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Tan Y, Huang Y, Xu C, Huang X, Li S, Yin Z. Long noncoding RNAs and mRNAs profiling in ovary during laying and broodiness in Taihe Black-Bone Silky Fowls (Gallus gallus Domesticus Brisson). BMC Genomics 2024; 25:357. [PMID: 38600449 PMCID: PMC11005167 DOI: 10.1186/s12864-024-10281-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2024] [Accepted: 04/02/2024] [Indexed: 04/12/2024] Open
Abstract
BACKGROUND Broodiness significantly impacts poultry egg production, particularly notable in specific breeds such as the black-boned Silky, characterized by pronounced broodiness. An understanding of the alterations in ovarian signaling is essential for elucidating the mechanisms that influence broodiness. However, comparative research on the characteristics of long non-coding RNAs (lncRNAs) in the ovaries of broody chickens (BC) and high egg-laying chickens (GC) remains scant. In this investigation, we employed RNA sequencing to assess the ovarian transcriptomes, which include both lncRNAs and mRNAs, in eight Taihe Black-Bone Silky Fowls (TBsf), categorized into broody and high egg-laying groups. This study aims to provide a clearer understanding of the genetic underpinnings associated with broodiness and egg production. RESULTS We have identified a total of 16,444 mRNAs and 18,756 lncRNAs, of which 349 mRNAs and 651 lncRNAs exhibited significantly different expression (DE) between the BC and GC groups. Furthermore, we have identified the cis-regulated and trans-regulated target genes of differentially abundant lncRNA transcripts and have constructed an lncRNA-mRNA trans-regulated interaction network linked to ovarian follicle development. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) annotation analyses have revealed that DE mRNAs and the target genes of DE lncRNAs are associated with pathways including neuroactive ligand-receptor interaction, CCR6 chemokine receptor binding, G-protein coupled receptor binding, cytokine-cytokine receptor interaction, and ECM-receptor interaction. CONCLUSION Our research presents a comprehensive compilation of lncRNAs and mRNAs linked to ovarian development. Additionally, it establishes a predictive interaction network involving differentially abundant lncRNAs and differentially expressed genes (DEGs) within TBsf. This significantly contributes to our understanding of the intricate interactions between lncRNAs and genes governing brooding behavior.
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Affiliation(s)
- Yuting Tan
- Zijingang Campus, Animal Science College, Zhejiang University, Hangzhou, 310058, China
| | - Yunyan Huang
- Zijingang Campus, Animal Science College, Zhejiang University, Hangzhou, 310058, China
| | - Chunhui Xu
- Zijingang Campus, Animal Science College, Zhejiang University, Hangzhou, 310058, China
| | - Xuan Huang
- Zijingang Campus, Animal Science College, Zhejiang University, Hangzhou, 310058, China
| | - Shibao Li
- Zijingang Campus, Animal Science College, Zhejiang University, Hangzhou, 310058, China
| | - Zhaozheng Yin
- Zijingang Campus, Animal Science College, Zhejiang University, Hangzhou, 310058, China.
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2
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Felício D, du Mérac TR, Amorim A, Martins S. Functional implications of paralog genes in polyglutamine spinocerebellar ataxias. Hum Genet 2023; 142:1651-1676. [PMID: 37845370 PMCID: PMC10676324 DOI: 10.1007/s00439-023-02607-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2023] [Accepted: 09/22/2023] [Indexed: 10/18/2023]
Abstract
Polyglutamine (polyQ) spinocerebellar ataxias (SCAs) comprise a group of autosomal dominant neurodegenerative disorders caused by (CAG/CAA)n expansions. The elongated stretches of adjacent glutamines alter the conformation of the native proteins inducing neurotoxicity, and subsequent motor and neurological symptoms. Although the etiology and neuropathology of most polyQ SCAs have been extensively studied, only a limited selection of therapies is available. Previous studies on SCA1 demonstrated that ATXN1L, a human duplicated gene of the disease-associated ATXN1, alleviated neuropathology in mice models. Other SCA-associated genes have paralogs (i.e., copies at different chromosomal locations derived from duplication of the parental gene), but their functional relevance and potential role in disease pathogenesis remain unexplored. Here, we review the protein homology, expression pattern, and molecular functions of paralogs in seven polyQ dominant ataxias-SCA1, SCA2, MJD/SCA3, SCA6, SCA7, SCA17, and DRPLA. Besides ATXN1L, we highlight ATXN2L, ATXN3L, CACNA1B, ATXN7L1, ATXN7L2, TBPL2, and RERE as promising functional candidates to play a role in the neuropathology of the respective SCA, along with the parental gene. Although most of these duplicates lack the (CAG/CAA)n region, if functionally redundant, they may compensate for a partial loss-of-function or dysfunction of the wild-type genes in SCAs. We aim to draw attention to the hypothesis that paralogs of disease-associated genes may underlie the complex neuropathology of dominant ataxias and potentiate new therapeutic strategies.
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Affiliation(s)
- Daniela Felício
- Instituto de Investigação e Inovação em Saúde (i3S), 4200-135, Porto, Portugal
- Institute of Molecular Pathology and Immunology of the University of Porto (IPATIMUP), 4200-135, Porto, Portugal
- Instituto Ciências Biomédicas Abel Salazar (ICBAS), Universidade do Porto, 4050-313, Porto, Portugal
| | - Tanguy Rubat du Mérac
- Instituto de Investigação e Inovação em Saúde (i3S), 4200-135, Porto, Portugal
- Institute of Molecular Pathology and Immunology of the University of Porto (IPATIMUP), 4200-135, Porto, Portugal
- Faculty of Science, University of Amsterdam, 1098 XH, Amsterdam, The Netherlands
| | - António Amorim
- Instituto de Investigação e Inovação em Saúde (i3S), 4200-135, Porto, Portugal
- Institute of Molecular Pathology and Immunology of the University of Porto (IPATIMUP), 4200-135, Porto, Portugal
- Department of Biology, Faculty of Sciences, University of Porto, 4169-007, Porto, Portugal
| | - Sandra Martins
- Instituto de Investigação e Inovação em Saúde (i3S), 4200-135, Porto, Portugal.
- Institute of Molecular Pathology and Immunology of the University of Porto (IPATIMUP), 4200-135, Porto, Portugal.
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3
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Role of the TATA-box binding protein (TBP) and associated family members in transcription regulation. Gene X 2022; 833:146581. [PMID: 35597524 DOI: 10.1016/j.gene.2022.146581] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2021] [Revised: 04/18/2022] [Accepted: 05/16/2022] [Indexed: 11/20/2022] Open
Abstract
The assembly of transcription complexes on eukaryotic promoters involves a series of steps, including chromatin remodeling, recruitment of TATA-binding protein (TBP)-containing complexes, the RNA polymerase II holoenzyme, and additional basal transcription factors. This review describes the transcriptional regulation by TBP and its corresponding homologs that constitute the TBP family and their interactions with promoter DNA. The C-terminal core domain of TBP is highly conserved and contains two structural repeats that fold into a saddle-like structure, essential for the interaction with the TATA-box on DNA. Based on the TBP C-terminal core domain similarity, three TBP-related factors (TRFs) or TBP-like factors (TBPLs) have been discovered in metazoans, TRF1, TBPL1, and TBPL2. TBP is autoregulated, and once bound to DNA, repressors such as Mot1 induce TBP to dissociate, while other factors such as NC2 and the NOT complex convert the active TBP/DNA complex into inactive, negatively regulating TBP. TFIIA antagonizes the TBP repressors but may be effective only in conjunction with the RNA polymerase II holoenzyme recruitment to the promoter by promoter-bound activators. TRF1 has been discovered inDrosophila melanogasterandAnophelesbut found absent in vertebrates and yeast. TBPL1 cannot bind to the TATA-box; instead, TBPL1 prefers binding to TATA-less promoters. However, TBPL1 shows a stronger association with TFIIA than TBP. The TCT core promoter element is present in most ribosomal protein genes inDrosophilaand humans, and TBPL1 is required for the transcription of these genes. TBP directly participates in the DNA repair mechanism, and TBPL1 mediates cell cycle arrest and apoptosis. TBPL2 is closely related to its TBP paralog, showing 95% sequence similarity with the TBP core domain. Like TBP, TBPL2 also binds to the TATA-box and shows interactions with TFIIA, TFIIB, and other basal transcription factors. Despite these advances, much remains to be explored in this family of transcription factors.
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4
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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: 16] [Impact Index Per Article: 5.3] [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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5
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Yu C, Cvetesic N, Hisler V, Gupta K, Ye T, Gazdag E, Negroni L, Hajkova P, Berger I, Lenhard B, Müller F, Vincent SD, Tora L. TBPL2/TFIIA complex establishes the maternal transcriptome through oocyte-specific promoter usage. Nat Commun 2020; 11:6439. [PMID: 33353944 PMCID: PMC7755920 DOI: 10.1038/s41467-020-20239-4] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2020] [Accepted: 11/20/2020] [Indexed: 01/28/2023] Open
Abstract
During oocyte growth, transcription is required to create RNA and protein reserves to achieve maternal competence. During this period, the general transcription factor TATA binding protein (TBP) is replaced by its paralogue, TBPL2 (TBP2 or TRF3), which is essential for RNA polymerase II transcription. We show that in oocytes TBPL2 does not assemble into a canonical TFIID complex. Our transcript analyses demonstrate that TBPL2 mediates transcription of oocyte-expressed genes, including mRNA survey genes, as well as specific endogenous retroviral elements. Transcription start site (TSS) mapping indicates that TBPL2 has a strong preference for TATA-like motif in core promoters driving sharp TSS selection, in contrast with canonical TBP/TFIID-driven TATA-less promoters that have broader TSS architecture. Thus, we show a role for the TBPL2/TFIIA complex in the establishment of the oocyte transcriptome by using a specific TSS recognition code.
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Affiliation(s)
- Changwei Yu
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, 67404, Illkirch, France
- Centre National de la Recherche Scientifique (CNRS), UMR7104, 67404, Illkirch, France
- Institut National de la Santé et de la Recherche Médicale (INSERM), U1258, 67404, Illkirch, France
- Université de Strasbourg, 67404, Illkirch, France
| | - Nevena Cvetesic
- Imperial College London, South Kensington Campus, London, SW7 2AZ, UK
| | - Vincent Hisler
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, 67404, Illkirch, France
- Centre National de la Recherche Scientifique (CNRS), UMR7104, 67404, Illkirch, France
- Institut National de la Santé et de la Recherche Médicale (INSERM), U1258, 67404, Illkirch, France
- Université de Strasbourg, 67404, Illkirch, France
| | - Kapil Gupta
- Max Planck Bristol Centre for Minimal Biology, University of Bristol, Cantock's Close, Bristol, BS8 1TS, UK
| | - Tao Ye
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, 67404, Illkirch, France
- Centre National de la Recherche Scientifique (CNRS), UMR7104, 67404, Illkirch, France
- Institut National de la Santé et de la Recherche Médicale (INSERM), U1258, 67404, Illkirch, France
- Université de Strasbourg, 67404, Illkirch, France
| | - Emese Gazdag
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, 67404, Illkirch, France
- Centre National de la Recherche Scientifique (CNRS), UMR7104, 67404, Illkirch, France
- Institut National de la Santé et de la Recherche Médicale (INSERM), U1258, 67404, Illkirch, France
- Université de Strasbourg, 67404, Illkirch, France
| | - Luc Negroni
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, 67404, Illkirch, France
- Centre National de la Recherche Scientifique (CNRS), UMR7104, 67404, Illkirch, France
- Institut National de la Santé et de la Recherche Médicale (INSERM), U1258, 67404, Illkirch, France
- Université de Strasbourg, 67404, Illkirch, France
| | - Petra Hajkova
- Imperial College London, South Kensington Campus, London, SW7 2AZ, UK
| | - Imre Berger
- Max Planck Bristol Centre for Minimal Biology, University of Bristol, Cantock's Close, Bristol, BS8 1TS, UK
| | - Boris Lenhard
- Imperial College London, South Kensington Campus, London, SW7 2AZ, UK
| | - Ferenc Müller
- Institute of Cancer and Genomic Sciences, College of Medical and Dental Sciences, University of Birmingham, Birmingham, B15 2TT, UK
| | - Stéphane D Vincent
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, 67404, Illkirch, France.
- Centre National de la Recherche Scientifique (CNRS), UMR7104, 67404, Illkirch, France.
- Institut National de la Santé et de la Recherche Médicale (INSERM), U1258, 67404, Illkirch, France.
- Université de Strasbourg, 67404, Illkirch, France.
| | - László Tora
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, 67404, Illkirch, France.
- Centre National de la Recherche Scientifique (CNRS), UMR7104, 67404, Illkirch, France.
- Institut National de la Santé et de la Recherche Médicale (INSERM), U1258, 67404, Illkirch, France.
- Université de Strasbourg, 67404, Illkirch, France.
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6
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TATA box-binding protein-related factor 3 drives the mesendoderm specification of human embryonic stem cells by globally interacting with the TATA box of key mesendodermal genes. Stem Cell Res Ther 2020; 11:196. [PMID: 32448362 PMCID: PMC7245780 DOI: 10.1186/s13287-020-01711-w] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2020] [Revised: 04/23/2020] [Accepted: 05/06/2020] [Indexed: 01/08/2023] Open
Abstract
BACKGROUND Mesendodermal formation during early gastrulation requires the expression of lineage-specific genes, while the regulatory mechanisms during this process have not yet been fully illustrated. TATA box-binding protein (TBP) and TBP-like factors are general transcription factors responsible for the transcription initiation by recruiting the preinitiation complex to promoter regions. However, the role of TBP family members in the regulation of mesendodermal specification remains largely unknown. METHODS We used an in vitro mesendodermal differentiation system of human embryonic stem cells (hESCs), combining with the microarray and quantitative polymerase chain reaction (qRT-PCR) analysis, loss of function and gain of function to determine the function of the TBP family member TBP-related factor 3 (TRF3) during mesendodermal differentiation of hESCs. The chromatin immunoprecipitation (ChIP) and biochemistry analysis were used to determine the binding of TRF3 to the promoter region of key mesendodermal genes. RESULTS The mesendodermal differentiation of hESCs was confirmed by the microarray gene expression profile, qRT-PCR, and immunocytochemical staining. The expression of TRF3 mRNA was enhanced during mesendodermal differentiation of hESCs. The TRF3 deficiency did not affect the pluripotent marker expression, alkaline phosphatase activity, and cell cycle distribution of undifferentiated hESCs or the expression of early neuroectodermal genes during neuroectodermal differentiation. During the mesendodermal differentiation, the expression of pluripotency markers decreased in both wild-type and TRF3 knockout (TRF3-/-) cells, while the TRF3 deficiency crippled the expression of the mesendodermal markers. The reintroduction of TRF3 into the TRF3-/- hESCs rescued inhibited mesendodermal differentiation. Mechanistically, the TRF3 binding profile was significantly shifted to the mesendodermal specification during mesendodermal differentiation of hESCs based on the ChIP-seq data. Moreover, ChIP and ChIP-qPCR analysis showed that TRF3 was enriched at core promoter regions of mesendodermal developmental genes, EOMESODERMIN, BRACHYURY, mix paired-like homeobox, and GOOSECOID homeobox, during mesendodermal differentiation of hESCs. CONCLUSIONS These results reveal that the TBP family member TRF3 is dispensable in the undifferentiated hESCs and the early neuroectodermal differentiation. However, it directs mesendodermal lineage commitment of hESCs via specifically promoting the transcription of key mesendodermal transcription factors. These findings provide new insights into the function and mechanisms of the TBP family member in hESC early lineage specification.
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7
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The RNA Polymerase II Core Promoter in Drosophila. Genetics 2019; 212:13-24. [PMID: 31053615 DOI: 10.1534/genetics.119.302021] [Citation(s) in RCA: 51] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2018] [Accepted: 03/05/2019] [Indexed: 11/18/2022] Open
Abstract
Transcription by RNA polymerase II initiates at the core promoter, which is sometimes referred to as the "gateway to transcription." Here, we describe the properties of the RNA polymerase II core promoter in Drosophila The core promoter is at a strategic position in the expression of genes, as it is the site of convergence of the signals that lead to transcriptional activation. Importantly, core promoters are diverse in terms of their structure and function. They are composed of various combinations of sequence motifs such as the TATA box, initiator (Inr), and downstream core promoter element (DPE). Different types of core promoters are transcribed via distinct mechanisms. Moreover, some transcriptional enhancers exhibit specificity for particular types of core promoters. These findings indicate that the core promoter is a central component of the transcriptional apparatus that regulates gene expression.
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8
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Liu C, Ma Y, Shang Y, Huo R, Li W. Post-translational regulation of the maternal-to-zygotic transition. Cell Mol Life Sci 2018; 75:1707-1722. [PMID: 29427077 PMCID: PMC11105290 DOI: 10.1007/s00018-018-2750-y] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2017] [Revised: 12/24/2017] [Accepted: 01/08/2018] [Indexed: 02/07/2023]
Abstract
The maternal-to-zygotic transition (MZT) is essential for the developmental control handed from maternal products to newly synthesized zygotic genome in the earliest stages of embryogenesis, including maternal component (mRNAs and proteins) degradation and zygotic genome activation (ZGA). Various protein post-translational modifications have been identified during the MZT, such as phosphorylation, methylation and ubiquitination. Precise post-translational regulation mechanisms are essential for the timely transition of early embryonic development. In this review, we summarize recent progress regarding the molecular mechanisms underlying post-translational regulation of maternal component degradation and ZGA during the MZT and discuss some important issues in the field.
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Affiliation(s)
- Chao Liu
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, 1 Beichen West Road, Chaoyang District, Beijing, 100101, People's Republic of China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049, People's Republic of China
| | - Yanjie Ma
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, 1 Beichen West Road, Chaoyang District, Beijing, 100101, People's Republic of China
- Department of Animal Science and Technology, Northeast Agricultural University, Haerbin, 150030, People's Republic of China
| | - Yongliang Shang
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, 1 Beichen West Road, Chaoyang District, Beijing, 100101, People's Republic of China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049, People's Republic of China
| | - Ran Huo
- State Key Laboratory of Reproductive Medicine, Department of Histology and Embryology, Nanjing Medical University, Nanjing, 210029, People's Republic of China.
- State Key Laboratory of Reproductive Medicine, Department of Histology and Embryology, Nanjing Medical University, Nanjing, 211166, People's Republic of China.
| | - Wei Li
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, 1 Beichen West Road, Chaoyang District, Beijing, 100101, People's Republic of China.
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049, People's Republic of China.
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9
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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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10
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A heterochromatin-dependent transcription machinery drives piRNA expression. Nature 2017; 549:54-59. [PMID: 28847004 PMCID: PMC5590728 DOI: 10.1038/nature23482] [Citation(s) in RCA: 159] [Impact Index Per Article: 22.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2017] [Accepted: 07/14/2017] [Indexed: 12/30/2022]
Abstract
Nuclear small RNA pathways safeguard genome integrity by establishing transcription-repressing heterochromatin at transposable elements. This inevitably also targets the transposon-rich source loci of the small RNAs themselves. How small RNA source loci are efficiently transcribed while transposon promoters are potently silenced is not understood. Here we show that, in Drosophila, transcription of PIWI-interacting RNA (piRNA) clusters-small RNA source loci in animal gonads-is enforced through RNA polymerase II pre-initiation complex formation within repressive heterochromatin. This is accomplished through Moonshiner, a paralogue of a basal transcription factor IIA (TFIIA) subunit, which is recruited to piRNA clusters via the heterochromatin protein-1 variant Rhino. Moonshiner triggers transcription initiation within piRNA clusters by recruiting the TATA-box binding protein (TBP)-related factor TRF2, an animal TFIID core variant. Thus, transcription of heterochromatic small RNA source loci relies on direct recruitment of the core transcriptional machinery to DNA via histone marks rather than sequence motifs, a concept that we argue is a recurring theme in evolution.
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11
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Nakazato A, Maeda R, Ishikawa K, Suzuki H, Tamura TA. TBP-like protein (TLP) represses myogenesis via inhibition of the myogenin promoter. Biochem Biophys Res Commun 2016; 479:814-819. [PMID: 27680312 DOI: 10.1016/j.bbrc.2016.09.127] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2016] [Accepted: 09/24/2016] [Indexed: 11/30/2022]
Abstract
TBP-like protein (TLP) is one of the metazoan-restricted transcription factors participating in development and differentiation, though the molecular mechanism by which TLP regulates these processes remains unclear. In this study, we investigated the relationship between TLP and myogenesis of mouse C2C12 myoblasts. We found that TLP gene expression decreases during myogenic differentiation. Overexpression and knockdown of TLP revealed that the levels of muscle-specific myosin heavy chain and the myogenic transcription factor myogenin are downregulated by TLP. TLP inhibits the progression of morphological change from myoblasts to myotubes, thereby suppressing myogenesis. We further show that TLP represses the promoter activity of myogenin. The proximal AT-rich sequence of the myogenin promoter is responsible for TLP-mediated transcriptional repression. The results of this study suggest that TLP inhibits myogenesis through downregulation of the myogenin gene.
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Affiliation(s)
- Aki Nakazato
- Department of Biology, Graduate School of Science, Chiba University, 1-33 Yayoicho, Inage-ku, Chiba, 263-8522, Japan
| | - Ryo Maeda
- Department of Biology, Graduate School of Science, Chiba University, 1-33 Yayoicho, Inage-ku, Chiba, 263-8522, Japan
| | - Kohei Ishikawa
- Department of Biology, Graduate School of Science, Chiba University, 1-33 Yayoicho, Inage-ku, Chiba, 263-8522, Japan
| | - Hidefumi Suzuki
- Department of Biology, Graduate School of Science, Chiba University, 1-33 Yayoicho, Inage-ku, Chiba, 263-8522, Japan
| | - Taka-Aki Tamura
- Department of Biology, Graduate School of Science, Chiba University, 1-33 Yayoicho, Inage-ku, Chiba, 263-8522, Japan.
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12
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Gazdag E, Jacobi UG, van Kruijsbergen I, Weeks DL, Veenstra GJC. Activation of a T-box-Otx2-Gsc gene network independent of TBP and TBP-related factors. Development 2016; 143:1340-50. [PMID: 26952988 PMCID: PMC4852510 DOI: 10.1242/dev.127936] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2015] [Accepted: 02/24/2016] [Indexed: 12/15/2022]
Abstract
Embryonic development relies on activating and repressing regulatory influences that are faithfully integrated at the core promoter of individual genes. In vertebrates, the basal machinery recognizing the core promoter includes TATA-binding protein (TBP) and two TBP-related factors. In Xenopus embryos, the three TBP family factors are all essential for development and are required for expression of distinct subsets of genes. Here, we report on a non-canonical TBP family-insensitive (TFI) mechanism of transcription initiation that involves mesoderm and organizer gene expression. Using TBP family single- and triple-knockdown experiments, α-amanitin treatment, transcriptome profiling and chromatin immunoprecipitation, we found that TFI gene expression cannot be explained by functional redundancy, is supported by active transcription and shows normal recruitment of the initiating form of RNA polymerase II to the promoter. Strikingly, recruitment of Gcn5 (also known as Kat2a), a co-activator that has been implicated in transcription initiation, to TFI gene promoters is increased upon depletion of TBP family factors. TFI genes are part of a densely connected TBP family-insensitive T-box-Otx2-Gsc interaction network. The results indicate that this network of genes bound by Vegt, Eomes, Otx2 and Gsc utilizes a novel, flexible and non-canonical mechanism of transcription that does not require TBP or TBP-related factors. Highlighted article: A network of embryonic genes, many of which are expressed in the mesoderm and the organiser, can initiate transcription through a non-canonical mechanism.
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Affiliation(s)
- Emese Gazdag
- Department of Molecular Developmental Biology, Radboud Institute for Molecular Life Sciences, Radboud University, 6500 HB Nijmegen, The Netherlands
| | - Ulrike G Jacobi
- Department of Molecular Developmental Biology, Radboud Institute for Molecular Life Sciences, Radboud University, 6500 HB Nijmegen, The Netherlands
| | - Ila van Kruijsbergen
- Department of Molecular Developmental Biology, Radboud Institute for Molecular Life Sciences, Radboud University, 6500 HB Nijmegen, The Netherlands
| | - Daniel L Weeks
- Department of Biochemistry, University of Iowa, Iowa City, IA 52242, USA
| | - Gert Jan C Veenstra
- Department of Molecular Developmental Biology, Radboud Institute for Molecular Life Sciences, Radboud University, 6500 HB Nijmegen, The Netherlands
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13
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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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14
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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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15
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Diversity in TAF proteomics: consequences for cellular differentiation and migration. Int J Mol Sci 2014; 15:16680-97. [PMID: 25244017 PMCID: PMC4200853 DOI: 10.3390/ijms150916680] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2014] [Revised: 08/25/2014] [Accepted: 08/27/2014] [Indexed: 12/31/2022] Open
Abstract
Development is a highly controlled process of cell proliferation and differentiation driven by mechanisms of dynamic gene regulation. Specific DNA binding factors for establishing cell- and tissue-specific transcriptional programs have been characterised in different cell and animal models. However, much less is known about the role of “core transcription machinery” during cell differentiation, given that general transcription factors and their spatiotemporally patterned activity govern different aspects of cell function. In this review, we focus on the role of TATA-box associated factor 4 (TAF4) and its functional isoforms generated by alternative splicing in controlling lineage-specific differentiation of normal mesenchymal stem cells and cancer stem cells. In the light of our recent findings, induction, control and maintenance of cell differentiation status implies diversification of the transcription initiation apparatus orchestrated by alternative splicing.
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16
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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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17
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Lee MT, Bonneau AR, Giraldez AJ. Zygotic genome activation during the maternal-to-zygotic transition. Annu Rev Cell Dev Biol 2014; 30:581-613. [PMID: 25150012 DOI: 10.1146/annurev-cellbio-100913-013027] [Citation(s) in RCA: 388] [Impact Index Per Article: 38.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Embryogenesis depends on a highly coordinated cascade of genetically encoded events. In animals, maternal factors contributed by the egg cytoplasm initially control development, whereas the zygotic nuclear genome is quiescent. Subsequently, the genome is activated, embryonic gene products are mobilized, and maternal factors are cleared. This transfer of developmental control is called the maternal-to-zygotic transition (MZT). In this review, we discuss recent advances toward understanding the scope, timing, and mechanisms that underlie zygotic genome activation at the MZT in animals. We describe high-throughput techniques to measure the embryonic transcriptome and explore how regulation of the cell cycle, chromatin, and transcription factors together elicits specific patterns of embryonic gene expression. Finally, we illustrate the interplay between zygotic transcription and maternal clearance and show how these two activities combine to reprogram two terminally differentiated gametes into a totipotent embryo.
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Affiliation(s)
- Miler T Lee
- Department of Genetics, Yale University School of Medicine, New Haven, Connecticut 06520; ,
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18
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Wang YL, Duttke SHC, Chen K, Johnston J, Kassavetis GA, Zeitlinger J, Kadonaga JT. TRF2, but not TBP, mediates the transcription of ribosomal protein genes. Genes Dev 2014; 28:1550-5. [PMID: 24958592 PMCID: PMC4102762 DOI: 10.1101/gad.245662.114] [Citation(s) in RCA: 57] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
The TCT core promoter element is present in most ribosomal protein (RP) genes in Drosophila and humans. Here we show that TBP (TATA box-binding protein)-related factor TRF2, but not TBP, is required for transcription of the TCT-dependent RP genes. In cells, TCT-dependent transcription, but not TATA-dependent transcription, increases or decreases upon overexpression or depletion of TRF2. In vitro, purified TRF2 activates TCT but not TATA promoters. ChIP-seq (chromatin immunoprecipitation [ChIP] combined with deep sequencing) experiments revealed the preferential localization of TRF2 at TCT versus TATA promoters. Hence, a specialized TRF2-based RNA polymerase II system functions in the synthesis of RPs and complements the RNA polymerase I and III systems.
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Affiliation(s)
- Yuan-Liang Wang
- Section of Molecular Biology, University of California at San Diego, La Jolla, California 92093, USA
| | - Sascha H C Duttke
- Section of Molecular Biology, University of California at San Diego, La Jolla, California 92093, USA
| | - Kai Chen
- Stowers Institute for Medical Research, Kansas City, Missouri 64110, USA
| | - Jeff Johnston
- Stowers Institute for Medical Research, Kansas City, Missouri 64110, USA
| | - George A Kassavetis
- Section of Molecular Biology, University of California at San Diego, La Jolla, California 92093, USA
| | - Julia Zeitlinger
- Stowers Institute for Medical Research, Kansas City, Missouri 64110, USA; Department of Pathology, University of Kansas Medical Center, Kansas City, Kansas 66160, USA
| | - James T Kadonaga
- Section of Molecular Biology, University of California at San Diego, La Jolla, California 92093, USA
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19
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Müller F, Tora L. Chromatin and DNA sequences in defining promoters for transcription initiation. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2013; 1839:118-28. [PMID: 24275614 DOI: 10.1016/j.bbagrm.2013.11.003] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/26/2013] [Revised: 11/11/2013] [Accepted: 11/11/2013] [Indexed: 01/29/2023]
Abstract
One of the key events in eukaryotic gene regulation and consequent transcription is the assembly of general transcription factors and RNA polymerase II into a functional pre-initiation complex at core promoters. An emerging view of complexity arising from a variety of promoter associated DNA motifs, their binding factors and recent discoveries in characterising promoter associated chromatin properties brings an old question back into the limelight: how is a promoter defined? In addition to position-dependent DNA sequence motifs, accumulating evidence suggests that several parallel acting mechanisms are involved in orchestrating a pattern marked by the state of chromatin and general transcription factor binding in preparation for defining transcription start sites. In this review we attempt to summarise these promoter features and discuss the available evidence pointing at their interactions in defining transcription initiation in developmental contexts. This article is part of a Special Issue entitled: Chromatin and epigenetic regulation of animal development.
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Affiliation(s)
- Ferenc Müller
- School of Clinical and Experimental Medicine, College of Medical and Dental Sciences, University of Birmingham, B15 2TT Edgbaston, Birmingham, UK.
| | - Làszlò Tora
- Cellular Signaling and Nuclear Dynamics Program, Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), UMR 7104 CNRS, UdS, INSERM U964, BP 10142, F-67404 Illkirch Cedex, CU de Strasbourg, France; School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, 637551, Singapore.
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20
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Verma N, Hung KH, Kang JJ, Barakat NH, Stumph WE. Differential utilization of TATA box-binding protein (TBP) and TBP-related factor 1 (TRF1) at different classes of RNA polymerase III promoters. J Biol Chem 2013; 288:27564-27570. [PMID: 23955442 DOI: 10.1074/jbc.c113.503094] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Abstract
In the fruit fly Drosophila melanogaster, RNA polymerase III transcription was found to be dependent not upon the canonical TATA box-binding protein (TBP) but instead upon the TBP-related factor 1 (TRF1) (Takada, S., Lis, J. T., Zhou, S., and Tjian, R. (2000) Cell 101, 459-469). Here we confirm that transcription of fly tRNA genes requires TRF1. However, we unexpectedly find that U6 snRNA gene promoters are occupied primarily by TBP in cells and that knockdown of TBP, but not TRF1, inhibits U6 transcription in cells. Moreover, U6 transcription in vitro effectively utilizes TBP, whereas TBP cannot substitute for TRF1 to promote tRNA transcription in vitro. Thus, in fruit flies, different classes of RNA polymerase III promoters differentially utilize TBP and TRF1 for the initiation of transcription.
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Affiliation(s)
- Neha Verma
- Molecular Biology Institute; Departments of Biology
| | - Ko-Hsuan Hung
- Molecular Biology Institute; Chemistry and Biochemistry, San Diego State University, San Diego, California 92182-1030
| | - Jin Joo Kang
- Molecular Biology Institute; Chemistry and Biochemistry, San Diego State University, San Diego, California 92182-1030
| | - Nermeen H Barakat
- Molecular Biology Institute; Chemistry and Biochemistry, San Diego State University, San Diego, California 92182-1030
| | - William E Stumph
- Molecular Biology Institute; Chemistry and Biochemistry, San Diego State University, San Diego, California 92182-1030.
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21
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Reinke V, Krause M, Okkema P. Transcriptional regulation of gene expression in C. elegans. ACTA ACUST UNITED AC 2013:1-34. [PMID: 23801596 DOI: 10.1895/wormbook.1.45.2] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
Protein coding gene sequences are converted to mRNA by the highly regulated process of transcription. The precise temporal and spatial control of transcription for many genes is an essential part of development in metazoans. Thus, understanding the molecular mechanisms underlying transcriptional control is essential to understanding cell fate determination during embryogenesis, post-embryonic development, many environmental interactions, and disease-related processes. Studies of transcriptional regulation in C. elegans exploit its genomic simplicity and physical characteristics to define regulatory events with single-cell and minute-time-scale resolution. When combined with the genetics of the system, C. elegans offers a unique and powerful vantage point from which to study how chromatin-associated proteins and their modifications interact with transcription factors and their binding sites to yield precise control of gene expression through transcriptional regulation.
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Affiliation(s)
- Valerie Reinke
- Department of Genetics, Yale University, New Haven, CT 06520, USA.
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22
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Akhtar W, Veenstra GJC. TBP-related factors: a paradigm of diversity in transcription initiation. Cell Biosci 2011; 1:23. [PMID: 21711503 PMCID: PMC3142196 DOI: 10.1186/2045-3701-1-23] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2011] [Accepted: 06/27/2011] [Indexed: 01/24/2023] Open
Abstract
TATA binding protein (TBP) is a key component of the eukaryotic transcription initiation machinery. It functions in several complexes involved in core promoter recognition and assembly of the pre-initiation complex. Through gene duplication eukaryotes have expanded their repertoire of TATA binding proteins, leading to a variable composition of the transcription machinery. In vertebrates this repertoire consists of TBP, TBP-like factor (TLF, also known as TBPL1, TRF2) and TBP2 (also known as TBPL2, TRF3). All three factors are essential, with TLF and TBP2 playing important roles in development and differentiation, in particular gametogenesis and early embryonic development, whereas TBP dominates somatic cell transcription. TBP-related factors may compete for promoters when co-expressed, but also show preferential interactions with subsets of promoters. Initiation factor switching occurs on account of differential expression of these proteins in gametes, embryos and somatic cells. Paralogs of TFIIA and TAF subunits account for additional variation in the transcription initiation complex. This variation in core promoter recognition accommodates the expanded regulatory capacity and specificity required for germ cells and embryonic development in higher eukaryotes.
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Affiliation(s)
- Waseem Akhtar
- Radboud University Nijmegen, Department of Molecular Biology, Faculty of Science, Nijmegen Centre for Molecular Life Sciences, Nijmegen, The Netherlands.
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23
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Gaudet J, McGhee JD. Recent advances in understanding the molecular mechanisms regulating C. elegans transcription. Dev Dyn 2010; 239:1388-404. [PMID: 20175193 DOI: 10.1002/dvdy.22246] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
Abstract
We review recent studies that have advanced our understanding of the molecular mechanisms regulating transcription in the nematode C. elegans. Topics covered include: (i) general properties of C. elegans promoters; (ii) transcription factors and transcription factor combinations involved in cell fate specification and cell differentiation; (iii) new roles for general transcription factors; (iv) nucleosome positioning in C. elegans "chromatin"; and (v) some characteristics of histone variants and histone modifications and their possible roles in controlling C. elegans transcription.
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Affiliation(s)
- Jeb Gaudet
- Department of Biochemistry and Molecular Biology, Alberta Children's Hospital Research Institute for Child and Maternal Health, University of Calgary, Calgary, Alberta, Canada
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24
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Abstract
Animal growth and development depend on the precise control of gene expression at the level of transcription. A central role in the regulation of developmental transcription is attributed to transcription factors that bind DNA enhancer elements, which are often located far from gene transcription start sites. Here, we review recent studies that have uncovered significant regulatory functions in developmental transcription for the TFIID basal transcription factors and for the DNA core promoter elements that are located close to transcription start sites.
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Affiliation(s)
- Uwe Ohler
- Institute for Genome Sciences & Policy, Departments of Biostatistics & Bioinformatics and Computer Science, Duke University, Durham, NC 27708, USA
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25
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D'Alessio JA, Wright KJ, Tjian R. Shifting players and paradigms in cell-specific transcription. Mol Cell 2009; 36:924-31. [PMID: 20064459 PMCID: PMC2807468 DOI: 10.1016/j.molcel.2009.12.011] [Citation(s) in RCA: 80] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2009] [Accepted: 12/08/2009] [Indexed: 01/28/2023]
Abstract
Historically, developmental-stage- and tissue-specific patterns of gene expression were assumed to be determined primarily by DNA regulatory sequences and their associated activators, while the general transcription machinery including core promoter recognition complexes, coactivators, and chromatin modifiers was held to be invariant. New evidence suggests that significant changes in these general transcription factors including TFIID, BAF, and Mediator may facilitate global changes in cell-type-specific transcription.
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Affiliation(s)
- Joseph A D'Alessio
- Howard Hughes Medical Institute, University of California, Berkeley, 94720, USA
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26
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Benoit B, He CH, Zhang F, Votruba SM, Tadros W, Westwood JT, Smibert CA, Lipshitz HD, Theurkauf WE. An essential role for the RNA-binding protein Smaug during the Drosophila maternal-to-zygotic transition. Development 2009; 136:923-32. [PMID: 19234062 DOI: 10.1242/dev.031815] [Citation(s) in RCA: 116] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Genetic control of embryogenesis switches from the maternal to the zygotic genome during the maternal-to-zygotic transition (MZT), when maternal mRNAs are destroyed, high-level zygotic transcription is initiated, the replication checkpoint is activated and the cell cycle slows. The midblastula transition (MBT) is the first morphological event that requires zygotic gene expression. The Drosophila MBT is marked by blastoderm cellularization and follows 13 cleavage-stage divisions. The RNA-binding protein Smaug is required for cleavage-independent maternal transcript destruction during the Drosophila MZT. Here, we show that smaug mutants also disrupt syncytial blastoderm stage cell-cycle delays, DNA replication checkpoint activation, cellularization, and high-level zygotic expression of protein coding and micro RNA genes. We also show that Smaug protein levels increase through the cleavage divisions and peak when the checkpoint is activated and zygotic transcription initiates, and that transgenic expression of Smaug in an anterior-to-posterior gradient produces a concomitant gradient in the timing of maternal transcript destruction, cleavage cell cycle delays, zygotic gene transcription, cellularization and gastrulation. Smaug accumulation thus coordinates progression through the MZT.
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Affiliation(s)
- Beatrice Benoit
- Program in Molecular Medicine, University of Massachusetts Medical School, 377 Plantation Street, Worcester, MA 01605, USA
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27
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Kopytova DV, Kopantseva MR, Nabirochkina EN, Vorobyova NE, Georgieva SG, Krasnov AN. Functions of transcription factor TRF2 Drosophila melanogaster. RUSS J GENET+ 2008. [DOI: 10.1134/s1022795408030034] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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28
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Bashirullah A, Lam G, Yin VP, Thummel CS. dTrf2 is required for transcriptional and developmental responses to ecdysone during Drosophila metamorphosis. Dev Dyn 2008; 236:3173-9. [PMID: 17948312 DOI: 10.1002/dvdy.21350] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022] Open
Abstract
The TATA box-binding protein (TBP) related factor 2 (TRF2) has been well characterized at a biochemical level and in cultured cells. Relatively little, however, is known about how TRF2 functions in specific biological pathways during development. Here, we show that Drosophila TRF2 (dTRF2) plays an essential role in responses to the steroid hormone ecdysone during the onset of metamorphosis. Hypomorphic dTrf2 mutations lead to developmental arrest during prepupal and early pupal stages with defects in major ecdysone-triggered biological responses, including puparium formation, anterior spiracle eversion, gas bubble translocation, adult head eversion, and larval salivary gland cell death. The transcription of key ecdysone-regulated target genes is delayed and reduced in dTrf2 mutants. dTrf2 appears to be required for the proper timing and levels of ecdysone-regulated gene expression required for entry into metamorphosis.
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Affiliation(s)
- Arash Bashirullah
- Department of Human Genetics, University of Utah School of Medicine, Salt Lake City, Utah 84112-5330, USA
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29
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30
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Isogai Y, Keles S, Prestel M, Hochheimer A, Tjian R. Transcription of histone gene cluster by differential core-promoter factors. Genes Dev 2007; 21:2936-49. [PMID: 17978101 PMCID: PMC2049195 DOI: 10.1101/gad.1608807] [Citation(s) in RCA: 83] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2007] [Accepted: 09/21/2007] [Indexed: 12/16/2022]
Abstract
The 100 copies of tandemly arrayed Drosophila linker (H1) and core (H2A/B and H3/H4) histone gene cluster are coordinately regulated during the cell cycle. However, the molecular mechanisms that must allow differential transcription of linker versus core histones prevalent during development remain elusive. Here, we used fluorescence imaging, biochemistry, and genetics to show that TBP (TATA-box-binding protein)-related factor 2 (TRF2) selectively regulates the TATA-less Histone H1 gene promoter, while TBP/TFIID targets core histone transcription. Importantly, TRF2-depleted polytene chromosomes display severe chromosomal structural defects. This selective usage of TRF2 and TBP provides a novel mechanism to differentially direct transcription within the histone cluster. Moreover, genome-wide chromatin immunoprecipitation (ChIP)-on-chip analyses coupled with RNA interference (RNAi)-mediated functional studies revealed that TRF2 targets several classes of TATA-less promoters of >1000 genes including those driving transcription of essential chromatin organization and protein synthesis genes. Our studies establish that TRF2 promoter recognition complexes play a significantly more central role in governing metazoan transcription than previously appreciated.
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Affiliation(s)
- Yoh Isogai
- Department of Molecular and Cell Biology, University of California at Berkeley, Berkeley, California 94720, USA
| | - Sündüz Keles
- Department of Statistics, Department of Biostatistics, and Department of Medical Informatics, University of Wisconsin at Madison, Madison, Wisconsin 53706, USA
| | - Matthias Prestel
- Adolf-Butenandt-Institut, Molekularbiologie, 80336 Munich, Germany
| | | | - Robert Tjian
- Department of Molecular and Cell Biology, University of California at Berkeley, Berkeley, California 94720, USA
- Howard Hughes Medical Institute, University of California at Berkeley, Berkeley, California 94720, USA
- Li Ka-Shing Center for Biomedical and Health Sciences, University of California at Berkeley, Berkeley, California 94720, USA
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31
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Variations in intracellular levels of TATA binding protein can affect specific genes by different mechanisms. Mol Cell Biol 2007; 28:83-92. [PMID: 17954564 DOI: 10.1128/mcb.00809-07] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
We previously showed that reduced intracellular levels of the TATA binding protein (TBP), brought about by tbp heterozygosity in DT40 cells, resulted in a mitotic delay reflecting reduced expression of the mitotic regulator cdc25B but did not significantly affect overall transcription. Here we extend these findings in several ways. We first provide evidence that the decrease in cdc25B expression reflects reduced activity of the cdc25B core promoter in the heterozygous (TBP-het) cells. Strikingly, mutations in a previously described repressor element that overlaps the TATA box restored promoter activity in TBP-het cells, supporting the idea that the sensitivity of this promoter to TBP levels reflects a competition between TBP and the repressor for DNA binding. To determine whether cells might have mechanisms to compensate for fluctuations in TBP levels, we next examined expression of the two known vertebrate TBP homologues, TLP and TBP2. Significantly, mRNAs encoding both were significantly overexpressed relative to levels observed in wild-type cells. In the case of TLP, this was shown to reflect regulation of the core promoter by both TBP and TLP. Together, our results indicate that variations in TBP levels can affect the transcription of specific promoters in distinct ways, but overall transcription may be buffered by corresponding alterations in the expression of TBP homologues.
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Jacobi UG, Akkers RC, Pierson ES, Weeks DL, Dagle JM, Veenstra GJC. TBP paralogs accommodate metazoan- and vertebrate-specific developmental gene regulation. EMBO J 2007; 26:3900-9. [PMID: 17703192 PMCID: PMC1994123 DOI: 10.1038/sj.emboj.7601822] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2007] [Accepted: 07/16/2007] [Indexed: 11/08/2022] Open
Abstract
In addition to TATA-binding protein (TBP), a key factor for transcription initiation, the metazoan-specific TBP-like factor TLF/TRF2 and the vertebrate-specific factor TBP2/TRF3 are known to be required for transcription of specific subsets of genes. We have combined an antisense-knockdown approach with transcriptome profiling to determine the significance and biological role of TBP-independent transcription in early gastrula-stage Xenopus laevis embryos. Here, we report that, although each of the TBP family members is essential for embryonic development, relatively few genes depend on TBP in the embryo. Most of the transcripts that depend on TBP in the embryo are also expressed maternally and in adult stages, and show no functional specialization. In contrast, TLF is linked to preferential expression in embryos and shows functional specialization in catabolism. A requirement for TBP2 is linked to vertebrate-specific embryonic genes and ventral-specific expression. Therefore TBP paralogs are essential for the gene-regulatory repertoire that is directly linked to early embryogenesis.
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Affiliation(s)
- Ulrike G Jacobi
- Department of Molecular Biology, Faculty of Science, Nijmegen Centre for Molecular Life Sciences, Radboud University Nijmegen, Nijmegen, The Netherlands
| | - Robert C Akkers
- Department of Molecular Biology, Faculty of Science, Nijmegen Centre for Molecular Life Sciences, Radboud University Nijmegen, Nijmegen, The Netherlands
| | - Elisabeth S Pierson
- Department of General Instruments, Radboud University Nijmegen, Nijmegen, The Netherlands
| | - Daniel L Weeks
- Department of Biochemistry, University of Iowa, Iowa City, IA, USA
| | - John M Dagle
- Department of Biochemistry, University of Iowa, Iowa City, IA, USA
- Department of Pediatrics, University of Iowa, Iowa City, IA, USA
| | - Gert Jan C Veenstra
- Department of Molecular Biology, Faculty of Science, Nijmegen Centre for Molecular Life Sciences, Radboud University Nijmegen, Nijmegen, The Netherlands
- Department of Molecular Biology, Nijmegen Centre for Molecular Life Sciences, Radboud University Nijmegen, Mol.Biol. M850/3.79, PO Box 9101, Nijmegen 6500, The Netherlands. Tel.: +31 24 3610541; Fax: +31 24 3610520; E-mail:
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Di Pietro C, Ragusa M, Duro L, Guglielmino MR, Barbagallo D, Carnemolla A, Laganà A, Buffa P, Angelica R, Rinaldi A, Calafato MS, Milicia I, Caserta C, Giugno R, Pulvirenti A, Giunta V, Rapisarda A, Di Pietro V, Grillo A, Messina A, Ferro A, Grzeschik KH, Purrello M. Genomics, evolution, and expression of TBPL2, a member of the TBP family. DNA Cell Biol 2007; 26:369-85. [PMID: 17570761 DOI: 10.1089/dna.2006.0527] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
TBPL2 is the most recently discovered and less characterized member of the TATA box binding protein (TBP) family that also comprises TBP, TATA box binding protein-like 1 (TBPL1), and Drosophila melanogaster TBP related factor (TRF). In this paper we report our in silico and in vitro data on (i) the genomics of the TBPL2 gene in Homo sapiens, Pan troglodytes, Mus musculus, Rattus norvegicus, Gallus gallus, Xenopus tropicalis, and Takifugu rubripes; (ii) its evolution and phylogenetic relationship with TBP, TBPL1, and TRF; (iii) the structure of the TBPL2 proteins that belong to the recently identified group of the intrinsically unstructured proteins (IUPs); and (iv) TBPL2 expression in different organs and cell types of Homo sapiens and Rattus norvegicus. Similar to TBP, both the TBPL2 gene and protein are bimodular. The 3' region of the gene encoding the DNA binding domain (DBD) was well conserved during evolution. Its high homology to vertebrate TBP suggests that TBPL2 also should bind to the TATA box and interact with the proteins binding to TBP carboxy-terminal domain, such as the TBP associated factors (TAFs). As already demonstrated for TBP, TBPL2 amino-terminal segment is intrinsically unstructured and, even though variable among vertebrates, comprises a highly conserved motif not found in any other known protein. Absence of TBPL2 from the genome of invertebrates and plants demonstrates its specific origin within the subphylum of vertebrates. Our RT-PCR analysis of human and rat RNA shows that, similar to TBP, TBPL2 is ubiquitously synthesized even though at variable levels that are at least two orders of magnitude lower. Higher expression of TBPL2 in the gonads than in other organs suggests that it could perform important functions in gametogenesis. Our genomic and expression data should contribute to clarify why TBP has a general master role within the transcription apparatus (TA), whereas both TBPL1 and TBPL2 perform tissue-specific functions.
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Affiliation(s)
- Cinzia Di Pietro
- Dipartimento di Scienze Biomediche-Unità di Biologia Genetica e BioInformatica, Università di Catania, Catania, Italy, EU
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Høiby T, Zhou H, Mitsiou DJ, Stunnenberg HG. A facelift for the general transcription factor TFIIA. ACTA ACUST UNITED AC 2007; 1769:429-36. [PMID: 17560669 DOI: 10.1016/j.bbaexp.2007.04.008] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2007] [Revised: 04/20/2007] [Accepted: 04/24/2007] [Indexed: 10/23/2022]
Abstract
TFIIA was classified as a general transcription factor when it was first identified. Since then it has been debated to what extent it can actually be regarded as "general". The most notable feature of TFIIA is the proteolytical cleavage of the TFIIAalphabeta into a TFIIAalpha and TFIIAbeta moiety which has long remained a mystery. Recent studies have showed that TFIIA is cleaved by Taspase1 which was initially identified as the protease for the proto-oncogene MLL. Cleavage of TFIIA does not appear to serve as a step required for its activation as the uncleaved TFIIA in the Taspase1 knock-outs adequately support bulk transcription. Instead, cleavage of TFIIA seems to affect its turn-over and may be a part of an intricate degradation mechanism that allows fine-tuning of cellular levels of TFIIA. Cleavage might also be responsible for switching transcription program as the uncleaved and cleaved TFIIA might have distinct promoter specificity during development and differentiation. This review will focus on functional characteristics of TFIIA and discuss novel insights in the role of this elusive transcription factor.
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Affiliation(s)
- Torill Høiby
- NCMLS, Department of Molecular Biology, 191, Radboud University of Nijmegen, PO Box 91001, 6500 HB Nijmegen, The Netherlands
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35
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Shima S, Aigaki T, Nojima T, Yamamoto D. Identification of trf2 mutants of Drosophila with defects in anterior spiracle eversion. ARCHIVES OF INSECT BIOCHEMISTRY AND PHYSIOLOGY 2007; 64:157-63. [PMID: 17366598 DOI: 10.1002/arch.20166] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/14/2023]
Abstract
TATA-box-binding protein (TBP)-related factor (Trf)2 is a member of the family of TBP-related factors present in metazoan organisms. In Drosophila, Trf2 immunoprecipitates with the nucleosome remodeling factor (NURF) chromatin remodeling complex and the DNA replication element (DRE)-binding factor DREF. When it forms a complex with DREF, Trf2 activates transcription from the DRE-binding sites of the proliferating cell nuclear antigen (PCNA) gene. Despite these observations at the molecular level, no mutations in the trf2 locus have been found in Drosophila. Here, we identify two P-element insertion alleles, PL28 and GS7403, as hypomorphic mutants with a decreased expression level of trf2. Pupae of these mutant alleles show failure in anterior spiracle eversion, a hallmark of mutations in the loci associated with ecdysteroid signaling.
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Affiliation(s)
- Seigo Shima
- Waseda University School of Human Sciences, Saitama, Japan
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36
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Kopytova DV, Krasnov AN. The family of TRF (TBP-like factors) proteins. RUSS J GENET+ 2007. [DOI: 10.1134/s1022795407030039] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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37
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Yang Y, Cao J, Huang L, Fang HY, Sheng HZ. Regulated expression of TATA-binding protein-related factor 3 (TRF3) during early embryogenesis. Cell Res 2007; 16:610-21. [PMID: 16721357 DOI: 10.1038/sj.cr.7310064] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
RNA polymerase (Pol) II transcription persists in TATA-box-binding protein (TBP)(-/-) mutant mouse embryos, indicating TBP-independent mechanisms for Pol II transcription in early development. TBP-related factor 3 (TRF3) has been proposed to substitute for TBP in TBP(-/-) mouse embryos. We examined the expression of TRF3 in maturing oocytes and early embryos and found that TRF3 was co-expressed with TBP in the meiotic oocytes and early embryos from the late one-cell stage onward. The amounts of TBP and TRF3 changed dynamically and correlated well with transcriptional activity. Chromatin immunoprecipitation (ChIP) assay revealed that different gene promoters in mouse embryonic stem (ES) cells recruited TRF3 and TBP selectively. Comparative analyses of TRF3 and TBP during cell cycle showed that both factors proceeded through cell cycle in a similar pace, except that TRF3 was slightly delayed than TBP in entering the nucleus when cells were exiting the M-phase. Data from expression and biochemical analyses therefore support the hypothesis that TRF3 plays a role in early mouse development. In addition, results from co-localization study suggest that TRF3 may be also involved in Pol I transcription.
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Affiliation(s)
- Ye Yang
- Laboratory of Stem Cell Biology, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China
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38
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Kopytova DV, Krasnov AN, Kopantceva MR, Nabirochkina EN, Nikolenko JV, Maksimenko O, Kurshakova MM, Lebedeva LA, Yerokhin MM, Simonova OB, Korochkin LI, Tora L, Georgiev PG, Georgieva SG. Two isoforms of Drosophila TRF2 are involved in embryonic development, premeiotic chromatin condensation, and proper differentiation of germ cells of both sexes. Mol Cell Biol 2006; 26:7492-505. [PMID: 17015475 PMCID: PMC1636870 DOI: 10.1128/mcb.00349-06] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The Drosophila TATA box-binding protein (TBP)-related factor 2 (TRF2 or TLF) was shown to control a subset of genes different from that controlled by TBP. Here, we have investigated the structure and functions of the trf2 gene. We demonstrate that it encodes two protein isoforms: the previously described 75-kDa TRF2 and a newly identified 175-kDa version in which the same sequence is preceded by a long N-terminal domain with coiled-coil motifs. Chromatography of Drosophila embryo extracts revealed that the long TRF2 is part of a multiprotein complex also containing ISWI. Both TRF2 forms are detected at the same sites on polytene chromosomes and have the same expression patterns, suggesting that they fulfill similar functions. A study of the manifestations of the trf2 mutation suggests an essential role of TRF2 during embryonic Drosophila development. The trf2 gene is strongly expressed in germ line cells of adult flies. High levels of TRF2 are found in nuclei of primary spermatocytes and trophocytes with intense transcription. In ovaries, TRF2 is present both in actively transcribing nurse cells and in the transcriptionally inactive oocyte nuclei. Moreover, TRF2 is essential for premeiotic chromatin condensation and proper differentiation of germ cells of both sexes.
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Affiliation(s)
- Daria V Kopytova
- Institute of Gene Biology, Russian Academy of Sciences, Vavilov St. 34/5, Moscow 119334, Russian Federation
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39
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Tanaka Y, Nanba YA, Park KA, Mabuchi T, Suenaga Y, Shiraishi S, Shimada M, Nakadai T, Tamura TA. Transcriptional repression of the mouse wee1 gene by TBP-related factor 2. Biochem Biophys Res Commun 2006; 352:21-8. [PMID: 17109819 DOI: 10.1016/j.bbrc.2006.10.175] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2006] [Accepted: 10/24/2006] [Indexed: 11/17/2022]
Abstract
TBP-related factor 2 (TRF2), one of the TBP family proteins, is involved in various cellular functions through its transcription stimulation activity. We previously reported that TRF2 is involved in reduction of wee1 mRNA in genotoxin-treated chicken cells. In this study, we investigated the role of TRF2 in wee1 gene expression. It was found that wee1 mRNA was decreased in hydroxyurea-treated NIH3T3 cells. Mouse wee1 promoter activity was repressed by TRF2 in mouse and chicken cells. Chromatin immunoprecipitation and plasmid immunoprecipitation analyses revealed that TRF2 is recruited to the wee1 promoter in accordance with the transcriptional repression. A mutant TRF2 that lacks TFIIA-binding capacity lost its repressive function. This mutant was less recruited to the wee1 promoter than was the wild-type one, and provided a decline in promoter-recruited TFIIA. Data in this study suggest that transcription repressive activity of TRF2 to wee1 promoter needs association with the promoter and TFIIA.
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Affiliation(s)
- Yuji Tanaka
- Department of Biology, Faculty of Science, Chiba University, 1-33 Yayoicho, Inage-ku, Chiba 263-8522, Japan
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40
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Abstract
In eukaryotes, the core promoter serves as a platform for the assembly of transcription preinitiation complex (PIC) that includes TFIIA, TFIIB, TFIID, TFIIE, TFIIF, TFIIH, and RNA polymerase II (pol II), which function collectively to specify the transcription start site. PIC formation usually begins with TFIID binding to the TATA box, initiator, and/or downstream promoter element (DPE) found in most core promoters, followed by the entry of other general transcription factors (GTFs) and pol II through either a sequential assembly or a preassembled pol II holoenzyme pathway. Formation of this promoter-bound complex is sufficient for a basal level of transcription. However, for activator-dependent (or regulated) transcription, general cofactors are often required to transmit regulatory signals between gene-specific activators and the general transcription machinery. Three classes of general cofactors, including TBP-associated factors (TAFs), Mediator, and upstream stimulatory activity (USA)-derived positive cofactors (PC1/PARP-1, PC2, PC3/DNA topoisomerase I, and PC4) and negative cofactor 1 (NC1/HMGB1), normally function independently or in combination to fine-tune the promoter activity in a gene-specific or cell-type-specific manner. In addition, other cofactors, such as TAF1, BTAF1, and negative cofactor 2 (NC2), can also modulate TBP or TFIID binding to the core promoter. In general, these cofactors are capable of repressing basal transcription when activators are absent and stimulating transcription in the presence of activators. Here we review the roles of these cofactors and GTFs, as well as TBP-related factors (TRFs), TAF-containing complexes (TFTC, SAGA, SLIK/SALSA, STAGA, and PRC1) and TAF variants, in pol II-mediated transcription, with emphasis on the events occurring after the chromatin has been remodeled but prior to the formation of the first phosphodiester bond.
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Affiliation(s)
- Mary C Thomas
- Department of Biochemistry, Case Western Reserve University School of Medicine, Cleveland, OH 44106-4935, USA
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Paul C, Lacroix M, Iankova I, Julien E, Schäfer BW, Labalette C, Wei Y, Le Cam A, Le Cam L, Sardet C. The LIM-only protein FHL2 is a negative regulator of E4F1. Oncogene 2006; 25:5475-84. [PMID: 16652157 DOI: 10.1038/sj.onc.1209567] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
The E1A-targeted transcription factor E4F1 is a key player in the control of mammalian embryonic and somatic cell proliferation and survival. Mouse embryos lacking E4F die at an early developmental stage, whereas enforced expression of E4F1 in various cell lines inhibits cell cycle progression. E4F1-antiproliferative effects have been shown to depend on its capacity to repress transcription and to interact with pRb and p53. Here we show that full-length E4F1 protein (p120(E4F1)) but not its E1A-activated and truncated form (p50(E4F1)), interacts directly in vitro and in vivo with the LIM-only protein FHL2, the product of the p53-responsive gene FHL2/DRAL (downregulated in rhabdomyosarcoma Lim protein). This E4F1-FHL2 association occurs in the nuclear compartment and inhibits the capacity of E4F1 to block cell proliferation. Consistent with this effect, ectopic expression of FHL2 inhibits E4F1 repressive effects on transcription and correlates with a reduction of nuclear E4F1-p53 complexes. Overall, these results suggest that FHL2/DRAL is an inhibitor of E4F1 activity. Finally, we show that endogenous E4F1-FHL2 complexes form in U2OS cells upon UV-light-induced nuclear accumulation of FHL2.
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Affiliation(s)
- C Paul
- Institut de Génétique Moleculaire, UMR 5535/IFR122, CNRS, Montpellier, France
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42
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Kopytova DV, Krasnov AN, Simonova OB, Modestova EA, Korochkin LI, Georgieva SG. Study of the lawc-trf2 gene of Drosophila melanogaster and the protein product of this gene. DOKL BIOCHEM BIOPHYS 2006; 405:380-2. [PMID: 16480132 DOI: 10.1007/s10628-005-0119-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Affiliation(s)
- D V Kopytova
- Institute of Gene Biology, Russian Academy of Sciences, ul. Vavilova 34/5, Moscow, 117334 Russia
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43
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DeJong J. Basic mechanisms for the control of germ cell gene expression. Gene 2006; 366:39-50. [PMID: 16326034 DOI: 10.1016/j.gene.2005.10.012] [Citation(s) in RCA: 51] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2005] [Revised: 09/23/2005] [Accepted: 10/10/2005] [Indexed: 11/17/2022]
Abstract
The patterns of gene expression in spermatocytes and oocytes are quite different from those in somatic cells. The messenger RNAs produced by these cells are not only required to support germ cell development but, in the case of oocytes, they are also used for maturation, fertilization, and early embryogenesis. Recent studies have begun to provide an explanation for how germ-cell-specific programs of gene expression are generated. Part of the answer comes from the observation that germ cells express core promoter-associated regulatory factors that are different from those expressed in somatic cells. These factors supplement or replace their somatic counterparts to direct expression during meiosis and gametogenesis. In addition, germ cell transcription involves the recognition and use of specialized core promoter sequences. Finally, transcription must occur on chromosomal DNA templates that are reorganized into new chromatin-packaging configurations using alternate histone subunits. This article will review recent advances in our understanding of the factors and mechanisms that control transcription in ovary and testis and will discuss models for germ cell gene expression.
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Affiliation(s)
- Jeff DeJong
- Department of Molecular and Cell Biology, University of Texas at Dallas, 2601 N. Floyd Road, Richardson, TX 75080, United States.
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44
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Chong JA, Moran MM, Teichmann M, Kaczmarek JS, Roeder R, Clapham DE. TATA-binding protein (TBP)-like factor (TLF) is a functional regulator of transcription: reciprocal regulation of the neurofibromatosis type 1 and c-fos genes by TLF/TRF2 and TBP. Mol Cell Biol 2005; 25:2632-43. [PMID: 15767669 PMCID: PMC1061635 DOI: 10.1128/mcb.25.7.2632-2643.2005] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The lack of direct targets for TATA-binding protein (TBP)-like factors (TLFs) confounds the understanding of their role in gene expression. Here we report that human TLF (also called TBP-related factor 2 [TRF2]) activates a number of different genes, including the neurofibromatosis type 1 (NF1) gene. The overexpression of TLF increases the amount of NF1 mRNA in cells. In vivo, TLF binds to and upregulates transcription from a fragment of the NF1 promoter. In vitro, purified TLF-TFIIA binds directly to the same NF1 promoter fragment that is required for TLF responsiveness in cells. Furthermore, targeted deletion of TLF in mice reduces NF1 levels. In contrast, TLF inhibits transcription driven by a fragment from the TATA-containing c-fos promoter by sequestering TFIIA. TBP affects the NF1 and c-fos promoters in a manner reciprocal to that of TLF, stimulating the c-fos promoter and inhibiting NF1 transcription. We conclude that TLF is a functional regulator of transcription with targets distinct from those of TBP.
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Affiliation(s)
- Jayhong A Chong
- Department of Cardiology, Children's Hospital, Enders 1309, 320 Longwood Ave., Boston, MA 02115, USA
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45
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Ruan JP, Arhin GK, Ullu E, Tschudi C. Functional characterization of a Trypanosoma brucei TATA-binding protein-related factor points to a universal regulator of transcription in trypanosomes. Mol Cell Biol 2004; 24:9610-8. [PMID: 15485927 PMCID: PMC522245 DOI: 10.1128/mcb.24.21.9610-9618.2004] [Citation(s) in RCA: 48] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Transcriptional mechanisms remain poorly understood in trypanosomatid protozoa. In particular, there is no knowledge about the function of basal transcription factors, and there is an apparent rarity of promoters for protein-coding genes transcribed by RNA polymerase (Pol) II. Here we describe a Trypanosoma brucei factor related to the TATA-binding protein (TBP). Although this TBP-related factor (TBP-related factor 4 [TRF4]) has about 31% identity to the TBP core domain, several key residues involved in TATA box binding are not conserved. Depletion of the T. brucei TRF4 (TbTRF4) by RNA interference revealed an essential role in RNA Pol I, II, and III transcription. Using chromatin immunoprecipitation, we further showed that TRF4 is recruited to the Pol I-transcribed procyclic acidic repetitive genes, Pol II-transcribed spliced leader RNA genes, and Pol III-transcribed U-snRNA and 7SL RNA genes, thus supporting a role for TbTRF4 in transcription performed by all three nuclear RNA polymerases. Finally, a search for TRF4 binding sites in the T. brucei genome led to the identification of such sites in the 3' portion of certain protein-coding genes, indicating a unique aspect of Pol II transcription in these organisms.
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Affiliation(s)
- Jia-Peng Ruan
- Department of Epidemiology and Public Health, Yale University Medical School, 295 Congress Ave., New Haven, CT 06536-0812, USA
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46
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Kieffer-Kwon P, Martianov I, Davidson I. Cell-specific nucleolar localization of TBP-related factor 2. Mol Biol Cell 2004; 15:4356-68. [PMID: 15269281 PMCID: PMC519132 DOI: 10.1091/mbc.e04-02-0138] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2004] [Revised: 06/09/2004] [Accepted: 06/30/2004] [Indexed: 01/05/2023] Open
Abstract
TATA-binding protein (TBP)-related factor 2 (TRF2) is one of four closely related RNA polymerase II transcription factors. We compared the intracellular localizations of TBP and TRF2 during the cell cycle and mitosis in HeLa cells. We show that during interphase, endogenous or exogenously expressed TRF2 is located almost exclusively in the nucleolus in HeLa or Cos cells. TRF2 localization is not affected by stress or mitotic stimuli, but TRF2 is rapidly released from the nucleolus upon inhibition of pol I transcription or treatment by RNase. These results suggest that localization of HeLa TRF2 requires a nucleolar-associated RNA species. In contrast, in 3T3 fibroblast cells, exogenously expressed TRF2 localizes to the nucleoplasm. Constitutive expression of ectopic TRF2 in 3T3 cells leads to a prolonged S phase of the cell cycle and reduced proliferation. Together with previous data, our results highlight the cell-specific localization and functions of TRF2. Furthermore, we show that during cell division, HeLa TRF2 and TBP are localized in the mitotic cytoplasm and TRF2 relocalizes into the nascent nucleoli immediately after mitosis, whereas TBP reassociates with the chromatin. Although partially contradictory results have been reported, our data are consistent with a model where only small proportion of the cellular TBP remains associated with specific promoter loci during mitosis.
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Affiliation(s)
- Philippe Kieffer-Kwon
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, Centre National de la Recherche Scientifique/Institut National de la Santé et de la Recherche Médicale/Université Louis Pasteur, 67404 Illkirch Cédex, France
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47
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Jallow Z, Jacobi UG, Weeks DL, Dawid IB, Veenstra GJC. Specialized and redundant roles of TBP and a vertebrate-specific TBP paralog in embryonic gene regulation in Xenopus. Proc Natl Acad Sci U S A 2004; 101:13525-30. [PMID: 15345743 PMCID: PMC518790 DOI: 10.1073/pnas.0405536101] [Citation(s) in RCA: 82] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The general transcription factor TATA-binding protein (TBP) is a key initiation factor involved in transcription by all three eukaryotic RNA polymerases. In addition, the related metazoan-specific TBP-like factor (TLF/TRF2) is essential for transcription of a distinct subset of genes. Here we characterize the vertebrate-specific TBP-like factor TBP2, using in vitro assays, in vivo antisense knockdown, and mRNA rescue experiments, as well as chromatin immunoprecipitation. We show that TBP2 is recruited to promoters in Xenopus oocytes in the absence of detectable TBP recruitment. Furthermore, TBP2 is essential for gastrulation and for the transcription of a subset of genes during Xenopus embryogenesis. In embryos, TBP2 protein is much less abundant than TBP, and moderate overexpression of TBP2 partially rescues an antisense knockdown of TBP levels and restores transcription of many TBP-dependent genes. TBP2 may be a TBP replacement factor in oocytes, whereas in embryos both TBP and TBP2 are required even though they exhibit partial redundancy and gene selectivity.
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Affiliation(s)
- Zainab Jallow
- Department of Molecular Biology, Radboud University Nijmegen Center for Molecular Life Sciences, 6500 HB Nijmegen, The Netherlands
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48
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Abstract
The TATA binding protein (TBP) is a subunit of several macromolecular complexes required for transcription by the three nuclear RNA polymerases. This observation led to the idea that TBP is a "universal" transcription factor. The discovery of three TBP-related factors and a macromolecular complex which lacks TBP but can support RNA polymerase II transcription in vitro has led to a reappraisal of the universal character of TBP. Several in vivo studies have rather shown that TBP plays a specific role in the activation of a subset of cellular genes controlling the cell cycle. In mammals, the aminoterminal region of TBP plays a highly selective role in the maternal immunotolerance of pregnancy.
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Affiliation(s)
- Irwin Davidson
- Institut de génétique et de biologie moléculaire et cellulaire, 1, rue Laurent Fries, 67404 Illkirch, France.
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Bártfai R, Balduf C, Hilton T, Rathmann Y, Hadzhiev Y, Tora L, Orbán L, Müller F. TBP2, a vertebrate-specific member of the TBP family, is required in embryonic development of zebrafish. Curr Biol 2004; 14:593-8. [PMID: 15062100 DOI: 10.1016/j.cub.2004.03.034] [Citation(s) in RCA: 69] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2003] [Revised: 01/29/2004] [Accepted: 02/13/2004] [Indexed: 11/16/2022]
Abstract
TATA binding protein (TBP) is a key regulator of RNA polymerase transcription. It binds to core promoters, often in large multiprotein complexes, and nucleates RNA polymerase II (Pol II) transcription initiation. In addition to the previously described TBP-like factor present in metazoans (TLF/TRF2/TRP/TLP), we describe a third, vertebrate-specific member of the TBP protein family from zebrafish, called TBP2. Evolutionary conserved TBP2 homologs were also found in human, mouse, frog, and pufferfish. The N-terminal domains of TBP2s are divergent amongst themselves and different from those of TBPs; however, the core domain of TBP2s and TBPs are almost identical. TBP2 binds the TATA box, interacts with TFIIA and TFIIB (similarly to TBP), and can mediate Pol II transcription initiation. However, TBP2 shows contrasting expression patterns in the gonads and during embryonic development in comparison to TBP, suggesting differential function. Knockdown of zebrafish TBP2 results in specific reduction of the protein level, leading to a phenotype, which indicates the requirement of TBP2 for embryonic patterning. The presence of three different TBP family members in vertebrates suggests the existence of developmental stage- and tissue-specific preinitiation complexes with specific requirements for different TBP family members.
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Affiliation(s)
- Richárd Bártfai
- Reproductive Genomics, Temasek Lifesciences Laboratory, 1 Research Link, The National University of Singapore, Singapore 117604, Singapore
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Walker AK, Shi Y, Blackwell TK. An extensive requirement for transcription factor IID-specific TAF-1 in Caenorhabditis elegans embryonic transcription. J Biol Chem 2004; 279:15339-47. [PMID: 14726532 DOI: 10.1074/jbc.m310731200] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The general transcription factor TFIID sets the mRNA start site and consists of TATA-binding protein and associated factors (TAF(II)s), some of which are also present in SPT-ADA-GCN5 (SAGA)-related complexes. In yeast, results of multiple studies indicate that TFIID-specific TAF(II)s are not required for the transcription of most genes, implying that intact TFIID may have a surprisingly specialized role in transcription. Relatively little is known about how TAF(II)s contribute to metazoan transcription in vivo, especially at developmental and tissue-specific genes. Previously, we investigated functions of four shared TFIID/SAGA TAF(II)s in Caenorhabditis elegans. Whereas TAF-4 was required for essentially all embryonic transcription, TAF-5, TAF-9, and TAF-10 were dispensable at multiple developmental and other metazoan-specific promoters. Here we show evidence that in C. elegans embryos transcription of most genes requires TFIID-specific TAF-1. TAF-1 is not as universally required as TAF-4, but it is essential for a greater proportion of transcription than TAF-5, -9, or -10 and is important for transcription of many developmental and other metazoan-specific genes. TAF-2, which binds core promoters with TAF-1, appears to be required for a similarly substantial proportion of transcription. C. elegans TAF-1 overlaps functionally with the coactivator p300/CBP (CBP-1), and at some genes it is required along with the TBP-like protein TLF(TRF2). We conclude that during C. elegans embryogenesis TAF-1 and TFIID have broad roles in transcription and development and that TFIID and TLF may act together at certain promoters. Our findings imply that in metazoans TFIID may be of widespread importance for transcription and for expression of tissue-specific genes.
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Affiliation(s)
- Amy K Walker
- Section of Developmental and Stem Cell Biology, Joslin Diabetes Center, Harvard Medical School, Boston, Massachusetts 02115, USA
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