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Lei P, Jiang Y, Zhao Y, Jiang M, Ji X, Ma L, Jin G, Li J, Zhang S, Kong D, Zhao X, Meng F. Functions of Basic Helix-Loop-Helix (bHLH) Proteins in the Regulation of Plant Responses to Cold, Drought, Salt, and Iron Deficiency: A Comprehensive Review. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2024; 72:10692-10709. [PMID: 38712500 DOI: 10.1021/acs.jafc.3c09665] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2024]
Abstract
Abiotic stresses including cold, drought, salt, and iron deficiency severely impair plant development, crop productivity, and geographic distribution. Several bodies of research have shed light on the pleiotropic functions of BASIC HELIX-LOOP-HELIX (bHLH) proteins in plant responses to these abiotic stresses. In this review, we mention the regulatory roles of bHLH TFs in response to stresses such as cold, drought, salt resistance, and iron deficiency, as well as in enhancing grain yield in plants, especially crops. The bHLH proteins bind to E/G-box motifs in the target promoter and interact with various other factors to form a complex regulatory network. Through this network, they cooperatively activate or repress the transcription of downstream genes, thereby regulating various stress responses. Finally, we present some perspectives for future research focusing on the molecular mechanisms that integrate and coordinate these abiotic stresses. Understanding these molecular mechanisms is crucial for the development of stress-tolerant crops.
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Affiliation(s)
- Pei Lei
- Jilin Provincial Key Laboratory of Tree and Grass Genetics and Breeding, College of Forestry and Grassland Science, Jilin Agricultural University, Changchun 130118, China
| | - Yaxuan Jiang
- College of Life Science, Northeast Forestry University, Hexing Road 26, Harbin 150040, China
| | - Yong Zhao
- College of Life Sciences, Baicheng Normal University, Baicheng 137099, China
| | - Mingquan Jiang
- Jilin Province Product Quality Supervision and Inspection Institute, Changchun 130022, China
| | - Ximei Ji
- Jilin Provincial Key Laboratory of Tree and Grass Genetics and Breeding, College of Forestry and Grassland Science, Jilin Agricultural University, Changchun 130118, China
- College of Life Science, Northeast Forestry University, Hexing Road 26, Harbin 150040, China
| | - Le Ma
- College of Life Science, Northeast Forestry University, Hexing Road 26, Harbin 150040, China
| | - Guangze Jin
- College of Life Science, Northeast Forestry University, Hexing Road 26, Harbin 150040, China
| | - Jianxin Li
- College of Life Science, Northeast Forestry University, Hexing Road 26, Harbin 150040, China
| | - Subin Zhang
- College of Life Science, Northeast Forestry University, Hexing Road 26, Harbin 150040, China
| | - Dexin Kong
- College of Life Science, Northeast Forestry University, Hexing Road 26, Harbin 150040, China
| | - Xiyang Zhao
- Jilin Provincial Key Laboratory of Tree and Grass Genetics and Breeding, College of Forestry and Grassland Science, Jilin Agricultural University, Changchun 130118, China
| | - Fanjuan Meng
- Jilin Provincial Key Laboratory of Tree and Grass Genetics and Breeding, College of Forestry and Grassland Science, Jilin Agricultural University, Changchun 130118, China
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Chen M, Dai Y, Liao J, Wu H, Lv Q, Huang Y, Liu L, Feng Y, Lv H, Zhou B, Peng D. TARGET OF MONOPTEROS: key transcription factors orchestrating plant development and environmental response. JOURNAL OF EXPERIMENTAL BOTANY 2024; 75:2214-2234. [PMID: 38195092 DOI: 10.1093/jxb/erae005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/06/2023] [Accepted: 01/04/2024] [Indexed: 01/11/2024]
Abstract
Plants have an incredible ability to sustain root and vascular growth after initiation of the embryonic root and the specification of vascular tissue in early embryos. Microarray assays have revealed that a group of transcription factors, TARGET OF MONOPTEROS (TMO), are important for embryonic root initiation in Arabidopsis. Despite the discovery of their auxin responsiveness early on, their function and mode of action remained unknown for many years. The advent of genome editing has accelerated the study of TMO transcription factors, revealing novel functions for biological processes such as vascular development, root system architecture, and response to environmental cues. This review covers recent achievements in understanding the developmental function and the genetic mode of action of TMO transcription factors in Arabidopsis and other plant species. We highlight the transcriptional and post-transcriptional regulation of TMO transcription factors in relation to their function, mainly in Arabidopsis. Finally, we provide suggestions for further research and potential applications in plant genetic engineering.
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Affiliation(s)
- Min Chen
- Faculty of Life Science and Biotechnology of Central South University of Forestry and Technology, 410004, Changsha, Hunan, China
| | - Yani Dai
- Faculty of Life Science and Biotechnology of Central South University of Forestry and Technology, 410004, Changsha, Hunan, China
| | - Jiamin Liao
- Faculty of Life Science and Biotechnology of Central South University of Forestry and Technology, 410004, Changsha, Hunan, China
| | - Huan Wu
- Faculty of Life Science and Biotechnology of Central South University of Forestry and Technology, 410004, Changsha, Hunan, China
| | - Qiang Lv
- Faculty of Life Science and Biotechnology of Central South University of Forestry and Technology, 410004, Changsha, Hunan, China
| | - Yu Huang
- Faculty of Life Science and Biotechnology of Central South University of Forestry and Technology, 410004, Changsha, Hunan, China
| | - Lichang Liu
- Faculty of Life Science and Biotechnology of Central South University of Forestry and Technology, 410004, Changsha, Hunan, China
| | - Yu Feng
- Faculty of Life Science and Biotechnology of Central South University of Forestry and Technology, 410004, Changsha, Hunan, China
| | - Hongxuan Lv
- Faculty of Life Science and Biotechnology of Central South University of Forestry and Technology, 410004, Changsha, Hunan, China
| | - Bo Zhou
- Faculty of Life Science and Biotechnology of Central South University of Forestry and Technology, 410004, Changsha, Hunan, China
- Huitong National Field Station for Scientific Observation and Research of Chinese Fir Plantation Ecosystem in Hunan Province, 438107, Huaihua, Hunan, China
- National Engineering Laboratory of Applied Technology for Forestry and Ecology in Southern China, 410004, Changsha, Hunan, China
- Forestry Biotechnology Hunan Key Laboratories, Hunan, China
- Key Laboratory of Cultivation and Protection for Non-Wood Forest Trees, Ministry of Education, Central South University of Forestry and Technology, 410004, Changsha, Hunan, China
- Yuelushan Laboratory Carbon Sinks Forests Variety Innovation Center, 410004, Changsha, Hunan, China
| | - Dan Peng
- Faculty of Life Science and Biotechnology of Central South University of Forestry and Technology, 410004, Changsha, Hunan, China
- Huitong National Field Station for Scientific Observation and Research of Chinese Fir Plantation Ecosystem in Hunan Province, 438107, Huaihua, Hunan, China
- Forestry Biotechnology Hunan Key Laboratories, Hunan, China
- Yuelushan Laboratory Carbon Sinks Forests Variety Innovation Center, 410004, Changsha, Hunan, China
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Chen X, Yao C, Liu J, Liu J, Fang J, Deng H, Yao Q, Kang T, Guo X. Basic helix-loop-helix (bHLH) gene family in rye (Secale cereale L.): genome-wide identification, phylogeny, evolutionary expansion and expression analyses. BMC Genomics 2024; 25:67. [PMID: 38233751 PMCID: PMC10792839 DOI: 10.1186/s12864-023-09911-3] [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: 05/15/2023] [Accepted: 12/15/2023] [Indexed: 01/19/2024] Open
Abstract
BACKGROUND Rye (Secale cereale), one of the drought and cold-tolerant crops, is an important component of the Triticae Dumortier family of Gramineae plants. Basic helix-loop-helix (bHLH), an important family of transcription factors, has played pivotal roles in regulating numerous intriguing biological processes in plant development and abiotic stress responses. However, no systemic analysis of the bHLH transcription factor family has yet been reported in rye. RESULTS In this study, 220 bHLH genes in S. cereale (ScbHLHs) were identified and named based on the chromosomal location. The evolutionary relationships, classifications, gene structures, motif compositions, chromosome localization, and gene replication events in these ScbHLH genes are systematically analyzed. These 220 ScbHLH members are divided into 21 subfamilies and one unclassified gene. Throughout evolution, the subfamilies 5, 9, and 18 may have experienced stronger expansion. The segmental duplications may have contributed significantly to the expansion of the bHLH family. To systematically analyze the evolutionary relationships of the bHLH family in different plants, we constructed six comparative genomic maps of homologous genes between rye and different representative monocotyledonous and dicotyledonous plants. Finally, the gene expression response characteristics of 22 ScbHLH genes in various biological processes and stress responses were analyzed. Some candidate genes, such as ScbHLH11, ScbHLH48, and ScbHLH172, related to tissue developments and environmental stresses were screened. CONCLUSIONS The results indicate that these ScbHLH genes exhibit characteristic expression in different tissues, grain development stages, and stress treatments. These findings provided a basis for a comprehensive understanding of the bHLH family in rye.
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Affiliation(s)
- Xingyu Chen
- Sichuan Industrial Institute of Antibiotics, School of Pharmacy, Chengdu University, Chengdu, 610106, PR China
| | - Caimei Yao
- Sichuan Industrial Institute of Antibiotics, School of Pharmacy, Chengdu University, Chengdu, 610106, PR China
| | - Jiahao Liu
- Sichuan Industrial Institute of Antibiotics, School of Pharmacy, Chengdu University, Chengdu, 610106, PR China
| | - Jintao Liu
- Sichuan Industrial Institute of Antibiotics, School of Pharmacy, Chengdu University, Chengdu, 610106, PR China
| | - Jingmei Fang
- Sichuan Industrial Institute of Antibiotics, School of Pharmacy, Chengdu University, Chengdu, 610106, PR China
| | - Hong Deng
- Sichuan Industrial Institute of Antibiotics, School of Pharmacy, Chengdu University, Chengdu, 610106, PR China
| | - Qian Yao
- Sichuan Industrial Institute of Antibiotics, School of Pharmacy, Chengdu University, Chengdu, 610106, PR China
| | - Tairan Kang
- School of Food and Biological Engineering, Chengdu University, Chengdu, 610106, PR China.
| | - Xiaoqiang Guo
- Sichuan Industrial Institute of Antibiotics, School of Pharmacy, Chengdu University, Chengdu, 610106, PR China.
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Wang L, Tan TK, Kim H, Kappei D, Tan SH, Look AT, Sanda T. ASCL1 characterizes adrenergic neuroblastoma via its pioneer function and cooperation with core regulatory circuit factors. Cell Rep 2023; 42:113541. [PMID: 38060444 DOI: 10.1016/j.celrep.2023.113541] [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: 05/19/2023] [Revised: 10/09/2023] [Accepted: 11/20/2023] [Indexed: 12/30/2023] Open
Abstract
Neuroblastoma originates from developing neural crest and can interconvert between the mesenchymal (MES) and adrenergic (ADRN) states, each of which are controlled by different sets of transcription factors forming the core regulatory circuit (CRC). However, the roles of CRC factors in induction and maintenance of specific state are poorly understood. Here, we demonstrate that overexpression of ASCL1, an ADRN CRC factor, in MES neuroblastoma cells opens closed chromatin at the promoters of key ADRN genes, accompanied by epigenetic activation and establishment of enhancer-promoter interactions, initiating the ADRN gene expression program. ASCL1 inhibits the transforming growth factor β-SMAD2/3 pathway but activates the bone morphogenetic protein SMAD1-ID3/4 pathway. ASCL1 and other CRC members potentiate each other's activity, increasing the expression of the original targets and inducing a new set of genes, thereby fully inducing the ADRN program. Our results demonstrate that ASCL1 serves as a pioneer factor and cooperates with CRC factors to characterize the ADRN gene expression program.
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Affiliation(s)
- Lu Wang
- Cancer Science Institute of Singapore, Singapore 117599, Singapore
| | - Tze King Tan
- Cancer Science Institute of Singapore, Singapore 117599, Singapore
| | - Hyoju Kim
- Cancer Science Institute of Singapore, Singapore 117599, Singapore
| | - Dennis Kappei
- Cancer Science Institute of Singapore, Singapore 117599, Singapore; Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117596, Singapore; NUS Center for Cancer Research, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Shi Hao Tan
- Cancer Science Institute of Singapore, Singapore 117599, Singapore
| | - A Thomas Look
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02216, USA; Division of Pediatric Hematology/Oncology, Boston Children's Hospital, Boston, MA 02215, USA
| | - Takaomi Sanda
- Cancer Science Institute of Singapore, Singapore 117599, Singapore; NUS Center for Cancer Research, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore; Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117599, Singapore.
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Thoben C, Pucker B. Automatic annotation of the bHLH gene family in plants. BMC Genomics 2023; 24:780. [PMID: 38102570 PMCID: PMC10722790 DOI: 10.1186/s12864-023-09877-2] [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: 05/10/2023] [Accepted: 12/06/2023] [Indexed: 12/17/2023] Open
Abstract
BACKGROUND The bHLH transcription factor family is named after the basic helix-loop-helix (bHLH) domain that is a characteristic element of their members. Understanding the function and characteristics of this family is important for the examination of a wide range of functions. As the availability of genome sequences and transcriptome assemblies has increased significantly, the need for automated solutions that provide reliable functional annotations is emphasised. RESULTS A phylogenetic approach was adapted for the automatic identification and functional annotation of the bHLH transcription factor family. The bHLH_annotator, designed for the automated functional annotation of bHLHs, was implemented in Python3. Sequences of bHLHs described in literature were collected to represent the full diversity of bHLH sequences. Previously described orthologs form the basis for the functional annotation assignment to candidates which are also screened for bHLH-specific motifs. The pipeline was successfully deployed on the two Arabidopsis thaliana accessions Col-0 and Nd-1, the monocot species Dioscorea dumetorum, and a transcriptome assembly of Croton tiglium. Depending on the applied search parameters for the initial candidates in the pipeline, species-specific candidates or members of the bHLH family which experienced domain loss can be identified. CONCLUSIONS The bHLH_annotator allows a detailed and systematic investigation of the bHLH family in land plant species and classifies candidates based on bHLH-specific characteristics, which distinguishes the pipeline from other established functional annotation tools. This provides the basis for the functional annotation of the bHLH family in land plants and the systematic examination of a wide range of functions regulated by this transcription factor family.
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Affiliation(s)
- Corinna Thoben
- Plant Biotechnology and Bioinformatics, Institute of Plant Biology & Braunschweig Integrated, Centre of Systems Biology (BRICS), TU Braunschweig, Braunschweig, Germany
| | - Boas Pucker
- Plant Biotechnology and Bioinformatics, Institute of Plant Biology & Braunschweig Integrated, Centre of Systems Biology (BRICS), TU Braunschweig, Braunschweig, Germany.
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Ding C, Gao J, Zhang S, Jiang N, Su D, Huang X, Zhang Z. The Basic/Helix-Loop-Helix Transcription Factor Family Gene RcbHLH112 Is a Susceptibility Gene in Gray Mould Resistance of Rose (Rosa Chinensis). Int J Mol Sci 2023; 24:16305. [PMID: 38003495 PMCID: PMC10671410 DOI: 10.3390/ijms242216305] [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: 09/15/2023] [Revised: 11/05/2023] [Accepted: 11/10/2023] [Indexed: 11/26/2023] Open
Abstract
The basic/helix-loop-helix (bHLH) family is a major family of transcription factors in plants. Although it has been reported that bHLH plays a defensive role against pathogen infection in plants, there is no comprehensive study on the bHLH-related defence response in rose (Rosa sp.). In this study, a genome-wide analysis of bHLH family genes (RcbHLHs) in rose was carried out, including their phylogenetic relationships, gene structure, chromosome localization and collinearity analysis. Via phylogenetic analysis, a total of 121 RcbHLH genes in the rose genome were divided into 21 sub-groups. These RcbHLHs are unevenly distributed in all 7 chromosomes of rose. The occurrence of gene duplication events indicates that whole-genome duplication and segmental duplication may play a key role in gene duplication. Ratios of non-synonymous to synonymous mutation frequency (Ka/Ks) analysis showed that the replicated RcbHLH genes mainly underwent purification selection, and their functional differentiation was limited. Gene expression analysis showed that 46 RcbHLHs were differentially expressed in rose petals upon B. cinerea infection. It is speculated that these RcbHLHs are candidate genes that regulate the response of rose plants to B. cinerea infection. Virus-induced gene silencing (VIGS) confirmed that RcbHLH112 in rose is a susceptibility factor for infection with B. cinerea. This study provides useful information for further study of the functions of the rose bHLH gene family.
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Affiliation(s)
- Chao Ding
- Shanxi Center for Testing of Functional Agro-Products, Shanxi Agricultural University, Taiyuan 030031, China
| | - Junzhao Gao
- Beijing Key Laboratory of Development and Quality Control of Ornamental Crops, Department of Ornamental Horticulture, China Agricultural University, Beijing 100107, China; (J.G.)
| | - Shiya Zhang
- Beijing Key Laboratory of Development and Quality Control of Ornamental Crops, Department of Ornamental Horticulture, China Agricultural University, Beijing 100107, China; (J.G.)
| | - Ning Jiang
- Beijing Key Laboratory of Development and Quality Control of Ornamental Crops, Department of Ornamental Horticulture, China Agricultural University, Beijing 100107, China; (J.G.)
| | - Dongtao Su
- Shanxi Center for Testing of Functional Agro-Products, Shanxi Agricultural University, Taiyuan 030031, China
| | - Xinzheng Huang
- Department of Entomology, MOA Key Lab of Pest Monitoring and Green Management, College of Plant Protection, China Agricultural University, Beijing 100193, China
| | - Zhao Zhang
- Beijing Key Laboratory of Development and Quality Control of Ornamental Crops, Department of Ornamental Horticulture, China Agricultural University, Beijing 100107, China; (J.G.)
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Du J, Wang J, Shan S, Mi T, Song Y, Xia Y, Ma S, Zhang G, Ma L, Niu N. Low-Temperature-Mediated Promoter Methylation Relates to the Expression of TaPOR2D, Affecting the Level of Chlorophyll Accumulation in Albino Wheat ( Triticum aestivum L.). Int J Mol Sci 2023; 24:14697. [PMID: 37834145 PMCID: PMC10573025 DOI: 10.3390/ijms241914697] [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: 08/02/2023] [Revised: 09/18/2023] [Accepted: 09/23/2023] [Indexed: 10/15/2023] Open
Abstract
Chlorophyll is an indispensable photoreceptor in plant photosynthesis. Its anabolic imbalance is detrimental to individual growth and development. As an essential epigenetic modification, DNA methylation can induce phenotypic variations, such as leaf color transformation, by regulating gene expression. Albino line XN1376B is a natural mutation of winter wheat cultivar XN1376; however, the regulatory mechanism of its albinism is still unclear. In this study, we found that low temperatures induced albinism in XN1376B. The number of chloroplasts decreased as the phenomenon of bleaching intensified and the fence tissue and sponge tissue slowly dissolved. We identified six distinct TaPOR (protochlorophyllide oxidoreductase) genes in the wheat genome, and TaPOR2D was deemed to be related to the phenomenon of albinism based on the expression in different color leaves (green leaves, white leaves and returned green leaves) and the analysis of promoters' cis-acting elements. TaPOR2D was localized to chloroplasts. TaPOR2D overexpression (TaPOR2D-OE) enhanced the chlorophyll significantly in Arabidopsis, especially at two weeks; the amount of chlorophyll was 6.46 mg/L higher than in WT. The methylation rate of the TaPOR2D promoter in low-temperature albino leaves is as high as 93%, whereas there was no methylation in green leaves. Correspondingly, three DNA methyltransferase genes (TaMET1, TaDRM and TaCMT) were up-regulated in white leaves. Our study clarified that the expression of TaPOR2D is associated with its promoter methylation at a low temperature; it affects the level of chlorophyll accumulation, which probably causes the abnormal development of plant chloroplasts in albino wheat XN1376B. The results provide a theoretical basis for in-depth analysis of the regulation of development of plant chloroplasts and color variation in wheat XN1376B leaves.
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Affiliation(s)
- Jingjing Du
- College of Agronomy, Northwest A & F University, Xianyang 712100, China; (J.D.); (J.W.); (S.S.); (T.M.); (Y.S.); (Y.X.); (S.M.); (G.Z.)
- Key Laboratory of Crop Heterosis of Shaanxi Province, Xianyang 712100, China
- Wheat Breeding Engineering Research Center of Ministry of Education, Xianyang 712100, China
| | - Junwei Wang
- College of Agronomy, Northwest A & F University, Xianyang 712100, China; (J.D.); (J.W.); (S.S.); (T.M.); (Y.S.); (Y.X.); (S.M.); (G.Z.)
- Key Laboratory of Crop Heterosis of Shaanxi Province, Xianyang 712100, China
- Wheat Breeding Engineering Research Center of Ministry of Education, Xianyang 712100, China
| | - Sicong Shan
- College of Agronomy, Northwest A & F University, Xianyang 712100, China; (J.D.); (J.W.); (S.S.); (T.M.); (Y.S.); (Y.X.); (S.M.); (G.Z.)
- Key Laboratory of Crop Heterosis of Shaanxi Province, Xianyang 712100, China
- Wheat Breeding Engineering Research Center of Ministry of Education, Xianyang 712100, China
| | - Tian Mi
- College of Agronomy, Northwest A & F University, Xianyang 712100, China; (J.D.); (J.W.); (S.S.); (T.M.); (Y.S.); (Y.X.); (S.M.); (G.Z.)
- Key Laboratory of Crop Heterosis of Shaanxi Province, Xianyang 712100, China
- Wheat Breeding Engineering Research Center of Ministry of Education, Xianyang 712100, China
| | - Yulong Song
- College of Agronomy, Northwest A & F University, Xianyang 712100, China; (J.D.); (J.W.); (S.S.); (T.M.); (Y.S.); (Y.X.); (S.M.); (G.Z.)
- Key Laboratory of Crop Heterosis of Shaanxi Province, Xianyang 712100, China
- Wheat Breeding Engineering Research Center of Ministry of Education, Xianyang 712100, China
| | - Yu Xia
- College of Agronomy, Northwest A & F University, Xianyang 712100, China; (J.D.); (J.W.); (S.S.); (T.M.); (Y.S.); (Y.X.); (S.M.); (G.Z.)
- Key Laboratory of Crop Heterosis of Shaanxi Province, Xianyang 712100, China
- Wheat Breeding Engineering Research Center of Ministry of Education, Xianyang 712100, China
| | - Shoucai Ma
- College of Agronomy, Northwest A & F University, Xianyang 712100, China; (J.D.); (J.W.); (S.S.); (T.M.); (Y.S.); (Y.X.); (S.M.); (G.Z.)
- Key Laboratory of Crop Heterosis of Shaanxi Province, Xianyang 712100, China
- Wheat Breeding Engineering Research Center of Ministry of Education, Xianyang 712100, China
| | - Gaisheng Zhang
- College of Agronomy, Northwest A & F University, Xianyang 712100, China; (J.D.); (J.W.); (S.S.); (T.M.); (Y.S.); (Y.X.); (S.M.); (G.Z.)
- Key Laboratory of Crop Heterosis of Shaanxi Province, Xianyang 712100, China
- Wheat Breeding Engineering Research Center of Ministry of Education, Xianyang 712100, China
| | - Lingjian Ma
- College of Agronomy, Northwest A & F University, Xianyang 712100, China; (J.D.); (J.W.); (S.S.); (T.M.); (Y.S.); (Y.X.); (S.M.); (G.Z.)
- Key Laboratory of Crop Heterosis of Shaanxi Province, Xianyang 712100, China
- Wheat Breeding Engineering Research Center of Ministry of Education, Xianyang 712100, China
| | - Na Niu
- College of Agronomy, Northwest A & F University, Xianyang 712100, China; (J.D.); (J.W.); (S.S.); (T.M.); (Y.S.); (Y.X.); (S.M.); (G.Z.)
- Key Laboratory of Crop Heterosis of Shaanxi Province, Xianyang 712100, China
- Wheat Breeding Engineering Research Center of Ministry of Education, Xianyang 712100, China
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García-Caballero D, Hart JR, Vogt PK. Long Non-Coding RNAs as "MYC Facilitators". PATHOPHYSIOLOGY 2023; 30:389-399. [PMID: 37755396 PMCID: PMC10534484 DOI: 10.3390/pathophysiology30030030] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2023] [Revised: 08/15/2023] [Accepted: 08/17/2023] [Indexed: 09/28/2023] Open
Abstract
In this article, we discuss a class of MYC-interacting lncRNAs (long non-coding RNAs) that share the following criteria: They are direct transcriptional targets of MYC. Their expression is coordinated with the expression of MYC. They are required for sustained MYC-driven cell proliferation, and they are not essential for cell survival. We refer to these lncRNAs as "MYC facilitators" and discuss two representative members of this class of lncRNAs, SNHG17 (small nuclear RNA host gene) and LNROP (long non-coding regulator of POU2F2). We also present a general hypothesis on the role of lncRNAs in MYC-mediated transcriptional regulation.
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Affiliation(s)
| | | | - Peter K. Vogt
- Department of Molecular Medicine, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA
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9
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Hammad M, Raftari M, Cesário R, Salma R, Godoy P, Emami SN, Haghdoost S. Roles of Oxidative Stress and Nrf2 Signaling in Pathogenic and Non-Pathogenic Cells: A Possible General Mechanism of Resistance to Therapy. Antioxidants (Basel) 2023; 12:1371. [PMID: 37507911 PMCID: PMC10376708 DOI: 10.3390/antiox12071371] [Citation(s) in RCA: 15] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2023] [Revised: 06/21/2023] [Accepted: 06/26/2023] [Indexed: 07/30/2023] Open
Abstract
The coordinating role of nuclear factor erythroid-2-related factor 2 (Nrf2) in cellular function is undeniable. Evidence indicates that this transcription factor exerts massive regulatory functions in multiple signaling pathways concerning redox homeostasis and xenobiotics, macromolecules, and iron metabolism. Being the master regulator of antioxidant system, Nrf2 controls cellular fate, influencing cell proliferation, differentiation, apoptosis, resistance to therapy, and senescence processes, as well as infection disease success. Because Nrf2 is the key coordinator of cell defence mechanisms, dysregulation of its signaling has been associated with carcinogenic phenomena and infectious and age-related diseases. Deregulation of this cytoprotective system may also interfere with immune response. Oxidative burst, one of the main microbicidal mechanisms, could be impaired during the initial phagocytosis of pathogens, which could lead to the successful establishment of infection and promote susceptibility to infectious diseases. There is still a knowledge gap to fill regarding the molecular mechanisms by which Nrf2 orchestrates such complex networks involving multiple pathways. This review describes the role of Nrf2 in non-pathogenic and pathogenic cells.
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Affiliation(s)
- Mira Hammad
- University of Caen Normandy, UMR6252 CIMAP/ARIA, GANIL, 14000 Caen, France
| | - Mohammad Raftari
- Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, 10691 Stockholm, Sweden
| | - Rute Cesário
- Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, 10691 Stockholm, Sweden
| | - Rima Salma
- University of Caen Normandy, UMR6252 CIMAP/ARIA, GANIL, 14000 Caen, France
| | - Paulo Godoy
- Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, 10691 Stockholm, Sweden
| | - S Noushin Emami
- Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, 10691 Stockholm, Sweden
- Natural Resources Institute, University of Greenwich, London ME4 4TB, UK
| | - Siamak Haghdoost
- University of Caen Normandy, UMR6252 CIMAP/ARIA, GANIL, 14000 Caen, France
- Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, 10691 Stockholm, Sweden
- Advanced Resource Center for HADrontherapy in Europe (ARCHADE), 14000 Caen, France
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10
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Zhang M, Feng B, Chen Y, Geng M, Li M, Zheng X, Zhang H, Zhang L, Tan B, Ye X, Wang W, Li J, Cheng J, Feng J. PpIBH1-1 limits internode elongation of peach shoot in a dose-dependent manner. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2023; 330:111630. [PMID: 36787849 DOI: 10.1016/j.plantsci.2023.111630] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/07/2022] [Revised: 12/20/2022] [Accepted: 02/03/2023] [Indexed: 06/18/2023]
Abstract
Peach [Prunus persica (L.) Batsch] annual shoots grow up quickly, which limits the lighting and ventilation of an orchard. Atypical bHLH proteins IBH1(INCREASED LEAF INCLINATION1 BINDING bHLH1) play substantial roles in regulating cell elongation and plant stature. In this study, three PpIBH1s (PpIBH1-1/-2/-3) were identified in peach genome and contain a conserved AS domain and a characteristic HLH domain. The transcript levels of three PpIBH1s positively correlated with internode length, which gradually increased from apex to base along the peach shoots. This positive correlation was further confirmed in apple and poplar shoots. And the PpIBH1s gene were highly expressed in the shoot tips collected from twelve dwarf peach cultivars (gid1c mutants). In tissue-specific expression analysis, PpIBH1-1 are more highly expressed in tissues at the growth-arrested stage than cell-elongating. Transgenic Arabidopsis lines showed that different plant heights depending on the dose of PpIBH1-1 transcripts. And the dwarfing PpIBH1-1 transgenic lines were caused by the shorted cell length. PpIBH1-1 interacted with two bHLH factors (PpACE2 and PpLP1). These results suggested that PpIBH1-1 probably prevents internode elongation of peach shoots in a dose-dependent manner. Our work provided a foundation for properly controlling the growth of annual peach branches.
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Affiliation(s)
- Mengmeng Zhang
- College of Horticulture, Henan Agricultural University, 95 Wenhua Road, Zhengzhou 450002, China
| | - Beibei Feng
- College of Horticulture, Henan Agricultural University, 95 Wenhua Road, Zhengzhou 450002, China
| | - Yun Chen
- College of Horticulture, Henan Agricultural University, 95 Wenhua Road, Zhengzhou 450002, China
| | - Mingxi Geng
- College of Horticulture, Henan Agricultural University, 95 Wenhua Road, Zhengzhou 450002, China
| | - Ming Li
- College of Horticulture, Henan Agricultural University, 95 Wenhua Road, Zhengzhou 450002, China
| | - Xianbo Zheng
- College of Horticulture, Henan Agricultural University, 95 Wenhua Road, Zhengzhou 450002, China
| | - Haipeng Zhang
- College of Horticulture, Henan Agricultural University, 95 Wenhua Road, Zhengzhou 450002, China
| | - Langlang Zhang
- College of Horticulture, Henan Agricultural University, 95 Wenhua Road, Zhengzhou 450002, China
| | - Bin Tan
- College of Horticulture, Henan Agricultural University, 95 Wenhua Road, Zhengzhou 450002, China
| | - Xia Ye
- College of Horticulture, Henan Agricultural University, 95 Wenhua Road, Zhengzhou 450002, China
| | - Wei Wang
- College of Horticulture, Henan Agricultural University, 95 Wenhua Road, Zhengzhou 450002, China
| | - Jidong Li
- College of Horticulture, Henan Agricultural University, 95 Wenhua Road, Zhengzhou 450002, China
| | - Jun Cheng
- College of Horticulture, Henan Agricultural University, 95 Wenhua Road, Zhengzhou 450002, China.
| | - Jiancan Feng
- College of Horticulture, Henan Agricultural University, 95 Wenhua Road, Zhengzhou 450002, China.
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11
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Zhang L, Chen W, Liu R, Shi B, Shu Y, Zhang H. Genome-wide characterization and expression analysis of bHLH gene family in physic nut ( Jatropha curcas L.). PeerJ 2022; 10:e13786. [PMID: 35966923 PMCID: PMC9373979 DOI: 10.7717/peerj.13786] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2022] [Accepted: 07/05/2022] [Indexed: 01/17/2023] Open
Abstract
The basic helix loop helix (bHLH) transcription factor perform essential roles in plant development and abiotic stress. Here, a total of 122 bHLH family members were identified from the physic nut (Jatropha curcas L.) genomic database. Chromosomal localization results showed that 120 members were located on 11 chromosomes. The phylogenetic tree manifested that the JcbHLHs could be grouped into 28 subfamilies. Syntenic analysis showed that there were 10 bHLH collinear genes among the physic nut, Arabidopsis thaliana and Oryza sativa. These genes, except JcbHLH84, were highly expressed in various tissues of the physic nut, implying a key role in plant development. Gene expression profiles showed that ten genes (especially JcbHLH33, JcbHLH45 and JcbHLH55) correspond to both salinity and drought stresses; while eight genes only respond to salinity and another eight genes only respond to drought stress. Moreover, the protein interaction network revealed that the JcbHLHs are involved in growth, development and stress signal transduction pathways. These discoveries will help to excavate several key genes may involve in salt or drought stresses and seed development, elucidate the complex transcriptional regulation mechanism of JcbHLH genes and provide the theoretical basis for stress response and genetic improvement of physic nut.
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Affiliation(s)
- Lin Zhang
- School of Environmental Engineering and Chemistry, Luoyang Institute of Science and Technology, Luoyang, Henan, China
| | - Wei Chen
- School of Environmental Engineering and Chemistry, Luoyang Institute of Science and Technology, Luoyang, Henan, China
| | - Rongrong Liu
- School of Environmental Engineering and Chemistry, Luoyang Institute of Science and Technology, Luoyang, Henan, China
| | - Ben Shi
- School of Environmental Engineering and Chemistry, Luoyang Institute of Science and Technology, Luoyang, Henan, China
| | - Youju Shu
- School of Environmental Engineering and Chemistry, Luoyang Institute of Science and Technology, Luoyang, Henan, China
| | - Haoyu Zhang
- School of Environmental Engineering and Chemistry, Luoyang Institute of Science and Technology, Luoyang, Henan, China
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12
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Edwards HE, Gorelick DA. The evolution and structure/function of bHLH-PAS transcription factor family. Biochem Soc Trans 2022; 50:1227-1243. [PMID: 35695677 PMCID: PMC10584024 DOI: 10.1042/bst20211225] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2022] [Revised: 05/23/2022] [Accepted: 05/24/2022] [Indexed: 02/06/2023]
Abstract
Proteins that contain basic helix-loop-helix (bHLH) and Per-Arnt-Sim motifs (PAS) function as transcription factors. bHLH-PAS proteins exhibit essential and diverse functions throughout the body, from cell specification and differentiation in embryonic development to the proper function of organs like the brain and liver in adulthood. bHLH-PAS proteins are divided into two classes, which form heterodimers to regulate transcription. Class I bHLH-PAS proteins are typically activated in response to specific stimuli, while class II proteins are expressed more ubiquitously. Here, we discuss the general structure and functions of bHLH-PAS proteins throughout the animal kingdom, including family members that do not fit neatly into the class I-class II organization. We review heterodimerization between class I and class II bHLH-PAS proteins, binding partner selectivity and functional redundancy. Finally, we discuss the evolution of bHLH-PAS proteins, and why a class I protein essential for cardiovascular development in vertebrates like chicken and fish is absent from mammals.
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Affiliation(s)
- Hailey E Edwards
- Center for Precision Environmental Health, Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, Texas, U.S.A
| | - Daniel A Gorelick
- Center for Precision Environmental Health, Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, Texas, U.S.A
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13
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Leung RF, George AM, Roussel EM, Faux MC, Wigle JT, Eisenstat DD. Genetic Regulation of Vertebrate Forebrain Development by Homeobox Genes. Front Neurosci 2022; 16:843794. [PMID: 35546872 PMCID: PMC9081933 DOI: 10.3389/fnins.2022.843794] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2021] [Accepted: 03/14/2022] [Indexed: 01/19/2023] Open
Abstract
Forebrain development in vertebrates is regulated by transcription factors encoded by homeobox, bHLH and forkhead gene families throughout the progressive and overlapping stages of neural induction and patterning, regional specification and generation of neurons and glia from central nervous system (CNS) progenitor cells. Moreover, cell fate decisions, differentiation and migration of these committed CNS progenitors are controlled by the gene regulatory networks that are regulated by various homeodomain-containing transcription factors, including but not limited to those of the Pax (paired), Nkx, Otx (orthodenticle), Gsx/Gsh (genetic screened), and Dlx (distal-less) homeobox gene families. This comprehensive review outlines the integral role of key homeobox transcription factors and their target genes on forebrain development, focused primarily on the telencephalon. Furthermore, links of these transcription factors to human diseases, such as neurodevelopmental disorders and brain tumors are provided.
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Affiliation(s)
- Ryan F. Leung
- Murdoch Children’s Research Institute, The Royal Children’s Hospital Melbourne, Parkville, VIC, Australia
- Department of Paediatrics, University of Melbourne, Parkville, VIC, Australia
| | - Ankita M. George
- Murdoch Children’s Research Institute, The Royal Children’s Hospital Melbourne, Parkville, VIC, Australia
| | - Enola M. Roussel
- Murdoch Children’s Research Institute, The Royal Children’s Hospital Melbourne, Parkville, VIC, Australia
| | - Maree C. Faux
- Murdoch Children’s Research Institute, The Royal Children’s Hospital Melbourne, Parkville, VIC, Australia
- Department of Paediatrics, University of Melbourne, Parkville, VIC, Australia
- Department of Surgery, Royal Melbourne Hospital, The University of Melbourne, Parkville, VIC, Australia
| | - Jeffrey T. Wigle
- Department of Biochemistry and Medical Genetics, Max Rady College of Medicine, Rady Faculty of Health Sciences, University of Manitoba, Winnipeg, MB, Canada
- Institute of Cardiovascular Sciences, St. Boniface Hospital Albrechtsen Research Centre, Winnipeg, MB, Canada
| | - David D. Eisenstat
- Murdoch Children’s Research Institute, The Royal Children’s Hospital Melbourne, Parkville, VIC, Australia
- Department of Paediatrics, University of Melbourne, Parkville, VIC, Australia
- Department of Medical Genetics, University of Alberta, Edmonton, AB, Canada
- Department of Pediatrics, University of Alberta, Edmonton, AB, Canada
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14
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He Z, Wang Z, Nie X, Qu M, Zhao H, Ji X, Wang Y. UNFERTILIZED EMBRYO SAC 12 phosphorylation plays a crucial role in conferring salt tolerance. PLANT PHYSIOLOGY 2022; 188:1385-1401. [PMID: 34904673 PMCID: PMC8825338 DOI: 10.1093/plphys/kiab549] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/20/2021] [Accepted: 10/28/2021] [Indexed: 06/14/2023]
Abstract
Arabidopsis (Arabidopsis thaliana) UNFERTILIZED EMBRYO SAC 12 (AtUNE12) belongs to the basic helix-loop-helix DNA-binding superfamily of proteins. However, its function is not well known. Here, we found that AtUNE12 plays an important role in mediating salt tolerance. AtUNE12 is a transcriptional activator located in the nucleus whose expression is induced by NaCl, mannitol, and abscisic acid. In addition to binding to the G-box "CACGTG", AtUNE12 also binds to the low temperature responsive element 15 (LTRE15) "CCGAC". Furthermore, the serine residue at position 108 of AtUNE12 is phosphorylated during the salt stress response, enabling AtUNE12 to trigger gene expression by binding to G-box and/or LTRE15 motifs. Phosphorylated AtUNE12 regulates the expression of the genes involved in ion transport leading to reduced Na+ accumulation and K+ loss. At the same time, phosphorylation of AtUNE12 also induces the expression of AtMYB61 to decrease stomatal aperture, leading to a reduced transpiration rate. Overall, AtUNE12 serves as a transcriptional activator that is induced and phosphorylated upon salt stress, and the induction and phosphorylation of AtUNE12 in turn activate the salt-overly-sensitive pathway and decrease the stomatal aperture, enabling improved salt tolerance.
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Affiliation(s)
- Zihang He
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin 150040, China
| | - Zhibo Wang
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin 150040, China
| | - Xianguang Nie
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin 150040, China
| | - Ming Qu
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin 150040, China
| | - Huimin Zhao
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin 150040, China
| | - Xiaoyu Ji
- College of Forestry, Shenyang Agricultural University, Shenyang 110866, China
| | - Yucheng Wang
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin 150040, China
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15
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Homodimeric and Heterodimeric Interactions among Vertebrate Basic Helix-Loop-Helix Transcription Factors. Int J Mol Sci 2021; 22:ijms222312855. [PMID: 34884664 PMCID: PMC8657788 DOI: 10.3390/ijms222312855] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2021] [Revised: 11/11/2021] [Accepted: 11/17/2021] [Indexed: 01/01/2023] Open
Abstract
The basic helix–loop–helix transcription factor (bHLH TF) family is involved in tissue development, cell differentiation, and disease. These factors have transcriptionally positive, negative, and inactive functions by combining dimeric interactions among family members. The best known bHLH TFs are the E-protein homodimers and heterodimers with the tissue-specific TFs or ID proteins. These cooperative and dynamic interactions result in a complex transcriptional network that helps define the cell’s fate. Here, the reported dimeric interactions of 67 vertebrate bHLH TFs with other family members are summarized in tables, including specifications of the experimental techniques that defined the dimers. The compilation of these extensive data underscores homodimers of tissue-specific bHLH TFs as a central part of the bHLH regulatory network, with relevant positive and negative transcriptional regulatory roles. Furthermore, some sequence-specific TFs can also form transcriptionally inactive heterodimers with each other. The function, classification, and developmental role for all vertebrate bHLH TFs in four major classes are detailed.
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16
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Li J, Li X, Han P, Liu H, Gong J, Zhou W, Shi B, Liu A, Xu L. Genome-wide investigation of bHLH genes and expression analysis under different biotic and abiotic stresses in Helianthus annuus L. Int J Biol Macromol 2021; 189:72-83. [PMID: 34411617 DOI: 10.1016/j.ijbiomac.2021.08.072] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2021] [Revised: 08/05/2021] [Accepted: 08/09/2021] [Indexed: 10/20/2022]
Abstract
The basic helix-loop-helix (bHLH) transcription factors play important roles in many processes such as plant growth, metabolism and response to biotic/abiotic stresses. Sunflower (Helianthus annuus) is a major oil crop, cultivated throughout the world. However, no systematic characterization of bHLH gene members in sunflower (HabHLH) and their functions involved in drought, cadmium tolerance and Orobanche cumana resistance has been reported yet. In this study, 183 HabHLH genes were identified and named according to their chromosomal locations. We classified these proteins into 21 subfamilies by phylogenetic tree analysis. Subsequently, DNA-binding patterns, sequence analysis, duplication analysis and gene structures were analyzed. All of the HabHLH genes were randomly distributed on 17 chromosomes, and 10 pairs of tandem duplicated genes and one pair of segmental duplicated genes were detected in the HabHLH family. Among the duplicated gene pairs, eight pairs of HabHLH genes suffer from positive selection. Moreover, qRT-PCR results revealed significant up-regulated expression of HabHLH024 gene in response to both abiotic (cadmium, drought) and biotic (Orobanche cumana) stresses, suggesting its important functions in response to different stresses. Therefore, HabHLH024 would be the potential candidate gene for the sunflower tolerance breeding.
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Affiliation(s)
- Juanjuan Li
- Zhejiang Province Key Laboratory of Plant Secondary Metabolism and Regulation, College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou 310018, China; Institute of Crop Science, Ministry of Agriculture and Rural Affairs Laboratory of Spectroscopy Sensing, Zhejiang University, Hangzhou 310058, China
| | - Xin Li
- Zhejiang Province Key Laboratory of Plant Secondary Metabolism and Regulation, College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou 310018, China
| | - Peng Han
- Department of Life Sciences, Changzhi University, Changzhi 046011, China
| | - Hui Liu
- UWA School of Agriculture and Environment and The UWA Institute of Agriculture, Faculty of Science, The University of Western Australia, WA 6009, Australia
| | - Jianchuan Gong
- Department of Life Sciences, Changzhi University, Changzhi 046011, China
| | - Weijun Zhou
- Institute of Crop Science, Ministry of Agriculture and Rural Affairs Laboratory of Spectroscopy Sensing, Zhejiang University, Hangzhou 310058, China
| | - Bixian Shi
- Institute of Economic Crops, Xinjiang Academy of Agricultural Sciences, Urumqi 830091, China
| | - Ake Liu
- Department of Life Sciences, Changzhi University, Changzhi 046011, China.
| | - Ling Xu
- Zhejiang Province Key Laboratory of Plant Secondary Metabolism and Regulation, College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou 310018, China.
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17
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Fan Y, Lai D, Yang H, Xue G, He A, Chen L, Feng L, Ruan J, Xiang D, Yan J, Cheng J. Genome-wide identification and expression analysis of the bHLH transcription factor family and its response to abiotic stress in foxtail millet (Setaria italica L.). BMC Genomics 2021; 22:778. [PMID: 34717536 PMCID: PMC8557513 DOI: 10.1186/s12864-021-08095-y] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2021] [Accepted: 10/18/2021] [Indexed: 12/04/2022] Open
Abstract
Background Members of the basic helix-loop-helix (bHLH) transcription factor family perform indispensable functions in various biological processes, such as plant growth, seed maturation, and abiotic stress responses. However, the bHLH family in foxtail millet (Setaria italica), an important food and feed crop, has not been thoroughly studied. Results In this study, 187 bHLH genes of foxtail millet (SibHLHs) were identified and renamed according to the chromosomal distribution of the SibHLH genes. Based on the number of conserved domains and gene structure, the SibHLH genes were divided into 21 subfamilies and two orphan genes via phylogenetic tree analysis. According to the phylogenetic tree, the subfamilies 15 and 18 may have experienced stronger expansion in the process of evolution. Then, the motif compositions, gene structures, chromosomal spread, and gene duplication events were discussed in detail. A total of sixteen tandem repeat events and thirty-eight pairs of segment duplications were identified in bHLH family of foxtail millet. To further investigate the evolutionary relationship in the SibHLH family, we constructed the comparative syntenic maps of foxtail millet associated with representative monocotyledons and dicotyledons species. Finally, the gene expression response characteristics of 15 typical SibHLH genes in different tissues and fruit development stages, and eight different abiotic stresses were analysed. The results showed that there were significant differences in the transcription levels of some SibHLH members in different tissues and fruit development stages, and different abiotic stresses, implying that SibHLH members might have different physiological functions. Conclusions In this study, we identified 187 SibHLH genes in foxtail millet and further analysed the evolution and expression patterns of the encoded proteins. The findings provide a comprehensive understanding of the bHLH family in foxtail millet, which will inform further studies on the functional characteristics of SibHLH genes. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-021-08095-y.
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Affiliation(s)
- Yu Fan
- College of Agriculture, Guizhou University, Huaxi District, Guiyang, Guizhou Province, 550025, People's Republic of China.,School of Food and Biological engineering, Chengdu University, Chengdu, 610106, People's Republic of China
| | - Dili Lai
- College of Agriculture, Guizhou University, Huaxi District, Guiyang, Guizhou Province, 550025, People's Republic of China
| | - Hao Yang
- College of Agriculture, Guizhou University, Huaxi District, Guiyang, Guizhou Province, 550025, People's Republic of China
| | - Guoxing Xue
- College of Agriculture, Guizhou University, Huaxi District, Guiyang, Guizhou Province, 550025, People's Republic of China
| | - Ailing He
- College of Agriculture, Guizhou University, Huaxi District, Guiyang, Guizhou Province, 550025, People's Republic of China
| | - Long Chen
- Department of Nursing, Sichuan Tianyi College, Mianzhu, 618200, People's Republic of China
| | - Liang Feng
- Chengdu Institute of Food Inspection, Chengdu, 610030, People's Republic of China
| | - Jingjun Ruan
- College of Agriculture, Guizhou University, Huaxi District, Guiyang, Guizhou Province, 550025, People's Republic of China
| | - Dabing Xiang
- School of Food and Biological engineering, Chengdu University, Chengdu, 610106, People's Republic of China
| | - Jun Yan
- School of Food and Biological engineering, Chengdu University, Chengdu, 610106, People's Republic of China.
| | - Jianping Cheng
- College of Agriculture, Guizhou University, Huaxi District, Guiyang, Guizhou Province, 550025, People's Republic of China.
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18
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Mechanisms of Binding Specificity among bHLH Transcription Factors. Int J Mol Sci 2021; 22:ijms22179150. [PMID: 34502060 PMCID: PMC8431614 DOI: 10.3390/ijms22179150] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2021] [Revised: 08/14/2021] [Accepted: 08/18/2021] [Indexed: 12/25/2022] Open
Abstract
The transcriptome of every cell is orchestrated by the complex network of interaction between transcription factors (TFs) and their binding sites on DNA. Disruption of this network can result in many forms of organism malfunction but also can be the substrate of positive natural selection. However, understanding the specific determinants of each of these individual TF-DNA interactions is a challenging task as it requires integrating the multiple possible mechanisms by which a given TF ends up interacting with a specific genomic region. These mechanisms include DNA motif preferences, which can be determined by nucleotide sequence but also by DNA’s shape; post-translational modifications of the TF, such as phosphorylation; and dimerization partners and co-factors, which can mediate multiple forms of direct or indirect cooperative binding. Binding can also be affected by epigenetic modifications of putative target regions, including DNA methylation and nucleosome occupancy. In this review, we describe how all these mechanisms have a role and crosstalk in one specific family of TFs, the basic helix-loop-helix (bHLH), with a very conserved DNA binding domain and a similar DNA preferred motif, the E-box. Here, we compile and discuss a rich catalog of strategies used by bHLH to acquire TF-specific genome-wide landscapes of binding sites.
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19
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Liang JJ, Peng H, Wang JJ, Liu XH, Ma L, Ni YR, Yang HJ, Zhang YQ, Ai WB, Wu JF. Relationship between the structure and function of the transcriptional regulator E2A. ACTA ACUST UNITED AC 2021; 28:15. [PMID: 34271975 PMCID: PMC8283981 DOI: 10.1186/s40709-021-00146-5] [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: 01/07/2021] [Accepted: 06/30/2021] [Indexed: 11/10/2022]
Abstract
E proteins are transcriptional regulators that regulate many developmental processes in animals and lymphocytosis and leukemia in Homo sapiens. In particular, E2A, a member of the E protein family, plays a major role in the transcriptional regulatory network that promotes the differentiation and development of B and T lymphocytes. E2A-mediated transcriptional regulation usually requires the formation of E2A dimers, which then bind to coregulators. In this review, we summarize the mechanisms by which E2A participates in transcriptional regulation from a structural perspective. More specifically, the C-terminal helix-loop-helix (HLH) region of the basic HLH (bHLH) domain first dimerizes, and then the activation domains of E2A bind to different coactivators or corepressors in different cell contexts, resulting in histone acetylation or deacetylation, respectively. Then, the N-terminal basic region (b) of the bHLH domain binds to or dissociates from a specific DNA motif (E-box sequence). Last, trans-activation or trans-repression occurs. We also summarize the properties of these E2A domains and their interactions with the domains of other proteins. The feasibility of developing drugs based on these domains is discussed.
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Affiliation(s)
- Jia-Jie Liang
- Medical College, China Three Gorges University, 8 Daxue Road, Xiling District, Yichang, 443002, China.,Institute of Organ Fibrosis and Targeted Drug Delivery, China Three Gorges University, 8 Daxue Road, Xiling District, Yichang, 443002, China.,Hubei Key Laboratory of Tumor Microenvironment and Immunotherapy, China Three Gorges University, 8 Daxue Road, Xiling District, Yichang, 443002, China
| | - Hu Peng
- Institute of Organ Fibrosis and Targeted Drug Delivery, China Three Gorges University, 8 Daxue Road, Xiling District, Yichang, 443002, China.,The Yiling Hospital of Yichang, 32 Donghu Road, Yi Ling District, Yichang, 443100, Hubei, China
| | - Jiao-Jiao Wang
- Medical College, China Three Gorges University, 8 Daxue Road, Xiling District, Yichang, 443002, China
| | - Xiao-Hui Liu
- Medical College, China Three Gorges University, 8 Daxue Road, Xiling District, Yichang, 443002, China
| | - Lan Ma
- Medical College, China Three Gorges University, 8 Daxue Road, Xiling District, Yichang, 443002, China.,Institute of Organ Fibrosis and Targeted Drug Delivery, China Three Gorges University, 8 Daxue Road, Xiling District, Yichang, 443002, China.,Hubei Key Laboratory of Tumor Microenvironment and Immunotherapy, China Three Gorges University, 8 Daxue Road, Xiling District, Yichang, 443002, China
| | - Yi-Ran Ni
- Medical College, China Three Gorges University, 8 Daxue Road, Xiling District, Yichang, 443002, China.,Institute of Organ Fibrosis and Targeted Drug Delivery, China Three Gorges University, 8 Daxue Road, Xiling District, Yichang, 443002, China.,Hubei Key Laboratory of Tumor Microenvironment and Immunotherapy, China Three Gorges University, 8 Daxue Road, Xiling District, Yichang, 443002, China
| | - Huai-Jie Yang
- The People's Hospital of China Three Gorges University, 31 Huti Subdistrict, Xi Ling District, Yichang, 443000, Hubei, China
| | - Yan-Qiong Zhang
- Medical College, China Three Gorges University, 8 Daxue Road, Xiling District, Yichang, 443002, China.,Institute of Organ Fibrosis and Targeted Drug Delivery, China Three Gorges University, 8 Daxue Road, Xiling District, Yichang, 443002, China.,Hubei Key Laboratory of Tumor Microenvironment and Immunotherapy, China Three Gorges University, 8 Daxue Road, Xiling District, Yichang, 443002, China
| | - Wen-Bing Ai
- The Yiling Hospital of Yichang, 32 Donghu Road, Yi Ling District, Yichang, 443100, Hubei, China.
| | - Jiang-Feng Wu
- Medical College, China Three Gorges University, 8 Daxue Road, Xiling District, Yichang, 443002, China. .,Institute of Organ Fibrosis and Targeted Drug Delivery, China Three Gorges University, 8 Daxue Road, Xiling District, Yichang, 443002, China. .,Hubei Key Laboratory of Tumor Microenvironment and Immunotherapy, China Three Gorges University, 8 Daxue Road, Xiling District, Yichang, 443002, China. .,The People's Hospital of China Three Gorges University, 31 Huti Subdistrict, Xi Ling District, Yichang, 443000, Hubei, China. .,The Yiling Hospital of Yichang, 32 Donghu Road, Yi Ling District, Yichang, 443100, Hubei, China.
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20
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Kaufman ML, Goodson NB, Park KU, Schwanke M, Office E, Schneider SR, Abraham J, Hensley A, Jones KL, Brzezinski JA. Initiation of Otx2 expression in the developing mouse retina requires a unique enhancer and either Ascl1 or Neurog2 activity. Development 2021; 148:dev199399. [PMID: 34143204 PMCID: PMC8254865 DOI: 10.1242/dev.199399] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2021] [Accepted: 05/10/2021] [Indexed: 11/20/2022]
Abstract
During retinal development, a large subset of progenitors upregulates the transcription factor Otx2, which is required for photoreceptor and bipolar cell formation. How these retinal progenitor cells initially activate Otx2 expression is unclear. To address this, we investigated the cis-regulatory network that controls Otx2 expression in mice. We identified a minimal enhancer element, DHS-4D, that drove expression in newly formed OTX2+ cells. CRISPR/Cas9-mediated deletion of DHS-4D reduced OTX2 expression, but this effect was diminished in postnatal development. Systematic mutagenesis of the enhancer revealed that three basic helix-loop-helix (bHLH) transcription factor-binding sites were required for its activity. Single cell RNA-sequencing of nascent Otx2+ cells identified the bHLH factors Ascl1 and Neurog2 as candidate regulators. CRISPR/Cas9 targeting of these factors showed that only the simultaneous loss of Ascl1 and Neurog2 prevented OTX2 expression. Our findings suggest that Ascl1 and Neurog2 act either redundantly or in a compensatory fashion to activate the DHS-4D enhancer and Otx2 expression. We observed redundancy or compensation at both the transcriptional and enhancer utilization levels, suggesting that the mechanisms governing Otx2 regulation in the retina are flexible and robust.
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Affiliation(s)
- Michael L. Kaufman
- Department of Ophthalmology, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Noah B. Goodson
- Department of Ophthalmology, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Ko Uoon Park
- Department of Ophthalmology, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Michael Schwanke
- Department of Ophthalmology, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Emma Office
- Department of Ophthalmology, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Sophia R. Schneider
- Department of Ophthalmology, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Joy Abraham
- Department of Ophthalmology, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Austin Hensley
- Department of Ophthalmology, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Kenneth L. Jones
- Department of Cell Biology, University of Oklahoma Health Sciences Center, Oklahoma City, OK 73104, USA
| | - Joseph A. Brzezinski
- Department of Ophthalmology, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
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21
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Tutukova S, Tarabykin V, Hernandez-Miranda LR. The Role of Neurod Genes in Brain Development, Function, and Disease. Front Mol Neurosci 2021; 14:662774. [PMID: 34177462 PMCID: PMC8221396 DOI: 10.3389/fnmol.2021.662774] [Citation(s) in RCA: 49] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2021] [Accepted: 05/11/2021] [Indexed: 01/14/2023] Open
Abstract
Transcriptional regulation is essential for the correct functioning of cells during development and in postnatal life. The basic Helix-loop-Helix (bHLH) superfamily of transcription factors is well conserved throughout evolution and plays critical roles in tissue development and tissue maintenance. A subgroup of this family, called neural lineage bHLH factors, is critical in the development and function of the central nervous system. In this review, we will focus on the function of one subgroup of neural lineage bHLH factors, the Neurod family. The Neurod family has four members: Neurod1, Neurod2, Neurod4, and Neurod6. Available evidence shows that these four factors are key during the development of the cerebral cortex but also in other regions of the central nervous system, such as the cerebellum, the brainstem, and the spinal cord. We will also discuss recent reports that link the dysfunction of these transcription factors to neurological disorders in humans.
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Affiliation(s)
- Svetlana Tutukova
- Institute of Neuroscience, Lobachevsky University of Nizhny Novgorod, Nizhny Novgorod, Russia.,Charité Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Institute for Cell- and Neurobiology, Berlin, Germany
| | - Victor Tarabykin
- Institute of Neuroscience, Lobachevsky University of Nizhny Novgorod, Nizhny Novgorod, Russia.,Charité Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Institute for Cell- and Neurobiology, Berlin, Germany
| | - Luis R Hernandez-Miranda
- Charité Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Institute for Cell- and Neurobiology, Berlin, Germany
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22
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Inamoto I, Sheoran I, Popa SC, Hussain M, Shin JA. Combining Rational Design and Continuous Evolution on Minimalist Proteins That Target the E-box DNA Site. ACS Chem Biol 2021; 16:35-44. [PMID: 33370105 DOI: 10.1021/acschembio.0c00684] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Protein-based therapeutics are part of the next-generation arsenal of drugs being developed against proto-oncoprotein Myc. We designed protein MEF to mimic the basic region/helix-loop-helix/leucine zipper (bHLHZ) domain of Max and Myc, which bind to the E-box motif (enhancer box, CACGTG). To make MEF, we started with our rationally designed ME47, a hybrid of the Max basic region and E47 HLH, that effectively inhibited tumor growth in a mouse model of breast cancer. We used phage-assisted continuous evolution (PACE), which uncovered mutations at Arg12 that contact the DNA phosphodiester backbone. The Arg12 mutations improved ME47's stability. We replaced Cys29 with Ala to eliminate potential undesired disulfide formation and fused the designed FosW leucine zipper to mutated ME47 to increase the dimerization interface and E-box targeting activity. This "franken-protein" MEF comprises the Max basic region, E47 HLH, and FosW leucine zipper. Compared with ME47, MEF gives 2-fold stronger binding to E-box and 4-fold increased specificity for E-box over nonspecific DNA. The synergistic combination of rational design and PACE allowed us to make MEF and demonstrates the power and utility of our two-pronged approach toward development of promising protein drugs with robust structure and DNA-binding function.
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Affiliation(s)
- Ichiro Inamoto
- Department of Chemistry, University of Toronto, 3359 Mississauga Road, Mississauga, ON L5L 1C6, Canada
| | - Inder Sheoran
- Department of Chemistry, University of Toronto, 3359 Mississauga Road, Mississauga, ON L5L 1C6, Canada
| | - Serban C. Popa
- Department of Chemistry, University of Toronto, 3359 Mississauga Road, Mississauga, ON L5L 1C6, Canada
| | - Montdher Hussain
- Department of Chemistry, University of Toronto, 3359 Mississauga Road, Mississauga, ON L5L 1C6, Canada
| | - Jumi A. Shin
- Department of Chemistry, University of Toronto, 3359 Mississauga Road, Mississauga, ON L5L 1C6, Canada
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23
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Desimio MG, Cesari E, Sorrenti M, De Felici M, Farini D. Stimulated by retinoic acid gene 8 (STRA8) interacts with the germ cell specific bHLH factor SOHLH1 and represses c-KIT expression in vitro. J Cell Mol Med 2020; 25:383-396. [PMID: 33236849 PMCID: PMC7810945 DOI: 10.1111/jcmm.16087] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2020] [Revised: 10/22/2020] [Accepted: 10/25/2020] [Indexed: 12/25/2022] Open
Abstract
STRA8 (Stimulated by Retinoic Acid Gene 8) controls the crucial decision of germ cells to engage meiotic division up and down‐regulating genes involved in the meiotic programme. It has been proven as an amplifier of genes involved in cell cycle control and chromosome events, however, how STRA8 functions as negative regulator are not well understood. In this study, we demonstrate that STRA8 can interact with itself and with other basic Helix‐Loop‐Helix (bHLH) transcription factors through its HLH domain and that this domain is important for its ability to negatively interfere with the Ebox‐mediated transcriptional activity of bHLH transcription factors. Significantly, we show that STRA8 interacts with TCF3/E47, a class I bHLH transcription factors, and with SOHLH1, a gonadal‐specific bHLH, in male germ cells obtained from prepuberal mouse testis. We demonstrated that STRA8, indirectly, is able to exert a negative control on the SOHLH1‐dependent stimulation of c‐KIT expression in late differentiating spermatogonia and preleptotene spermatocytes. Although part of this results were obtained only ‘in vitro’, they support the notion that STRA8 interacting with different transcription factors, besides its established role as ‘amplifier’ of meiotic programme, is able to finely modulate the balance between spermatogonia proliferation, differentiation and acquisition of meiotic competence.
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Affiliation(s)
- Maria Giovanna Desimio
- Department of Biomedicine and Prevention, Section of Histology and Embryology, University Tor Vergata, Rome, Italy
| | - Eleonora Cesari
- Department of Neuroscience, Section of Human Anatomy, Catholic University of the Sacred Heart, Rome, Italy
| | - Maria Sorrenti
- Department of Biomedicine and Prevention, Section of Histology and Embryology, University Tor Vergata, Rome, Italy
| | - Massimo De Felici
- Department of Biomedicine and Prevention, Section of Histology and Embryology, University Tor Vergata, Rome, Italy
| | - Donatella Farini
- Department of Biomedicine and Prevention, Section of Histology and Embryology, University Tor Vergata, Rome, Italy
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24
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Analyses of functional conservation and divergence reveal requirement of bHLH010/089/091 for pollen development at elevated temperature in Arabidopsis. J Genet Genomics 2020; 47:477-492. [DOI: 10.1016/j.jgg.2020.09.001] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2020] [Revised: 09/01/2020] [Accepted: 09/02/2020] [Indexed: 01/03/2023]
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25
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Fautsch MP, Wieben ED, Baratz KH, Bhattacharyya N, Sadan AN, Hafford-Tear NJ, Tuft SJ, Davidson AE. TCF4-mediated Fuchs endothelial corneal dystrophy: Insights into a common trinucleotide repeat-associated disease. Prog Retin Eye Res 2020; 81:100883. [PMID: 32735996 PMCID: PMC7988464 DOI: 10.1016/j.preteyeres.2020.100883] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2020] [Revised: 06/24/2020] [Accepted: 07/04/2020] [Indexed: 12/13/2022]
Abstract
Fuchs endothelial corneal dystrophy (FECD) is a common cause for heritable visual loss in the elderly. Since the first description of an association between FECD and common polymorphisms situated within the transcription factor 4 (TCF4) gene, genetic and molecular studies have implicated an intronic CTG trinucleotide repeat (CTG18.1) expansion as a causal variant in the majority of FECD patients. To date, several non-mutually exclusive mechanisms have been proposed that drive and/or exacerbate the onset of disease. These mechanisms include (i) TCF4 dysregulation; (ii) toxic gain-of-function from TCF4 repeat-containing RNA; (iii) toxic gain-of-function from repeat-associated non-AUG dependent (RAN) translation; and (iv) somatic instability of CTG18.1. However, the relative contribution of these proposed mechanisms in disease pathogenesis is currently unknown. In this review, we summarise research implicating the repeat expansion in disease pathogenesis, define the phenotype-genotype correlations between FECD and CTG18.1 expansion, and provide an update on research tools that are available to study FECD as a trinucleotide repeat expansion disease. Furthermore, ongoing international research efforts to develop novel CTG18.1 expansion-mediated FECD therapeutics are highlighted and we provide a forward-thinking perspective on key unanswered questions that remain in the field. FECD is a common, age-related corneal dystrophy. The majority of cases are associated with expansion of a CTG repeat (CTG18.1). FECD is the most common trinucleotide repeat expansion disease in humans. Evidence supports multiple molecular mechanisms underlying the pathophysiology. Novel CTG18.1-targeted therapeutics are in development.
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Affiliation(s)
- Michael P Fautsch
- Department of Ophthalmology, 200 1st St SW, Mayo Clinic, Rochester, MN, 55905, USA.
| | - Eric D Wieben
- Department of Biochemistry and Molecular Biology, 200 1st St SW, Mayo Clinic, Rochester, MN, USA.
| | - Keith H Baratz
- Department of Ophthalmology, 200 1st St SW, Mayo Clinic, Rochester, MN, 55905, USA.
| | | | - Amanda N Sadan
- University College London Institute of Ophthalmology, London, ECIV 9EL, UK.
| | | | - Stephen J Tuft
- University College London Institute of Ophthalmology, London, ECIV 9EL, UK; Moorfields Eye Hospital, London, EC1V 2PD, UK.
| | - Alice E Davidson
- University College London Institute of Ophthalmology, London, ECIV 9EL, UK.
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26
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Yamazaki T, Liu L, Conlon EG, Manley JL. Burkitt lymphoma-related TCF3 mutations alter TCF3 alternative splicing by disrupting hnRNPH1 binding. RNA Biol 2020; 17:1383-1390. [PMID: 32449435 DOI: 10.1080/15476286.2020.1772559] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Burkitt lymphoma (BL) is an aggressive B-cell lymphoma characterized by translocation and deregulation of the proto-oncogene c-MYC. Transcription factor 3 (TCF3) has also been shown to be involved in BL pathogenesis. In BL, TCF3 is constitutively active, and/or expression of its transcriptional targets are altered as a result of BL-associated mutations. Here, we found that BL-related TCF3 mutations affect TCF3 alternative splicing, in part by reducing binding of the splicing regulator hnRNPH1 to exon 18b. This leads to greater exon 18b inclusion, thereby generating more of the mutated E47 isoform of TCF3. Interestingly, upregulation of E47 dysregulates the expression of TCF3 targets PTPN6, and perhaps CCND3, which are known to be involved in BL pathogenesis. Our findings thus reveal a mechanism by which TCF3 somatic mutations affect multilayered gene regulation underlying BL pathogenesis.
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Affiliation(s)
- Takashi Yamazaki
- Department of Biological Sciences, Columbia University , New York, NY, USA.,Neuroscience Drug Discovery Unit, Takeda Pharmaceutical Co. Ltd ., Fujisawa, Japan
| | - Lizhi Liu
- Department of Biological Sciences, Columbia University , New York, NY, USA
| | - Erin G Conlon
- Department of Biological Sciences, Columbia University , New York, NY, USA.,Laboratory of Molecular Neuro-oncology, Rockefeller University , New York, NY, USA
| | - James L Manley
- Department of Biological Sciences, Columbia University , New York, NY, USA
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27
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Olig2 SUMOylation protects against genotoxic damage response by antagonizing p53 gene targeting. Cell Death Differ 2020; 27:3146-3161. [PMID: 32483381 PMCID: PMC7560653 DOI: 10.1038/s41418-020-0569-1] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2019] [Revised: 05/19/2020] [Accepted: 05/20/2020] [Indexed: 01/05/2023] Open
Abstract
Posttranslational modifications of nuclear proteins, including transcription factors, nuclear receptors, and their coregulators, have attracted much attention in cancer research. Although phosphorylation of oligodendrocyte transcription factor 2 (Olig2) may contribute to the notorious resistance of gliomas to radiation and genotoxic drugs, the precise mechanisms remain elusive. We show here that in addition to phosphorylation, Olig2 is also conjugated by small ubiquitin-like modifier-1 (SUMO1) at three lysine residues K27, K76, and K112. SUMOylation is required for Olig2 to suppress p53-mediated cell cycle arrest and apoptosis induced by genotoxic damage, and to enhance resistance to temozolomide (TMZ) in glioma. Both SUMOylation and triple serine motif (TSM) phosphorylation of Olig2 are required for the antiapoptotic function. Olig2 SUMOylation enhances its genetic targeting ability, which in turn occludes p53 recruitment to Cdkn1a promoter for DNA-damage responses. Our work uncovers a SUMOylation-dependent regulatory mechanism of Olig2 in regulating cancer survival.
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28
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Xia Y, Li Z, Wang J, Li Y, Ren Y, Du J, Song Q, Ma S, Song Y, Zhao H, Yang Z, Zhang G, Niu N. Isolation and Identification of a TaTDR-Like Wheat Gene Encoding a bHLH Domain Protein, Which Negatively Regulates Chlorophyll Biosynthesis in Arabidopsis. Int J Mol Sci 2020; 21:ijms21020629. [PMID: 31963591 PMCID: PMC7014150 DOI: 10.3390/ijms21020629] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2019] [Revised: 01/12/2020] [Accepted: 01/15/2020] [Indexed: 11/26/2022] Open
Abstract
Chlorophyll biosynthesis plays a vital role in chloroplast development and photosynthesis in plants. In this study, we identified an orthologue of the rice gene TDR (Oryza sativa L., Tapetum Degeneration Retardation) in wheat (Triticum aestivum L.) called TaTDR-Like (TaTDRL) by sequence comparison. TaTDRL encodes a putative 557 amino acid protein with a basic helix-loop-helix (bHLH) conserved domain at the C-terminal (295–344 aa). The TaTDRL protein localised to the nucleus and displayed transcriptional activation activity in a yeast hybrid system. TaTDRL was expressed in the leaf tissue and expression was induced by dark treatment. Here, we revealed the potential function of TaTDRL gene in wheat by utilizing transgenic Arabidopsis plants TaTDRL overexpressing (TaTDRL-OE) and TaTDRL-EAR (EAR-motif, a repression domain of only 12 amino acids). Compared with wild-type plants (WT), both TaTDRL-OE and TaTDRL-EAR were characterized by a deficiency of chlorophyll. Moreover, the expression level of the chlorophyll-related gene AtPORC (NADPH:protochlorophyllide oxidoreductase C) in TaTDRL-OE and TaTDRL-EAR was lower than that of WT. We found that TaTDRL physically interacts with wheat Phytochrome Interacting Factor 1 (PIF1) and Arabadopsis PIF1, suggesting that TaTDRL regulates light signaling during dark or light treatment. In summary, TaTDRL may respond to dark or light treatment and negatively regulate chlorophyll biosynthesis by interacting with AtPIF1 in transgenic Arabidopsis.
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Affiliation(s)
- Yu Xia
- Key Laboratory of Crop Heterosis of Shaanxi Province, Wheat Breeding Engineering Research Center, Ministry of Education, College of Agronomy, Northwest A & F University, Yangling 712100, Shaanxi, China; (Y.X.); (Z.L.); (J.W.); (Y.L.); (Y.R.); (J.D.); (Q.S.); (S.M.); (Y.S.); (Z.Y.)
| | - Zheng Li
- Key Laboratory of Crop Heterosis of Shaanxi Province, Wheat Breeding Engineering Research Center, Ministry of Education, College of Agronomy, Northwest A & F University, Yangling 712100, Shaanxi, China; (Y.X.); (Z.L.); (J.W.); (Y.L.); (Y.R.); (J.D.); (Q.S.); (S.M.); (Y.S.); (Z.Y.)
| | - Junwei Wang
- Key Laboratory of Crop Heterosis of Shaanxi Province, Wheat Breeding Engineering Research Center, Ministry of Education, College of Agronomy, Northwest A & F University, Yangling 712100, Shaanxi, China; (Y.X.); (Z.L.); (J.W.); (Y.L.); (Y.R.); (J.D.); (Q.S.); (S.M.); (Y.S.); (Z.Y.)
| | - Yanhong Li
- Key Laboratory of Crop Heterosis of Shaanxi Province, Wheat Breeding Engineering Research Center, Ministry of Education, College of Agronomy, Northwest A & F University, Yangling 712100, Shaanxi, China; (Y.X.); (Z.L.); (J.W.); (Y.L.); (Y.R.); (J.D.); (Q.S.); (S.M.); (Y.S.); (Z.Y.)
| | - Yang Ren
- Key Laboratory of Crop Heterosis of Shaanxi Province, Wheat Breeding Engineering Research Center, Ministry of Education, College of Agronomy, Northwest A & F University, Yangling 712100, Shaanxi, China; (Y.X.); (Z.L.); (J.W.); (Y.L.); (Y.R.); (J.D.); (Q.S.); (S.M.); (Y.S.); (Z.Y.)
| | - Jingjing Du
- Key Laboratory of Crop Heterosis of Shaanxi Province, Wheat Breeding Engineering Research Center, Ministry of Education, College of Agronomy, Northwest A & F University, Yangling 712100, Shaanxi, China; (Y.X.); (Z.L.); (J.W.); (Y.L.); (Y.R.); (J.D.); (Q.S.); (S.M.); (Y.S.); (Z.Y.)
| | - Qilu Song
- Key Laboratory of Crop Heterosis of Shaanxi Province, Wheat Breeding Engineering Research Center, Ministry of Education, College of Agronomy, Northwest A & F University, Yangling 712100, Shaanxi, China; (Y.X.); (Z.L.); (J.W.); (Y.L.); (Y.R.); (J.D.); (Q.S.); (S.M.); (Y.S.); (Z.Y.)
| | - Shoucai Ma
- Key Laboratory of Crop Heterosis of Shaanxi Province, Wheat Breeding Engineering Research Center, Ministry of Education, College of Agronomy, Northwest A & F University, Yangling 712100, Shaanxi, China; (Y.X.); (Z.L.); (J.W.); (Y.L.); (Y.R.); (J.D.); (Q.S.); (S.M.); (Y.S.); (Z.Y.)
| | - Yulong Song
- Key Laboratory of Crop Heterosis of Shaanxi Province, Wheat Breeding Engineering Research Center, Ministry of Education, College of Agronomy, Northwest A & F University, Yangling 712100, Shaanxi, China; (Y.X.); (Z.L.); (J.W.); (Y.L.); (Y.R.); (J.D.); (Q.S.); (S.M.); (Y.S.); (Z.Y.)
| | - Huiyan Zhao
- College of Plant Protection, Northwest A & F University, Yangling 712100, Shaanxi, China;
| | - Zhiquan Yang
- Key Laboratory of Crop Heterosis of Shaanxi Province, Wheat Breeding Engineering Research Center, Ministry of Education, College of Agronomy, Northwest A & F University, Yangling 712100, Shaanxi, China; (Y.X.); (Z.L.); (J.W.); (Y.L.); (Y.R.); (J.D.); (Q.S.); (S.M.); (Y.S.); (Z.Y.)
| | - Gaisheng Zhang
- Key Laboratory of Crop Heterosis of Shaanxi Province, Wheat Breeding Engineering Research Center, Ministry of Education, College of Agronomy, Northwest A & F University, Yangling 712100, Shaanxi, China; (Y.X.); (Z.L.); (J.W.); (Y.L.); (Y.R.); (J.D.); (Q.S.); (S.M.); (Y.S.); (Z.Y.)
- Correspondence: (G.Z.); (N.N.)
| | - Na Niu
- Key Laboratory of Crop Heterosis of Shaanxi Province, Wheat Breeding Engineering Research Center, Ministry of Education, College of Agronomy, Northwest A & F University, Yangling 712100, Shaanxi, China; (Y.X.); (Z.L.); (J.W.); (Y.L.); (Y.R.); (J.D.); (Q.S.); (S.M.); (Y.S.); (Z.Y.)
- Correspondence: (G.Z.); (N.N.)
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29
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Kiss Z, Mudryj M, Ghosh PM. Non-circadian aspects of BHLHE40 cellular function in cancer. Genes Cancer 2020; 11:1-19. [PMID: 32577154 PMCID: PMC7289903 DOI: 10.18632/genesandcancer.201] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2019] [Accepted: 02/27/2020] [Indexed: 02/06/2023] Open
Abstract
While many genes specifically act as oncogenes or tumor suppressors, others are tumor promoters or suppressors in a context-dependent manner. Here we will review the basic-helix-loop-helix (BHLH) protein BHLHE40, (also known as BHLHB2, STRA13, DEC1, or SHARP2) which is overexpressed in gastric, breast, and brain tumors; and downregulated in colorectal, esophageal, pancreatic and lung cancer. As a transcription factor, BHLHE40 is expressed in the nucleus, where it binds to target gene promoters containing the E-box hexanucleotide sequence, but can also be expressed in the cytoplasm, where it stabilizes cyclin E, preventing cyclin E-mediated DNA replication and cell cycle progression. In different organs BHLHE40 regulates different targets; hence may have different impacts on tumorigenesis. BHLHE40 promotes PI3K/Akt/mTOR activation in breast cancer, activating tumor progression, but suppresses STAT1 expression in clear cell carcinoma, triggering tumor suppression. Target specificity likely depends on cooperation with other transcription factors. BHLHE40 is activated in lung and esophageal carcinoma by the tumor suppressor p53 inducing senescence and suppressing tumor growth, but is also activated under hypoxic conditions by HIF-1α in gastric cancer and hepatocellular carcinomas, stimulating tumor progression. Thus, BHLHE40 is a multi-functional protein that mediates the promotion or suppression of cancer in a context dependent manner.
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Affiliation(s)
- Zsofia Kiss
- VA Northern California Health Care System, Sacramento, CA, USA
- Department of Urology, University of California Davis School of Medicine, Sacramento, CA, USA
| | - Maria Mudryj
- VA Northern California Health Care System, Sacramento, CA, USA
- Department of Microbiology and Immunology, University of California, Davis, CA, USA
| | - Paramita M. Ghosh
- VA Northern California Health Care System, Sacramento, CA, USA
- Department of Urology, University of California Davis School of Medicine, Sacramento, CA, USA
- Department of Biochemistry and Molecular Medicine, University of California Davis School of Medicine, Sacramento, CA, USA
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30
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Yang J, Horton JR, Li J, Huang Y, Zhang X, Blumenthal RM, Cheng X. Structural basis for preferential binding of human TCF4 to DNA containing 5-carboxylcytosine. Nucleic Acids Res 2019; 47:8375-8387. [PMID: 31081034 PMCID: PMC6895265 DOI: 10.1093/nar/gkz381] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2019] [Revised: 04/27/2019] [Accepted: 04/30/2019] [Indexed: 12/11/2022] Open
Abstract
The psychiatric risk-associated transcription factor 4 (TCF4) is linked to schizophrenia. Rare TCF4 coding variants are found in individuals with Pitt-Hopkins syndrome-an intellectual disability and autism spectrum disorder. TCF4 contains a C-terminal basic-helix-loop-helix (bHLH) DNA binding domain which recognizes the enhancer-box (E-box) element 5'-CANNTG-3' (where N = any nucleotide). A subset of the TCF4-occupancy sites have the expanded consensus binding specificity 5'-C(A/G)-CANNTG-3', with an added outer Cp(A/G) dinucleotide; for example in the promoter for CNIH3, a gene involved in opioid dependence. In mammalian genomes, particularly brain, the CpG and CpA dinucleotides can be methylated at the 5-position of cytosine (5mC), and then may undergo successive oxidations to the 5-hydroxymethyl (5hmC), 5-formyl (5fC), and 5-carboxyl (5caC) forms. We find that, in the context of 5'-0CG-1CA-2CG-3TG-3'(where the numbers indicate successive dinucleotides), modification of the central E-box 2CG has very little effect on TCF4 binding, E-box 1CA modification has a negative influence on binding, while modification of the flanking 0CG, particularly carboxylation, has a strong positive impact on TCF4 binding to DNA. Crystallization of TCF4 in complex with unmodified or 5caC-modified oligonucleotides revealed that the basic region of bHLH domain adopts multiple conformations, including an extended loop going through the DNA minor groove, or the N-terminal portion of a long helix binding in the DNA major groove. The different protein conformations enable arginine 576 (R576) to interact, respectively, with a thymine in the minor groove, a phosphate group of DNA backbone, or 5caC in the major groove. The Pitt-Hopkins syndrome mutations affect five arginine residues in the basic region, two of them (R569 and R576) involved in 5caC recognition. Our analyses indicate, and suggest a structural basis for, the preferential recognition of 5caC by a transcription factor centrally important in brain development.
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Affiliation(s)
- Jie Yang
- Department of Molecular and Cellular Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - John R Horton
- Department of Molecular and Cellular Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Jia Li
- Center for Epigenetics & Disease Prevention, Institute of Biosciences and Technology, Texas A&M University, Houston, TX 77030, USA
| | - Yun Huang
- Center for Epigenetics & Disease Prevention, Institute of Biosciences and Technology, Texas A&M University, Houston, TX 77030, USA
| | - Xing Zhang
- Department of Molecular and Cellular Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Robert M Blumenthal
- Department of Medical Microbiology and Immunology, and Program in Bioinformatics, The University of Toledo College of Medicine and Life Sciences, Toledo, OH 43614, USA
| | - Xiaodong Cheng
- Department of Molecular and Cellular Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
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Wang BT, Yu XY, Zhu YJ, Zhuang M, Zhang ZM, Jin L, Jin FJ. Research progress on the basic helix-loop-helix transcription factors of Aspergillus species. ADVANCES IN APPLIED MICROBIOLOGY 2019; 109:31-59. [PMID: 31677646 DOI: 10.1016/bs.aambs.2019.09.001] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Basic helix-loop-helix (bHLH) proteins belong to a superfamily of transcription factors, and they are widely distributed in eukaryotic organisms. Members of the bHLH protein family can form homodimers or heterodimers with themselves or other family members, and they often play bifunctional roles as activators and repressors to uniquely regulate the transcription of downstream target genes. The bHLH transcription factors are usually involved in developmental processes, including cellular proliferation and differentiation. Therefore, these transcription factors often play crucial roles in regulating growth, development, and differentiation in eukaryotes. Aspergillus species fungi are widely distributed in the environment, and they play important roles not only in the decomposition of organic matter as an important environmental microorganism but also in the fermentation and the food processing industry. Furthermore, some pathogenic fungi, such as Aspergillus flavus and Aspergillus fumigatus, affect the environment and human health in important ways. Recent research has shown that some Aspergillus bHLH proteins are significantly involved in the regulation of asexual and sexual reproduction, secondary metabolite production, carbohydrate metabolism, conidial and sclerotial production, among other processes. Here, we review the regulatory mechanisms and biological functions of the bHLH transcription factors of the Aspergillus genus to provide a theoretical reference for further study on the growth and development of Aspergillus and the functions of bHLHs.
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Affiliation(s)
- Bao-Teng Wang
- College of Biology and the Environment, Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, China
| | - Xing-Ye Yu
- College of Biology and the Environment, Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, China
| | - Yun-Jia Zhu
- College of Biology and the Environment, Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, China
| | - Miao Zhuang
- College of Biology and the Environment, Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, China
| | - Zhi-Min Zhang
- College of Biology and the Environment, Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, China
| | - Long Jin
- College of Biology and the Environment, Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, China
| | - Feng-Jie Jin
- College of Biology and the Environment, Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, China.
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Mao TY, Liu YY, Zhu HH, Zhang J, Yang JX, Fu Q, Wang N, Wang Z. Genome-wide analyses of the bHLH gene family reveals structural and functional characteristics in the aquatic plant Nelumbo nucifera. PeerJ 2019; 7:e7153. [PMID: 31231599 PMCID: PMC6573809 DOI: 10.7717/peerj.7153] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2019] [Accepted: 05/17/2019] [Indexed: 12/20/2022] Open
Abstract
Lotus (Nelumbo nucifera Gaertn.) is an economically important aquatic plant with multiple applications, but water salinity and cold stress seriously affect lotus yield and distribution. The basic helix-loop-helix (bHLH) transcription factors (TFs) play a vital role in plant growth and development, metabolic regulation processes and responses to environmental changes. However, systematic analyses of the bHLH TF family in lotus has not yet been reported. Here, we report the identification and description of bHLH genes in lotus (NnbHLHs) with a focus on functional prediction, particularly for those involved in stress resistance. In all, 115 NnbHLHs were identified in the lotus genome and classified into 19 subfamilies. The chromosomal distribution, physicochemical properties, bHLH domain, conserved motif compositions and evolution of these 115 NnbHLHs were further analyzed. To better understand the functions of the lotus bHLH family, gene ontology, cis-element, and phylogenetic analyses were conducted. NnbHLHs were predicted to be involved in plant development, metabolic regulation and responses to stress, in accordance with previous findings. Overall, 15 NnbHLHs were further investigated with functional prediction via quantitative real-time PCR analyses. Meanwhile, expression profiles of NnbHLHs in four tissues indicated that many NnbHLHs showed tissue preference in their expression. This study is supposed to provide a good foundation for further research into the functions and evolution of NnbHLHs, and identifies candidate genes for stress resistance in lotus.
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Affiliation(s)
- Tian-Yu Mao
- Key Laboratory of Horticultural Plant Biology, College of Horticulture and Forestry Sciences, Huazhong Agriculture University, Wuhan, China.,Key Laboratory of Urban Agriculture in Central China, Ministry of Agriculture and Rural Affairs, Wuhan, China
| | - Yao-Yao Liu
- Key Laboratory of Horticultural Plant Biology, College of Horticulture and Forestry Sciences, Huazhong Agriculture University, Wuhan, China.,Key Laboratory of Urban Agriculture in Central China, Ministry of Agriculture and Rural Affairs, Wuhan, China
| | - Huan-Huan Zhu
- Key Laboratory of Horticultural Plant Biology, College of Horticulture and Forestry Sciences, Huazhong Agriculture University, Wuhan, China.,Key Laboratory of Urban Agriculture in Central China, Ministry of Agriculture and Rural Affairs, Wuhan, China
| | - Jie Zhang
- Key Laboratory of Horticultural Plant Biology, College of Horticulture and Forestry Sciences, Huazhong Agriculture University, Wuhan, China.,Key Laboratory of Urban Agriculture in Central China, Ministry of Agriculture and Rural Affairs, Wuhan, China
| | - Ju-Xiang Yang
- Key Laboratory of Horticultural Plant Biology, College of Horticulture and Forestry Sciences, Huazhong Agriculture University, Wuhan, China.,Key Laboratory of Urban Agriculture in Central China, Ministry of Agriculture and Rural Affairs, Wuhan, China
| | - Qiang Fu
- Key Laboratory of Horticultural Plant Biology, College of Horticulture and Forestry Sciences, Huazhong Agriculture University, Wuhan, China.,Key Laboratory of Urban Agriculture in Central China, Ministry of Agriculture and Rural Affairs, Wuhan, China
| | - Nian Wang
- Key Laboratory of Horticultural Plant Biology, College of Horticulture and Forestry Sciences, Huazhong Agriculture University, Wuhan, China.,Key Laboratory of Urban Agriculture in Central China, Ministry of Agriculture and Rural Affairs, Wuhan, China
| | - Ze Wang
- Key Laboratory of Horticultural Plant Biology, College of Horticulture and Forestry Sciences, Huazhong Agriculture University, Wuhan, China.,Key Laboratory of Urban Agriculture in Central China, Ministry of Agriculture and Rural Affairs, Wuhan, China
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Abstract
In this review from Murre, the evolution of HLH genes, the structures of HLH domains, and the elaborate activities of HLH proteins in multicellular life are discussed. Helix–loop–helix (HLH) proteins are dimeric transcription factors that control lineage- and developmental-specific gene programs. Genes encoding for HLH proteins arose in unicellular organisms >600 million years ago and then duplicated and diversified from ancestral genes across the metazoan and plant kingdoms to establish multicellularity. Hundreds of HLH proteins have been identified with diverse functions in a wide variety of cell types. HLH proteins orchestrate lineage specification, commitment, self-renewal, proliferation, differentiation, and homing. HLH proteins also regulate circadian clocks, protect against hypoxic stress, promote antigen receptor locus assembly, and program transdifferentiation. HLH proteins deposit or erase epigenetic marks, activate noncoding transcription, and sequester chromatin remodelers across the chromatin landscape to dictate enhancer–promoter communication and somatic recombination. Here the evolution of HLH genes, the structures of HLH domains, and the elaborate activities of HLH proteins in multicellular life are discussed.
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Affiliation(s)
- Cornelis Murre
- Division of Biological Sciences, University of California at San Diego, La Jolla, California 92903, USA
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del Olmo Toledo V, Puccinelli R, Fordyce PM, Pérez JC. Diversification of DNA binding specificities enabled SREBP transcription regulators to expand the repertoire of cellular functions that they govern in fungi. PLoS Genet 2018; 14:e1007884. [PMID: 30596634 PMCID: PMC6329520 DOI: 10.1371/journal.pgen.1007884] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2018] [Revised: 01/11/2019] [Accepted: 12/08/2018] [Indexed: 01/08/2023] Open
Abstract
The Sterol Regulatory Element Binding Proteins (SREBPs) are basic-helix-loop-helix transcription regulators that control the expression of sterol biosynthesis genes in higher eukaryotes and some fungi. Surprisingly, SREBPs do not regulate sterol biosynthesis in the ascomycete yeasts (Saccharomycotina) as this role was handed off to an unrelated transcription regulator in this clade. The SREBPs, nonetheless, expanded in fungi such as the ascomycete yeasts Candida spp., raising questions about their role and evolution in these organisms. Here we report that the fungal SREBPs diversified their DNA binding preferences concomitantly with an expansion in function. We establish that several branches of fungal SREBPs preferentially bind non-palindromic DNA sequences, in contrast to the palindromic DNA motifs recognized by most basic-helix-loop-helix proteins (including SREBPs) in higher eukaryotes. Reconstruction and biochemical characterization of the likely ancestor protein suggest that an intrinsic DNA binding promiscuity in the family was resolved by alternative mechanisms in different branches of fungal SREBPs. Furthermore, we show that two SREBPs in the human commensal yeast Candida albicans drive a transcriptional cascade that inhibits a morphological switch under anaerobic conditions. Preventing this morphological transition enhances C. albicans colonization of the mammalian intestine, the fungus' natural niche. Thus, our results illustrate how diversification in DNA binding preferences enabled the functional expansion of a family of eukaryotic transcription regulators.
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Affiliation(s)
- Valentina del Olmo Toledo
- Interdisciplinary Center for Clinical Research, University Hospital Würzburg, Würzburg, Germany
- Institute for Molecular Infection Biology, University Würzburg, Würzburg, Germany
| | - Robert Puccinelli
- Department of Genetics, Stanford University, Stanford, California, United States of America
- Chan Zuckerberg Biohub, San Francisco, California, United States of America
| | - Polly M. Fordyce
- Department of Genetics, Stanford University, Stanford, California, United States of America
- Chan Zuckerberg Biohub, San Francisco, California, United States of America
- Department of Bioengineering, Stanford University, Stanford, California, United States of America
- Stanford CheM-H Institute, Stanford University, Stanford, California, United States of America
| | - J. Christian Pérez
- Interdisciplinary Center for Clinical Research, University Hospital Würzburg, Würzburg, Germany
- Institute for Molecular Infection Biology, University Würzburg, Würzburg, Germany
- * E-mail:
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Wei K, Chen H. Comparative functional genomics analysis of bHLH gene family in rice, maize and wheat. BMC PLANT BIOLOGY 2018; 18:309. [PMID: 30497403 PMCID: PMC6267037 DOI: 10.1186/s12870-018-1529-5] [Citation(s) in RCA: 46] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/12/2018] [Accepted: 11/15/2018] [Indexed: 05/22/2023]
Abstract
BACKGROUND The basic helix-loop-helix transcription factors play important roles in diverse cellular and molecular processes. Comparative functional genomics can provide powerful approaches to draw inferences about gene function and evolution among species. The comprehensive comparison of bHLH gene family in different gramineous plants has not yet been reported. RESULTS In this study, a total of 183, 231 and 571 bHLHs were identified in rice, maize and wheat genomes respectively, and 1154 bHLH genes from the three species and Arabidopsis were classified into 36 subfamilies. Of the identified genes, 110 OsbHLHs, 188 ZmbHLHs and 209 TabHLHs with relatively high mRNA abundances were detected in one or more tissues during development, and some of them exhibited tissue-specific expression such as TabHLH454-459, ZmbHLH099-101 and OsbHLH037 in root, TabHLH559-562, - 046, - 047 and ZmbHLH010, - 072, - 226 in leaf, TabHLH216-221, - 333, - 335, - 340 and OsbHLH005, - 141 in inflorescence, TabHLH081, ZmbHLH139 and OsbHLH144 in seed. Forty five, twenty nine and thirty one differentially expressed bHLHs were respectively detected in wheat, maize and rice under drought stresses using RNA-seq technology. Among them, the expressions of TabHLH046, - 047, ZmbHLH097, - 098, OsbHLH006 and - 185 were strongly induced, whereas TabHLH303, - 562, ZmbHLH155, - 154, OsbHLH152 and - 113 showed significant down-regulation. Twenty two TabHLHs were induced after stripe rust infection at 24 h and nine of them were suppressed at 72 hpi, whereas 28 and 6 TabHLHs exhibited obviously down- and up-regulation after powdery mildew attack respectively. Forty one ZmbHLHs were differentially expressed in response to F. verticillioides infection. Twenty two co-expression modules were identified by the WGCNA, some of which were associated with particular tissue types. And GO enrichment analysis for the modules showed that some TabHLHs were involved in the control of several biological processes, such as tapetal PCD, lipid metabolism, iron absorption, stress responses and signal regulation. CONCLUSION The present study identifies the bHLH family in rice, maize and wheat genomes, and detailedly discusses the evolutionary relationships, expression and function of bHLHs. This study provides some novel and detail information about bHLHs, and may facilitate understanding the molecular basis of the plant growth, development and stress physiology.
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Affiliation(s)
- Kaifa Wei
- School of Biological Sciences and Biotechnology, Minnan Normal University, 36 Xian-Qian-Zhi Street, Zhangzhou, 363000 Fujian China
| | - Huiqin Chen
- School of Life Sciences, Tsinghua University, Beijing, 100084 China
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36
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Wu H, Shao Q. The role of inhibitor of binding or differentiation 2 in the development and differentiation of immune cells. Immunobiology 2018; 224:142-146. [PMID: 30340915 DOI: 10.1016/j.imbio.2018.09.006] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2018] [Revised: 09/05/2018] [Accepted: 09/19/2018] [Indexed: 12/24/2022]
Abstract
Inhibitor of binding or differentiation 2 (Id2), a member of helix-loop-helix (HLH) transcriptional factors, is recently reported as an important regulator of the development or differentiation of immune cells. It has been demonstrated that Id2 plays a critical role in the early lymphopoiesis. However, it has been discovered recently that Id2 displays new functions in different immune cells. In the adaptive immune cells, Id2 is required for determining T-cell subsets and B cells. In addition, Id2 is also involved in the development of innate immune cells, including dendritic cells (DCs), natural killer (NK) cells, and other innate lymphoid cells (ILCs). Here, we review the current reports about the role of Id2 in the development or differentiation of main immune cells.
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Affiliation(s)
- Haojie Wu
- Reproductive Sciences Institute of Jiangsu University, Zhenjiang 212001, Jiangsu, P.R. China; Department of Immunology, Key Laboratory of Medical Science and Laboratory Medicine of Jiangsu Province, School of Medicine, Jiangsu University, Zhenjiang 212013, Jiangsu, P.R. China
| | - Qixiang Shao
- Reproductive Sciences Institute of Jiangsu University, Zhenjiang 212001, Jiangsu, P.R. China; Department of Immunology, Key Laboratory of Medical Science and Laboratory Medicine of Jiangsu Province, School of Medicine, Jiangsu University, Zhenjiang 212013, Jiangsu, P.R. China.
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37
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Ramos A, Miow QH, Liang X, Lin QS, Putti TC, Lim YP. Phosphorylation of E-box binding USF-1 by PI3K/AKT enhances its transcriptional activation of the WBP2 oncogene in breast cancer cells. FASEB J 2018; 32:fj201801167RR. [PMID: 30183375 DOI: 10.1096/fj.201801167rr] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/28/2024]
Abstract
WW domain binding protein 2 (WBP2), a transcriptional coactivator, plays a vital role in breast tumorigenesis. It positively regulates estrogen receptor, Hippo, and Wnt pathways, which subsequently enhance the transcription of downstream target genes contributing to cancer. Understanding the regulation of the expression and activity of WBP2 oncoprotein has implication in cancer therapy. We have previously reported that WBP2 is regulated at the post-translational and post-transcriptional levels. However, its regulation at the transcriptional level is not known. In this study, the minimal promoter region of WBP2 that is critical for its transcription was identified. The E-box motif in the WBP2 promoter was demonstrated to be essential for its transcription. The E-box binding protein upstream stimulatory factor 1 (USF-1) was discovered to be a key transcription factor for WBP2 by yeast one-hybrid analysis and was validated through reporter and chromatin immunoprecipitation assays and tandem mass spectrometry, which also suggested that USF-1 acts by regulating a network of genes, in addition to WBP2, associated with cell movement, proliferation, cell-cycle, and survival cellular processes. USF-1 is overexpressed in majority of the breast cancer cell lines and tissues tested, and has profound effects on cancer cell proliferation. USF-1-mediated transcription of WBP2 was demonstrated to be inducible by insulin, which led to AKT-mediated phosphorylation of USF-1 that modulated its ability to bind to the WBP2 promoter and activate its transcription. This study sheds new light onto the regulation of the WBP2 oncogene at the transcriptional level by a novel oncogenic transcription factor, USF-1. USF-1 is a potential drug target for treatment of WBP2-positive breast cancer.-Ramos, A., Miow, Q. H., Liang, X., Lin, Q. S., Putti, T. C., Lim, Y. P. Phosphorylation of E-box binding USF-1 by PI3K/AKT enhances its transcriptional activation of the WBP2 oncogene in breast cancer cells.
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Affiliation(s)
- Alisha Ramos
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - Qing Hao Miow
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - Xu Liang
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - Qing Song Lin
- Department of Biological Sciences, Faculty of Science, National University of Singapore, Singapore
| | | | - Yoon Pin Lim
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
- National University Cancer Institute, National University of Singapore, Singapore
- NUS Graduate School for Integrative Sciences and Engineering, National University of Singapore, Singapore
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Guo J, Liu C, Wang P, Cheng Q, Sun L, Yang W, Shen H. The Aborted Microspores ( AMS)-Like Gene Is Required for Anther and Microspore Development in Pepper ( Capsicum annuum L.). Int J Mol Sci 2018; 19:ijms19051341. [PMID: 29724052 PMCID: PMC5983743 DOI: 10.3390/ijms19051341] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2018] [Revised: 04/27/2018] [Accepted: 04/30/2018] [Indexed: 12/01/2022] Open
Abstract
Pepper (Capsicum annuum L.) is an economically important vegetable crop worldwide. Although many genes associated with anther and pollen development have been identified, little is known about the mechanism of pollen abortion in pepper. Here, we identified and isolated two putative aborted microspore (AMS) isoforms from pepper flowers: CaAMS1 and CaAMS2. Sequence analysis showed that CaAMS2 was generated by retention of the fourth intron in CaAMS1 pre-mRNA. CaAMS1 encodes a putative protein with a basic helix-loop-helix (bHLH) domain belonging to the MYC subfamily of bHLH transcription factors, and it is localized to the nucleus. Truncated CaAMS2-1 and CaAMS2-2 are produced by alternative splicing. Quantitative real-time PCR analysis showed that CaAMS (referred to CaAMS1 and CaAMS2-2) was preferentially expressed in stamens and its expression level gradually decreases with flower development. RNA in situ hybridization analysis showed that CaAMS is strongly expressed in the tapetum at the tetrad and uninucleate stages. Downregulation of CaAMS led to partial shortened filaments, shriveled, indehiscent stamens and abortive pollens in pepper flowers. Several genes involved in pollen exine formation were downregulated in defective CaAMS-silenced anthers. Thus, CaAMS seems to play an important role in pepper tapetum and pollen development by regulating a complex genetic network.
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Affiliation(s)
- Jinju Guo
- Beijing Key Laboratory of Growth and Developmental Regulation for Protected Vegetable Crops, Department of Vegetable Science, College of Horticulture, China Agricultural University, Beijing 100193, China.
| | - Chen Liu
- Beijing Key Laboratory of Growth and Developmental Regulation for Protected Vegetable Crops, Department of Vegetable Science, College of Horticulture, China Agricultural University, Beijing 100193, China.
- Shandong Key Laboratory of Greenhouse Vegetable Biology, Institute of Vegetables and Flowers, Shandong Academy of Agricultural Sciences, Shandong Branch of National Vegetable Improvement Center, Jinan 250100, China.
| | - Peng Wang
- Beijing Key Laboratory of Growth and Developmental Regulation for Protected Vegetable Crops, Department of Vegetable Science, College of Horticulture, China Agricultural University, Beijing 100193, China.
| | - Qing Cheng
- Beijing Key Laboratory of Growth and Developmental Regulation for Protected Vegetable Crops, Department of Vegetable Science, College of Horticulture, China Agricultural University, Beijing 100193, China.
| | - Liang Sun
- Beijing Key Laboratory of Growth and Developmental Regulation for Protected Vegetable Crops, Department of Vegetable Science, College of Horticulture, China Agricultural University, Beijing 100193, China.
| | - Wencai Yang
- Beijing Key Laboratory of Growth and Developmental Regulation for Protected Vegetable Crops, Department of Vegetable Science, College of Horticulture, China Agricultural University, Beijing 100193, China.
| | - Huolin Shen
- Beijing Key Laboratory of Growth and Developmental Regulation for Protected Vegetable Crops, Department of Vegetable Science, College of Horticulture, China Agricultural University, Beijing 100193, China.
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The Recombinant Inhibitor of DNA Binding Id2 Forms Multimeric Structures via the Helix-Loop-Helix Domain and the Nuclear Export Signal. Int J Mol Sci 2018; 19:ijms19041105. [PMID: 29642431 PMCID: PMC5979349 DOI: 10.3390/ijms19041105] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2018] [Revised: 03/31/2018] [Accepted: 04/03/2018] [Indexed: 12/24/2022] Open
Abstract
The inhibitor of DNA binding and cell differentiation 2 (Id2) is a helix-loop-helix (HLH) protein that acts as negative dominant regulator of basic-HLH transcription factors during development and in cancer. The structural properties of Id2 have been investigated so far by using synthetic or recombinant fragments reproducing single domains (N-terminus, HLH, C-terminus): the HLH domain tends to dimerize into a four-helix bundle, whereas the flanking regions are flexible. In this work, the intact protein was expressed in E. coli, solubilized from inclusion bodies with urea, purified and dissolved in water at pH~4. Under these conditions, Id2 was obtained with both cysteine residues disulfide-bonded to β-mercaptoethanol that was present during the solubilization process. Moreover, it existed in a self-assembled state, in which the N-terminus remained highly flexible, while the HLH domain and, surprisingly, part of the C-terminus, which corresponds to the nuclear export signal (NES), both were involved in slowly tumbling, rigid structures. The protein oligomers also formed twisted fibrils that were several micrometers long and up to 80 nm thick. These results show that self-assembly decreases the backbone flexibility of those two protein regions (HLH and NES) that are important for interaction with basic-HLH transcription factors or for nucleocytoplasmic shuttling.
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40
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Dong H, Zhao H, Li S, Han Z, Hu G, Liu C, Yang G, Wang G, Xie W, Xing Y. Genome-wide association studies reveal that members of bHLH subfamily 16 share a conserved function in regulating flag leaf angle in rice (Oryza sativa). PLoS Genet 2018; 14:e1007323. [PMID: 29617374 PMCID: PMC5902044 DOI: 10.1371/journal.pgen.1007323] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2018] [Revised: 04/16/2018] [Accepted: 03/20/2018] [Indexed: 11/19/2022] Open
Abstract
As a major component of ideal plant architecture, leaf angle especially flag leaf angle (FLA) makes a large contribution to grain yield in rice. We utilized a worldwide germplasm collection to elucidate the genetic basis of FLA that would be helpful for molecular design breeding in rice. Genome-wide association studies (GWAS) identified a total of 40 and 32 QTLs for FLA in Wuhan and Hainan, respectively. Eight QTLs were commonly detected in both conditions. Of these, 2 and 3 QTLs were identified in the indica and japonica subpopulations, respectively. In addition, the candidates of 5 FLA QTLs were verified by haplotype-level association analysis. These results indicate diverse genetic bases for FLA between the indica and japonica subpopulations. Three candidates, OsbHLH153, OsbHLH173 and OsbHLH174, quickly responded to BR and IAA involved in plant architecture except for OsbHLH173, whose expression level was too low to be detected; their overexpression in plants increased rice leaf angle. Together with previous studies, it was concluded that all 6 members in bHLH subfamily 16 had the conserved function in regulating FLA in rice. A comparison with our previous GWAS for tiller angle (TA) showed only one QTL had pleiotropic effects on FLA and TA, which explained low similarity of the genetic basis between FLA and TA. An ideal plant architecture is expected to be efficiently developed by combining favorable alleles for FLA from indica with favorable alleles for TA from japonica by inter-subspecies hybridization.
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Affiliation(s)
- Haijiao Dong
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan, China
| | - Hu Zhao
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan, China
| | - Shuangle Li
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan, China
| | - Zhongmin Han
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan, China
| | - Gang Hu
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan, China
| | - Chang Liu
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan, China
| | - Gaiyu Yang
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan, China
| | - Gongwei Wang
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan, China
| | - Weibo Xie
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan, China
| | - Yongzhong Xing
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan, China
- Hubei Collaborative Innovation Center for Grain Industry, Yangtze University, Jingzhou, China
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41
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Zhao K, Li S, Yao W, Zhou B, Li R, Jiang T. Characterization of the basic helix-loop-helix gene family and its tissue-differential expression in response to salt stress in poplar. PeerJ 2018; 6:e4502. [PMID: 29576971 PMCID: PMC5857177 DOI: 10.7717/peerj.4502] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2017] [Accepted: 02/23/2018] [Indexed: 11/23/2022] Open
Abstract
The basic helix–loop–helix (bHLH) transcription factor gene family is one of the largest gene families and extensively involved in plant growth, development, and stress responses. However, limited studies are available on the gene family in poplar. In this study, we focused on 202 bHLH genes, exploring their DNA and protein sequences and physicochemical properties. According to their protein sequence similarities, we classified the genes into 25 groups with specific motif structures. In order to explore their expressions, we performed gene expression profiling using RNA-Seq and identified 19 genes that display tissue-differential expression patterns without treatment. Furthermore, we also performed gene expression profiling under salt stress. We found 74 differentially expressed genes (DEGs), which are responsive to the treatment. A total of 18 of the 19 genes correspond well to the DEGs. We validated the results using reverse transcription quantitative real-time PCR. This study lays the foundation for future studies on gene cloning, transgenes, and biological mechanisms.
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Affiliation(s)
- Kai Zhao
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, China
| | - Shuxuan Li
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, China
| | - Wenjing Yao
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, China.,Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Harbin, China
| | - Boru Zhou
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, China
| | - Renhua Li
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, China
| | - Tingbo Jiang
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, China
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42
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Casey BH, Kollipara RK, Pozo K, Johnson JE. Intrinsic DNA binding properties demonstrated for lineage-specifying basic helix-loop-helix transcription factors. Genome Res 2018; 28:484-496. [PMID: 29500235 PMCID: PMC5880239 DOI: 10.1101/gr.224360.117] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2017] [Accepted: 02/28/2018] [Indexed: 12/27/2022]
Abstract
During development, transcription factors select distinct gene programs, providing the necessary regulatory complexity for temporal and tissue-specific gene expression. How related factors retain specificity, especially when they recognize the same DNA motifs, is not understood. We address this paradox using basic helix-loop-helix (bHLH) transcription factors ASCL1, ASCL2, and MYOD1, crucial mediators of lineage specification. In vivo, these factors recognize the same DNA motifs, yet bind largely different genomic sites and regulate distinct transcriptional programs. This suggests that their ability to identify regulatory targets is defined either by the cellular environment of the partially defined lineages in which they are endogenously expressed, or by intrinsic properties of the factors themselves. To distinguish between these mechanisms, we directly compared the chromatin binding properties of this subset of bHLH factors when ectopically expressed in embryonic stem cells, presenting them with a common chromatin landscape and cellular components. We find that these factors retain distinct binding sites; thus, specificity of binding is an intrinsic property not requiring a restricted landscape or lineage-specific cofactors. Although the ASCL factors and MYOD1 have some distinct DNA motif preference, it is not sufficient to explain the extent of the differential binding. All three factors can bind inaccessible chromatin and induce changes in chromatin accessibility and H3K27ac. A reiterated pattern of DNA binding motifs is uniquely enriched in inaccessible chromatin at sites bound by these bHLH factors. These combined properties define a subclass of lineage-specific bHLH factors and provide context for their central roles in development and disease.
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Affiliation(s)
- Bradford H Casey
- Department of Neuroscience, UT Southwestern Medical Center, Dallas, Texas 75390, USA
| | - Rahul K Kollipara
- McDermott Center for Human Growth and Development, UT Southwestern Medical Center, Dallas, Texas 75390, USA
| | - Karine Pozo
- Department of Neuroscience, UT Southwestern Medical Center, Dallas, Texas 75390, USA
| | - Jane E Johnson
- Department of Neuroscience, UT Southwestern Medical Center, Dallas, Texas 75390, USA.,Department of Pharmacology, UT Southwestern Medical Center, Dallas, Texas 75390, USA
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43
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Crystal Structure of Tetrameric Arabidopsis MYC2 Reveals the Mechanism of Enhanced Interaction with DNA. Cell Rep 2018; 19:1334-1342. [PMID: 28514654 DOI: 10.1016/j.celrep.2017.04.057] [Citation(s) in RCA: 43] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2017] [Revised: 03/09/2017] [Accepted: 04/20/2017] [Indexed: 01/17/2023] Open
Abstract
Jasmonates (JAs) are essential plant hormones that play important roles in the regulation of plant growth and the response to environmental stress. In the JA signaling pathway, the core transcription factors are a class of basic helix-loop-helix (bHLH) proteins, including MYC2, MYC3, and MYC4, that have different regulatory capacities. Here, we report the 2.7 Å crystal structure of the MYC2 bHLH domain complexed with G-box DNA, showing a cis-tetrameric structure. Biochemical assays confirmed that full-length MYC2 forms a stable homo-tetramer both in solution and in DNA-bound states, whereas MYC3 forms only a homodimer. Isothermal titration calorimetry (ITC) assays demonstrated that tetramerization enhanced DNA binding affinity, and fluorescence resonance energy transfer (FRET) assay indicated DNA looping potential of tetrameric MYC2. Luciferase assay further confirmed the importance of tetramerization in transcriptional regulation. Our studies provide a mechanistic explanation for the regulatory differences of MYC transcription factors.
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44
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Inamoto I, Shin JA. Peptide therapeutics that directly target transcription factors. Pept Sci (Hoboken) 2018. [DOI: 10.1002/pep2.24048] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Ichiro Inamoto
- Department of Chemistry; University of Toronto, 3359 Mississauga Road; Mississauga Ontario L5L 1C6 Canada
| | - Jumi A. Shin
- Department of Chemistry; University of Toronto, 3359 Mississauga Road; Mississauga Ontario L5L 1C6 Canada
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45
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Tsigelny IF, Mukthavaram R, Kouznetsova VL, Chao Y, Babic I, Nurmemmedov E, Pastorino S, Jiang P, Calligaris D, Agar N, Scadeng M, Pingle SC, Wrasidlo W, Makale MT, Kesari S. Multiple spatially related pharmacophores define small molecule inhibitors of OLIG2 in glioblastoma. Oncotarget 2017; 8:22370-22384. [PMID: 26517684 PMCID: PMC5410230 DOI: 10.18632/oncotarget.5633] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2015] [Accepted: 10/14/2015] [Indexed: 01/05/2023] Open
Abstract
Transcription factors (TFs) are a major class of protein signaling molecules that play key cellular roles in cancers such as the highly lethal brain cancer—glioblastoma (GBM). However, the development of specific TF inhibitors has proved difficult owing to expansive protein-protein interfaces and the absence of hydrophobic pockets. We uniquely defined the dimerization surface as an expansive parental pharmacophore comprised of several regional daughter pharmacophores. We targeted the OLIG2 TF which is essential for GBM survival and growth, we hypothesized that small molecules able to fit each subpharmacophore would inhibit OLIG2 activation. The most active compound was OLIG2 selective, it entered the brain, and it exhibited potent anti-GBM activity in cell-based assays and in pre-clinical mouse orthotopic models. These data suggest that (1) our multiple pharmacophore approach warrants further investigation, and (2) our most potent compounds merit detailed pharmacodynamic, biophysical, and mechanistic characterization for potential preclinical development as GBM therapeutics.
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Affiliation(s)
- Igor F Tsigelny
- Department of Neurosciences, University of California San Diego, La Jolla, CA, USA.,San Diego Supercomputer Center, University of California San Diego, La Jolla, CA, USA.,Translational Neuro-oncology Laboratories, Moores Cancer Center, University of California San Diego, La Jolla, CA, USA
| | - Rajesh Mukthavaram
- Translational Neuro-oncology Laboratories, Moores Cancer Center, University of California San Diego, La Jolla, CA, USA
| | - Valentina L Kouznetsova
- San Diego Supercomputer Center, University of California San Diego, La Jolla, CA, USA.,Translational Neuro-oncology Laboratories, Moores Cancer Center, University of California San Diego, La Jolla, CA, USA
| | - Ying Chao
- Translational Neuro-oncology Laboratories, Moores Cancer Center, University of California San Diego, La Jolla, CA, USA
| | - Ivan Babic
- Translational Neuro-oncology Laboratories, Moores Cancer Center, University of California San Diego, La Jolla, CA, USA
| | | | - Sandra Pastorino
- Translational Neuro-oncology Laboratories, Moores Cancer Center, University of California San Diego, La Jolla, CA, USA
| | - Pengfei Jiang
- Translational Neuro-oncology Laboratories, Moores Cancer Center, University of California San Diego, La Jolla, CA, USA
| | - David Calligaris
- Harvard Medical School, Department of Neurosurgery, Brigham and Women's Hospital, Boston, MA, USA
| | - Nathalie Agar
- Harvard Medical School, Department of Neurosurgery, Brigham and Women's Hospital, Boston, MA, USA
| | - Miriam Scadeng
- FMRI Research Center, Department of Radiology, University of California San Diego, La Jolla, CA, USA
| | - Sandeep C Pingle
- Translational Neuro-oncology Laboratories, Moores Cancer Center, University of California San Diego, La Jolla, CA, USA
| | - Wolfgang Wrasidlo
- Department of Neurosciences, University of California San Diego, La Jolla, CA, USA.,Translational Neuro-oncology Laboratories, Moores Cancer Center, University of California San Diego, La Jolla, CA, USA
| | - Milan T Makale
- Translational Neuro-oncology Laboratories, Moores Cancer Center, University of California San Diego, La Jolla, CA, USA
| | - Santosh Kesari
- Department of Neurosciences, University of California San Diego, La Jolla, CA, USA.,Translational Neuro-oncology Laboratories, Moores Cancer Center, University of California San Diego, La Jolla, CA, USA.,Current Address: John Wayne Cancer Institute at Providence Saint John's Health Center, Santa Monica, CA, USA
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46
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Chen E, Wang X, Gong Q, Butt HI, Chen Y, Zhang C, Yang Z, Wu Z, Ge X, Zhang X, Li F, Zhang X. A novel GhBEE1-Like gene of cotton causes anther indehiscence in transgenic Arabidopsis under uncontrolled transcription level. Gene 2017; 627:49-56. [PMID: 28600178 DOI: 10.1016/j.gene.2017.06.007] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2017] [Revised: 05/12/2017] [Accepted: 06/05/2017] [Indexed: 11/18/2022]
Abstract
Male-sterile lines are very important for selective breeding, and anther dehiscence defect is an effective way to generate male-sterile lines. Although several bHLH-family proteins in Arabidopsis have been characterized, little is known about the role of bHLH-family proteins in cotton. Here, we isolated a novel bHLH protein from cotton (Gossypium hirsutum), named GhBEE1-Like. Protein domain analysis showed that GhBEE1-Like contained a basic domain and an HLH domain. Subcellular localization analysis revealed that GhBEE1-Like was a nuclear-localized protein. Expression pattern analysis showed GhBEE1-Like was highly expressed in floral organs, and its expression was induced by the active brassinosteroid (BR) substance 24-epi-BL. GhBEE1-Like overexpression in Arabidopsis resulted in two types of transgenic lines, one with normal anther dehiscence and the other with defective anther dehiscence. Semi-qRT-PCR and qRT-PCR analyses revealed that GhBEE1-Like transcript levels acted as a check-point determining how anther dehiscence proceeds in these transgenic lines; regulated transcript levels result in normal anther dehiscence, whereas uncontrolled transcript levels lead to anther indehiscence. These results suggest that GhBEE1-Like plays an important role via its accumulation in regulating anther dehiscence. Therefore, controlling the level of GhBEE1-Like expression in cotton could be a convenient tool for generating male-sterile lines to use in selective breeding.
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Affiliation(s)
- Eryong Chen
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, China; Huazhong Agricultural University, Wuhan 430070, China
| | - Xiaoqian Wang
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, China
| | - Qian Gong
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, China
| | - Hamama Islam Butt
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, China
| | - Yanli Chen
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, China
| | - Chaojun Zhang
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, China
| | - Zuoren Yang
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, China
| | - Zhixia Wu
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, China
| | - Xiaoyang Ge
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, China
| | | | - Fuguang Li
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, China
| | - Xueyan Zhang
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, China.
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47
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Zhang D, Li G, Wang Y. A genome-wide identification and analysis of basic helix-loop-helix transcription factors in cattle. Gene 2017; 626:241-250. [PMID: 28536080 DOI: 10.1016/j.gene.2017.05.036] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2017] [Revised: 04/02/2017] [Accepted: 05/15/2017] [Indexed: 12/16/2022]
Abstract
Basic helix-loop-helix (BHLH) transcription factors comprise a large family of regulatory proteins and play critical roles in the developmental processes of higher organisms. Complete lists of BHLH family members have been identified in about 50 organisms, including fruit fly, zebrafish, mouse, giant panda, worm, yeast, rice and apple. Cattle, Bos taurus, is important for agriculture and animal nutrition, and is also a good model organism for health research. In the present study, 116 putative BHLHs were identified in the cattle genome. Phylogenetic analyses revealed that 111 Bos taurus BHLH (BtBHLH: Bos taurus BHLH) members belong to 44 families, with 48, 26, 16, 4, 13 and 4 members in group A, B, C, D, E and F respectively, and the remaining 5 BtBHLHs are orphan members. All of them were named and assigned into the corresponding BHLH families based on acceptable bootstrap values from in-group phylogenetic analyses with orthologous BHLHs from mouse and other mammalian species. A comparison between annotations deposited in the GenBank and KEGG databases with our analyses indicated that the annotations of 2 of the 116 BtBHLH members were inconsistent with our analytical results. Microarray evidence and expressed sequence tags of only 14 BtBHLH genes was now not available. Chromosomal locations of the BtBHLHs showed that the distribution of the BtBHLHs was uneven and some genes, e.g., BtOligo, BtHes and BtMyf6, may arise from gene duplication. The test of positive selection showed episodic positive selection occurs only in 5 families among the studied mammalian BHLHs. These results provide a solid basis for further studies on BHLH protein regulation of key growth and developmental processes.
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Affiliation(s)
- Debao Zhang
- Shanghai Huaxin High Biotechnology Company Limited, 1150 Guiqiao Road, Shanghai 201206, PR China.
| | - Guanying Li
- Shanghai Huaxin High Biotechnology Company Limited, 1150 Guiqiao Road, Shanghai 201206, PR China.
| | - Yong Wang
- School of Food and Biological Engineering, Jiangsu University, 301 Xuefu Road, Zhenjiang 212013, PR China.
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48
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Kim J, Lee HJ, Jung YJ, Kang KK, Tyagi W, Kovach M, Sweeney M, McCouch S, Cho YG. Functional properties of an alternative, tissue-specific promoter for rice NADPH-dependent dihydroflavonol reductase. PLoS One 2017; 12:e0183722. [PMID: 28841686 PMCID: PMC5571921 DOI: 10.1371/journal.pone.0183722] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2017] [Accepted: 08/09/2017] [Indexed: 11/23/2022] Open
Abstract
NADPH-dependent dihydroflavonol reductase (DFR) plays an important role in both anthocyanin biosynthesis and proanthocyanidin synthesis in plants. A specific and quantitative RT-PCR assay for transcription from the DFR promoter detected high expression with limited variability in rice tissues. A 440 bp minimal promoter region was identified by transfection of β-glucuronidase (GUS) reporter constructs into Jeokjinju variety. Alignment of the region with orthologous promoters revealed three conserved segments containing both bHLH (-386 to -381) and Myb (-368 to -362) binding sites. Transfection of β-glucuronidase constructs with targeted point mutations in the minimal promoter defined two sites important for promoter function to the transcription factor binding consensus sequences. The expression study showed that the bHLH binding domain (-386 to -381) is essential for DFR expression, and that a Myb binding domain (-368 to -362) is also required for full expression of the DFR gene, while the two bHLH binding domains (-104 to -99 and -27 to -22) nearest to the transcriptional start site are not necessary for DFR expression.
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Affiliation(s)
- Joonki Kim
- Department of Crop Science, Chungbuk National University, Cheongju, Korea
| | - Hye-Jung Lee
- Department of Crop Science, Chungbuk National University, Cheongju, Korea
| | - Yu-Jin Jung
- Department of Horticultural Life Science, Hankyong National University, Ansung, Korea
| | - Kwon-Kyoo Kang
- Department of Horticultural Life Science, Hankyong National University, Ansung, Korea
| | - Wricha Tyagi
- Department of Plant Breeding and Genetics, Cornell University, Ithaca, New York, United States of America
| | - Michael Kovach
- Department of Plant Breeding and Genetics, Cornell University, Ithaca, New York, United States of America
| | - Megan Sweeney
- Department of Plant Breeding and Genetics, Cornell University, Ithaca, New York, United States of America
| | - Susan McCouch
- Department of Plant Breeding and Genetics, Cornell University, Ithaca, New York, United States of America
- * E-mail: (SRM); (YGC)
| | - Yong-Gu Cho
- Department of Crop Science, Chungbuk National University, Cheongju, Korea
- * E-mail: (SRM); (YGC)
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49
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Niu X, Guan Y, Chen S, Li H. Genome-wide analysis of basic helix-loop-helix (bHLH) transcription factors in Brachypodium distachyon. BMC Genomics 2017; 18:619. [PMID: 28810832 PMCID: PMC5558667 DOI: 10.1186/s12864-017-4044-4] [Citation(s) in RCA: 56] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2017] [Accepted: 08/09/2017] [Indexed: 01/21/2023] Open
Abstract
BACKGROUND As a superfamily of transcription factors (TFs), the basic helix-loop-helix (bHLH) proteins have been characterized functionally in many plants with a vital role in the regulation of diverse biological processes including growth, development, response to various stresses, and so on. However, no systemic analysis of the bHLH TFs has been reported in Brachypodium distachyon, an emerging model plant in Poaceae. RESULTS A total of 146 bHLH TFs were identified in the Brachypodium distachyon genome and classified into 24 subfamilies. BdbHLHs in the same subfamily share similar protein motifs and gene structures. Gene duplication events showed a close relationship to rice, maize and sorghum, and segment duplications might play a key role in the expansion of this gene family. The amino acid sequence of the bHLH domains were quite conservative, especially Leu-27 and Leu-54. Based on the predicted binding activities, the BdbHLHs were divided into DNA binding and non-DNA binding types. According to the gene ontology (GO) analysis, BdbHLHs were speculated to function in homodimer or heterodimer manner. By integrating the available high throughput data in public database and results of quantitative RT-PCR, we found the expression profiles of BdbHLHs were different, implying their differentiated functions. CONCLUSION One hundred fourty-six BdbHLHs were identified and their conserved domains, sequence features, phylogenetic relationship, chromosomal distribution, GO annotations, gene structures, gene duplication and expression profiles were investigated. Our findings lay a foundation for further evolutionary and functional elucidation of BdbHLH genes.
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Affiliation(s)
- Xin Niu
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling, China
| | - Yuxiang Guan
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling, China
| | - Shoukun Chen
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling, China
| | - Haifeng Li
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling, China
- Xinjiang Agricultural Vocational Technical College, Changji, China
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50
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Bouard C, Terreux R, Tissier A, Jacqueroud L, Vigneron A, Ansieau S, Puisieux A, Payen L. Destabilization of the TWIST1/E12 complex dimerization following the R154P point-mutation of TWIST1: an in silico approach. BMC STRUCTURAL BIOLOGY 2017; 17:6. [PMID: 28521820 PMCID: PMC5437649 DOI: 10.1186/s12900-017-0076-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/03/2017] [Accepted: 05/02/2017] [Indexed: 11/24/2022]
Abstract
Background The bHLH transcription factor TWIST1 plays a key role in the embryonic development and in tumorigenesis. Some loss-of-function mutations of the TWIST1 gene have been shown to cause an autosomal dominant craniosynostosis, known as the Saethre-Chotzen syndrome (SCS). Although the functional impacts of many TWIST1 mutations have been experimentally reported, little is known on the molecular mechanisms underlying their loss-of-function. In a previous study, we highlighted the predictive value of in silico molecular dynamics (MD) simulations in deciphering the molecular function of TWIST1 residues. Results Here, since the substitution of the arginine 154 amino acid by a glycine residue (R154G) is responsible for the SCS phenotype and the substitution of arginine 154 by a proline experimentally decreases the dimerizing ability of TWIST1, we investigated the molecular impact of this point mutation using MD approaches. Consistently, MD simulations highlighted a clear decrease in the stability of the α-helix during the dimerization of the mutated R154P TWIST1/E12 dimer compared to the wild-type TE complex, which was further confirmed in vitro using immunoassays. Conclusions Our study demonstrates that MD simulations provide a structural explanation for the loss-of-function associated with the SCS TWIST1 mutation and provides a proof of concept of the predictive value of these MD simulations. This in silico methodology could be used to determine reliable pharmacophore sites, leading to the application of docking approaches in order to identify specific inhibitors of TWIST1 complexes. Electronic supplementary material The online version of this article (doi:10.1186/s12900-017-0076-x) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Charlotte Bouard
- Inserm UMR-S1052, Centre de Recherche en Cancérologie de Lyon, Lyon, 69373, France.,CNRS UMR5286, Centre de Recherche en Cancérologie de Lyon, Lyon, 69373, France.,LabEX DEVweCAN, Lyon, France.,UNIV UMR1052, Lyon, 69008, France.,Centre Léon Bérard, Lyon, 69373, France
| | - Raphael Terreux
- Université de Lyon1, ISPB, Lyon, 69008, France.,Pole Rhône-Alpes de Bioinformatique - Lyon Gerland (PRABI-LG), Lyon, 69007, France.,CNRS UMR 5305, Lyon, France
| | - Agnès Tissier
- Inserm UMR-S1052, Centre de Recherche en Cancérologie de Lyon, Lyon, 69373, France.,CNRS UMR5286, Centre de Recherche en Cancérologie de Lyon, Lyon, 69373, France.,LabEX DEVweCAN, Lyon, France.,UNIV UMR1052, Lyon, 69008, France.,Centre Léon Bérard, Lyon, 69373, France
| | - Laurent Jacqueroud
- Inserm UMR-S1052, Centre de Recherche en Cancérologie de Lyon, Lyon, 69373, France.,CNRS UMR5286, Centre de Recherche en Cancérologie de Lyon, Lyon, 69373, France.,LabEX DEVweCAN, Lyon, France.,UNIV UMR1052, Lyon, 69008, France.,Centre Léon Bérard, Lyon, 69373, France
| | - Arnaud Vigneron
- Inserm UMR-S1052, Centre de Recherche en Cancérologie de Lyon, Lyon, 69373, France.,CNRS UMR5286, Centre de Recherche en Cancérologie de Lyon, Lyon, 69373, France.,LabEX DEVweCAN, Lyon, France.,UNIV UMR1052, Lyon, 69008, France.,Centre Léon Bérard, Lyon, 69373, France
| | - Stéphane Ansieau
- Inserm UMR-S1052, Centre de Recherche en Cancérologie de Lyon, Lyon, 69373, France.,CNRS UMR5286, Centre de Recherche en Cancérologie de Lyon, Lyon, 69373, France.,LabEX DEVweCAN, Lyon, France.,UNIV UMR1052, Lyon, 69008, France.,Centre Léon Bérard, Lyon, 69373, France
| | - Alain Puisieux
- Inserm UMR-S1052, Centre de Recherche en Cancérologie de Lyon, Lyon, 69373, France.,CNRS UMR5286, Centre de Recherche en Cancérologie de Lyon, Lyon, 69373, France.,LabEX DEVweCAN, Lyon, France.,UNIV UMR1052, Lyon, 69008, France.,Centre Léon Bérard, Lyon, 69373, France.,Université de Lyon1, ISPB, Lyon, 69008, France.,Institut Universitaire de France, Paris, 75231, France
| | - Léa Payen
- Inserm UMR-S1052, Centre de Recherche en Cancérologie de Lyon, Lyon, 69373, France. .,CNRS UMR5286, Centre de Recherche en Cancérologie de Lyon, Lyon, 69373, France. .,LabEX DEVweCAN, Lyon, France. .,UNIV UMR1052, Lyon, 69008, France. .,Centre Léon Bérard, Lyon, 69373, France. .,Université de Lyon1, ISPB, Lyon, 69008, France. .,Laboratoire de Biochimie et Biologie Moléculaire (CHLS), Hospices Civils de Lyon, Lyon, 69003, France.
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