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Sloutskin A, Itzhak D, Vogler G, Pozeilov H, Ideses D, Alter H, Adato O, Shachar H, Doniger T, Shohat-Ophir G, Frasch M, Bodmer R, Duttke SH, Juven-Gershon T. From promoter motif to cardiac function: a single DPE motif affects transcription regulation and organ function in vivo. Development 2024; 151:dev202355. [PMID: 38958007 DOI: 10.1242/dev.202355] [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: 09/18/2023] [Accepted: 06/26/2024] [Indexed: 07/04/2024]
Abstract
Transcription initiates at the core promoter, which contains distinct core promoter elements. Here, we highlight the complexity of transcriptional regulation by outlining the effect of core promoter-dependent regulation on embryonic development and the proper function of an organism. We demonstrate in vivo the importance of the downstream core promoter element (DPE) in complex heart formation in Drosophila. Pioneering a novel approach using both CRISPR and nascent transcriptomics, we show the effects of mutating a single core promoter element within the natural context. Specifically, we targeted the downstream core promoter element (DPE) of the endogenous tin gene, encoding the Tinman transcription factor, a homologue of human NKX2-5 associated with congenital heart diseases. The 7 bp substitution mutation results in massive perturbation of the Tinman regulatory network that orchestrates dorsal musculature, which is manifested as physiological and anatomical changes in the cardiac system, impaired specific activity features, and significantly compromised viability of adult flies. Thus, a single motif can have a critical impact on embryogenesis and, in the case of DPE, functional heart formation.
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Affiliation(s)
- Anna Sloutskin
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gan 5290002, Israel
| | - Dekel Itzhak
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gan 5290002, Israel
| | - Georg Vogler
- Development, Aging and Regeneration Program, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA 92037, USA
| | - Hadar Pozeilov
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gan 5290002, Israel
| | - Diana Ideses
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gan 5290002, Israel
| | - Hadar Alter
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gan 5290002, Israel
| | - Orit Adato
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gan 5290002, Israel
| | - Hadar Shachar
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gan 5290002, Israel
| | - Tirza Doniger
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gan 5290002, Israel
| | - Galit Shohat-Ophir
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gan 5290002, Israel
| | - Manfred Frasch
- Division of Developmental Biology, Department of Biology, Friedrich-Alexander University of Erlangen-Nürnberg, Erlangen 91058, Germany
| | - Rolf Bodmer
- Development, Aging and Regeneration Program, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA 92037, USA
| | - Sascha H Duttke
- School of Molecular Biosciences, College of Veterinary Medicine, Washington State University, Pullman, WA 99164, USA
| | - Tamar Juven-Gershon
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gan 5290002, Israel
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He YJ, Lu G, Xu BJ, Mao QZ, Qi YH, Jiao GY, Weng HT, Tian YZ, Huang HJ, Zhang CX, Chen JP, Li JM. Maintenance of persistent transmission of a plant arbovirus in its insect vector mediated by the Toll-Dorsal immune pathway. Proc Natl Acad Sci U S A 2024; 121:e2315982121. [PMID: 38536757 PMCID: PMC10998634 DOI: 10.1073/pnas.2315982121] [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: 09/14/2023] [Accepted: 03/01/2024] [Indexed: 04/08/2024] Open
Abstract
Throughout evolution, arboviruses have developed various strategies to counteract the host's innate immune defenses to maintain persistent transmission. Recent studies have shown that, in addition to bacteria and fungi, the innate Toll-Dorsal immune system also plays an essential role in preventing viral infections in invertebrates. However, whether the classical Toll immune pathway is involved in maintaining the homeostatic process to ensure the persistent and propagative transmission of arboviruses in insect vectors remain unclear. In this study, we revealed that the transcription factor Dorsal is actively involved in the antiviral defense of an insect vector (Laodelphax striatellus) by regulating the target gene, zinc finger protein 708 (LsZN708), which mediates downstream immune-related effectors against infection with the plant virus (Rice stripe virus, RSV). In contrast, an antidefense strategy involving the use of the nonstructural-protein (NS4) to antagonize host antiviral defense through competitive binding to Dorsal from the MSK2 kinase was employed by RSV; this competitive binding inhibited Dorsal phosphorylation and reduced the antiviral response of the host insect. Our study revealed the molecular mechanism through which Toll-Dorsal-ZN708 mediates the maintenance of an arbovirus homeostasis in insect vectors. Specifically, ZN708 is a newly documented zinc finger protein targeted by Dorsal that mediates the downstream antiviral response. This study will contribute to our understanding of the successful transmission and spread of arboviruses in plant or invertebrate hosts.
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Affiliation(s)
- Yu-Juan He
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Key Laboratory of Biotechnology in Plant Protection of Ministry of Agriculture and Zhejiang Province, Institute of Plant Virology, Ningbo University, Ningbo315211, China
| | - Gang Lu
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Key Laboratory of Biotechnology in Plant Protection of Ministry of Agriculture and Zhejiang Province, Institute of Plant Virology, Ningbo University, Ningbo315211, China
| | - Bo-Jie Xu
- School of Basic Medical Sciences, Health Science Center, Ningbo University, Ningbo315211, China
| | - Qian-Zhuo Mao
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Key Laboratory of Biotechnology in Plant Protection of Ministry of Agriculture and Zhejiang Province, Institute of Plant Virology, Ningbo University, Ningbo315211, China
| | - Yu-Hua Qi
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Key Laboratory of Biotechnology in Plant Protection of Ministry of Agriculture and Zhejiang Province, Institute of Plant Virology, Ningbo University, Ningbo315211, China
| | - Gao-Yang Jiao
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Key Laboratory of Biotechnology in Plant Protection of Ministry of Agriculture and Zhejiang Province, Institute of Plant Virology, Ningbo University, Ningbo315211, China
| | - Hai-Tao Weng
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Key Laboratory of Biotechnology in Plant Protection of Ministry of Agriculture and Zhejiang Province, Institute of Plant Virology, Ningbo University, Ningbo315211, China
| | - Yan-Zhen Tian
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Key Laboratory of Biotechnology in Plant Protection of Ministry of Agriculture and Zhejiang Province, Institute of Plant Virology, Ningbo University, Ningbo315211, China
| | - Hai-Jian Huang
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Key Laboratory of Biotechnology in Plant Protection of Ministry of Agriculture and Zhejiang Province, Institute of Plant Virology, Ningbo University, Ningbo315211, China
| | - Chuan-Xi Zhang
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Key Laboratory of Biotechnology in Plant Protection of Ministry of Agriculture and Zhejiang Province, Institute of Plant Virology, Ningbo University, Ningbo315211, China
| | - Jian-Ping Chen
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Key Laboratory of Biotechnology in Plant Protection of Ministry of Agriculture and Zhejiang Province, Institute of Plant Virology, Ningbo University, Ningbo315211, China
| | - Jun-Min Li
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Key Laboratory of Biotechnology in Plant Protection of Ministry of Agriculture and Zhejiang Province, Institute of Plant Virology, Ningbo University, Ningbo315211, China
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Sloutskin A, Itzhak D, Vogler G, Ideses D, Alter H, Shachar H, Doniger T, Frasch M, Bodmer R, Duttke SH, Juven-Gershon T. A single DPE core promoter motif contributes to in vivo transcriptional regulation and affects cardiac function. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.06.11.544490. [PMID: 37398300 PMCID: PMC10312617 DOI: 10.1101/2023.06.11.544490] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/04/2023]
Abstract
Transcription is initiated at the core promoter, which confers specific functions depending on the unique combination of core promoter elements. The downstream core promoter element (DPE) is found in many genes related to heart and mesodermal development. However, the function of these core promoter elements has thus far been studied primarily in isolated, in vitro or reporter gene settings. tinman (tin) encodes a key transcription factor that regulates the formation of the dorsal musculature and heart. Pioneering a novel approach utilizing both CRISPR and nascent transcriptomics, we show that a substitution mutation of the functional tin DPE motif within the natural context of the core promoter results in a massive perturbation of Tinman's regulatory network orchestrating dorsal musculature and heart formation. Mutation of endogenous tin DPE reduced the expression of tin and distinct target genes, resulting in significantly reduced viability and an overall decrease in adult heart function. We demonstrate the feasibility and importance of characterizing DNA sequence elements in vivo in their natural context, and accentuate the critical impact a single DPE motif has during Drosophila embryogenesis and functional heart formation.
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Affiliation(s)
- Anna Sloutskin
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gan, Israel
| | - Dekel Itzhak
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gan, Israel
| | - Georg Vogler
- Development, Aging and Regeneration Program, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA, USA
| | - Diana Ideses
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gan, Israel
| | - Hadar Alter
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gan, Israel
| | - Hadar Shachar
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gan, Israel
| | - Tirza Doniger
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gan, Israel
| | - Manfred Frasch
- Division of Developmental Biology, Department of Biology, Friedrich-Alexander University of Erlangen-Nürnberg, Erlangen, Germany
| | - Rolf Bodmer
- Development, Aging and Regeneration Program, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA, USA
| | - Sascha H Duttke
- School of Molecular Biosciences, College of Veterinary Medicine, Washington State University, Pullman, WA, USA
| | - Tamar Juven-Gershon
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gan, Israel
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Li L, Waymack R, Gad M, Wunderlich Z. Two promoters integrate multiple enhancer inputs to drive wild-type knirps expression in the Drosophila melanogaster embryo. Genetics 2021; 219:6372693. [PMID: 34849867 DOI: 10.1093/genetics/iyab154] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2021] [Accepted: 09/12/2021] [Indexed: 11/13/2022] Open
Abstract
Proper development depends on precise spatiotemporal gene expression patterns. Most developmental genes are regulated by multiple enhancers and often by multiple core promoters that generate similar transcripts. We hypothesize that multiple promoters may be required either because enhancers prefer a specific promoter or because multiple promoters serve as a redundancy mechanism. To test these hypotheses, we studied the expression of the knirps locus in the early Drosophila melanogaster embryo, which is mediated by multiple enhancers and core promoters. We found that one of these promoters resembles a typical "sharp" developmental promoter, while the other resembles a "broad" promoter usually associated with housekeeping genes. Using synthetic reporter constructs, we found that some, but not all, enhancers in the locus show a preference for one promoter, indicating that promoters provide both redundancy and specificity. By analyzing the reporter dynamics, we identified specific burst properties during the transcription process, namely burst size and frequency, that are most strongly tuned by the combination of promoter and enhancer. Using locus-sized reporters, we discovered that enhancers with no promoter preference in a synthetic setting have a preference in the locus context. Our results suggest that the presence of multiple promoters in a locus is due both to enhancer preference and a need for redundancy and that "broad" promoters with dispersed transcription start sites are common among developmental genes. They also imply that it can be difficult to extrapolate expression measurements from synthetic reporters to the locus context, where other variables shape a gene's overall expression pattern.
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Affiliation(s)
- Lily Li
- Department of Developmental and Cell Biology, University of California, Irvine, Irvine, CA 92697, USA
| | - Rachel Waymack
- Department of Developmental and Cell Biology, University of California, Irvine, Irvine, CA 92697, USA
| | - Mario Gad
- Department of Developmental and Cell Biology, University of California, Irvine, Irvine, CA 92697, USA
| | - Zeba Wunderlich
- Department of Developmental and Cell Biology, University of California, Irvine, Irvine, CA 92697, USA.,Department of Biology, Boston University, Boston, MA 02215, USA
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Sloutskin A, Shir-Shapira H, Freiman RN, Juven-Gershon T. The Core Promoter Is a Regulatory Hub for Developmental Gene Expression. Front Cell Dev Biol 2021; 9:666508. [PMID: 34568311 PMCID: PMC8461331 DOI: 10.3389/fcell.2021.666508] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2021] [Accepted: 08/25/2021] [Indexed: 11/13/2022] Open
Abstract
The development of multicellular organisms and the uniqueness of each cell are achieved by distinct transcriptional programs. Multiple processes that regulate gene expression converge at the core promoter region, an 80 bp region that directs accurate transcription initiation by RNA polymerase II (Pol II). In recent years, it has become apparent that the core promoter region is not a passive DNA component, but rather an active regulatory module of transcriptional programs. Distinct core promoter compositions were demonstrated to result in different transcriptional outputs. In this mini-review, we focus on the role of the core promoter, particularly its downstream region, as the regulatory hub for developmental genes. The downstream core promoter element (DPE) was implicated in the control of evolutionarily conserved developmental gene regulatory networks (GRNs) governing body plan in both the anterior-posterior and dorsal-ventral axes. Notably, the composition of the basal transcription machinery is not universal, but rather promoter-dependent, highlighting the importance of specialized transcription complexes and their core promoter target sequences as key hubs that drive embryonic development, differentiation and morphogenesis across metazoan species. The extent of transcriptional activation by a specific enhancer is dependent on its compatibility with the relevant core promoter. The core promoter content also regulates transcription burst size. Overall, while for many years it was thought that the specificity of gene expression is primarily determined by enhancers, it is now clear that the core promoter region comprises an important regulatory module in the intricate networks of developmental gene expression.
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Affiliation(s)
- Anna Sloutskin
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gan, Israel
| | - Hila Shir-Shapira
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gan, Israel
| | - Richard N. Freiman
- Department of Molecular Biology, Cell Biology and Biochemistry, Brown University, Providence, RI, United States
| | - Tamar Juven-Gershon
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gan, Israel
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Dreos R, Sloutskin A, Malachi N, Ideses D, Bucher P, Juven-Gershon T. Computational identification and experimental characterization of preferred downstream positions in human core promoters. PLoS Comput Biol 2021; 17:e1009256. [PMID: 34383743 PMCID: PMC8384218 DOI: 10.1371/journal.pcbi.1009256] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2020] [Revised: 08/24/2021] [Accepted: 07/07/2021] [Indexed: 12/02/2022] Open
Abstract
Metazoan core promoters, which direct the initiation of transcription by RNA polymerase II (Pol II), may contain short sequence motifs termed core promoter elements/motifs (e.g. the TATA box, initiator (Inr) and downstream core promoter element (DPE)), which recruit Pol II via the general transcription machinery. The DPE was discovered and extensively characterized in Drosophila, where it is strictly dependent on both the presence of an Inr and the precise spacing from it. Since the Drosophila DPE is recognized by the human transcription machinery, it is most likely that some human promoters contain a downstream element that is similar, though not necessarily identical, to the Drosophila DPE. However, only a couple of human promoters were shown to contain a functional DPE, and attempts to computationally detect human DPE-containing promoters have mostly been unsuccessful. Using a newly-designed motif discovery strategy based on Expectation-Maximization probabilistic partitioning algorithms, we discovered preferred downstream positions (PDP) in human promoters that resemble the Drosophila DPE. Available chromatin accessibility footprints revealed that Drosophila and human Inr+DPE promoter classes are not only highly structured, but also similar to each other, particularly in the proximal downstream region. Clustering of the corresponding sequence motifs using a neighbor-joining algorithm strongly suggests that canonical Inr+DPE promoters could be common to metazoan species. Using reporter assays we demonstrate the contribution of the identified downstream positions to the function of multiple human promoters. Furthermore, we show that alteration of the spacing between the Inr and PDP by two nucleotides results in reduced promoter activity, suggesting a spacing dependency of the newly discovered human PDP on the Inr. Taken together, our strategy identified novel functional downstream positions within human core promoters, supporting the existence of DPE-like motifs in human promoters. Transcription of genes by the RNA polymerase II enzyme initiates at a genomic region termed the core promoter. The core promoter is a regulatory region that may contain diverse short DNA sequence motifs/elements that confer specific properties to it. Interestingly, core promoter motifs can be located both upstream and downstream of the transcription start site. Variable compositions of core promoter elements were identified. The initiator (Inr) motif and the downstream core promoter element (DPE) is a combination of elements that has been identified and extensively characterized in fruit flies. Although a few Inr+DPE -containing human promoters were identified, the presence of transcriptionally important downstream core promoter positions within human promoters has been a matter of controversy in the literature. Here, using a newly-designed motif discovery strategy, we discovered preferred downstream positions in human promoters that resemble fruit fly DPE. Clustering of the corresponding sequence motifs in eight additional species indicated that such promoters could be common to multicellular non-plant organisms. Importantly, functional characterization of the newly discovered preferred downstream positions supports the existence of Inr+DPE-containing promoters in human genes.
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Affiliation(s)
- René Dreos
- Swiss Institute of Bioinformatics (SIB), Lausanne, Switzerland
| | - Anna Sloutskin
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan, Israel
| | - Nati Malachi
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan, Israel
| | - Diana Ideses
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan, Israel
| | - Philipp Bucher
- Swiss Institute of Bioinformatics (SIB), Lausanne, Switzerland
- School of Life Sciences, Swiss Federal Institute of Technology, Lausanne, Switzerland
- * E-mail: (PB); (TJG)
| | - Tamar Juven-Gershon
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan, Israel
- * E-mail: (PB); (TJG)
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Levi T, Sloutskin A, Kalifa R, Juven-Gershon T, Gerlitz O. Efficient In Vivo Introduction of Point Mutations Using ssODN and a Co-CRISPR Approach. Biol Proced Online 2020; 22:14. [PMID: 32684853 PMCID: PMC7362497 DOI: 10.1186/s12575-020-00123-7] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2020] [Accepted: 05/06/2020] [Indexed: 12/20/2022] Open
Abstract
Background The generation of point mutations is a major tool for evaluating the roles of specific nucleotides or amino acids within the regulatory or functional landscape. However, examination of these mutations in vivo requires the generation of animals carrying only the relevant point mutations at the endogenous genomic loci, which is technically challenging. The CRISPR-Cas9 based genome editing greatly facilitates the generation of such genetically modified animals; however, most of the described methods use double-strand DNA (dsDNA) as the donor template. The dsDNA plasmids frequently undergo undesired integration events into the targeted genomic locus. The use of a single-strand oligodeoxynucleotide (ssODN) as the donor template prevents this complication and is therefore the preferred choice for introducing point mutations, as well as short sequences such as protein tags. Results We successfully applied the CRISPR-based white co-conversion strategy with a ssODN template, instead of the originally described dsDNA plasmid, to create genetically modified Drosophila melanogaster strains. We used the technique to easily introduce point mutations in two distinct chromosomes. Using the generated flies, we were able to demonstrate the in vivo importance of the respective mutations. For the Nucleoporin107 (Nup107) gene, the 1090G > A mutation was confirmed to affect ovarian development, while for the tinman (tin) gene, the regulatory role of the downstream core promoter element (DPE) was demonstrated within the developing Drosophila melanogaster embryo. Conclusions The described approach has facilitated the successful generation of point mutations in two different chromosomes, by two different labs. Distinct phenotypes associated with the newly-generated genotype were identified, thus exemplifying the importance of investigating the in vivo role of specific nucleotides. In addition, detailed guidelines, recommendations and crossing schemes are provided in order to support the generation of additional genetically modified animals by the scientific community.
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Affiliation(s)
- Tgst Levi
- Department of Developmental Biology and Cancer Research, Faculty of Medicine, Institute for Medical Research Israel-Canada, Hebrew University, Jerusalem, Israel
| | - Anna Sloutskin
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gan, Israel
| | - Rachel Kalifa
- Department of Developmental Biology and Cancer Research, Faculty of Medicine, Institute for Medical Research Israel-Canada, Hebrew University, Jerusalem, Israel
| | - Tamar Juven-Gershon
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gan, Israel
| | - Offer Gerlitz
- Department of Developmental Biology and Cancer Research, Faculty of Medicine, Institute for Medical Research Israel-Canada, Hebrew University, Jerusalem, Israel
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Bicoid-Dependent Activation of the Target Gene hunchback Requires a Two-Motif Sequence Code in a Specific Basal Promoter. Mol Cell 2019; 75:1178-1187.e4. [PMID: 31402096 DOI: 10.1016/j.molcel.2019.06.038] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2018] [Revised: 05/14/2019] [Accepted: 06/25/2019] [Indexed: 01/08/2023]
Abstract
In complex genetic loci, individual enhancers interact most often with specific basal promoters. Here we investigate the activation of the Bicoid target gene hunchback (hb), which contains two basal promoters (P1 and P2). Early in embryogenesis, P1 is silent, while P2 is strongly activated. In vivo deletion of P2 does not cause activation of P1, suggesting that P2 contains intrinsic sequence motifs required for activation. We show that a two-motif code (a Zelda binding site plus TATA) is required and sufficient for P2 activation. Zelda sites are present in the promoters of many embryonically expressed genes, but the combination of Zelda plus TATA does not seem to be a general code for early activation or Bicoid-specific activation per se. Because Zelda sites are also found in Bicoid-dependent enhancers, we propose that simultaneous binding to both enhancers and promoters independently synchronizes chromatin accessibility and facilitates correct enhancer-promoter interactions.
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lncRNA PSORS1C3 is regulated by glucocorticoids and fine-tunes OCT4 expression in non-pluripotent cells. Sci Rep 2019; 9:8370. [PMID: 31182783 PMCID: PMC6557835 DOI: 10.1038/s41598-019-44827-7] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2018] [Accepted: 05/20/2019] [Indexed: 11/29/2022] Open
Abstract
OCT4 is a transcription factor known for its regulatory roles in stemness, tumorigenesis and stress response. Considering its versatile functions, expression of OCT4 is regulated at different levels. PSORS1C3, a long non-coding RNA overlapped with OCT4, has a putative association with immune mediated diseases; however, its exact functions remained to be elucidated. Here, we demonstrated that PSORS1C3 is regulated by glucocorticoids (GC), has two endogenously active promoters, promoter 0 and 1, and two sets of transcripts, short and long variants. According to our findings, PSORS1C3 promoters behaved differently during neural differentiation of NT2 cells and glucocorticoid receptor (GR) activation. In both processes the expression pattern of short variants differed from that of long variants and was similar to OCT4 expression. Furthermore, our data revealed that PSORS1C3’s promoter 0 could act as an enhancer for OCT4 in non-pluripotent cells, where its deletion caused a significant decrease in OCT4 expression. Meanwhile, during GR activation promoter 0 functioned as a negative regulator and alleviated transcription induction of OCT4 after GC treatment. Altogether, our work clarified the structure and regulation of PSORS1C3, explained its relation to immune-related disease through GR signaling and introduced it as a novel fine-tuner of OCT4 expression in non-pluripotent cells.
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10
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Shir-Shapira H, Sloutskin A, Adato O, Ovadia-Shochat A, Ideses D, Zehavi Y, Kassavetis G, Kadonaga JT, Unger R, Juven-Gershon T. Identification of evolutionarily conserved downstream core promoter elements required for the transcriptional regulation of Fushi tarazu target genes. PLoS One 2019; 14:e0215695. [PMID: 30998799 PMCID: PMC6472829 DOI: 10.1371/journal.pone.0215695] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2019] [Accepted: 04/07/2019] [Indexed: 12/21/2022] Open
Abstract
The regulation of transcription initiation is critical for developmental and cellular processes. RNA polymerase II (Pol II) is recruited by the basal transcription machinery to the core promoter where Pol II initiates transcription. The core promoter encompasses the region from -40 to +40 bp relative to the +1 transcription start site (TSS). Core promoters may contain one or more core promoter motifs that confer specific properties to the core promoter, such as the TATA box, initiator (Inr) and motifs that are located downstream of the TSS, namely, motif 10 element (MTE), the downstream core promoter element (DPE) and the Bridge, a bipartite core promoter element. We had previously shown that Caudal, an enhancer-binding homeodomain transcription factor and a key regulator of the Hox gene network, is a DPE-specific activator. Interestingly, pair-rule proteins have been implicated in enhancer-promoter communication at the engrailed locus. Fushi tarazu (Ftz) is an enhancer-binding homeodomain transcription factor encoded by the ftz pair-rule gene. Ftz works in concert with its co-factor, Ftz-F1, to activate transcription. Here, we examined whether Ftz and Ftz-F1 activate transcription with a preference for a specific core promoter motif. Our analysis revealed that similarly to Caudal, Ftz and Ftz-F1 activate the promoter containing a TATA box mutation to significantly higher levels than the promoter containing a DPE mutation, thus demonstrating a preference for the DPE motif. We further discovered that Ftz target genes are enriched for a combination of functional downstream core promoter elements that are conserved among Drosophila species. Thus, the unique combination (Inr, Bridge and DPE) of functional downstream core promoter elements within Ftz target genes highlights the complexity of transcriptional regulation via the core promoter in the transcription of different developmental gene regulatory networks.
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Affiliation(s)
- Hila Shir-Shapira
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gan, Israel
| | - Anna Sloutskin
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gan, Israel
| | - Orit Adato
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gan, Israel
| | - Avital Ovadia-Shochat
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gan, Israel
| | - Diana Ideses
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gan, Israel
| | - Yonathan Zehavi
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gan, Israel
| | - George Kassavetis
- Section of Molecular Biology, University of California, San Diego, La Jolla, CA, United States of America
| | - James T. Kadonaga
- Section of Molecular Biology, University of California, San Diego, La Jolla, CA, United States of America
| | - Ron Unger
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gan, Israel
| | - Tamar Juven-Gershon
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gan, Israel
- * E-mail:
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11
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Wu K, Jia Z, Wang Q, Wei Z, Zhou Z, Liu X. Identification, expression analysis, and the regulating function on C/EBPs of KLF10 in Dalian purple sea urchin, Strongylocentrotus nudus. Genome 2017; 60:837-849. [PMID: 28891718 DOI: 10.1139/gen-2017-0033] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Accumulating evidence indicates that Krüppel-like factors (KLFs) play important roles in fat biology via the regulation of CCAAT/enhancer binding proteins (C/EBPs). However, KLFs and C/EBPs have not been identified from Strongylocentrotus nudus, and their roles in this species are not clear. In this study, the full-length cDNA of S. nudus KLF10 (SnKLF10) and three cDNA fragments of S. nudus C/EBPs (SnC/EBPs) were obtained. Examination of tissue distribution and expression patterns during gonadal development implied that SnKLF10 and SnC/EBPs play important roles in gonadal lipogenesis. The presence of transcription factor-binding sites (TFBSs) for KLFs in SnC/EBPs, and the results of an over-expression assay, revealed that SnKLF10 negatively regulates the transcription of SnC/EBPs. In addition, the core promoter regions of SnC/EBPs were determined, and multiple TFBSs for transcription factor (TFs) were identified, which are potential regulators of SnC/EBP transcription. Taken together, these results suggest that SnC/EBP genes are potential targets of SnKLF10, and that SnKLF10 plays a role in lipogenesis by repressing the transcription of SnC/EBPs. These findings provide information for further studies of KLF10 in invertebrates and provide new insight into the regulatory mechanisms of C/EBP transcription.
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Affiliation(s)
- Kaikai Wu
- a College of Animal Science and Technology, Northwest A&F University, Shaanxi Key Laboratory of Molecular Biology for Agriculture, Yangling 712100, China
| | - Zhiying Jia
- a College of Animal Science and Technology, Northwest A&F University, Shaanxi Key Laboratory of Molecular Biology for Agriculture, Yangling 712100, China
| | - Qi'ai Wang
- a College of Animal Science and Technology, Northwest A&F University, Shaanxi Key Laboratory of Molecular Biology for Agriculture, Yangling 712100, China
| | - Zhenlin Wei
- b Biological Science Department, Dezhou University, Dezhou, Shandong 253023, China
| | - Zunchun Zhou
- c Liaoning Key Laboratory of Marine Fishery Molecular Biology, Liaoning Ocean and Fisheries Science Research Institute, Dalian, Liaoning 116023, China
| | - Xiaolin Liu
- a College of Animal Science and Technology, Northwest A&F University, Shaanxi Key Laboratory of Molecular Biology for Agriculture, Yangling 712100, China
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12
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Abstract
This review by Vo ngoc et al. expands the view of the RNA polymerase II core promoter, which is comprised of classical DNA sequence motifs, sequence-specific DNA-binding transcription factors, chromatin signals, and DNA structure. The signals that direct the initiation of transcription ultimately converge at the core promoter, which is the gateway to transcription. Here we provide an overview of the RNA polymerase II core promoter in bilateria (bilaterally symmetric animals). The core promoter is diverse in terms of its composition and function yet is also punctilious, as it acts with strict rules and precision. We additionally describe an expanded view of the core promoter that comprises the classical DNA sequence motifs, sequence-specific DNA-binding transcription factors, chromatin signals, and DNA structure. This model may eventually lead to a more unified conceptual understanding of the core promoter.
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Affiliation(s)
- Long Vo Ngoc
- Section of Molecular Biology, University of California at San Diego, La Jolla, California 92093, USA
| | - Yuan-Liang Wang
- Section of Molecular Biology, University of California at San Diego, La Jolla, California 92093, USA
| | - George A Kassavetis
- Section of Molecular Biology, University of California at San Diego, La Jolla, California 92093, USA
| | - James T Kadonaga
- Section of Molecular Biology, University of California at San Diego, La Jolla, California 92093, USA
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13
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Schor IE, Degner JF, Harnett D, Cannavò E, Casale FP, Shim H, Garfield DA, Birney E, Stephens M, Stegle O, Furlong EEM. Promoter shape varies across populations and affects promoter evolution and expression noise. Nat Genet 2017; 49:550-558. [PMID: 28191888 DOI: 10.1038/ng.3791] [Citation(s) in RCA: 58] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2016] [Accepted: 01/20/2017] [Indexed: 12/29/2022]
Abstract
Animal promoters initiate transcription either at precise positions (narrow promoters) or dispersed regions (broad promoters), a distinction referred to as promoter shape. Although highly conserved, the functional properties of promoters with different shapes and the genetic basis of their evolution remain unclear. Here we used natural genetic variation across a panel of 81 Drosophila lines to measure changes in transcriptional start site (TSS) usage, identifying thousands of genetic variants affecting transcript levels (strength) or the distribution of TSSs within a promoter (shape). Our results identify promoter shape as a molecular trait that can evolve independently of promoter strength. Broad promoters typically harbor shape-associated variants, with signatures of adaptive selection. Single-cell measurements demonstrate that variants modulating promoter shape often increase expression noise, whereas heteroallelic interactions with other promoter variants alleviate these effects. These results uncover new functional properties of natural promoters and suggest the minimization of expression noise as an important factor in promoter evolution.
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Affiliation(s)
- Ignacio E Schor
- European Molecular Biology Laboratory (EMBL) Genome Biology Unit, Heidelberg, Germany
| | - Jacob F Degner
- European Molecular Biology Laboratory (EMBL) Genome Biology Unit, Heidelberg, Germany
| | - Dermot Harnett
- European Molecular Biology Laboratory (EMBL) Genome Biology Unit, Heidelberg, Germany
| | - Enrico Cannavò
- European Molecular Biology Laboratory (EMBL) Genome Biology Unit, Heidelberg, Germany
| | - Francesco P Casale
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Hinxton, UK
| | - Heejung Shim
- Department of Statistics, Purdue University, West Lafayette, Indiana, USA
| | - David A Garfield
- European Molecular Biology Laboratory (EMBL) Genome Biology Unit, Heidelberg, Germany
| | - Ewan Birney
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Hinxton, UK
| | - Matthew Stephens
- Department of Human Genetics, University of Chicago, Chicago, Illinois, USA
| | - Oliver Stegle
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Hinxton, UK
| | - Eileen E M Furlong
- European Molecular Biology Laboratory (EMBL) Genome Biology Unit, Heidelberg, Germany
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14
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Wragg J, Müller F. Transcriptional Regulation During Zygotic Genome Activation in Zebrafish and Other Anamniote Embryos. ADVANCES IN GENETICS 2016; 95:161-94. [PMID: 27503357 DOI: 10.1016/bs.adgen.2016.05.001] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Embryo development commences with the fusion of two terminally differentiated haploid gametes into the totipotent fertilized egg, which through a series of major cellular and molecular transitions generate a pluripotent cell mass. The activation of the zygotic genome occurs during the so-called maternal to zygotic transition and prepares the embryo for zygotic takeover from maternal factors, in the control of the development of cellular lineages during differentiation. Recent advances in next generation sequencing technologies have allowed the dissection of the genomic and epigenomic processes mediating this transition. These processes include reorganization of the chromatin structure to a transcriptionally permissive state, changes in composition and function of structural and regulatory DNA-binding proteins, and changeover of the transcriptome as it is overhauled from that deposited by the mother in the oocyte to a zygotically transcribed complement. Zygotic genome activation in zebrafish occurs 10 cell cycles after fertilization and provides an ideal experimental platform for elucidating the temporal sequence and dynamics of establishment of a transcriptionally active chromatin state and helps in identifying the determinants of transcription activation at polymerase II transcribed gene promoters. The relatively large number of pluripotent cells generated by the fast cell divisions before zygotic transcription provides sufficient biomass for next generation sequencing technology approaches to establish the temporal dynamics of events and suggest causative relationship between them. However, genomic and genetic technologies need to be improved further to capture the earliest events in development, where cell number is a limiting factor. These technologies need to be complemented with precise, inducible genetic interference studies using the latest genome editing tools to reveal the function of candidate determinants and to confirm the predictions made by classic embryological tools and genome-wide assays. In this review we summarize recent advances in the characterization of epigenetic regulation, transcription control, and gene promoter function during zygotic genome activation and how they fit with old models for the mechanisms of the maternal to zygotic transition. This review will focus on the zebrafish embryo but draw comparisons with other vertebrate model systems and refer to invertebrate models where informative.
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Affiliation(s)
- J Wragg
- University of Birmingham, Birmingham, United Kingdom
| | - F Müller
- University of Birmingham, Birmingham, United Kingdom
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15
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Sloutskin A, Danino YM, Orenstein Y, Zehavi Y, Doniger T, Shamir R, Juven-Gershon T. ElemeNT: a computational tool for detecting core promoter elements. Transcription 2016. [PMID: 26226151 PMCID: PMC4581360 DOI: 10.1080/21541264.2015.1067286] [Citation(s) in RCA: 51] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Core promoter elements play a pivotal role in the transcriptional output, yet they are often detected manually within sequences of interest. Here, we present 2 contributions to the detection and curation of core promoter elements within given sequences. First, the Elements Navigation Tool (ElemeNT) is a user-friendly web-based, interactive tool for prediction and display of putative core promoter elements and their biologically-relevant combinations. Second, the CORE database summarizes ElemeNT-predicted core promoter elements near CAGE and RNA-seq-defined Drosophila melanogaster transcription start sites (TSSs). ElemeNT's predictions are based on biologically-functional core promoter elements, and can be used to infer core promoter compositions. ElemeNT does not assume prior knowledge of the actual TSS position, and can therefore assist in annotation of any given sequence. These resources, freely accessible at http://lifefaculty.biu.ac.il/gershon-tamar/index.php/resources, facilitate the identification of core promoter elements as active contributors to gene expression.
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Affiliation(s)
- Anna Sloutskin
- a The Mina and Everard Goodman Faculty of Life Sciences ; Bar-Ilan University ; Ramat Gan , Israel
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16
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Even DY, Kedmi A, Basch-Barzilay S, Ideses D, Tikotzki R, Shir-Shapira H, Shefi O, Juven-Gershon T. Engineered Promoters for Potent Transient Overexpression. PLoS One 2016; 11:e0148918. [PMID: 26872062 PMCID: PMC4752495 DOI: 10.1371/journal.pone.0148918] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2015] [Accepted: 01/23/2016] [Indexed: 12/25/2022] Open
Abstract
The core promoter, which is generally defined as the region to which RNA Polymerase II is recruited to initiate transcription, plays a pivotal role in the regulation of gene expression. The core promoter consists of different combinations of several short DNA sequences, termed core promoter elements or motifs, which confer specific functional properties to each promoter. Earlier studies that examined the ability to modulate gene expression levels via the core promoter, led to the design of strong synthetic core promoters, which combine different core elements into a single core promoter. Here, we designed a new core promoter, termed super core promoter 3 (SCP3), which combines four core promoter elements (the TATA box, Inr, MTE and DPE) into a single promoter that drives prolonged and potent gene expression. We analyzed the effect of core promoter architecture on the temporal dynamics of reporter gene expression by engineering EGFP expression vectors that are driven by distinct core promoters. We used live cell imaging and flow cytometric analyses in different human cell lines to demonstrate that SCPs, particularly the novel SCP3, drive unusually strong long-term EGFP expression. Importantly, this is the first demonstration of long-term expression in transiently transfected mammalian cells, indicating that engineered core promoters can provide a novel non-viral strategy for biotechnological as well as gene-therapy-related applications that require potent expression for extended time periods.
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Affiliation(s)
- Dan Y. Even
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan, 5290002, Israel
| | - Adi Kedmi
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan, 5290002, Israel
| | - Shani Basch-Barzilay
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan, 5290002, Israel
| | - Diana Ideses
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan, 5290002, Israel
| | - Ravid Tikotzki
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan, 5290002, Israel
| | - Hila Shir-Shapira
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan, 5290002, Israel
| | - Orit Shefi
- Faculty of Engineering and Bar-Ilan Institute of Nanotechnologies and Advanced Materials, Bar-Ilan University, Ramat-Gan, 5290002, Israel
| | - Tamar Juven-Gershon
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan, 5290002, Israel
- * E-mail:
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17
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Macías F, López MC, Thomas MC. The Trypanosomatid Pr77-hallmark contains a downstream core promoter element essential for transcription activity of the Trypanosoma cruzi L1Tc retrotransposon. BMC Genomics 2016; 17:105. [PMID: 26861854 PMCID: PMC4748587 DOI: 10.1186/s12864-016-2427-6] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2015] [Accepted: 02/01/2016] [Indexed: 01/11/2023] Open
Abstract
Background Trypanosomatid genomes are highly colonized by non-LTR retroelements that make up to 5 % of the nuclear genome. These elements are mainly accumulated in the strand switch regions (SSRs) where polycistronic transcription is initiated and have a 77 nt-long sequence - Pr77 - at their 5′ ends. L1Tc is the best represented retrotransposon in the Trypanosoma cruzi genome and is a potentially functional autonomous element that encodes its own retrotransposition machinery. The Pr77 of the T. cruzi L1Tc element activates gene transcription via RNA polymerase II, generating abundant, unspliced transcripts which are translated. Results The present manuscript describes the identification of a downstream core promoter element (DPE) in the L1Tc Pr77 sequence. Just four nucleotides long (CGTG), it covers in Pr77 positions +25 to +28 of the described L1Tc transcription start site. The Pr77-DPE motif is conserved in terms of sequence composition and position in the Pr77 of most trypanosomatid non-LTR retrotransposons, independent of the coding or non-coding capacity of these retroelements. Transcription assays in T. cruzi stable transfectants with vector containing point mutations at 17 locations of the Pr77 nucleotide sequence evidence that the DPE motif is essential for the promoter function of Pr77. Furthermore, the obtained data show that other nucleotides also contributed to the promoter function of Pr77. In addition, the presented results indicate that parasite nuclear proteins specifically bind to different regions of the Pr77 sequence although the strongest binding is to the DPE motif. Moreover, it is shown that the DPE sense single-stranded sequence is being required in DNA-protein recognition of nuclear factors. Conclusions The Pr77 sequence present in most of non-LTR retrotransposons of trypanosomatids contains a downstream core promoter element (DPE) which is conserved in terms of nucleotide composition and location. The Pr77-DPE motif is essential for the transcriptional activity of Pr77 although other nucleotides are also involved. DPE has a high affinity binding for nuclear proteins in T. cruzi. The wide retroelement-mediated distribution of Pr77 suggests that it may represent an important tool for regulating gene expression in trypanosomatids. Electronic supplementary material The online version of this article (doi:10.1186/s12864-016-2427-6) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Francisco Macías
- Instituto de Parasitología y Biomedicina López-Neyra, Consejo Superior de Investigaciones Científicas (IPBLN-CSIC), PTS Granada, Avda. del Conocimiento S/N, 18016, Granada, Spain.
| | - Manuel Carlos López
- Instituto de Parasitología y Biomedicina López-Neyra, Consejo Superior de Investigaciones Científicas (IPBLN-CSIC), PTS Granada, Avda. del Conocimiento S/N, 18016, Granada, Spain.
| | - M Carmen Thomas
- Instituto de Parasitología y Biomedicina López-Neyra, Consejo Superior de Investigaciones Científicas (IPBLN-CSIC), PTS Granada, Avda. del Conocimiento S/N, 18016, Granada, Spain.
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18
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Xu M, Gonzalez-Hurtado E, Martinez E. Core promoter-specific gene regulation: TATA box selectivity and Initiator-dependent bi-directionality of serum response factor-activated transcription. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2016; 1859:553-63. [PMID: 26824723 DOI: 10.1016/j.bbagrm.2016.01.005] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/27/2015] [Revised: 12/31/2015] [Accepted: 01/23/2016] [Indexed: 11/15/2022]
Abstract
Gene-specific activation by enhancers involves their communication with the basal RNA polymerase II transcription machinery at the core promoter. Core promoters are diverse and may contain a variety of sequence elements such as the TATA box, the Initiator (INR), and the downstream promoter element (DPE) recognized, respectively, by the TATA-binding protein (TBP) and TBP-associated factors of the TFIID complex. Core promoter elements contribute to the gene selectivity of enhancers, and INR/DPE-specific enhancers and activators have been identified. Here, we identify a TATA box-selective activating sequence upstream of the human β-actin (ACTB) gene that mediates serum response factor (SRF)-induced transcription from TATA-dependent but not INR-dependent promoters and requires the TATA-binding/bending activity of TBP, which is otherwise dispensable for transcription from a TATA-less promoter. The SRF-dependent ACTB sequence is stereospecific on TATA promoters but activates in an orientation-independent manner a composite TATA/INR-containing promoter. More generally, we show that SRF-regulated genes of the actin/cytoskeleton/contractile family tend to have a TATA box. These results suggest distinct TATA-dependent and INR-dependent mechanisms of TFIID-mediated transcription in mammalian cells that are compatible with only certain stereospecific combinations of activators, and that a TBP-TATA binding mechanism is important for SRF activation of the actin/cytoskeleton-related gene family.
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Affiliation(s)
- Muyu Xu
- Department of Biochemistry, University of California, Riverside, CA 92521, USA
| | - Elsie Gonzalez-Hurtado
- Department of Biochemistry, University of California, Riverside, CA 92521, USA; MARC U-STAR Program, University of California, Riverside, CA 92521, USA
| | - Ernest Martinez
- Department of Biochemistry, University of California, Riverside, CA 92521, USA; MARC U-STAR Program, University of California, Riverside, CA 92521, USA.
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19
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Zehavi Y, Sloutskin A, Kuznetsov O, Juven-Gershon T. The core promoter composition establishes a new dimension in developmental gene networks. Nucleus 2015; 5:298-303. [PMID: 25482118 DOI: 10.4161/nucl.29838] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Developmental processes are highly dependent on transcriptional regulation by RNA polymerase II, which initiates transcription at the core promoter. The dorsal-ventral gene regulatory network (GRN) includes multiple genes that are activated by different nuclear concentrations of the Dorsal transcription factor along the dorsal-ventral axis. Downstream core promoter element (DPE)-containing genes are conserved and highly prevalent among Dorsal target genes. Moreover, the DPE motif is functional in multiple Dorsal target genes, as mutation of the DPE results in the loss of transcriptional activity. Furthermore, analysis of hybrid enhancer-promoter constructs reveals that the core promoter composition plays a pivotal role in the transcriptional output. Importantly, we provide in vivo evidence that expression driven by the homeotic Antennapedia P2 promoter during Drosophila embryogenesis is dependent on the DPE. Taken together, we propose that transcriptional regulation results from the interplay between enhancers and core promoter composition, thus establishing a novel dimension in developmental GRNs.
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Affiliation(s)
- Yonathan Zehavi
- a The Mina and Everard Goodman Faculty of Life Sciences; Bar-Ilan University; Ramat Gan, Israel
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20
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Boija A, Mannervik M. A time of change: Dynamics of chromatin and transcriptional regulation during nuclear programming in earlyDrosophiladevelopment. Mol Reprod Dev 2015; 82:735-46. [DOI: 10.1002/mrd.22517] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2015] [Accepted: 06/10/2015] [Indexed: 12/20/2022]
Affiliation(s)
- Ann Boija
- Department of Molecular Biosciences; The Wenner-Gren Institute; Stockholm University; Stockholm Sweden
| | - Mattias Mannervik
- Department of Molecular Biosciences; The Wenner-Gren Institute; Stockholm University; Stockholm Sweden
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21
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Watanabe K, Yabe M, Kasahara K, Kokubo T. A Random Screen Using a Novel Reporter Assay System Reveals a Set of Sequences That Are Preferred as the TATA or TATA-Like Elements in the CYC1 Promoter of Saccharomyces cerevisiae. PLoS One 2015; 10:e0129357. [PMID: 26046838 PMCID: PMC4457894 DOI: 10.1371/journal.pone.0129357] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2015] [Accepted: 05/08/2015] [Indexed: 12/11/2022] Open
Abstract
In Saccharomyces cerevisiae, the core promoters of class II genes contain either TATA or TATA-like elements to direct accurate transcriptional initiation. Genome-wide analyses show that the consensus sequence of the TATA element is TATAWAWR (8 bp), whereas TATA-like elements carry one or two mismatches to this consensus. The fact that several functionally distinct TATA sequences have been identified indicates that these elements may function, at least to some extent, in a gene-specific manner. The purpose of the present study was to identify functional TATA sequences enriched in one particular core promoter and compare them with the TATA or TATA-like elements that serve as the pre-initiation complex (PIC) assembly sites on the yeast genome. For this purpose, we conducted a randomized screen of the TATA element in the CYC1 promoter by using a novel reporter assay system and identified several hundreds of unique sequences that were tentatively classified into nine groups. The results indicated that the 7 bp TATA element (i.e., TATAWAD) and several sets of TATA-like sequences are preferred specifically by this promoter. Furthermore, we find that the most frequently isolated TATA-like sequence, i.e., TATTTAAA, is actually utilized as a functional core promoter element for the endogenous genes, e.g., ADE5,7 and ADE6. Collectively, these results indicate that the sequence requirements for the functional TATA or TATA-like elements in one particular core promoter are not as stringent. However, the variation of these sequences differs significantly from that of the PIC assembly sites on the genome, presumably depending on promoter structures and reflecting the gene-specific function of these sequences.
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Affiliation(s)
- Kiyoshi Watanabe
- Molecular and Cellular Biology Laboratory, Graduate School of Medical Life Science, Yokohama City University, Yokohama, Kanagawa, Japan
| | - Makoto Yabe
- Molecular and Cellular Biology Laboratory, Graduate School of Medical Life Science, Yokohama City University, Yokohama, Kanagawa, Japan
| | - Koji Kasahara
- Molecular and Cellular Biology Laboratory, Graduate School of Medical Life Science, Yokohama City University, Yokohama, Kanagawa, Japan
| | - Tetsuro Kokubo
- Molecular and Cellular Biology Laboratory, Graduate School of Medical Life Science, Yokohama City University, Yokohama, Kanagawa, Japan
- * E-mail:
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22
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Shir-Shapira H, Sharabany J, Filderman M, Ideses D, Ovadia-Shochat A, Mannervik M, Juven-Gershon T. Structure-Function Analysis of the Drosophila melanogaster Caudal Transcription Factor Provides Insights into Core Promoter-preferential Activation. J Biol Chem 2015; 290:17293-305. [PMID: 26018075 DOI: 10.1074/jbc.m114.632109] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2014] [Indexed: 11/06/2022] Open
Abstract
Regulation of RNA polymerase II transcription is critical for the proper development, differentiation, and growth of an organism. The RNA polymerase II core promoter is the ultimate target of a multitude of transcription factors that control transcription initiation. Core promoters encompass the RNA start site and consist of functional elements such as the TATA box, initiator, and downstream core promoter element (DPE), which confer specific properties to the core promoter. We have previously discovered that Drosophila Caudal, which is a master regulator of genes involved in development and differentiation, is a DPE-specific transcriptional activator. Here, we show that the mouse Caudal-related homeobox (Cdx) proteins (mCdx1, mCdx2, and mCdx4) are also preferential core promoter transcriptional activators. To elucidate the mechanism that enables Caudal to preferentially activate DPE transcription, we performed structure-function analysis. Using a systematic series of deletion mutants (all containing the intact DNA-binding homeodomain) we discovered that the C-terminal region of Caudal contributes to the preferential activation of the fushi tarazu (ftz) Caudal target gene. Furthermore, the region containing both the homeodomain and the C terminus of Caudal was sufficient to confer core promoter-preferential activation to the heterologous GAL4 DNA-binding domain. Importantly, we discovered that Drosophila CREB-binding protein (dCBP) is a co-activator for Caudal-regulated activation of ftz. Strikingly, dCBP conferred the ability to preferentially activate the DPE-dependent ftz reporter to mini-Caudal proteins that were unable to preferentially activate ftz transcription themselves. Taken together, it is the unique combination of dCBP and Caudal that enables the co-activation of ftz in a core promoter-preferential manner.
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Affiliation(s)
- Hila Shir-Shapira
- From The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gan 52900, Israel and
| | - Julia Sharabany
- From The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gan 52900, Israel and
| | - Matan Filderman
- From The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gan 52900, Israel and
| | - Diana Ideses
- From The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gan 52900, Israel and
| | - Avital Ovadia-Shochat
- From The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gan 52900, Israel and
| | - Mattias Mannervik
- The Wenner-Gren Institute, Developmental Biology, Stockholm University, Arrhenius Laboratories E3, SE-106 91 Stockholm, Sweden
| | - Tamar Juven-Gershon
- From The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gan 52900, Israel and
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23
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Lubliner S, Regev I, Lotan-Pompan M, Edelheit S, Weinberger A, Segal E. Core promoter sequence in yeast is a major determinant of expression level. Genome Res 2015; 25:1008-17. [PMID: 25969468 PMCID: PMC4484384 DOI: 10.1101/gr.188193.114] [Citation(s) in RCA: 68] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2014] [Accepted: 05/11/2015] [Indexed: 11/24/2022]
Abstract
The core promoter is the regulatory sequence to which RNA polymerase is recruited and where it acts to initiate transcription. Here, we present the first comprehensive study of yeast core promoters, providing massively parallel measurements of core promoter activity and of TSS locations and relative usage for thousands of native and designed sequences. We found core promoter activity to be highly correlated to the activity of the entire promoter and that sequence variation in different core promoter regions substantially tunes its activity in a predictable way. We also show that location, orientation, and flanking bases critically affect TATA element function, that transcription initiation in highly active core promoters is focused within a narrow region, that poly(dA:dT) orientation has a functional consequence at the 3' end of promoters, and that orthologous core promoters across yeast species have conserved activities. Our results demonstrate the importance of core promoters in the quantitative study of gene regulation.
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Affiliation(s)
- Shai Lubliner
- Department of Computer Science and Applied Mathematics, Weizmann Institute of Science, 7610001 Rehovot, Israel
| | - Ifat Regev
- Department of Computer Science and Applied Mathematics, Weizmann Institute of Science, 7610001 Rehovot, Israel; Department of Molecular Cell Biology, Weizmann Institute of Science, 7610001 Rehovot, Israel
| | - Maya Lotan-Pompan
- Department of Computer Science and Applied Mathematics, Weizmann Institute of Science, 7610001 Rehovot, Israel; Department of Molecular Cell Biology, Weizmann Institute of Science, 7610001 Rehovot, Israel
| | - Sarit Edelheit
- Department of Molecular Genetics, Weizmann Institute of Science, 7610001 Rehovot, Israel
| | - Adina Weinberger
- Department of Computer Science and Applied Mathematics, Weizmann Institute of Science, 7610001 Rehovot, Israel; Department of Molecular Cell Biology, Weizmann Institute of Science, 7610001 Rehovot, Israel
| | - Eran Segal
- Department of Computer Science and Applied Mathematics, Weizmann Institute of Science, 7610001 Rehovot, Israel; Department of Molecular Cell Biology, Weizmann Institute of Science, 7610001 Rehovot, Israel
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24
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Danino YM, Even D, Ideses D, Juven-Gershon T. The core promoter: At the heart of gene expression. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2015; 1849:1116-31. [PMID: 25934543 DOI: 10.1016/j.bbagrm.2015.04.003] [Citation(s) in RCA: 99] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/17/2015] [Revised: 04/19/2015] [Accepted: 04/23/2015] [Indexed: 12/17/2022]
Abstract
The identities of different cells and tissues in multicellular organisms are determined by tightly controlled transcriptional programs that enable accurate gene expression. The mechanisms that regulate gene expression comprise diverse multiplayer molecular circuits of multiple dedicated components. The RNA polymerase II (Pol II) core promoter establishes the center of this spatiotemporally orchestrated molecular machine. Here, we discuss transcription initiation, diversity in core promoter composition, interactions of the basal transcription machinery with the core promoter, enhancer-promoter specificity, core promoter-preferential activation, enhancer RNAs, Pol II pausing, transcription termination, Pol II recycling and translation. We further discuss recent findings indicating that promoters and enhancers share similar features and may not substantially differ from each other, as previously assumed. Taken together, we review a broad spectrum of studies that highlight the importance of the core promoter and its pivotal role in the regulation of metazoan gene expression and suggest future research directions and challenges.
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Affiliation(s)
- Yehuda M Danino
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gan 5290002, Israel
| | - Dan Even
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gan 5290002, Israel
| | - Diana Ideses
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gan 5290002, Israel
| | - Tamar Juven-Gershon
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gan 5290002, Israel.
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25
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Abstract
Transcriptional regulation is pivotal for development and differentiation of organisms. Transcription of eukaryotic protein-coding genes by RNA polymerase II (Pol II) initiates at the core promoter. Core promoters, which encompass the transcription start site, may contain functional core promoter elements, such as the TATA box, initiator, TCT and downstream core promoter element. TRF2 (TATA-box-binding protein-related factor 2) does not bind TATA box-containing promoters. Rather, it is recruited to core promoters via sequences other than the TATA box. We review the recent findings implicating TRF2 as a basal transcription factor in the regulation of diverse biological processes and specialized transcriptional programs.
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Key Words
- BREd, downstream TFIIB recognition element
- BREu, upstream TFIIB recognition element
- ChIP, Chromatin immunoprecipitation
- DPE
- DPE, downstream core promoter element
- Inr, initiator
- MTE, motif ten element
- PIC, preinitiation complex
- Pol II, RNA polymerase II
- RNA Pol II transcription
- TAF, TBP-associated factor
- TBP, TATA-box binding protein
- TBP-related factors
- TCT
- TFIIA (transcription factor, RNA polymerase II A)
- TFIIB (transcription factor, RNA polymerase II B)
- TFIID (transcription factor, RNA polymerase II D)
- TRF, TATA-box-binding protein-related factor
- TRF2
- TSS, transcription start site
- core promoter elements/motifs
- embryonic development
- histone gene cluster
- ribosomal protein genes
- spermiogenesis
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Affiliation(s)
- Yonathan Zehavi
- a The Mina and Everard Goodman Faculty of Life Sciences , Bar-Ilan University , Ramat Gan , 5290002 , Israel
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26
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Abstract
Kadonaga and colleagues present novel molecular insights into TATA-box-binding protein (TBP) family members and the evolution of complex animal body plans. They demonstrate that the TBP-related factor 2 (TRF2), which activates TATA-less core promoters, first arose in a common ancestor to the bilaterians and hypothesize that this new TRF2-based transcription system facilitated the evolution of bilateria. The development of a complex body plan requires a diversity of regulatory networks. Here we consider the concept of TATA-box-binding protein (TBP) family proteins as “system factors” that each supports a distinct set of transcriptional programs. For instance, TBP activates TATA-box-dependent core promoters, whereas TBP-related factor 2 (TRF2) activates TATA-less core promoters that are dependent on a TCT or downstream core promoter element (DPE) motif. These findings led us to investigate the evolution of TRF2. TBP occurs in Archaea and eukaryotes, but TRF2 evolved prior to the emergence of the bilateria and subsequent to the evolutionary split between bilaterians and nonbilaterian animals. Unlike TBP, TRF2 does not bind to the TATA box and could thus function as a new system factor that is largely independent of TBP. We postulate that this TRF2-based system served as the foundation for new transcriptional programs, such as those involved in triploblasty and body plan development, that facilitated the evolution of bilateria.
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Affiliation(s)
- Sascha H C Duttke
- Section of Molecular Biology, University of California at San Diego, La Jolla, California 92093, USA
| | - Russell F Doolittle
- Section of Molecular Biology, University of California at San Diego, La Jolla, California 92093, USA; Department of Chemistry and Biochemistry, University of California at San Diego, La Jolla, California 92093, USA
| | - Yuan-Liang Wang
- Section of Molecular Biology, University of California at San Diego, La Jolla, California 92093, USA
| | - James T Kadonaga
- Section of Molecular Biology, University of California at San Diego, La Jolla, California 92093, USA;
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27
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Abstract
Transcription of protein-coding genes is highly dependent on the RNA polymerase II core promoter. Core promoters, generally defined as the regions that direct transcription initiation, consist of functional core promoter motifs (such as the TATA-box, initiator [Inr], and downstream core promoter element [DPE]) that confer specific properties to the core promoter. The known basal transcription factors that support TATA-dependent transcription are insufficient for in vitro transcription of DPE-dependent promoters. In search of a transcription factor that supports DPE-dependent transcription, we used a biochemical complementation approach and identified the Drosophila TBP (TATA-box-binding protein)-related factor 2 (TRF2) as an enriched factor in the fractions that support DPE-dependent transcription. We demonstrate that the short TRF2 isoform preferentially activates DPE-dependent promoters. DNA microarray analysis reveals the enrichment of DPE promoters among short TRF2 up-regulated genes. Using primer extension analysis and reporter assays, we show the importance of the DPE in transcriptional regulation of TRF2 target genes. It was previously shown that, unlike TBP, TRF2 fails to bind DNA containing TATA-boxes. Using microfluidic affinity analysis, we discovered that short TRF2-bound DNA oligos are enriched for Inr and DPE motifs. Taken together, our findings highlight the role of short TRF2 as a preferential core promoter regulator.
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