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Liao B, Liang P, Tong L, Lu L, Lu Y, Zheng R, Zheng X, Chen J, Hao Z. The Role of Liriodendron Dof Gene Family in Abiotic Stress Response. PLANTS (BASEL, SWITZERLAND) 2024; 13:2009. [PMID: 39065535 PMCID: PMC11281171 DOI: 10.3390/plants13142009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/19/2024] [Revised: 07/18/2024] [Accepted: 07/19/2024] [Indexed: 07/28/2024]
Abstract
The DOF (DNA-binding with one finger) transcription factors are exclusive to plants and play crucial roles in plant growth, development, and environmental adaptation. Although extensive research has been conducted on the Dof gene family in Arabidopsis, maize, and Solanum, investigations concerning the role of this gene family in Liriodendron remain unreported, leaving its biological function largely unknown. In this study, we performed a comprehensive genome-wide identification of the Dof gene family based on the Liriodendron genome, resulting in the discovery of a total of 17 LcDof gene members. Based on the results of phylogenetic analysis, the 17 LcDof proteins were classified into eight subfamilies. The motif analysis revealed the diverse nature of motifs within the D1 subfamily, which includes a distinct type of Dof transcription factor known as CDF (Cycling Dof Factor). We further characterized the chromosomal distribution, gene structure, conserved protein motifs, and cis-elements in the promoter regions. Additionally, utilizing transcriptome data from Liriodendron hybrids and conducting RT-qPCR experiments, we investigated the expression patterns of LhDofs under various abiotic stresses such as drought, cold, and heat stress. Notably, we found that several LhDofs, particularly LhDof4 and LhDof6, were significantly upregulated in response to abiotic stress. Furthermore, we cloned LhDof4 and LhDof6 genes and found that its encoding protein was mainly located in the nucleus by transient transformation in Liriodendron hybrids protoplast. Subsequently, we used LhDof6-overexpressing Liriodendron hybrid seedlings. We found that overexpression of LhDof6 enhanced the cold tolerance of the plants, increasing their survival rate at -20 °C. This result was further validated by changes in physiological indicators.
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Affiliation(s)
- Bojun Liao
- State Key Laboratory of Tree Genetics and Breeding, Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing 210037, China; (B.L.); (P.L.); (L.T.); (L.L.); (Y.L.)
- Key Laboratory of Forest Genetics & Biotechnology of Ministry of Education, Nanjing Forestry University, Nanjing 210037, China
| | - Pengxiang Liang
- State Key Laboratory of Tree Genetics and Breeding, Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing 210037, China; (B.L.); (P.L.); (L.T.); (L.L.); (Y.L.)
- Key Laboratory of Forest Genetics & Biotechnology of Ministry of Education, Nanjing Forestry University, Nanjing 210037, China
| | - Lu Tong
- State Key Laboratory of Tree Genetics and Breeding, Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing 210037, China; (B.L.); (P.L.); (L.T.); (L.L.); (Y.L.)
- Key Laboratory of Forest Genetics & Biotechnology of Ministry of Education, Nanjing Forestry University, Nanjing 210037, China
| | - Lu Lu
- State Key Laboratory of Tree Genetics and Breeding, Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing 210037, China; (B.L.); (P.L.); (L.T.); (L.L.); (Y.L.)
- Key Laboratory of Forest Genetics & Biotechnology of Ministry of Education, Nanjing Forestry University, Nanjing 210037, China
| | - Ye Lu
- State Key Laboratory of Tree Genetics and Breeding, Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing 210037, China; (B.L.); (P.L.); (L.T.); (L.L.); (Y.L.)
- Key Laboratory of Forest Genetics & Biotechnology of Ministry of Education, Nanjing Forestry University, Nanjing 210037, China
| | - Renhua Zheng
- Fujian Academy of Forestry, Fuzhou 350012, China; (R.Z.); (X.Z.)
- National Germplasm Bank of Chinese Fir at Fujian Yangkou Forest Farm, Shunchang, Nanping 353211, China
| | - Xueyan Zheng
- Fujian Academy of Forestry, Fuzhou 350012, China; (R.Z.); (X.Z.)
- National Germplasm Bank of Chinese Fir at Fujian Yangkou Forest Farm, Shunchang, Nanping 353211, China
| | - Jinhui Chen
- State Key Laboratory of Tree Genetics and Breeding, Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing 210037, China; (B.L.); (P.L.); (L.T.); (L.L.); (Y.L.)
- Key Laboratory of Forest Genetics & Biotechnology of Ministry of Education, Nanjing Forestry University, Nanjing 210037, China
| | - Zhaodong Hao
- State Key Laboratory of Tree Genetics and Breeding, Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing 210037, China; (B.L.); (P.L.); (L.T.); (L.L.); (Y.L.)
- Key Laboratory of Forest Genetics & Biotechnology of Ministry of Education, Nanjing Forestry University, Nanjing 210037, China
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Sokolov V, Kyrchanova O, Klimenko N, Fedotova A, Ibragimov A, Maksimenko O, Georgiev P. New Drosophila promoter-associated architectural protein Mzfp1 interacts with CP190 and is required for housekeeping gene expression and insulator activity. Nucleic Acids Res 2024; 52:6886-6905. [PMID: 38769058 PMCID: PMC11229372 DOI: 10.1093/nar/gkae393] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2023] [Revised: 04/20/2024] [Accepted: 05/10/2024] [Indexed: 05/22/2024] Open
Abstract
In Drosophila, a group of zinc finger architectural proteins recruits the CP190 protein to the chromatin, an interaction that is essential for the functional activity of promoters and insulators. In this study, we describe a new architectural C2H2 protein called Madf and Zinc-Finger Protein 1 (Mzfp1) that interacts with CP190. Mzfp1 has an unusual structure that includes six C2H2 domains organized in a C-terminal cluster and two tandem MADF domains. Mzfp1 predominantly binds to housekeeping gene promoters located in both euchromatin and heterochromatin genome regions. In vivo mutagenesis studies showed that Mzfp1 is an essential protein, and both MADF domains and the CP190 interaction region are required for its functional activity. The C2H2 cluster is sufficient for the specific binding of Mzfp1 to regulatory elements, while the second MADF domain is required for Mzfp1 recruitment to heterochromatin. Mzfp1 binds to the proximal part of the Fub boundary that separates regulatory domains of the Ubx and abd-A genes in the Bithorax complex. Mzfp1 participates in Fub functions in cooperation with the architectural proteins Pita and Su(Hw). Thus, Mzfp1 is a new architectural C2H2 protein involved in the organization of active promoters and insulators in Drosophila.
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Affiliation(s)
- Vladimir Sokolov
- Department of the Control of Genetic Processes, Institute of Gene Biology, Russian Academy of Sciences, Moscow 119334, Russia
| | - Olga Kyrchanova
- Department of the Control of Genetic Processes, Institute of Gene Biology, Russian Academy of Sciences, Moscow 119334, Russia
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Institute of Gene Biology, Russian Academy of Sciences, Moscow 119334, Russia
| | - Natalia Klimenko
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Institute of Gene Biology, Russian Academy of Sciences, Moscow 119334, Russia
| | - Anna Fedotova
- Department of the Control of Genetic Processes, Institute of Gene Biology, Russian Academy of Sciences, Moscow 119334, Russia
| | - Airat Ibragimov
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Institute of Gene Biology, Russian Academy of Sciences, Moscow 119334, Russia
| | - Oksana Maksimenko
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Institute of Gene Biology, Russian Academy of Sciences, Moscow 119334, Russia
| | - Pavel Georgiev
- Department of the Control of Genetic Processes, Institute of Gene Biology, Russian Academy of Sciences, Moscow 119334, Russia
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3
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Chavan A, Isenhart R, Nguyen SC, Kotb NM, Harke J, Sintsova A, Ulukaya G, Uliana F, Ashiono C, Kutay U, Pegoraro G, Rangan P, Joyce EF, Jagannathan M. A nuclear architecture screen in Drosophila identifies Stonewall as a link between chromatin position at the nuclear periphery and germline stem cell fate. Genes Dev 2024; 38:415-435. [PMID: 38866555 PMCID: PMC11216176 DOI: 10.1101/gad.351424.123] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2023] [Accepted: 05/21/2024] [Indexed: 06/14/2024]
Abstract
The association of genomic loci to the nuclear periphery is proposed to facilitate cell type-specific gene repression and influence cell fate decisions. However, the interplay between gene position and expression remains incompletely understood, in part because the proteins that position genomic loci at the nuclear periphery remain unidentified. Here, we used an Oligopaint-based HiDRO screen targeting ∼1000 genes to discover novel regulators of nuclear architecture in Drosophila cells. We identified the heterochromatin-associated protein Stonewall (Stwl) as a factor promoting perinuclear chromatin positioning. In female germline stem cells (GSCs), Stwl binds and positions chromatin loci, including GSC differentiation genes, at the nuclear periphery. Strikingly, Stwl-dependent perinuclear positioning is associated with transcriptional repression, highlighting a likely mechanism for Stwl's known role in GSC maintenance and ovary homeostasis. Thus, our study identifies perinuclear anchors in Drosophila and demonstrates the importance of gene repression at the nuclear periphery for cell fate.
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Affiliation(s)
- Ankita Chavan
- Institute of Biochemistry, Department of Biology, Eidgenössische Technische Hochschule (ETH) Zürich, Zürich 8093, Switzerland
- Bringing Materials to Life Consortium, ETH Zürich, Zürich 8093, Switzerland
- Life Science Zürich Graduate School, Zürich 8057, Switzerland
| | - Randi Isenhart
- Penn Epigenetics Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
| | - Son C Nguyen
- Penn Epigenetics Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
| | - Noor M Kotb
- Department of Cell, Developmental, and Regenerative Biology, Black Family Stem Cell Institute, Icahn School of Medicine at Mount Sinai, New York, New York 10029, USA
| | - Jailynn Harke
- Penn Epigenetics Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
| | - Anna Sintsova
- Institute of Microbiology, Department of Biology, ETH Zürich, Zürich 8093, Switzerland
| | - Gulay Ulukaya
- Bioinformatics for Next-Generation Sequencing (BiNGS) Core, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, New York 10029, USA
| | - Federico Uliana
- Institute of Biochemistry, Department of Biology, Eidgenössische Technische Hochschule (ETH) Zürich, Zürich 8093, Switzerland
| | - Caroline Ashiono
- Institute of Biochemistry, Department of Biology, Eidgenössische Technische Hochschule (ETH) Zürich, Zürich 8093, Switzerland
| | - Ulrike Kutay
- Institute of Biochemistry, Department of Biology, Eidgenössische Technische Hochschule (ETH) Zürich, Zürich 8093, Switzerland
| | - Gianluca Pegoraro
- High-Throughput Imaging Facility (HiTIF), National Cancer Institute, National Institutes of Health, Bethesda, Maryland 20892, USA
| | - Prashanth Rangan
- Department of Cell, Developmental, and Regenerative Biology, Black Family Stem Cell Institute, Icahn School of Medicine at Mount Sinai, New York, New York 10029, USA
| | - Eric F Joyce
- Penn Epigenetics Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA;
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
| | - Madhav Jagannathan
- Institute of Biochemistry, Department of Biology, Eidgenössische Technische Hochschule (ETH) Zürich, Zürich 8093, Switzerland;
- Bringing Materials to Life Consortium, ETH Zürich, Zürich 8093, Switzerland
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4
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Zhang ZB, Xiong T, Wang XJ, Chen YR, Wang JL, Guo CL, Ye ZY. Lineage-specific gene duplication and expansion of DUF1216 gene family in Brassicaceae. PLoS One 2024; 19:e0302292. [PMID: 38626181 PMCID: PMC11020792 DOI: 10.1371/journal.pone.0302292] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2024] [Accepted: 04/01/2024] [Indexed: 04/18/2024] Open
Abstract
Proteins containing domain of unknown function (DUF) are prevalent in eukaryotic genome. The DUF1216 proteins possess a conserved DUF1216 domain resembling to the mediator protein of Arabidopsis RNA polymerase II transcriptional subunit-like protein. The DUF1216 family are specifically existed in Brassicaceae, however, no comprehensive evolutionary analysis of DUF1216 genes have been performed. We performed a first comprehensive genome-wide analysis of DUF1216 proteins in Brassicaceae. Totally 284 DUF1216 genes were identified in 27 Brassicaceae species and classified into four subfamilies on the basis of phylogenetic analysis. The analysis of gene structure and conserved motifs revealed that DUF1216 genes within the same subfamily exhibited similar intron/exon patterns and motif composition. The majority members of DUF1216 genes contain a signal peptide in the N-terminal, and the ninth position of the signal peptide in most DUF1216 is cysteine. Synteny analysis revealed that segmental duplication is a major mechanism for expanding of DUF1216 genes in Brassica oleracea, Brassica juncea, Brassica napus, Lepidium meyneii, and Brassica carinata, while in Arabidopsis thaliana and Capsella rubella, tandem duplication plays a major role in the expansion of the DUF1216 gene family. The analysis of Ka/Ks (non-synonymous substitution rate/synonymous substitution rate) ratios for DUF1216 paralogous indicated that most of gene pairs underwent purifying selection. DUF1216 genes displayed a specifically high expression in reproductive tissues in most Brassicaceae species, while its expression in Brassica juncea was specifically high in root. Our studies offered new insights into the phylogenetic relationships, gene structures and expressional patterns of DUF1216 members in Brassicaceae, which provides a foundation for future functional analysis.
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Affiliation(s)
- Zai-Bao Zhang
- School of Life and Health Science, Huzhou College, Huzhou, Zhejiang, China
| | - Tao Xiong
- College of Life Science, Xinyang Normal University, Xinyang, Henan, China
| | - Xiao-Jia Wang
- College of International Education, Xinyang Normal University, Xinyang, Henan, China
| | - Yu-Rui Chen
- College of International Education, Xinyang Normal University, Xinyang, Henan, China
| | - Jing-Lei Wang
- College of International Education, Xinyang Normal University, Xinyang, Henan, China
| | - Cong-Li Guo
- College of International Education, Xinyang Normal University, Xinyang, Henan, China
| | - Zi-Yi Ye
- School of Life and Health Science, Huzhou College, Huzhou, Zhejiang, China
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5
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Palumbo RJ, Yang Y, Feigon J, Hanes SD. Catalytic activity of the Bin3/MePCE methyltransferase domain is dispensable for 7SK snRNP function in Drosophila melanogaster. Genetics 2024; 226:iyad203. [PMID: 37982586 PMCID: PMC10763541 DOI: 10.1093/genetics/iyad203] [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: 05/31/2023] [Revised: 10/27/2023] [Accepted: 11/13/2023] [Indexed: 11/21/2023] Open
Abstract
Methylphosphate Capping Enzyme (MePCE) monomethylates the gamma phosphate at the 5' end of the 7SK noncoding RNA, a modification thought to protect 7SK from degradation. 7SK serves as a scaffold for assembly of a snRNP complex that inhibits transcription by sequestering the positive elongation factor P-TEFb. While much is known about the biochemical activity of MePCE in vitro, little is known about its functions in vivo, or what roles-if any-there are for regions outside the conserved methyltransferase domain. Here, we investigated the role of Bin3, the Drosophila ortholog of MePCE, and its conserved functional domains in Drosophila development. We found that bin3 mutant females had strongly reduced rates of egg-laying, which was rescued by genetic reduction of P-TEFb activity, suggesting that Bin3 promotes fecundity by repressing P-TEFb. bin3 mutants also exhibited neuromuscular defects, analogous to a patient with MePCE haploinsufficiency. These defects were also rescued by genetic reduction of P-TEFb activity, suggesting that Bin3 and MePCE have conserved roles in promoting neuromuscular function by repressing P-TEFb. Unexpectedly, we found that a Bin3 catalytic mutant (Bin3Y795A) could still bind and stabilize 7SK and rescue all bin3 mutant phenotypes, indicating that Bin3 catalytic activity is dispensable for 7SK stability and snRNP function in vivo. Finally, we identified a metazoan-specific motif (MSM) outside of the methyltransferase domain and generated mutant flies lacking this motif (Bin3ΔMSM). Bin3ΔMSM mutant flies exhibited some-but not all-bin3 mutant phenotypes, suggesting that the MSM is required for a 7SK-independent, tissue-specific function of Bin3.
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Affiliation(s)
- Ryan J Palumbo
- Department of Biochemistry & Molecular Biology, SUNY Upstate Medical University, Syracuse, NY 13210, USA
| | - Yuan Yang
- Department of Chemistry and Biochemistry, University of California, Los Angeles, CA 90095, USA
| | - Juli Feigon
- Department of Chemistry and Biochemistry, University of California, Los Angeles, CA 90095, USA
| | - Steven D Hanes
- Department of Biochemistry & Molecular Biology, SUNY Upstate Medical University, Syracuse, NY 13210, USA
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6
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Chavan A, Isenhart R, Nguyen SC, Kotb N, Harke J, Sintsova A, Ulukaya G, Uliana F, Ashiono C, Kutay U, Pegoraro G, Rangan P, Joyce EF, Jagannathan M. A nuclear architecture screen in Drosophila identifies Stonewall as a link between chromatin position at the nuclear periphery and germline stem cell fate. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.11.17.567611. [PMID: 38014085 PMCID: PMC10680830 DOI: 10.1101/2023.11.17.567611] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/29/2023]
Abstract
The association of genomic loci to the nuclear periphery is proposed to facilitate cell-type specific gene repression and influence cell fate decisions. However, the interplay between gene position and expression remains incompletely understood, in part because the proteins that position genomic loci at the nuclear periphery remain unidentified. Here, we used an Oligopaint-based HiDRO screen targeting ~1000 genes to discover novel regulators of nuclear architecture in Drosophila cells. We identified the heterochromatin-associated protein, Stonewall (Stwl), as a factor promoting perinuclear chromatin positioning. In female germline stem cells (GSCs), Stwl binds and positions chromatin loci, including GSC differentiation genes, at the nuclear periphery. Strikingly, Stwl-dependent perinuclear positioning is associated with transcriptional repression, highlighting a likely mechanism for Stwl's known role in GSC maintenance and ovary homeostasis. Thus, our study identifies perinuclear anchors in Drosophila and demonstrates the importance of gene repression at the nuclear periphery for cell fate.
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Affiliation(s)
- Ankita Chavan
- Institute of Biochemistry, Department of Biology, ETH Zürich, Switzerland
- Bringing Materials to Life Consortium, ETH Zürich, Switzerland
- Life Science Zurich Graduate School, Zürich, Switzerland
- These authors contributed equally
| | - Randi Isenhart
- Penn Epigenetics Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
- These authors contributed equally
| | - Son C. Nguyen
- Penn Epigenetics Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Noor Kotb
- Department of Cell, Developmental and Regenerative Biology, Black Family Stem Cell Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Jailynn Harke
- Penn Epigenetics Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Anna Sintsova
- Institute of Microbiology, Department of Biology, ETH Zürich, Switzerland
| | - Gulay Ulukaya
- Bioinformatics for Next Generation Sequencing (BiNGS) core, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Federico Uliana
- Institute of Biochemistry, Department of Biology, ETH Zürich, Switzerland
| | - Caroline Ashiono
- Institute of Biochemistry, Department of Biology, ETH Zürich, Switzerland
| | - Ulrike Kutay
- Institute of Biochemistry, Department of Biology, ETH Zürich, Switzerland
| | - Gianluca Pegoraro
- High Throughput Imaging Facility (HiTIF), National Cancer Institute, NIH, Bethesda, MD 20892 USA
| | - Prashanth Rangan
- Department of Cell, Developmental and Regenerative Biology, Black Family Stem Cell Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Eric F. Joyce
- Penn Epigenetics Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Madhav Jagannathan
- Institute of Biochemistry, Department of Biology, ETH Zürich, Switzerland
- Bringing Materials to Life Consortium, ETH Zürich, Switzerland
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Melnikova L, Molodina V, Babosha V, Kostyuchenko M, Georgiev P, Golovnin A. The MADF-BESS Protein CP60 Is Recruited to Insulators via CP190 and Has Redundant Functions in Drosophila. Int J Mol Sci 2023; 24:15029. [PMID: 37834476 PMCID: PMC10573801 DOI: 10.3390/ijms241915029] [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: 08/25/2023] [Revised: 10/03/2023] [Accepted: 10/05/2023] [Indexed: 10/15/2023] Open
Abstract
Drosophila CP190 and CP60 are transcription factors that are associated with centrosomes during mitosis. CP190 is an essential transcription factor and preferentially binds to housekeeping gene promoters and insulators through interactions with architectural proteins, including Su(Hw) and dCTCF. CP60 belongs to a family of transcription factors that contain the N-terminal MADF domain and the C-terminal BESS domain, which is characterized by the ability to homodimerize. In this study, we show that the conserved CP60 region adjacent to MADF is responsible for interacting with CP190. In contrast to the well-characterized MADF-BESS transcriptional activator Adf-1, CP60 is recruited to most chromatin sites through its interaction with CP190, and the MADF domain is likely involved in protein-protein interactions but not in DNA binding. The deletion of the Map60 gene showed that CP60 is not an essential protein, despite the strong and ubiquitous expression of CP60 at all stages of Drosophila development. Although CP60 is a stable component of the Su(Hw) insulator complex, the inactivation of CP60 does not affect the enhancer-blocking activity of the Su(Hw)-dependent gypsy insulator. Overall, our results indicate that CP60 has an important but redundant function in transcriptional regulation as a partner of the CP190 protein.
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Affiliation(s)
- Larisa Melnikova
- Department of Drosophila Molecular Genetics, Institute of Gene Biology, Russian Academy of Sciences, 34/5 Vavilov Street, Moscow 119334, Russia; (L.M.)
| | - Varvara Molodina
- Department of Drosophila Molecular Genetics, Institute of Gene Biology, Russian Academy of Sciences, 34/5 Vavilov Street, Moscow 119334, Russia; (L.M.)
| | - Valentin Babosha
- Department of the Control of Genetic Processes, Institute of Gene Biology, Russian Academy of Sciences, 34/5 Vavilov Street, Moscow 119334, Russia (P.G.)
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Institute of Gene Biology, Russian Academy of Sciences, 34/5 Vavilov Street, Moscow 119334, Russia
| | - Margarita Kostyuchenko
- Department of Drosophila Molecular Genetics, Institute of Gene Biology, Russian Academy of Sciences, 34/5 Vavilov Street, Moscow 119334, Russia; (L.M.)
| | - Pavel Georgiev
- Department of the Control of Genetic Processes, Institute of Gene Biology, Russian Academy of Sciences, 34/5 Vavilov Street, Moscow 119334, Russia (P.G.)
| | - Anton Golovnin
- Department of Drosophila Molecular Genetics, Institute of Gene Biology, Russian Academy of Sciences, 34/5 Vavilov Street, Moscow 119334, Russia; (L.M.)
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8
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Broitman-Maduro G, Sun S, Kikuchi T, Maduro MF. The GATA factor ELT-3 specifies endoderm in Caenorhabditis angaria in an ancestral gene network. Development 2022; 149:277064. [PMID: 36196618 PMCID: PMC9720673 DOI: 10.1242/dev.200984] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2022] [Accepted: 09/20/2022] [Indexed: 11/07/2022]
Abstract
ABSTRACT
Endoderm specification in Caenorhabditis elegans occurs through a network in which maternally provided SKN-1/Nrf, with additional input from POP-1/TCF, activates the GATA factor cascade MED-1,2→END-1,3→ELT-2,7. Orthologues of the MED, END and ELT-7 factors are found only among nematodes closely related to C. elegans, raising the question of how gut is specified in their absence in more distant species in the genus. We find that the C. angaria, C. portoensis and C. monodelphis orthologues of the GATA factor gene elt-3 are expressed in the early E lineage, just before their elt-2 orthologues. In C. angaria, Can-pop-1(RNAi), Can-elt-3(RNAi) and a Can-elt-3 null mutation result in a penetrant ‘gutless’ phenotype. Can-pop-1 is necessary for Can-elt-3 activation, showing that it acts upstream. Forced early E lineage expression of Can-elt-3 in C. elegans can direct the expression of a Can-elt-2 transgene and rescue an elt-7 end-1 end-3; elt-2 quadruple mutant strain to viability. Our results demonstrate an ancestral mechanism for gut specification and differentiation in Caenorhabditis involving a simpler POP-1→ELT-3→ELT-2 gene network.
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Affiliation(s)
- Gina Broitman-Maduro
- University of California 1 Department of Molecular, Cell and Systems Biology , , Riverside, CA 92521 , USA
| | - Simo Sun
- Faculty of Medicine, University of Miyazaki 2 Department of Infectious Diseases , , 5200 Kihara, Miyazaki 889-1692 , Japan
- Graduate School of Frontier Sciences, The University of Tokyo 3 Department of Integrated Biosciences , , Chiba 277-8562 , Japan
| | - Taisei Kikuchi
- Faculty of Medicine, University of Miyazaki 2 Department of Infectious Diseases , , 5200 Kihara, Miyazaki 889-1692 , Japan
- Graduate School of Frontier Sciences, The University of Tokyo 3 Department of Integrated Biosciences , , Chiba 277-8562 , Japan
| | - Morris F. Maduro
- University of California 1 Department of Molecular, Cell and Systems Biology , , Riverside, CA 92521 , USA
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Zinshteyn D, Barbash DA. Stonewall prevents expression of ectopic genes in the ovary and accumulates at insulator elements in D. melanogaster. PLoS Genet 2022; 18:e1010110. [PMID: 35324887 PMCID: PMC8982855 DOI: 10.1371/journal.pgen.1010110] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2021] [Revised: 04/05/2022] [Accepted: 02/18/2022] [Indexed: 11/29/2022] Open
Abstract
Germline stem cells (GSCs) are the progenitor cells of the germline for the lifetime of an animal. In Drosophila, these cells reside in a cellular niche that is required for both their maintenance (self-renewal) and differentiation (asymmetric division resulting in a daughter cell that differs from the GSC). The stem cell—daughter cell transition is tightly regulated by a number of processes, including an array of proteins required for genome stability. The germline stem-cell maintenance factor Stonewall (Stwl) associates with heterochromatin, but its molecular function is poorly understood. We performed RNA-Seq on stwl mutant ovaries and found significant derepression of many transposon families but not heterochromatic genes. We also discovered inappropriate expression of multiple classes of genes. Most prominent are testis-enriched genes, including the male germline sex-determination switch Phf7, the differentiation factor bgcn, and a large testis-specific gene cluster on chromosome 2, all of which are upregulated or ectopically expressed in stwl mutant ovaries. Surprisingly, we also found that RNAi knockdown of stwl in somatic S2 cells results in ectopic expression of these testis genes. Using parallel ChIP-Seq and RNA-Seq experiments in S2 cells, we discovered that Stwl localizes upstream of transcription start sites and at heterochromatic sequences including repetitive sequences associated with telomeres. Stwl is also enriched at bgcn, suggesting that it directly regulates this essential differentiation factor. Finally, we identify Stwl binding motifs that are shared with known insulator binding proteins. We propose that Stwl affects gene regulation, including repression of male transcripts in the female germline, by binding insulators and establishing chromatin boundaries. Stem cells are defined by their ability to divide asymmetrically, resulting in a differentiated cell and a stem cell daughter. In fruit flies, sperm and egg production begins with germline stem cells (GSCs). The ability of a GSC to differentiate or self-renew is tightly regulated by a myriad of factors. Some of these are transcription factors, which are responsible for activating or suppressing other genes to promote one state in favor of another. Stonewall is an ovarian nuclear protein required for GSC self-renewal, whose molecular function is poorly understood. Here we show that Stonewall is responsible for preventing the activation of “male” molecular programming in the fruit fly ovary. When Stonewall is absent from the ovary, egg production is terminated and testis-specific genes become highly expressed, including the male transcript of Phf7, which induces male sexual identity in female germ cells. We also show that Stonewall is likely localizing to genomic insulators, which are regions of the genome that shield genes from nearby regulators. Our findings suggest that Stonewall helps to organize the genome in ovarian germ cells and prevent expression of male genes.
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Affiliation(s)
- Daniel Zinshteyn
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York, United States of America
| | - Daniel A. Barbash
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York, United States of America
- * E-mail:
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10
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Cai QC, Chen CX, Liu HY, Zhang W, Han YF, Zhang Q, Zhou GF, Xu S, Liu T, Xiao W, Zhu QS, Luo KJ. Interactions of Vank proteins from Microplitis bicoloratus bracovirus with host Dip3 suppress eIF4E expression. DEVELOPMENTAL AND COMPARATIVE IMMUNOLOGY 2021; 118:103994. [PMID: 33417999 DOI: 10.1016/j.dci.2021.103994] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/12/2020] [Revised: 12/31/2020] [Accepted: 12/31/2020] [Indexed: 06/12/2023]
Abstract
Microplitis bicoloratus bracovirus (MbBV) inhibits the immune response of the host Spodoptera litura by disrupting nuclear factor (NF)-κB signaling and downstream gene expression. However, the underlying molecular mechanisms are not well understood. Herein, we report that viral ankyrin (Vank) proteins interacted with host dorsal-interacting protein 3 (Dip3) to selectively inhibit the transcription of eukaryotic translation initiation factor 4 E (eIF4E). Dip3 and Vank proteins were co-expressed and colocalized in the nucleus. Furthermore, ectopic expression of Dip3 rescued the transcription of some NF-κB-dependent genes suppressed by Vank proteins, including eIF4E. Co-immunoprecipitation and pull-down assays confirmed that Vank proteins interacted with and bound to full-length Dip3, which including MADF, DNA-binding protein, BESS, and protein-protein interaction motifs as well as non-motif sequences. In vivo, RNAi-mediated dip3 silencing decreased eIF4E levels and was accompanied by an immunosuppressive phenotype in S. litura. Our results provided novel insights into the regulation of host transcription during immune suppression by viral proteins that modulate nuclear NF-κB signaling.
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Affiliation(s)
- Qiu-Chen Cai
- School of Life Sciences, Yunnan University, Kunming, 650500, PR China; Key Laboratory of the University in Yunnan Province for International Cooperation in Intercellular Communications and Regulations, Yunnan University, Kunming, 650500, PR China; Biocontrol Engineering Research Centre of Crop Disease & Pest in Yunnan Province, Kunming, 650500, PR China
| | - Chang-Xu Chen
- School of Life Sciences, Yunnan University, Kunming, 650500, PR China; Key Laboratory of the University in Yunnan Province for International Cooperation in Intercellular Communications and Regulations, Yunnan University, Kunming, 650500, PR China; Biocontrol Engineering Research Centre of Crop Disease & Pest in Yunnan Province, Kunming, 650500, PR China
| | - Hong-Yu Liu
- School of Life Sciences, Yunnan University, Kunming, 650500, PR China; Key Laboratory of the University in Yunnan Province for International Cooperation in Intercellular Communications and Regulations, Yunnan University, Kunming, 650500, PR China; Biocontrol Engineering Research Centre of Crop Disease & Pest in Yunnan Province, Kunming, 650500, PR China
| | - Wei Zhang
- School of Life Sciences, Yunnan University, Kunming, 650500, PR China; Key Laboratory of the University in Yunnan Province for International Cooperation in Intercellular Communications and Regulations, Yunnan University, Kunming, 650500, PR China; Biocontrol Engineering Research Centre of Crop Disease & Pest in Yunnan Province, Kunming, 650500, PR China
| | - Yun-Feng Han
- School of Life Sciences, Yunnan University, Kunming, 650500, PR China; Key Laboratory of the University in Yunnan Province for International Cooperation in Intercellular Communications and Regulations, Yunnan University, Kunming, 650500, PR China; Biocontrol Engineering Research Centre of Crop Disease & Pest in Yunnan Province, Kunming, 650500, PR China
| | - Qi Zhang
- School of Life Sciences, Yunnan University, Kunming, 650500, PR China; Key Laboratory of the University in Yunnan Province for International Cooperation in Intercellular Communications and Regulations, Yunnan University, Kunming, 650500, PR China; Biocontrol Engineering Research Centre of Crop Disease & Pest in Yunnan Province, Kunming, 650500, PR China
| | - Gui-Fang Zhou
- School of Life Sciences, Yunnan University, Kunming, 650500, PR China; Key Laboratory of the University in Yunnan Province for International Cooperation in Intercellular Communications and Regulations, Yunnan University, Kunming, 650500, PR China; Biocontrol Engineering Research Centre of Crop Disease & Pest in Yunnan Province, Kunming, 650500, PR China
| | - Sha Xu
- School of Life Sciences, Yunnan University, Kunming, 650500, PR China
| | - Tian Liu
- Key Laboratory of the University in Yunnan Province for International Cooperation in Intercellular Communications and Regulations, Yunnan University, Kunming, 650500, PR China
| | - Wei Xiao
- School of Life Sciences, Yunnan University, Kunming, 650500, PR China; Key Laboratory of the University in Yunnan Province for International Cooperation in Intercellular Communications and Regulations, Yunnan University, Kunming, 650500, PR China
| | - Qi-Shun Zhu
- School of Life Sciences, Yunnan University, Kunming, 650500, PR China; Key Laboratory of the University in Yunnan Province for International Cooperation in Intercellular Communications and Regulations, Yunnan University, Kunming, 650500, PR China
| | - Kai-Jun Luo
- School of Life Sciences, Yunnan University, Kunming, 650500, PR China; Key Laboratory of the University in Yunnan Province for International Cooperation in Intercellular Communications and Regulations, Yunnan University, Kunming, 650500, PR China; Biocontrol Engineering Research Centre of Crop Disease & Pest in Yunnan Province, Kunming, 650500, PR China.
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Bai X, Xu J, Shao X, Luo W, Niu Z, Gao C, Wan D. A Novel Gene Coding γ-Aminobutyric Acid Transporter May Improve the Tolerance of Populus euphratica to Adverse Environments. FRONTIERS IN PLANT SCIENCE 2019; 10:1083. [PMID: 31572409 PMCID: PMC6749060 DOI: 10.3389/fpls.2019.01083] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/27/2019] [Accepted: 08/08/2019] [Indexed: 05/28/2023]
Abstract
Novel genes provide important genetic resource for organism innovation. However, the evidence from genetic experiment is limited. In plants, γ-aminobutyric acid (GABA) transporters (GATs) primarily transport GABA and further involve in plant growth, development, and response to various stresses. In this study, we have identified the GATs family in Populus species and characterized their functional evolution and divergence in a desert poplar species (Populus euphratica). We found that the GATs underwent genus-specific expansion via multiple whole-genome duplications in Populus species. The purifying selection were identified across those GATs evolution and divergence in poplar diversity, except two paralogous PeuGAT2 and PeuGAT3 from P. euphratica. The both genes arose from a tandem duplication event about 49 million years ago and have experienced strong positive selection, suggesting that the divergence in PeuGAT3 protein function/structure might define gene function better than in expression pattern. Both PeuGAT genes were functionally characterized in Arabidopsis and poplar, respectively. The overexpression of PeuGAT3 increased the thickness of xylem cells walls in both Arabidopsis and poplar and enhanced the lignin content of xylem tissues and the proline accumulation in poplar leaves, all of which may improve tolerance of salt/drought stress in desert poplars. Our findings help clarify the genetic mechanisms underpinning high tolerance in desert poplars and suggest that PeuGAT3 could be an attractive candidate gene for engineering trees with improved brown-rot resistance.
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Parey E, Crombach A. Evolution of the Drosophila melanogaster Chromatin Landscape and Its Associated Proteins. Genome Biol Evol 2019; 11:660-677. [PMID: 30689829 PMCID: PMC6411481 DOI: 10.1093/gbe/evz019] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/24/2019] [Indexed: 12/30/2022] Open
Abstract
In the nucleus of eukaryotic cells, genomic DNA associates with numerous protein complexes and RNAs, forming the chromatin landscape. Through a genome-wide study of chromatin-associated proteins in Drosophila cells, five major chromatin types were identified as a refinement of the traditional binary division into hetero- and euchromatin. These five types were given color names in reference to the Greek word chroma. They are defined by distinct but overlapping combinations of proteins and differ in biological and biochemical properties, including transcriptional activity, replication timing, and histone modifications. In this work, we assess the evolutionary relationships of chromatin-associated proteins and present an integrated view of the evolution and conservation of the fruit fly Drosophila melanogaster chromatin landscape. We combine homology prediction across a wide range of species with gene age inference methods to determine the origin of each chromatin-associated protein. This provides insight into the evolution of the different chromatin types. Our results indicate that for the euchromatic types, YELLOW and RED, young associated proteins are more specialized than old ones; and for genes found in either chromatin type, intron/exon structure is lineage-specific. Next, we provide evidence that a subset of GREEN-associated proteins is involved in a centromere drive in D. melanogaster. Our results on BLUE chromatin support the hypothesis that the emergence of Polycomb Group proteins is linked to eukaryotic multicellularity. In light of these results, we discuss how the regulatory complexification of chromatin links to the origins of eukaryotic multicellularity.
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Affiliation(s)
- Elise Parey
- Center for Interdisciplinary Research in Biology (CIRB), Collège de France, CNRS, INSERM, PSL Université Paris, France.,Institut de Biologie de l'Ecole Normale Supérieure (IBENS), Ecole Normale Supérieure, CNRS, INSERM, PSL Université Paris, Paris, France
| | - Anton Crombach
- Center for Interdisciplinary Research in Biology (CIRB), Collège de France, CNRS, INSERM, PSL Université Paris, France.,Inria, Antenne Lyon La Doua, Villeurbanne, France.,Université de Lyon, INSA-Lyon, LIRIS, UMR 5205, Villeurbanne, France
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13
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Guo Z, Qin J, Zhou X, Zhang Y. Insect Transcription Factors: A Landscape of Their Structures and Biological Functions in Drosophila and beyond. Int J Mol Sci 2018; 19:ijms19113691. [PMID: 30469390 PMCID: PMC6274879 DOI: 10.3390/ijms19113691] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2018] [Revised: 11/16/2018] [Accepted: 11/16/2018] [Indexed: 12/17/2022] Open
Abstract
Transcription factors (TFs) play essential roles in the transcriptional regulation of functional genes, and are involved in diverse physiological processes in living organisms. The fruit fly Drosophila melanogaster, a simple and easily manipulated organismal model, has been extensively applied to study the biological functions of TFs and their related transcriptional regulation mechanisms. It is noteworthy that with the development of genetic tools such as CRISPR/Cas9 and the next-generation genome sequencing techniques in recent years, identification and dissection the complex genetic regulatory networks of TFs have also made great progress in other insects beyond Drosophila. However, unfortunately, there is no comprehensive review that systematically summarizes the structures and biological functions of TFs in both model and non-model insects. Here, we spend extensive effort in collecting vast related studies, and attempt to provide an impartial overview of the progress of the structure and biological functions of current documented TFs in insects, as well as the classical and emerging research methods for studying their regulatory functions. Consequently, considering the importance of versatile TFs in orchestrating diverse insect physiological processes, this review will assist a growing number of entomologists to interrogate this understudied field, and to propel the progress of their contributions to pest control and even human health.
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Affiliation(s)
- Zhaojiang Guo
- Department of Plant Protection, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China.
| | - Jianying Qin
- Department of Plant Protection, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China.
- Longping Branch, Graduate School of Hunan University, Changsha 410125, China.
| | - Xiaomao Zhou
- Longping Branch, Graduate School of Hunan University, Changsha 410125, China.
| | - Youjun Zhang
- Department of Plant Protection, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China.
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Bao R, Dia SE, Issa HA, Alhusein D, Friedrich M. Comparative Evidence of an Exceptional Impact of Gene Duplication on the Developmental Evolution of Drosophila and the Higher Diptera. Front Ecol Evol 2018. [DOI: 10.3389/fevo.2018.00063] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
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15
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Stonewall and Brickwall: Two Partially Redundant Determinants Required for the Maintenance of Female Germline in Drosophila. G3-GENES GENOMES GENETICS 2018; 8:2027-2041. [PMID: 29669801 PMCID: PMC5982830 DOI: 10.1534/g3.118.200192] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Proper specification of germline stem cells (GSCs) in Drosophila ovaries depends on niche derived non-autonomous signaling and cell autonomous components of transcriptional machinery. Stonewall (Stwl), a MADF-BESS family protein, is one of the cell intrinsic transcriptional regulators involved in the establishment and/or maintenance of GSC fate in Drosophila ovaries. Here we report identification and functional characterization of another member of the same protein family, CG3838/ Brickwall (Brwl) with analogous functions. Loss of function alleles of brwl exhibit age dependent progressive degeneration of the developing ovarioles and loss of GSCs. Supporting the conclusion that the structural deterioration of mutant egg chambers is a result of apoptotic cell death, activated caspase levels are considerably elevated in brwl- ovaries. Moreover, as in the case of stwl mutants, on several instances, loss of brwl activity results in fusion of egg chambers and misspecification of the oocyte. Importantly, brwl phenotypes can be partially rescued by germline specific over-expression of stwl arguing for overlapping yet distinct functional capabilities of the two proteins. Taken together with our phylogenetic analysis, these data suggest that brwl and stwl likely share a common MADF-BESS ancestor and they are expressed in overlapping spatiotemporal domains to ensure robust development of the female germline.
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16
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Richhariya S, Jayakumar S, Abruzzi K, Rosbash M, Hasan G. A pupal transcriptomic screen identifies Ral as a target of store-operated calcium entry in Drosophila neurons. Sci Rep 2017; 7:42586. [PMID: 28195208 PMCID: PMC5307359 DOI: 10.1038/srep42586] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2016] [Accepted: 01/12/2017] [Indexed: 12/20/2022] Open
Abstract
Transcriptional regulation by Store-operated Calcium Entry (SOCE) is well studied in non-excitable cells. However, the role of SOCE has been poorly documented in neuronal cells with more complicated calcium dynamics. Previous reports demonstrated a requirement for SOCE in neurons that regulate Drosophila flight bouts. We refine this requirement temporally to the early pupal stage and use RNA-sequencing to identify SOCE mediated gene expression changes in the developing Drosophila pupal nervous system. Down regulation of dStim, the endoplasmic reticular calcium sensor and a principal component of SOCE in the nervous system, altered the expression of 131 genes including Ral, a small GTPase. Disruption of Ral function in neurons impaired flight, whereas ectopic expression of Ral in SOCE-compromised neurons restored flight. Through live imaging of calcium transients from cultured pupal neurons, we confirmed that Ral does not participate in SOCE, but acts downstream of it. These results identify neuronal SOCE as a mechanism that regulates expression of specific genes during development of the pupal nervous system and emphasizes the relevance of SOCE-regulated gene expression to flight circuit maturation.
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Affiliation(s)
- Shlesha Richhariya
- National Centre for Biological Sciences, Tata Institute of Fundamental Research, Bangalore 560065, India
| | - Siddharth Jayakumar
- National Centre for Biological Sciences, Tata Institute of Fundamental Research, Bangalore 560065, India
- Manipal University, Manipal 576104, India
| | - Katharine Abruzzi
- Howard Hughes Medical Institute, National Center for Behavioral Genomics, Department of Biology, Brandeis University, Waltham, MA 02454, USA
| | - Michael Rosbash
- Howard Hughes Medical Institute, National Center for Behavioral Genomics, Department of Biology, Brandeis University, Waltham, MA 02454, USA
| | - Gaiti Hasan
- National Centre for Biological Sciences, Tata Institute of Fundamental Research, Bangalore 560065, India
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Chakraborty M, Jarvis ED. Brain evolution by brain pathway duplication. Philos Trans R Soc Lond B Biol Sci 2016; 370:rstb.2015.0056. [PMID: 26554045 PMCID: PMC4650129 DOI: 10.1098/rstb.2015.0056] [Citation(s) in RCA: 68] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Understanding the mechanisms of evolution of brain pathways for complex behaviours is still in its infancy. Making further advances requires a deeper understanding of brain homologies, novelties and analogies. It also requires an understanding of how adaptive genetic modifications lead to restructuring of the brain. Recent advances in genomic and molecular biology techniques applied to brain research have provided exciting insights into how complex behaviours are shaped by selection of novel brain pathways and functions of the nervous system. Here, we review and further develop some insights to a new hypothesis on one mechanism that may contribute to nervous system evolution, in particular by brain pathway duplication. Like gene duplication, we propose that whole brain pathways can duplicate and the duplicated pathway diverge to take on new functions. We suggest that one mechanism of brain pathway duplication could be through gene duplication, although other mechanisms are possible. We focus on brain pathways for vocal learning and spoken language in song-learning birds and humans as example systems. This view presents a new framework for future research in our understanding of brain evolution and novel behavioural traits.
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Affiliation(s)
- Mukta Chakraborty
- Department of Neurobiology, Duke University Medical Center, Durham, NC 27713, USA Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA
| | - Erich D Jarvis
- Department of Neurobiology, Duke University Medical Center, Durham, NC 27713, USA Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA
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18
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Fu CL, Wang XF, Cheng Q, Wang D, Hirose S, Liu QX. The T-box transcription factor Midline regulates wing development by repressing wingless and hedgehog in Drosophila. Sci Rep 2016; 6:27981. [PMID: 27301278 PMCID: PMC4908378 DOI: 10.1038/srep27981] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2016] [Accepted: 05/27/2016] [Indexed: 12/21/2022] Open
Abstract
Wingless (Wg) and Hedgehog (Hh) signaling pathways are key players in animal development. However, regulation of the expression of wg and hh are not well understood. Here, we show that Midline (Mid), an evolutionarily conserved transcription factor, expresses in the wing disc of Drosophila and plays a vital role in wing development. Loss or knock down of mid in the wing disc induced hyper-expression of wingless (wg) and yielded cocked and non-flat wings. Over-expression of mid in the wing disc markedly repressed the expression of wg, DE-Cadherin (DE-Cad) and armadillo (arm), and resulted in a small and blistered wing. In addition, a reduction in the dose of mid enhanced phenotypes of a gain-of-function mutant of hedgehog (hh). We also observed repression of hh upon overexpression of mid in the wing disc. Taken together, we propose that Mid regulates wing development by repressing wg and hh in Drosophila.
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Affiliation(s)
- Chong-Lei Fu
- Laboratory of Developmental Genetics, Shandong Agricultural University, Tai'an, Shandong 271018, China
| | - Xian-Feng Wang
- Laboratory of Developmental Genetics, Shandong Agricultural University, Tai'an, Shandong 271018, China
| | - Qian Cheng
- Laboratory of Developmental Genetics, Shandong Agricultural University, Tai'an, Shandong 271018, China
| | - Dan Wang
- Laboratory of Developmental Genetics, Shandong Agricultural University, Tai'an, Shandong 271018, China
| | - Susumu Hirose
- Department of Developmental Genetics, National Institute of Genetics, Mishima, Shizuoka 411-8540, Japan
| | - Qing-Xin Liu
- Laboratory of Developmental Genetics, Shandong Agricultural University, Tai'an, Shandong 271018, China
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Vidal NM, Grazziotin AL, Iyer LM, Aravind L, Venancio TM. Transcription factors, chromatin proteins and the diversification of Hemiptera. INSECT BIOCHEMISTRY AND MOLECULAR BIOLOGY 2016; 69:1-13. [PMID: 26226651 PMCID: PMC4732926 DOI: 10.1016/j.ibmb.2015.07.001] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/30/2014] [Revised: 06/29/2015] [Accepted: 07/03/2015] [Indexed: 06/04/2023]
Abstract
Availability of complete genomes provides a means to explore the evolution of enormous developmental, morphological, and behavioral diversity among insects. Hemipterans in particular show great diversity of both morphology and life history within a single order. To better understand the role of transcription regulators in the diversification of hemipterans, using sequence profile searches and hidden Markov models we computationally analyzed transcription factors (TFs) and chromatin proteins (CPs) in the recently available Rhodnius prolixus genome along with 13 other insect and 4 non-insect arthropod genomes. We generated a comprehensive collection of TFs and CPs across arthropods including 303 distinct types of domains in TFs and 139 in CPs. This, along with the availability of two hemipteran genomes, R. prolixus and Acyrthosiphon pisum, helped us identify possible determinants for their dramatic morphological and behavioral divergence. We identified five domain families (i.e. Pipsqueak, SAZ/MADF, THAP, FLYWCH and BED finger) as having undergone differential patterns of lineage-specific expansion in hemipterans or within hemipterans relative to other insects. These expansions appear to be at least in part driven by transposons, with the DNA-binding domains of transposases having provided the raw material for emergence of new TFs. Our analysis suggests that while R. prolixus probably retains a state closer to the ancestral hemipteran, A. pisum represents a highly derived state, with the emergence of asexual reproduction potentially favoring genome duplication and transposon expansion. Both hemipterans are predicted to possess active DNA methylation systems. However, in the course of their divergence, aphids seem to have expanded the ancestral hemipteran DNA methylation along with a distinctive linkage to the histone methylation system, as suggested by expansion of SET domain methylases, including those fused to methylated CpG recognition domains. Thus, differential use of DNA methylation and histone methylation might have played a role in emergence of polyphenism and cyclic parthenogenesis from the ancestral hemipteran.
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Affiliation(s)
- Newton M Vidal
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA; Laboratório de Química e Função de Proteínas e Peptídeos, Centro de Biociências e Biotecnologia, Universidade Estadual do Norte Fluminense Darcy Ribeiro, Campos dos Goytacazes, RJ, Brazil; Instituto Nacional de Ciência e Tecnologia em Entomologia Molecular (INCT-EM), Rio de Janeiro, RJ, Brazil.
| | - Ana Laura Grazziotin
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA; Laboratório de Química e Função de Proteínas e Peptídeos, Centro de Biociências e Biotecnologia, Universidade Estadual do Norte Fluminense Darcy Ribeiro, Campos dos Goytacazes, RJ, Brazil.
| | - Lakshminarayan M Iyer
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA.
| | - L Aravind
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA.
| | - Thiago M Venancio
- Laboratório de Química e Função de Proteínas e Peptídeos, Centro de Biociências e Biotecnologia, Universidade Estadual do Norte Fluminense Darcy Ribeiro, Campos dos Goytacazes, RJ, Brazil; Instituto Nacional de Ciência e Tecnologia em Entomologia Molecular (INCT-EM), Rio de Janeiro, RJ, Brazil.
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20
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Rao Z, Duan J, Xia Q, Feng Q. In silico identification of BESS-DC genes and expression analysis in the silkworm, Bombyx mori. Gene 2016; 575:478-487. [DOI: 10.1016/j.gene.2015.09.024] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2015] [Revised: 09/10/2015] [Accepted: 09/11/2015] [Indexed: 11/15/2022]
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21
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Ellis K, Friedman C, Yedvobnick B. Drosophila domino Exhibits Genetic Interactions with a Wide Spectrum of Chromatin Protein-Encoding Loci. PLoS One 2015; 10:e0142635. [PMID: 26555684 PMCID: PMC4640824 DOI: 10.1371/journal.pone.0142635] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2015] [Accepted: 10/23/2015] [Indexed: 11/18/2022] Open
Abstract
The Drosophila domino gene encodes protein of the SWI2/SNF2 family that has widespread roles in transcription, replication, recombination and DNA repair. Here, the potential relationship of Domino protein to other chromatin-associated proteins has been investigated through a genetic interaction analysis. We scored for genetic modification of a domino wing margin phenotype through coexpression of RNAi directed against a set of previously characterized and more newly characterized chromatin-encoding loci. A set of other SWI2/SNF2 loci were also assayed for interaction with domino. Our results show that the majority of tested loci exhibit synergistic enhancement or suppression of the domino wing phenotype. Therefore, depression in domino function sensitizes the wing margin to alterations in the activity of numerous chromatin components. In several cases the genetic interactions are associated with changes in the level of cell death measured across the dorsal-ventral margin of the wing imaginal disc. These results highlight the broad realms of action of many chromatin proteins and suggest significant overlap with Domino function in fundamental cell processes, including cell proliferation, cell death and cell signaling.
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Affiliation(s)
- Kaitlyn Ellis
- Biology Department, Emory University, Atlanta, Georgia, United States of America
| | - Chloe Friedman
- Biology Department, Emory University, Atlanta, Georgia, United States of America
| | - Barry Yedvobnick
- Biology Department, Emory University, Atlanta, Georgia, United States of America
- * E-mail:
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