1
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Veronezi GMB, Ramachandran S. Nucleation and spreading maintain Polycomb domains every cell cycle. Cell Rep 2024; 43:114090. [PMID: 38607915 PMCID: PMC11179494 DOI: 10.1016/j.celrep.2024.114090] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2022] [Revised: 02/07/2024] [Accepted: 03/26/2024] [Indexed: 04/14/2024] Open
Abstract
Gene repression by the Polycomb pathway is essential for metazoan development. Polycomb domains, characterized by trimethylation of histone H3 lysine 27 (H3K27me3), carry the memory of repression and hence need to be maintained to counter the dilution of parental H3K27me3 with unmodified H3 during replication. Yet, how locus-specific H3K27me3 is maintained through replication is unclear. To understand H3K27me3 recovery post-replication, we first define nucleation sites within each Polycomb domain in mouse embryonic stem cells. To map dynamics of H3K27me3 domains across the cell cycle, we develop CUT&Flow (coupling cleavage under target and tagmentation with flow cytometry). We show that post-replication recovery of Polycomb domains occurs by nucleation and spreading, using the same nucleation sites used during de novo domain formation. By using Polycomb repressive complex 2 (PRC2) subunit-specific inhibitors, we find that PRC2 targets nucleation sites post-replication independent of pre-existing H3K27me3. Thus, competition between H3K27me3 deposition and nucleosome turnover drives both de novo domain formation and maintenance during every cell cycle.
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Affiliation(s)
- Giovana M B Veronezi
- Molecular Biology Graduate Program, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA; Department of Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Srinivas Ramachandran
- Department of Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA; RNA Bioscience Initiative, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA.
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2
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Ito S, Umehara T, Koseki H. Polycomb-mediated histone modifications and gene regulation. Biochem Soc Trans 2024; 52:151-161. [PMID: 38288743 DOI: 10.1042/bst20230336] [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: 11/14/2023] [Revised: 01/03/2024] [Accepted: 01/05/2024] [Indexed: 02/29/2024]
Abstract
Polycomb repressive complexes 1 and 2 (PRC1 and PRC2) are transcriptional repressor complexes that play a fundamental role in epigenomic regulation and the cell-fate decision; these complexes are widely conserved in multicellular organisms. PRC1 is an E3 ubiquitin (ub) ligase that generates histone H2A ubiquitinated at lysine (K) 119 (H2AK119ub1), whereas PRC2 is a histone methyltransferase that specifically catalyzes tri-methylation of histone H3K27 (H3K27me3). Genome-wide analyses have confirmed that these two key epigenetic marks highly overlap across the genome and contribute to gene repression. We are now beginning to understand the molecular mechanisms that enable PRC1 and PRC2 to identify their target sites in the genome and communicate through feedback mechanisms to create Polycomb chromatin domains. Recently, it has become apparent that PRC1-induced H2AK119ub1 not only serves as a docking site for PRC2 but also affects the dynamics of the H3 tail, both of which enhance PRC2 activity, suggesting that trans-tail communication between H2A and H3 facilitates the formation of the Polycomb chromatin domain. In this review, we discuss the emerging principles that define how PRC1 and PRC2 establish the Polycomb chromatin domain and regulate gene expression in mammals.
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Affiliation(s)
- Shinsuke Ito
- Laboratory of Developmental Genetics, RIKEN Center for Integrative Medical Sciences, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
| | - Takashi Umehara
- Laboratory of Developmental Genetics, RIKEN Center for Integrative Medical Sciences, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
- Laboratory for Epigenetics Drug Discovery, RIKEN Center for Biosystems Dynamics Research, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
| | - Haruhiko Koseki
- Laboratory of Developmental Genetics, RIKEN Center for Integrative Medical Sciences, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
- Department of Cellular and Molecular Medicine, Graduate School of Medicine, Chiba University, 1-8-1 Inohana, Chuo-ku, Chiba 260-8670, Japan
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Shirahama Y, Yamamoto K. The E2F6 Transcription Factor is Associated with the Mammalian SUZ12-Containing Polycomb Complex. Kurume Med J 2023; 67:171-183. [PMID: 36464274 DOI: 10.2739/kurumemedj.ms674006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/05/2022]
Abstract
The Polycomb group protein (PcG) SUZ12 forms Polycomb repressive complexes together with histone methyltransferase EZH2. Although the complexes have been demonstrated to be involved in epigenetic maintenance of gene expression in a transcriptional repressive state, it is unclear how they are recruited to the target genes. Here we report that SUZ12 directly interacts with site-specific transcriptional repressor E2F6 and forms a complex together with EZH2. SUZ12 interacts with E2F6 selectively among the E2F family proteins and E2F6- containing SUZ12-EZH2 complex was biochemically purified from HEK293 cells stably expressing Flag-tagged SUZ12. Chromatin immunoprecipitation assays revealed the target genes of the E2F6-SUZ12-EZH2 complex. Contrary to expectation, the promoter regions of these genes are not or only weakly tri-methylated at histone H3-K27, and their expression is down-regulated by depletion of EZH2. Given that the transactivation function of SUZ12-EZH2 has been previously reported, the inhibitory effect on E2F6-mediated transcriptional repression by physical interaction can be considered a candidate mechanism of gene activation by these PcGs.
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Affiliation(s)
- Yuko Shirahama
- Department of Medical Biochemistry, Kurume University School of Medicine
| | - Ken Yamamoto
- Department of Medical Biochemistry, Kurume University School of Medicine
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4
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Liu JN, Fang H, Liang Q, Dong Y, Wang C, Yan L, Ma X, Zhou R, Lang X, Gai S, Wang L, Xu S, Yang KQ, Wu D. Genomic analyses provide insights into the evolution and salinity adaptation of halophyte Tamarix chinensis. Gigascience 2022; 12:giad053. [PMID: 37494283 PMCID: PMC10370455 DOI: 10.1093/gigascience/giad053] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2023] [Revised: 06/09/2023] [Accepted: 06/29/2023] [Indexed: 07/28/2023] Open
Abstract
BACKGROUND The woody halophyte Tamarix chinensis is a pioneer tree species in the coastal wetland ecosystem of northern China, exhibiting high resistance to salt stress. However, the genetic information underlying salt tolerance in T. chinensis remains to be seen. Here we present a genomic investigation of T. chinensis to elucidate the underlying mechanism of its high resistance to salinity. RESULTS Using a combination of PacBio and high-throughput chromosome conformation capture data, a chromosome-level T. chinensis genome was assembled with a size of 1.32 Gb and scaffold N50 of 110.03 Mb. Genome evolution analyses revealed that T. chinensis significantly expanded families of HAT and LIMYB genes. Whole-genome and tandem duplications contributed to the expansion of genes associated with the salinity adaptation of T. chinensis. Transcriptome analyses were performed on root and shoot tissues during salt stress and recovery, and several hub genes responding to salt stress were identified. WRKY33/40, MPK3/4, and XBAT31 were critical in responding to salt stress during early exposure, while WRKY40, ZAT10, AHK4, IRX9, and CESA4/8 were involved in responding to salt stress during late stress and recovery. In addition, PER7/27/57/73 encoding class III peroxidase and MCM3/4/5/7 encoding DNA replication licensing factor maintained up/downregulation during salt stress and recovery stages. CONCLUSIONS The results presented here reveal the genetic mechanisms underlying salt adaptation in T. chinensis, thus providing important genomic resources for evolutionary studies on tamarisk and plant salt tolerance genetic improvement.
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Affiliation(s)
- Jian Ning Liu
- College of Forestry, Shandong Agricultural University, Taian 271018, China
| | - Hongcheng Fang
- College of Forestry, Shandong Agricultural University, Taian 271018, China
- State Forestry and Grassland Administration Key Laboratory of Silviculture in the Downstream Areas of the Yellow River, Shandong Agricultural University, Taian 271018, China
- Shandong Taishan Forest Ecosystem Research Station, Shandong Agricultural University, Taian 271018, China
| | - Qiang Liang
- College of Forestry, Shandong Agricultural University, Taian 271018, China
- State Forestry and Grassland Administration Key Laboratory of Silviculture in the Downstream Areas of the Yellow River, Shandong Agricultural University, Taian 271018, China
- Shandong Taishan Forest Ecosystem Research Station, Shandong Agricultural University, Taian 271018, China
| | - Yuhui Dong
- College of Forestry, Shandong Agricultural University, Taian 271018, China
- State Forestry and Grassland Administration Key Laboratory of Silviculture in the Downstream Areas of the Yellow River, Shandong Agricultural University, Taian 271018, China
- Shandong Taishan Forest Ecosystem Research Station, Shandong Agricultural University, Taian 271018, China
| | - Changxi Wang
- College of Forestry, Shandong Agricultural University, Taian 271018, China
| | - Liping Yan
- Shandong Provincial Academy of Forestry, Jinan 250014, China
| | - Xinmei Ma
- College of Forestry, Shandong Agricultural University, Taian 271018, China
| | - Rui Zhou
- College of Forestry, Shandong Agricultural University, Taian 271018, China
| | - Xinya Lang
- College of Forestry, Shandong Agricultural University, Taian 271018, China
| | - Shasha Gai
- College of Forestry, Shandong Agricultural University, Taian 271018, China
| | - Lichang Wang
- College of Forestry, Shandong Agricultural University, Taian 271018, China
| | - Shengyi Xu
- College of Forestry, Shandong Agricultural University, Taian 271018, China
| | - Ke Qiang Yang
- College of Forestry, Shandong Agricultural University, Taian 271018, China
- State Forestry and Grassland Administration Key Laboratory of Silviculture in the Downstream Areas of the Yellow River, Shandong Agricultural University, Taian 271018, China
- Shandong Taishan Forest Ecosystem Research Station, Shandong Agricultural University, Taian 271018, China
| | - Dejun Wu
- Shandong Provincial Academy of Forestry, Jinan 250014, China
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Liu J, Jiang Y, Huang H, Xu J, Wu Y, Wang Q, Zhu Y, Zheng B, Shen C, Qian W, Shen J. BMI-1 promotes breast cancer proliferation and metastasis through different mechanisms in different subtypes. Cancer Sci 2022; 114:449-462. [PMID: 36285479 PMCID: PMC9899611 DOI: 10.1111/cas.15623] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2022] [Revised: 09/18/2022] [Accepted: 10/06/2022] [Indexed: 02/07/2023] Open
Abstract
Breast cancer is among the most common malignant cancers in women. B-cell-specific Moloney murine leukemia virus integration site 1 (BMI-1) is a transcriptional repressor that has been shown to be involved in tumorigenesis, the cell cycle, and stem cell maintenance. In our study, increased expression of BMI-1 was found in both human triple negative breast cancer and luminal A-type breast cancer tissues compared with adjacent tissues. We also found that knockdown of BMI-1 significantly suppressed cell proliferation and migration in vitro and in vivo. Further mechanistic research demonstrated that BMI-1 directly bound to the promoter region of CDKN2D/BRCA1 and inhibited its transcription in MCF-7/MDA-MB-231. More importantly, we discovered that knockdown of CDKN2D/BRCA1 could promote cell proliferation and migration after repression by PTC-209. Our results reveal that BMI-1 transcriptionally suppressed BRCA1 in TNBC cell lines whereas, in luminal A cell lines, CDKN2D was the target gene. This provides a reference for the precise treatment of different types of breast cancer in clinical practice.
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Affiliation(s)
- Jin‐yan Liu
- Department of Breast and Thyroid SurgeryThe Affiliated Suzhou Hospital of Nanjing Medical University, Gusu School, Nanjing Medical UniversitySuzhouChina
| | - Yan‐nan Jiang
- Department of Breast and Thyroid SurgeryThe Affiliated Suzhou Hospital of Nanjing Medical University, Gusu School, Nanjing Medical UniversitySuzhouChina
| | - Hai Huang
- Department of Breast and Thyroid SurgeryThe Affiliated Suzhou Hospital of Nanjing Medical University, Gusu School, Nanjing Medical UniversitySuzhouChina
| | - Jin‐fu Xu
- State Key Laboratory of Reproductive Medicine, Department of Histology and EmbryologyNanjing Medical UniversityNanjingChina
| | - Ying‐hui Wu
- Department of Orthopaedic SurgeryThe Affiliated Suzhou Hospital of Nanjing Medical University, Gusu School, Nanjing Medical University, Suzhou Municipal HospitalSuzhouChina
| | - Qiang Wang
- Department of Orthopaedic SurgeryThe Affiliated Suzhou Hospital of Nanjing Medical University, Gusu School, Nanjing Medical University, Suzhou Municipal HospitalSuzhouChina
| | - Yue Zhu
- Department of Breast and Thyroid SurgeryThe Affiliated Suzhou Hospital of Nanjing Medical University, Gusu School, Nanjing Medical UniversitySuzhouChina
| | - Bo Zheng
- State Key Laboratory of Reproductive Medicine, Center for Reproduction and GeneticsThe Affiliated Suzhou Hospital of Nanjing Medical University, Gusu School, Nanjing Medical UniversitySuzhouChina
| | - Cong Shen
- State Key Laboratory of Reproductive Medicine, Center for Reproduction and GeneticsThe Affiliated Suzhou Hospital of Nanjing Medical University, Gusu School, Nanjing Medical UniversitySuzhouChina
| | - Wei‐feng Qian
- Department of Breast and Thyroid SurgeryThe Affiliated Suzhou Hospital of Nanjing Medical University, Gusu School, Nanjing Medical UniversitySuzhouChina
| | - Jun Shen
- Department of Orthopaedic SurgeryThe Affiliated Suzhou Hospital of Nanjing Medical University, Gusu School, Nanjing Medical University, Suzhou Municipal HospitalSuzhouChina
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6
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Beaven R, Denholm B. Early patterning followed by tissue growth establishes distal identity in Drosophila Malpighian tubules. Front Cell Dev Biol 2022; 10:947376. [PMID: 36060795 PMCID: PMC9437309 DOI: 10.3389/fcell.2022.947376] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2022] [Accepted: 07/28/2022] [Indexed: 12/03/2022] Open
Abstract
Specification and elaboration of proximo-distal (P-D) axes for structures or tissues within a body occurs secondarily from that of the main axes of the body. Our understanding of the mechanism(s) that pattern P-D axes is limited to a few examples such as vertebrate and invertebrate limbs. Drosophila Malpighian/renal tubules (MpTs) are simple epithelial tubules, with a defined P-D axis. How this axis is patterned is not known, and provides an ideal context to understand patterning mechanisms of a secondary axis. Furthermore, epithelial tubules are widespread, and their patterning is not well understood. Here, we describe the mechanism that establishes distal tubule and show this is a radically different mechanism to that patterning the proximal MpT. The distal domain is patterned in two steps: distal identity is specified in a small group of cells very early in MpT development through Wingless/Wnt signalling. Subsequently, this population is expanded by proliferation to generate the distal MpT domain. This mechanism enables distal identity to be established in the tubule in a domain of cells much greater than the effective range of Wingless.
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Affiliation(s)
| | - Barry Denholm
- Deanery of Biomedical Sciences, The University of Edinburgh, Edinburgh, United Kingdom
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7
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Zhai F, Li J, Ye M, Jin X. The functions and effects of CUL3-E3 ligases mediated non-degradative ubiquitination. Gene X 2022; 832:146562. [PMID: 35580799 DOI: 10.1016/j.gene.2022.146562] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2022] [Revised: 03/30/2022] [Accepted: 05/06/2022] [Indexed: 02/09/2023] Open
Abstract
Ubiquitination of substrates usually have two fates: one is degraded by 26S proteasome, and the other is non-degradative ubiquitination modification which is associated with cell cycle regulation, chromosome inactivation, protein transportation, tumorigenesis, achondroplasia, and neurological diseases. Cullin3 (CUL3), a scaffold protein, binding with the Bric-a-Brac-Tramtrack-Broad-complex (BTB) domain of substrates recognition adaptor and RING-finger protein 1 (RBX1) form ubiquitin ligases (E3). Based on the current researches, this review has summarized the functions and effects of CUL3-E3 ligases mediated non-degradative ubiquitination.
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Affiliation(s)
- Fengguang Zhai
- The Affiliated Hospital of Medical School, Ningbo University, Ningbo 315020, China; Department of Biochemistry and Molecular Biology, Zhejiang Key Laboratory of Pathphysiology, Medical School of Ningbo University, Ningbo 315211, China
| | - Jingyun Li
- The Affiliated Hospital of Medical School, Ningbo University, Ningbo 315020, China; Department of Biochemistry and Molecular Biology, Zhejiang Key Laboratory of Pathphysiology, Medical School of Ningbo University, Ningbo 315211, China
| | - Meng Ye
- The Affiliated Hospital of Medical School, Ningbo University, Ningbo 315020, China; Department of Biochemistry and Molecular Biology, Zhejiang Key Laboratory of Pathphysiology, Medical School of Ningbo University, Ningbo 315211, China.
| | - Xiaofeng Jin
- The Affiliated Hospital of Medical School, Ningbo University, Ningbo 315020, China; Department of Biochemistry and Molecular Biology, Zhejiang Key Laboratory of Pathphysiology, Medical School of Ningbo University, Ningbo 315211, China.
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8
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Amemiya HM, Goss TJ, Nye TM, Hurto RL, Simmons LA, Freddolino PL. Distinct heterochromatin-like domains promote transcriptional memory and silence parasitic genetic elements in bacteria. EMBO J 2022; 41:e108708. [PMID: 34961960 PMCID: PMC8804932 DOI: 10.15252/embj.2021108708] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2021] [Revised: 11/22/2021] [Accepted: 11/29/2021] [Indexed: 02/03/2023] Open
Abstract
There is increasing evidence that prokaryotes maintain chromosome structure, which in turn impacts gene expression. We recently characterized densely occupied, multi-kilobase regions in the E. coli genome that are transcriptionally silent, similar to eukaryotic heterochromatin. These extended protein occupancy domains (EPODs) span genomic regions containing genes encoding metabolic pathways as well as parasitic elements such as prophages. Here, we investigate the contributions of nucleoid-associated proteins (NAPs) to the structuring of these domains, by examining the impacts of deleting NAPs on EPODs genome-wide in E. coli and B. subtilis. We identify key NAPs contributing to the silencing of specific EPODs, whose deletion opens a chromosomal region for RNA polymerase binding at genes contained within that region. We show that changes in E. coli EPODs facilitate an extra layer of transcriptional regulation, which prepares cells for exposure to exotic carbon sources. Furthermore, we distinguish novel xenogeneic silencing roles for the NAPs Fis and Hfq, with the presence of at least one being essential for cell viability in the presence of domesticated prophages. Our findings reveal previously unrecognized mechanisms through which genomic architecture primes bacteria for changing metabolic environments and silences harmful genomic elements.
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Affiliation(s)
- Haley M Amemiya
- Cellular and Molecular Biology ProgramUniversity of Michigan Medical SchoolAnn ArborMIUSA,Department of Computational Medicine and BioinformaticsUniversity of Michigan Medical SchoolAnn ArborMIUSA,Present address:
Broad Institute of MIT and HarvardCambridgeMAUSA
| | - Thomas J Goss
- Department of Biological ChemistryUniversity of Michigan Medical SchoolAnn ArborMIUSA
| | - Taylor M Nye
- Department of Molecular, Cellular, and Developmental BiologyUniversity of MichiganAnn ArborMIUSA,Present address:
Department of Molecular MicrobiologyWashington University in St. Louis School of MedicineSt. LouisMOUSA
| | - Rebecca L Hurto
- Department of Biological ChemistryUniversity of Michigan Medical SchoolAnn ArborMIUSA
| | - Lyle A Simmons
- Department of Molecular, Cellular, and Developmental BiologyUniversity of MichiganAnn ArborMIUSA
| | - Peter L Freddolino
- Cellular and Molecular Biology ProgramUniversity of Michigan Medical SchoolAnn ArborMIUSA,Department of Computational Medicine and BioinformaticsUniversity of Michigan Medical SchoolAnn ArborMIUSA,Department of Biological ChemistryUniversity of Michigan Medical SchoolAnn ArborMIUSA
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9
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Larkin A, Ames A, Seman M, Ragunathan K. Investigating Mitotic Inheritance of Histone Modifications Using Tethering Strategies. Methods Mol Biol 2022; 2529:419-440. [PMID: 35733025 DOI: 10.1007/978-1-0716-2481-4_18] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
The covalent and reversible modification of histones enables cells to establish heritable gene expression patterns without altering their genetic blueprint. Epigenetic mechanisms regulate gene expression in two separate ways: (1) establishment, which depends on sequence-specific DNA- or RNA-binding proteins that recruit histone-modifying enzymes to unique genomic loci, and (2) maintenance, which is sequence-independent and depends on the autonomous propagation of preexisting chromatin states during DNA replication. Only a subset of the vast repertoire of histone modifications in the genome is heritable. Here, we describe a synthetic biology approach to tether histone-modifying enzymes to engineer chromatin states in living cells and evaluate their potential for mitotic inheritance. In S. pombe, fusing the H3K9 methyltransferase, Clr4, to the tetracycline-inducible TetR DNA-binding domain facilitates rapid and reversible control of heterochromatin assembly. We describe a framework to successfully implement an inducible heterochromatin establishment system and evaluate its molecular properties. We anticipate that our innovative genetic strategy will be broadly applicable to the discovery of protein complexes and separation-of-function alleles of heterochromatin-associated factors with unique roles in epigenetic inheritance.
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Affiliation(s)
- Ajay Larkin
- Department of Biological Chemistry, University of Michigan, Ann Arbor, MI, USA
| | - Amanda Ames
- Department of Biological Chemistry, University of Michigan, Ann Arbor, MI, USA
| | - Melissa Seman
- Cellular and Molecular Biology Program, University of Michigan, Ann Arbor, MI, USA
| | - Kaushik Ragunathan
- Department of Biological Chemistry, University of Michigan, Ann Arbor, MI, USA.
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10
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Amemiya HM, Schroeder J, Freddolino PL. Nucleoid-associated proteins shape chromatin structure and transcriptional regulation across the bacterial kingdom. Transcription 2021; 12:182-218. [PMID: 34499567 PMCID: PMC8632127 DOI: 10.1080/21541264.2021.1973865] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2021] [Revised: 08/15/2021] [Accepted: 08/18/2021] [Indexed: 01/21/2023] Open
Abstract
Genome architecture has proven to be critical in determining gene regulation across almost all domains of life. While many of the key components and mechanisms of eukaryotic genome organization have been described, the interplay between bacterial DNA organization and gene regulation is only now being fully appreciated. An increasing pool of evidence has demonstrated that the bacterial chromosome can reasonably be thought of as chromatin, and that bacterial chromosomes contain transcriptionally silent and transcriptionally active regions analogous to heterochromatin and euchromatin, respectively. The roles played by histones in eukaryotic systems appear to be shared across a range of nucleoid-associated proteins (NAPs) in bacteria, which function to compact, structure, and regulate large portions of bacterial chromosomes. The broad range of extant NAPs, and the extent to which they differ from species to species, has raised additional challenges in identifying and characterizing their roles in all but a handful of model bacteria. Here we review the regulatory roles played by NAPs in several well-studied bacteria and use the resulting state of knowledge to provide a working definition for NAPs, based on their function, binding pattern, and expression levels. We present a screening procedure which can be applied to any species for which transcriptomic data are available. Finally, we note that NAPs tend to play two major regulatory roles - xenogeneic silencers and developmental regulators - and that many unrecognized potential NAPs exist in each bacterial species examined.
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Affiliation(s)
- Haley M. Amemiya
- University of Michigan Medical School, Ann Arbor, MI, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Computational Medicine and Bioinformatics, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Jeremy Schroeder
- Department of Biological Chemistry, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Peter L. Freddolino
- Department of Computational Medicine and Bioinformatics, University of Michigan Medical School, Ann Arbor, MI, USA
- Department of Biological Chemistry, University of Michigan Medical School, Ann Arbor, MI, USA
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11
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Tang Y, Zhao L, Yu X, Zhang J, Qian L, Jin J, Lu R, Zhou Y. Inhibition of EZH2 primes the cardiac gene activation via removal of epigenetic repression during human direct cardiac reprogramming. Stem Cell Res 2021; 53:102365. [PMID: 34087994 PMCID: PMC8238038 DOI: 10.1016/j.scr.2021.102365] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/05/2020] [Revised: 04/12/2021] [Accepted: 04/21/2021] [Indexed: 12/12/2022] Open
Abstract
Cardiovascular disease, until now, is still the leading cause of death in the United States. Due to the limited regenerative capacity of adult hearts, the damage caused by heart injury cannot be reversed and eventually progress into heart failure. In need of cardiovascular disease treatment, many therapies aimed at either cell transplantation or cell regeneration have been proposed. Direct reprogramming of somatic cells into induced cardiomyocytes (iCMs) is considered to be a promising strategy for regenerative medicine. The induction of cardiomyocytes from non-myocytes can be achieved efficiently via ectopic expression of reprogramming factors both in vitro and in vivo in the mouse model, however, the generation of human induced cardiomyocyte-like cells (hiCMs) remains challenging. The inefficiency of hiCMs production called for the identification of the additional epigenetic memories in non-myocytes which might be damping the hiCM reprogramming. Here, we conducted an unbiased loss-of-function screening focusing on epigenetic regulators and identified enhancer of zeste homolog 2 (EZH2) as an important epigenetic barrier during hiCM reprogramming. We found that the removal of EZH2 via genetic knockdown or treatment of EZH2 selective degrader significantly increased the hiCM reprogramming efficiency and led to profound activation of cardiac genes and repression of collagen and extracellular matrix genes. Furthermore, EZH2 inhibitors targeting its catalytic activity also promotes hiCM reprogramming, suggesting that EZH2 may restrain cardiac conversion through H3K27me3-mediated gene repression. Indeed, genomic profiling of H3K27me3 revealed a subset of cardiac genes that remain repressed with high levels of H3K27me3 despite of the delivery of the reprogramming factors. Inhibition of EZH2, however, leads to reduced H3K27me3 occupancy and robust activation of these cardiac genes. Taken together, our data suggested that EZH2 inhibition facilitates the activation of cardiac genes in fibroblasts and eases the production of hiCMs.
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Affiliation(s)
- Yawen Tang
- Department of Biomedical Engineering, University of Alabama at Birmingham, Birmingham, AL 35233, USA
| | - Lianzhong Zhao
- Division of Hematology/Oncology, Department of Medicine, University of Alabama at Birmingham, Birmingham, AL 35294, USA; O'Neal Comprehensive Cancer Center, University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - Xufen Yu
- Mount Sinai Center for Therapeutics Discovery, Departments of Pharmacological Sciences and Oncological Sciences, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Jianyi Zhang
- Department of Biomedical Engineering, University of Alabama at Birmingham, Birmingham, AL 35233, USA
| | - Li Qian
- Department of Pathology and Laboratory Medicine, McAllister Heart Institute, Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Jian Jin
- Mount Sinai Center for Therapeutics Discovery, Departments of Pharmacological Sciences and Oncological Sciences, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Rui Lu
- Division of Hematology/Oncology, Department of Medicine, University of Alabama at Birmingham, Birmingham, AL 35294, USA; O'Neal Comprehensive Cancer Center, University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - Yang Zhou
- Department of Biomedical Engineering, University of Alabama at Birmingham, Birmingham, AL 35233, USA.
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12
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Cheng Y, Pitoniak A, Wang J, Bohmann D. Preserving transcriptional stress responses as an anti-aging strategy. Aging Cell 2021; 20:e13297. [PMID: 33474790 PMCID: PMC7884037 DOI: 10.1111/acel.13297] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2020] [Revised: 11/09/2020] [Accepted: 12/07/2020] [Indexed: 12/30/2022] Open
Abstract
The progressively increasing frailty, morbidity and mortality of aging organisms coincides with, and may be causally related to, their waning ability to adapt to environmental perturbations. Transcriptional responses to challenges, such as oxidative stress or pathogens, diminish with age. This effect is manifest in the declining function of the stress responsive transcription factor Nrf2. Protective gene expression programs that are controlled by the Drosophila Nrf2 homolog, CncC, support homeostasis and longevity. Age‐associated chromatin changes make these genes inaccessible to CncC binding and render them inert to signal‐dependent transcriptional activation in old animals. In a previous paper, we have reported that overexpression of the CncC dimerization partner Maf‐S counteracts this degenerative effect and preserves organism fitness. Building on this work, we show here that Maf‐S overexpression prevents loss of chromatin accessibility and maintains gene responsiveness. Moreover, the same outcome, along with an extension of lifespan, can be achieved by inducing CncC target gene expression pharmacologically throughout adult life. Thus, pharmacological or dietary interventions that can preserve stress responsive gene expression may be feasible anti‐aging strategies.
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Affiliation(s)
- Yang Cheng
- Department of Biomedical Genetics University of Rochester Medical Center Rochester New York USA
| | - Andrew Pitoniak
- Department of Biomedical Genetics University of Rochester Medical Center Rochester New York USA
| | - Julia Wang
- Medical Scientist Training Program Baylor College of Medicine Houston Texas USA
| | - Dirk Bohmann
- Department of Biomedical Genetics University of Rochester Medical Center Rochester New York USA
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13
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Xu H, Wang J, Liang Y, Fu Y, Li S, Huang J, Xu H, Zou W, Chen B. TriTag: an integrative tool to correlate chromatin dynamics and gene expression in living cells. Nucleic Acids Res 2021; 48:e127. [PMID: 33104788 PMCID: PMC7736787 DOI: 10.1093/nar/gkaa906] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2020] [Revised: 08/29/2020] [Accepted: 10/21/2020] [Indexed: 02/07/2023] Open
Abstract
A wealth of single-cell imaging studies have contributed novel insights into chromatin organization and gene regulation. However, a comprehensive understanding of spatiotemporal gene regulation requires developing tools to combine multiple monitoring systems in a single study. Here, we report a versatile tag, termed TriTag, which integrates the functional capabilities of CRISPR-Tag (DNA labeling), MS2 aptamer (RNA imaging) and fluorescent protein (protein tracking). Using this tag, we correlate changes in chromatin dynamics with the progression of endogenous gene expression, by recording both transcriptional bursting and protein production. This strategy allows precise measurements of gene expression at single-allele resolution across the cell cycle or in response to stress. TriTag enables capturing an integrated picture of gene expression, thus providing a powerful tool to study transcriptional heterogeneity and regulation.
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Affiliation(s)
- Haiyue Xu
- Department of Cell Biology, and Bone Marrow Transplantation Center of the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou 310058, China
| | - Junyan Wang
- Department of Cell Biology, and Bone Marrow Transplantation Center of the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou 310058, China
| | - Ying Liang
- Department of Cell Biology, and Bone Marrow Transplantation Center of the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou 310058, China
| | - Yujuan Fu
- Department of Cell Biology, and Bone Marrow Transplantation Center of the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou 310058, China
| | - Sihui Li
- Department of Cell Biology, and Bone Marrow Transplantation Center of the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou 310058, China
| | - Jinghan Huang
- School of Physics and Astronomy, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Heng Xu
- School of Physics and Astronomy, Shanghai Jiao Tong University, Shanghai 200240, China.,Institute of Natural Sciences, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Wei Zou
- The Fourth Affiliated Hospital, Zhejiang University School of Medicine, Yiwu 322000, China.,Insititute of Translational Medicine, Zhejiang University, Hangzhou 310003, China
| | - Baohui Chen
- Department of Cell Biology, and Bone Marrow Transplantation Center of the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou 310058, China.,Institute of Hematology, Zhejiang University & Zhejiang Engineering Laboratory for Stem Cell and Immunotherapy, Hangzhou 310058, China.,Zhejiang Laboratory for Systems & Precision Medicine, Zhejiang University Medical Center, Hangzhou 311121, China.,Zhejiang Provincial Key Laboratory of Genetic & Developmental Disorders, Hangzhou 310058, China
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14
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Batra R, Gautam T, Pal S, Chaturvedi D, Rakhi, Jan I, Balyan HS, Gupta PK. Identification and characterization of SET domain family genes in bread wheat (Triticum aestivum L.). Sci Rep 2020; 10:14624. [PMID: 32884064 PMCID: PMC7471321 DOI: 10.1038/s41598-020-71526-5] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2020] [Accepted: 08/18/2020] [Indexed: 01/21/2023] Open
Abstract
SET domain genes (SDGs) that are involved in histone methylation have been examined in many plant species, but have never been examined in bread wheat; the histone methylation caused due to SDGs is associated with regulation of gene expression at the transcription level. We identified a total of 166 bread wheat TaSDGs, which carry some interesting features including the occurrence of tandem/interspersed duplications, SSRs (simple sequence repeats), transposable elements, lncRNAs and targets for miRNAs along their lengths and transcription factor binding sites (TFBS) in the promoter regions. Only 130 TaSDGs encoded proteins with complete SET domain, the remaining 36 proteins had truncated SET domain. The TaSDG encoded proteins were classified into six classes (I–V and VII). In silico expression analysis indicated relatively higher expression (FPKM > 20) of eight of the 130 TaSDGs in different tissues, and downregulation of 30 TaSDGs under heat and drought at the seedling stage. qRT-PCR was also conducted to validate the expression of seven genes at the seedling stage in pairs of contrasting genotypes in response to abiotic stresses (water and heat) and biotic stress (leaf rust). These genes were generally downregulated in response to the three stresses examined.
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Affiliation(s)
- Ritu Batra
- Department of Genetics and Plant Breeding, CCS University, Meerut, Uttar Pradesh, 250004, India
| | - Tinku Gautam
- Department of Genetics and Plant Breeding, CCS University, Meerut, Uttar Pradesh, 250004, India
| | - Sunita Pal
- Department of Genetics and Plant Breeding, CCS University, Meerut, Uttar Pradesh, 250004, India
| | - Deepti Chaturvedi
- Department of Genetics and Plant Breeding, CCS University, Meerut, Uttar Pradesh, 250004, India
| | - Rakhi
- Department of Genetics and Plant Breeding, CCS University, Meerut, Uttar Pradesh, 250004, India
| | - Irfat Jan
- Department of Genetics and Plant Breeding, CCS University, Meerut, Uttar Pradesh, 250004, India
| | - Harindra Singh Balyan
- Department of Genetics and Plant Breeding, CCS University, Meerut, Uttar Pradesh, 250004, India
| | - Pushpendra Kumar Gupta
- Department of Genetics and Plant Breeding, CCS University, Meerut, Uttar Pradesh, 250004, India.
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15
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Bheda P, Aguilar-Gómez D, Becker NB, Becker J, Stavrou E, Kukhtevich I, Höfer T, Maerkl S, Charvin G, Marr C, Kirmizis A, Schneider R. Single-Cell Tracing Dissects Regulation of Maintenance and Inheritance of Transcriptional Reinduction Memory. Mol Cell 2020; 78:915-925.e7. [DOI: 10.1016/j.molcel.2020.04.016] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2019] [Revised: 02/15/2020] [Accepted: 04/15/2020] [Indexed: 10/24/2022]
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16
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Chandrashekar DS, Chakravarthi BVSK, Robinson AD, Anderson JC, Agarwal S, Balasubramanya SAH, Eich ML, Bajpai AK, Davuluri S, Guru MS, Guru AS, Naik G, Della Manna DL, Acharya KK, Carskadon S, Manne U, Crossman DK, Ferguson JE, Grizzle WE, Palanisamy N, Willey CD, Crowley MR, Netto GJ, Yang ES, Varambally S, Sonpavde G. Therapeutically actionable PAK4 is amplified, overexpressed, and involved in bladder cancer progression. Oncogene 2020; 39:4077-4091. [PMID: 32231273 DOI: 10.1038/s41388-020-1275-7] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2019] [Revised: 03/09/2020] [Accepted: 03/13/2020] [Indexed: 12/30/2022]
Abstract
Muscle-invasive bladder carcinomas (MIBCs) are aggressive genitourinary malignancies. Metastatic urothelial carcinoma of the bladder is generally incurable by current chemotherapy and leads to early mortality. Recent studies have identified molecular subtypes of MIBCs with different sensitivities to frontline therapy, suggesting tumor heterogeneity. We have performed multi-omic profiling of the kinome in bladder cancer patients with the goal of identify therapeutic targets. Our analyses revealed amplification, overexpression, and elevated kinase activity of P21 (RAC1) activated kinase 4 (PAK4) in a subset of Bladder cancer (BLCA). Using bladder cancer cells, we confirmed the role of PAK4 in BLCA cell proliferation and invasion. Furthermore, we observed that a PAK4 inhibitor was effective in curtailing growth of BLCA cells. Transcriptomic analyses identified elevated expression of another kinase, protein tyrosine kinase 6 (PTK6), upon treatment with a PAK4 inhibitor and RNA interference of PAK4. Treatment with a combination of kinase inhibitors (vandetanib and dasatinib) showed enhanced sensitivity compared with either drug alone. Thus, PAK4 may be therapeutically actionable for a subset of MIBC patients with amplified and/or overexpressed PAK4 in their tumors. Our results also indicate that combined inhibition of PAK4 and PTK6 may overcome resistance to PAK4. These observations warrant clinical investigations with selected BLCA patients.
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Affiliation(s)
| | | | - Alyncia D Robinson
- Department of Pathology, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Joshua C Anderson
- Department of Radiation Oncology, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Sumit Agarwal
- Department of Pathology, University of Alabama at Birmingham, Birmingham, AL, USA
| | | | - Marie-Lisa Eich
- Department of Pathology, University of Alabama at Birmingham, Birmingham, AL, USA
| | | | | | - Maya S Guru
- Department of Medicine, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Arjun S Guru
- Department of Medicine, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Gurudatta Naik
- Division of Hematology and Oncology, University of Alabama at Birmingham, Birmingham, AL, USA.,O'Neal Comprehensive Cancer Center, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Deborah L Della Manna
- Department of Radiation Oncology, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Kshitish K Acharya
- Shodhaka Life Sciences Private Limited, Bengaluru, India.,Institute of Bioinformatics and Applied Biotechnology (IBAB), Biotech Park, Electronic City, Bengaluru, 560100, Karnataka, India
| | - Shannon Carskadon
- Vattikuti Urology Institute, Department of Urology, Henry Ford Health System, Detroit, MI, 48202, USA
| | - Upender Manne
- Department of Pathology, University of Alabama at Birmingham, Birmingham, AL, USA.,O'Neal Comprehensive Cancer Center, University of Alabama at Birmingham, Birmingham, AL, USA
| | - David K Crossman
- Department of Genetics, University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - James E Ferguson
- Department of Urology, University of Alabama at Birmingham, Birmingham, AL, USA
| | - William E Grizzle
- Department of Pathology, University of Alabama at Birmingham, Birmingham, AL, USA.,Department of Urology, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Nallasivam Palanisamy
- Vattikuti Urology Institute, Department of Urology, Henry Ford Health System, Detroit, MI, 48202, USA
| | - Christopher D Willey
- Department of Radiation Oncology, University of Alabama at Birmingham, Birmingham, AL, USA.,Department of Urology, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Michael R Crowley
- Department of Genetics, University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - George J Netto
- Department of Pathology, University of Alabama at Birmingham, Birmingham, AL, USA.,O'Neal Comprehensive Cancer Center, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Eddy S Yang
- Department of Radiation Oncology, University of Alabama at Birmingham, Birmingham, AL, USA.,O'Neal Comprehensive Cancer Center, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Sooryanarayana Varambally
- Department of Pathology, University of Alabama at Birmingham, Birmingham, AL, USA. .,O'Neal Comprehensive Cancer Center, University of Alabama at Birmingham, Birmingham, AL, USA. .,Informatics Institute, University of Alabama at Birmingham, Birmingham, AL, USA.
| | - Guru Sonpavde
- Department of Medicine, Dana-Farber Cancer Institute, Boston, MA, USA.
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17
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Zhang X, Murray B, Mo G, Shern JF. The Role of Polycomb Repressive Complex in Malignant Peripheral Nerve Sheath Tumor. Genes (Basel) 2020; 11:genes11030287. [PMID: 32182803 PMCID: PMC7140867 DOI: 10.3390/genes11030287] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2020] [Revised: 02/24/2020] [Accepted: 03/02/2020] [Indexed: 12/24/2022] Open
Abstract
Malignant peripheral nerve sheath tumors (MPNSTs) are aggressive soft tissue sarcomas that can arise most frequently in patients with neurofibromatosis type 1 (NF1). Despite an increasing understanding of the molecular mechanisms that underlie these tumors, there remains limited therapeutic options for this aggressive disease. One potentially critical finding is that a significant proportion of MPNSTs exhibit recurrent mutations in the genes EED or SUZ12, which are key components of the polycomb repressive complex 2 (PRC2). Tumors harboring these genetic lesions lose the marker of transcriptional repression, trimethylation of lysine residue 27 on histone H3 (H3K27me3) and have dysregulated oncogenic signaling. Given the recurrence of PRC2 alterations, intensive research efforts are now underway with a focus on detailing the epigenetic and transcriptomic consequences of PRC2 loss as well as development of novel therapeutic strategies for targeting these lesions. In this review article, we will summarize the recent findings of PRC2 in MPNST tumorigenesis, including highlighting the functions of PRC2 in normal Schwann cell development and nerve injury repair, as well as provide commentary on the potential therapeutic vulnerabilities of a PRC2 deficient tumor cell.
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Affiliation(s)
- Xiyuan Zhang
- Pediatric Oncology Branch, Tumor Evolution and Genomics Section, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA; (X.Z.); (B.M.); (G.M.)
| | - Béga Murray
- Pediatric Oncology Branch, Tumor Evolution and Genomics Section, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA; (X.Z.); (B.M.); (G.M.)
- The Patrick G Johnston Centre for Cancer Research, Queen’s University Belfast, 97 Lisburn road, Belfast BT9 7AE, UK
| | - George Mo
- Pediatric Oncology Branch, Tumor Evolution and Genomics Section, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA; (X.Z.); (B.M.); (G.M.)
- SUNY Downstate Health Sciences University, Brooklyn, NY 11203, USA
| | - Jack F. Shern
- Pediatric Oncology Branch, Tumor Evolution and Genomics Section, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA; (X.Z.); (B.M.); (G.M.)
- Correspondence:
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18
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Abstract
Background Organisms can be primed by metabolic exposures to continue expressing response genes even once the metabolite is no longer available, and can affect the speed and magnitude of responsive gene expression during subsequent exposures. This “metabolic transcriptional memory” can have a profound impact on the survivability of organisms in fluctuating environments. Scope of review Here I present several examples of metabolic transcriptional memory in the microbial world and discuss what is known so far regarding the underlying mechanisms, which mainly focus on chromatin modifications, protein inheritance, and broad changes in metabolic network. From these lessons learned in microbes, some insights into the yet understudied human metabolic memory can be gained. I thus discuss the implications of metabolic memory in disease progression in humans – i.e., the memory of high blood sugar exposure and the resulting effects on diabetic complications. Major conclusions Carbon source shifts from glucose to other less preferred sugars such as lactose, galactose, and maltose for energy metabolism as well as starvation of a signal transduction precursor sugar inositol are well-studied examples of metabolic transcriptional memory in Escherichia coli and Saccharomyces cerevisiae. Although the specific factors guiding metabolic transcriptional memory are not necessarily conserved from microbes to humans, the same basic mechanisms are in play, as is observed in hyperglycemic memory. Exploration of new metabolic transcriptional memory systems as well as further detailed mechanistic analyses of known memory contexts in microbes is therefore central to understanding metabolic memory in humans, and may be of relevance for the successful treatment of the ever-growing epidemic of diabetes. Metabolic exposures can prime genes to have memory. Memory of carbon source shifts occurs in all kingdoms of life. Memory is maintained through multiple mechanisms including chromatin modifications, proteins, and metabolic network. Metabolic transcriptional memory in unicellular organisms is a part of “bet-hedging” strategies to ensure survival. Hyperglycemic memory in humans contributes to diabetes and aging.
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Affiliation(s)
- Poonam Bheda
- Institute of Functional Epigenetics, Helmholtz Zentrum München, Neuherberg, Germany.
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19
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Genomic organization of Polycomb Response Elements and its functional implication in Drosophila and other insects. J Biosci 2020. [DOI: 10.1007/s12038-019-9975-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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20
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Hamada A, Torre C, Drancourt M, Ghigo E. Trained Immunity Carried by Non-immune Cells. Front Microbiol 2019; 9:3225. [PMID: 30692968 PMCID: PMC6340064 DOI: 10.3389/fmicb.2018.03225] [Citation(s) in RCA: 73] [Impact Index Per Article: 14.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2018] [Accepted: 12/11/2018] [Indexed: 12/21/2022] Open
Abstract
“Trained immunity” is a term proposed by Netea to describe the ability of an organism to develop an exacerbated immunological response to protect against a second infection independent of the adaptative immunity. This immunological memory can last from 1 week to several months and is only described in innate immune cells such as monocytes, macrophages, and natural killer cells. Paradoxically, the lifespan of these cells in the blood is shorter than the duration of trained immunity. This observation suggested that trained immunity could be carried by long lifespan cells such as stem cells and non-immune cells like fibroblasts. It is now evident that in addition to performing their putative function in the development and maintenance of tissue homeostasis, non-immune cells also play an important role in the response to pathogens by producing anti-microbial factors, with long-term inflammation suggesting that non-immune cells can be trained to confer long-lasting immunological memory. This review provides a summary of the current relevant knowledge about the cells which possess immunological memory and discusses the possibility that non-immune cells may carry immunological memory and mechanisms that might be involved.
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Affiliation(s)
- Attoumani Hamada
- IRD, MEPHI, Institut Hospitalier Universitaire Méditerranée Infection, Aix-Marseille University, Marseille, France
| | - Cédric Torre
- IRD, MEPHI, Institut Hospitalier Universitaire Méditerranée Infection, Aix-Marseille University, Marseille, France
| | - Michel Drancourt
- IRD, MEPHI, Institut Hospitalier Universitaire Méditerranée Infection, Aix-Marseille University, Marseille, France
| | - Eric Ghigo
- IRD, MEPHI, Institut Hospitalier Universitaire Méditerranée Infection, Aix-Marseille University, Marseille, France
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21
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Tong AH, Tan J, Zhang JH, Xu FJ, Li FY, Cao CY. Overexpression of RYBP inhibits proliferation, invasion, and chemoresistance to cisplatin in anaplastic thyroid cancer cells via the EGFR pathway. J Biochem Mol Toxicol 2018; 33:e22241. [PMID: 30431689 DOI: 10.1002/jbt.22241] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2018] [Revised: 08/19/2018] [Accepted: 09/07/2018] [Indexed: 12/28/2022]
Affiliation(s)
- Ai-Hua Tong
- Department of Endocrinology; Linyi Central Hospital; Linyi City China
| | - Juan Tan
- Department of Endocrinology; Linyi Central Hospital; Linyi City China
| | - Jin-Hua Zhang
- Department of Endocrinology; Linyi Central Hospital; Linyi City China
| | - Fang-Jiang Xu
- Department of Endocrinology; Linyi Central Hospital; Linyi City China
| | - Fu-Yuan Li
- Department of Endocrinology; Linyi Central Hospital; Linyi City China
| | - Chun-Yu Cao
- Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences; Beijing China
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22
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Snell-Rood EC, Kobiela, ME, Sikkink, KL, Shephard AM. Mechanisms of Plastic Rescue in Novel Environments. ANNUAL REVIEW OF ECOLOGY EVOLUTION AND SYSTEMATICS 2018. [DOI: 10.1146/annurev-ecolsys-110617-062622] [Citation(s) in RCA: 72] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Adaptive phenotypic plasticity provides a mechanism of developmental rescue in novel and rapidly changing environments. Understanding the underlying mechanism of plasticity is important for predicting both the likelihood that a developmental response is adaptive and associated life-history trade-offs that could influence patterns of subsequent evolutionary rescue. Although evolved developmental switches may move organisms toward a new adaptive peak in a novel environment, such mechanisms often result in maladaptive responses. The induction of generalized physiological mechanisms in new environments is relatively more likely to result in adaptive responses to factors such as novel toxins, heat stress, or pathogens. Developmental selection forms of plasticity, which rely on within-individual selective processes, such as shaping of tissue architecture, trial-and-error learning, or acquired immunity, are particularly likely to result in adaptive plasticity in a novel environment. However, both the induction of plastic responses and the ability to be plastic through developmental selection come with significant costs, resulting in delays in reproduction, increased individual investment, and reduced fecundity. Thus, we might expect complex interactions between plastic responses that allow survival in novel environments and subsequent evolutionary responses at the population level.
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Affiliation(s)
- Emilie C. Snell-Rood
- Department of Ecology, Evolution and Behavior, University of Minnesota, St. Paul, Minnesota 55108, USA;, , ,
| | - Megan E. Kobiela,
- Department of Ecology, Evolution and Behavior, University of Minnesota, St. Paul, Minnesota 55108, USA;, , ,
| | - Kristin L. Sikkink,
- Department of Ecology, Evolution and Behavior, University of Minnesota, St. Paul, Minnesota 55108, USA;, , ,
| | - Alexander M. Shephard
- Department of Ecology, Evolution and Behavior, University of Minnesota, St. Paul, Minnesota 55108, USA;, , ,
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23
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Huang W, Liang J, Feng Y, Jia Z, Jiang L, Cai W, Paul C, Gu JG, Stambrook PJ, Millard RW, Zhu XL, Zhu P, Wang Y. Heterogeneity of adult masseter muscle satellite cells with cardiomyocyte differentiation potential. Exp Cell Res 2018; 371:20-30. [PMID: 29842877 PMCID: PMC7291879 DOI: 10.1016/j.yexcr.2018.05.028] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2017] [Revised: 05/21/2018] [Accepted: 05/24/2018] [Indexed: 01/25/2023]
Abstract
Although resident cardiac stem cells have been reported, regeneration of functional cardiomyocytes (CMs) remains a challenge. The present study identifies an alternative progenitor source for CM regeneration without the need for genetic manipulation or invasive heart biopsy procedures. Unlike limb skeletal muscles, masseter muscles (MM) in the mouse head are developed from Nkx2-5 mesodermal progenitors. Adult masseter muscle satellite cells (MMSCs) display heterogeneity in developmental origin and cell phenotypes. The heterogeneous MMSCs that can be characterized by cell sorting based on stem cell antigen-1 (Sca1) show different lineage potential. While cardiogenic potential is preserved in Sca1+ MMSCs as shown by expression of cardiac progenitor genes (including Nkx2-5), skeletal myogenic capacity is maintained in Sca1- MMSCs with Pax7 expression. Sca1+ MMSC-derived beating cells express cardiac genes and exhibit CM-like morphology. Electrophysiological properties of MMSC-derived CMs are demonstrated by calcium transients and action potentials. These findings show that MMSCs could serve as a novel cell source for cardiomyocyte replacement.
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Affiliation(s)
- Wei Huang
- Department of Pathology and Laboratory Medicine, University of Cincinnati College of Medicine, Cincinnati, OH, USA
| | - Jialiang Liang
- Department of Pathology and Laboratory Medicine, University of Cincinnati College of Medicine, Cincinnati, OH, USA
| | - Yuliang Feng
- Department of Pathology and Laboratory Medicine, University of Cincinnati College of Medicine, Cincinnati, OH, USA
| | - Zhanfeng Jia
- Department of Anesthesiology, University of Cincinnati College of Medicine, Cincinnati, OH, USA
| | - Lin Jiang
- Department of Pathology and Laboratory Medicine, University of Cincinnati College of Medicine, Cincinnati, OH, USA
| | - Wenfeng Cai
- Department of Pathology and Laboratory Medicine, University of Cincinnati College of Medicine, Cincinnati, OH, USA
| | - Christian Paul
- Department of Pathology and Laboratory Medicine, University of Cincinnati College of Medicine, Cincinnati, OH, USA
| | - Jianguo G Gu
- Department of Anesthesiology, University of Cincinnati College of Medicine, Cincinnati, OH, USA
| | - Peter J Stambrook
- Department of Molecular Genetics, Biochemistry, and Microbiology, University of Cincinnati College of Medicine, Cincinnati, OH, USA
| | - Ronald W Millard
- Pharmacology and Cell Biophysics, University of Cincinnati College of Medicine, Cincinnati, OH, USA
| | - Xiao-Lan Zhu
- Department of Cardiac Surgery, Guangdong Cardiovascular Institute, Guangdong General Hospital, Guangdong Academy of Medical Sciences, Guangzhou 510080, China
| | - Ping Zhu
- Department of Cardiac Surgery, Guangdong Cardiovascular Institute, Guangdong General Hospital, Guangdong Academy of Medical Sciences, Guangzhou 510080, China.
| | - Yigang Wang
- Department of Pathology and Laboratory Medicine, University of Cincinnati College of Medicine, Cincinnati, OH, USA.
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24
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Zhang T, Wei G, Millard CJ, Fischer R, Konietzny R, Kessler BM, Schwabe JWR, Brockdorff N. A variant NuRD complex containing PWWP2A/B excludes MBD2/3 to regulate transcription at active genes. Nat Commun 2018; 9:3798. [PMID: 30228260 PMCID: PMC6143588 DOI: 10.1038/s41467-018-06235-9] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2017] [Accepted: 08/03/2018] [Indexed: 02/07/2023] Open
Abstract
Transcriptional regulation by chromatin is a highly dynamic process directed through the recruitment and coordinated action of epigenetic modifiers and readers of these modifications. Using an unbiased proteomic approach to find interactors of H3K36me3, a modification enriched on active chromatin, here we identify PWWP2A and HDAC2 among the top interactors. PWWP2A and its paralog PWWP2B form a stable complex with NuRD subunits MTA1/2/3:HDAC1/2:RBBP4/7, but not with MBD2/3, p66α/β, and CHD3/4. PWWP2A competes with MBD3 for binding to MTA1, thus defining a new variant NuRD complex that is mutually exclusive with the MBD2/3 containing NuRD. In mESCs, PWWP2A/B is most enriched at highly transcribed genes. Loss of PWWP2A/B leads to increases in histone acetylation predominantly at highly expressed genes, accompanied by decreases in Pol II elongation. Collectively, these findings suggest a role for PWWP2A/B in regulating transcription through the fine-tuning of histone acetylation dynamics at actively transcribed genes. Transcription regulation requires recruitment of different epigenetic regulators to the chromatin. Here the authors provide evidence that an H3K36me3 reader PWWP2A forms a variant NuRD complex and plays a role in regulating transcription and histone acetylation dynamics.
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Affiliation(s)
- Tianyi Zhang
- Developmental Epigenetics, Department of Biochemistry, University of Oxford, Oxford, OX1 3QU, United Kingdom
| | - Guifeng Wei
- Developmental Epigenetics, Department of Biochemistry, University of Oxford, Oxford, OX1 3QU, United Kingdom
| | - Christopher J Millard
- Leicester Institute for Structural and Chemical Biology and Department of Molecular and Cell Biology, University of Leicester, Leicester, LE1 7RH, United Kingdom
| | - Roman Fischer
- Target Discovery Institute, Nuffield Department of Medicine, University of Oxford, Roosevelt Drive, Oxford, OX3 7FZ, United Kingdom
| | - Rebecca Konietzny
- Target Discovery Institute, Nuffield Department of Medicine, University of Oxford, Roosevelt Drive, Oxford, OX3 7FZ, United Kingdom.,Agilent Technologies, Hewlett-Packard-Str. 8, 76337, Waldbronn, Germany
| | - Benedikt M Kessler
- Target Discovery Institute, Nuffield Department of Medicine, University of Oxford, Roosevelt Drive, Oxford, OX3 7FZ, United Kingdom
| | - John W R Schwabe
- Leicester Institute for Structural and Chemical Biology and Department of Molecular and Cell Biology, University of Leicester, Leicester, LE1 7RH, United Kingdom
| | - Neil Brockdorff
- Developmental Epigenetics, Department of Biochemistry, University of Oxford, Oxford, OX1 3QU, United Kingdom.
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25
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Liang Y, Yang Y, Guo R, Gao S, Guo X, Li D, Wang M, Koseki H, Li X. PCL2 regulates p53 stability and functions as a tumor suppressor in breast cancer. Sci Bull (Beijing) 2018; 63:629-639. [PMID: 36658883 DOI: 10.1016/j.scib.2018.03.012] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2017] [Revised: 03/13/2018] [Accepted: 03/14/2018] [Indexed: 01/21/2023]
Abstract
Polycomblike2 (PCL2) is a well-known component of polycomb repressive complex 2 (PRC2) and plays important roles in H3K27 methylation and homeotic gene silencing. However, the involvement of PCL2 in breast cancer development remains unclear. Here, we established PCL2 as a tumor suppressor gene in breast cancer. Expression level of PCL2 was significantly downregulated in breast cancer tissue samples observed at different TNM stages. Ectopic expression of PCL2 could significantly inhibit cell proliferation and promoted apoptosis. PCL2 also remarkably elevated levels of p53 and its targets by increasing p53 stability. Mechanistically, PCL2 protected p53 proteins from MDM2-mediated ubiquitination and degradation by sequestering MDM2 into the nucleolus. Overexpression of PCL2 also suppressed migration and invasion by inhibiting epithelial-mesenchymal transition. PCL2 expression was correlated with E-cadherin expression and was inversely correlated with vimentin expression. Furthermore, PCL2 knockdown could attenuate anti-tumor effect of MLN4924. Taken together, our findings indicated that PCL2 played a tumor suppressor role in development and progression of breast cancer and may be a prognostic and predictive marker for breast cancer.
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Affiliation(s)
- Yiran Liang
- Department of Cell Biology, Shandong University School of Basic Medical Sciences, Jinan 250012, China; Department of Breast Surgery, Qilu Hospital of Shandong University, Jinan 250012, China
| | - Yang Yang
- Department of Cell Biology, Shandong University School of Basic Medical Sciences, Jinan 250012, China
| | - Renbo Guo
- Department of Urology, Shandong Cancer Hospital Affiliated to Shandong University, Jinan 250117, China
| | - Shuang Gao
- Department of Cell Biology, Shandong University School of Basic Medical Sciences, Jinan 250012, China
| | - Xinghong Guo
- Department of Cell Biology, Shandong University School of Basic Medical Sciences, Jinan 250012, China
| | - Danyang Li
- Department of Cell Biology, Shandong University School of Basic Medical Sciences, Jinan 250012, China
| | - Meng Wang
- Department of Cell Biology, Shandong University School of Basic Medical Sciences, Jinan 250012, China
| | - Haruhiko Koseki
- Laboratory for Developmental Genetics, RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa 230-0045, Japan
| | - Xiangzhi Li
- Department of Cell Biology, Shandong University School of Basic Medical Sciences, Jinan 250012, China.
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26
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Chereji RV, Clark DJ. Major Determinants of Nucleosome Positioning. Biophys J 2018; 114:2279-2289. [PMID: 29628211 DOI: 10.1016/j.bpj.2018.03.015] [Citation(s) in RCA: 49] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2017] [Revised: 02/27/2018] [Accepted: 03/08/2018] [Indexed: 12/21/2022] Open
Abstract
The compact structure of the nucleosome limits DNA accessibility and inhibits the binding of most sequence-specific proteins. Nucleosomes are not randomly located on the DNA but positioned with respect to the DNA sequence, suggesting models in which critical binding sites are either exposed in the linker, resulting in activation, or buried inside a nucleosome, resulting in repression. The mechanisms determining nucleosome positioning are therefore of paramount importance for understanding gene regulation and other events that occur in chromatin, such as transcription, replication, and repair. Here, we review our current understanding of the major determinants of nucleosome positioning: DNA sequence, nonhistone DNA-binding proteins, chromatin-remodeling enzymes, and transcription. We outline the major challenges for the future: elucidating the precise mechanisms of chromatin opening and promoter activation, identifying the complexes that occupy promoters, and understanding the multiscale problem of chromatin fiber organization.
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Affiliation(s)
- Răzvan V Chereji
- Division of Developmental Biology, Eunice Kennedy Shriver National Institute for Child Health and Human Development, National Institutes of Health, Bethesda, Maryland.
| | - David J Clark
- Division of Developmental Biology, Eunice Kennedy Shriver National Institute for Child Health and Human Development, National Institutes of Health, Bethesda, Maryland.
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An Evolutionary Conserved Epigenetic Mark of Polycomb Response Elements Implemented by Trx/MLL/COMPASS. Mol Cell 2017; 63:318-328. [PMID: 27447986 DOI: 10.1016/j.molcel.2016.06.018] [Citation(s) in RCA: 47] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2016] [Revised: 04/07/2016] [Accepted: 06/10/2016] [Indexed: 12/20/2022]
Abstract
Polycomb response elements (PREs) are specific DNA sequences that stably maintain the developmental pattern of gene expression. Drosophila PREs are well characterized, whereas the existence of PREs in mammals remains debated. Accumulating evidence supports a model in which CpG islands recruit Polycomb group (PcG) complexes; however, which subset of CGIs is selected to serve as PREs is unclear. Trithorax (Trx) positively regulates gene expression in Drosophila and co-occupies PREs to antagonize Polycomb-dependent silencing. Here we demonstrate that Trx-dependent H3K4 dimethylation (H3K4me2) marks Drosophila PREs and maintains the developmental expression pattern of nearby genes. Similarly, the mammalian Trx homolog, MLL1, deposits H3K4me2 at CpG-dense regions that could serve as PREs. In the absence of MLL1 and H3K4me2, H3K27me3 levels, a mark of Polycomb repressive complex 2 (PRC2), increase at these loci. By inhibiting PRC2-dependent H3K27me3 in the absence of MLL1, we can rescue expression of these loci, demonstrating a functional balance between MLL1 and PRC2 activities at these sites. Thus, our study provides rules for identifying cell-type-specific functional mammalian PREs within the human genome.
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28
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The Role of Epigenetic Mechanisms in the Regulation of Gene Expression in the Nervous System. J Neurosci 2017; 36:11427-11434. [PMID: 27911745 DOI: 10.1523/jneurosci.2492-16.2016] [Citation(s) in RCA: 94] [Impact Index Per Article: 13.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2016] [Revised: 08/29/2016] [Accepted: 08/31/2016] [Indexed: 11/21/2022] Open
Abstract
Neuroepigenetics is a newly emerging field in neurobiology that addresses the epigenetic mechanism of gene expression regulation in various postmitotic neurons, both over time and in response to environmental stimuli. In addition to its fundamental contribution to our understanding of basic neuronal physiology, alterations in these neuroepigenetic mechanisms have been recently linked to numerous neurodevelopmental, psychiatric, and neurodegenerative disorders. This article provides a selective review of the role of DNA and histone modifications in neuronal signal-induced gene expression regulation, plasticity, and survival and how targeting these mechanisms could advance the development of future therapies. In addition, we discuss a recent discovery on how double-strand breaks of genomic DNA mediate the rapid induction of activity-dependent gene expression in neurons.
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29
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Brici D, Zhang Q, Reinhardt S, Dahl A, Hartmann H, Schmidt K, Goveas N, Huang J, Gahurova L, Kelsey G, Anastassiadis K, Stewart AF, Kranz A. Setd1b, encoding a histone 3 lysine 4 methyltransferase, is a maternal effect gene required for the oogenic gene expression program. Development 2017; 144:2606-2617. [PMID: 28619824 DOI: 10.1242/dev.143347] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2016] [Accepted: 06/02/2017] [Indexed: 12/16/2022]
Abstract
Germ cell development involves major reprogramming of the epigenome to prime the zygote for totipotency. Histone 3 lysine 4 (H3K4) methylations are universal epigenetic marks mediated in mammals by six H3K4 methyltransferases related to fly Trithorax, including two yeast Set1 orthologs: Setd1a and Setd1b. Whereas Setd1a plays no role in oogenesis, we report that Setd1b deficiency causes female sterility in mice. Oocyte-specific Gdf9-iCre conditional knockout (Setd1bGdf9 cKO) ovaries develop through all stages; however, follicular loss accumulated with age and unfertilized metaphase II (MII) oocytes exhibited irregularities of the zona pellucida and meiotic spindle. Most Setd1bGdf9 cKO zygotes remained in the pronuclear stage and displayed polyspermy in the perivitelline space. Expression profiling of Setd1bGdf9 cKO MII oocytes revealed (1) that Setd1b promotes the expression of the major oocyte transcription factors including Obox1, 2, 5, 7, Meis2 and Sall4; and (2) twice as many mRNAs were upregulated than downregulated, suggesting that Setd1b also promotes the expression of negative regulators of oocyte development with multiple Zfp-KRAB factors implicated. Together, these findings indicate that Setd1b serves as maternal effect gene through regulation of the oocyte gene expression program.
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Affiliation(s)
- David Brici
- Genomics, Biotechnology Center, Technische Universität Dresden, BioInnovationsZentrum, Tatzberg 47, Dresden 01307, Germany
| | - Qinyu Zhang
- Genomics, Biotechnology Center, Technische Universität Dresden, BioInnovationsZentrum, Tatzberg 47, Dresden 01307, Germany
| | - Susanne Reinhardt
- Deep Sequencing Group SFB 655, Biotechnology Center, Technische Universität Dresden, 01307 Dresden, Germany
| | - Andreas Dahl
- Deep Sequencing Group SFB 655, Biotechnology Center, Technische Universität Dresden, 01307 Dresden, Germany
| | - Hella Hartmann
- Light Microscopy Core Facility of the Biotechnology Center/Center for Regenerative Therapies Dresden, Technische Universität Dresden, 01307 Dresden, Germany
| | - Kerstin Schmidt
- Stem Cell Engineering, Biotechnology Center, Technische Universität Dresden, BioInnovationsZentrum, Tatzberg 47, Dresden 01307, Germany
| | - Neha Goveas
- Genomics, Biotechnology Center, Technische Universität Dresden, BioInnovationsZentrum, Tatzberg 47, Dresden 01307, Germany
| | - Jiahao Huang
- Epigenetics Programme, The Babraham Institute, Cambridge, CB22 3AT, UK
| | - Lenka Gahurova
- Epigenetics Programme, The Babraham Institute, Cambridge, CB22 3AT, UK
| | - Gavin Kelsey
- Epigenetics Programme, The Babraham Institute, Cambridge, CB22 3AT, UK
| | - Konstantinos Anastassiadis
- Stem Cell Engineering, Biotechnology Center, Technische Universität Dresden, BioInnovationsZentrum, Tatzberg 47, Dresden 01307, Germany
| | - A Francis Stewart
- Genomics, Biotechnology Center, Technische Universität Dresden, BioInnovationsZentrum, Tatzberg 47, Dresden 01307, Germany
| | - Andrea Kranz
- Genomics, Biotechnology Center, Technische Universität Dresden, BioInnovationsZentrum, Tatzberg 47, Dresden 01307, Germany
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Mu Y, Liu Y, Bai L, Li S, He C, Yan Y, Yu X, Li Y. Cucumber CsBPCs Regulate the Expression of CsABI3 during Seed Germination. FRONTIERS IN PLANT SCIENCE 2017; 8:459. [PMID: 28421094 PMCID: PMC5376566 DOI: 10.3389/fpls.2017.00459] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/23/2016] [Accepted: 03/16/2017] [Indexed: 05/11/2023]
Abstract
Cucumber seeds with shallow dormancy start to germinate in fruit that are harvested late. ABSCISIC ACID INSENSITIVE3 (ABI3), a transcription factor in the abscisic acid (ABA) signaling pathway, is one of the most important regulators in the transition from late embryogenesis to germination. Our analysis found a candidate cis-regulatory motif for cucumber BASIC PENTACYSTEINE (CsBPC) in the promoter of CsABI3. Yeast one-hybrid and chromatin immunoprecipitation (ChIP) assays showed that CsBPCs bound to the promoter of CsABI3. Examination of β-glucuronidase (GUS) activity driven by the CsABI3 promoter in transgenic Arabidopsis thaliana plants overexpressing CsBPCs and a Nicotiana benthamiana (tobacco) luciferase assay indicated that CsBPCs inhibited the expression of CsABI3. Transgenic plants overexpressing CsBPCs were constructed to confirm that CsBPCs participates in the control of seed germination. This study of the cucumber BPC-ABI3 pathway will help to explore and characterize the molecular mechanisms underlying seed germination and will provide necessary information for seed conservation in agriculture and forestry.
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Connelly KE, Dykhuizen EC. Compositional and functional diversity of canonical PRC1 complexes in mammals. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2016; 1860:233-245. [PMID: 28007606 DOI: 10.1016/j.bbagrm.2016.12.006] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/06/2016] [Revised: 12/12/2016] [Accepted: 12/15/2016] [Indexed: 12/17/2022]
Abstract
The compositional complexity of Polycomb Repressive Complex 1 (PRC1) increased dramatically during vertebrate evolution. What is considered the "canonical" PRC1 complex consists of four subunits originally identified as regulators of body segmentation in Drosophila. In mammals, each of these four canonical subunits consists of two to six paralogs that associate in a combinatorial manner to produce over a hundred possible distinct PRC1 complexes with unknown function. Genetic studies have begun to define the phenotypic roles for different PRC1 paralogs; however, relating these phenotypes to unique biochemical and transcriptional function for the different paralogs has been challenging. In this review, we attempt to address how the compositional diversity of canonical PRC1 complexes relates to unique roles for individual PRC1 paralogs in transcriptional regulation. This review focuses primarily on PRC1 complex composition, genome targeting, and biochemical function.
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Affiliation(s)
- Katelyn E Connelly
- Department of Medicinal Chemistry and Molecular Pharmacology, College of Pharmacy, Purdue University, 201 S. University St., West Lafayette, IN 47907, USA
| | - Emily C Dykhuizen
- Department of Medicinal Chemistry and Molecular Pharmacology, College of Pharmacy, Purdue University, 201 S. University St., West Lafayette, IN 47907, USA; Purdue University Center for Cancer Research, 201 S. University St., West Lafayette, IN 47907, USA.
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32
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Zhu X, Yan M, Luo W, Liu W, Ren Y, Bei C, Tang G, Chen R, Tan S. Expression and clinical significance of PcG-associated protein RYBP in hepatocellular carcinoma. Oncol Lett 2016; 13:141-150. [PMID: 28123534 PMCID: PMC5244986 DOI: 10.3892/ol.2016.5380] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2015] [Accepted: 11/01/2016] [Indexed: 12/13/2022] Open
Abstract
Ring1 and YY1 binding protein (RYBP), a member of the polycomb group proteins, has been implicated in transcription repression and tumor cell-specific apoptosis. Previously, RYBP has been reported as a putative tumor suppressor in cancer tissues by regulating mouse double minute 2 homolog-p53 signaling. However, the exact role and underlying mechanisms of RYBP in cancer remain to be fully elucidated. The present study investigated the expression profile of RYBP in hepatocellular carcinoma (HCC) and examined the association between the expression of RYBP and metastasis of HCC. It was found that RYBP was downregulated in HCC tissues, compared with matched adjacent non-tumor tissues, as detected by reverse transcription-quantitative polymerase chain reaction and immunohistochemistry. In addition, Kaplan-Meier survival analysis showed that the negative expression of RYBP was associated with decreased overall survival rates in patients with HCC. It was also found that RYBP was associated with zinc finger E-box binding homeobox 1 and zinc finger E-box binding homeobox 2, which were overexpressed in HCC and correlated with epithelial-mesenchymal transition. The results of the present study suggested the importance of RYBP in HCC and its possible mechanism in the metastasis of HCC.
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Affiliation(s)
- Xiaonian Zhu
- Department of Epidemiology and Statistics, School of Public Health, Guilin Medical University, Guilin, Guangxi 541000, P.R. China
| | - Meng Yan
- Department of Hepatobiliary Surgery, The Affiliated Hospital of Guilin Medical University, Guilin, Guangxi 541000, P.R. China; Department of General Surgery, First Central Hospital of Baoding, Baoding, Hebei 071000, P.R. China
| | - Wei Luo
- Department of Hepatobiliary Surgery, The Affiliated Hospital of Guilin Medical University, Guilin, Guangxi 541000, P.R. China
| | - Wei Liu
- Department of Hepatobiliary Surgery, The Affiliated Hospital of Guilin Medical University, Guilin, Guangxi 541000, P.R. China
| | - Yuan Ren
- Department of Epidemiology and Statistics, School of Public Health, Guilin Medical University, Guilin, Guangxi 541000, P.R. China
| | - Chunhua Bei
- Department of Epidemiology and Statistics, School of Public Health, Guilin Medical University, Guilin, Guangxi 541000, P.R. China
| | - Guifang Tang
- Department of Hepatology, Nanxishan Hospital of Guangxi Zhuang Autonomous Region, Guilin, Guangxi 541000, P.R. China
| | - Ruiling Chen
- Department of Hepatology, Nanxishan Hospital of Guangxi Zhuang Autonomous Region, Guilin, Guangxi 541000, P.R. China
| | - Shengkui Tan
- Department of Epidemiology and Statistics, School of Public Health, Guilin Medical University, Guilin, Guangxi 541000, P.R. China; Department of Hepatobiliary Surgery, The Affiliated Hospital of Guilin Medical University, Guilin, Guangxi 541000, P.R. China
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Yamada T, Kanoh M, Nabe S, Yasuoka T, Suzuki J, Matsumoto A, Kuwahara M, Maruyama S, Fujimoto T, Sakisuka R, Yasukawa M, Yamashita M. Menin Plays a Critical Role in the Regulation of the Antigen-Specific CD8+ T Cell Response upon Listeria Infection. THE JOURNAL OF IMMUNOLOGY 2016; 197:4079-4089. [PMID: 27798149 DOI: 10.4049/jimmunol.1502295] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/27/2015] [Accepted: 09/12/2016] [Indexed: 02/06/2023]
Abstract
Menin, a tumor suppressor protein, is encoded by the MEN1 gene in humans. Certain germinal mutations of MEN1 induce an autosomal-dominant syndrome that is characterized by concurrent parathyroid adenomas and several other tumor types. Although menin is also expressed in hematopoietic lineages, its role in CD8+ T cells remains unclear. We generated Meninflox/flox CD4-Cre (Menin-KO) mice by crossing Meninflox/flox mice with CD4-Cre transgenic (Tg) mice to determine the role of menin in CD8+ T cells. Wild-type (WT) and Menin-KO mice were infected with Listeria monocytogenes expressing OVA to analyze the immune response of Ag-specific CD8+ T cells. Menin deficiency resulted in an impaired primary immune response by CD8+ T cells. On day 7, there were fewer Menin-KO OVA-specific CD8+ T cells compared with WT cells. Next, we adoptively transferred WT and Menin-KO OT-1 Tg CD8+ T cells into congenic recipient mice and infected them with L. monocytogenes expressing OVA to determine the CD8+ T cell-intrinsic effect. Menin-KO OT-1 Tg CD8+ T cells were outcompeted by the WT cells upon infection. Increased expression of Blimp-1 and T-bet, cell cycle inhibitors, and proapoptotic genes was observed in the Menin-KO OT-1 Tg CD8+ T cells upon infection. These data suggest that menin inhibits differentiation into terminal effectors and positively controls proliferation and survival of Ag-specific CD8+ T cells that are activated upon infection. Collectively, our study uncovered an important role for menin in the immune response of CD8+ T cells to infection.
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Affiliation(s)
- Takeshi Yamada
- Department of Infection and Host Defenses, Graduate School of Medicine, Ehime University, Shitsukawa, Toon, Ehime 791-0295, Japan;
| | - Makoto Kanoh
- Department of Infection and Host Defenses, Graduate School of Medicine, Ehime University, Shitsukawa, Toon, Ehime 791-0295, Japan
| | - Shogo Nabe
- Department of Hematology, Clinical Immunology, and Infectious diseases, Graduate School of Medicine, Ehime University, Shitsukawa, Toon, Ehime 791-0295, Japan
| | - Toshiaki Yasuoka
- Department of Obstetrics and Gynecology, Graduate School of Medicine, Ehime University, Shitsukawa, Toon, Ehime 791-0295, Japan
| | - Junpei Suzuki
- Department of Hematology, Clinical Immunology, and Infectious diseases, Graduate School of Medicine, Ehime University, Shitsukawa, Toon, Ehime 791-0295, Japan.,Department of Immunology, Graduate School of Medicine, Ehime University, Shitsukawa, Toon, Ehime 791-0295, Japan; and.,Translational Research Center, Ehime University Hospital, Shitsukawa, Toon, Ehime 791-0295, Japan
| | - Akira Matsumoto
- Department of Infection and Host Defenses, Graduate School of Medicine, Ehime University, Shitsukawa, Toon, Ehime 791-0295, Japan
| | - Makoto Kuwahara
- Department of Immunology, Graduate School of Medicine, Ehime University, Shitsukawa, Toon, Ehime 791-0295, Japan; and.,Translational Research Center, Ehime University Hospital, Shitsukawa, Toon, Ehime 791-0295, Japan
| | - Saho Maruyama
- Department of Immunology, Graduate School of Medicine, Ehime University, Shitsukawa, Toon, Ehime 791-0295, Japan; and
| | - Takuya Fujimoto
- Department of Infection and Host Defenses, Graduate School of Medicine, Ehime University, Shitsukawa, Toon, Ehime 791-0295, Japan
| | - Ryo Sakisuka
- Department of Infection and Host Defenses, Graduate School of Medicine, Ehime University, Shitsukawa, Toon, Ehime 791-0295, Japan
| | - Masaki Yasukawa
- Department of Hematology, Clinical Immunology, and Infectious diseases, Graduate School of Medicine, Ehime University, Shitsukawa, Toon, Ehime 791-0295, Japan
| | - Masakatsu Yamashita
- Department of Immunology, Graduate School of Medicine, Ehime University, Shitsukawa, Toon, Ehime 791-0295, Japan; and.,Translational Research Center, Ehime University Hospital, Shitsukawa, Toon, Ehime 791-0295, Japan
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34
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Gallardo M, Calaf GM. Curcumin inhibits invasive capabilities through epithelial mesenchymal transition in breast cancer cell lines. Int J Oncol 2016; 49:1019-27. [DOI: 10.3892/ijo.2016.3598] [Citation(s) in RCA: 42] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2016] [Accepted: 03/22/2016] [Indexed: 11/05/2022] Open
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35
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Abstract
The central nervous system (CNS) underlies memory, perception, decision-making, and behavior in numerous organisms. However, neural networks have no monopoly on the signaling functions that implement these remarkable algorithms. It is often forgotten that neurons optimized cellular signaling modes that existed long before the CNS appeared during evolution, and were used by somatic cellular networks to orchestrate physiology, embryonic development, and behavior. Many of the key dynamics that enable information processing can, in fact, be implemented by different biological hardware. This is widely exploited by organisms throughout the tree of life. Here, we review data on memory, learning, and other aspects of cognition in a range of models, including single celled organisms, plants, and tissues in animal bodies. We discuss current knowledge of the molecular mechanisms at work in these systems, and suggest several hypotheses for future investigation. The study of cognitive processes implemented in aneural contexts is a fascinating, highly interdisciplinary topic that has many implications for evolution, cell biology, regenerative medicine, computer science, and synthetic bioengineering.
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Affiliation(s)
- František Baluška
- Department of Plant Cell Biology, IZMB, University of Bonn Bonn, Germany
| | - Michael Levin
- Biology Department, Tufts Center for Regenerative and Developmental Biology, Tufts University Medford, MA, USA
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36
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Song Y, Wu F, Wu J. Targeting histone methylation for cancer therapy: enzymes, inhibitors, biological activity and perspectives. J Hematol Oncol 2016; 9:49. [PMID: 27316347 PMCID: PMC4912745 DOI: 10.1186/s13045-016-0279-9] [Citation(s) in RCA: 98] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2016] [Accepted: 06/07/2016] [Indexed: 12/31/2022] Open
Abstract
Post-translational methylation of histone lysine or arginine residues plays important roles in gene regulation and other physiological processes. Aberrant histone methylation caused by a gene mutation, translocation, or overexpression can often lead to initiation of a disease such as cancer. Small molecule inhibitors of such histone modifying enzymes that correct the abnormal methylation could be used as novel therapeutics for these diseases, or as chemical probes for investigation of epigenetics. Discovery and development of histone methylation modulators are in an early stage and undergo a rapid expansion in the past few years. A number of highly potent and selective compounds have been reported, together with extensive preclinical studies of their biological activity. Several compounds have been in clinical trials for safety, pharmacokinetics, and efficacy, targeting several types of cancer. This review summarizes the biochemistry, structures, and biology of cancer-relevant histone methylation modifying enzymes, small molecule inhibitors and their preclinical and clinical antitumor activities. Perspectives for targeting histone methylation for cancer therapy are also discussed.
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Affiliation(s)
- Yongcheng Song
- Department of Pharmacology, Baylor College of Medicine, 1 Baylor Plaza, Houston, TX, 77030, USA. .,Dan L. Duncan Cancer Center, Baylor College of Medicine, 1 Baylor Plaza, Houston, TX, 77030, USA.
| | - Fangrui Wu
- Department of Pharmacology, Baylor College of Medicine, 1 Baylor Plaza, Houston, TX, 77030, USA
| | - Jingyu Wu
- Department of Pharmacology, Baylor College of Medicine, 1 Baylor Plaza, Houston, TX, 77030, USA
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Liedtke S, Sacchetti B, Laitinen A, Donsante S, Klöckers R, Laitinen S, Riminucci M, Kogler G. Low oxygen tension reveals distinct HOX codes in human cord blood-derived stromal cells associated with specific endochondral ossification capacities in vitro and in vivo. J Tissue Eng Regen Med 2016; 11:2725-2736. [PMID: 27214005 DOI: 10.1002/term.2167] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2015] [Revised: 12/21/2015] [Accepted: 02/03/2016] [Indexed: 12/17/2022]
Abstract
Effects of oxygen tension on the generation, expansion, proliferation and differentiation of stromal cell types is widely described in the literature. However, data on the internal heterogeneity of applied cell populations at different O2 levels and possible impacts on differentiation potentials are controversial. Here, the expression of 39 human HOX genes was determined in neonatal cord blood stromal cells and linked to differentiation-associated signatures. In cord blood, unrestricted somatic stromal cells (USSCs), lacking HOX gene expression, and cord blood-derived multipotent stromal cells (CB-MSCs), expressing about 20 HOX genes, are distinguished by their specific HOX code. Interestingly, 74% of the clones generated at 21% O2 were HOX-negative USSCs, whereas 73% of upcoming clones at 3% O2 were HOX-positive CB-MSCs. In order to better categorize distinct cell lines generated at 3% O2 , the expression of all 39 HOX genes within HOX clusters A, B, C and D were tested and new subtypes defined: cells negative in all four HOX clusters (USSCs); cells positive in all four clusters (CB-MSCsABCD ); and subpopulations missing a single cluster (CB-MSCsACD and CB-MSCsBCD ). Comprehensive qPCR analyses of established chondro-osteomarkers revealed subtype-specific signatures verifiably associated with in vitro and in vivo differentiation capacity. The data presented here underline the necessity of better characterizing distinct cell populations at a clonal level, taking advantage of the inherent specific HOX code as a distinguishing feature between individual subtypes. Moreover, the correlation of subtype-specific molecular signatures with in vitro and in vivo bone formation is discussed. Copyright © 2016 John Wiley & Sons, Ltd.
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Affiliation(s)
- Stefanie Liedtke
- Institute of Transplantation Diagnostics and Cell Therapeutics, Heinrich-Heine-University Medical Centre, Düsseldorf, Germany
| | - Benedetto Sacchetti
- Stem Cell Laboratory, Department of Molecular Medicine, Sapienza University, Rome, Italy
| | - Anita Laitinen
- Research and Development, Medical Services, Finnish Red Cross Blood Service, Helsinki, Finland
| | - Samantha Donsante
- Stem Cell Laboratory, Department of Molecular Medicine, Sapienza University, Rome, Italy
| | - Robert Klöckers
- Institute of Transplantation Diagnostics and Cell Therapeutics, Heinrich-Heine-University Medical Centre, Düsseldorf, Germany
| | - Saara Laitinen
- Research and Development, Medical Services, Finnish Red Cross Blood Service, Helsinki, Finland
| | - Mara Riminucci
- Stem Cell Laboratory, Department of Molecular Medicine, Sapienza University, Rome, Italy
| | - Gesine Kogler
- Institute of Transplantation Diagnostics and Cell Therapeutics, Heinrich-Heine-University Medical Centre, Düsseldorf, Germany
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Hu T, Jin Y, Li H, Amombo E, Fu J. Stress memory induced transcriptional and metabolic changes of perennial ryegrass (Lolium perenne) in response to salt stress. PHYSIOLOGIA PLANTARUM 2016; 156:54-69. [PMID: 25913889 DOI: 10.1111/ppl.12342] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/05/2015] [Revised: 04/02/2015] [Accepted: 04/02/2015] [Indexed: 05/18/2023]
Abstract
Preexposure to a stress could induce stable signals and reactions on plant physiology and gene expression during future encounters as a 'stress memory'. In this study, we found that two trainable genes, BPSP encoding putative brown plant hopper susceptibility protein and sucs encoding sucrose synthase displayed transcriptional memory for their considerably higher transcript levels during two or more subsequent stresses (S3, S4) relative to the initial stress (S0), and their expression returning to basal transcript levels (non-stressed) during the recovery states (R1, R2 and R3). Removing the repetitive stress/recovery exercise, activated transcriptional memory from two trainable genes persisted for at least 4 days in perennial ryegrass. The pretrainable genes with stress memory effort had higher response to the subsequent elevated NaCl concentration treatment than the non-trainable plants, which was confirmed by lower electrolyte leakage and minimum H2 O2 and O2 (-) accumulation. Salt stress elevated the content of 41 metabolites in perennial ryegrass leaves, and sugars and sugar alcohol accounted for more than 74.1% of the total metabolite content. The salt stress memory was associated with higher contents of 11 sugars and 1 sugar alcohol in the pretrainable grass leaves. Similarly, six sugars showed greater content in the pretrainable grass roots. These novel phenomena associated with transcriptional memory and metabolite profiles could lead to new insights into improving plant salinity acclimation process.
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Affiliation(s)
- Tao Hu
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Science, Wuhan 430074, China
| | - Yupei Jin
- Institute of Molecular Biology, China Three Gorges University, Yichang 443002, China
| | - Huiying Li
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Science, Wuhan 430074, China
| | - Erick Amombo
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Science, Wuhan 430074, China
| | - Jinmin Fu
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Science, Wuhan 430074, China
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Hsp90 as a "Chaperone" of the Epigenome: Insights and Opportunities for Cancer Therapy. Adv Cancer Res 2015; 129:107-40. [PMID: 26916003 DOI: 10.1016/bs.acr.2015.09.003] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
The cellular functions of Hsp90 have historically been attributed to its ability to chaperone client proteins involved in signal transduction. Although numerous stimuli and the signaling cascades they activate contribute to cancer progression, many of these pathways ultimately require transcriptional effectors to elicit tumor-promoting effects. Despite this obvious connection, the majority of studies evaluating Hsp90 function in malignancy have focused upon its regulation of cytosolic client proteins, and particularly members of receptor and/or kinase families. However, in recent years, Hsp90 has emerged as a pivotal orchestrator of nuclear events. Discovery of an expanding repertoire of Hsp90 clients has illuminated a vital role for Hsp90 in overseeing nuclear events and influencing gene transcription. Hence, this chapter will cast a spotlight upon several regulatory themes involving Hsp90-dependent nuclear functions. Highlighted topics include a summary of chaperone-dependent regulation of key transcription factors (TFs) and epigenetic effectors in malignancy, as well as a discussion of how the complex interplay among a subset of these TFs and epigenetic regulators may generate feed-forward loops that further support cancer progression. This chapter will also highlight less recognized indirect mechanisms whereby Hsp90-supported signaling may impinge upon epigenetic regulation. Finally, the relevance of these nuclear events is discussed within the framework of Hsp90's capacity to enable phenotypic variation and drug resistance. These newly acquired insights expanding our understanding of Hsp90 function support the collective notion that nuclear clients are major beneficiaries of Hsp90 action, and their impairment is likely responsible for many of the anticancer effects elicited by Hsp90-targeted approaches.
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Abstract
SUMMARY The involvement of RNA interference (RNAi) in heterochromatin formation has become clear largely through studies in the fission yeast Schizosaccharomyces pombe and plants like Arabidopsis thaliana. This article discusses how heterochromatic small interfering RNAs are produced and how the RNAi machinery participates in the formation and function of heterochromatin.
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Affiliation(s)
| | - Danesh Moazed
- Department of Cell Biology, Harvard Medical School, Boston, Massachusetts 02115-5730
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Frege T, Uversky VN. Intrinsically disordered proteins in the nucleus of human cells. Biochem Biophys Rep 2015; 1:33-51. [PMID: 29124132 PMCID: PMC5668563 DOI: 10.1016/j.bbrep.2015.03.003] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2015] [Accepted: 03/11/2015] [Indexed: 12/16/2022] Open
Abstract
Intrinsically disordered proteins are known to perform a variety of important functions such as macromolecular recognition, promiscuous binding, and signaling. They are crucial players in various cellular pathway and processes, where they often have key regulatory roles. Among vital cellular processes intimately linked to the intrinsically disordered proteins is transcription, an intricate biological performance predominantly developing inside the cell nucleus. With this work, we gathered information about proteins that exist in various compartments and sub-nuclear bodies of the nucleus of the human cells, with the goal of identifying which ones are highly disordered and which functions are ascribed to the disordered nuclear proteins.
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Affiliation(s)
- Telma Frege
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, FL 33612, USA
- GenomeNext LLC, 175 South 3rd Street, Suite 200, Columbus OH 43215, USA
| | - Vladimir N. Uversky
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, FL 33612, USA
- USF Health Byrd Alzheimer׳s Research Institute, Morsani College of Medicine, University of South Florida, Tampa, FL 33612, USA
- Department of Biology, Faculty of Science, King Abdulaziz University, P.O. Box 80203, Jeddah 21589, Saudi Arabia
- Institute for Biological Instrumentation, Russian Academy of Sciences, 142290 Pushchino, Moscow Region, Russia
- Laboratory of Structural Dynamics, Stability and Folding of Proteins, Institute of Cytology, Russian Academy of Sciences, St. Petersburg, Russia
- Correspondence to: Department of Molecular, Medicine, Morsani College of Medicine, University of South Florida, 12901 Bruce B. Downs Boulevard, MDC07, Tampa, FL 33612, USA. Tel.: +1 813 974 5816; fax: +1 813 974 7357.
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Hu T, Liu SQ, Amombo E, Fu JM. Stress memory induced rearrangements of HSP transcription, photosystem II photochemistry and metabolism of tall fescue (Festuca arundinacea Schreb.) in response to high-temperature stress. FRONTIERS IN PLANT SCIENCE 2015; 6:403. [PMID: 26136755 PMCID: PMC4468413 DOI: 10.3389/fpls.2015.00403] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/03/2015] [Accepted: 05/19/2015] [Indexed: 05/20/2023]
Abstract
When plants are pre-exposed to stress, they can produce some stable signals and physiological reactions that may be carried forward as "stress memory". However, there is insufficient information about plants' stress memory responses mechanisms. Here, two tall fescue genotypes, heat-tolerant PI 574522 and heat-sensitive PI 512315, were subjected to recurring high-temperature pre-acclimation treatment. Two heat shock protein (HSP) genes, LMW-HSP and HMW-HSP, exhibited transcriptional memory for their higher transcript abundance during one or more subsequent stresses (S2, S3, S4) relative to the first stress (S1), and basal transcript levels during the recovery states (R1, R2, and R3). Activated transcriptional memory from two trainable genes could persist up to 4 days, and induce higher thermotolerance in tall fescue. This was confirmed by greater turf quality and lower electrolyte leakage. Pre-acclimation treatment inhibited the decline at steps of O-J-I-P and energy transport fluxes in active Photosystem II reaction center (PSII RC) for both tall fescue genotypes. The heat stress memory was associated with major shifts in leaf metabolite profiles. Furthermore, there was an exclusive increase in leaf organic acids (citric acid, malic acid, tris phosphoric acid, threonic acid), sugars (sucrose, glucose, idose, allose, talose, glucoheptose, tagatose, psicose), amino acids (serine, proline, pyroglutamic acid, glycine, alanine), and one fatty acid (butanoic acid) in pre-acclimated plants. These observations involved in transcriptional memory, PSII RC energy transport and metabolite profiles could provide new insights into the plant high-temperature response process.
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Affiliation(s)
| | | | | | - Jin-Min Fu
- *Correspondence: Jin-Min Fu, Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan 430074, Hubei, China
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Conrad LJ, Khanday I, Johnson C, Guiderdoni E, An G, Vijayraghavan U, Sundaresan V. The polycomb group gene EMF2B is essential for maintenance of floral meristem determinacy in rice. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2014; 80:883-94. [PMID: 25279942 DOI: 10.1111/tpj.12688] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/26/2013] [Revised: 09/12/2014] [Accepted: 09/19/2014] [Indexed: 05/23/2023]
Abstract
Polycomb Repressive Complex 2 (PRC2) represses the transcriptional activity of target genes through trimethylation of lysine 27 of histone H3. The functions of plant PRC2 have been chiefly described in Arabidopsis, but specific functions in other plant species, especially cereals, are still largely unknown. Here we characterize mutants in the rice EMF2B gene, an ortholog of the Arabidopsis EMBRYONIC FLOWER2 (EMF2) gene. Loss of EMF2B in rice results in complete sterility, and mutant flowers have severe floral organ defects and indeterminacy that resemble loss-of-function mutants in E-function floral organ specification genes. Transcriptome analysis identified the E-function genes OsMADS1, OsMADS6 and OsMADS34 as differentially expressed in the emf2b mutant compared with wild type. OsMADS1 and OsMADS6, known to be required for meristem determinacy in rice, have reduced expression in the emf2b mutant, whereas OsMADS34 which interacts genetically with OsMADS1 was ectopically expressed. Chromatin immunoprecipitation for H3K27me3 followed by quantitative (q)RT-PCR showed that all three genes are presumptive targets of PRC2 in the meristem. Therefore, in rice, and possibly other cereals, PRC2 appears to play a major role in floral meristem determinacy through modulation of the expression of E-function genes.
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Affiliation(s)
- Liza J Conrad
- Plant Biology Department, University of California Davis, 1 Shields Ave, Davis, CA 95616, USA
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Kingston RE, Tamkun JW. Transcriptional regulation by trithorax-group proteins. Cold Spring Harb Perspect Biol 2014; 6:a019349. [PMID: 25274705 DOI: 10.1101/cshperspect.a019349] [Citation(s) in RCA: 72] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
The trithorax group of genes (trxG) was identified in mutational screens that examined developmental phenotypes and suppression of Polycomb mutant phenotypes. The protein products of these genes are primarily involved in gene activation, although some can also have repressive effects. There is no central function for these proteins. Some move nucleosomes about on the genome in an ATP-dependent manner, some covalently modify histones such as methylating lysine 4 of histone H3, and some directly interact with the transcription machinery or are a part of that machinery. It is interesting to consider why these specific members of large families of functionally related proteins have strong developmental phenotypes.
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Affiliation(s)
- Robert E Kingston
- Department of Molecular Biology, Massachusetts General Hospital, Boston, Massachusetts 02114
| | - John W Tamkun
- Department of Molecular, Cell and Developmental Biology, University of California, Santa Cruz, Santa Cruz, California 95064
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45
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Chen Y, Lian G, Zhang Q, Zeng L, Qian C, Chen S, Huang K. Overexpression of Bmi-1 induces the malignant transformation of gastric epithelial cells in vitro. Oncol Res 2014; 21:33-41. [PMID: 24330850 DOI: 10.3727/096504013x13786659070316] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Abstract
Oncogene Bmi-1 (B-cell-specific Moloney murine leukemia virus integration site 1) has attracted much attention for its involvement in the initiation of a variety of tumors. Our previous study showed that Bmi-1 was highly expressed in gastric cancer and correlated with patient prognosis. However, whether aberrant Bmi-1 expression was critical for the transformation of gastric epithelial cells remains unknown. In this study, we stably expressed Bmi-1 in a human gastric epithelial immortalized cell line, GES-1. The overexpression of Bmi-1 promoted cell growth and proliferation, inhibited apoptosis, enhanced clone formation capability, possessed the characteristics of anchorage-independent growth, and increased migration and invasion abilities. Therefore, our findings demonstrated that ectopic expression of Bmi-1 played an important role in the malignant transformation of gastric epithelial cells.
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Affiliation(s)
- Yinting Chen
- Department of Gastroenterology, Sun Yat-Sen Memorial Hospital of Sun Yat-Sen University, Guangzhou, China
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Yang YA, Kim J, Yu J. Influence of oncogenic transcription factors on chromatin conformation and implications in prostate cancer. APPLICATION OF CLINICAL GENETICS 2014; 7:81-91. [PMID: 24876790 PMCID: PMC4036145 DOI: 10.2147/tacg.s35598] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
In recent years, facilitated by rapid technological advances, we are becoming more adept at probing the molecular processes, which take place in the nucleus, that are crucial for the hierarchical regulation and organization of chromatin architecture. With an unprecedented level of resolution, a detailed atlas of chromosomal structures (histone displacement, variants, modifications, chromosome territories, and DNA looping) and mechanisms underlying their establishment, provides invaluable insight into physiological as well as pathological phenomena. In this review, we will focus on prostate cancer, a prevalent malignancy in men worldwide, and for which a curative treatment strategy is yet to be attained. We aim to catalog the most frequently observed oncogenic alterations associated with chromatin conformation, while emphasizing the TMPRSS2-ERG fusion, which is found in more than one-half of prostate cancer patients and its functions in compromising the chromatin landscape in prostate cancer.
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Affiliation(s)
- Yeqing Angela Yang
- Division of Hematology/Oncology, Department of Medicine, Northwestern University, Feinberg School of Medicine, Chicago, IL, USA
| | - Jung Kim
- Division of Hematology/Oncology, Department of Medicine, Northwestern University, Feinberg School of Medicine, Chicago, IL, USA
| | - Jindan Yu
- Division of Hematology/Oncology, Department of Medicine, Northwestern University, Feinberg School of Medicine, Chicago, IL, USA ; Robert H Lurie Comprehensive Cancer Center, Northwestern University, Feinberg School of Medicine, Chicago, IL, USA
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47
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Hajjari M, Behmanesh M, Jahani MM. In silico finding of Putative Cis-Acting Elements for the Tethering of Polycomb Repressive Complex2 in Human Genome. Bioinformation 2014; 10:187-90. [PMID: 24966518 PMCID: PMC4070047 DOI: 10.6026/97320630010187] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2014] [Accepted: 03/21/2014] [Indexed: 11/23/2022] Open
Abstract
Polycomb Repressive Complex2 maintains a predetermined state of transcription which constitutes a cellular memory stable over many cell divisions. Since this complex acts through the regulation of chromatin structure, it is important to understand how it is recruited to chromatin. The specific target sequences of this complex such as PRE (polycomb repressive element) have not been completely recognized in human genome. In this study, we have compared the target sequences of this complex with non-target genes in tumor cell lines. Through in silico and statistical analyses, we have identified some motifs which are over-represented in target genes against non-target genes. Analyzing these motifs shows some transcription factors which are potential recruiters of Polycomb repressive complex2.
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Affiliation(s)
- Mohammadreza Hajjari
- Department of Genetics, Shahid Chamran University of Ahvaz, Ahvaz, Iran
- Department of Genetics, School of Biological Sciences, Tarbiat Modares University, Tehran, Iran
| | - Mehrdad Behmanesh
- Department of Genetics, School of Biological Sciences, Tarbiat Modares University, Tehran, Iran
| | - Mohammad Mehdi Jahani
- Department of Genetics, Shahid Chamran University of Ahvaz, Ahvaz, Iran
- Department of Genetics, School of Biological Sciences, Tarbiat Modares University, Tehran, Iran
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Basu A, Dasari V, Mishra RK, Khosla S. The CpG island encompassing the promoter and first exon of human DNMT3L gene is a PcG/TrX response element (PRE). PLoS One 2014; 9:e93561. [PMID: 24743422 PMCID: PMC3990577 DOI: 10.1371/journal.pone.0093561] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2013] [Accepted: 03/07/2014] [Indexed: 01/27/2023] Open
Abstract
DNMT3L, a member of DNA methyltransferases family, is present only in mammals. As it provides specificity to the action of de novo methyltransferases, DNMT3A and DNMT3B and interacts with histone H3, DNMT3L has been invoked as the molecule that can read the histone code and translate it into DNA methylation. It plays an important role in the initiation of genomic imprints during gametogenesis and in nuclear reprogramming. With important functions attributed to it, it is imperative that the DNMT3L expression is tightly controlled. Previously, we had identified a CpG island within the human DNMT3L promoter and first exon that showed loss of DNA methylation in cancer samples. Here we show that this Differentially Methylated CpG island within DNMT3L (DNMT3L DMC) acts to repress transcription, is a Polycomb/Trithorax Response Element (PRE) and interacts with both PRC1 and PRC2 Polycomb repressive complexes. In addition, it adopts inactive chromatin conformation and is associated with other inactive chromatin-specific proteins like SUV39H1 and HP1. The presence of DNMT3L DMC also influences the adjacent promoter to adopt repressive histone post-translational modifications. Due to its association with multiple layers of repressive epigenetic modifications, we believe that PRE within the DNMT3L DMC is responsible for the tight regulation of DNMT3L expression and the aberrant epigenetic modifications of this region leading to DNMT3L overexpression could be the reason of nuclear programming during carcinogenesis.
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Affiliation(s)
- Amitava Basu
- Centre for DNA Fingerprinting and Diagnostics (CDFD), Nampally, Hyderabad, India
| | - Vasanthi Dasari
- Centre for Cellular and Molecular Biology (CCMB), Council of Scientific and Industrial Research (CSIR), Hyderabad, India
| | - Rakesh K. Mishra
- Centre for Cellular and Molecular Biology (CCMB), Council of Scientific and Industrial Research (CSIR), Hyderabad, India
| | - Sanjeev Khosla
- Centre for DNA Fingerprinting and Diagnostics (CDFD), Nampally, Hyderabad, India
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EZH2 expands breast stem cells through activation of NOTCH1 signaling. Proc Natl Acad Sci U S A 2014; 111:3098-103. [PMID: 24516139 DOI: 10.1073/pnas.1308953111] [Citation(s) in RCA: 144] [Impact Index Per Article: 14.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Breast cancer is the second-leading cause of cancer-related deaths in women, but the details of how it begins remain elusive. Increasing evidence supports the association of aggressive triple-negative (TN) breast cancer with heightened expression of the Polycomb group protein Enhancer of Zeste Homolog 2 (EZH2) and increased tumor-initiating cells (TICs). However, mechanistic links between EZH2 and TICs are unclear, and direct demonstration of a tumorigenic function of EZH2 in vivo is lacking. Here, we identify an unrecognized EZH2/NOTCH1 axis that controls breast TICs in TN breast carcinomas. EZH2 overexpression increases NOTCH1 expression and signaling, and inhibition of NOTCH1 activity prevents EZH2-mediated stem cell expansion in nontumorigenic breast cells. We uncover a unique role of EZH2 in activating, rather than repressing, NOTCH1 signaling through binding to the NOTCH1 promoter in TN breast cancer cells. EZH2 binding is independent of its catalytic histone H3 lysine 27 methyltransferase activity and of the Polycomb Repressive Complex 2 but corresponds instead to transcriptional activation marks. In vivo, EZH2 knockdown decreases the onset and volume of xenografts derived from TN breast TICs. Conversely, transgenic EZH2 overexpression accelerates mammary tumor initiation and increases NOTCH1 activation in mouse mammary tumor virus-neu mice. Consonant with these findings, in clinical samples, high levels of EZH2 are significantly associated with activated NOTCH1 protein and increased TICs in TN invasive carcinomas. These data reveal a functional and mechanistic link between EZH2 levels, NOTCH1 signaling activation, and TICs, and provide previously unidentified evidence that EZH2 enhances breast cancer initiation.
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50
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Pulianmackal AJ, Kareem AVK, Durgaprasad K, Trivedi ZB, Prasad K. Competence and regulatory interactions during regeneration in plants. FRONTIERS IN PLANT SCIENCE 2014; 5:142. [PMID: 24782880 PMCID: PMC3990048 DOI: 10.3389/fpls.2014.00142] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/05/2014] [Accepted: 03/25/2014] [Indexed: 05/08/2023]
Abstract
The ability to regenerate is widely exploited by multitudes of organisms ranging from unicellular bacteria to multicellular plants for their propagation and repair. But the levels of competence for regeneration vary from species to species. While variety of living cells of a plant display regeneration ability, only a few set of cells maintain their stemness in mammals. This highly pliable nature of plant cells in-terms of regeneration can be attributed to their high developmental plasticity. De novo organ initiation can be relatively easily achieved in plants by proper hormonal regulations. Elevated levels of plant hormone auxin induces the formation of proliferating mass of pluripotent cells called callus, which predominantly express lateral root meristem markers and hence is having an identity similar to lateral root primordia. Organ formation can be induced from the callus by modulating the ratio of hormones. An alternative for de novo organogenesis is by the forced expression of plant specific transcription factors. The mechanisms by which plant cells attain competence for regeneration on hormonal treatment or forced expression remain largely elusive. Recent studies have provided some insight into how the epigenetic modifications in plants affect this competence. In this review we discuss the present understanding of regenerative biology in plants and scrutinize the future prospectives of this topic. While discussing about the regeneration in the sporophyte of angiosperms which is well studied, here we outline the regenerative biology of the gametophytic phase and discuss about various strategies of regeneration that have evolved in the domain of life so that a common consensus on the entire process of regeneration can be made.
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Affiliation(s)
| | | | | | | | - Kalika Prasad
- *Correspondence: Kalika Prasad, School of Biology Indian Institute of Science Education and Research, Thiruvananthapuram, India e-mail:
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