1
|
Li J, Guo D, Bai J, Wang H, Wang C, Wang Y, Guo X, Xu B, Liu Z. Isolation of the AccCDK8 gene of Apis cerana cerana and its functional analysis under pesticide and heavy metal stress. Biochimie 2024; 218:57-68. [PMID: 37704078 DOI: 10.1016/j.biochi.2023.09.012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2023] [Revised: 07/25/2023] [Accepted: 09/10/2023] [Indexed: 09/15/2023]
Abstract
Environmental pollution has gained negative attention in recent years. The pesticides and heavy metals are top list of environmental toxicants directly endangering the survival and development of Apis cerana cerana. Cyclin-dependent kinases (CDKs) are heteromeric serine/threonine kinases that participate in cell cycle regulation and have a vital role in pesticide and heavy metal stress in Apis cerana cerana. In this experiment, we filtered out CDK8 gene from Apis cerana cerana (AccCDK8) and investigated its functions of pesticide and heavy metals resistance. Sequence analysis indicated that AccCDK8 is highly homologous to multiple CDK8s and contains a highly conserved CDK active site sequence. Phylogenetic analysis showed that AmCDK8 and AccCDK8 were closely related evolutionarily in Apis mellifera. Transcriptome analysis revealed that AccCDK8 expression was differentially affected after exposure to pesticide and heavy metal stresses. This indicates that AccCDK8 has a significant role in the resistance of Apis cerana cerana to pesticide and heavy metal stresses. It has implications for studying the function of CDK in other insects in response to stress.
Collapse
Affiliation(s)
- Jing Li
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Taian, Shandong, 271018, People's Republic of China
| | - Dezheng Guo
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Taian, Shandong, 271018, People's Republic of China
| | - Jinhao Bai
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Taian, Shandong, 271018, People's Republic of China
| | - Hongfang Wang
- College of Animal Science and Technology, Shandong Agricultural University, Taian, Shandong, 271018, People's Republic of China
| | - Chen Wang
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Taian, Shandong, 271018, People's Republic of China
| | - Ying Wang
- College of Animal Science and Technology, Shandong Agricultural University, Taian, Shandong, 271018, People's Republic of China
| | - Xingqi Guo
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Taian, Shandong, 271018, People's Republic of China
| | - Baohua Xu
- College of Animal Science and Technology, Shandong Agricultural University, Taian, Shandong, 271018, People's Republic of China
| | - Zhenguo Liu
- College of Animal Science and Technology, Shandong Agricultural University, Taian, Shandong, 271018, People's Republic of China.
| |
Collapse
|
2
|
Li T, Tang HC, Tsai KL. Unveiling the noncanonical activation mechanism of CDKs: insights from recent structural studies. Front Mol Biosci 2023; 10:1290631. [PMID: 38028546 PMCID: PMC10666765 DOI: 10.3389/fmolb.2023.1290631] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2023] [Accepted: 10/27/2023] [Indexed: 12/01/2023] Open
Abstract
The Cyclin-dependent kinases (CDKs) play crucial roles in a range of essential cellular processes. While the classical two-step activation mechanism is generally applicable to cell cycle-related CDKs, both CDK7 and CDK8, involved in transcriptional regulation, adopt distinct mechanisms for kinase activation. In both cases, binding to their respective cyclin partners results in only partial activity, while their full activation requires the presence of an additional subunit. Recent structural studies of these two noncanonical kinases have provided unprecedented insights into their activation mechanisms, enabling us to understand how the third subunit coordinates the T-loop stabilization and enhances kinase activity. In this review, we summarize the structure and function of CDK7 and CDK8 within their respective functional complexes, while also describing their noncanonical activation mechanisms. These insights open new avenues for targeted drug discovery and potential therapeutic interventions in various diseases related to CDK7 and CDK8.
Collapse
Affiliation(s)
- Tao Li
- Department of Biochemistry and Molecular Biology, McGovern Medical School, University of Texas Health Science Center at Houston, Houston, TX, United States
| | - Hui-Chi Tang
- Department of Biochemistry and Molecular Biology, McGovern Medical School, University of Texas Health Science Center at Houston, Houston, TX, United States
| | - Kuang-Lei Tsai
- Department of Biochemistry and Molecular Biology, McGovern Medical School, University of Texas Health Science Center at Houston, Houston, TX, United States
- MD Anderson Cancer Center UTHealth Graduate School of Biomedical Sciences, Houston, TX, United States
| |
Collapse
|
3
|
Pluta AJ, Studniarek C, Murphy S, Norbury CJ. Cyclin-dependent kinases: Masters of the eukaryotic universe. WILEY INTERDISCIPLINARY REVIEWS. RNA 2023; 15:e1816. [PMID: 37718413 PMCID: PMC10909489 DOI: 10.1002/wrna.1816] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/05/2023] [Revised: 07/21/2023] [Accepted: 08/03/2023] [Indexed: 09/19/2023]
Abstract
A family of structurally related cyclin-dependent protein kinases (CDKs) drives many aspects of eukaryotic cell function. Much of the literature in this area has considered individual members of this family to act primarily either as regulators of the cell cycle, the context in which CDKs were first discovered, or as regulators of transcription. Until recently, CDK7 was the only clear example of a CDK that functions in both processes. However, new data points to several "cell-cycle" CDKs having important roles in transcription and some "transcriptional" CDKs having cell cycle-related targets. For example, novel functions in transcription have been demonstrated for the archetypal cell cycle regulator CDK1. The increasing evidence of the overlap between these two CDK types suggests that they might play a critical role in coordinating the two processes. Here we review the canonical functions of cell-cycle and transcriptional CDKs, and provide an update on how these kinases collaborate to perform important cellular functions. We also provide a brief overview of how dysregulation of CDKs contributes to carcinogenesis, and possible treatment avenues. This article is categorized under: RNA Interactions with Proteins and Other Molecules > RNA-Protein Complexes RNA Processing > 3' End Processing RNA Processing > Splicing Regulation/Alternative Splicing.
Collapse
Affiliation(s)
| | | | - Shona Murphy
- Sir William Dunn School of PathologyUniversity of OxfordOxfordUK
| | - Chris J. Norbury
- Sir William Dunn School of PathologyUniversity of OxfordOxfordUK
| |
Collapse
|
4
|
Lambert É, Puwakdandawa K, Tao YF, Robert F. From structure to molecular condensates: emerging mechanisms for Mediator function. FEBS J 2023; 290:286-309. [PMID: 34698446 DOI: 10.1111/febs.16250] [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: 08/13/2021] [Revised: 10/15/2021] [Accepted: 10/25/2021] [Indexed: 02/05/2023]
Abstract
Mediator is a large modular protein assembly whose function as a coactivator of transcription is conserved in all eukaryotes. The Mediator complex can integrate and relay signals from gene-specific activators bound at enhancers to activate the general transcription machinery located at promoters. It has thus been described as a bridge between these elements during initiation of transcription. Here, we review recent studies on Mediator relating to its structure, gene specificity and general requirement, roles in chromatin architecture as well as novel concepts involving phase separation and transcriptional bursting. We revisit the mechanism of action of Mediator and ultimately put forward models for its mode of action in gene activation.
Collapse
Affiliation(s)
- Élie Lambert
- Institut de recherches cliniques de Montréal, Canada
| | | | - Yi Fei Tao
- Institut de recherches cliniques de Montréal, Canada
| | - François Robert
- Institut de recherches cliniques de Montréal, Canada.,Département de Médecine, Faculté de Médecine, Université de Montréal, Canada
| |
Collapse
|
5
|
Agrawal R, Jiří F, Thakur JK. The kinase module of the Mediator complex: an important signalling processor for the development and survival of plants. JOURNAL OF EXPERIMENTAL BOTANY 2021; 72:224-240. [PMID: 32945869 DOI: 10.1093/jxb/eraa439] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/16/2020] [Accepted: 09/16/2020] [Indexed: 05/06/2023]
Abstract
Mediator, a multisubunit protein complex, is a signal processor that conveys regulatory information from transcription factors to RNA polymerase II and therefore plays an important role in the regulation of gene expression. This megadalton complex comprises four modules, namely, the head, middle, tail, and kinase modules. The first three modules form the core part of the complex, whereas association of the kinase module is facultative. The kinase module is able to alter the function of Mediator and has been established as a major transcriptional regulator of numerous developmental and biochemical processes. The kinase module consists of MED12, MED13, CycC, and kinase CDK8. Upon association with Mediator, the kinase module can alter its structure and function dramatically. In the past decade, research has established that the kinase module is very important for plant growth and development, and in the fight against biotic and abiotic challenges. However, there has been no comprehensive review discussing these findings in detail and depth. In this review, we survey the regulation of kinase module subunits and highlight their many functions in plants. Coordination between the subunits to process different signals for optimum plant growth and development is also discussed.
Collapse
Affiliation(s)
- Rekha Agrawal
- Plant Mediator Lab, National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi, India
| | - Fajkus Jiří
- Mendel Centre for Plant Genomics and Proteomics, Central European Institute of Technology, Masaryk University, Brno, Czech Republic
| | - Jitendra K Thakur
- Plant Mediator Lab, National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi, India
| |
Collapse
|
6
|
Li YC, Chao TC, Kim HJ, Cholko T, Chen SF, Li G, Snyder L, Nakanishi K, Chang CE, Murakami K, Garcia BA, Boyer TG, Tsai KL. Structure and noncanonical Cdk8 activation mechanism within an Argonaute-containing Mediator kinase module. SCIENCE ADVANCES 2021; 7:eabd4484. [PMID: 33523904 PMCID: PMC7810384 DOI: 10.1126/sciadv.abd4484] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/22/2020] [Accepted: 11/25/2020] [Indexed: 05/02/2023]
Abstract
The Cdk8 kinase module (CKM) in Mediator, comprising Med13, Med12, CycC, and Cdk8, regulates RNA polymerase II transcription through kinase-dependent and -independent functions. Numerous pathogenic mutations causative for neurodevelopmental disorders and cancer congregate in CKM subunits. However, the structure of the intact CKM and the mechanism by which Cdk8 is non-canonically activated and functionally affected by oncogenic CKM alterations are poorly understood. Here, we report a cryo-electron microscopy structure of Saccharomyces cerevisiae CKM that redefines prior CKM structural models and explains the mechanism of Med12-dependent Cdk8 activation. Med12 interacts extensively with CycC and activates Cdk8 by stabilizing its activation (T-)loop through conserved Med12 residues recurrently mutated in human tumors. Unexpectedly, Med13 has a characteristic Argonaute-like bi-lobal architecture. These findings not only provide a structural basis for understanding CKM function and pathological dysfunction, but also further impute a previously unknown regulatory mechanism of Mediator in transcriptional modulation through its Med13 Argonaute-like features.
Collapse
Affiliation(s)
- Yi-Chuan Li
- Department of Biochemistry and Molecular Biology, McGovern Medical School, University of Texas Health Science Center at Houston, Houston, TX, USA
| | - Ti-Chun Chao
- Department of Biochemistry and Molecular Biology, McGovern Medical School, University of Texas Health Science Center at Houston, Houston, TX, USA
| | - Hee Jong Kim
- Biochemistry and Molecular Biophysics Graduate Group, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Timothy Cholko
- Department of Chemistry, University of California, Riverside, CA, USA
| | - Shin-Fu Chen
- Department of Biochemistry and Molecular Biology, McGovern Medical School, University of Texas Health Science Center at Houston, Houston, TX, USA
| | - Guojie Li
- Department of Biochemistry and Molecular Biology, McGovern Medical School, University of Texas Health Science Center at Houston, Houston, TX, USA
| | - Laura Snyder
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Kotaro Nakanishi
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH, USA
| | - Chia-En Chang
- Department of Chemistry, University of California, Riverside, CA, USA
| | - Kenji Murakami
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Benjamin A Garcia
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Epigenetics Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Thomas G Boyer
- Department of Molecular Medicine, University of Texas Health Science Center at San Antonio, San Antonio, TX, USA.
| | - Kuang-Lei Tsai
- Department of Biochemistry and Molecular Biology, McGovern Medical School, University of Texas Health Science Center at Houston, Houston, TX, USA.
- MD Anderson Cancer Center UTHealth Graduate School of Biomedical Sciences, Houston, TX, USA
| |
Collapse
|
7
|
Liu Q, Bischof S, Harris CJ, Zhong Z, Zhan L, Nguyen C, Rashoff A, Barshop WD, Sun F, Feng S, Potok M, Gallego-Bartolome J, Zhai J, Wohlschlegel JA, Carey MF, Long JA, Jacobsen SE. The characterization of Mediator 12 and 13 as conditional positive gene regulators in Arabidopsis. Nat Commun 2020; 11:2798. [PMID: 32493925 PMCID: PMC7271234 DOI: 10.1038/s41467-020-16651-5] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2020] [Accepted: 05/14/2020] [Indexed: 12/18/2022] Open
Abstract
Mediator 12 (MED12) and MED13 are components of the Mediator multi-protein complex, that facilitates the initial steps of gene transcription. Here, in an Arabidopsis mutant screen, we identify MED12 and MED13 as positive gene regulators, both of which contribute broadly to morc1 de-repressed gene expression. Both MED12 and MED13 are preferentially required for the expression of genes depleted in active chromatin marks, a chromatin signature shared with morc1 re-activated loci. We further discover that MED12 tends to interact with genes that are responsive to environmental stimuli, including light and radiation. We demonstrate that light-induced transient gene expression depends on MED12, and is accompanied by a concomitant increase in MED12 enrichment during induction. In contrast, the steady-state expression level of these genes show little dependence on MED12, suggesting that MED12 is primarily required to aid the expression of genes in transition from less-active to more active states. Mediator is a multiprotein complex required to activate gene transcription by RNAPII. Here, the authors report that MED12 and MED13 are conditional positive regulators that facilitate the expression of genes depleted in active chromatin marks and the induction of gene expression in response to environmental stimuli in Arabidopsis.
Collapse
Affiliation(s)
- Qikun Liu
- School of Advanced Agricultural Sciences, Peking University, 100871, Beijing, China. .,Department of Molecular, Cell and Developmental Biology, University of California at Los Angeles, Los Angeles, CA, 90095, USA.
| | - Sylvain Bischof
- Department of Molecular, Cell and Developmental Biology, University of California at Los Angeles, Los Angeles, CA, 90095, USA.,Department of Plant and Microbial Biology and Zurich-Basel Plant Science Center, University of Zurich, Zollikerstrasse 107, 8008, Zurich, Switzerland
| | - C Jake Harris
- Department of Molecular, Cell and Developmental Biology, University of California at Los Angeles, Los Angeles, CA, 90095, USA
| | - Zhenhui Zhong
- Department of Molecular, Cell and Developmental Biology, University of California at Los Angeles, Los Angeles, CA, 90095, USA.,Basic Forestry and Proteomics Center, Fujian Agriculture and Forestry University, 350002, Fuzhou, China
| | - Lingyu Zhan
- Department of Molecular, Cell and Developmental Biology, University of California at Los Angeles, Los Angeles, CA, 90095, USA
| | - Calvin Nguyen
- Department of Molecular, Cell and Developmental Biology, University of California at Los Angeles, Los Angeles, CA, 90095, USA
| | - Andrew Rashoff
- Department of Molecular, Cell and Developmental Biology, University of California at Los Angeles, Los Angeles, CA, 90095, USA
| | - William D Barshop
- Department of Biological Chemistry, David Geffen School of Medicine, University of California at Los Angeles, Los Angeles, CA, 90095, USA
| | - Fei Sun
- Department of Biological Chemistry, David Geffen School of Medicine, University of California at Los Angeles, Los Angeles, CA, 90095, USA
| | - Suhua Feng
- Department of Molecular, Cell and Developmental Biology, University of California at Los Angeles, Los Angeles, CA, 90095, USA
| | - Magdalena Potok
- Department of Molecular, Cell and Developmental Biology, University of California at Los Angeles, Los Angeles, CA, 90095, USA
| | - Javier Gallego-Bartolome
- Department of Molecular, Cell and Developmental Biology, University of California at Los Angeles, Los Angeles, CA, 90095, USA
| | - Jixian Zhai
- Institute of Plant and Food Science, Department of Biology, Southern University of Science and Technology, Shenzhen, China
| | - James A Wohlschlegel
- Department of Biological Chemistry, David Geffen School of Medicine, University of California at Los Angeles, Los Angeles, CA, 90095, USA
| | - Michael F Carey
- Department of Biological Chemistry, David Geffen School of Medicine, University of California at Los Angeles, Los Angeles, CA, 90095, USA
| | - Jeffrey A Long
- Department of Molecular, Cell and Developmental Biology, University of California at Los Angeles, Los Angeles, CA, 90095, USA
| | - Steven E Jacobsen
- Department of Molecular, Cell and Developmental Biology, University of California at Los Angeles, Los Angeles, CA, 90095, USA. .,Howard Hughes Medical Institute, University of California at Los Angeles, Los Angeles, CA, 90095, USA.
| |
Collapse
|
8
|
Wang X, Mittal P, Castro CA, Rajkovic G, Rajkovic A. Med12 regulates ovarian steroidogenesis, uterine development and maternal effects in the mammalian egg. Biol Reprod 2019; 97:822-834. [PMID: 29126187 DOI: 10.1093/biolre/iox143] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2017] [Accepted: 11/07/2017] [Indexed: 12/21/2022] Open
Abstract
The transcriptional factor MED12 is part of the essential mediator transcriptional complex that acts as a transcriptional coactivator in all eukaryotes. Missense gain-of-function mutations in human MED12 are associated with uterine leiomyomas, yet the role of MED12 deficiency in tumorigenesis and reproductive biology has not been fully explored. We generated a Med12 reproductive conditional knockout mouse model to evaluate its role in uterine mesenchyme, granulosa cells, and oocytes. Mice heterozygous for Med12 deficiency in granulosa cells and uterus (Med12fl/+ Amhr2-Cre) were subfertile, while mice homozygous for Med12 deficiency in granulosa cells and uterus (Med12fl/fl Amhr2-Cre) were infertile. Morphological and histological analysis of the Med12fl/fl Amhr2-Cre reproductive tract revealed atrophic uteri and hyperchromatic granulosa cells with disrupted expression of Lhcgr, Esr1, and Esr2. Med12fl/fl Amhr2-Cre mice estrous cycle was disrupted, and serum analysis showed blunted rise in estradiol in response to pregnant mare serum gonadotropin. Uterine atrophy was partially rescued by exogenous steroid supplementation with dysregulation of Notch1 and Smo expression in steroid supplemented Med12fl/fl Amhr2-Cre uteri, indicating intrinsic uterine defects. Oocyte-specific ablation of Med12 caused infertility without disrupting normal folliculogenesis and ovulation, consistent with maternal effects of Med12 in early embryo development. These results show the critical importance of Med12 in reproductive tract development and that Med12 loss of function does not cause tumorigenesis in reproductive tissues.
Collapse
Affiliation(s)
- Xinye Wang
- Tsinghua MD Program, Tsinghua University School of Medicine, Beijing, China.,Department of Obstetrics, Gynecology and Reproductive Sciences, Magee-Womens Research Institute, Pittsburgh, Pennsylvania, USA
| | - Priya Mittal
- Department of Human Genetics, Graduate School of Public Health, University of Pittsburgh, Pittsburgh, Pennsylvania, USA.,Department of Oncology, St. Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - Carlos A Castro
- Department of Obstetrics, Gynecology and Reproductive Sciences, Magee-Womens Research Institute, Pittsburgh, Pennsylvania, USA
| | - Gabriel Rajkovic
- Department of Obstetrics, Gynecology and Reproductive Sciences, Magee-Womens Research Institute, Pittsburgh, Pennsylvania, USA
| | - Aleksandar Rajkovic
- Department of Obstetrics, Gynecology and Reproductive Sciences, Magee-Womens Research Institute, Pittsburgh, Pennsylvania, USA.,Department of Human Genetics, Graduate School of Public Health, University of Pittsburgh, Pittsburgh, Pennsylvania, USA.,Department of Pathology, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| |
Collapse
|
9
|
Zeng Z, Wu J, Kovalchuk A, Raffaello T, Wen Z, Liu M, Asiegbu FO. Genome-wide DNA methylation and transcriptomic profiles in the lifestyle strategies and asexual development of the forest fungal pathogen Heterobasidion parviporum. Epigenetics 2019; 14:16-40. [PMID: 30633603 PMCID: PMC6380393 DOI: 10.1080/15592294.2018.1564426] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2018] [Revised: 12/03/2018] [Accepted: 12/20/2018] [Indexed: 12/18/2022] Open
Abstract
Heterobasidion parviporum is the most devastating fungal pathogen of conifer forests in Northern Europe. The fungus has dual life strategies, necrotrophy on living trees and saprotrophy on dead woods. DNA cytosine methylation is an important epigenetic modification in eukaryotic organisms. Our presumption is that the lifestyle transition and asexual development in H. parviporum could be driven by epigenetic effects. Involvements of DNA methylation in the regulation of aforementioned processes have never been studied thus far. RNA-seq identified lists of highly induced genes enriched in carbohydrate-active enzymes during necrotrophic interaction with host trees and saprotrophic sawdust growth. It also highlighted signaling- and transcription factor-related genes potentially associated with the transition of saprotrophic to necrotrophic lifestyle and groups of primary cellular activities throughout asexual development. Whole-genome bisulfite sequencing revealed that DNA methylation displayed pronounced preference in CpG dinucleotide context across the genome and mostly targeted transposable element (TE)-rich regions. TE methylation level demonstrated a strong negative correlation with TE expression, reinforcing the protective function of DNA methylation in fungal genome stability. Small groups of genes putatively subject to methylation transcriptional regulation in response to saprotrophic and necrotrophic growth in comparison with free-living mycelia were also explored. Our study reported on the first methylome map of a forest pathogen. Analysis of transcriptome and methylome variations associated with asexual development and different lifestyle strategies provided further understanding of basic biological processes in H. parviporum. More importantly, our work raised additional potential roles of DNA methylation in fungi apart from controlling the proliferation of TEs.
Collapse
Affiliation(s)
- Zhen Zeng
- Department of Forest Sciences, University of Helsinki, Helsinki, Finland
| | - Jiayao Wu
- Department of Forest Sciences, University of Helsinki, Helsinki, Finland
| | - Andriy Kovalchuk
- Department of Forest Sciences, University of Helsinki, Helsinki, Finland
| | - Tommaso Raffaello
- Department of Forest Sciences, University of Helsinki, Helsinki, Finland
| | - Zilan Wen
- Department of Forest Sciences, University of Helsinki, Helsinki, Finland
| | - Mengxia Liu
- Department of Forest Sciences, University of Helsinki, Helsinki, Finland
| | - Fred O. Asiegbu
- Department of Forest Sciences, University of Helsinki, Helsinki, Finland
| |
Collapse
|
10
|
CDK8 regulates the angiogenesis of pancreatic cancer cells in part via the CDK8-β-catenin-KLF2 signal axis. Exp Cell Res 2018; 369:304-315. [PMID: 29856990 DOI: 10.1016/j.yexcr.2018.05.033] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2018] [Revised: 05/18/2018] [Accepted: 05/28/2018] [Indexed: 11/20/2022]
Abstract
BACKGROUND CDK8 is associated with the transcriptional Mediator complex and has been shown to regulate several transcription factors implicated in cancer. As a pancreatic cancer oncogene, the role of CDK8 in cancer angiogenesis remains unclear. Here, we investigated the contribution of CDK8 in pancreatic cancer angiogenesis and examined the underlying molecular mechanisms. METHODS CDK8 expression was evaluated via immunohistochemistry, western blotting, and qRT-PCR in relation to the clinicopathological characteristics of pancreatic cancer patients. The effects of silencing or overexpressing CDK8 on cancer angiogenesis were assessed in vitro by western blotting assays in pancreatic cancer cell lines and in vivo with nude mice xenograft models. RESULTS Compared with adjacent normal tissues, pancreatic cancer tissues showed upregulation of CDK8 expression, which was inversely correlated with T grade, liver metastasis, size, lymph node metastasis and poor survival. CDK8 overexpression promoted angiogenesis in pancreatic cancer via activation of the CDK8-β-catenin-KLF2 signaling axis, as demonstrated by the upregulation and downregulation of signals representing the rate-limiting steps in angiogenesis. Silencing CDK8 inhibited angiogenesis in pancreatic cancer in vitro. Additionally, these results were confirmed in nude mice xenograft models in vivo. CONCLUSIONS CDK8 promotes angiogenesis in pancreatic cancer via activation of the CDK8-β-catenin-KLF2 signaling axis, thus providing valid targets for the treatment of pancreatic cancer.
Collapse
|
11
|
Asadollahi R, Zweier M, Gogoll L, Schiffmann R, Sticht H, Steindl K, Rauch A. Genotype-phenotype evaluation of MED13L defects in the light of a novel truncating and a recurrent missense mutation. Eur J Med Genet 2017. [PMID: 28645799 DOI: 10.1016/j.ejmg.2017.06.004] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
A decade after the designation of MED13L as a gene and its link to intellectual disability (ID) and dextro-looped transposition of great arteries in 2003, we previously described a recognizable syndrome due to MED13L haploinsufficiency. Subsequent reports of 22 further patients diagnosed by genome-wide testing further delineated the syndrome with expansion of the phenotypic spectrum and showed reduced penetrance for congenital heart defects. We now report two novel patients identified by whole exome sequencing, one with a de novo MED13L truncating mutation and the other with a de novo missense mutation. The first patient indicates some facial resemblance to Kleefstra syndrome as a novel differential diagnosis, and the second patient shows, for the first time, recurrence of a MED13L missense mutation (p.(Asp860Gly)). Notably, our in silico modelling predicted this missense mutation to decrease the stability of an alpha-helix and thereby affecting the MED13L secondary structure, while the majority of published missense mutations remain variants of uncertain significance. Review of the reported patients with MED13L haploinsufficiency indicates moderate to severe ID and facial anomalies in all patients, as well as severe speech delay and muscular hypotonia in the majority. Further common signs include abnormal MRI findings of myelination defects and abnormal corpus callosum, ataxia and coordination problems, autistic features, seizures/abnormal EEG, or congenital heart defects, present in about 20-50% of the patients. With reference to facial anomalies, the majority of patients were reported to show broad/prominent forehead, low set ears, bitemporal narrowing, upslanting palpebral fissures, depressed/flat nasal bridge, bulbous nose, and abnormal chin, but macroglossia and horizontal eyebrows were also observed in ∼30%. The latter are especially important in the differential diagnosis of 1p36 deletion and Kleefstra syndromes, while the more common facial gestalt shows some resemblance to 22q11.2 deletion syndrome. Despite the fact that MED13L was found to be one of the most common ID genes in the Deciphering Developmental Disorders Study, further detailed patient descriptions are needed to explore the full clinical spectrum, potential genotype-phenotype correlations, as well as the role of missense mutations and potential mutational hotspots along the gene.
Collapse
Affiliation(s)
- Reza Asadollahi
- Institute of Medical Genetics, University of Zurich, Schlieren-Zurich, Switzerland
| | - Markus Zweier
- Institute of Medical Genetics, University of Zurich, Schlieren-Zurich, Switzerland
| | - Laura Gogoll
- Institute of Medical Genetics, University of Zurich, Schlieren-Zurich, Switzerland
| | - Raphael Schiffmann
- Institute of Metabolic Disease, Baylor Scott & White Research Institute, Dallas, TX, USA
| | - Heinrich Sticht
- Institute of Biochemistry, University of Erlangen-Nuremberg, Erlangen, Germany
| | - Katharina Steindl
- Institute of Medical Genetics, University of Zurich, Schlieren-Zurich, Switzerland
| | - Anita Rauch
- Institute of Medical Genetics, University of Zurich, Schlieren-Zurich, Switzerland; Neuroscience Center Zurich, University of Zurich, Zurich, Switzerland; Zurich Center of Integrative Human Physiology, University of Zurich, Zurich, Switzerland.
| |
Collapse
|
12
|
Banyai G, Szilagyi Z, Baraznenok V, Khorosjutina O, Gustafsson CM. Cyclin C influences the timing of mitosis in fission yeast. Mol Biol Cell 2017; 28:1738-1744. [PMID: 28515143 PMCID: PMC5491182 DOI: 10.1091/mbc.e16-11-0787] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2016] [Revised: 05/04/2017] [Accepted: 05/09/2017] [Indexed: 12/25/2022] Open
Abstract
A number of genes are periodically transcribed during cell cycle progression. How the periodic transcription patterns of these genes are achieved is not completely understood. Cyclin C, a component of Mediator, plays an essential role in periodic transcription and the timing of cell cycle progression. The multiprotein Mediator complex is required for the regulated transcription of nearly all RNA polymerase II–dependent genes. Mediator contains the Cdk8 regulatory subcomplex, which directs periodic transcription and influences cell cycle progression in fission yeast. Here we investigate the role of CycC, the cognate cyclin partner of Cdk8, in cell cycle control. Previous reports suggested that CycC interacts with other cellular Cdks, but a fusion of CycC to Cdk8 reported here did not cause any obvious cell cycle phenotypes. We find that Cdk8 and CycC interactions are stabilized within the Mediator complex and the activity of Cdk8-CycC is regulated by other Mediator components. Analysis of a mutant yeast strain reveals that CycC, together with Cdk8, primarily affects M-phase progression but mutations that release Cdk8 from CycC control also affect timing of entry into S phase.
Collapse
Affiliation(s)
- Gabor Banyai
- Institute of Biomedicine, University of Gothenburg, SE-40530 Gothenburg, Sweden
| | - Zsolt Szilagyi
- Institute of Biomedicine, University of Gothenburg, SE-40530 Gothenburg, Sweden
| | | | - Olga Khorosjutina
- Department of Biosciences and Nutrition, Karolinska Institutet, SE-17177 Stockholm, Sweden
| | - Claes M Gustafsson
- Institute of Biomedicine, University of Gothenburg, SE-40530 Gothenburg, Sweden
| |
Collapse
|
13
|
Mittal P, Wang X, Rajkovic A. The Role of Mediator Complex Subunit 12 in Leiomyoma Biology. CURRENT GENETIC MEDICINE REPORTS 2016. [DOI: 10.1007/s40142-016-0106-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
|
14
|
Jeronimo C, Langelier MF, Bataille AR, Pascal JM, Pugh BF, Robert F. Tail and Kinase Modules Differently Regulate Core Mediator Recruitment and Function In Vivo. Mol Cell 2016; 64:455-466. [PMID: 27773677 DOI: 10.1016/j.molcel.2016.09.002] [Citation(s) in RCA: 103] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2016] [Revised: 07/22/2016] [Accepted: 08/31/2016] [Indexed: 01/09/2023]
Abstract
Mediator is a highly conserved transcriptional coactivator organized into four modules, namely Tail, Middle, Head, and Kinase (CKM). Previous work suggests regulatory roles for Tail and CKM, but an integrated model for these activities is lacking. Here, we analyzed the genome-wide distribution of Mediator subunits in wild-type and mutant yeast cells in which RNA polymerase II promoter escape is blocked, allowing detection of transient Mediator forms. We found that although all modules are recruited to upstream activated regions (UAS), assembly of Mediator within the pre-initiation complex is accompanied by the release of CKM. Interestingly, our data show that CKM regulates Mediator-UAS interaction rather than Mediator-promoter association. In addition, although Tail is required for Mediator recruitment to UAS, Tailless Mediator nevertheless interacts with core promoters. Collectively, our data suggest that the essential function of Mediator is mediated by Head and Middle at core promoters, while Tail and CKM play regulatory roles.
Collapse
Affiliation(s)
- Célia Jeronimo
- Institut de recherches cliniques de Montréal, 110 Avenue des Pins Ouest, Montréal, QC H2W 1R7, Canada
| | - Marie-France Langelier
- Département de Biochimie et Médecine Moléculaire, Faculté de Médecine, Université de Montréal, 2900 Boulevard Edouard-Montpetit, Montréal, QC H3T 1J4, Canada
| | - Alain R Bataille
- Center for Eukaryotic Gene Regulation, Department of Biochemistry and Molecular Biology, The Pennsylvania State University, 456A North Frear Laboratory, University Park, PA 16802, USA
| | - John M Pascal
- Département de Biochimie et Médecine Moléculaire, Faculté de Médecine, Université de Montréal, 2900 Boulevard Edouard-Montpetit, Montréal, QC H3T 1J4, Canada
| | - B Franklin Pugh
- Center for Eukaryotic Gene Regulation, Department of Biochemistry and Molecular Biology, The Pennsylvania State University, 456A North Frear Laboratory, University Park, PA 16802, USA
| | - François Robert
- Institut de recherches cliniques de Montréal, 110 Avenue des Pins Ouest, Montréal, QC H2W 1R7, Canada; Département de Médecine, Faculté de Médecine, Université de Montréal, 2900 Boulevard Edouard-Montpetit, Montréal, QC H3T 1J4, Canada.
| |
Collapse
|
15
|
Buendía-Monreal M, Gillmor CS. Mediator: A key regulator of plant development. Dev Biol 2016; 419:7-18. [PMID: 27287881 DOI: 10.1016/j.ydbio.2016.06.009] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2016] [Revised: 06/01/2016] [Accepted: 06/06/2016] [Indexed: 10/21/2022]
Abstract
Mediator is a multiprotein complex that regulates transcription at the level of RNA pol II assembly, as well as through regulation of chromatin architecture, RNA processing and recruitment of epigenetic marks. Though its modular structure is conserved in eukaryotes, its subunit composition has diverged during evolution and varies in response to environmental and tissue-specific inputs, suggesting different functions for each subunit and/or Mediator conformation. In animals, Mediator has been implicated in the control of differentiation and morphogenesis through modulation of numerous signaling pathways. In plants, studies have revealed roles for Mediator in regulation of cell division, cell fate and organogenesis, as well as developmental timing and hormone responses. We begin this review with an overview of biochemical mechanisms of yeast and animal Mediator that are likely to be conserved in all eukaryotes, as well as a brief discussion of the role of Mediator in animal development. We then present a comprehensive review of studies of the role of Mediator in plant development. Finally, we point to important questions for future research on the role of Mediator as a master coordinator of development.
Collapse
Affiliation(s)
- Manuel Buendía-Monreal
- Laboratorio Nacional de Genómica para la Biodiversidad (Langebio), Unidad de Genómica Avanzada, CINVESTAV-IPN, Irapuato, Guanajuato, Mexico
| | - C Stewart Gillmor
- Laboratorio Nacional de Genómica para la Biodiversidad (Langebio), Unidad de Genómica Avanzada, CINVESTAV-IPN, Irapuato, Guanajuato, Mexico.
| |
Collapse
|
16
|
Humbert A, Bovier E, Sellem CH, Sainsard-Chanet A. Deletion of the MED13 and CDK8 subunits of the Mediator improves the phenotype of a long-lived respiratory deficient mutant of Podospora anserina. Fungal Genet Biol 2015; 82:228-37. [PMID: 26231682 DOI: 10.1016/j.fgb.2015.07.010] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2015] [Revised: 07/27/2015] [Accepted: 07/28/2015] [Indexed: 01/18/2023]
Abstract
In Podospora anserina, the loss of function of the cytochrome segment of the mitochondrial respiratory chain is viable. This is due to the presence in this organism, as in most filamentous fungi, of an alternative respiratory oxidase (AOX) that provides a bypass to the cytochrome pathway. However mutants lacking a functional cytochrome pathway present multiple phenotypes including poorly colored thin mycelium and slow growth. In a large genetic screen based on the improvement of these phenotypes, we isolated a large number of independent suppressor mutations. Most of them led to the constitutive overexpression of the aox gene. In this study, we characterize a new suppressor mutation that does not affect the production of AOX. It is a loss-of-function mutation in the gene encoding the MED13 subunit of the kinase module of the Mediator complex. Inactivation of the cdk8 gene encoding another subunit of the same module also results in partial suppression of a cytochrome-deficient mutant. Analysis of strains lacking the MED13 or CDK8 subunits points to the importance of these subunits as regulators involved in diverse physiological processes such as growth, longevity and sexual development. Interestingly, transcriptional analyses indicate that in P. anserina, loss of the respiratory cytochrome pathway results in the up-regulation of glycolysis-related genes revealing a new type of retrograde regulation. The loss of MED13 augments the up-regulation of some of these genes.
Collapse
Affiliation(s)
- Adeline Humbert
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Sud, Avenue de la Terrasse, 91198 Gif-sur-Yvette cedex, France
| | - Elodie Bovier
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Sud, Avenue de la Terrasse, 91198 Gif-sur-Yvette cedex, France
| | - Carole H Sellem
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Sud, Avenue de la Terrasse, 91198 Gif-sur-Yvette cedex, France
| | - Annie Sainsard-Chanet
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Sud, Avenue de la Terrasse, 91198 Gif-sur-Yvette cedex, France.
| |
Collapse
|
17
|
Samanta S, Thakur JK. Importance of Mediator complex in the regulation and integration of diverse signaling pathways in plants. FRONTIERS IN PLANT SCIENCE 2015; 6:757. [PMID: 26442070 PMCID: PMC4584954 DOI: 10.3389/fpls.2015.00757] [Citation(s) in RCA: 69] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/26/2015] [Accepted: 09/04/2015] [Indexed: 05/19/2023]
Abstract
Basic transcriptional machinery in eukaryotes is assisted by a number of cofactors, which either increase or decrease the rate of transcription. Mediator complex is one such cofactor, and recently has drawn a lot of interest because of its integrative power to converge different signaling pathways before channeling the transcription instructions to the RNA polymerase II machinery. Like yeast and metazoans, plants do possess the Mediator complex across the kingdom, and its isolation and subunit analyses have been reported from the model plant, Arabidopsis. Genetic, and molecular analyses have unraveled important regulatory roles of Mediator subunits at every stage of plant life cycle starting from flowering to embryo and organ development, to even size determination. It also contributes immensely to the survival of plants against different environmental vagaries by the timely activation of its resistance mechanisms. Here, we have provided an overview of plant Mediator complex starting from its discovery to regulation of stoichiometry of its subunits. We have also reviewed involvement of different Mediator subunits in different processes and pathways including defense response pathways evoked by diverse biotic cues. Wherever possible, attempts have been made to provide mechanistic insight of Mediator's involvement in these processes.
Collapse
Affiliation(s)
| | - Jitendra K. Thakur
- *Correspondence: Jitendra K. Thakur, Plant Mediator Lab, National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi-110067, India
| |
Collapse
|
18
|
Gillmor CS, Silva-Ortega CO, Willmann MR, Buendía-Monreal M, Poethig RS. The Arabidopsis Mediator CDK8 module genes CCT (MED12) and GCT (MED13) are global regulators of developmental phase transitions. Development 2014; 141:4580-9. [PMID: 25377553 DOI: 10.1242/dev.111229] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
Temporal coordination of developmental programs is necessary for normal ontogeny, but the mechanism by which this is accomplished is still poorly understood. We have previously shown that two components of the Mediator CDK8 module encoded by CENTER CITY (CCT; Arabidopsis MED12) and GRAND CENTRAL (GCT; Arabidopsis MED13) are required for timing of pattern formation during embryogenesis. A morphological, molecular and genomic analysis of the post-embryonic phenotype of gct and cct mutants demonstrated that these genes also promote at least three subsequent developmental transitions: germination, vegetative phase change, and flowering. Genetic and molecular analyses indicate that GCT and CCT operate in parallel to gibberellic acid, a phytohormone known to regulate these same three transitions. We demonstrate that the delay in vegetative phase change in gct and cct is largely due to overexpression of miR156, and that the delay in flowering is due in part to upregulation of FLC. Thus, GCT and CCT coordinate vegetative and floral transitions by repressing the repressors miR156 and FLC. Our results suggest that MED12 and MED13 act as global regulators of developmental timing by fine-tuning the expression of temporal regulatory genes.
Collapse
Affiliation(s)
- C Stewart Gillmor
- Laboratorio Nacional de Genómica para la Biodiversidad (Langebio), Unidad de Genómica Avanzada, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional (CINVESTAV-IPN), Irapuato, Guanajuato, 36821, Mexico Department of Biology, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Claudia O Silva-Ortega
- Laboratorio Nacional de Genómica para la Biodiversidad (Langebio), Unidad de Genómica Avanzada, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional (CINVESTAV-IPN), Irapuato, Guanajuato, 36821, Mexico
| | - Matthew R Willmann
- Department of Biology, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Manuel Buendía-Monreal
- Laboratorio Nacional de Genómica para la Biodiversidad (Langebio), Unidad de Genómica Avanzada, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional (CINVESTAV-IPN), Irapuato, Guanajuato, 36821, Mexico
| | - R Scott Poethig
- Department of Biology, University of Pennsylvania, Philadelphia, PA 19104, USA
| |
Collapse
|
19
|
Lindsay AK, Morales DK, Liu Z, Grahl N, Zhang A, Willger SD, Myers LC, Hogan DA. Analysis of Candida albicans mutants defective in the Cdk8 module of mediator reveal links between metabolism and biofilm formation. PLoS Genet 2014; 10:e1004567. [PMID: 25275466 PMCID: PMC4183431 DOI: 10.1371/journal.pgen.1004567] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2014] [Accepted: 06/30/2014] [Indexed: 12/29/2022] Open
Abstract
Candida albicans biofilm formation is a key virulence trait that involves hyphal growth and adhesin expression. Pyocyanin (PYO), a phenazine secreted by Pseudomonas aeruginosa, inhibits both C. albicans biofilm formation and development of wrinkled colonies. Using a genetic screen, we identified two mutants, ssn3Δ/Δ and ssn8Δ/Δ, which continued to wrinkle in the presence of PYO. Ssn8 is a cyclin-like protein and Ssn3 is similar to cyclin-dependent kinases; both proteins are part of the heterotetrameric Cdk8 module that forms a complex with the transcriptional co-regulator, Mediator. Ssn3 kinase activity was also required for PYO sensitivity as a kinase dead mutant maintained a wrinkled colony morphology in the presence of PYO. Furthermore, similar phenotypes were observed in mutants lacking the other two components of the Cdk8 module-Srb8 and Srb9. Through metabolomics analyses and biochemical assays, we showed that a compromised Cdk8 module led to increases in glucose consumption, glycolysis-related transcripts, oxidative metabolism and ATP levels even in the presence of PYO. In the mutant, inhibition of respiration to levels comparable to the PYO-treated wild type inhibited wrinkled colony development. Several lines of evidence suggest that PYO does not act through Cdk8. Lastly, the ssn3 mutant was a hyperbiofilm former, and maintained higher biofilm formation in the presence of PYO than the wild type. Together these data provide novel insights into the role of the Cdk8 module of Mediator in regulation of C. albicans physiology and the links between respiratory activity and both wrinkled colony and biofilm development.
Collapse
Affiliation(s)
- Allia K. Lindsay
- Department of Microbiology and Immunology, Geisel School of Medicine at Dartmouth, Hanover, New Hampshire, United States of America
| | - Diana K. Morales
- Department of Microbiology and Immunology, Geisel School of Medicine at Dartmouth, Hanover, New Hampshire, United States of America
| | - Zhongle Liu
- Department of Biochemistry, Geisel School of Medicine at Dartmouth, Hanover, New Hampshire, United States of America
| | - Nora Grahl
- Department of Microbiology and Immunology, Geisel School of Medicine at Dartmouth, Hanover, New Hampshire, United States of America
| | - Anda Zhang
- Department of Biochemistry, Geisel School of Medicine at Dartmouth, Hanover, New Hampshire, United States of America
| | - Sven D. Willger
- Department of Microbiology and Immunology, Geisel School of Medicine at Dartmouth, Hanover, New Hampshire, United States of America
| | - Lawrence C. Myers
- Department of Biochemistry, Geisel School of Medicine at Dartmouth, Hanover, New Hampshire, United States of America
| | - Deborah A. Hogan
- Department of Microbiology and Immunology, Geisel School of Medicine at Dartmouth, Hanover, New Hampshire, United States of America
- * E-mail:
| |
Collapse
|
20
|
Genomics of uterine leiomyomas: insights from high-throughput sequencing. Fertil Steril 2014; 102:621-9. [PMID: 25106763 DOI: 10.1016/j.fertnstert.2014.06.050] [Citation(s) in RCA: 143] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2014] [Revised: 06/27/2014] [Accepted: 06/27/2014] [Indexed: 02/07/2023]
Abstract
Uterine leiomyomas are benign smooth-muscle tumors of extremely low malignant potential. Early work utilizing classical cytogenetics revealed that a subset of uterine leiomyomas harbor recurrent chromosomal rearrangements, such as translocations affecting the HMGA2 gene. Our understanding of the genetics of many tumor types has deepened remarkably with the emergence of next-generation sequencing technologies. Exome sequencing identified that the majority of leiomyomas display highly specific MED12 mutations. Further studies suggest that these MED12 hotspot mutations are also frequent in breast fibroadenomas, but not in other human tumors. Whole-genome sequencing showed that a subset of leiomyomas display complex chromosomal rearrangements resembling chromothripsis. These were formed in a single event of chromosomal breakage and random reassembly involving one or a limited number of chromosomes. Although most leiomyomas have been shown to arise independently, these studies also revealed that distinct nodules within a uterus may display identical genetic changes indicating a common clonal origin. A minority of leiomyomas were also found to display deletions within the COL4A5-COL4A6 genes, leading to upregulation of the adjacent gene IRS4. The findings derived from high-throughput sequencing combined with previous knowledge have led to an emerging molecular classification of leiomyomas, suggesting that there are several distinct pathogenic pathways involved in leiomyoma formation. The evidence points to at least 4 molecular subclasses: leiomyomas with MED12 mutation, FH inactivation, HMGA2 overexpression, and COL4A6-COL4A5 deletion. Elucidating the molecular pathogenesis of leiomyomas should be relevant for developing treatments for this very common disease.
Collapse
|
21
|
Mao F, Yang X, Fu L, Lv X, Zhang Z, Wu W, Yang S, Zhou Z, Zhang L, Zhao Y. The Kto-Skd complex can regulate ptc expression by interacting with Cubitus interruptus (Ci) in the Hedgehog signaling pathway. J Biol Chem 2014; 289:22333-41. [PMID: 24962581 DOI: 10.1074/jbc.m114.560995] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The hedgehog (Hh) signaling pathway plays a very important role in metazoan development by controlling pattern formation. Drosophila imaginal discs are subdivided into anterior and posterior compartments that derive from adjacent cell populations. The anterior/posterior (A/P) boundaries, which are critical to maintaining the position of organizers, are established by a complex mechanism involving Hh signaling. Here, we uncover the regulation of ptc in the Hh signaling pathway by two subunits of mediator complex, Kto and Skd, which can also regulate boundary location. Collectively, we provide further evidence that Kto-Skd affects the A/P-axial development of the whole wing disc. Kto can interact with Cubitus interruptus (Ci), bind to the Ci-binding region on ptc promoter, which are both regulated by Hh signals to down-regulate ptc expression.
Collapse
Affiliation(s)
- Feifei Mao
- From the State Key Laboratory of Cell Biology, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 320 Yue-Yang Road, Shanghai 200031, China
| | - Xiaofeng Yang
- From the State Key Laboratory of Cell Biology, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 320 Yue-Yang Road, Shanghai 200031, China
| | - Lin Fu
- From the State Key Laboratory of Cell Biology, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 320 Yue-Yang Road, Shanghai 200031, China
| | - Xiangdong Lv
- From the State Key Laboratory of Cell Biology, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 320 Yue-Yang Road, Shanghai 200031, China
| | - Zhao Zhang
- From the State Key Laboratory of Cell Biology, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 320 Yue-Yang Road, Shanghai 200031, China
| | - Wenqing Wu
- From the State Key Laboratory of Cell Biology, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 320 Yue-Yang Road, Shanghai 200031, China
| | - Siqi Yang
- From the State Key Laboratory of Cell Biology, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 320 Yue-Yang Road, Shanghai 200031, China
| | - Zhaocai Zhou
- From the State Key Laboratory of Cell Biology, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 320 Yue-Yang Road, Shanghai 200031, China
| | - Lei Zhang
- From the State Key Laboratory of Cell Biology, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 320 Yue-Yang Road, Shanghai 200031, China
| | - Yun Zhao
- From the State Key Laboratory of Cell Biology, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 320 Yue-Yang Road, Shanghai 200031, China
| |
Collapse
|
22
|
Mäkinen N, Heinonen HR, Sjöberg J, Taipale J, Vahteristo P, Aaltonen LA. Mutation analysis of components of the Mediator kinase module in MED12 mutation-negative uterine leiomyomas. Br J Cancer 2014; 110:2246-9. [PMID: 24642626 PMCID: PMC4007231 DOI: 10.1038/bjc.2014.138] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2013] [Revised: 02/14/2014] [Accepted: 02/21/2014] [Indexed: 02/06/2023] Open
Abstract
Background: Kinase module of Mediator complex (‘CDK8 submodule') consists of four subunits: CDK8, Cyclin C, MED12, and MED13. Recently, we reported recurrent MED12 mutations in 70% of uterine leiomyomas. The aim of this study was to analyse whether mutations in other components of the module contribute to the development of these lesions. Methods: Mutation screening of altogether 70 MED12 mutation-negative uterine leiomyomas was carried out by direct sequencing. Results: None of the tumours displayed somatic mutations in the coding regions of CDK8/CDK19, CCNC, or MED13. Conclusions: Mutations in CDK8/CDK19, CCNC, and MED13 do not frequently contribute to genesis of uterine leiomyomas.
Collapse
Affiliation(s)
- N Mäkinen
- Department of Medical Genetics, Genome-Scale Biology Research Program, University of Helsinki, PO Box 63, 00014 Helsinki, Finland
| | - H-R Heinonen
- Department of Medical Genetics, Genome-Scale Biology Research Program, University of Helsinki, PO Box 63, 00014 Helsinki, Finland
| | - J Sjöberg
- Department of Obstetrics and Gynecology, Helsinki University Central Hospital, PO Box 140, 00029 Helsinki, Finland
| | - J Taipale
- 1] Genome-Scale Biology Research Program and Department of Pathology, Haartman Institute, University of Helsinki, PO Box 63, 00014 Helsinki, Finland [2] Science for Life Laboratory, Department of Biosciences and Nutrition, Karolinska Institute, Stockholm, Sweden
| | - P Vahteristo
- Department of Medical Genetics, Genome-Scale Biology Research Program, University of Helsinki, PO Box 63, 00014 Helsinki, Finland
| | - L A Aaltonen
- Department of Medical Genetics, Genome-Scale Biology Research Program, University of Helsinki, PO Box 63, 00014 Helsinki, Finland
| |
Collapse
|
23
|
Corden JL. RNA polymerase II C-terminal domain: Tethering transcription to transcript and template. Chem Rev 2013; 113:8423-55. [PMID: 24040939 PMCID: PMC3988834 DOI: 10.1021/cr400158h] [Citation(s) in RCA: 136] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Jeffry L Corden
- Department of Molecular Biology and Genetics, The Johns Hopkins University School of Medicine , 725 North Wolfe Street, Baltimore Maryland 21205, United States
| |
Collapse
|
24
|
Emerging roles of Cdk8 in cell cycle control. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2013; 1829:916-20. [DOI: 10.1016/j.bbagrm.2013.04.010] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/05/2013] [Revised: 04/22/2013] [Accepted: 04/24/2013] [Indexed: 12/12/2022]
|
25
|
Differential regulation of white-opaque switching by individual subunits of Candida albicans mediator. EUKARYOTIC CELL 2013; 12:1293-304. [PMID: 23873866 DOI: 10.1128/ec.00137-13] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
The multisubunit eukaryotic Mediator complex integrates diverse positive and negative gene regulatory signals and transmits them to the core transcription machinery. Mutations in individual subunits within the complex can lead to decreased or increased transcription of certain subsets of genes, which are highly specific to the mutated subunit. Recent studies suggest a role for Mediator in epigenetic silencing. Using white-opaque morphological switching in Candida albicans as a model, we have shown that Mediator is required for the stability of both the epigenetic silenced (white) and active (opaque) states of the bistable transcription circuit driven by the master regulator Wor1. Individual deletions of eight C. albicans Mediator subunits have shown that different Mediator subunits have dramatically diverse effects on the directionality, frequency, and environmental induction of epigenetic switching. Among the Mediator deletion mutants analyzed, only Med12 has a steady-state transcriptional effect on the components of the Wor1 circuit that clearly corresponds to its effect on switching. The MED16 and MED9 genes have been found to be among a small subset of genes that are required for the stability of both the white and opaque states. Deletion of the Med3 subunit completely destabilizes the opaque state, even though the Wor1 transcription circuit is intact and can be driven by ectopic expression of Wor1. The highly impaired ability of the med3 deletion mutant to mate, even when Wor1 expression is ectopically induced, reveals that the activation of the Wor1 circuit can be decoupled from the opaque state and one of its primary biological consequences.
Collapse
|
26
|
Burroughs AM, Iyer LM, Aravind L. Two novel PIWI families: roles in inter-genomic conflicts in bacteria and Mediator-dependent modulation of transcription in eukaryotes. Biol Direct 2013; 8:13. [PMID: 23758928 PMCID: PMC3702460 DOI: 10.1186/1745-6150-8-13] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2013] [Accepted: 06/05/2013] [Indexed: 01/12/2023] Open
Abstract
Background The PIWI module, found in the PIWI/AGO superfamily of proteins, is a critical component of several cellular pathways including germline maintenance, chromatin organization, regulation of splicing, RNA interference, and virus suppression. It binds a guide strand which helps it target complementary nucleic strands. Results Here we report the discovery of two divergent, novel families of PIWI modules, the first such to be described since the initial discovery of the PIWI/AGO superfamily over a decade ago. Both families display conservation patterns consistent with the binding of oligonucleotide guide strands. The first family is bacterial in distribution and is typically encoded by a distinctive three-gene operon alongside genes for a restriction endonuclease fold enzyme and a helicase of the DinG family. The second family is found only in eukaryotes. It is the core conserved module of the Med13 protein, a subunit of the CDK8 subcomplex of the transcription regulatory Mediator complex. Conclusions Based on the presence of the DinG family helicase, which specifically acts on R-loops, we infer that the first family of PIWI modules is part of a novel RNA-dependent restriction system which could target invasive DNA from phages, plasmids or conjugative transposons. It is predicted to facilitate restriction of actively transcribed invading DNA by utilizing RNA guides. The PIWI family found in the eukaryotic Med13 proteins throws new light on the regulatory switch through which the CDK8 subcomplex modulates transcription at Mediator-bound promoters of highly transcribed genes. We propose that this involves recognition of small RNAs by the PIWI module in Med13 resulting in a conformational switch that propagates through the Mediator complex. Reviewers This article was reviewed by Sandor Pongor, Frank Eisenhaber and Balaji Santhanam.
Collapse
Affiliation(s)
- A Maxwell Burroughs
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
| | | | | |
Collapse
|
27
|
Matsuzawa T, Kageyama Y, Ooishi K, Kawamukai M, Takegawa K. The zinc finger protein Gsf1 regulates Gsf2-dependent flocculation in fission yeast. FEMS Yeast Res 2013; 13:259-66. [PMID: 23311928 DOI: 10.1111/1567-1364.12029] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2012] [Revised: 12/15/2012] [Accepted: 01/01/2013] [Indexed: 11/30/2022] Open
Abstract
Fission yeast flocculates nonsexually by induction of the flocculin encoded by gsf2(+) which is controlled by the positive regulator Mbx2. Here, we report a novel gene designated gsf1(+) found to be a negative regulator of nonsexual flocculation. We identified gsf1(+) as a multicopy suppressor of a sam2 mutation, which caused growth sensitivity to Ca(2+) and also found a nonsense mutation in gsf1(+) in a previously isolated gsf1 mutant. The gsf1(+) gene encodes a 547-aa protein containing a Zn(2)-Cys(6) binuclear cluster-type zinc finger motif. The Gsf1 protein localized in the nucleus, consistent with a role as a transcription factor. Deletion of gsf1(+) resulted in nonsexual flocculation inducible by CaCl2 , which was suppressed by the addition of EDTA or galactose. Both gsf2(+) and mbx2(+) were highly expressed in the gsf1 mutant. gsf1∆ gsf2∆ and gsf1∆ mbx2∆ double mutants did not flocculate, suggesting that gsf1(+) is an upstream regulator. In addition, the gsf1 mutant was sensitive to CaCl2 , KCl, HU, and TBZ, consistent with the possibility that gsf1(+) plays a role in functions unrelated to flocculation. Taken together, these results suggest that nonsexual flocculation in fission yeast is negatively controlled by Gsf1, which controls expression of mbx2(+) and gsf2(+) .
Collapse
Affiliation(s)
- Tomohiko Matsuzawa
- Department of Bioscience & Biotechnology, Faculty of Agriculture, Kyushu University, Fukuoka, Japan
| | | | | | | | | |
Collapse
|
28
|
Ansari SA, Morse RH. Selective role of Mediator tail module in the transcription of highly regulated genes in yeast. Transcription 2012; 3:110-4. [PMID: 22771944 DOI: 10.4161/trns.19840] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
The tail module subunits of Mediator complex are targets of activators both in yeast and metazoans. Here we discuss recent evidence from studies in yeast for tail module specificity for SAGA-dependent, TATA-containing genes including highly regulated stress response genes, and for independent recruitment and function of the tail module.
Collapse
Affiliation(s)
- Suraiya A Ansari
- Laboratory of Molecular Genetics, Wadsworth Center, New York State Department of Health, Albany, NY, USA.
| | | |
Collapse
|
29
|
Drogat J, Migeot V, Mommaerts E, Mullier C, Dieu M, van Bakel H, Hermand D. Cdk11-cyclinL controls the assembly of the RNA polymerase II mediator complex. Cell Rep 2012; 2:1068-76. [PMID: 23122962 DOI: 10.1016/j.celrep.2012.09.027] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2012] [Revised: 08/30/2012] [Accepted: 09/24/2012] [Indexed: 10/27/2022] Open
Abstract
The large Mediator (L-Mediator) is a general coactivator of RNA polymerase II transcription and is formed by the reversible association of the small Mediator (S-Mediator) and the kinase-module-harboring Cdk8. It is not known how the kinase module association/dissociation is regulated. We describe the fission yeast Cdk11-L-type cyclin pombe (Lcp1) complex and show that its inactivation alters the global expression profile in a manner very similar to that of mutations of the kinase module. Cdk11 is broadly distributed onto chromatin and phosphorylates the Med27 and Med4 Mediator subunits on conserved residues. The association of the kinase module and the S-Mediator is strongly decreased by the inactivation of either Cdk11 or the mutation of its target residues on the Mediator. These results show that Cdk11-Lcp1 regulates the association of the kinase module and the S-Mediator to form the L-Mediator complex.
Collapse
Affiliation(s)
- Julie Drogat
- Namur Research College (NARC), The University of Namur, Namur 5000 Belgium
| | | | | | | | | | | | | |
Collapse
|
30
|
Pointner J, Persson J, Prasad P, Norman-Axelsson U, Strålfors A, Khorosjutina O, Krietenstein N, Svensson JP, Ekwall K, Korber P. CHD1 remodelers regulate nucleosome spacing in vitro and align nucleosomal arrays over gene coding regions in S. pombe. EMBO J 2012; 31:4388-403. [PMID: 23103765 DOI: 10.1038/emboj.2012.289] [Citation(s) in RCA: 80] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2012] [Accepted: 09/28/2012] [Indexed: 11/09/2022] Open
Abstract
Nucleosome positioning governs access to eukaryotic genomes. Many genes show a stereotypic organisation at their 5'end: a nucleosome free region just upstream of the transcription start site (TSS) followed by a regular nucleosomal array over the coding region. The determinants for this pattern are unclear, but nucleosome remodelers are likely critical. Here we study the role of remodelers in global nucleosome positioning in S. pombe and the corresponding changes in expression. We find a striking evolutionary shift in remodeler usage between budding and fission yeast. The S. pombe RSC complex does not seem to be involved in nucleosome positioning, despite its prominent role in S. cerevisiae. While S. pombe lacks ISWI-type remodelers, it has two CHD1-type ATPases, Hrp1 and Hrp3. We demonstrate nucleosome spacing activity for Hrp1 and Hrp3 in vitro, and that together they are essential for linking regular genic arrays to most TSSs in vivo. Impaired arrays in the absence of either or both remodelers may lead to increased cryptic antisense transcription, but overall gene expression levels are only mildly affected.
Collapse
Affiliation(s)
- Julia Pointner
- Adolf-Butenandt-Institut, University of Munich, Munich, Germany
| | | | | | | | | | | | | | | | | | | |
Collapse
|
31
|
Conaway RC, Conaway JW. The Mediator complex and transcription elongation. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2012; 1829:69-75. [PMID: 22983086 DOI: 10.1016/j.bbagrm.2012.08.017] [Citation(s) in RCA: 109] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/04/2012] [Revised: 08/14/2012] [Accepted: 08/29/2012] [Indexed: 11/25/2022]
Abstract
BACKGROUND Mediator is an evolutionarily conserved multisubunit RNA polymerase II (Pol II) coregulatory complex. Although Mediator was initially found to play a critical role in the regulation of the initiation of Pol II transcription, recent studies have brought to light an expanded role for Mediator at post-initiation stages of transcription. SCOPE OF REVIEW We provide a brief description of the structure of Mediator and its function in the regulation of Pol II transcription initiation, and we summarize recent findings implicating Mediator in the regulation of various stages of Pol II transcription elongation. MAJOR CONCLUSIONS Emerging evidence is revealing new roles for Mediator in nearly all stages of Pol II transcription, including initiation, promoter escape, elongation, pre-mRNA processing, and termination. GENERAL SIGNIFICANCE Mediator plays a central role in the regulation of gene expression by impacting nearly all stages of mRNA synthesis. This article is part of a Special Issue entitled: RNA polymerase II Transcript Elongation.
Collapse
Affiliation(s)
- Ronald C Conaway
- Stowers Institute for Medical Research, Kansas City, MO 64110, USA.
| | | |
Collapse
|
32
|
Sansó M, Lee KM, Viladevall L, Jacques PÉ, Pagé V, Nagy S, Racine A, St. Amour CV, Zhang C, Shokat KM, Schwer B, Robert F, Fisher RP, Tanny JC. A positive feedback loop links opposing functions of P-TEFb/Cdk9 and histone H2B ubiquitylation to regulate transcript elongation in fission yeast. PLoS Genet 2012; 8:e1002822. [PMID: 22876190 PMCID: PMC3410854 DOI: 10.1371/journal.pgen.1002822] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2012] [Accepted: 05/24/2012] [Indexed: 11/25/2022] Open
Abstract
Transcript elongation by RNA polymerase II (RNAPII) is accompanied by conserved patterns of histone modification. Whereas histone modifications have established roles in transcription initiation, their functions during elongation are not understood. Mono-ubiquitylation of histone H2B (H2Bub1) plays a key role in coordinating co-transcriptional histone modification by promoting site-specific methylation of histone H3. H2Bub1 also regulates gene expression through an unidentified, methylation-independent mechanism. Here we reveal bidirectional communication between H2Bub1 and Cdk9, the ortholog of metazoan positive transcription elongation factor b (P-TEFb), in the fission yeast Schizosaccharomyces pombe. Chemical and classical genetic analyses indicate that lowering Cdk9 activity or preventing phosphorylation of its substrate, the transcription processivity factor Spt5, reduces H2Bub1 in vivo. Conversely, mutations in the H2Bub1 pathway impair Cdk9 recruitment to chromatin and decrease Spt5 phosphorylation. Moreover, an Spt5 phosphorylation-site mutation, combined with deletion of the histone H3 Lys4 methyltransferase Set1, phenocopies morphologic and growth defects due to H2Bub1 loss, suggesting independent, partially redundant roles for Cdk9 and Set1 downstream of H2Bub1. Surprisingly, mutation of the histone H2B ubiquitin-acceptor residue relaxes the Cdk9 activity requirement in vivo, and cdk9 mutations suppress cell-morphology defects in H2Bub1-deficient strains. Genome-wide analyses by chromatin immunoprecipitation also demonstrate opposing effects of Cdk9 and H2Bub1 on distribution of transcribing RNAPII. Therefore, whereas mutual dependence of H2Bub1 and Spt5 phosphorylation indicates positive feedback, mutual suppression by cdk9 and H2Bub1-pathway mutations suggests antagonistic functions that must be kept in balance to regulate elongation. Loss of H2Bub1 disrupts that balance and leads to deranged gene expression and aberrant cell morphologies, revealing a novel function of a conserved, co-transcriptional histone modification. Modification of histone proteins is an important transcriptional regulatory mechanism in eukaryotic cells. Although various histone modifications are found primarily within the coding regions of transcribed genes, how they influence transcription elongation remains unclear. Among these modifications is mono-ubiquitylation of histone H2B (H2Bub1), which is needed for co-transcriptional methylation of histone H3 at specific sites. Here we show that H2Bub1 and Cdk9, the kinase component of positive transcription elongation factor b (P-TEFb), are jointly regulated by a positive feedback loop: Cdk9 activity is needed for co-transcriptional H2Bub1, and H2Bub1 in turn stimulates Cdk9 activity toward one of its major substrates, the conserved elongation factor Spt5. We provide genetic evidence that the combined action of H2Bub1 on Spt5 phosphorylation and histone methylation accounts for the gene-regulatory effects of this modification. Surprisingly, our genetic and genome-wide studies indicate that P-TEFb and H2Bub1 act in opposition on elongating RNA polymerase. We suggest that the positive feedback linking P-TEFb and H2Bub1 helps to maintain a balance between their opposing actions. These results highlight a novel regulatory role for a conserved histone modification during transcription elongation.
Collapse
Affiliation(s)
- Miriam Sansó
- Department of Structural and Chemical Biology, Mount Sinai School of Medicine, New York, New York, United States of America
| | - Karen M. Lee
- Department of Structural and Chemical Biology, Mount Sinai School of Medicine, New York, New York, United States of America
| | - Laia Viladevall
- Department of Structural and Chemical Biology, Mount Sinai School of Medicine, New York, New York, United States of America
| | | | - Viviane Pagé
- Department of Pharmacology and Therapeutics, McGill University, Montréal, Canada
| | - Stephen Nagy
- Department of Pharmacology and Therapeutics, McGill University, Montréal, Canada
| | - Ariane Racine
- Department of Pharmacology and Therapeutics, McGill University, Montréal, Canada
| | - Courtney V. St. Amour
- Programs in Biochemistry, Cell and Molecular Biology, Weill Cornell Medical College, New York, New York, United States of America
| | - Chao Zhang
- Howard Hughes Medical Institute and Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, California, United States of America
| | - Kevan M. Shokat
- Howard Hughes Medical Institute and Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, California, United States of America
| | - Beate Schwer
- Department of Microbiology and Immunology, Weill Cornell Medical College, New York, New York, United States of America
| | - François Robert
- Institut de Recherches Cliniques de Montréal, Montréal, Canada
| | - Robert P. Fisher
- Department of Structural and Chemical Biology, Mount Sinai School of Medicine, New York, New York, United States of America
- * E-mail: (RPF); (JCT)
| | - Jason C. Tanny
- Department of Pharmacology and Therapeutics, McGill University, Montréal, Canada
- * E-mail: (RPF); (JCT)
| |
Collapse
|
33
|
Liu Z, Myers LC. Med5(Nut1) and Med17(Srb4) are direct targets of mediator histone H4 tail interactions. PLoS One 2012; 7:e38416. [PMID: 22693636 PMCID: PMC3367926 DOI: 10.1371/journal.pone.0038416] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2012] [Accepted: 05/09/2012] [Indexed: 11/18/2022] Open
Abstract
The Mediator complex transmits activation signals from DNA bound transcription factors to the core transcription machinery. In addition to its canonical role in transcriptional activation, recent studies have demonstrated that S. cerevisiae Mediator can interact directly with nucleosomes, and their histone tails. Mutations in Mediator subunits have shown that Mediator and certain chromatin structures mutually impact each other structurally and functionally in vivo. We have taken a UV photo cross-linking approach to further delineate the molecular basis of Mediator chromatin interactions and help determine whether the impact of certain Mediator mutants on chromatin is direct. Specifically, by using histone tail peptides substituted with an amino acid analog that is a UV activatible crosslinker, we have identified specific subunits within Mediator that participate in histone tail interactions. Using Mediator purified from mutant yeast strains we have evaluated the impact of these subunits on histone tail binding. This analysis has identified the Med5 subunit of Mediator as a target for histone tail interactions and suggests that the previously observed effect of med5 mutations on telomeric heterochromatin and silencing is direct.
Collapse
Affiliation(s)
- Zhongle Liu
- Department of Biochemistry, Dartmouth Medical School, Hanover, New Hampshire, United States of America
| | - Lawrence C. Myers
- Department of Biochemistry, Dartmouth Medical School, Hanover, New Hampshire, United States of America
- * E-mail:
| |
Collapse
|
34
|
The Tlo proteins are stoichiometric components of Candida albicans mediator anchored via the Med3 subunit. EUKARYOTIC CELL 2012; 11:874-84. [PMID: 22562472 DOI: 10.1128/ec.00095-12] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
The amplification of the TLO (for telomere-associated) genes in Candida albicans, compared to its less pathogenic, close relative Candida dubliniensis, suggests a role in virulence. Little, however, is known about the function of the Tlo proteins. We have purified the Mediator coactivator complex from C. albicans (caMediator) and found that Tlo proteins are a stoichiometric component of caMediator. Many members of the Tlo family are expressed, and each is a unique member of caMediator. Protein expression analysis of individual Tlo proteins, as well as the purification of tagged Tlo proteins, demonstrate that there is a large free population of Tlo proteins in addition to the Mediator-associated population. Coexpression and copurification of Tloα12 and caMed3 in Escherichia coli established a direct physical interaction between the two proteins. We have also made a C. albicans med3Δ/Δ strain and purified an intact Mediator from this strain. The analysis of the composition of the med3Δ Mediator shows that it lacks a Tlo subunit. Regarding Mediator function, the med3Δ/Δ strain serves as a substitute for the difficult-to-make tloΔ/Δ C. albicans strain. A potential role of the TLO and MED3 genes in virulence is supported by the inability of the med3Δ/Δ strain to form normal germ tubes. This study of caMediator structure provides initial clues to the mechanism of action of the Tlo genes and a platform for further mechanistic studies of caMediator's involvement in gene regulatory patterns that underlie pathogenesis.
Collapse
|
35
|
Abstract
Temporal changes in transcription programs are coupled to control of cell growth and division. We here report that Mediator, a conserved coregulator of eukaryotic transcription, is part of a regulatory pathway that controls mitotic entry in fission yeast. The Mediator subunit cyclin-dependent kinase 8 (Cdk8) phosphorylates the forkhead 2 (Fkh2) protein in a periodic manner that coincides with gene activation during mitosis. Phosphorylation prevents degradation of the Fkh2 transcription factor by the proteasome, thus ensuring cell cycle-dependent variations in Fkh2 levels. Interestingly, Cdk8-dependent phosphorylation of Fkh2 controls mitotic entry, and mitotic entry is delayed by inactivation of the Cdk8 kinase activity or mutations replacing the phosphorylated serine residues of Fkh2. In addition, mutations in Fkh2, which mimic protein phosphorylation, lead to premature mitotic entry. Therefore, Fkh2 regulates not only the onset of mitotic transcription but also the correct timing of mitotic entry via effects on the Wee1 kinase. Our findings thus establish a new pathway linking the Mediator complex to control of mitotic transcription and regulation of mitotic entry in fission yeast.
Collapse
|
36
|
Galbraith MD, Donner AJ, Espinosa JM. CDK8: a positive regulator of transcription. Transcription 2012; 1:4-12. [PMID: 21327159 DOI: 10.4161/trns.1.1.12373] [Citation(s) in RCA: 167] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2010] [Revised: 05/12/2010] [Accepted: 05/13/2010] [Indexed: 01/09/2023] Open
Abstract
CDK8 belongs to a group of cyclin-dependent kinases involved in transcriptional regulation from yeast to mammals. CDK8 associates with the Mediator complex, but functions outside of Mediator are also likely. Historically, CDK8 has been described mostly as a transcriptional repressor, but a growing body of research provides unequivocal evidence for various roles of CDK8 in gene activation. Several transcriptional programs of biomedical importance employ CDK8 as a co-activator, including the p53 network, the Wnt/β-catenin pathway, the serum response network, and those governed by SMADs and the thyroid hormone receptor, thus highlighting the importance of further investigation into this enigmatic transcriptional regulator.
Collapse
|
37
|
Imura Y, Kobayashi Y, Yamamoto S, Furutani M, Tasaka M, Abe M, Araki T. CRYPTIC PRECOCIOUS/MED12 is a novel flowering regulator with multiple target steps in Arabidopsis. PLANT & CELL PHYSIOLOGY 2012; 53:287-303. [PMID: 22247249 PMCID: PMC3278046 DOI: 10.1093/pcp/pcs002] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/19/2011] [Accepted: 01/05/2012] [Indexed: 05/22/2023]
Abstract
The proper timing of flowering is of crucial importance for reproductive success of plants. Regulation of flowering is orchestrated by inputs from both environmental and endogenous signals such as daylength, light quality, temperature and hormones, and key flowering regulators construct several parallel and interactive genetic pathways. This integrative regulatory network has been proposed to create robustness as well as plasticity of the regulation. Although knowledge of key genes and their regulation has been accumulated, there still remains much to learn about how they are organized into an integrative regulatory network. Here, we have analyzed the CRYPTIC PRECOCIOUS (CRP) gene for the Arabidopsis counterpart of the MED12 subunit of the Mediator. A novel dominant mutant, crp-1D, which causes up-regulation of SUPPRESSOR OF OVEREXPRESSION OF CONSTANS 1 (SOC1), FRUITFULL (FUL) and APETALA1 (AP1) expression in a FLOWERING LOCUS T (FT)-dependent manner, was identified in an enhancer screen of the early-flowering phenotype of 35S::FT. Genetic and molecular analysis of both crp-1D and crp loss-of-function alleles showed that MED12/CRP is required not only for proper regulation of SOC1, FUL and AP1, but also for up-regulation of FT, TWIN SISTER OF FT (TSF) and FD, and down-regulation of FLOWERING LOCUS C (FLC). These observations suggest that MED12/CRP is a novel flowering regulator with multiple regulatory target steps both upstream and downstream of the key flowering regulators including FT florigen. Our work, taken together with recent studies of other Mediator subunit genes, supports an emerging view that the Mediator plays multiple roles in the regulation of flowering.
Collapse
Affiliation(s)
- Yuri Imura
- Graduate School of Biostudies, Kyoto University, Kyoto, 606-8501 Japan
| | - Yasushi Kobayashi
- Graduate School of Science, Kyoto University, Kyoto, 606-8502 Japan
- Department of Molecular Biology, Max Planck Institute for Developmental Biology, D-72076 Tübingen, Germany
| | - Sumiko Yamamoto
- Graduate School of Science, Kyoto University, Kyoto, 606-8502 Japan
- Genome Informatics Laboratory, CIB-DDBJ, National Institute of Genetics, ROIS, Shizuoka, 411-8540 Japan
| | - Masahiko Furutani
- Graduate School of Biological Sciences, Nara Institute of Science and Technology, Nara, 630-0101 Japan
| | - Masao Tasaka
- Graduate School of Biological Sciences, Nara Institute of Science and Technology, Nara, 630-0101 Japan
| | - Mitsutomo Abe
- Graduate School of Biostudies, Kyoto University, Kyoto, 606-8501 Japan
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, 113-0033 Japan
| | - Takashi Araki
- Graduate School of Biostudies, Kyoto University, Kyoto, 606-8501 Japan
- *Corresponding author: E-mail, ; Fax, +81-75-753-6470.
| |
Collapse
|
38
|
Xu W, Ji JY. Dysregulation of CDK8 and Cyclin C in tumorigenesis. J Genet Genomics 2011; 38:439-52. [PMID: 22035865 PMCID: PMC9792140 DOI: 10.1016/j.jgg.2011.09.002] [Citation(s) in RCA: 60] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2011] [Revised: 09/05/2011] [Accepted: 09/06/2011] [Indexed: 01/23/2023]
Abstract
Appropriately controlled gene expression is fundamental for normal growth and survival of all living organisms. In eukaryotes, the transcription of protein-coding mRNAs is dependent on RNA polymerase II (Pol II). The multi-subunit transcription cofactor Mediator complex is proposed to regulate most, if not all, of the Pol II-dependent transcription. Here we focus our discussion on two subunits of the Mediator complex, cyclin-dependent kinase 8 (CDK8) and its regulatory partner Cyclin C (CycC), because they are either mutated or amplified in a variety of human cancers. CDK8 functions as an oncoprotein in melanoma and colorectal cancers, thus there are considerable interests in developing drugs specifically targeting the CDK8 kinase activity. However, to evaluate the feasibility of targeting CDK8 for cancer therapy and to understand how their dysregulation contributes to tumorigenesis, it is essential to elucidate the in vivo function and regulation of CDK8-CycC, which are still poorly understood in multi-cellular organisms. We summarize the evidence linking their dysregulation to various cancers and present our bioinformatics and computational analyses on the structure and evolution of CDK8. We also discuss the implications of these observations in tumorigenesis. Because most of the Mediator subunits, including CDK8 and CycC, are highly conserved during eukaryotic evolution, we expect that investigations using model organisms such as Drosophila will provide important insights into the function and regulation of CDK8 and CycC in different cellular and developmental contexts.
Collapse
Affiliation(s)
- Wu Xu
- Department of Chemistry, University of Louisiana at Lafayette, P.O. Box 44370, Lafayette, LA 70504, USA
| | - Jun-Yuan Ji
- Department of Molecular and Cellular Medicine, College of Medicine, Texas A&M Health Science Center, College Station, TX 77843, USA
- Corresponding author: Tel: +1 979 845 6389, fax: +1 979 847 9481. (J.-Y. Ji)
| |
Collapse
|
39
|
Unraveling framework of the ancestral Mediator complex in human diseases. Biochimie 2011; 94:579-87. [PMID: 21983542 DOI: 10.1016/j.biochi.2011.09.016] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2011] [Accepted: 09/15/2011] [Indexed: 01/13/2023]
Abstract
Mediator (MED) is a fundamental component of the RNA polymerase II-mediated transcription machinery. This multiprotein complex plays a pivotal role in the regulation of eukaryotic mRNA synthesis. The yeast Mediator complex consists of 26 different subunits. Recent studies indicate additional pathogenic roles for Mediator, for example during transcription elongation and non-coding RNA production. Mediator subunits have been emerging also to have pathophysiological roles suggesting MED-dependent therapeutic targets involving in several diseases, such as cancer, cardiovascular disease (CVD), metabolic and neurological disorders.
Collapse
|
40
|
Conaway RC, Conaway JW. Origins and activity of the Mediator complex. Semin Cell Dev Biol 2011; 22:729-34. [PMID: 21821140 DOI: 10.1016/j.semcdb.2011.07.021] [Citation(s) in RCA: 90] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2011] [Revised: 07/19/2011] [Accepted: 07/20/2011] [Indexed: 11/16/2022]
Abstract
The Mediator is a large, multisubunit RNA polymerase II transcriptional regulator that was first identified in Saccharomyces cerevisiae as a factor required for responsiveness of Pol II and the general initiation factors to DNA binding transactivators. Since its discovery in yeast, Mediator has been shown to be an integral and highly evolutionarily conserved component of the Pol II transcriptional machinery with critical roles in multiple stages of transcription, from regulation of assembly of the Pol II initiation complex to regulation of Pol II elongation. Here we provide a brief overview of the evolutionary origins of Mediator, its subunit composition, and its remarkably diverse collection of activities in Pol II transcription.
Collapse
Affiliation(s)
- Ronald C Conaway
- Stowers Institute for Medical Research, 1000 E. 50th Street, Kansas City, MO 64110, USA.
| | | |
Collapse
|
41
|
Janody F, Treisman JE. Requirements for mediator complex subunits distinguish three classes of notch target genes at the Drosophila wing margin. Dev Dyn 2011; 240:2051-9. [PMID: 21793099 DOI: 10.1002/dvdy.22705] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/15/2011] [Indexed: 11/11/2022] Open
Abstract
Spatial and temporal gene regulation relies on a combinatorial code of sequence-specific transcription factors that must be integrated by the general transcriptional machinery. A key link between the two is the mediator complex, which consists of a core complex that reversibly associates with the accessory kinase module. We show here that genes activated by Notch signaling at the dorsal-ventral boundary of the Drosophila wing disc fall into three classes that are affected differently by the loss of kinase module subunits. One class requires all four kinase module subunits for activation, while the others require only Med12 and Med13, either for activation or for repression. These distinctions do not result from different requirements for the Notch coactivator Mastermind or the corepressors Hairless and Groucho. We propose that interactions with the kinase module through distinct cofactors allow the DNA-binding protein Suppressor of Hairless to carry out both its activator and repressor functions.
Collapse
Affiliation(s)
- Florence Janody
- Kimmel Center for Biology and Medicine of the Skirball Institute, NYU School of Medicine, Department of Cell Biology, New York, New York, USA
| | | |
Collapse
|
42
|
Zhu X, Zhang Y, Bjornsdottir G, Liu Z, Quan A, Costanzo M, Dávila López M, Westholm JO, Ronne H, Boone C, Gustafsson CM, Myers LC. Histone modifications influence mediator interactions with chromatin. Nucleic Acids Res 2011; 39:8342-54. [PMID: 21742760 PMCID: PMC3201872 DOI: 10.1093/nar/gkr551] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
The Mediator complex transmits activation signals from DNA bound transcription factors to the core transcription machinery. Genome wide localization studies have demonstrated that Mediator occupancy not only correlates with high levels of transcription, but that the complex also is present at transcriptionally silenced locations. We provide evidence that Mediator localization is guided by an interaction with histone tails, and that this interaction is regulated by their post-translational modifications. A quantitative, high-density genetic interaction map revealed links between Mediator components and factors affecting chromatin structure, especially histone deacetylases. Peptide binding assays demonstrated that pure wild-type Mediator forms stable complexes with the tails of Histone H3 and H4. These binding assays also showed Mediator-histone H4 peptide interactions are specifically inhibited by acetylation of the histone H4 lysine 16, a residue critical in transcriptional silencing. Finally, these findings were validated by tiling array analysis that revealed a broad correlation between Mediator and nucleosome occupancy in vivo, but a negative correlation between Mediator and nucleosomes acetylated at histone H4 lysine 16. Our studies show that chromatin structure and the acetylation state of histones are intimately connected to Mediator localization.
Collapse
Affiliation(s)
- Xuefeng Zhu
- Department of Biochemistry and Cell Biology, University of Gothenburg, SE-405 30 Gothenburg, Sweden
| | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
43
|
Abstract
MicroRNAs (miRNAs) are a class of posttranscriptional regulators that have recently introduced an additional level of intricacy to our understanding of gene regulation. There are currently over 10,000 miRNAs that have been identified in a range of species including metazoa, mycetozoa, viridiplantae, and viruses, of which 940, to date, are found in humans. It is estimated that more than 60% of human protein-coding genes harbor miRNA target sites in their 3′ untranslated region and, thus, are potentially regulated by these molecules in health and disease. This review will first briefly describe the discovery, structure, and mode of function of miRNAs in mammalian cells, before elaborating on their roles and significance during development and pathogenesis in the various mammalian organs, while attempting to reconcile their functions with our existing knowledge of their targets. Finally, we will summarize some of the advances made in utilizing miRNAs in therapeutics.
Collapse
Affiliation(s)
- Danish Sayed
- Cardiovascular Research Institute, Department of Cell Biology and Molecular Medicine, University of Medicine and Dentistry of New Jersey, Newark, New Jersey
| | - Maha Abdellatif
- Cardiovascular Research Institute, Department of Cell Biology and Molecular Medicine, University of Medicine and Dentistry of New Jersey, Newark, New Jersey
| |
Collapse
|
44
|
Conaway RC, Conaway JW. Function and regulation of the Mediator complex. Curr Opin Genet Dev 2011; 21:225-30. [PMID: 21330129 PMCID: PMC3086004 DOI: 10.1016/j.gde.2011.01.013] [Citation(s) in RCA: 236] [Impact Index Per Article: 16.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2010] [Accepted: 01/18/2011] [Indexed: 11/18/2022]
Abstract
Over the past few years, advances in biochemical and genetic studies of the structure and function of the Mediator complex have shed new light on its subunit architecture and its mechanism of action in transcription by RNA polymerase II (pol II). The development of improved methods for reconstitution of recombinant Mediator subassemblies is enabling more in-depth analyses of basic features of the mechanisms by which Mediator interacts with and controls the activity of pol II and the general initiation factors. The discovery and characterization of multiple, functionally distinct forms of Mediator characterized by the presence or absence of the Cdk8 kinase module have led to new insights into how Mediator functions in both Pol II transcription activation and repression. Finally, progress in studies of the mechanisms by which the transcriptional activation domains (ADs) of DNA binding transcription factors target Mediator have brought to light unexpected complexities in the way Mediator participates in signal transduction.
Collapse
Affiliation(s)
- Ronald C Conaway
- Stowers Institute for Medical Research, 1000 E. 50th Street, Kansas City, MO 64110, USA
| | | |
Collapse
|
45
|
Khorosjutina O, Wanrooij PH, Walfridsson J, Szilagyi Z, Zhu X, Baraznenok V, Ekwall K, Gustafsson CM. A chromatin-remodeling protein is a component of fission yeast mediator. J Biol Chem 2010; 285:29729-37. [PMID: 20622008 DOI: 10.1074/jbc.m110.153858] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The multiprotein Mediator complex is an important regulator of RNA polymerase II-dependent genes in eukaryotic cells. In contrast to the situation in many other eukaryotes, the conserved Med15 protein is not a stable component of Mediator isolated from fission yeast. We here demonstrate that Med15 exists in a protein complex together with Hrp1, a CHD1 ATP-dependent chromatin-remodeling protein. The Med15-Hrp1 subcomplex is not a component of the core Mediator complex but can interact with the L-Mediator conformation. Deletion of med15(+) and hrp1(+) causes very similar effects on global steady-state levels of mRNA, and genome-wide analyses demonstrate that Med15 associates with a distinct subset of Hrp1-bound gene promoters. Our findings therefore indicate that Mediator may directly influence histone density at regulated promoters.
Collapse
Affiliation(s)
- Olga Khorosjutina
- From the Division of Metabolic Diseases, Karolinska Institutet, SE-141 86 Stockholm, Sweden
| | | | | | | | | | | | | | | |
Collapse
|
46
|
Shahi P, Gulshan K, Näär AM, Moye-Rowley WS. Differential roles of transcriptional mediator subunits in regulation of multidrug resistance gene expression in Saccharomyces cerevisiae. Mol Biol Cell 2010; 21:2469-82. [PMID: 20505076 PMCID: PMC2903675 DOI: 10.1091/mbc.e09-10-0899] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Abstract
Med12 is a transcriptional Mediator subunit most typically associated with negative control of gene expression. Here Med12 is demonstrated to serve as a positive regulator required for activation of multidrug resistance gene expression in yeast cells lacking their mitochondrial genome. The multiprotein transcriptional Mediator complex provides a key link between RNA polymerase II and upstream transcriptional activator proteins. Previous work has established that the multidrug resistance transcription factors Pdr1 and Pdr3 interact with the Mediator component Med15/Gal11 to drive normal levels of expression of the ATP-binding cassette transporter-encoding gene PDR5 in Saccharomyces cerevisiae. PDR5 transcription is induced upon loss of the mitochondrial genome (ρ0 cells) and here we provide evidence that this ρ0 induction is Med15 independent. A search through other known Mediator components determined that Med12/Srb8, a member of the CDK8 Mediator submodule, is required for ρ0 activation of PDR5 transcription. The CDK8 submodule contains the cyclin C homologue (CycC/Srb11), cyclin-dependent kinase Cdk8/Srb10, and the large Med13/Srb9 protein. Loss of these other proteins did not lead to the same block in PDR5 induction. Chromatin immunoprecipitation analyses demonstrated that Med15 is associated with the PDR5 promoter in both ρ+ and ρ0, whereas Med12 recruitment to this target promoter is highly responsive to loss of the mitochondrial genome. Coimmunoprecipitation experiments revealed that association of Pdr3 with Med12 can only be detected in ρ0 cells. These experiments uncover the unique importance of Med12 in activated transcription of PDR5 seen in ρ0 cells.
Collapse
Affiliation(s)
- Puja Shahi
- Department of Molecular Physiology and Biophysics, Carver College of Medicine, University of Iowa, Iowa City, IA 52242, USA
| | | | | | | |
Collapse
|
47
|
Takada I, Tsuji N, Youn MY, Fujiyama S, Okada M, Imai Y, Kondo S, Kitakawa H, Yasuda H, Kato S. Purification and identification of estrogen receptor alpha co-regulators in osteoclasts. Ann N Y Acad Sci 2010; 1192:201-7. [DOI: 10.1111/j.1749-6632.2009.05215.x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
|
48
|
Proshkina GM, Shpakovskiĭ GV. [The functional interaction of an RNA polymerase II Rpb11 subunit with the Med18 subunit (Srb5) of the Saccharomyces cerevisiae mediator complex]. RUSSIAN JOURNAL OF BIOORGANIC CHEMISTRY 2010; 35:572-6. [PMID: 19928061 DOI: 10.1134/s1068162009040153] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
The SRB5 gene encoding the Med18 (Srb5) subunit of the mediator complex of the Saccharomyces cerevisiae transcription apparatus was identified in the C-terminal region of the yeast RNA polymerase II Rpb11 subunit as a multicopy suppressor of the Leu111Ala (L111A) point mutation. Thus, the functional interaction between one of the mediator components and the core of the major transcription enzyme was first shown. It is also essential that the suppressed point mutation was located in the short C-terminal region of the Rpb11subunit, which plays an important role for the evolution of the eukaryotic transcription apparatus, as was demonstrated in our previous studies.
Collapse
|
49
|
Cyclin-dependent kinase 8 positively cooperates with Mediator to promote thyroid hormone receptor-dependent transcriptional activation. Mol Cell Biol 2010; 30:2437-48. [PMID: 20231357 DOI: 10.1128/mcb.01541-09] [Citation(s) in RCA: 56] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
Mediator is a multisubunit assemblage of proteins originally identified in humans as a coactivator bound to thyroid hormone receptors (TRs) and essential for thyroid hormone (T3)-dependent transcription. Cyclin-dependent kinase 8 (CDK8), cyclin C, MED12, and MED13 form a variably associated Mediator subcomplex (termed the CDK8 module) whose functional role in TR-dependent transcription remains unclear. Using in vitro and cellular approaches, we show here that Mediator complexes containing the CDK8 module are specifically recruited into preinitiation complexes at the TR target gene type I deiodinase (DioI) together with RNA polymerase II (Pol II) in a TR- and T3-dependent manner. We found that CDK8 is essential for robust T3-dependent Dio1 transcription and that CDK8 knockdown via RNA interference decreased Pol II occupancy, and also the recruitment of the Pol II kinase CDK9, at the DioI promoter. Chromatin immunoprecipitation revealed CDK8 occupancy at the DioI promoter concurrent with active transcription, thus suggesting CDK8 involvement in transcriptional reinitiation. Mutagenesis assays showed that CDK8 kinase activity is necessary for full T3-dependent DioI activation, whereas in vitro kinase studies indicated that CDK8 may contribute to Pol II phosphorylation. Collectively, our data suggest CDK8 plays an important coactivator role in TR-dependent transcription by promoting Pol II recruitment and activation at TR target gene promoters.
Collapse
|
50
|
Gillmor CS, Park MY, Smith MR, Pepitone R, Kerstetter RA, Poethig RS. The MED12-MED13 module of Mediator regulates the timing of embryo patterning in Arabidopsis. Development 2010; 137:113-22. [PMID: 20023166 DOI: 10.1242/dev.043174] [Citation(s) in RCA: 93] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
The Arabidopsis embryo becomes patterned into central and peripheral domains during the first few days after fertilization. A screen for mutants that affect this process identified two genes, GRAND CENTRAL (GCT)and CENTER CITY (CCT). Mutations in GCT and CCT delay the specification of central and peripheral identity and the globular-to-heart transition, but have little or no effect on the initial growth rate of the embryo. Mutant embryos eventually recover and undergo relatively normal patterning, albeit at an inappropriate size. GCT and CCT were identified as the Arabidopsis orthologs of MED13 and MED12 - evolutionarily conserved proteins that act in association with the Mediator complex to negatively regulate transcription. The predicted function of these proteins combined with the effect of gct and cct on embryo development suggests that MED13 and MED12 regulate pattern formation during Arabidopsis embryogenesis by transiently repressing a transcriptional program that interferes with this process. Their mutant phenotype reveals the existence of a previously unknown temporal regulatory mechanism in plant embryogenesis.
Collapse
Affiliation(s)
- C Stewart Gillmor
- Department of Biological Sciences, University of Pennsylvania, Philadelphia, PA 19104, USA
| | | | | | | | | | | |
Collapse
|