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Cornwell AB, Zhang Y, Thondamal M, Johnson DW, Thakar J, Samuelson AV. The C. elegans Myc-family of transcription factors coordinate a dynamic adaptive response to dietary restriction. GeroScience 2024:10.1007/s11357-024-01197-x. [PMID: 38878153 DOI: 10.1007/s11357-024-01197-x] [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: 02/16/2024] [Accepted: 05/08/2024] [Indexed: 06/25/2024] Open
Abstract
Dietary restriction (DR), the process of decreasing overall food consumption over an extended period of time, has been shown to increase longevity across evolutionarily diverse species and delay the onset of age-associated diseases in humans. In Caenorhabditis elegans, the Myc-family transcription factors (TFs) MXL-2 (Mlx) and MML-1 (MondoA/ChREBP), which function as obligate heterodimers, and PHA-4 (orthologous to FOXA) are both necessary for the full physiological benefits of DR. However, the adaptive transcriptional response to DR and the role of MML-1::MXL-2 and PHA-4 remains elusive. We identified the transcriptional signature of C. elegans DR, using the eat-2 genetic model, and demonstrate broad changes in metabolic gene expression in eat-2 DR animals, which requires both mxl-2 and pha-4. While the requirement for these factors in DR gene expression overlaps, we found many of the DR genes exhibit an opposing change in relative gene expression in eat-2;mxl-2 animals compared to wild-type, which was not observed in eat-2 animals with pha-4 loss. Surprisingly, we discovered more than 2000 genes synthetically dysregulated in eat-2;mxl-2, out of which the promoters of down-regulated genes were substantially enriched for PQM-1 and ELT-1/3 GATA TF binding motifs. We further show functional deficiencies of the mxl-2 loss in DR outside of lifespan, as eat-2;mxl-2 animals exhibit substantially smaller brood sizes and lay a proportion of dead eggs, indicating that MML-1::MXL-2 has a role in maintaining the balance between resource allocation to the soma and to reproduction under conditions of chronic food scarcity. While eat-2 animals do not show a significantly different metabolic rate compared to wild-type, we also find that loss of mxl-2 in DR does not affect the rate of oxygen consumption in young animals. The gene expression signature of eat-2 mutant animals is consistent with optimization of energy utilization and resource allocation, rather than induction of canonical gene expression changes associated with acute metabolic stress, such as induction of autophagy after TORC1 inhibition. Consistently, eat-2 animals are not substantially resistant to stress, providing further support to the idea that chronic DR may benefit healthspan and lifespan through efficient use of limited resources rather than broad upregulation of stress responses, and also indicates that MML-1::MXL-2 and PHA-4 may have distinct roles in promotion of benefits in response to different pro-longevity stimuli.
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Affiliation(s)
- Adam B Cornwell
- Department of Biomedical Genetics, University of Rochester Medical Center, 601 Elmwood Avenue, Rochester, NY, 14642, USA
| | - Yun Zhang
- Department of Biomedical Genetics, University of Rochester Medical Center, 601 Elmwood Avenue, Rochester, NY, 14642, USA
| | - Manjunatha Thondamal
- Department of Biomedical Genetics, University of Rochester Medical Center, 601 Elmwood Avenue, Rochester, NY, 14642, USA
- MURTI Centre and Department of Biotechnology, School of Technology, Gandhi Institute of Technology and Management (GITAM), Visakhapatnam, Andhra Pradesh, 530045, India
| | - David W Johnson
- Department of Biomedical Genetics, University of Rochester Medical Center, 601 Elmwood Avenue, Rochester, NY, 14642, USA
- Department of Math and Science, Genesee Community College, One College Rd, Batavia, NY, 14020, USA
| | - Juilee Thakar
- Department of Biomedical Genetics, University of Rochester Medical Center, 601 Elmwood Avenue, Rochester, NY, 14642, USA
- Department of Biostatistics and Computational Biology, University of Rochester Medical Center, 601 Elmwood Avenue, Rochester, NY, 14642, USA
- Department of Microbiology and Immunology, University of Rochester Medical Center, 601 Elmwood Avenue, Rochester, NY, 14642, USA
| | - Andrew V Samuelson
- Department of Biomedical Genetics, University of Rochester Medical Center, 601 Elmwood Avenue, Rochester, NY, 14642, USA.
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Galli M, Chen Z, Ghandour T, Chaudhry A, Gregory J, Li M, Zhang X, Dong Y, Song G, Walley JW, Chuck G, Whipple C, Kaeppler HF, Huang SSC, Gallavotti A. Transcription factor binding site divergence across maize inbred lines drives transcriptional and phenotypic variation. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.31.596834. [PMID: 38895211 PMCID: PMC11185568 DOI: 10.1101/2024.05.31.596834] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/21/2024]
Abstract
Regulatory elements are important constituents of plant genomes that have shaped ancient and modern crops. Their identification, function, and diversity in crop genomes however are poorly characterized, thus limiting our ability to harness their power for further agricultural advances using induced or natural variation. Here, we use DNA affinity purification-sequencing (DAP-seq) to map transcription factor (TF) binding events for 200 maize TFs belonging to 30 distinct families and heterodimer pairs in two distinct inbred lines historically used for maize hybrid plant production, providing empirical binding site annotation for 5.3% of the maize genome. TF binding site comparison in B73 and Mo17 inbreds reveals widespread differences, driven largely by structural variation, that correlate with gene expression changes. TF binding site presence-absence variation helps clarify complex QTL such as vgt1, an important determinant of maize flowering time, and DICE, a distal enhancer involved in herbivore resistance. Modification of TF binding regions via CRISPR-Cas9 mediated editing alters target gene expression and phenotype. Our functional catalog of maize TF binding events enables collective and comparative TF binding analysis, and highlights its value for agricultural improvement.
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Affiliation(s)
- Mary Galli
- Waksman Institute of Microbiology, Rutgers University, Piscataway, NJ, 08854-8020, USA
| | - Zongliang Chen
- Waksman Institute of Microbiology, Rutgers University, Piscataway, NJ, 08854-8020, USA
| | - Tara Ghandour
- Center for Genomics and Systems Biology, Department of Biology, New York University, New York, NY 10003, USA
| | - Amina Chaudhry
- Waksman Institute of Microbiology, Rutgers University, Piscataway, NJ, 08854-8020, USA
| | - Jason Gregory
- Waksman Institute of Microbiology, Rutgers University, Piscataway, NJ, 08854-8020, USA
| | - Miaomiao Li
- Center for Genomics and Systems Biology, Department of Biology, New York University, New York, NY 10003, USA
| | - Xuan Zhang
- Department of Genetics, University of Georgia, Athens, GA, USA
| | - Yinxin Dong
- Department of Genetics, University of Georgia, Athens, GA, USA
| | - Gaoyuan Song
- Department of Plant Pathology, Entomology, and Microbiology, Iowa State University; Ames, IA, 50011
| | - Justin W. Walley
- Department of Plant Pathology, Entomology, and Microbiology, Iowa State University; Ames, IA, 50011
| | - George Chuck
- Plant Gene Expression Center, Albany, CA 94710, USA
| | - Clinton Whipple
- Department of Biology, Brigham Young University, 4102 LSB, Provo, UT 84602, USA
| | - Heidi F. Kaeppler
- Department of Agronomy, University of Wisconsin, Madison, WI, USA
- Wisconsin Crop Innovation Center, University of Wisconsin, Middleton, WI, USA
| | - Shao-shan Carol Huang
- Center for Genomics and Systems Biology, Department of Biology, New York University, New York, NY 10003, USA
| | - Andrea Gallavotti
- Waksman Institute of Microbiology, Rutgers University, Piscataway, NJ, 08854-8020, USA
- Department of Plant Biology, Rutgers University, New Brunswick, NJ, 08901, USA
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3
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Yan Z, Zhang F, Mu C, Ma C, Yao G, Sun Y, Hou J, Leng B, Liu X. The ZmbHLH47-ZmSnRK2.9 Module Promotes Drought Tolerance in Maize. Int J Mol Sci 2024; 25:4957. [PMID: 38732175 PMCID: PMC11084430 DOI: 10.3390/ijms25094957] [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: 04/11/2024] [Revised: 04/29/2024] [Accepted: 04/30/2024] [Indexed: 05/13/2024] Open
Abstract
Drought stress globally poses a significant threat to maize (Zea mays L.) productivity and the underlying molecular mechanisms of drought tolerance remain elusive. In this study, we characterized ZmbHLH47, a basic helix-loop-helix (bHLH) transcription factor, as a positive regulator of drought tolerance in maize. ZmbHLH47 expression was notably induced by both drought stress and abscisic acid (ABA). Transgenic plants overexpressing ZmbHLH47 displayed elevated drought tolerance and ABA responsiveness, while the zmbhlh47 mutant exhibited increased drought sensitivity and reduced ABA sensitivity. Mechanistically, it was revealed that ZmbHLH47 could directly bind to the promoter of ZmSnRK2.9 gene, a member of the subgroup III SnRK2 kinases, activating its expression. Furthermore, ZmSnRK2.9-overexpressing plants exhibited enhanced ABA sensitivity and drought tolerance, whereas the zmsnrk2.9 mutant displayed a decreased sensitivity to both. Notably, overexpressing ZmbHLH47 in the zmsnrk2.9 mutant closely resembled the zmsnrk2.9 mutant, indicating the importance of the ZmbHLH47-ZmSnRK2.9 module in ABA response and drought tolerance. These findings provided valuable insights and a potential genetic resource for enhancing the environmental adaptability of maize.
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Affiliation(s)
- Zhenwei Yan
- Maize Research Institute, Shandong Academy of Agricultural Sciences, Jinan 250100, China; (Z.Y.); (F.Z.); (C.M.); (G.Y.)
| | - Fajun Zhang
- Maize Research Institute, Shandong Academy of Agricultural Sciences, Jinan 250100, China; (Z.Y.); (F.Z.); (C.M.); (G.Y.)
| | - Chunhua Mu
- Maize Research Institute, Shandong Academy of Agricultural Sciences, Jinan 250100, China; (Z.Y.); (F.Z.); (C.M.); (G.Y.)
| | - Changle Ma
- College of Life Sciences, Shandong Normal University, Jinan 250300, China;
| | - Guoqi Yao
- Maize Research Institute, Shandong Academy of Agricultural Sciences, Jinan 250100, China; (Z.Y.); (F.Z.); (C.M.); (G.Y.)
| | - Yue Sun
- College of Agronomy, Qingdao Agricultural University, Qingdao 266109, China;
| | - Jing Hou
- School of Agriculture, Ludong University, Yantai 264001, China;
| | - Bingying Leng
- Maize Research Institute, Shandong Academy of Agricultural Sciences, Jinan 250100, China; (Z.Y.); (F.Z.); (C.M.); (G.Y.)
| | - Xia Liu
- Maize Research Institute, Shandong Academy of Agricultural Sciences, Jinan 250100, China; (Z.Y.); (F.Z.); (C.M.); (G.Y.)
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Nie XY, Menet JS. Circadian regulation of stereotypic chromatin conformations at enhancers. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.04.24.590818. [PMID: 38712031 PMCID: PMC11071494 DOI: 10.1101/2024.04.24.590818] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2024]
Abstract
Cooperation between the circadian transcription factor (TF) CLOCK:BMAL1 and other TFs at cis-regulatory elements (CREs) is critical to daily rhythms of transcription. Yet, the modalities of this cooperation are unclear. Here, we analyzed the co-binding of multiple TFs on single DNA molecules in mouse liver using single molecule footprinting (SMF). We found that SMF reads clustered in stereotypic chromatin states that reflect distinguishable organization of TFs and nucleosomes, and that were remarkably conserved between all samples. DNA protection at CLOCK:BMAL1 binding motif (E-box) varied between CREs, from E-boxes being solely bound by CLOCK:BMAL1 to situations where other TFs competed with CLOCK:BMAL1 for E-box binding. SMF also uncovered CLOCK:BMAL1 cooperative binding at E-boxes separated by 250 bp, which structurally altered the CLOCK:BMAL1-DNA interface. Importantly, we discovered multiple nucleosomes with E-boxes at entry/exit sites that were removed upon CLOCK:BMAL1 DNA binding, thereby promoting the formation of open chromatin states that facilitate DNA binding of other TFs and that were associated with rhythmic transcription. These results demonstrate the utility of SMF for studying how CLOCK:BMAL1 and other TFs regulate stereotypical chromatin states at CREs to promote transcription.
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Affiliation(s)
- Xinyu Y. Nie
- Department of Biology, Center for Biological Clock Research, Texas A&M University, College Station, TX
| | - Jerome S. Menet
- Department of Biology, Center for Biological Clock Research, Texas A&M University, College Station, TX
- Interdisciplinary Program of Genetics, Texas A&M University, College Station, TX
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Wu C, Cai D, Li J, Lin Z, Wei W, Shan W, Chen J, Lu W, Su X, Kuang J. Banana MabHLH28 positively regulates the expression of softening-related genes to mediate fruit ripening independently or via cooperating with MaWRKY49/111. HORTICULTURE RESEARCH 2024; 11:uhae053. [PMID: 38706579 PMCID: PMC11069428 DOI: 10.1093/hr/uhae053] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/02/2023] [Accepted: 02/17/2024] [Indexed: 05/07/2024]
Abstract
Texture softening is a physiological indicator of fruit ripening, which eventually contributes to fruit quality and the consumer's acceptance. Despite great progress having been made in identification of the genes related to fruit softening, the upstream transcriptional regulatory pathways of these softening-related genes are not fully elucidated. Here, a novel bHLH gene, designated as MabHLH28, was identified because of its significant upregulation in banana fruit ripening. DAP-Seq analysis revealed that MabHLH28 bound to the core sequence of 'CAYGTG' presented in promoter regions of fruit softening-associated genes, such as the genes related to cell wall modification (MaPG3, MaPE1, MaPL5, MaPL8, MaEXP1, MaEXP2, MaEXPA2, and MaEXPA15) and starch degradation (MaGWD1 and MaLSF2), and these bindings were validated by EMSA and DLR assays. Transient overexpression and knockdown of MabHLH28 in banana fruit resulted in up- and down-regulation of softening-related genes, thereby hastening and postponing fruit ripening. Furthermore, overexpression of MabHLH28 in tomato accelerated the ripening process by elevating the accumulation of softening-associated genes. In addition, MabHLH28 showed interaction withMaWRKY49/111 and itself to form protein complexes, which could combinatorically strengthen the transcription of softening-associated genes. Taken together, our findings suggest that MabHLH28 mediates fruit softening by upregulating the expression of softening-related genes either alone or in combination with MaWRKY49/111.
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Affiliation(s)
- Chaojie Wu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources/Guangdong Provincial Key Laboratory of Postharvest Science of Fruits and Vegetables/Engineering Research Center of Southern Horticultural Products Preservation, Ministry of Education, College of Horticulture, South China Agricultural University, Guangzhou 510642, China
| | - Danling Cai
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources/Guangdong Provincial Key Laboratory of Postharvest Science of Fruits and Vegetables/Engineering Research Center of Southern Horticultural Products Preservation, Ministry of Education, College of Horticulture, South China Agricultural University, Guangzhou 510642, China
| | - Jun Li
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources/Guangdong Provincial Key Laboratory of Postharvest Science of Fruits and Vegetables/Engineering Research Center of Southern Horticultural Products Preservation, Ministry of Education, College of Horticulture, South China Agricultural University, Guangzhou 510642, China
| | - Zengxiang Lin
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources/Guangdong Provincial Key Laboratory of Postharvest Science of Fruits and Vegetables/Engineering Research Center of Southern Horticultural Products Preservation, Ministry of Education, College of Horticulture, South China Agricultural University, Guangzhou 510642, China
| | - Wei Wei
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources/Guangdong Provincial Key Laboratory of Postharvest Science of Fruits and Vegetables/Engineering Research Center of Southern Horticultural Products Preservation, Ministry of Education, College of Horticulture, South China Agricultural University, Guangzhou 510642, China
| | - Wei Shan
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources/Guangdong Provincial Key Laboratory of Postharvest Science of Fruits and Vegetables/Engineering Research Center of Southern Horticultural Products Preservation, Ministry of Education, College of Horticulture, South China Agricultural University, Guangzhou 510642, China
| | - Jianye Chen
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources/Guangdong Provincial Key Laboratory of Postharvest Science of Fruits and Vegetables/Engineering Research Center of Southern Horticultural Products Preservation, Ministry of Education, College of Horticulture, South China Agricultural University, Guangzhou 510642, China
| | - Wangjin Lu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources/Guangdong Provincial Key Laboratory of Postharvest Science of Fruits and Vegetables/Engineering Research Center of Southern Horticultural Products Preservation, Ministry of Education, College of Horticulture, South China Agricultural University, Guangzhou 510642, China
| | - Xinguo Su
- Agronomy Dean, Guangdong AIB Polytechnic College, Guangzhou 510507, China
| | - Jianfei Kuang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources/Guangdong Provincial Key Laboratory of Postharvest Science of Fruits and Vegetables/Engineering Research Center of Southern Horticultural Products Preservation, Ministry of Education, College of Horticulture, South China Agricultural University, Guangzhou 510642, China
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6
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Mikheeva SA, Funk CC, Horner PJ, Rostomily RC, Mikheev AM. Novel TCF4:TCF12 heterodimer inhibits glioblastoma growth. Mol Oncol 2024; 18:517-527. [PMID: 37507199 PMCID: PMC10920085 DOI: 10.1002/1878-0261.13496] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2023] [Revised: 06/15/2023] [Accepted: 07/24/2023] [Indexed: 07/30/2023] Open
Abstract
TWIST1 (TW) is a pro-oncogenic basic helix-loop-helix (bHLH) transcription factor and promotes the hallmark features of malignancy (e.g., cell invasion, cancer cell stemness, and treatment resistance), which contribute to poor prognoses of glioblastoma (GBM). We previously reported that specific TW dimerization motifs regulate unique cellular phenotypes in GBM. For example, the TW:E12 heterodimer increases periostin (POSTN) expression and promotes cell invasion. TW dimer-specific transcriptional regulation requires binding to the regulatory E-box consensus sequences, but alternative bHLH dimers that balance TW dimer activity in regulating pro-oncogenic TW target genes are unknown. We leveraged the ENCODE DNase I hypersensitivity data to identify E-box sites and tethered TW:E12 and TW:TW proteins to validate dimer binding to E-boxes in vitro. Subsequently, TW knockdown revealed a novel TCF4:TCF12 bHLH dimer occupying the same TW E-box site that, when expressed as a tethered TCF4:TCF12 dimer, markedly repressed POSTN expression and extended animal survival. These observations support TCF4:TCF12 as a novel dimer with tumor-suppressor activity in GBM that functions in part through displacement of and/or competitive inhibition of pro-oncogenic TW dimers at E-box sites.
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Affiliation(s)
- Svetlana A. Mikheeva
- Department of Neurosurgery, Center for NeuroregenerationHouston Methodist Research InstituteTexasUSA
| | - Cory C. Funk
- Institute for Systems BiologySeattleWashingtonUSA
| | - Philip J. Horner
- Department of Neurosurgery, Center for NeuroregenerationHouston Methodist Research InstituteTexasUSA
- Department of NeurosurgeryUniversity of WashingtonSeattleWashingtonUSA
- Institute for Stem Cell and Regenerative MedicineUniversity of WashingtonSeattleWashingtonUSA
| | - Robert C. Rostomily
- Department of Neurosurgery, Center for NeuroregenerationHouston Methodist Research InstituteTexasUSA
- Department of NeurosurgeryUniversity of WashingtonSeattleWashingtonUSA
- Institute for Stem Cell and Regenerative MedicineUniversity of WashingtonSeattleWashingtonUSA
| | - Andrei M. Mikheev
- Department of Neurosurgery, Center for NeuroregenerationHouston Methodist Research InstituteTexasUSA
- Department of NeurosurgeryUniversity of WashingtonSeattleWashingtonUSA
- Institute for Stem Cell and Regenerative MedicineUniversity of WashingtonSeattleWashingtonUSA
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7
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Liu H, Zhao X, Bi J, Dong X, Zhang C. A natural mutation in the promoter of the aconitase gene ZjACO3 influences fruit citric acid content in jujube. HORTICULTURE RESEARCH 2024; 11:uhae003. [PMID: 38464475 PMCID: PMC10923642 DOI: 10.1093/hr/uhae003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/31/2023] [Accepted: 12/30/2023] [Indexed: 03/12/2024]
Abstract
Jujube (Ziziphus jujuba Mill.) is the most economically important fruit tree of the Rhamnaceae and was domesticated from wild or sour jujube (Z. jujuba Mill. var. spinosa Hu). During the process of domestication, there was a substantial reduction in the content of organic acids, particularly malate and citrate, which greatly influence the taste and nutritional value of the fruit. We previously demonstrated that ZjALMT4 is crucial for malate accumulation. However, the mechanism of citrate degradation in jujube remains poorly understood. In the present study, aconitase ZjACO3 was shown to participate in citric acid degradation in the cytoplasm through the GABA pathway. Interestingly, we discovered an E-box mutation in the ZjACO3 promoter (-484A > G; CAAGTG in sour jujube mutated to CAGGTG in cultivated jujube) that was strongly correlated with fruit citrate content; 'A' represented a high-citrate genotype and 'G' represented a low-citrate genotype. We developed and validated an ACO-based Kompetitive allele-specific PCR (KASP) marker for determining citric acid content. Yeast one-hybrid screening, transient dual-luciferase assays, and overexpression analyses showed that the transcription factor ZjbHLH113 protein directly binds to CAGGTG in the promoter of ZjACO3 in cultivated jujube plants, transcriptionally activating ZjACO3 expression, and enhancing citric acid degradation. Conversely, binding ability of the ZjbHLH113 protein to CAAGTG was weakened in sour jujube, thereby promoting citrate accumulation in the fruit. These findings will assist in elucidating the mechanism by which ZjACO3 modulates citrate accumulation in sour jujube and its cultivars.
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Affiliation(s)
- Hanxiao Liu
- State Forestry and Grassland Administration Key Laboratory of Silviculture in Downstream Areas of the Yellow River, College of Forestry, Shandong Agricultural University, Tai’an, Shandong, 271018, China
| | - Xiangning Zhao
- State Forestry and Grassland Administration Key Laboratory of Silviculture in Downstream Areas of the Yellow River, College of Forestry, Shandong Agricultural University, Tai’an, Shandong, 271018, China
| | - Jingxin Bi
- State Forestry and Grassland Administration Key Laboratory of Silviculture in Downstream Areas of the Yellow River, College of Forestry, Shandong Agricultural University, Tai’an, Shandong, 271018, China
| | - Xiaochang Dong
- Shandong Institute of Pomology, Shandong Academy of Agricultural Sciences, Tai’an, 271000, China
| | - Chunmei Zhang
- State Forestry and Grassland Administration Key Laboratory of Silviculture in Downstream Areas of the Yellow River, College of Forestry, Shandong Agricultural University, Tai’an, Shandong, 271018, China
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8
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Bernardini A, Tora L. Co-translational Assembly Pathways of Nuclear Multiprotein Complexes Involved in the Regulation of Gene Transcription. J Mol Biol 2024; 436:168382. [PMID: 38061625 DOI: 10.1016/j.jmb.2023.168382] [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: 10/25/2023] [Revised: 11/24/2023] [Accepted: 12/01/2023] [Indexed: 12/18/2023]
Abstract
Most factors that regulate gene transcription in eukaryotic cells are multimeric, often large, protein complexes. The understanding of the biogenesis pathways of such large and heterogeneous protein assemblies, as well as the dimerization partner choice among transcription factors, is crucial to interpret and control gene expression programs and consequent cell fate decisions. Co-translational assembly (Co-TA) is thought to play key roles in the biogenesis of protein complexes by directing complex formation during protein synthesis. In this review we discuss the principles of Co-TA with a special focus for the assembly of transcription regulatory complexes. We outline the expected molecular advantages of establishing co-translational interactions, pointing at the available, or missing, evidence for each of them. We hypothesize different molecular mechanisms based on Co-TA to explain the allocation "dilemma" of paralog proteins and subunits shared by different transcription complexes. By taking as a paradigm the different assembly pathways employed by three related transcription regulatory complexes (TFIID, SAGA and ATAC), we discuss alternative Co-TA strategies for nuclear multiprotein complexes and the widespread - yet specific - use of Co-TA for the formation of nuclear complexes involved in gene transcription. Ultimately, we outlined a series of open questions which demand well-defined lines of research to investigate the principles of gene regulation that rely on the coordinated assembly of protein complexes.
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Affiliation(s)
- Andrea Bernardini
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, Illkirch, France; Centre National de la Recherche Scientifique, UMR7104, Illkirch, France; Institut National de la Santé et de la Recherche Médicale, U964 Illkirch, France; Université de Strasbourg, Illkirch, France.
| | - László Tora
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, Illkirch, France; Centre National de la Recherche Scientifique, UMR7104, Illkirch, France; Institut National de la Santé et de la Recherche Médicale, U964 Illkirch, France; Université de Strasbourg, Illkirch, France.
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9
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Jiang Y, Curran-French S, Koh SWH, Jamil I, Gu B, Argirò L, Lopez SG, Martins C, Saalbach G, Moubayidin L. O-glycosylation of the transcription factor SPATULA promotes style development in Arabidopsis. NATURE PLANTS 2024; 10:283-299. [PMID: 38278950 PMCID: PMC10881398 DOI: 10.1038/s41477-023-01617-4] [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: 03/22/2023] [Accepted: 12/21/2023] [Indexed: 01/28/2024]
Abstract
O-linked β-N-acetylglucosamine (O-GlcNAc) and O-fucose are two sugar-based post-translational modifications whose mechanistic role in plant signalling and transcriptional regulation is still largely unknown. Here we investigated how two O-glycosyltransferase enzymes of Arabidopsis thaliana, SPINDLY (SPY) and SECRET AGENT (SEC), promote the activity of the basic helix-loop-helix transcription factor SPATULA (SPT) during morphogenesis of the plant female reproductive organ apex, the style. SPY and SEC modify amino-terminal residues of SPT in vivo and in vitro by attaching O-fucose and O-GlcNAc, respectively. This post-translational regulation does not impact SPT homo- and heterodimerization events, although it enhances the affinity of SPT for the kinase PINOID gene locus and its transcriptional repression. Our findings offer a mechanistic example of the effect of O-GlcNAc and O-fucose on the activity of a plant transcription factor and reveal previously unrecognized roles for SEC and SPY in orchestrating style elongation and shape.
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Affiliation(s)
- Yuxiang Jiang
- Department of Cell and Developmental Biology, John Innes Centre, Norwich, UK
| | | | - Samuel W H Koh
- Department of Cell and Developmental Biology, John Innes Centre, Norwich, UK
| | - Iqra Jamil
- Department of Cell and Developmental Biology, John Innes Centre, Norwich, UK
| | - Benguo Gu
- Department of Cell and Developmental Biology, John Innes Centre, Norwich, UK
| | - Luca Argirò
- Department of Cell and Developmental Biology, John Innes Centre, Norwich, UK
| | - Sergio G Lopez
- Department of Cell and Developmental Biology, John Innes Centre, Norwich, UK
| | - Carlo Martins
- Department of Molecular Microbiology, John Innes Centre, Norwich, UK
| | - Gerhard Saalbach
- Department of Molecular Microbiology, John Innes Centre, Norwich, UK
| | - Laila Moubayidin
- Department of Cell and Developmental Biology, John Innes Centre, Norwich, UK.
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10
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Dwivedi S, Singh D, Singh N, Trivedi PK. Advances in regulatory mechanism(s) and biotechnological approaches to modulate nicotine content in tobacco. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2024; 207:108397. [PMID: 38316099 DOI: 10.1016/j.plaphy.2024.108397] [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: 10/23/2023] [Revised: 01/12/2024] [Accepted: 01/22/2024] [Indexed: 02/07/2024]
Abstract
More than 8 million deaths are caused by tobacco-related diseases every year. A staggering 1.2 million of those fatalities occur due to second-hand smoke exposure among non-smokers, but more than 7 million are due to direct tobacco use among smokers. Nicotine acts as the key ingredient triggering the addiction. The United States Food and Drug Administration (FDA) has classified more than 90 chemical components of tobacco and related smoke as hazardous or potentially hazardous leading to cancer, cardiovascular, respiratory, and reproductive disorders. Hence, reducing nicotine content has been the foremost objective to reduce health and death risks. Therefore, various biotechnological approaches for developing tobacco varieties with low nicotine concentrations are urgently required for the welfare of humankind. In recent years, numerous advancements have been made in nicotine-based tobacco research, suggesting regulatory components involved in nicotine biosynthesis and developing nicotine-less tobacco varieties through biotechnological approaches. This review highlights the various regulatory components and major approaches used to modulate nicotine content in tobacco cultivars.
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Affiliation(s)
- Shambhavi Dwivedi
- CSIR-Central Institute of Medicinal and Aromatic Plants (CSIR-CIMAP), Lucknow, India
| | - Deeksha Singh
- CSIR-Central Institute of Medicinal and Aromatic Plants (CSIR-CIMAP), Lucknow, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India
| | - Nivedita Singh
- CSIR-Central Institute of Medicinal and Aromatic Plants (CSIR-CIMAP), Lucknow, India
| | - Prabodh Kumar Trivedi
- CSIR-Central Institute of Medicinal and Aromatic Plants (CSIR-CIMAP), Lucknow, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India.
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11
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Mitra R, Li J, Sagendorf JM, Jiang Y, Chiu TP, Rohs R. DeepPBS: Geometric deep learning for interpretable prediction of protein-DNA binding specificity. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.12.15.571942. [PMID: 38293168 PMCID: PMC10827229 DOI: 10.1101/2023.12.15.571942] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/01/2024]
Abstract
Predicting specificity in protein-DNA interactions is a challenging yet essential task for understanding gene regulation. Here, we present Deep Predictor of Binding Specificity (DeepPBS), a geometric deep-learning model designed to predict binding specificity across protein families based on protein-DNA structures. The DeepPBS architecture allows investigation of different family-specific recognition patterns. DeepPBS can be applied to predicted structures, and can aid in the modeling of protein-DNA complexes. DeepPBS is interpretable and can be used to calculate protein heavy atom-level importance scores, demonstrated as a case-study on p53-DNA interface. When aggregated at the protein residue level, these scores conform well with alanine scanning mutagenesis experimental data. The inference time for DeepPBS is sufficiently fast for analyzing simulation trajectories, as demonstrated on a molecular-dynamics simulation of a Drosophila Hox-DNA tertiary complex with its cofactor. DeepPBS and its corresponding data resources offer a foundation for machine-aided protein-DNA interaction studies, guiding experimental choices and complex design, as well as advancing our understanding of molecular interactions.
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12
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Paquette AR, Boddy CN. Double Stranded DNA Binding Stapled Peptides: An Emerging Tool for Transcriptional Regulation. Chembiochem 2023; 24:e202300594. [PMID: 37750576 DOI: 10.1002/cbic.202300594] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2023] [Revised: 09/25/2023] [Accepted: 09/26/2023] [Indexed: 09/27/2023]
Abstract
Stapled peptides have rapidly established themselves as a powerful technique to mimic α-helical interactions with a short peptide sequence. There are many examples of stapled peptides that successfully disrupt α-helix-mediated protein-protein interactions, with an example currently in clinical trials. DNA-protein interactions are also often mediated by α-helices and are involved in all transcriptional regulation processes. Unlike DNA-binding small molecules, which typically lack DNA sequence selectivity, DNA-binding proteins bind with high affinity and high selectivity. These are ideal candidates for the design DNA-binding stapled peptides. Despite the parallel to protein-protein interaction disrupting stapled peptides and the need for sequence specific DNA binders, there are very few DNA-binding stapled peptides. In this review we examine all the known DNA-binding stapled peptides. Their design concepts are compared to stapled peptides that disrupt protein-protein interactions and based on the few examples in the literature, DNA-binding stapled peptide trends are discussed.
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Affiliation(s)
- André R Paquette
- Department of Chemistry and Biomolecular Sciences, The University of Ottawa, Ottawa, ON, K1N 6N5, Canada
| | - Christopher N Boddy
- Department of Chemistry and Biomolecular Sciences, The University of Ottawa, Ottawa, ON, K1N 6N5, Canada
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13
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Cornwell A, Zhang Y, Thondamal M, Johnson DW, Thakar J, Samuelson AV. The C. elegans Myc-family of transcription factors coordinate a dynamic adaptive response to dietary restriction. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.11.22.568222. [PMID: 38045350 PMCID: PMC10690244 DOI: 10.1101/2023.11.22.568222] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/05/2023]
Abstract
Dietary restriction (DR), the process of decreasing overall food consumption over an extended period of time, has been shown to increase longevity across evolutionarily diverse species and delay the onset of age-associated diseases in humans. In Caenorhabditis elegans, the Myc-family transcription factors (TFs) MXL-2 (Mlx) and MML-1 (MondoA/ChREBP), which function as obligate heterodimers, and PHA-4 (orthologous to forkhead box transcription factor A) are both necessary for the full physiological benefits of DR. However, the adaptive transcriptional response to DR and the role of MML-1::MXL-2 and PHA-4 remains elusive. We identified the transcriptional signature of C. elegans DR, using the eat-2 genetic model, and demonstrate broad changes in metabolic gene expression in eat-2 DR animals, which requires both mxl-2 and pha-4. While the requirement for these factors in DR gene expression overlaps, we found many of the DR genes exhibit an opposing change in relative gene expression in eat-2;mxl-2 animals compared to wild-type, which was not observed in eat-2 animals with pha-4 loss. We further show functional deficiencies of the mxl-2 loss in DR outside of lifespan, as eat-2;mxl-2 animals exhibit substantially smaller brood sizes and lay a proportion of dead eggs, indicating that MML-1::MXL-2 has a role in maintaining the balance between resource allocation to the soma and to reproduction under conditions of chronic food scarcity. While eat-2 animals do not show a significantly different metabolic rate compared to wild-type, we also find that loss of mxl-2 in DR does not affect the rate of oxygen consumption in young animals. The gene expression signature of eat-2 mutant animals is consistent with optimization of energy utilization and resource allocation, rather than induction of canonical gene expression changes associated with acute metabolic stress -such as induction of autophagy after TORC1 inhibition. Consistently, eat-2 animals are not substantially resistant to stress, providing further support to the idea that chronic DR may benefit healthspan and lifespan through efficient use of limited resources rather than broad upregulation of stress responses, and also indicates that MML-1::MXL-2 and PHA-4 may have different roles in promotion of benefits in response to different pro-longevity stimuli.
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Affiliation(s)
- Adam Cornwell
- Department of Biomedical Genetics, University of Rochester Medical Center, 601 Elmwood Avenue, Rochester, NY 14642, USA
| | - Yun Zhang
- Department of Biomedical Genetics, University of Rochester Medical Center, 601 Elmwood Avenue, Rochester, NY 14642, USA
| | - Manjunatha Thondamal
- Department of Biomedical Genetics, University of Rochester Medical Center, 601 Elmwood Avenue, Rochester, NY 14642, USA
- Department of Biological Sciences, GITAM University, Andhra Pradesh, India
| | - David W Johnson
- Department of Biomedical Genetics, University of Rochester Medical Center, 601 Elmwood Avenue, Rochester, NY 14642, USA
- Department of Math and Science, Genesee Community College, One College Rd Batavia, NY 14020, USA
| | - Juilee Thakar
- Department of Biomedical Genetics, University of Rochester Medical Center, 601 Elmwood Avenue, Rochester, NY 14642, USA
- Department of Biostatistics and Computational Biology, University of Rochester Medical Center, 601 Elmwood Avenue, Rochester, NY 14642, USA
- Department of Microbiology and Immunology, University of Rochester Medical Center, 601 Elmwood Avenue, Rochester, NY 14642, USA
| | - Andrew V Samuelson
- Department of Biomedical Genetics, University of Rochester Medical Center, 601 Elmwood Avenue, Rochester, NY 14642, USA
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Vazana-Netzarim R, Elmalem Y, Sofer S, Bruck H, Danino N, Sarig U. Distinct HAND2/HAND2-AS1 Expression Levels May Fine-Tune Mesenchymal and Epithelial Cell Plasticity of Human Mesenchymal Stem Cells. Int J Mol Sci 2023; 24:16546. [PMID: 38003736 PMCID: PMC10672054 DOI: 10.3390/ijms242216546] [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: 09/21/2023] [Revised: 11/09/2023] [Accepted: 11/13/2023] [Indexed: 11/26/2023] Open
Abstract
We previously developed several successful decellularization strategies that yielded porcine cardiac extracellular matrices (pcECMs) exhibiting tissue-specific bioactivity and bioinductive capacity when cultured with various pluripotent and multipotent stem cells. Here, we study the tissue-specific effects of the pcECM on seeded human mesenchymal stem cell (hMSC) phenotypes using reverse transcribed quantitative polymerase chain reaction (RT-qPCR) arrays for cardiovascular related gene expression. We further corroborated interesting findings at the protein level (flow cytometry and immunological stains) as well as bioinformatically using several mRNA sequencing and protein databases of normal and pathologic adult and embryonic (organogenesis stage) tissue expression. We discovered that upon the seeding of hMSCs on the pcECM, they displayed a partial mesenchymal-to-epithelial transition (MET) toward endothelial phenotypes (CD31+) and morphologies, which were preceded by an early spike (~Day 3 onward after seeding) in HAND2 expression at both the mRNA and protein levels compared to that in plate controls. The CRISPR-Cas9 knockout (KO) of HAND2 and its associated antisense long non-coding RNA (HAND2-AS1) regulatory region resulted in proliferation arrest, hypertrophy, and senescent-like morphology. Bioinformatic analyses revealed that HAND2 and HAND2-AS1 are highly correlated in expression and are expressed in many different tissue types albeit at distinct yet tightly regulated expression levels. Deviation (downregulation or upregulation) from these basal tissue expression levels is associated with a long list of pathologies. We thus suggest that HAND2 expression levels may possibly fine-tune hMSCs' plasticity through affecting senescence and mesenchymal-to-epithelial transition states, through yet unknown mechanisms. Targeting this pathway may open up a promising new therapeutic approach for a wide range of diseases, including cancer, degenerative disorders, and aging. Nevertheless, further investigation is required to validate these findings and better understand the molecular players involved, potential inducers and inhibitors of this pathway, and eventually potential therapeutic applications.
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Affiliation(s)
- Rachel Vazana-Netzarim
- The Dr. Miriam and Sheldon Adelson School of Medicine, Department of Morphological Sciences and Teratology, Ariel University, Ariel 4070000, Israel; (R.V.-N.); (N.D.)
| | - Yishay Elmalem
- Department of Chemical Engineering, Faculty of Engineering, Ariel University, Ariel 4070000, Israel (S.S.); (H.B.)
| | - Shachar Sofer
- Department of Chemical Engineering, Faculty of Engineering, Ariel University, Ariel 4070000, Israel (S.S.); (H.B.)
| | - Hod Bruck
- Department of Chemical Engineering, Faculty of Engineering, Ariel University, Ariel 4070000, Israel (S.S.); (H.B.)
| | - Naama Danino
- The Dr. Miriam and Sheldon Adelson School of Medicine, Department of Morphological Sciences and Teratology, Ariel University, Ariel 4070000, Israel; (R.V.-N.); (N.D.)
| | - Udi Sarig
- The Dr. Miriam and Sheldon Adelson School of Medicine, Department of Morphological Sciences and Teratology, Ariel University, Ariel 4070000, Israel; (R.V.-N.); (N.D.)
- Department of Chemical Engineering, Faculty of Engineering, Ariel University, Ariel 4070000, Israel (S.S.); (H.B.)
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15
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Tan Z, Lu D, Yu Y, Li L, Dong W, Xu L, Yang Q, Wan X, Liang H. Genome-Wide Identification and Characterization of the bHLH Gene Family and Its Response to Abiotic Stresses in Carthamus tinctorius. PLANTS (BASEL, SWITZERLAND) 2023; 12:3764. [PMID: 37960120 PMCID: PMC10648185 DOI: 10.3390/plants12213764] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/14/2023] [Revised: 10/16/2023] [Accepted: 11/02/2023] [Indexed: 11/15/2023]
Abstract
The basic helix-loop-helix (bHLH) transcription factors possess DNA-binding and dimerization domains and are involved in various biological and physiological processes, such as growth and development, the regulation of secondary metabolites, and stress response. However, the bHLH gene family in C. tinctorius has not been investigated. In this study, we performed a genome-wide identification and analysis of bHLH transcription factors in C. tinctorius. A total of 120 CtbHLH genes were identified, distributed across all 12 chromosomes, and classified into 24 subfamilies based on their phylogenetic relationships. Moreover, the 120 CtbHLH genes were subjected to comprehensive analyses, including protein sequence alignment, evolutionary assessment, motif prediction, and the analysis of promoter cis-acting elements. The promoter region analysis revealed that CtbHLH genes encompass cis-acting elements and were associated with various aspects of plant growth and development, responses to phytohormones, as well as responses to both abiotic and biotic stresses. Expression profiles, sourced from transcriptome databases, indicated distinct expression patterns among these CtbHLH genes, which appeared to be either tissue-specific or specific to certain cultivars. To further explore their functionality, we determined the expression levels of fifteen CtbHLH genes known to harbor motifs related to abiotic and hormone responses. This investigation encompassed treatments with ABA, salt, drought, and MeJA. The results demonstrated substantial variations in the expression patterns of CtbHLH genes in response to these abiotic and hormonal treatments. In summary, our study establishes a solid foundation for future inquiries into the roles and regulatory mechanisms of the CtbHLH gene family.
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Affiliation(s)
- Zhengwei Tan
- Institute of Chinese Herbel Medicines, Henan Academy of Agricultural Sciences, Zhengzhou 450002, China; (Z.T.); (D.L.); (Y.Y.); (L.L.); (W.D.); (L.X.); (Q.Y.)
- Henan Sesame Research Center, Henan Academy of Agricultural Sciences, Zhengzhou 450002, China
| | - Dandan Lu
- Institute of Chinese Herbel Medicines, Henan Academy of Agricultural Sciences, Zhengzhou 450002, China; (Z.T.); (D.L.); (Y.Y.); (L.L.); (W.D.); (L.X.); (Q.Y.)
- Henan Sesame Research Center, Henan Academy of Agricultural Sciences, Zhengzhou 450002, China
| | - Yongliang Yu
- Institute of Chinese Herbel Medicines, Henan Academy of Agricultural Sciences, Zhengzhou 450002, China; (Z.T.); (D.L.); (Y.Y.); (L.L.); (W.D.); (L.X.); (Q.Y.)
- Henan Sesame Research Center, Henan Academy of Agricultural Sciences, Zhengzhou 450002, China
| | - Lei Li
- Institute of Chinese Herbel Medicines, Henan Academy of Agricultural Sciences, Zhengzhou 450002, China; (Z.T.); (D.L.); (Y.Y.); (L.L.); (W.D.); (L.X.); (Q.Y.)
- Henan Sesame Research Center, Henan Academy of Agricultural Sciences, Zhengzhou 450002, China
| | - Wei Dong
- Institute of Chinese Herbel Medicines, Henan Academy of Agricultural Sciences, Zhengzhou 450002, China; (Z.T.); (D.L.); (Y.Y.); (L.L.); (W.D.); (L.X.); (Q.Y.)
- Henan Sesame Research Center, Henan Academy of Agricultural Sciences, Zhengzhou 450002, China
| | - Lanjie Xu
- Institute of Chinese Herbel Medicines, Henan Academy of Agricultural Sciences, Zhengzhou 450002, China; (Z.T.); (D.L.); (Y.Y.); (L.L.); (W.D.); (L.X.); (Q.Y.)
- Henan Sesame Research Center, Henan Academy of Agricultural Sciences, Zhengzhou 450002, China
| | - Qing Yang
- Institute of Chinese Herbel Medicines, Henan Academy of Agricultural Sciences, Zhengzhou 450002, China; (Z.T.); (D.L.); (Y.Y.); (L.L.); (W.D.); (L.X.); (Q.Y.)
- Henan Sesame Research Center, Henan Academy of Agricultural Sciences, Zhengzhou 450002, China
| | - Xiufu Wan
- State Key Laboratory for Quality Ensurance and Sustainable Use of Dao-di Herbs, National Resource Center for Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijng 100700, China;
| | - Huizhen Liang
- Institute of Chinese Herbel Medicines, Henan Academy of Agricultural Sciences, Zhengzhou 450002, China; (Z.T.); (D.L.); (Y.Y.); (L.L.); (W.D.); (L.X.); (Q.Y.)
- Henan Sesame Research Center, Henan Academy of Agricultural Sciences, Zhengzhou 450002, China
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16
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Żak M, Støle TP, Plagnol V, Daudet N. Regulation of otic neurosensory specification by Notch and Wnt signalling: insights from RNA-seq screenings in the embryonic chicken inner ear. Front Cell Dev Biol 2023; 11:1245330. [PMID: 37900277 PMCID: PMC10600479 DOI: 10.3389/fcell.2023.1245330] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2023] [Accepted: 09/25/2023] [Indexed: 10/31/2023] Open
Abstract
The Notch and Wnt signalling pathways play key roles in the formation of inner ear sensory organs, but little is known about their transcriptional effectors and targets in this context. Here, we perturbed Notch and Wnt activities in the embryonic chicken otic vesicle using pharmacological treatment or in ovo electroporation of plasmid DNA, and used RNA-Seq to analyse the resulting changes in gene expression. Compared to pharmacological treatments, in ovo electroporation changed the expression of fewer genes, a likely consequence of the variability and mosaicism of transfection. The pharmacological inhibition of Notch activity induced a rapid change in the expression of known effectors of this pathway and genes associated with neurogenesis, consistent with a switch towards an otic neurosensory fate. The Wnt datasets contained many genes associated with a neurosensory biological function, confirming the importance of this pathway for neurosensory specification in the otocyst. Finally, the results of a preliminary gain-of-function screening of selected transcription factors and Wnt signalling components suggest that the endogenous programs of otic neurosensory specification are very robust, and in general unaffected by the overexpression of a single factor. Altogether this work provides new insights into the effectors and candidate targets of the Notch and Wnt pathways in the early developing inner ear and could serve as a useful reference for future functional genomics experiments in the embryonic avian inner ear.
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Affiliation(s)
- Magdalena Żak
- UCL Ear Institute, University College London, London, United Kingdom
| | - Thea P. Støle
- UCL Ear Institute, University College London, London, United Kingdom
| | - Vincent Plagnol
- Genetics Institute, University College London, London, United Kingdom
| | - Nicolas Daudet
- UCL Ear Institute, University College London, London, United Kingdom
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17
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Mahajan M, Sarkar A, Mondal S. Cell cycle protein BORA is associated with colorectal cancer progression by AURORA-PLK1 cascades: a bioinformatics analysis. J Cell Commun Signal 2023; 17:773-791. [PMID: 36538275 PMCID: PMC10409947 DOI: 10.1007/s12079-022-00719-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2022] [Accepted: 12/14/2022] [Indexed: 12/24/2022] Open
Abstract
Colorectal cancer (CRC) is the third most diagnosed cancer in the world. A better understanding of the molecular mechanism of CRC is essential for making novel strategies for the CRC management and its prevention. The present study aims to explore the molecular mechanism through integrated bioinformatics analysis by analyzing genes and their co-expression pattern in normal and CRC states. GSE110223, GSE110224 and GSE113513 gene expression profiles were analyzed in this study. The co-expression networks for normal and tumor samples were constructed separately and analyzed to identify the modules, sub-networks and key genes. Gene regulatory network analysis was done to understand the regulatory mechanism of selected genes. Survival analysis was performed for the identified sub-networks and key genes to understand their role in CRC progression. A total of seven modules were detected and the KEGG pathway analysis revealed these modules were mainly enriched with cell cycle, metabolism and signaling-related pathways. E2F6 and ETV4 transcription factors regulating the activity of multiple genes of identified modules were found to be up-regulated in CRC. Six Sub-networks and seven key genes, BORA, CCT7, DTL, RUVBL1, RUVBL2, THEM6 and TMEM97 associated with the CRC progression were identified. Disease-gene association analysis identified a novel association of the BORA gene with CRC that activates and regulates the AURORA-PLK1 cascades in the cell cycle. Survival analysis indicates that the overexpressed BORA is associated with unfavourable overall survival in CRC. The mechanistic role of BORA in the regulation of cell cycle progression suggests that BORA might act as a potential therapeutic target for CRC.
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Affiliation(s)
- Mohita Mahajan
- Department of Biological Sciences, Birla Institute of Technology and Science, Pilani, K.K. Birla Goa Campus, Zuarinagar, Goa 403726 India
| | - Angshuman Sarkar
- Department of Biological Sciences, Birla Institute of Technology and Science, Pilani, K.K. Birla Goa Campus, Zuarinagar, Goa 403726 India
| | - Sukanta Mondal
- Department of Biological Sciences, Birla Institute of Technology and Science, Pilani, K.K. Birla Goa Campus, Zuarinagar, Goa 403726 India
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18
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Gruss MJ, O’Callaghan C, Donnellan M, Corsi AK. A Twist-Box domain of the C. elegans Twist homolog, HLH-8, plays a complex role in transcriptional regulation. Genetics 2023; 224:iyad066. [PMID: 37067863 PMCID: PMC10411555 DOI: 10.1093/genetics/iyad066] [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: 11/04/2022] [Revised: 11/04/2022] [Accepted: 03/21/2023] [Indexed: 04/18/2023] Open
Abstract
TWIST1 is a basic helix-loop-helix (bHLH) transcription factor in humans that functions in mesoderm differentiation. TWIST1 primarily regulates genes as a transcriptional repressor often through TWIST-Box domain-mediated protein-protein interactions. The TWIST-Box also can function as an activation domain requiring 3 conserved, equidistant amino acids (LXXXFXXXR). Autosomal dominant mutations in TWIST1, including 2 reported in these conserved amino acids (F187L and R191M), lead to craniofacial defects in Saethre-Chotzen syndrome (SCS). Caenorhabditis elegans has a single TWIST1 homolog, HLH-8, that functions in the differentiation of the muscles responsible for egg laying and defecation. Null alleles in hlh-8 lead to severely egg-laying defective and constipated animals due to defects in the corresponding muscles. TWIST1 and HLH-8 share sequence identity in their bHLH regions; however, the domain responsible for the transcriptional activity of HLH-8 is unknown. Sequence alignment suggests that HLH-8 has a TWIST-Box LXXXFXXXR motif; however, its function also is unknown. CRISPR/Cas9 genome editing was utilized to generate a domain deletion and several missense mutations, including those analogous to SCS patients, in the 3 conserved HLH-8 amino acids to investigate their functional role. The TWIST-Box alleles did not phenocopy hlh-8 null mutants. The strongest phenotype detected was a retentive (Ret) phenotype with late-stage embryos in the hermaphrodite uterus. Further, GFP reporters of HLH-8 downstream target genes (arg-1::gfp and egl-15::gfp) revealed tissue-specific, target-specific, and allele-specific defects. Overall, the TWIST-Box in HLH-8 is partially required for the protein's transcriptional activity, and the conserved amino acids contribute unequally to the domain's function.
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Affiliation(s)
- Michael J Gruss
- Department of Biology, The Catholic University of America, 620 Michigan Ave., NE, Washington, D.C. 20064USA
| | - Colleen O’Callaghan
- Department of Biology, The Catholic University of America, 620 Michigan Ave., NE, Washington, D.C. 20064USA
| | - Molly Donnellan
- Department of Biology, The Catholic University of America, 620 Michigan Ave., NE, Washington, D.C. 20064USA
| | - Ann K Corsi
- Department of Biology, The Catholic University of America, 620 Michigan Ave., NE, Washington, D.C. 20064USA
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19
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Xue G, Fan Y, Zheng C, Yang H, Feng L, Chen X, Yang Y, Yao X, Weng W, Kong L, Liu C, Cheng J, Ruan J. bHLH transcription factor family identification, phylogeny, and its response to abiotic stress in Chenopodium quinoa. FRONTIERS IN PLANT SCIENCE 2023; 14:1171518. [PMID: 37476176 PMCID: PMC10355129 DOI: 10.3389/fpls.2023.1171518] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/22/2023] [Accepted: 04/21/2023] [Indexed: 07/22/2023]
Abstract
The second-largest transcription factor superfamily in plants is that of the basic helix-loop-helix (bHLH) family, which plays an important complex physiological role in plant growth, tissue development, and environmental adaptation. Systematic research on the Chenopodium quinoa bHLH family will enable a better understanding of this species. Herein, authors used a variety of bioinformatics methods and quantitative Real-Time Polymerase Chain Reaction (qRT-PCR) to explore the evolution and function of the 218 CqbHLH genes identified. A total of 218 CqbHLH transcription factor genes were identified in the whole genome, located on 18 chromosomes. A phylogenetic tree was constructed using the CqbHLH and AtbHLH proteins to determine their homology, and the members were divided into 20 subgroups and one unclustered gene. Authors also analyzed 218 CqbHLH genes, conservative motifs, chromosome diffusion, and gene replication. The author constructed one Neighbor-Joining (NJ) tree and a collinearity analysis map of the bHLH family in C. quinoa and six other plant species to study the evolutionary relationship and homology among multiple species. In addition, the expression levels of 20 CqbHLH members from different subgroups in various tissues, different fruit developmental stages, and six abiotic stresses were analyzed. Authors identified 218 CqbHLH genes and studied their biological functions, providing a basis for better understanding and further studying the bHLH family in quinoa.
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Affiliation(s)
- Guoxing Xue
- College of Agriculture, Guizhou University, Guiyang, Guizhou, China
| | - Yue Fan
- College of Food Science and Engineering, Xinjiang Institute of Technology, Aksu, China
| | - Chunyu Zheng
- College of Food Science and Engineering, Xinjiang Institute of Technology, Aksu, China
| | - Hao Yang
- Agricultural Service Center of Langde Town, Kaili, Guizhou, China
| | - Liang Feng
- Chengdu Institute of Food Inspection, Chengdu, Sichuan, China
| | - Xingyu Chen
- College of Agriculture, Guizhou University, Guiyang, Guizhou, China
| | - Yanqi Yang
- College of Agriculture, Guizhou University, Guiyang, Guizhou, China
| | - Xin Yao
- College of Agriculture, Guizhou University, Guiyang, Guizhou, China
| | - Wenfeng Weng
- College of Agriculture, Guizhou University, Guiyang, Guizhou, China
| | - Lingyan Kong
- The First Senior Middle School of Yuanyang County, Xinxiang, Henan, China
| | - Chuang Liu
- Henan Institute of Technology, Xinxiang, Henan, China
| | - Jianping Cheng
- College of Agriculture, Guizhou University, Guiyang, Guizhou, China
| | - Jingjun Ruan
- College of Agriculture, Guizhou University, Guiyang, Guizhou, China
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20
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Michael AK, Stoos L, Crosby P, Eggers N, Nie XY, Makasheva K, Minnich M, Healy KL, Weiss J, Kempf G, Cavadini S, Kater L, Seebacher J, Vecchia L, Chakraborty D, Isbel L, Grand RS, Andersch F, Fribourgh JL, Schübeler D, Zuber J, Liu AC, Becker PB, Fierz B, Partch CL, Menet JS, Thomä NH. Cooperation between bHLH transcription factors and histones for DNA access. Nature 2023; 619:385-393. [PMID: 37407816 PMCID: PMC10338342 DOI: 10.1038/s41586-023-06282-3] [Citation(s) in RCA: 18] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2022] [Accepted: 06/02/2023] [Indexed: 07/07/2023]
Abstract
The basic helix-loop-helix (bHLH) family of transcription factors recognizes DNA motifs known as E-boxes (CANNTG) and includes 108 members1. Here we investigate how chromatinized E-boxes are engaged by two structurally diverse bHLH proteins: the proto-oncogene MYC-MAX and the circadian transcription factor CLOCK-BMAL1 (refs. 2,3). Both transcription factors bind to E-boxes preferentially near the nucleosomal entry-exit sites. Structural studies with engineered or native nucleosome sequences show that MYC-MAX or CLOCK-BMAL1 triggers the release of DNA from histones to gain access. Atop the H2A-H2B acidic patch4, the CLOCK-BMAL1 Per-Arnt-Sim (PAS) dimerization domains engage the histone octamer disc. Binding of tandem E-boxes5-7 at endogenous DNA sequences occurs through direct interactions between two CLOCK-BMAL1 protomers and histones and is important for circadian cycling. At internal E-boxes, the MYC-MAX leucine zipper can also interact with histones H2B and H3, and its binding is indirectly enhanced by OCT4 elsewhere on the nucleosome. The nucleosomal E-box position and the type of bHLH dimerization domain jointly determine the histone contact, the affinity and the degree of competition and cooperativity with other nucleosome-bound factors.
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Affiliation(s)
- Alicia K Michael
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland
- University of Basel, Basel, Switzerland
| | - Lisa Stoos
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland
- University of Basel, Basel, Switzerland
| | - Priya Crosby
- Department of Chemistry and Biochemistry, University of California, Santa Cruz, Santa Cruz, CA, USA
| | - Nikolas Eggers
- Biomedical Center, Molecular Biology Division, Ludwig-Maximilians-Universität, Munich, Germany
| | - Xinyu Y Nie
- Department of Biology, Center for Biological Clock Research, Texas A&M University, College Station, TX, USA
| | - Kristina Makasheva
- Institute of Chemical Sciences and Engineering, Ecole Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | - Martina Minnich
- Research Institute of Molecular Pathology, Vienna BioCenter, Vienna, Austria
| | - Kelly L Healy
- Department of Physiology and Aging, College of Medicine, University of Florida, Gainesville, FL, USA
| | - Joscha Weiss
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland
- University of Basel, Basel, Switzerland
| | - Georg Kempf
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland
| | - Simone Cavadini
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland
| | - Lukas Kater
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland
| | - Jan Seebacher
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland
| | - Luca Vecchia
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland
| | - Deyasini Chakraborty
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland
- University of Basel, Basel, Switzerland
| | - Luke Isbel
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland
| | - Ralph S Grand
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland
| | - Florian Andersch
- Research Institute of Molecular Pathology, Vienna BioCenter, Vienna, Austria
| | - Jennifer L Fribourgh
- Department of Chemistry and Biochemistry, University of California, Santa Cruz, Santa Cruz, CA, USA
| | - Dirk Schübeler
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland
- University of Basel, Basel, Switzerland
| | - Johannes Zuber
- Research Institute of Molecular Pathology, Vienna BioCenter, Vienna, Austria
- Medical University of Vienna, Vienna, Austria
| | - Andrew C Liu
- Department of Physiology and Aging, College of Medicine, University of Florida, Gainesville, FL, USA
| | - Peter B Becker
- Biomedical Center, Molecular Biology Division, Ludwig-Maximilians-Universität, Munich, Germany
| | - Beat Fierz
- Institute of Chemical Sciences and Engineering, Ecole Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | - Carrie L Partch
- Department of Chemistry and Biochemistry, University of California, Santa Cruz, Santa Cruz, CA, USA
| | - Jerome S Menet
- Department of Biology, Center for Biological Clock Research, Texas A&M University, College Station, TX, USA
| | - Nicolas H Thomä
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland.
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21
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Plant E, Bellefroid M, Van Lint C. A complex network of transcription factors and epigenetic regulators involved in bovine leukemia virus transcriptional regulation. Retrovirology 2023; 20:11. [PMID: 37268923 DOI: 10.1186/s12977-023-00623-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2023] [Accepted: 05/09/2023] [Indexed: 06/04/2023] Open
Abstract
Bovine Leukemia Virus (BLV) is the etiological agent of enzootic bovine leukosis, a disease characterized by the neoplastic proliferation of B cells in cattle. While most European countries have introduced efficient eradication programs, BLV is still present worldwide and no treatment is available. A major feature of BLV infection is the viral latency, which enables the escape from the host immune system, the maintenance of a persistent infection and ultimately the tumoral development. BLV latency is a multifactorial phenomenon resulting in the silencing of viral genes due to genetic and epigenetic repressions of the viral promoter located in the 5' Long Terminal Repeat (5'LTR). However, viral miRNAs and antisense transcripts are expressed from two different proviral regions, respectively the miRNA cluster and the 3'LTR. These latter transcripts are expressed despite the viral latency affecting the 5'LTR and are increasingly considered to take part in tumoral development. In the present review, we provide a summary of the experimental evidence that has enabled to characterize the molecular mechanisms regulating each of the three BLV transcriptional units, either through cis-regulatory elements or through epigenetic modifications. Additionally, we describe the recently identified BLV miRNAs and antisense transcripts and their implications in BLV-induced tumorigenesis. Finally, we discuss the relevance of BLV as an experimental model for the closely related human T-lymphotropic virus HTLV-1.
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Affiliation(s)
- Estelle Plant
- Service of Molecular Virology, Department of Molecular Biology (DBM), Université Libre de Bruxelles (ULB), 6041, Gosselies, Belgium
| | - Maxime Bellefroid
- Service of Molecular Virology, Department of Molecular Biology (DBM), Université Libre de Bruxelles (ULB), 6041, Gosselies, Belgium
| | - Carine Van Lint
- Service of Molecular Virology, Department of Molecular Biology (DBM), Université Libre de Bruxelles (ULB), 6041, Gosselies, Belgium.
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22
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Santos VC, Ostler JB, Harrison KS, Jones C. Slug, a Stress-Induced Transcription Factor, Stimulates Herpes Simplex Virus 1 Replication and Transactivates a cis-Regulatory Module within the VP16 Promoter. J Virol 2023; 97:e0007323. [PMID: 37022165 PMCID: PMC10134811 DOI: 10.1128/jvi.00073-23] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2023] [Accepted: 03/16/2023] [Indexed: 04/07/2023] Open
Abstract
Stress-mediated activation of the glucocorticoid receptor (GR) and specific stress-induced transcription factors stimulate herpes simplex virus 1 (HSV-1) productive infection, explant-induced reactivation, and immediate early (IE) promoters that drive expression of infected cell protein 0 (ICP0), ICP4, and ICP27. Several published studies concluded the virion tegument protein VP16, ICP0, and/or ICP4 drives early steps of reactivation from latency. Notably, VP16 protein expression was induced in trigeminal ganglionic neurons of Swiss Webster or C57BL/6J mice during early stages of stress-induced reactivation. If VP16 mediates reactivation, we hypothesized stress-induced cellular transcription factors would stimulate its expression. To address this hypothesis, we tested whether stress-induced transcription factors transactivate a VP16 cis-regulatory module (CRM) located upstream of the VP16 TATA box (-249 to -30). Initial studies revealed the VP16 CRM cis-activated a minimal promoter more efficiently in mouse neuroblastoma cells (Neuro-2A) than mouse fibroblasts (NIH-3T3). GR and Slug, a stress-induced transcription factor that binds enhancer boxes (E-boxes), were the only stress-induced transcription factors examined that transactivated the VP16 CRM construct. GR- and Slug-mediated transactivation was reduced to basal levels when the E-box, two 1/2 GR response elements (GREs), or NF-κB binding site was mutated. Previous studies revealed GR and Slug cooperatively transactivated the ICP4 CRM, but not ICP0 or ICP27. Silencing of Slug expression in Neuro-2A cells significantly reduced viral replication, indicating Slug-mediated transactivation of ICP4 and VP16 CRM activity correlates with enhanced viral replication and reactivation from latency. IMPORTANCE Herpes simplex virus 1 (HSV-1) establishes lifelong latency in several types of neurons. Periodically cellular stressors trigger reactivation from latency. Viral regulatory proteins are not abundantly expressed during latency, indicating cellular transcription factors mediate early stages of reactivation. Notably, the glucocorticoid receptor (GR) and certain stress-induced transcription factors transactivate cis-regulatory modules (CRMs) essential for expression of infected cell protein 0 (ICP0) and ICP4, key viral transcriptional regulatory proteins linked to triggering reactivation from latency. Virion protein 16 (VP16) specifically transactivates IE promoter and was also reported to mediate early stages of reactivation from latency. GR and Slug, a stress-induced enhancer box (E-box) binding protein, transactivate a minimal promoter downstream of VP16 CRM, and these transcription factors occupy VP16 CRM sequences in transfected cells. Notably, Slug stimulates viral replication in mouse neuroblastoma cells suggesting Slug, by virtue of transactivating VP16 and ICP4 CRM sequences, can trigger reactivation in certain neurons.
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Affiliation(s)
- Vanessa Claire Santos
- Oklahoma State University, College of Veterinary Medicine, Department of Veterinary Pathobiology, Stillwater, Oklahoma, USA
| | - Jeffery B. Ostler
- Oklahoma State University, College of Veterinary Medicine, Department of Veterinary Pathobiology, Stillwater, Oklahoma, USA
| | - Kelly S. Harrison
- Oklahoma State University, College of Veterinary Medicine, Department of Veterinary Pathobiology, Stillwater, Oklahoma, USA
| | - Clinton Jones
- Oklahoma State University, College of Veterinary Medicine, Department of Veterinary Pathobiology, Stillwater, Oklahoma, USA
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23
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Ge Y, Chen X, Nan N, Bard J, Wu F, Yergeau D, Liu T, Wang J, Mu X. Key transcription factors influence the epigenetic landscape to regulate retinal cell differentiation. Nucleic Acids Res 2023; 51:2151-2176. [PMID: 36715342 PMCID: PMC10018358 DOI: 10.1093/nar/gkad026] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2022] [Revised: 01/05/2023] [Accepted: 01/09/2023] [Indexed: 01/31/2023] Open
Abstract
How the diverse neural cell types emerge from multipotent neural progenitor cells during central nervous system development remains poorly understood. Recent scRNA-seq studies have delineated the developmental trajectories of individual neural cell types in many neural systems including the neural retina. Further understanding of the formation of neural cell diversity requires knowledge about how the epigenetic landscape shifts along individual cell lineages and how key transcription factors regulate these changes. In this study, we dissect the changes in the epigenetic landscape during early retinal cell differentiation by scATAC-seq and identify globally the enhancers, enriched motifs, and potential interacting transcription factors underlying the cell state/type specific gene expression in individual lineages. Using CUT&Tag, we further identify the enhancers bound directly by four key transcription factors, Otx2, Atoh7, Pou4f2 and Isl1, including those dependent on Atoh7, and uncover the sequential and combinatorial interactions of these factors with the epigenetic landscape to control gene expression along individual retinal cell lineages such as retinal ganglion cells (RGCs). Our results reveal a general paradigm in which transcription factors collaborate and compete to regulate the emergence of distinct retinal cell types such as RGCs from multipotent retinal progenitor cells (RPCs).
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Affiliation(s)
- Yichen Ge
- Department of Ophthalmology/Ross Eye Institute, Jacobs School of Medicine and Biomedical Sciences, University at Buffalo, Buffalo, NY, USA
| | - Xushen Chen
- Department of Ophthalmology/Ross Eye Institute, Jacobs School of Medicine and Biomedical Sciences, University at Buffalo, Buffalo, NY, USA
| | - Nan Nan
- Department of Ophthalmology/Ross Eye Institute, Jacobs School of Medicine and Biomedical Sciences, University at Buffalo, Buffalo, NY, USA
- Department of Biostatistics, School of Public Health and Health Professions, University at Buffalo, Buffalo, NY, USA
| | - Jonathan Bard
- New York State Center of Excellence in Bioinformatics and Life Sciences, University at Buffalo, Buffalo, NY, USA
| | - Fuguo Wu
- Department of Ophthalmology/Ross Eye Institute, Jacobs School of Medicine and Biomedical Sciences, University at Buffalo, Buffalo, NY, USA
| | - Donald Yergeau
- New York State Center of Excellence in Bioinformatics and Life Sciences, University at Buffalo, Buffalo, NY, USA
| | - Tao Liu
- Department of Biostatistics & Bioinformatics, Roswell Park Comprehensive Cancer Center, Buffalo, NY, USA
| | - Jie Wang
- Correspondence may also be addressed to Jie Wang.
| | - Xiuqian Mu
- To whom correspondence should be addressed. Tel: +1 716 881 7463; Fax: +1 716 887 2991;
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24
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Genetic Variation in Transcription Factor Binding Sites. Int J Mol Sci 2023; 24:ijms24055038. [PMID: 36902467 PMCID: PMC10003035 DOI: 10.3390/ijms24055038] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2023] [Accepted: 02/16/2023] [Indexed: 03/08/2023] Open
Abstract
The interaction between transcription factors (TFs) and DNA is the core process that determines the state of a cell's transcriptome [...].
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25
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Politano D, Gana S, Pezzotti E, Berardinelli A, Pasca L, Carmen Barbero V, Pichiecchio A, Maria Valente E, Errichiello E. A novel variant in NEUROD2 in a patient with Rett-like phenotype points to Glu130 codon as a mutational hotspot. Brain Dev 2023; 45:179-184. [PMID: 36446697 DOI: 10.1016/j.braindev.2022.11.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/18/2022] [Revised: 10/25/2022] [Accepted: 11/14/2022] [Indexed: 11/27/2022]
Abstract
BACKGROUND NEUROD2, encoding the neurogenic differentiation factor 2, is essential for neurodevelopment. To date, heterozygous missense variants in this gene have been identified in eight patients (from six unrelated families) with epileptic encephalopathy and developmental delay. CASE REPORT We describe a child with initial clinical suspicion of Rett/Rett-like syndrome, in whom exome sequencing detected a novel de novo variant (c.388G > A, p.Glu130Lys) in NEUROD2. Interestingly, a missense change affecting the same codon, c.388G > C (p.Glu130Gln), was previously identified in other two patients. CONCLUSIONS Our results suggest that Glu130 might represent a potential mutational hotspot of NEUROD2. Furthermore, the clinical findings (especially the absence of clinically overt seizures) strengthen the NEUROD2-phenotypic spectrum, implying that developmental delay may also manifest isolatedly. We suggest inclusion of NEUROD2-associated developmental and epileptic encephalopathies (DEEs) in the differential diagnosis of atypical Rett syndrome as well as gene panels related to autism spectrum disorder.
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Affiliation(s)
- Davide Politano
- Department of Brain and Behavioral Sciences, University of Pavia, Pavia, Italy
| | - Simone Gana
- Medical Genetics Unit, IRCCS Mondino Foundation, Pavia, Italy
| | - Elena Pezzotti
- Department of Brain and Behavioral Sciences, University of Pavia, Pavia, Italy
| | - Angela Berardinelli
- Department of Child Neurology and Psychiatry, IRCCS Mondino Foundation, Pavia, Italy
| | - Ludovica Pasca
- Department of Brain and Behavioral Sciences, University of Pavia, Pavia, Italy; Department of Child Neurology and Psychiatry, IRCCS Mondino Foundation, Pavia, Italy
| | | | - Anna Pichiecchio
- Department of Brain and Behavioral Sciences, University of Pavia, Pavia, Italy; Department of Neuroradiology, Advanced Imaging and Radiomics Center, IRCCS Mondino Foundation, Pavia, Italy
| | - Enza Maria Valente
- Medical Genetics Unit, IRCCS Mondino Foundation, Pavia, Italy; Department of Molecular Medicine, University of Pavia, Pavia, Italy
| | - Edoardo Errichiello
- Medical Genetics Unit, IRCCS Mondino Foundation, Pavia, Italy; Department of Molecular Medicine, University of Pavia, Pavia, Italy.
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26
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Ge L, Zhao G, Lan C, Song H, Qi D, Huang P, Ke X, Cui H. MESP2 binds competitively to TCF4 to suppress gastric cancer progression by regulating the SKP2/p27 axis. Cell Death Discov 2023; 9:79. [PMID: 36854722 PMCID: PMC9975210 DOI: 10.1038/s41420-023-01367-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2022] [Revised: 02/07/2023] [Accepted: 02/13/2023] [Indexed: 03/02/2023] Open
Abstract
Gastric cancer (GC) is a major cause of human deaths worldwide, and is notorious for its high incidence and mortality rates. Mesoderm Posterior Basic Helix-loop-helix (bHLH) transcription factor 2 (MESP2) acts as a transcription factor with a conserved bHLH domain. However, whether MESP2 contributes to tumorigenesis and its potential molecular mechanisms, remain unexplored. Noticeably, MESP2 expression levels are decreased in GC tissues and cell lines compared to those in normal tissue. Further, in vitro and in vivo experiments have confirmed that MESP2 overexpression suppresses GC cell growth, migration, and invasion, whereas MESP2 knockdown results in the exact opposite. Here, we present the first report that MESP2 binds to transcription factor 7-like 2 (TCF7L2/TCF4) to inhibit the activation of the TCF4/beta-catenin transcriptional complex, decrease the occupancy of the complex on the S-phase kinase Associated Protein 2 (SKP2) promoter, and promote p27 accumulation. MESP2 knockdown facilitated tumorigenesis, which was partially suppressed by SKP2 knockdown. Taken together, we conclude that MESP2 binds competitively to TCF4 to suppress GC progression by regulating the SKP2/p27 axis, thus offering a potential therapeutic strategy for future treatment.
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Affiliation(s)
- Lingjun Ge
- grid.263906.80000 0001 0362 4044State Key Laboratory of Silkworm Genome Biology, Southwest University, Chongqing, 400716 China
| | - Gaichao Zhao
- grid.263906.80000 0001 0362 4044State Key Laboratory of Silkworm Genome Biology, Southwest University, Chongqing, 400716 China
| | - Chao Lan
- grid.263906.80000 0001 0362 4044State Key Laboratory of Silkworm Genome Biology, Southwest University, Chongqing, 400716 China
| | - Houji Song
- grid.263906.80000 0001 0362 4044Cancer Center, Medical Research Institute, Southwest University, Chongqing, 400716 China
| | - Dan Qi
- grid.263906.80000 0001 0362 4044Cancer Center, Medical Research Institute, Southwest University, Chongqing, 400716 China
| | - Pan Huang
- grid.263906.80000 0001 0362 4044State Key Laboratory of Silkworm Genome Biology, Southwest University, Chongqing, 400716 China
| | - Xiaoxue Ke
- State Key Laboratory of Silkworm Genome Biology, Southwest University, Chongqing, 400716, China. .,Cancer Center, Medical Research Institute, Southwest University, Chongqing, 400716, China.
| | - Hongjuan Cui
- State Key Laboratory of Silkworm Genome Biology, Southwest University, Chongqing, 400716, China. .,Cancer Center, Medical Research Institute, Southwest University, Chongqing, 400716, China.
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27
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In Silico Examination of Single Nucleotide Missense Mutations in NHLH2, a Gene Linked to Infertility and Obesity. Int J Mol Sci 2023; 24:ijms24043193. [PMID: 36834605 PMCID: PMC9968165 DOI: 10.3390/ijms24043193] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2022] [Revised: 01/25/2023] [Accepted: 01/30/2023] [Indexed: 02/09/2023] Open
Abstract
Continual advances in our understanding of the human genome have led to exponential increases in known single nucleotide variants. The characterization of each of the variants lags behind. For researchers needing to study a single gene, or multiple genes in a pathway, there must be ways to narrow down pathogenic variants from those that are silent or pose less pathogenicity. In this study, we use the NHLH2 gene which encodes the nescient helix-loop-helix 2 (Nhlh2) transcription factor in a systematic analysis of all missense mutations to date in the gene. The NHLH2 gene was first described in 1992. Knockout mice created in 1997 indicated a role for this protein in body weight control, puberty, and fertility, as well as the motivation for sex and exercise. Only recently have human carriers of NHLH2 missense variants been characterized. Over 300 missense variants for the NHLH2 gene are listed in the NCBI single nucleotide polymorphism database (dbSNP). Using in silico tools, predicted pathogenicity of the variants narrowed the missense variants to 37 which were predicted to affect NHLH2 function. These 37 variants cluster around the basic-helix-loop-helix and DNA binding domains of the transcription factor, and further analysis using in silico tools provided 21 SNV resulting in 22 amino acid changes for future wet lab analysis. The tools used, findings, and predictions for the variants are discussed considering the known function of the NHLH2 transcription factor. Overall use of these in silico tools and analysis of these data contribute to our knowledge of a protein which is both involved in the human genetic syndrome, Prader-Willi syndrome, and in controlling genes involved in body weight control, fertility, puberty, and behavior in the general population, and may provide a systematic methodology for others to characterize variants for their gene of interest.
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28
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Chang S, Li Q, Huang B, Chen W, Tan H. Genome-wide identification and characterisation of bHLH transcription factors in Artemisia annua. BMC PLANT BIOLOGY 2023; 23:63. [PMID: 36721100 PMCID: PMC9890702 DOI: 10.1186/s12870-023-04063-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/13/2022] [Accepted: 01/13/2023] [Indexed: 06/18/2023]
Abstract
BACKGROUND A. annua (also named Artemisia annua, sweet wormwood) is the main source of the anti-malarial drug artemisinin, which is synthesised and stored in its trichomes. Members of the basic Helix-Loop-Helix (bHLH) family of transcription factors (TFs) have been implicated in artemisinin biosynthesis in A. annua and in trichome development in other plant species. RESULTS Here, we have systematically identified and characterised 226 putative bHLH TFs in A. annua. All of the proteins contain a HLH domain, 213 of which also contain the basic motif that mediates DNA binding of HLH dimers. Of these, 22 also contained a Myc domain that permits dimerisation with other families of TFs; only two proteins lacking the basic motif contained a Myc domain. Highly conserved GO annotations reflected the transcriptional regulatory role of the identified TFs, and suggested conserved roles in biological processes such as iron homeostasis, and guard cell and endosperm development. Expression analysis revealed that three genes (AabHLH80, AabHLH96, and AaMyc-bHLH3) exhibited spatiotemporal expression patterns similar to genes encoding key enzymes in artemisinin synthesis. CONCLUSIONS This comprehensive analysis of bHLH TFs provides a new resource to direct further analysis into key molecular mechanisms underlying and regulating artemisinin biosynthesis and trichome development, as well as other biological processes, in the key medicinal plant A. annua.
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Affiliation(s)
- Shuwei Chang
- Department Chinese Medicine Authentication, College of Pharmacy, Naval Medical University (Second Military Medical University), Shanghai, China
- Department of Pharmacy, Shanghai Fourth People’s Hospital Affiliated to Tongji University School of Medicine, Shanghai, China
| | - Qi Li
- Department Chinese Medicine Authentication, College of Pharmacy, Naval Medical University (Second Military Medical University), Shanghai, China
| | - Baokang Huang
- Department Chinese Medicine Authentication, College of Pharmacy, Naval Medical University (Second Military Medical University), Shanghai, China
| | - Wansheng Chen
- Department Chinese Medicine Authentication, College of Pharmacy, Naval Medical University (Second Military Medical University), Shanghai, China
| | - Hexin Tan
- Department Chinese Medicine Authentication, College of Pharmacy, Naval Medical University (Second Military Medical University), Shanghai, China
- Department of Pharmacy, Shanghai Fourth People’s Hospital Affiliated to Tongji University School of Medicine, Shanghai, China
- Shanghai Key Laboratory for Pharmaceutical Metabolite Research, Shanghai, China
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29
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Kaiyrlykyzy A, Umbayev B, Masoud AR, Baibulatova A, Tsoy A, Olzhayev F, Alzhanova D, Zholdasbekova G, Davletov K, Akilzhanova A, Askarova S. Circulating adiponectin levels, expression of adiponectin receptors, and methylation of adiponectin gene promoter in relation to Alzheimer's disease. BMC Med Genomics 2022; 15:262. [PMID: 36527105 PMCID: PMC9756783 DOI: 10.1186/s12920-022-01420-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2022] [Accepted: 12/13/2022] [Indexed: 12/23/2022] Open
Abstract
BACKGROUND The role of adiponectin (ADIPOQ) in Alzheimer's disease (AD) has been documented, however, demonstrating controversial results. In this study, we investigated blood serum ADIPOQ levels, methylation of the adiponectin gene promoter, and adiponectin receptors (AdipoR1 and AdipoR2) expression in blood samples isolated from AD patients and healthy controls. METHODS We performed a case-control study including 248 subjects (98 AD patients and 150 healthy controls); ADIPOQ serum levels, AdipoR1, and AdipoR2 levels in PBMC were measured by ELISA Kits, and ADIPOQ gene methylation was analyzed using methyl-specific PCR. RESULTS Serum adiponectin levels were threefold higher in the AD group compared to the controls. We have also found a positive correlation between adiponectin and MMSE scores and high-density lipoprotein cholesterol (HDL-C) in AD patients. A significant difference in the proportion of methylation of the CpG sites at - 74 nt of the ADIPOQ gene promoter was detected in AD cases, and the levels of adiponectin in blood serum were significantly higher in methylated samples in the AD group compared to controls. The amount of AdipoR1 was significantly higher among AD subjects, while the expression of AdipoR2 did not vary between AD patients and controls. CONCLUSION These findings may contribute to a deeper understanding of the etiological factors leading to the development of dementia and may serve as a basis for the development of predictive biomarkers of AD.
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Affiliation(s)
- Aiym Kaiyrlykyzy
- grid.428191.70000 0004 0495 7803Center for Life Sciences, National Laboratory Astana, Nazarbayev University, 53 Kabanbay Batyr Avenue, Astana, Kazakhstan ,grid.77184.3d0000 0000 8887 5266Faculty of Medicine and Public Health, al-Farabi Kazakh National University, Almaty, Kazakhstan
| | - Bauyrzhan Umbayev
- grid.428191.70000 0004 0495 7803Center for Life Sciences, National Laboratory Astana, Nazarbayev University, 53 Kabanbay Batyr Avenue, Astana, Kazakhstan
| | - Abdul-Razak Masoud
- grid.428191.70000 0004 0495 7803Center for Life Sciences, National Laboratory Astana, Nazarbayev University, 53 Kabanbay Batyr Avenue, Astana, Kazakhstan ,grid.259237.80000000121506076Louisiana Tech University, Ruston, LA USA
| | - Aida Baibulatova
- grid.428191.70000 0004 0495 7803Center for Life Sciences, National Laboratory Astana, Nazarbayev University, 53 Kabanbay Batyr Avenue, Astana, Kazakhstan
| | - Andrey Tsoy
- grid.428191.70000 0004 0495 7803Center for Life Sciences, National Laboratory Astana, Nazarbayev University, 53 Kabanbay Batyr Avenue, Astana, Kazakhstan
| | - Farkhad Olzhayev
- grid.428191.70000 0004 0495 7803Center for Life Sciences, National Laboratory Astana, Nazarbayev University, 53 Kabanbay Batyr Avenue, Astana, Kazakhstan
| | - Dinara Alzhanova
- grid.501850.90000 0004 0467 386XDepartment of Neurology and Psychiatry, Astana Medical University, Astana, Kazakhstan ,Open Clinic, Astana, Kazakhstan
| | - Gulnaz Zholdasbekova
- grid.443557.40000 0004 0400 6856Karaganda State Medical University, Karaganda, Kazakhstan
| | - Kairat Davletov
- grid.443453.10000 0004 0387 8740Asfendiyarov Kazakh National Medical University, Almaty, Kazakhstan
| | - Ainur Akilzhanova
- grid.428191.70000 0004 0495 7803Center for Life Sciences, National Laboratory Astana, Nazarbayev University, 53 Kabanbay Batyr Avenue, Astana, Kazakhstan
| | - Sholpan Askarova
- grid.428191.70000 0004 0495 7803Center for Life Sciences, National Laboratory Astana, Nazarbayev University, 53 Kabanbay Batyr Avenue, Astana, Kazakhstan
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30
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False-positive IRESes from Hoxa9 and other genes resulting from errors in mammalian 5' UTR annotations. Proc Natl Acad Sci U S A 2022; 119:e2122170119. [PMID: 36037358 PMCID: PMC9456764 DOI: 10.1073/pnas.2122170119] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Hyperconserved genomic sequences have great promise for understanding core biological processes. It has been recently proposed that scores of hyperconserved 5' untranslated regions (UTRs), also known as transcript leaders (hTLs), encode internal ribosome entry sites (IRESes) that drive cap-independent translation, in part, via interactions with ribosome expansion segments. However, the direct functional significance of such interactions has not yet been definitively demonstrated. We provide evidence that the putative IRESes previously reported in Hox gene hTLs are rarely included in transcript leaders. Instead, these regions function independently as transcriptional promoters. In addition, we find the proposed RNA structure of the putative Hoxa9 IRES is not conserved. Instead, sequences previously shown to be essential for putative IRES activity encode a hyperconserved transcription factor binding site (E-box) that contributes to its promoter activity and is bound by several transcription factors, including USF1 and USF2. Similar E-box sequences enhance the promoter activities of other putative Hoxa gene IRESes. Moreover, we provide evidence that the vast majority of hTLs with putative IRES activity overlap transcriptional promoters, enhancers, and 3' splice sites that are most likely responsible for their reported IRES activities. These results argue strongly against recently reported widespread IRES-like activities from hTLs and contradict proposed interactions between ribosomal expansion segment ES9S and putative IRESes. Furthermore, our work underscores the importance of accurate transcript annotations, controls in bicistronic reporter assays, and the power of synthesizing publicly available data from multiple sources.
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31
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Lynch AW, Theodoris CV, Long HW, Brown M, Liu XS, Meyer CA. MIRA: joint regulatory modeling of multimodal expression and chromatin accessibility in single cells. Nat Methods 2022; 19:1097-1108. [PMID: 36068320 PMCID: PMC9517733 DOI: 10.1038/s41592-022-01595-z] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2021] [Accepted: 07/26/2022] [Indexed: 02/06/2023]
Abstract
Rigorously comparing gene expression and chromatin accessibility in the same single cells could illuminate the logic of how coupling or decoupling of these mechanisms regulates fate commitment. Here we present MIRA, probabilistic multimodal models for integrated regulatory analysis, a comprehensive methodology that systematically contrasts transcription and accessibility to infer the regulatory circuitry driving cells along cell state trajectories. MIRA leverages topic modeling of cell states and regulatory potential modeling of individual gene loci. MIRA thereby represents cell states in an efficient and interpretable latent space, infers high-fidelity cell state trees, determines key regulators of fate decisions at branch points and exposes the variable influence of local accessibility on transcription at distinct loci. Applied to epidermal differentiation and embryonic brain development from two different multimodal platforms, MIRA revealed that early developmental genes were tightly regulated by local chromatin landscape whereas terminal fate genes were titrated without requiring extensive chromatin remodeling.
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Affiliation(s)
- Allen W Lynch
- Department of Data Science, Dana-Farber Cancer Institute, Boston, MA, USA.,Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Christina V Theodoris
- Department of Data Science, Dana-Farber Cancer Institute, Boston, MA, USA.,Division of Genetics and Genomics, Boston Children's Hospital, Boston, MA, USA.,Harvard Medical School Genetics Training Program, Boston, MA, USA
| | - Henry W Long
- Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA, USA.,Department of Medical Oncology, Dana-Farber Cancer Institute, Brigham and Women's Hospital, and Harvard Medical School, Boston, MA, USA
| | - Myles Brown
- Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA, USA.,Department of Medical Oncology, Dana-Farber Cancer Institute, Brigham and Women's Hospital, and Harvard Medical School, Boston, MA, USA
| | - X Shirley Liu
- Department of Data Science, Dana-Farber Cancer Institute, Boston, MA, USA. .,Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA, USA. .,Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA, USA.
| | - Clifford A Meyer
- Department of Data Science, Dana-Farber Cancer Institute, Boston, MA, USA. .,Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA, USA. .,Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA, USA.
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32
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Hersbach BA, Fischer DS, Masserdotti G, Deeksha, Mojžišová K, Waltzhöni T, Rodriguez-Terrones D, Heinig M, Theis FJ, Götz M, Stricker SH. Probing cell identity hierarchies by fate titration and collision during direct reprogramming. Mol Syst Biol 2022; 18:e11129. [PMID: 36106915 PMCID: PMC9476893 DOI: 10.15252/msb.202211129] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2022] [Revised: 08/01/2022] [Accepted: 08/17/2022] [Indexed: 11/17/2022] Open
Abstract
Despite the therapeutic promise of direct reprogramming, basic principles concerning fate erasure and the mechanisms to resolve cell identity conflicts remain unclear. To tackle these fundamental questions, we established a single‐cell protocol for the simultaneous analysis of multiple cell fate conversion events based on combinatorial and traceable reprogramming factor expression: Collide‐seq. Collide‐seq revealed the lack of a common mechanism through which fibroblast‐specific gene expression loss is initiated. Moreover, we found that the transcriptome of converting cells abruptly changes when a critical level of each reprogramming factor is attained, with higher or lower levels not contributing to major changes. By simultaneously inducing multiple competing reprogramming factors, we also found a deterministic system, in which titration of fates against each other yields dominant or colliding fates. By investigating one collision in detail, we show that reprogramming factors can disturb cell identity programs independent of their ability to bind their target genes. Taken together, Collide‐seq has shed light on several fundamental principles of fate conversion that may aid in improving current reprogramming paradigms.
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Affiliation(s)
- Bob A Hersbach
- Institute of Stem Cell Research, Helmholtz Zentrum München, German Research Center for Environmental Health, Oberschleißheim, Germany.,Division of Physiological Genomics, Biomedical Center Munich, Ludwig-Maximilians University, Munich, Germany.,Graduate School of Systemic Neurosciences, Biocenter, Ludwig-Maximilians University, Munich, Germany
| | - David S Fischer
- Institute of Computational Biology, Helmholtz Zentrum München, German Research Center for Environmental Health, Oberschleißheim, Germany.,TUM School of Life Sciences Weihenstephan, Technical University of Munich, Freising, Germany.,Department of Informatics, Technical University of Munich, Munich, Germany
| | - Giacomo Masserdotti
- Institute of Stem Cell Research, Helmholtz Zentrum München, German Research Center for Environmental Health, Oberschleißheim, Germany.,Division of Physiological Genomics, Biomedical Center Munich, Ludwig-Maximilians University, Munich, Germany
| | - Deeksha
- Institute of Stem Cell Research, Helmholtz Zentrum München, German Research Center for Environmental Health, Oberschleißheim, Germany.,Division of Physiological Genomics, Biomedical Center Munich, Ludwig-Maximilians University, Munich, Germany
| | - Karolina Mojžišová
- Institute of Computational Biology, Helmholtz Zentrum München, German Research Center for Environmental Health, Oberschleißheim, Germany
| | - Thomas Waltzhöni
- Institute of Computational Biology, Helmholtz Zentrum München, German Research Center for Environmental Health, Oberschleißheim, Germany.,Core Facility Genomics, Helmholtz Zentrum München, Oberschleißheim, Germany
| | - Diego Rodriguez-Terrones
- Institute of Computational Biology, Helmholtz Zentrum München, German Research Center for Environmental Health, Oberschleißheim, Germany
| | - Matthias Heinig
- Institute of Computational Biology, Helmholtz Zentrum München, German Research Center for Environmental Health, Oberschleißheim, Germany.,Department of Informatics, Technical University of Munich, Munich, Germany
| | - Fabian J Theis
- Institute of Computational Biology, Helmholtz Zentrum München, German Research Center for Environmental Health, Oberschleißheim, Germany.,TUM School of Life Sciences Weihenstephan, Technical University of Munich, Freising, Germany.,Department of Informatics, Technical University of Munich, Munich, Germany.,German Excellence Cluster of Systems Neurology, Biomedical Center Munich, Munich, Germany
| | - Magdalena Götz
- Institute of Stem Cell Research, Helmholtz Zentrum München, German Research Center for Environmental Health, Oberschleißheim, Germany.,Division of Physiological Genomics, Biomedical Center Munich, Ludwig-Maximilians University, Munich, Germany.,German Excellence Cluster of Systems Neurology, Biomedical Center Munich, Munich, Germany
| | - Stefan H Stricker
- Institute of Stem Cell Research, Helmholtz Zentrum München, German Research Center for Environmental Health, Oberschleißheim, Germany.,Division of Physiological Genomics, Biomedical Center Munich, Ludwig-Maximilians University, Munich, Germany
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33
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Bachu VS, Kandoi S, Park KU, Kaufman ML, Schwanke M, Lamba DA, Brzezinski JA. An enhancer located in a Pde6c intron drives transient expression in the cone photoreceptors of developing mouse and human retinas. Dev Biol 2022; 488:131-150. [PMID: 35644251 PMCID: PMC10676565 DOI: 10.1016/j.ydbio.2022.05.012] [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: 01/27/2022] [Revised: 04/29/2022] [Accepted: 05/19/2022] [Indexed: 02/04/2023]
Abstract
How cone photoreceptors are formed during retinal development is only partially known. This is in part because we do not fully understand the gene regulatory network responsible for cone genesis. We reasoned that cis-regulatory elements (enhancers) active in nascent cones would be regulated by the same upstream network that controls cone formation. To dissect this network, we searched for enhancers active in developing cones. By electroporating enhancer-driven fluorescent reporter plasmids, we observed that a sequence within an intron of the cone-specific Pde6c gene acted as an enhancer in developing mouse cones. Similar fluorescent reporter plasmids were used to generate stable transgenic human induced pluripotent stem cells that were then grown into three-dimensional human retinal organoids. These organoids contained fluorescently labeled cones, demonstrating that the Pde6c enhancer was also active in human cones. We observed that enhancer activity was transient and labeled a minor population of developing rod photoreceptors in both mouse and human systems. This cone-enriched pattern argues that the Pde6c enhancer is activated in cells poised between rod and cone fates. Additionally, it suggests that the Pde6c enhancer is activated by the same regulatory network that selects or stabilizes cone fate choice. To further understand this regulatory network, we identified essential enhancer sequence regions through a series of mutagenesis experiments. This suggested that the Pde6c enhancer was regulated by transcription factor binding at five or more locations. Binding site predictions implicated transcription factor families known to control photoreceptor formation and families not previously associated with cone development. These results provide a framework for deciphering the gene regulatory network that controls cone genesis in both human and mouse systems. Our new transgenic human stem cell lines provide a tool for determining which cone developmental mechanisms are shared and distinct between mice and humans.
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Affiliation(s)
- Vismaya S Bachu
- Department of Ophthalmology, University of Colorado Anschutz Medical Campus, Aurora, CO, USA; Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Sangeetha Kandoi
- Department of Ophthalmology, University of California San Francisco, San Francisco, CA, USA; Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, University of California San Francisco, San Francisco, CA, USA
| | - Ko Uoon Park
- Department of Ophthalmology, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Michael L Kaufman
- Department of Ophthalmology, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Michael Schwanke
- Department of Ophthalmology, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Deepak A Lamba
- Department of Ophthalmology, University of California San Francisco, San Francisco, CA, USA; Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, University of California San Francisco, San Francisco, CA, USA
| | - Joseph A Brzezinski
- Department of Ophthalmology, University of Colorado Anschutz Medical Campus, Aurora, CO, USA.
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34
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Kim JY, Park M, Ohn J, Seong RH, Chung JH, Kim KH, Jo SJ, Kwon O. Twist2-driven chromatin remodeling governs the postnatal maturation of dermal fibroblasts. Cell Rep 2022; 39:110821. [PMID: 35584664 DOI: 10.1016/j.celrep.2022.110821] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2021] [Revised: 03/05/2022] [Accepted: 04/22/2022] [Indexed: 12/17/2022] Open
Abstract
Dermal fibroblasts lose stem cell potency after birth, which prevents regenerative healing. However, the underlying intracellular mechanisms are largely unknown. We uncover the postnatal maturation of papillary fibroblasts (PFs) driven by the extensive Twist2-mediated remodeling of chromatin accessibility. A loss of the regenerative ability of postnatal PFs occurs with decreased H3K27ac levels. Single-cell transcriptomics, assay for transposase-accessible chromatin sequencing (ATAC-seq), and chromatin immunoprecipitation sequencing (ChIP-seq) reveal the postnatal maturation trajectory associated with the loss of the regenerative trajectory in PFs, which is characterized by a marked decrease in chromatin accessibility and H3K27ac modifications. Histone deacetylase inhibition delays spontaneous chromatin remodeling, thus maintaining the regenerative ability of postnatal PFs. Genomic analysis identifies Twist2 as a major regulator within chromatin regions with decreased accessibility during the postnatal period. When Twist2 is genetically deleted in dermal fibroblasts, the intracellular cascade of postnatal maturation is significantly delayed. Our findings reveal the comprehensive intracellular mechanisms underlying intrinsic postnatal changes in dermal fibroblasts.
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Affiliation(s)
- Jin Yong Kim
- Department of Dermatology, Seoul National University College of Medicine, Seoul 03080, Korea; Laboratory of Cutaneous Aging and Hair Research, Biomedical Research Institute, Seoul National University Hospital, Seoul 03080, Korea; Institute of Human-Environment Interface Biology, Medical Research Center, Seoul National University, Seoul 03080, Korea; Department of Dermatology, Columbia University, New York 10032, NY, USA
| | - Minji Park
- Department of Dermatology, Seoul National University College of Medicine, Seoul 03080, Korea; Laboratory of Cutaneous Aging and Hair Research, Biomedical Research Institute, Seoul National University Hospital, Seoul 03080, Korea; Institute of Human-Environment Interface Biology, Medical Research Center, Seoul National University, Seoul 03080, Korea; Department of Biomedical Sciences, Seoul National University College of Medicine, Seoul 03080, Korea
| | - Jungyoon Ohn
- Department of Dermatology, Seoul National University College of Medicine, Seoul 03080, Korea; Laboratory of Cutaneous Aging and Hair Research, Biomedical Research Institute, Seoul National University Hospital, Seoul 03080, Korea; Institute of Human-Environment Interface Biology, Medical Research Center, Seoul National University, Seoul 03080, Korea
| | - Rho Hyun Seong
- Department of Biological Sciences, Institute of Molecular Biology and Genetics, Seoul National University, Seoul 08826, Korea
| | - Jin Ho Chung
- Department of Dermatology, Seoul National University College of Medicine, Seoul 03080, Korea; Laboratory of Cutaneous Aging and Hair Research, Biomedical Research Institute, Seoul National University Hospital, Seoul 03080, Korea; Institute of Human-Environment Interface Biology, Medical Research Center, Seoul National University, Seoul 03080, Korea; Department of Biomedical Sciences, Seoul National University College of Medicine, Seoul 03080, Korea
| | - Kyu Han Kim
- Department of Dermatology, Seoul National University College of Medicine, Seoul 03080, Korea; Laboratory of Cutaneous Aging and Hair Research, Biomedical Research Institute, Seoul National University Hospital, Seoul 03080, Korea; Institute of Human-Environment Interface Biology, Medical Research Center, Seoul National University, Seoul 03080, Korea
| | - Seong Jin Jo
- Department of Dermatology, Seoul National University College of Medicine, Seoul 03080, Korea; Laboratory of Cutaneous Aging and Hair Research, Biomedical Research Institute, Seoul National University Hospital, Seoul 03080, Korea; Institute of Human-Environment Interface Biology, Medical Research Center, Seoul National University, Seoul 03080, Korea.
| | - Ohsang Kwon
- Department of Dermatology, Seoul National University College of Medicine, Seoul 03080, Korea; Laboratory of Cutaneous Aging and Hair Research, Biomedical Research Institute, Seoul National University Hospital, Seoul 03080, Korea; Institute of Human-Environment Interface Biology, Medical Research Center, Seoul National University, Seoul 03080, Korea; Department of Biomedical Sciences, Seoul National University College of Medicine, Seoul 03080, Korea; Genomic Medicine Institute, Medical Research Center, Seoul National University College of Medicine, Seoul 03080, Korea.
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35
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Homologous basic helix–loop–helix transcription factors induce distinct deformations of torsionally-stressed DNA: a potential transcription regulation mechanism. QRB DISCOVERY 2022. [PMID: 37529292 PMCID: PMC10392670 DOI: 10.1017/qrd.2022.5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022] Open
Abstract
Abstract
Changing torsional restraints on DNA is essential for the regulation of transcription. Torsional stress, introduced by RNA polymerase, can propagate along chromatin facilitating topological transitions and modulating the specific binding of transcription factors (TFs) to DNA. Despite the importance, the mechanistic details on how torsional stress impacts the TFs-DNA complexation remain scarce. Herein, we address the impact of torsional stress on DNA complexation with homologous human basic helix–loop–helix (BHLH) hetero- and homodimers: MycMax, MadMax and MaxMax. The three TF dimers exhibit specificity towards the same DNA consensus sequence, the E-box response element, while regulating different transcriptional pathways. Using microseconds-long atomistic molecular dynamics simulations together with the torsional restraint that controls DNA total helical twist, we gradually over- and underwind naked and complexed DNA to a maximum of ± 5°/bp step. We observe that the binding of the BHLH dimers results in a similar increase in DNA torsional rigidity. However, under torsional stress the BHLH dimers induce distinct DNA deformations, characterised by changes in DNA grooves geometry and a significant asymmetric DNA bending. Supported by bioinformatics analyses, our data suggest that torsional stress may contribute to the execution of differential transcriptional programs of the homologous TFs by modulating their collaborative interactions.
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