] [Revised: 05/16/2016] [Accepted: 05/17/2016] [Indexed: 01/10/2023]
Abstract
The combinatorial action of transcription factors drives cell-type-specific gene expression patterns. However, transcription factor binding and gene regulation occur in the context of chromatin, which modulates DNA accessibility. High-resolution chromatin interaction maps have defined units of chromatin that are in spatial proximity, called topologically associated domains (TADs). TADs can be further classified based on expression activity, replication timing, or the histone marks or non-histone proteins associated with them. Independently, other chromatin domains have been defined by their likelihood to interact with non-DNA structures, such as the nuclear lamina. Lamina-associated domains (LADs) correlate with low gene expression and late replication timing. TADs and LADs have recently been evaluated with respect to cell-type-specific gene expression. The results shed light on the relevance of these forms of chromatin organization for transcriptional regulation, and address specifically how chromatin sequestration influences cell fate decisions during organismal development.
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Affiliation(s)
- Adriana Gonzalez-Sandoval
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland; Faculty of Natural Sciences, University of Basel, Basel, Switzerland
| | - Susan M Gasser
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland; Faculty of Natural Sciences, University of Basel, Basel, Switzerland.
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van Arensbergen J, van Steensel B, Bussemaker HJ. In search of the determinants of enhancer-promoter interaction specificity. Trends Cell Biol. 2014;24:695-702. [PMID: 25160912 DOI: 10.1016/j.tcb.2104.07.004] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Although it was originally believed that enhancers activate only the nearest promoter, recent global analyses enabled by high-throughput technology suggest that the network of enhancer-promoter interactions is far more complex. The mechanisms that determine the specificity of enhancer-promoter interactions are still poorly understood, but they are thought to include biochemical compatibility, constraints imposed by the three-dimensional architecture of chromosomes, insulator elements, and possibly the effects of local chromatin composition. In this review, we assess the current insights into these determinants, and highlight the functional genomic approaches that will lead the way towards better mechanistic understanding.
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van Arensbergen J, van Steensel B, Bussemaker HJ. In search of the determinants of enhancer-promoter interaction specificity. Trends Cell Biol 2014; 24:695-702. [PMID: 25160912 DOI: 10.1016/j.tcb.2014.07.004] [Citation(s) in RCA: 120] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2014] [Revised: 07/15/2014] [Accepted: 07/21/2014] [Indexed: 02/07/2023]
Abstract
Although it was originally believed that enhancers activate only the nearest promoter, recent global analyses enabled by high-throughput technology suggest that the network of enhancer-promoter interactions is far more complex. The mechanisms that determine the specificity of enhancer-promoter interactions are still poorly understood, but they are thought to include biochemical compatibility, constraints imposed by the three-dimensional architecture of chromosomes, insulator elements, and possibly the effects of local chromatin composition. In this review, we assess the current insights into these determinants, and highlight the functional genomic approaches that will lead the way towards better mechanistic understanding.
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Affiliation(s)
- Joris van Arensbergen
- Division of Gene Regulation, Netherlands Cancer Institute, 1066 CX Amsterdam, The Netherlands
| | - Bas van Steensel
- Division of Gene Regulation, Netherlands Cancer Institute, 1066 CX Amsterdam, The Netherlands.
| | - Harmen J Bussemaker
- Department of Biological Sciences, Columbia University, New York, NY 10027, USA; Center for Computational Biology and Bioinformatics, Columbia University, New York, NY 10032, USA.
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Abstract
The scs and scs' elements were proposed to function as chromatin domain boundaries for the 87A7 heat shock locus in Drosophila melanogaster. Here we report the identification and characterization of SBP (scs binding protein), a component of the scs nucleoprotein complex. SBP binds specifically to a 24-bp region of scs in vitro and is associated with scs in vivo. Multiple copies of an oligonucleotide containing the SBP recognition sequence are capable of blocking enhancer-promoter interactions in transgene assays. Mutations in the oligonucleotide that disrupt SBP binding in vitro also eliminate enhancer-blocking activity in vivo. We show that SBP is encoded by the zeste-white 5 gene and that mutations in zeste-white 5 reduce the enhancer-blocking activity of the multimerized oligonucleotides.
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Affiliation(s)
- M Gaszner
- Department of Molecular Biology, Princeton University, Princeton, New Jersey 08544 USA
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