1
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Kozlowski P. Thirty Years with ERH: An mRNA Splicing and Mitosis Factor Only or Rather a Novel Genome Integrity Protector? Cells 2023; 12:2449. [PMID: 37887293 PMCID: PMC10605862 DOI: 10.3390/cells12202449] [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: 08/29/2023] [Revised: 10/10/2023] [Accepted: 10/12/2023] [Indexed: 10/28/2023] Open
Abstract
ERH is a 100 to about 110 aa nuclear protein with unique primary and three-dimensional structures that are very conserved from simple eukaryotes to humans, albeit some species have lost its gene, with most higher fungi being a noteworthy example. Initially, studies on Drosophila melanogaster implied its function in pyrimidine metabolism. Subsequently, research on Xenopus laevis suggested that it acts as a transcriptional repressor. Finally, studies in humans pointed to a role in pre-mRNA splicing and in mitosis but further research, also in Caenorhabditis elegans and Schizosaccharomyces pombe, demonstrated its much broader activity, namely involvement in the biogenesis of mRNA, and miRNA, piRNA and some other ncRNAs, and in repressive heterochromatin formation. ERH interacts with numerous, mostly taxon-specific proteins, like Mmi1 and Mei2 in S. pombe, PID-3/PICS-1, TOST-1 and PID-1 in C. elegans, and DGCR8, CIZ1, PDIP46/SKAR and SAFB1/2 in humans. There are, however, some common themes in this wide range of processes and partners, such as: (a) ERH homodimerizes to form a scaffold for several complexes involved in the metabolism of nucleic acids, (b) all these RNAs are RNA polymerase II transcripts, (c) pre-mRNAs, whose splicing depends on ERH, are enriched in transcripts of DNA damage response and DNA metabolism genes, and (d) heterochromatin is formed to silence unwanted transcription, e.g., from repetitive elements. Thus, it seems that ERH has been adopted for various pathways that serve to maintain genome integrity.
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Affiliation(s)
- Piotr Kozlowski
- Department of Molecular Biology, Institute of Biochemistry, Faculty of Biology, University of Warsaw, Miecznikowa 1, 02-096 Warsaw, Poland
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2
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Pang K, Li ML, Hao L, Shi ZD, Feng H, Chen B, Ma YY, Xu H, Pan D, Chen ZS, Han CH. ERH Gene and Its Role in Cancer Cells. Front Oncol 2022; 12:900496. [PMID: 35677162 PMCID: PMC9169799 DOI: 10.3389/fonc.2022.900496] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2022] [Accepted: 04/05/2022] [Indexed: 12/12/2022] Open
Abstract
Cancer is a major public health problem worldwide. Studies on oncogenes and tumor-targeted therapies have become an important part of cancer treatment development. In this review, we summarize and systematically introduce the gene enhancer of rudimentary homolog (ERH), which encodes a highly conserved small molecule protein. ERH mainly exists as a protein partner in human cells. It is involved in pyrimidine metabolism and protein complexes, acts as a transcriptional repressor, and participates in cell cycle regulation. Moreover, it is involved in DNA damage repair, mRNA splicing, the process of microRNA hairpins as well as erythroid differentiation. There are many related studies on the role of ERH in cancer cells; however, there are none on tumor-targeted therapeutic drugs or related therapies based on the expression of ERH. This study will provide possible directions for oncologists to further their research studies in this field.
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Affiliation(s)
- Kun Pang
- Department of Urology, Xuzhou Central Hospital, Affiliated Central Hospital of Xuzhou Medical University, Xuzhou, China
| | - Mei-Li Li
- Department of Ophthalmology, The Affiliated Xuzhou Municipal Hospital of Xuzhou Medical University, Xuzhou First People's Hospital, Xuzhou, China.,Department of Ophthalmology, Eye Disease Prevention and Treatment Institute of Xuzhou, Xuzhou, China
| | - Lin Hao
- Department of Urology, Xuzhou Central Hospital, Affiliated Central Hospital of Xuzhou Medical University, Xuzhou, China
| | - Zhen-Duo Shi
- Department of Urology, Xuzhou Central Hospital, Affiliated Central Hospital of Xuzhou Medical University, Xuzhou, China
| | - Harry Feng
- STEM Academic Department, Wyoming Seminary, Kingston, PA, United States
| | - Bo Chen
- Department of Urology, Xuzhou Central Hospital, Affiliated Central Hospital of Xuzhou Medical University, Xuzhou, China
| | - Yu-Yang Ma
- Graduate School, Bengbu Medical College, Bengbu, China
| | - Hao Xu
- Graduate School, Bengbu Medical College, Bengbu, China
| | - Deng Pan
- Graduate School, Bengbu Medical College, Bengbu, China
| | - Zhe-Sheng Chen
- College of Pharmacy and Health Sciences, St. John's University, New York, NY, United States
| | - Cong-Hui Han
- Department of Urology, Xuzhou Central Hospital, Affiliated Central Hospital of Xuzhou Medical University, Xuzhou, China
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3
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Ohtsuka H, Shimasaki T, Aiba H. Response to leucine in Schizosaccharomyces pombe (fission yeast). FEMS Yeast Res 2022; 22:6553821. [PMID: 35325114 PMCID: PMC9041340 DOI: 10.1093/femsyr/foac020] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2021] [Revised: 03/08/2022] [Accepted: 03/22/2022] [Indexed: 11/13/2022] Open
Abstract
Leucine (Leu) is a branched-chain, essential amino acid in animals, including humans. Fungi, including the fission yeast Schizosaccharomyces pombe, can biosynthesize Leu, but deletion of any of the genes in this biosynthesis leads to Leu auxotrophy. In this yeast, although a mutation in the Leu biosynthetic pathway, leu1-32, is clearly inconvenient for this species, it has increased its usefulness as a model organism in laboratories worldwide. Leu auxotrophy produces intracellular responses and phenotypes different from those of the prototrophic strains, depending on the growing environment, which necessitates a certain degree of caution in the analysis and interpretation of the experimental results. Under amino acid starvation, the amino acid-auxotrophic yeast induces cellular responses, which are conserved in higher organisms without the ability of synthesizing amino acids. This mini-review focuses on the roles of Leu in S. pombe and discusses biosynthetic pathways, contribution to experimental convenience using a plasmid specific for Leu auxotrophic yeast, signaling pathways, and phenotypes caused by Leu starvation. An accurate understanding of the intracellular responses brought about by Leu auxotrophy can contribute to research in various fields using this model organism and to the understanding of intracellular responses in higher organisms that cannot synthesize Leu.
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Affiliation(s)
- Hokuto Ohtsuka
- Laboratory of Molecular Microbiology, Department of Basic Medicinal Sciences, Graduate School of Pharmaceutical Sciences, Nagoya University, Chikusa-ku, Nagoya 464-8601, Japan
| | - Takafumi Shimasaki
- Laboratory of Molecular Microbiology, Department of Basic Medicinal Sciences, Graduate School of Pharmaceutical Sciences, Nagoya University, Chikusa-ku, Nagoya 464-8601, Japan
| | - Hirofumi Aiba
- Laboratory of Molecular Microbiology, Department of Basic Medicinal Sciences, Graduate School of Pharmaceutical Sciences, Nagoya University, Chikusa-ku, Nagoya 464-8601, Japan
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4
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Kwon SC, Jang H, Shen S, Baek SC, Kim K, Yang J, Kim J, Kim JS, Wang S, Shi Y, Li F, Kim VN. ERH facilitates microRNA maturation through the interaction with the N-terminus of DGCR8. Nucleic Acids Res 2020; 48:11097-11112. [PMID: 33035348 PMCID: PMC7641749 DOI: 10.1093/nar/gkaa827] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2020] [Revised: 09/14/2020] [Accepted: 10/02/2020] [Indexed: 01/28/2023] Open
Abstract
The microprocessor complex cleaves the primary transcript of microRNA (pri-miRNA) to initiate miRNA maturation. Microprocessor is known to consist of RNase III DROSHA and dsRNA-binding DGCR8. Here, we identify Enhancer of Rudimentary Homolog (ERH) as a new component of Microprocessor. Through a crystal structure and biochemical experiments, we reveal that ERH uses its hydrophobic groove to bind to a conserved region in the N-terminus of DGCR8, in a 2:2 stoichiometry. Knock-down of ERH or deletion of the DGCR8 N-terminus results in a reduced processing of suboptimal pri-miRNAs in polycistronic miRNA clusters. ERH increases the processing of suboptimal pri-miR-451 in a manner dependent on its neighboring pri-miR-144. Thus, the ERH dimer may mediate 'cluster assistance' in which Microprocessor is loaded onto a poor substrate with help from a high-affinity substrate in the same cluster. Our study reveals a role of ERH in the miRNA biogenesis pathway.
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Affiliation(s)
- S Chul Kwon
- Center for RNA Research, Institute for Basic Science, Seoul 08826, Korea.,School of Biological Sciences, Seoul National University, Seoul 08826, Korea.,School of Biomedical Sciences, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
| | - Harim Jang
- Center for RNA Research, Institute for Basic Science, Seoul 08826, Korea.,School of Biological Sciences, Seoul National University, Seoul 08826, Korea
| | - Siyuan Shen
- Hefei National Laboratory for Physical Sciences at Microscale, School of Life Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui 230026, China
| | - S Chan Baek
- Center for RNA Research, Institute for Basic Science, Seoul 08826, Korea.,School of Biological Sciences, Seoul National University, Seoul 08826, Korea
| | - Kijun Kim
- Center for RNA Research, Institute for Basic Science, Seoul 08826, Korea.,School of Biological Sciences, Seoul National University, Seoul 08826, Korea
| | - Jihye Yang
- Center for RNA Research, Institute for Basic Science, Seoul 08826, Korea.,School of Biological Sciences, Seoul National University, Seoul 08826, Korea
| | - Jeesoo Kim
- Center for RNA Research, Institute for Basic Science, Seoul 08826, Korea.,School of Biological Sciences, Seoul National University, Seoul 08826, Korea
| | - Jong-Seo Kim
- Center for RNA Research, Institute for Basic Science, Seoul 08826, Korea.,School of Biological Sciences, Seoul National University, Seoul 08826, Korea
| | - Suman Wang
- Hefei National Laboratory for Physical Sciences at Microscale, School of Life Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui 230026, China
| | - Yunyu Shi
- Hefei National Laboratory for Physical Sciences at Microscale, School of Life Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui 230026, China
| | - Fudong Li
- Hefei National Laboratory for Physical Sciences at Microscale, School of Life Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui 230026, China
| | - V Narry Kim
- Center for RNA Research, Institute for Basic Science, Seoul 08826, Korea.,School of Biological Sciences, Seoul National University, Seoul 08826, Korea
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5
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Schwer B, Sanchez AM, Shuman S. Inactivation of fission yeast Erh1 de-represses pho1 expression: evidence that Erh1 is a negative regulator of prt lncRNA termination. RNA (NEW YORK, N.Y.) 2020; 26:1334-1344. [PMID: 32546512 PMCID: PMC7491324 DOI: 10.1261/rna.076463.120] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/16/2020] [Accepted: 06/01/2020] [Indexed: 05/08/2023]
Abstract
Fission yeast Erh1 exists in a complex with RNA-binding protein Mmi1. Deletion of erh1 up-regulates the phosphate homeostasis gene pho1, which is normally repressed by transcription in cis of a 5' flanking prt lncRNA. Here we present evidence that de-repression of pho1 by erh1Δ is achieved through precocious 3'-processing/termination of prt lncRNA synthesis, to wit: (i) erh1Δ does not affect the activity of the prt or pho1 promoters per se; (ii) de-repression by erh1Δ depends on CPF (cleavage and polyadenylation factor) subunits Ctf1, Dis2, Ssu72, Swd22, and Ppn1 and on termination factor Rhn1; (iii) de-repression requires synthesis by the Asp1 IPP kinase of inositol 1-pyrophosphates (1-IPPs); (iv) de-repression is effaced by mutating Thr4 of the RNA polymerase II CTD to alanine; and (v) erh1Δ exerts an additive effect on pho1 de-repression in combination with mutating CTD Ser7 to alanine and with deletion of the IPP pyrophosphatase Aps1. These findings point to Erh1 as an antagonist of lncRNA termination in the prt-pho1 axis. In contrast, in mmi1Δ cells there is a reduction in pho1 mRNA and increase in the formation of a prt-pho1 read-through transcript, consistent with Mmi1 being an agonist of prt termination. We envision that Erh1 acts as a brake on Mmi1's ability to promote CPF-dependent termination during prt lncRNA synthesis. Consistent with this idea, erh1Δ de-repression of pho1 was eliminated by mutating the Mmi1-binding sites in the prt lncRNA.
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Affiliation(s)
- Beate Schwer
- Department of Microbiology and Immunology, Weill Cornell Medical College, New York, New York 10065, USA
| | - Ana M Sanchez
- Department of Microbiology and Immunology, Weill Cornell Medical College, New York, New York 10065, USA
- Gerstner Sloan Kettering Graduate School of Biomedical Sciences, New York, New York 10065, USA
| | - Stewart Shuman
- Molecular Biology Program, Sloan Kettering Institute, New York, New York 10065, USA
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6
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Formation of S. pombe Erh1 homodimer mediates gametogenic gene silencing and meiosis progression. Sci Rep 2020; 10:1034. [PMID: 31974447 PMCID: PMC6978305 DOI: 10.1038/s41598-020-57872-4] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2019] [Accepted: 12/23/2019] [Indexed: 11/17/2022] Open
Abstract
Timely and accurate expression of the genetic information relies on the integration of environmental cues and the activation of regulatory networks involving transcriptional and post-transcriptional mechanisms. In fission yeast, meiosis-specific transcripts are selectively targeted for degradation during mitosis by the EMC complex, composed of Erh1, the ortholog of human ERH, and the YTH family RNA-binding protein Mmi1. Here, we present the crystal structure of Erh1 and show that it assembles as a homodimer. Mutations of amino acid residues to disrupt Erh1 homodimer formation result in loss-of-function phenotypes, similar to erh1∆ cells: expression of meiotic genes is derepressed in mitotic cells and meiosis progression is severely compromised. Interestingly, formation of Erh1 homodimer is dispensable for interaction with Mmi1, suggesting that only fully assembled EMC complexes consisting of two Mmi1 molecules bridged by an Erh1 dimer are functionally competent. We also show that Erh1 does not contribute to Mmi1-dependent down-regulation of the meiosis regulator Mei2, supporting the notion that Mmi1 performs additional functions beyond EMC. Overall, our results provide a structural basis for the assembly of the EMC complex and highlight its biological relevance in gametogenic gene silencing and meiosis progression.
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7
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Xu X, Yanagida M. Suppressor screening reveals common kleisin-hinge interaction in condensin and cohesin, but different modes of regulation. Proc Natl Acad Sci U S A 2019; 116:10889-10898. [PMID: 31072933 PMCID: PMC6561158 DOI: 10.1073/pnas.1902699116] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Abstract
Cohesin and condensin play fundamental roles in sister chromatid cohesion and chromosome segregation, respectively. Both consist of heterodimeric structural maintenance of chromosomes (SMC) subunits, which possess a head (containing ATPase) and a hinge, intervened by long coiled coils. Non-SMC subunits (Cnd1, Cnd2, and Cnd3 for condensin; Rad21, Psc3, and Mis4 for cohesin) bind to the SMC heads. Here, we report a large number of spontaneous extragenic suppressors for fission yeast condensin and cohesin mutants, and their sites were determined by whole-genome sequencing. Mutants of condensin's non-SMC subunits were rescued by impairing the SUMOylation pathway. Indeed, SUMOylation of Cnd2, Cnd3, and Cut3 occurs in midmitosis, and Cnd3 K870 SUMOylation functionally opposes Cnd subunits. In contrast, cohesin mutants rad21 and psc3 were rescued by loss of the RNA elimination pathway (Erh1, Mmi1, and Red1), and loader mutant mis4 was rescued by loss of Hrp1-mediated chromatin remodeling. In addition, distinct regulations were discovered for condensin and cohesin hinge mutants. Mutations in the N-terminal helix bundle [containing a helix-turn-helix (HTH) motif] of kleisin subunits (Cnd2 and Rad21) rescue virtually identical hinge interface mutations in cohesin and condensin, respectively. These mutations may regulate kleisin's interaction with the coiled coil at the SMC head, thereby revealing a common, but previously unknown, suppression mechanism between the hinge and the kleisin N domain, which is required for successful chromosome segregation. We propose that in both condensin and cohesin, the head (or kleisin) and hinge may interact and collaboratively regulate the resulting coiled coils to hold and release chromosomal DNAs.
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Affiliation(s)
- Xingya Xu
- G0 Cell Unit, Okinawa Institute of Science and Technology Graduate University, Onna-son, 904-0495 Okinawa, Japan
| | - Mitsuhiro Yanagida
- G0 Cell Unit, Okinawa Institute of Science and Technology Graduate University, Onna-son, 904-0495 Okinawa, Japan
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8
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Xie G, Vo TV, Thillainadesan G, Holla S, Zhang B, Jiang Y, Lv M, Xu Z, Wang C, Balachandran V, Shi Y, Li F, Grewal SIS. A conserved dimer interface connects ERH and YTH family proteins to promote gene silencing. Nat Commun 2019; 10:251. [PMID: 30651569 PMCID: PMC6335422 DOI: 10.1038/s41467-018-08273-9] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2018] [Accepted: 12/21/2018] [Indexed: 12/18/2022] Open
Abstract
Gene regulatory mechanisms rely on a complex network of RNA processing factors to prevent untimely gene expression. In fission yeast, the highly conserved ortholog of human ERH, called Erh1, interacts with the YTH family RNA binding protein Mmi1 to form the Erh1-Mmi1 complex (EMC) implicated in gametogenic gene silencing. However, the structural basis of EMC assembly and its functions are poorly understood. Here, we present the co-crystal structure of the EMC that consists of Erh1 homodimers interacting with Mmi1 in a 2:2 stoichiometry via a conserved molecular interface. Structure-guided mutation of the Mmi1Trp112 residue, which is required for Erh1 binding, causes defects in facultative heterochromatin assembly and gene silencing while leaving Mmi1-mediated transcription termination intact. Indeed, EMC targets masked in mmi1∆ due to termination defects are revealed in mmi1W112A. Our study delineates EMC requirements in gene silencing and identifies an ERH interface required for interaction with an RNA binding protein.
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Affiliation(s)
- Guodong Xie
- Hefei National Laboratory for Physical Sciences at the Microscale, School of Life Sciences, University of Science and Technology of China, 230026, Hefei, China
| | - Tommy V Vo
- Laboratory of Biochemistry and Molecular Biology, National Cancer Institute, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Gobi Thillainadesan
- Laboratory of Biochemistry and Molecular Biology, National Cancer Institute, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Sahana Holla
- Laboratory of Biochemistry and Molecular Biology, National Cancer Institute, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Beibei Zhang
- Hefei National Laboratory for Physical Sciences at the Microscale, School of Life Sciences, University of Science and Technology of China, 230026, Hefei, China
| | - Yiyang Jiang
- Hefei National Laboratory for Physical Sciences at the Microscale, School of Life Sciences, University of Science and Technology of China, 230026, Hefei, China
| | - Mengqi Lv
- Hefei National Laboratory for Physical Sciences at the Microscale, School of Life Sciences, University of Science and Technology of China, 230026, Hefei, China
| | - Zheng Xu
- Hefei National Laboratory for Physical Sciences at the Microscale, School of Life Sciences, University of Science and Technology of China, 230026, Hefei, China
| | - Chongyuan Wang
- Hefei National Laboratory for Physical Sciences at the Microscale, School of Life Sciences, University of Science and Technology of China, 230026, Hefei, China
| | - Vanivilasini Balachandran
- Laboratory of Biochemistry and Molecular Biology, National Cancer Institute, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Yunyu Shi
- Hefei National Laboratory for Physical Sciences at the Microscale, School of Life Sciences, University of Science and Technology of China, 230026, Hefei, China
| | - Fudong Li
- Hefei National Laboratory for Physical Sciences at the Microscale, School of Life Sciences, University of Science and Technology of China, 230026, Hefei, China.
| | - Shiv I S Grewal
- Laboratory of Biochemistry and Molecular Biology, National Cancer Institute, National Institutes of Health, Bethesda, MD, 20892, USA.
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9
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Shichino Y, Otsubo Y, Kimori Y, Yamamoto M, Yamashita A. YTH-RNA-binding protein prevents deleterious expression of meiotic proteins by tethering their mRNAs to nuclear foci. eLife 2018; 7:32155. [PMID: 29424342 PMCID: PMC5807050 DOI: 10.7554/elife.32155] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2017] [Accepted: 01/31/2018] [Indexed: 12/24/2022] Open
Abstract
Accurate and extensive regulation of meiotic gene expression is crucial to distinguish germ cells from somatic cells. In the fission yeast Schizosaccharomyces pombe, a YTH family RNA-binding protein, Mmi1, directs the nuclear exosome-mediated elimination of meiotic transcripts during vegetative proliferation. Mmi1 also induces the formation of facultative heterochromatin at a subset of its target genes. Here, we show that Mmi1 prevents the mistimed expression of meiotic proteins by tethering their mRNAs to the nuclear foci. Mmi1 interacts with itself with the assistance of a homolog of Enhancer of Rudimentary, Erh1. Mmi1 self-interaction is required for foci formation, target transcript elimination, their nuclear retention, and protein expression inhibition. We propose that nuclear foci formed by Mmi1 are not only the site of RNA degradation, but also of sequestration of meiotic transcripts from the translation machinery.
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Affiliation(s)
- Yuichi Shichino
- Laboratory of Cell Responses, National Institute for Basic Biology, Okazaki, Japan
| | - Yoko Otsubo
- Laboratory of Cell Responses, National Institute for Basic Biology, Okazaki, Japan
| | - Yoshitaka Kimori
- Department of Imaging Science, Center for Novel Science Initiatives, National Institutes of Natural Sciences, Okazaki, Japan.,Laboratory of Biological Diversity, National Institute for Basic Biology, Okazaki, Japan.,Department of Basic Biology, School of Life Science, SOKENDAI (The Graduate University for Advanced Studies), Okazaki, Japan
| | - Masayuki Yamamoto
- Laboratory of Cell Responses, National Institute for Basic Biology, Okazaki, Japan.,Department of Basic Biology, School of Life Science, SOKENDAI (The Graduate University for Advanced Studies), Okazaki, Japan
| | - Akira Yamashita
- Laboratory of Cell Responses, National Institute for Basic Biology, Okazaki, Japan.,Department of Basic Biology, School of Life Science, SOKENDAI (The Graduate University for Advanced Studies), Okazaki, Japan
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10
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Emerging Roles for Ciz1 in Cell Cycle Regulation and as a Driver of Tumorigenesis. Biomolecules 2016; 7:biom7010001. [PMID: 28036012 PMCID: PMC5372713 DOI: 10.3390/biom7010001] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2016] [Revised: 12/12/2016] [Accepted: 12/14/2016] [Indexed: 12/19/2022] Open
Abstract
Precise duplication of the genome is a prerequisite for the health and longevity of multicellular organisms. The temporal regulation of origin specification, replication licensing, and firing at replication origins is mediated by the cyclin-dependent kinases. Here the role of Cip1 interacting Zinc finger protein 1 (Ciz1) in regulation of cell cycle progression is discussed. Ciz1 contributes to regulation of the G1/S transition in mammalian cells. Ciz1 contacts the pre-replication complex (pre-RC) through cell division cycle 6 (Cdc6) interactions and aids localization of cyclin A- cyclin-dependent kinase 2 (CDK2) activity to chromatin and the nuclear matrix during initiation of DNA replication. We discuss evidence that Ciz1 serves as a kinase sensor that regulates both initiation of DNA replication and prevention of re-replication. Finally, the emerging role for Ciz1 in cancer biology is discussed. Ciz1 is overexpressed in common tumors and tumor growth is dependent on Ciz1 expression, suggesting that Ciz1 is a driver of tumor growth. We present evidence that Ciz1 may contribute to deregulation of the cell cycle due to its ability to alter the CDK activity thresholds that are permissive for initiation of DNA replication. We propose that Ciz1 may contribute to oncogenesis by induction of DNA replication stress and that Ciz1 may be a multifaceted target in cancer therapy.
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11
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Sugiyama T, Thillainadesan G, Chalamcharla VR, Meng Z, Balachandran V, Dhakshnamoorthy J, Zhou M, Grewal SIS. Enhancer of Rudimentary Cooperates with Conserved RNA-Processing Factors to Promote Meiotic mRNA Decay and Facultative Heterochromatin Assembly. Mol Cell 2016; 61:747-759. [PMID: 26942678 DOI: 10.1016/j.molcel.2016.01.029] [Citation(s) in RCA: 66] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2015] [Revised: 12/22/2015] [Accepted: 01/27/2016] [Indexed: 12/21/2022]
Abstract
Erh1, the fission yeast homolog of Enhancer of rudimentary, is implicated in meiotic mRNA elimination during vegetative growth, but its function is poorly understood. We show that Erh1 and the RNA-binding protein Mmi1 form a stoichiometric complex, called the Erh1-Mmi1 complex (EMC), to promote meiotic mRNA decay and facultative heterochromatin assembly. To perform these functions, EMC associates with two distinct complexes, Mtl1-Red1 core (MTREC) and CCR4-NOT. Whereas MTREC facilitates assembly of heterochromatin islands coating meiotic genes silenced by the nuclear exosome, CCR4-NOT promotes RNAi-dependent heterochromatin domain (HOOD) formation at EMC-target loci. CCR4-NOT also assembles HOODs at retrotransposons and regulated genes containing cryptic introns. We find that CCR4-NOT facilitates HOOD assembly through its association with the conserved Pir2/ARS2 protein, and also maintains rDNA integrity and silencing by promoting heterochromatin formation. Our results reveal connections among Erh1, CCR4-NOT, Pir2/ARS2, and RNAi, which target heterochromatin to regulate gene expression and protect genome integrity.
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Affiliation(s)
- Tomoyasu Sugiyama
- Laboratory of Biochemistry and Molecular Biology, National Cancer Institute, Bethesda, MD 20892, USA
| | - Gobi Thillainadesan
- Laboratory of Biochemistry and Molecular Biology, National Cancer Institute, Bethesda, MD 20892, USA
| | - Venkata R Chalamcharla
- Laboratory of Biochemistry and Molecular Biology, National Cancer Institute, Bethesda, MD 20892, USA
| | - Zhaojing Meng
- Laboratory of Proteomics and Analytical Technologies, Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA
| | - Vanivilasini Balachandran
- Laboratory of Biochemistry and Molecular Biology, National Cancer Institute, Bethesda, MD 20892, USA
| | - Jothy Dhakshnamoorthy
- Laboratory of Biochemistry and Molecular Biology, National Cancer Institute, Bethesda, MD 20892, USA
| | - Ming Zhou
- Laboratory of Proteomics and Analytical Technologies, Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA
| | - Shiv I S Grewal
- Laboratory of Biochemistry and Molecular Biology, National Cancer Institute, Bethesda, MD 20892, USA.
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12
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Enhancer of Rudimentary Homolog Affects the Replication Stress Response through Regulation of RNA Processing. Mol Cell Biol 2015; 35:2979-90. [PMID: 26100022 DOI: 10.1128/mcb.01276-14] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2014] [Accepted: 06/11/2015] [Indexed: 12/21/2022] Open
Abstract
Accurate replication of DNA is imperative for the maintenance of genomic integrity. We identified Enhancer of Rudimentary Homolog (ERH) using a whole-genome RNA interference (RNAi) screen to discover novel proteins that function in the replication stress response. Here we report that ERH is important for DNA replication and recovery from replication stress. ATR pathway activity is diminished in ERH-deficient cells. The reduction in ATR signaling corresponds to a decrease in the expression of multiple ATR pathway genes, including ATR itself. ERH interacts with multiple RNA processing complexes, including splicing regulators. Furthermore, splicing of ATR transcripts is deficient in ERH-depleted cells. Transcriptome-wide analysis indicates that ERH depletion affects the levels of ∼1,500 transcripts, with DNA replication and repair genes being highly enriched among those with reduced expression. Splicing defects were evident in ∼750 protein-coding genes, which again were enriched for DNA metabolism genes. Thus, ERH regulation of RNA processing is needed to ensure faithful DNA replication and repair.
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Weng MT, Luo J. The enigmatic ERH protein: its role in cell cycle, RNA splicing and cancer. Protein Cell 2014; 4:807-12. [PMID: 24078386 DOI: 10.1007/s13238-013-3056-3] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2013] [Accepted: 08/26/2013] [Indexed: 12/21/2022] Open
Abstract
Enhancer of rudimentary homolog (ERH) is a small, highly conserved protein among eukaryotes. Since its discovery nearly 20 years ago, its molecular function has remained enigmatic. It has been implicated to play a role in transcriptional regulation and in cell cycle. We recently showed that ERH binds to the Sm complex and is required for the mRNA splicing of the mitotic motor protein CENP-E. Furthermore, cancer cells driven by mutations in the KRAS oncogene are particularly sensitive to RNAi-mediated suppression of ERH function, and ERH expression is inversely correlated with survival in colorectal cancer patients whose tumors harbor KRAS mutation. These recent findings indicate that ERH plays an important role in cell cycle through its mRNA splicing activity and is critically required for genomic stability and cancer cell survival.
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Banko MI, Krzyzanowski MK, Turcza P, Maniecka Z, Kulis M, Kozlowski P. Identification of amino acid residues of ERH required for its recruitment to nuclear speckles and replication foci in HeLa cells. PLoS One 2013; 8:e74885. [PMID: 24015320 PMCID: PMC3755989 DOI: 10.1371/journal.pone.0074885] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2013] [Accepted: 08/07/2013] [Indexed: 11/18/2022] Open
Abstract
ERH is a small, highly evolutionarily conserved nuclear protein of unknown function. Its three-dimensional structure is absolutely unique and it can form a homodimer through a β sheet surface. ERH has been shown to interact, among others, with PDIP46/SKAR and Ciz1. When coexpressed with the latter protein, ERH accumulates in replication foci in the nucleus of HeLa cells. Here, we report that when ERH is coexpressed with PDIP46/SKAR in HeLa cells, it is recruited to nuclear speckles, and identify amino acid residues critical for targeting ERH to both these subnuclear structures. ERH H3A Q9A shows a diminished recruitment to nuclear speckles but it is recruited to replication foci. ERH E37A T51A is very poorly recruited to replication foci while still accumulating in nuclear speckles. Consequently, ERH H3A Q9A E37A T51A is recruited neither to nuclear speckles nor to replication foci. The lack of interactions of these three ERH forms with PDIP46/SKAR and/or Ciz1 was further confirmed in vitro by GST pull-down assay. The residues whose substitutions interfere with the accumulation in nuclear speckles are situated on the β sheet surface of ERH, indicating that only the monomer of ERH can interact with PDIP46/SKAR. Substitutions affecting the recruitment to replication foci map to the other side of ERH, near a long loop between the α1 and α2 helices, thus both the monomer and the dimer of ERH could interact with Ciz1. The construction of the ERH mutants not recruited to nuclear speckles or replication foci will facilitate further studies on ERH actions in these subnuclear structures.
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Affiliation(s)
- Monika I. Banko
- Department of Molecular Biology, Faculty of Biology, University of Warsaw, Warsaw, Poland
| | - Marek K. Krzyzanowski
- Department of Molecular Biology, Faculty of Biology, University of Warsaw, Warsaw, Poland
| | - Paulina Turcza
- Department of Molecular Biology, Faculty of Biology, University of Warsaw, Warsaw, Poland
| | - Zuzanna Maniecka
- Department of Molecular Biology, Faculty of Biology, University of Warsaw, Warsaw, Poland
| | - Marta Kulis
- Department of Molecular Biology, Faculty of Biology, University of Warsaw, Warsaw, Poland
| | - Piotr Kozlowski
- Department of Molecular Biology, Faculty of Biology, University of Warsaw, Warsaw, Poland
- * E-mail:
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Yamashita A, Takayama T, Iwata R, Yamamoto M. A novel factor Iss10 regulates Mmi1-mediated selective elimination of meiotic transcripts. Nucleic Acids Res 2013; 41:9680-7. [PMID: 23980030 PMCID: PMC3834831 DOI: 10.1093/nar/gkt763] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
A number of meiosis-specific transcripts are selectively eliminated during the mitotic cell cycle in fission yeast. Mmi1, an RNA-binding protein, plays a crucial role in this selective elimination. Mmi1 recognizes a specific region, namely, the determinant of selective removal (DSR) on meiotic transcripts and induces nuclear exosome-mediated elimination. During meiosis, Mmi1 is sequestered by a chromosome-associated dot structure, Mei2 dot, allowing meiosis-specific transcripts to be stably expressed. Red1, a zinc-finger protein, is also known to participate in the Mmi1/DSR elimination system, although its molecular function has remained elusive. To uncover the detailed molecular mechanisms underlying the Mmi1/DSR elimination system, we sought to identify factors that interact genetically with Mmi1. Here, we show that one of the identified factors, Iss10, is involved in the Mmi1/DSR system by regulating the interaction between Mmi1 and Red1. In cells lacking Iss10, association of Red1 with Mmi1 is severely impaired, and target transcripts of Mmi1 are ectopically expressed in the mitotic cycle. During meiosis, Iss10 is downregulated, resulting in dissociation of Red1 from Mmi1 and subsequent suppression of Mmi1 activity.
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Affiliation(s)
- Akira Yamashita
- Laboratory of Gene Function, Kazusa DNA Research Institute, 2-6-7 Kazusa-kamatari, Kisarazu, Chiba, 292-0818, Japan and Department of Biophysics and Biochemistry, Graduate School of Science, University of Tokyo, Hongo, Tokyo, 113-0033, Japan
- *To whom correspondence should be addressed. Tel: +81 438 52 3954; Fax: +81 438 52 3925;
| | - Tomomi Takayama
- Laboratory of Gene Function, Kazusa DNA Research Institute, 2-6-7 Kazusa-kamatari, Kisarazu, Chiba, 292-0818, Japan and Department of Biophysics and Biochemistry, Graduate School of Science, University of Tokyo, Hongo, Tokyo, 113-0033, Japan
| | - Ryo Iwata
- Laboratory of Gene Function, Kazusa DNA Research Institute, 2-6-7 Kazusa-kamatari, Kisarazu, Chiba, 292-0818, Japan and Department of Biophysics and Biochemistry, Graduate School of Science, University of Tokyo, Hongo, Tokyo, 113-0033, Japan
| | - Masayuki Yamamoto
- Laboratory of Gene Function, Kazusa DNA Research Institute, 2-6-7 Kazusa-kamatari, Kisarazu, Chiba, 292-0818, Japan and Department of Biophysics and Biochemistry, Graduate School of Science, University of Tokyo, Hongo, Tokyo, 113-0033, Japan
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