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Shakes LA, Wolf HM, Norford DC, Grant DJ, Chatterjee PK. Harnessing mobile genetic elements to explore gene regulation. Mob Genet Elements 2014; 4:e29759. [PMID: 25054085 PMCID: PMC4092005 DOI: 10.4161/mge.29759] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2014] [Revised: 06/20/2014] [Accepted: 06/27/2014] [Indexed: 11/19/2022] Open
Abstract
Sequences that regulate expression of a gene in cis but are located at large distances along the DNA from the gene, as found with most developmentally regulated genes in higher vertebrates, are difficult to identify if those sequences are not conserved across species. Mutating suspected gene-regulatory sequences to alter expression then becomes a hit-or-miss affair. The relaxed specificity of transposon insertions offers an opportunity to develop alternate strategies, to scan in an unbiased manner, pieces of chromosomal DNA cloned in BACs for transcription enhancing elements. This article illustrates how insertions of Tn10 with enhancer-traps into BAC DNA containing the gene, and its germ-line expression in zebrafish, have identified distal regulatory elements functionally. Transposition of Tn10 first introduces the enhancer-trap with a loxP site randomly into BAC DNA. Cre-recombination between the inserted loxP and the loxP endogenous to a BAC-end positions the enhancer-trap to the newly created truncated end of BAC DNA. The procedure generates a library of integration-ready enhancer-trap BACs with progressive truncations from an end in a single experiment. Individual enhancer-trap BACs from the library can be evaluated functionally in zebrafish or mice. Furthermore, the ability to readily alter sequences in a small transposon plasmid containing a regulatory domain of the gene allows re-introduction of altered parts of a BAC back into itself. It serves as a useful strategy to functionally dissect multiple discontinuous regulatory domains of a gene quickly. These methodologies have been successfully used in identifying novel regulatory domains of the Amyloid Precursor Protein (appb) gene in zebrafish, and provided important clues for regulation of the gene in humans.
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Affiliation(s)
- Leighcraft A Shakes
- Julius L. Chambers Biomedical/ Biotechnology Research Institute and Department of Chemistry; North Carolina Central University; Durham, NC USA
| | - Hope M Wolf
- Julius L. Chambers Biomedical/ Biotechnology Research Institute and Department of Chemistry; North Carolina Central University; Durham, NC USA
| | - Derek C Norford
- Julius L. Chambers Biomedical/ Biotechnology Research Institute and Department of Chemistry; North Carolina Central University; Durham, NC USA
| | - Delores J Grant
- Julius L. Chambers Biomedical/ Biotechnology Research Institute and Department of Chemistry; North Carolina Central University; Durham, NC USA
| | - Pradeep K Chatterjee
- Julius L. Chambers Biomedical/ Biotechnology Research Institute and Department of Chemistry; North Carolina Central University; Durham, NC USA
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Blackledge NP, Farcas AM, Kondo T, King HW, McGouran JF, Hanssen LLP, Ito S, Cooper S, Kondo K, Koseki Y, Ishikura T, Long HK, Sheahan TW, Brockdorff N, Kessler BM, Koseki H, Klose RJ. Variant PRC1 complex-dependent H2A ubiquitylation drives PRC2 recruitment and polycomb domain formation. Cell 2014; 157:1445-1459. [PMID: 24856970 PMCID: PMC4048464 DOI: 10.1016/j.cell.2014.05.004] [Citation(s) in RCA: 533] [Impact Index Per Article: 53.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2013] [Revised: 03/10/2014] [Accepted: 05/02/2014] [Indexed: 11/30/2022]
Abstract
Chromatin modifying activities inherent to polycomb repressive complexes PRC1 and PRC2 play an essential role in gene regulation, cellular differentiation, and development. However, the mechanisms by which these complexes recognize their target sites and function together to form repressive chromatin domains remain poorly understood. Recruitment of PRC1 to target sites has been proposed to occur through a hierarchical process, dependent on prior nucleation of PRC2 and placement of H3K27me3. Here, using a de novo targeting assay in mouse embryonic stem cells we unexpectedly discover that PRC1-dependent H2AK119ub1 leads to recruitment of PRC2 and H3K27me3 to effectively initiate a polycomb domain. This activity is restricted to variant PRC1 complexes, and genetic ablation experiments reveal that targeting of the variant PCGF1/PRC1 complex by KDM2B to CpG islands is required for normal polycomb domain formation and mouse development. These observations provide a surprising PRC1-dependent logic for PRC2 occupancy at target sites in vivo.
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Affiliation(s)
- Neil P Blackledge
- Laboratory of Chromatin Biology and Transcription, Department of Biochemistry, University of Oxford, Oxford, OX1 3QU, UK
| | - Anca M Farcas
- Laboratory of Chromatin Biology and Transcription, Department of Biochemistry, University of Oxford, Oxford, OX1 3QU, UK
| | - Takashi Kondo
- Laboratory of Developmental Genetics, RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa 230-0045, Japan
| | - Hamish W King
- Laboratory of Chromatin Biology and Transcription, Department of Biochemistry, University of Oxford, Oxford, OX1 3QU, UK
| | - Joanna F McGouran
- Ubiquitin Proteolysis Group, Central Proteomics Facility, Target Discovery Institute, Nuffield Department of Medicine, University of Oxford, OX3 7BN, UK
| | - Lars L P Hanssen
- Laboratory of Chromatin Biology and Transcription, Department of Biochemistry, University of Oxford, Oxford, OX1 3QU, UK
| | - Shinsuke Ito
- Laboratory of Developmental Genetics, RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa 230-0045, Japan
| | - Sarah Cooper
- Laboratory of Developmental Epigenetics, Department of Biochemistry, University of Oxford, Oxford, OX1 3QU, UK
| | - Kaori Kondo
- Laboratory of Developmental Genetics, RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa 230-0045, Japan
| | - Yoko Koseki
- Laboratory of Developmental Genetics, RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa 230-0045, Japan
| | - Tomoyuki Ishikura
- Laboratory of Developmental Genetics, RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa 230-0045, Japan
| | - Hannah K Long
- Laboratory of Chromatin Biology and Transcription, Department of Biochemistry, University of Oxford, Oxford, OX1 3QU, UK
| | - Thomas W Sheahan
- Laboratory of Chromatin Biology and Transcription, Department of Biochemistry, University of Oxford, Oxford, OX1 3QU, UK
| | - Neil Brockdorff
- Laboratory of Developmental Epigenetics, Department of Biochemistry, University of Oxford, Oxford, OX1 3QU, UK
| | - Benedikt M Kessler
- Ubiquitin Proteolysis Group, Central Proteomics Facility, Target Discovery Institute, Nuffield Department of Medicine, University of Oxford, OX3 7BN, UK
| | - Haruhiko Koseki
- Laboratory of Developmental Genetics, RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa 230-0045, Japan
| | - Robert J Klose
- Laboratory of Chromatin Biology and Transcription, Department of Biochemistry, University of Oxford, Oxford, OX1 3QU, UK.
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Chatterjee PK, Shakes LA, Wolf HM, Mujalled MA, Zhou C, Hatcher C, Norford DC. Identifying Distal cis-acting Gene-Regulatory Sequences by Expressing BACs Functionalized with loxP-Tn10 Transposons in Zebrafish. RSC Adv 2013; 3:8604-8617. [PMID: 24772295 DOI: 10.1039/c3ra40332g] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Bacterial Artificial Chromosomes (BACs) are large pieces of DNA from the chromosomes of organisms propagated faithfully in bacteria as large extra-chromosomal plasmids. Expression of genes contained in BACs can be monitored after functionalizing the BAC DNA with reporter genes and other sequences that allow stable maintenance and propagation of the DNA in the new host organism. The DNA in BACs can be altered within its bacterial host in several ways. Here we discuss one such approach, using Tn10 mini-transposons, to introduce exogenous sequences into BACs for a variety of purposes. The largely random insertions of Tn10 transposons carrying lox sites have been used to position mammalian cell-selectable antibiotic resistance genes, enhancer-traps and inverted repeat ends of the vertebrate transposon Tol2 precisely at the ends of the genomic DNA insert in BACs. These modified BACs are suitable for expression in zebrafish or mouse, and have been used to functionally identify important long-range gene regulatory sequences in both species. Enhancer-trapping using BACs should prove uniquely useful in analyzing multiple discontinuous DNA domains that act in concert to regulate expression of a gene, and is not limited by genome accessibility issues of traditional enhancer-trapping methods.
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Affiliation(s)
- Pradeep K Chatterjee
- Julius L. Chambers Biomedical/ Biotechnology Research Institute & Department of Chemistry, North Carolina Central University, 1801 Fayetteville Street, Durham, NC 27707, USA
| | - Leighcraft A Shakes
- Julius L. Chambers Biomedical/ Biotechnology Research Institute & Department of Chemistry, North Carolina Central University, 1801 Fayetteville Street, Durham, NC 27707, USA
| | - Hope M Wolf
- Julius L. Chambers Biomedical/ Biotechnology Research Institute & Department of Chemistry, North Carolina Central University, 1801 Fayetteville Street, Durham, NC 27707, USA
| | - Mohammad A Mujalled
- Julius L. Chambers Biomedical/ Biotechnology Research Institute & Department of Chemistry, North Carolina Central University, 1801 Fayetteville Street, Durham, NC 27707, USA
| | - Constance Zhou
- Julius L. Chambers Biomedical/ Biotechnology Research Institute & Department of Chemistry, North Carolina Central University, 1801 Fayetteville Street, Durham, NC 27707, USA
| | - Charles Hatcher
- Julius L. Chambers Biomedical/ Biotechnology Research Institute & Department of Chemistry, North Carolina Central University, 1801 Fayetteville Street, Durham, NC 27707, USA
| | - Derek C Norford
- Julius L. Chambers Biomedical/ Biotechnology Research Institute & Department of Chemistry, North Carolina Central University, 1801 Fayetteville Street, Durham, NC 27707, USA
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Shakes LA, Du H, Wolf HM, Hatcher C, Norford DC, Precht P, Sen R, Chatterjee PK. Using BAC transgenesis in zebrafish to identify regulatory sequences of the amyloid precursor protein gene in humans. BMC Genomics 2012; 13:451. [PMID: 22947103 PMCID: PMC3546842 DOI: 10.1186/1471-2164-13-451] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2012] [Accepted: 08/24/2012] [Indexed: 12/23/2022] Open
Abstract
Background Non-coding DNA in and around the human Amyloid Precursor Protein (APP) gene that is central to Alzheimer’s disease (AD) shares little sequence similarity with that of appb in zebrafish. Identifying DNA domains regulating expression of the gene in such situations becomes a challenge. Taking advantage of the zebrafish system that allows rapid functional analyses of gene regulatory sequences, we previously showed that two discontinuous DNA domains in zebrafish appb are important for expression of the gene in neurons: an enhancer in intron 1 and sequences 28–31 kb upstream of the gene. Here we identify the putative transcription factor binding sites responsible for this distal cis-acting regulation, and use that information to identify a regulatory region of the human APP gene. Results Functional analyses of intron 1 enhancer mutations in enhancer-trap BACs expressed as transgenes in zebrafish identified putative binding sites of two known transcription factor proteins, E4BP4/ NFIL3 and Forkhead, to be required for expression of appb. A cluster of three E4BP4 sites at −31 kb is also shown to be essential for neuron-specific expression, suggesting that the dependence of expression on upstream sequences is mediated by these E4BP4 sites. E4BP4/ NFIL3 and XFD1 sites in the intron enhancer and E4BP4/ NFIL3 sites at −31 kb specifically and efficiently bind the corresponding zebrafish proteins in vitro. These sites are statistically over-represented in both the zebrafish appb and the human APP genes, although their locations are different. Remarkably, a cluster of four E4BP4 sites in intron 4 of human APP exists in actively transcribing chromatin in a human neuroblastoma cell-line, SHSY5Y, expressing APP as shown using chromatin immunoprecipitation (ChIP) experiments. Thus although the two genes share little sequence conservation, they appear to share the same regulatory logic and are regulated by a similar set of transcription factors. Conclusion The results suggest that the clock-regulated and immune system modulator transcription factor E4BP4/ NFIL3 likely regulates the expression of both appb in zebrafish and APP in humans. It suggests potential human APP gene regulatory pathways, not on the basis of comparing DNA primary sequences with zebrafish appb but on the model of conservation of transcription factors.
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Affiliation(s)
- Leighcraft A Shakes
- Julius L. Chambers Biomedical/ Biotechnology Research Institute & Department of Chemistry, North Carolina Central University, 1801 Fayetteville Street, Durham, NC 27707, USA
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