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Dai Y, Zhong Y, Pan R, Yuan L, Fu Y, Chen Y, Du J, Li M, Wang X, Liu H, Shi C, Liu G, Zhu P, Shimeld S, Zhou X, Li G. Evolutionary origin of the chordate nervous system revealed by amphioxus developmental trajectories. Nat Ecol Evol 2024; 8:1693-1710. [PMID: 39025981 DOI: 10.1038/s41559-024-02469-7] [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: 06/12/2023] [Accepted: 06/17/2024] [Indexed: 07/20/2024]
Abstract
The common ancestor of all vertebrates had a highly sophisticated nervous system, but questions remain about the evolution of vertebrate neural cell types. The amphioxus, a chordate that diverged before the origin of vertebrates, can inform vertebrate evolution. Here we develop and analyse a single-cell RNA-sequencing dataset from seven amphioxus embryo stages to understand chordate cell type evolution and to study vertebrate neural cell type origins. We identified many new amphioxus cell types, including homologues to the vertebrate hypothalamus and neurohypophysis, rooting the evolutionary origin of these structures. On the basis of ancestor-descendant reconstruction of cell trajectories of the amphioxus and other species, we inferred expression dynamics of transcription factor genes throughout embryogenesis and identified three ancient developmental routes forming chordate neurons. We characterized cell specification at the mechanistic level and generated mutant lines to examine the function of five key transcription factors involved in neural specification. Our results show three developmental origins for the vertebrate nervous system: an anterior FoxQ2-dependent mechanism that is deeply conserved in invertebrates, a less-conserved route leading to more posterior neurons in the vertebrate spinal cord and a mechanism for specifying neuromesoderm progenitors that is restricted to chordates. The evolution of neuromesoderm progenitors may have led to a dramatic shift in posterior neural and mesodermal cell fate decisions and the body elongation process in a stem chordate.
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Affiliation(s)
- Yichen Dai
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiamen, China
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Beijing, China
| | - Yanhong Zhong
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiamen, China
| | - Rongrong Pan
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiamen, China
| | - Liang Yuan
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiamen, China
- School of Life Sciences, Xinjiang Normal University, Urumqi, China
| | - Yongheng Fu
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiamen, China
| | - Yuwei Chen
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiamen, China
| | - Juan Du
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Beijing, China
| | - Meng Li
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Beijing, China
| | - Xiao Wang
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Beijing, China
| | - Huimin Liu
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiamen, China
| | - Chenggang Shi
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiamen, China
| | - Gaoming Liu
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Beijing, China
| | - Pingfen Zhu
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Beijing, China
| | | | - Xuming Zhou
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Beijing, China.
| | - Guang Li
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiamen, China.
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Rodriguez-Gil JL, Nagy PL, Francke U. Optical genome mapping with genome sequencing identifies subtelomeric Xq28 deletion and inserted 7p22.3 duplication in a male with multisystem developmental disorder. Am J Med Genet A 2024:e63814. [PMID: 39011850 DOI: 10.1002/ajmg.a.63814] [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: 11/01/2023] [Revised: 03/24/2024] [Accepted: 06/27/2024] [Indexed: 07/17/2024]
Abstract
We report a 17-year-old male with supravalvular stenosis, initial failure to thrive and delayed early development, short stature, acromelia, dysmorphic facial features, hypertelorism, macrocephaly, syringomyelia, hypertension, and anxiety disorder. Fluorescent in situ hybridization (FISH), chromosomal microarray analysis (CMA), and exome sequencing (ES) were nondiagnostic. Combined optical genome mapping (OGM) and genome sequencing (GS) showed a complex rearrangement including an X chromosome with a 22.5 kb deletion in band Xq28 replaced by a 61.4 kb insertion of duplicated chromosome 7p22.3 material. The deletion removes the distal 3' untranslated region (UTR) of FUNDC2, the entire CMC4 and MTCP1, and the first five exons of BRCC3. Transcriptome analysis revealed absent expression of CMC4 and MTCP1 and BRCC3 with normal transcript level of FUNDC2. The inserted duplication includes only one known gene: UNCX. Similar overlapping Xq28 deletions have been reported to be associated with Moyamoya disease (MMD), short stature, hypergonadotropic hypogonadism (HH), and facial dysmorphism. Although he has short stature, our patient does not have signs of Moyamoya arteriopathy or hypogonadism. The structurally abnormal X chromosome was present in his mother, but not in his unaffected brother, maternal uncle, or maternal grandparents. We propose that the combination of his absent Xq28 and duplicated 7p22.3 genomic material is responsible for his phenotype. This case highlights the potential of combined OGM and GS for detecting complex structural variants compared with standard of care genetic testing such as CMA and ES.
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Affiliation(s)
- Jorge L Rodriguez-Gil
- Department of Pediatrics, Division of Medical Genetics, Stanford University School of Medicine, Stanford, California, USA
- Department of Pediatrics, Division of Neonatal and Developmental Medicine, Stanford University, Stanford, California, USA
| | | | - Uta Francke
- Department of Pediatrics, Division of Medical Genetics, Stanford University School of Medicine, Stanford, California, USA
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Sánchez RS, Lazarte MA, Abdala VSL, Sánchez SS. Antagonistic regulation of homeologous uncx.L and uncx.S genes orchestrates myotome and sclerotome differentiation in the evolutionarily divergent vertebral column of Xenopus laevis. JOURNAL OF EXPERIMENTAL ZOOLOGY. PART B, MOLECULAR AND DEVELOPMENTAL EVOLUTION 2024; 342:350-367. [PMID: 38155515 DOI: 10.1002/jez.b.23235] [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: 06/19/2023] [Revised: 12/04/2023] [Accepted: 12/05/2023] [Indexed: 12/30/2023]
Abstract
In anurans, the vertebral column diverges widely from that of other tetrapods; yet the molecular mechanisms underlying its morphogenesis remain largely unexplored. In this study, we investigate the role of the homeologous uncx.L and uncx.S genes in the vertebral column morphogenesis of the allotetraploid frog Xenopus laevis. We initiated our study by cloning the uncx orthologous genes in the anuran Xenopus and determining their spatial expression patterns using in situ hybridization. Additionally, we employed gain-of-function and loss-of-function approaches through dexamethasone-inducible uncx constructs and antisense morpholino oligonucleotides, respectively. Comparative analysis of the messenger RNA sequences of homeologous uncx genes revealed that the uncx.L variant lacks the eh1-like repressor domain. Our spatial expression analysis indicated that in the presomitic mesoderm and somites, the transcripts of uncx.L and uncx.S are located in overlapping domains. Alterations in the function of uncx genes significantly impact the development and differentiation of the sclerotome and myotome, resulting in axial skeleton malformations. Our findings suggest a scenario where the homeologous genes uncx.L and uncx.S exhibit antagonistic functions during somitogenesis. Specifically, uncx.S appears to be crucial for sclerotome development and differentiation, while uncx.L primarily influences myotome development. Postallotetraploidization, the uncx.L gene in X. laevis evolved to lose its eh1-like repressor domain, transforming into a "native dominant negative" variant that potentially competes with uncx.S for the same target genes. Finally, the histological analysis revealed that uncx.S expression is necessary for the correct formation of pedicles and neural arch of the vertebrae, and uncx.L is required for trunk muscle development.
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Affiliation(s)
- Romel S Sánchez
- Instituto Superior de Investigaciones Biológicas (INSIBIO), CONICET and Instituto de Biología "Dr. Francisco D. Barbieri, Facultad de Bioquímica, Química y Farmacia, Universidad Nacional de Tucumán, San Miguel de Tucumán, Argentina
- Cátedra de Biología General, Facultad de Ciencias Naturales e Instituto Miguel Lillo, Universidad Nacional de Tucumán, San Miguel de Tucumán, Argentina
- Cátedra de Fisiología, Departamento Biomédico, Facultad de Medicina, Universidad Nacional de Tucumán, San Miguel de Tucumán, Argentina
| | - María A Lazarte
- Instituto de Biodiversidad Neotropical (IBN), CONICET, Facultad de Ciencias Naturales e IML, Universidad Nacional de Tucumán, Yerba Buena, Tucumán, Argentina
| | - Virginia S L Abdala
- Cátedra de Biología General, Facultad de Ciencias Naturales e Instituto Miguel Lillo, Universidad Nacional de Tucumán, San Miguel de Tucumán, Argentina
- Instituto de Biodiversidad Neotropical (IBN), CONICET, Facultad de Ciencias Naturales e IML, Universidad Nacional de Tucumán, Yerba Buena, Tucumán, Argentina
| | - Sara S Sánchez
- Instituto Superior de Investigaciones Biológicas (INSIBIO), CONICET and Instituto de Biología "Dr. Francisco D. Barbieri, Facultad de Bioquímica, Química y Farmacia, Universidad Nacional de Tucumán, San Miguel de Tucumán, Argentina
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4
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England SJ, Rusnock AK, Mujcic A, Kowalchuk A, de Jager S, Hilinski WC, Juárez-Morales JL, Smith ME, Grieb G, Banerjee S, Lewis KE. Molecular analyses of zebrafish V0v spinal interneurons and identification of transcriptional regulators downstream of Evx1 and Evx2 in these cells. Neural Dev 2023; 18:8. [PMID: 38017520 PMCID: PMC10683209 DOI: 10.1186/s13064-023-00176-w] [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: 08/23/2023] [Accepted: 10/12/2023] [Indexed: 11/30/2023] Open
Abstract
BACKGROUND V0v spinal interneurons are highly conserved, glutamatergic, commissural neurons that function in locomotor circuits. We have previously shown that Evx1 and Evx2 are required to specify the neurotransmitter phenotype of these cells. However, we still know very little about the gene regulatory networks that act downstream of these transcription factors in V0v cells. METHODS To identify candidate members of V0v gene regulatory networks, we FAC-sorted wild-type and evx1;evx2 double mutant zebrafish V0v spinal interneurons and expression-profiled them using microarrays and single cell RNA-seq. We also used in situ hybridization to compare expression of a subset of candidate genes in evx1;evx2 double mutants and wild-type siblings. RESULTS Our data reveal two molecularly distinct subtypes of zebrafish V0v spinal interneurons at 48 h and suggest that, by this stage of development, evx1;evx2 double mutant cells transfate into either inhibitory spinal interneurons, or motoneurons. Our results also identify 25 transcriptional regulator genes that require Evx1/2 for their expression in V0v interneurons, plus a further 11 transcriptional regulator genes that are repressed in V0v interneurons by Evx1/2. Two of the latter genes are hmx2 and hmx3a. Intriguingly, we show that Hmx2/3a, repress dI2 interneuron expression of skor1a and nefma, two genes that require Evx1/2 for their expression in V0v interneurons. This suggests that Evx1/2 might regulate skor1a and nefma expression in V0v interneurons by repressing Hmx2/3a expression. CONCLUSIONS This study identifies two molecularly distinct subsets of zebrafish V0v spinal interneurons, as well as multiple transcriptional regulators that are strong candidates for acting downstream of Evx1/2 to specify the essential functional characteristics of these cells. Our data further suggest that in the absence of both Evx1 and Evx2, V0v spinal interneurons initially change their neurotransmitter phenotypes from excitatory to inhibitory and then, later, start to express markers of distinct types of inhibitory spinal interneurons, or motoneurons. Taken together, our findings significantly increase our knowledge of V0v and spinal development and move us closer towards the essential goal of identifying the complete gene regulatory networks that specify this crucial cell type.
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Affiliation(s)
| | | | - Amra Mujcic
- Biology Department, Syracuse University, Syracuse, NY, USA
| | | | - Sarah de Jager
- Physiology, Development and Neuroscience Department, Cambridge University, Cambridge, UK
| | | | - José L Juárez-Morales
- Biology Department, Syracuse University, Syracuse, NY, USA
- Programa de IxM-CONAHCYT, Centro de Investigaciones Biológicas del Noroeste, S.C. (CIBNOR), La Paz, Baja California Sur, México
| | | | - Ginny Grieb
- Biology Department, Syracuse University, Syracuse, NY, USA
| | - Santanu Banerjee
- Biological Sciences Department, SUNY-Cortland, Cortland, NY, USA
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5
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Zhang Y, Jin Y, Wang H, He L, Zhang Y, Liu Q, Xin Y, Li X. Identification of Genes Associated with Decreasing Abundance of Monocytes in Long-Term Peritoneal Dialysis Patients. Int J Gen Med 2023; 16:5017-5030. [PMID: 37942472 PMCID: PMC10629397 DOI: 10.2147/ijgm.s435041] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2023] [Accepted: 10/19/2023] [Indexed: 11/10/2023] Open
Abstract
Purpose Chronic kidney disease (CKD) will become an end-stage renal disease (ESRD) at stage 5. Peritoneal dialysis (PD) is required for renal replacement therapy. This study aims to identify monocytes-related genes in peritoneal cells from long-term PD (LPD) patients and short-term PD (SPD) patients. Methods Bulk RNA-seq data (GSE125498 dataset) and ScRNA-seq data (GSE130888) were downloaded to identify differentially expressed genes, monocytes-related genes, and monocytes marker genes in LPD patients. Immune infiltration was analyzed in the GSE125498 dataset. Core genes associated with monocytes changes were screened out, followed by functional analysis and expression validation using RT-PCR. Results Monocytes are the most abundant immune cell in PD. The number of monocytes was remarkably decreased in LPD compared with SPD. A total of 16 up-regulated core genes negatively correlated with the abundance of monocytes were obtained in LPD. The expression of 16 core genes was lower in monocyte clusters than that in other cell clusters. In addition, LCK, CD3G, CD3E, CD3D, and LAT were involved in the signaling pathways of Th1 and Th2 cell differentiation, T cell receptor signaling pathway, and Th17 cell differentiation. CD2 was involved in hematopoietic cell lineage signaling pathway. Conclusion Identification of monocytes related-genes and related signaling pathways could be helpful in understanding the molecular mechanism of monocytes changes during PD.
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Affiliation(s)
- Yinghui Zhang
- Department of Nephrology, General Hospital of Northern Theater Command, Shenyang, Liaoning Province, People’s Republic of China
| | - Yanhua Jin
- Department of Nephrology, General Hospital of Northern Theater Command, Shenyang, Liaoning Province, People’s Republic of China
| | - Huan Wang
- Department of Nephrology, General Hospital of Northern Theater Command, Shenyang, Liaoning Province, People’s Republic of China
| | - Long He
- Organ Transplant Center, General Hospital of Northern Theater Command, Shenyang, Liaoning Province, People’s Republic of China
| | - Yanning Zhang
- Department of Nephrology, General Hospital of Northern Theater Command, Shenyang, Liaoning Province, People’s Republic of China
| | - Qi Liu
- Department of Nephrology, General Hospital of Northern Theater Command, Shenyang, Liaoning Province, People’s Republic of China
| | - Yu Xin
- Department of Nephrology, General Hospital of Northern Theater Command, Shenyang, Liaoning Province, People’s Republic of China
| | - Xueyu Li
- Nursing Department, General Hospital of Northern Theater Command, Shenyang, Liaoning Province, People’s Republic of China
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6
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England SJ, Woodard AK, Mujcic A, Kowalchuk A, de Jager S, Hilinski WC, Juárez-Morales JL, Smith ME, Grieb G, Banerjee S, Lewis KE. Molecular Analyses of V0v Spinal Interneurons and Identification of Transcriptional Regulators Downstream of Evx1 and Evx2 in these Cells. RESEARCH SQUARE 2023:rs.3.rs-3290462. [PMID: 37693471 PMCID: PMC10491344 DOI: 10.21203/rs.3.rs-3290462/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/12/2023]
Abstract
Background V0v spinal interneurons are highly conserved, glutamatergic, commissural neurons that function in locomotor circuits. We have previously shown that Evx1 and Evx2 are required to specify the neurotransmitter phenotype of these cells. However, we still know very little about the gene regulatory networks that act downstream of these transcription factors in V0v cells. Methods To identify candidate members of V0v gene regulatory networks, we FAC-sorted WT and evx1;evx2 double mutant zebrafish V0v spinal interneurons and expression-profiled them using microarrays and single cell RNA-seq. We also used in situ hybridization to compare expression of a subset of candidate genes in evx1;evx2 double mutants and wild-type siblings. Results Our data reveal two molecularly distinct subtypes of V0v spinal interneurons at 48 h and suggest that, by this stage of development, evx1;evx2 double mutant cells transfate into either inhibitory spinal interneurons, or motoneurons. Our results also identify 25 transcriptional regulator genes that require Evx1/2 for their expression in V0v interneurons, plus a further 11 transcriptional regulator genes that are repressed in V0v interneurons by Evx1/2. Two of the latter genes are hmx2 and hmx3a. Intriguingly, we show that Hmx2/3a, repress dI2 interneuronal expression of skor1a and nefma, two genes that require Evx1/2 for their expression in V0v interneurons. This suggests that Evx1/2 might regulate skor1a and nefma expression in V0v interneurons by repressing Hmx2/3a expression. Conclusions This study identifies two molecularly distinct subsets of V0v spinal interneurons, as well as multiple transcriptional regulators that are strong candidates for acting downstream of Evx1/2 to specify the essential functional characteristics of these cells. Our data further suggest that in the absence of both Evx1 and Evx2, V0v spinal interneurons initially change their neurotransmitter phenotypes from excitatory to inhibitory and then, later, start to express markers of distinct types of inhibitory spinal interneurons, or motoneurons. Taken together, our findings significantly increase our knowledge of V0v and spinal development and move us closer towards the essential goal of identifying the complete gene regulatory networks that specify this crucial cell type.
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7
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Yonezawa Y, Guo L, Kakinuma H, Otomo N, Yoshino S, Takeda K, Nakajima M, Shiraki T, Ogura Y, Takahashi Y, Koike Y, Minami S, Uno K, Kawakami N, Ito M, Yonezawa I, Watanabe K, Kaito T, Yanagida H, Taneichi H, Harimaya K, Taniguchi Y, Shigematsu H, Iida T, Demura S, Sugawara R, Fujita N, Yagi M, Okada E, Hosogane N, Kono K, Chiba K, Kotani T, Sakuma T, Akazawa T, Suzuki T, Nishida K, Kakutani K, Tsuji T, Sudo H, Iwata A, Sato T, Inami S, Nakamura M, Matsumoto M, Terao C, Watanabe K, Okamoto H, Ikegawa S. Identification of a Functional Susceptibility Variant for Adolescent Idiopathic Scoliosis that Upregulates Early Growth Response 1 (EGR1)-Mediated UNCX Expression. J Bone Miner Res 2023; 38:144-153. [PMID: 36342191 DOI: 10.1002/jbmr.4738] [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: 07/22/2022] [Revised: 10/23/2022] [Accepted: 11/03/2022] [Indexed: 11/09/2022]
Abstract
Adolescent idiopathic scoliosis (AIS) is a serious health problem affecting 3% of live births all over the world. Many loci associated with AIS have been identified by previous genome wide association studies, but their biological implication remains mostly unclear. In this study, we evaluated the AIS-associated variants in the 7p22.3 locus by combining in silico, in vitro, and in vivo analyses. rs78148157 was located in an enhancer of UNCX, a homeobox gene and its risk allele upregulated the UNCX expression. A transcription factor, early growth response 1 (EGR1), transactivated the rs78148157-located enhancer and showed a higher binding affinity for the risk allele of rs78148157. Furthermore, zebrafish larvae with UNCX messenger RNA (mRNA) injection developed body curvature and defective neurogenesis in a dose-dependent manner. rs78148157 confers the genetic susceptibility to AIS by enhancing the EGR1-regulated UNCX expression. © 2022 American Society for Bone and Mineral Research (ASBMR).
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Affiliation(s)
- Yoshiro Yonezawa
- Department of Orthopedic Surgery, Keio University School of Medicine, Tokyo, Japan.,Laboratory for Bone and Joint Diseases, RIKEN Center for Integrative Medical Sciences, Tokyo, Japan
| | - Long Guo
- Laboratory for Bone and Joint Diseases, RIKEN Center for Integrative Medical Sciences, Tokyo, Japan.,Department of Laboratory Animal Science, School of Basic Medical Sciences, Xi'an Jiaotong University, Xi'an, China
| | - Hisaya Kakinuma
- Laboratory for Neural Circuit Dynamics of Decision Making, RIKEN Brain Science Institute, Saitama, Japan
| | - Nao Otomo
- Department of Orthopedic Surgery, Keio University School of Medicine, Tokyo, Japan
| | - Soichiro Yoshino
- Laboratory for Statistical and Translational Genetics, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan.,Department of Orthopaedic Surgery, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Kazuki Takeda
- Department of Orthopedic Surgery, Keio University School of Medicine, Tokyo, Japan
| | - Masahiro Nakajima
- Laboratory for Bone and Joint Diseases, RIKEN Center for Integrative Medical Sciences, Tokyo, Japan
| | - Toshiyuki Shiraki
- Laboratory for Neural Circuit Dynamics of Decision Making, RIKEN Brain Science Institute, Saitama, Japan
| | - Yoji Ogura
- Department of Orthopedic Surgery, Keio University School of Medicine, Tokyo, Japan
| | - Yohei Takahashi
- Department of Orthopedic Surgery, Keio University School of Medicine, Tokyo, Japan
| | - Yoshinao Koike
- Laboratory for Statistical and Translational Genetics, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan.,Department of Orthopedic Surgery, Graduate School of Medical Sciences, Hokkaido University, Sapporo, Japan
| | - Shohei Minami
- Department of Orthopedic Surgery, Seirei Sakura Citizen Hospital, Chiba, Japan
| | - Koki Uno
- Department of Orthopedic Surgery, National Hospital Organization, Kobe Medical Center, Kobe, Japan
| | | | - Manabu Ito
- Department of Orthopedic Surgery, National Hospital Organization Hokkaido Medical Center, Sapporo, Japan
| | - Ikuho Yonezawa
- Department of Orthopedic Surgery, Juntendo University School of Medicine, Tokyo, Japan
| | - Kei Watanabe
- Department of Orthopedic Surgery, Niigata University Medical and Dental General Hospital, Niigata, Japan
| | - Takashi Kaito
- Department of Orthopedic Surgery, Osaka University Graduate School of Medicine, Suita, Japan
| | - Haruhisa Yanagida
- Department of Orthopedic Surgery, Fukuoka Children's Hospital, Fukuoka, Japan
| | - Hiroshi Taneichi
- Department of Orthopedic Surgery, Dokkyo Medical University School of Medicine, Tochigi, Japan
| | - Katsumi Harimaya
- Department of Orthopedic Surgery, Kyushu University Beppu Hospital, Beppu, Japan
| | - Yuki Taniguchi
- Department of Orthopedic, Surgery, Faculty of Medicine, The University of Tokyo, Tokyo, Japan
| | - Hideki Shigematsu
- Department of Orthopedic Surgery, Nara Medical University, Nara, Japan
| | - Takahiro Iida
- Department of Orthopedic Surgery, Dokkyo Medical University Koshigaya Hospital, Saitama, Japan
| | - Satoru Demura
- Department of Orthopedic Surgery, Kanazawa University Hospital, Kanazawa, Japan
| | - Ryo Sugawara
- Department of Orthopedic Surgery, Jichi Medical University, Tochigi, Japan
| | - Nobuyuki Fujita
- Department of Orthopedic Surgery, Fujita Health University, Nagoya, Japan
| | - Mitsuru Yagi
- Department of Orthopedic Surgery, Keio University School of Medicine, Tokyo, Japan
| | - Eijiro Okada
- Department of Orthopedic Surgery, Keio University School of Medicine, Tokyo, Japan
| | - Naobumi Hosogane
- Department of Orthopedic Surgery, Kyorin University School of Medicine, Tokyo, Japan
| | - Katsuki Kono
- Department of Orthopedic Surgery, Kono Orthopaedic Clinic, Tokyo, Japan
| | - Kazuhiro Chiba
- Department of Orthopedic Surgery, National Defense Medical College, Saitama, Japan
| | - Toshiaki Kotani
- Department of Orthopedic Surgery, Seirei Sakura Citizen Hospital, Chiba, Japan
| | - Tsuyoshi Sakuma
- Department of Orthopedic Surgery, Seirei Sakura Citizen Hospital, Chiba, Japan
| | - Tsutomu Akazawa
- Department of Orthopedic Surgery, Seirei Sakura Citizen Hospital, Chiba, Japan
| | - Teppei Suzuki
- Department of Orthopedic Surgery, National Hospital Organization, Kobe Medical Center, Kobe, Japan
| | - Kotaro Nishida
- Department of Orthopedic Surgery, Kobe University Graduate School of Medicine, Kobe, Japan
| | - Kenichiro Kakutani
- Department of Orthopedic Surgery, Kobe University Graduate School of Medicine, Kobe, Japan
| | - Taichi Tsuji
- Department of Orthopedic Surgery, Meijo Hospital, Nagoya, Japan
| | - Hideki Sudo
- Department of Advanced Medicine for Spine and Spinal Cord Disorders, Hokkaido University Graduate School of Medicine, Sapporo, Japan
| | - Akira Iwata
- Department of Preventive and Therapeutic Research for Metastatic Bone Tumor, Faculty of Medicine and Graduate School of Medicine, Hokkaido University, Sapporo, Japan
| | - Tatsuya Sato
- Department of Orthopedic Surgery, Juntendo University School of Medicine, Tokyo, Japan
| | - Satoshi Inami
- Department of Orthopedic Surgery, Dokkyo Medical University School of Medicine, Tochigi, Japan
| | - Masaya Nakamura
- Department of Orthopedic Surgery, Keio University School of Medicine, Tokyo, Japan
| | - Morio Matsumoto
- Department of Orthopedic Surgery, Keio University School of Medicine, Tokyo, Japan
| | - Chikashi Terao
- Laboratory for Statistical and Translational Genetics, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - Kota Watanabe
- Department of Orthopedic Surgery, Keio University School of Medicine, Tokyo, Japan
| | - Hitoshi Okamoto
- Laboratory for Neural Circuit Dynamics of Decision Making, RIKEN Brain Science Institute, Saitama, Japan
| | - Shiro Ikegawa
- Laboratory for Bone and Joint Diseases, RIKEN Center for Integrative Medical Sciences, Tokyo, Japan
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Identification and Validation of Marketing Weight-Related SNP Markers Using SLAF Sequencing in Male Yangzhou Geese. Genes (Basel) 2021; 12:genes12081203. [PMID: 34440377 PMCID: PMC8393582 DOI: 10.3390/genes12081203] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2021] [Revised: 07/27/2021] [Accepted: 07/29/2021] [Indexed: 11/17/2022] Open
Abstract
Growth performance is a complex economic trait for avian production. The swan goose (Anser cygnoides) has never been exploited genetically like chickens or other waterfowl species such as ducks. Traditional phenotypic selection is still the main method for genetic improvement of geese body weight. In this study, specific locus amplified fragment sequencing (SLAF-seq) with bulked segregant analysis (BSA) was conducted for discovering and genotyping single nucleotide polymorphisms (SNPs) associated with marketing weight trait in male geese. A total of 149,045 SNPs were obtained from 427,093 SLAF tags with an average sequencing depth of 44.97-fold and a Q30 value of 93.26%. After SNPs' filtering, a total of 12,917 SNPs were included in the study. The 31 highest significant SNPs-which had different allelic frequencies-were further validated by individual-based AS-PCR genotyping in two populations. The association between 10 novel SNPs and the marketing weight of male geese was confirmed. The 10 significant SNPs were involved in linear regression model analysis, which confirmed single-SNP associations and revealed three types of SNP networks for marketing weight. The 10 significant SNPs were located within or close to 10 novel genes, which were identified. The qPCR analysis showed significant difference between genotypes of each SNP in seven genes. Developed SLAF-seq and identified genes will enrich growth performance studies, promoting molecular breeding applications to boost the marketing weight of Chinese geese.
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9
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Miao Z, Balzer MS, Ma Z, Liu H, Wu J, Shrestha R, Aranyi T, Kwan A, Kondo A, Pontoglio M, Kim J, Li M, Kaestner KH, Susztak K. Single cell regulatory landscape of the mouse kidney highlights cellular differentiation programs and disease targets. Nat Commun 2021; 12:2277. [PMID: 33859189 PMCID: PMC8050063 DOI: 10.1038/s41467-021-22266-1] [Citation(s) in RCA: 118] [Impact Index Per Article: 39.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2020] [Accepted: 02/28/2021] [Indexed: 12/19/2022] Open
Abstract
Determining the epigenetic program that generates unique cell types in the kidney is critical for understanding cell-type heterogeneity during tissue homeostasis and injury response. Here, we profile open chromatin and gene expression in developing and adult mouse kidneys at single cell resolution. We show critical reliance of gene expression on distal regulatory elements (enhancers). We reveal key cell type-specific transcription factors and major gene-regulatory circuits for kidney cells. Dynamic chromatin and expression changes during nephron progenitor differentiation demonstrates that podocyte commitment occurs early and is associated with sustained Foxl1 expression. Renal tubule cells follow a more complex differentiation, where Hfn4a is associated with proximal and Tfap2b with distal fate. Mapping single nucleotide variants associated with human kidney disease implicates critical cell types, developmental stages, genes, and regulatory mechanisms. The single cell multi-omics atlas reveals key chromatin remodeling events and gene expression dynamics associated with kidney development.
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Affiliation(s)
- Zhen Miao
- Renal, Electrolyte, and Hypertension Division, Department of Medicine, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA, USA
- Institute for Diabetes, Obesity, and Metabolism, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA, USA
- Graduate Group in Genomics and Computational Biology, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA, USA
| | - Michael S Balzer
- Renal, Electrolyte, and Hypertension Division, Department of Medicine, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA, USA
- Institute for Diabetes, Obesity, and Metabolism, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA, USA
| | - Ziyuan Ma
- Renal, Electrolyte, and Hypertension Division, Department of Medicine, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA, USA
- Institute for Diabetes, Obesity, and Metabolism, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA, USA
| | - Hongbo Liu
- Renal, Electrolyte, and Hypertension Division, Department of Medicine, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA, USA
- Institute for Diabetes, Obesity, and Metabolism, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA, USA
| | - Junnan Wu
- Renal, Electrolyte, and Hypertension Division, Department of Medicine, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA, USA
- Institute for Diabetes, Obesity, and Metabolism, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA, USA
| | - Rojesh Shrestha
- Renal, Electrolyte, and Hypertension Division, Department of Medicine, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA, USA
- Institute for Diabetes, Obesity, and Metabolism, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA, USA
| | - Tamas Aranyi
- Renal, Electrolyte, and Hypertension Division, Department of Medicine, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA, USA
- Institute for Diabetes, Obesity, and Metabolism, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA, USA
| | - Amy Kwan
- Department of Genetics, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA, USA
| | - Ayano Kondo
- Department of Genetics, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA, USA
| | - Marco Pontoglio
- Epigenetics and Development Laboratory, Université de Paris Inserm U1151/CNRS UMR 8253, Institut Necker Enfants Malades, Paris, France
| | - Junhyong Kim
- Department of Biology, University of Pennsylvania, Philadelphia, PA, USA
| | - Mingyao Li
- Department of Epidemiology and Biostatistics, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA, USA
| | - Klaus H Kaestner
- Institute for Diabetes, Obesity, and Metabolism, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA, USA
- Department of Genetics, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA, USA
| | - Katalin Susztak
- Renal, Electrolyte, and Hypertension Division, Department of Medicine, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA, USA.
- Institute for Diabetes, Obesity, and Metabolism, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA, USA.
- Department of Genetics, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA, USA.
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Lacin H, Williamson WR, Card GM, Skeath JB, Truman JW. Unc-4 acts to promote neuronal identity and development of the take-off circuit in the Drosophila CNS. eLife 2020; 9:55007. [PMID: 32216875 PMCID: PMC7156266 DOI: 10.7554/elife.55007] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2020] [Accepted: 03/27/2020] [Indexed: 12/14/2022] Open
Abstract
The Drosophila ventral nerve cord (VNC) is composed of thousands of neurons born from a set of individually identifiable stem cells. The VNC harbors neuronal circuits required to execute key behaviors, such as flying and walking. Leveraging the lineage-based functional organization of the VNC, we investigated the developmental and molecular basis of behavior by focusing on lineage-specific functions of the homeodomain transcription factor, Unc-4. We found that Unc-4 functions in lineage 11A to promote cholinergic neurotransmitter identity and suppress the GABA fate. In lineage 7B, Unc-4 promotes proper neuronal projections to the leg neuropil and a specific flight-related take-off behavior. We also uncovered that Unc-4 acts peripherally to promote proprioceptive sensory organ development and the execution of specific leg-related behaviors. Through time-dependent conditional knock-out of Unc-4, we found that its function is required during development, but not in the adult, to regulate the above events.
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Affiliation(s)
- Haluk Lacin
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, United States.,Department of Genetics, Washington University, Saint Louis, United States
| | - W Ryan Williamson
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, United States
| | - Gwyneth M Card
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, United States
| | - James B Skeath
- Department of Genetics, Washington University, Saint Louis, United States
| | - James W Truman
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, United States.,Friday Harbor Laboratories, University of Washington, Friday Harbor, United States
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