1
|
Huang Z, Liu D, Zhang Y, Lu W, Hu L, Zhang J, Xie L, Chen S. PITX1 as a grading, prognostic and tumor-infiltrating immune cells marker for chondrosarcoma: a public database-based immunoassay and tissue sample analysis. Front Oncol 2025; 15:1477649. [PMID: 40342824 PMCID: PMC12060168 DOI: 10.3389/fonc.2025.1477649] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2024] [Accepted: 03/24/2025] [Indexed: 05/11/2025] Open
Abstract
Background Chondrosarcoma (CHS) is a rare bone cancer originating from chondrocytes, with high-grade cases associated with high mortality rates. However, the prognostic factors and therapeutic targets for CHS have not been studied. Methods Graded gene differential analysis was conducted on 97 CHS tissues to identify genes associated with CHS grading. Additionally, we performed GO and KEGG enrichment analyses of the differentially-expressed genes (DEGs), as well as GSEA analysis, differential expression analysis, survival analysis, and univariable and multifactorial COX analysis of paired-like homology structural domain transcription factor 1 (PITX1). Furthermore, our findings investigated the relationship between tumor-infiltrating immune cells (TICs) in CHS tumors using CIBERSORT to calculate proportions and differences. Our findings also explored the associations among gene expression patterns, survival prognosis, TICs, and immune checkpoints across various cancer types. Finally, immunohistochemical staining was carried out on self-collected clinical samples to assess PITX1 expression levels and correlate them with clinical information. Results Gene differential expression analysis revealed a strong correlation between PITX1 expression and tumor grade. GO, KEGG enrichment, and GSEA analysis demonstrated the association of PITX1 with cell proliferation-related processes, such as cell cycle regulation and mitosis, and differentiation-related processes, such as RNA processing. PITX1 expression was associated with tumor stage and survival outcomes. Immunoassay indicated a positive correlation between PITX1 levels and TICs, immune checkpoints, and graded TICs. Pan-cancer analysis confirmed the differential expression of the PITX1 gene across multiple cancers, impacting survival prognosis, TIC patterns, and immune checkpoint regulation. Lastly, our 75 collection of clinical patient tissue samples exhibited varying levels of PITX1 expression across different cancer grades while also demonstrating a significant association with tumor differentiation and metastasis. Conclusion PITX1 is a novel biomarker for distinguishing between high-grade and low-grade CHS, serving as a prognostic indicator for patients with this condition and presenting a promising target for immunotherapy. These findings offer innovative insights into the treatment of CHS.
Collapse
Affiliation(s)
- Zikun Huang
- Department of Orthopaedics, First Affiliated Hospital of Shantou University Medical College, Shantou, China
- Department of Pathology, Shantou University Medical College, Shantou, Guangdong, China
| | - Dongchen Liu
- Department of Pathology, Shantou University Medical College, Shantou, Guangdong, China
- Department of Radiotherapy, Cancer Hospital of Shantou University Medical College, Shantou, Guangdong, China
- Clinical Research Center, Cancer Hospital of Shantou University Medical College, Shantou, Guangdong, China
| | - Ying Zhang
- Department of Radiotherapy, Cancer Hospital of Shantou University Medical College, Shantou, Guangdong, China
- Clinical Research Center, Cancer Hospital of Shantou University Medical College, Shantou, Guangdong, China
| | - Weiqing Lu
- Department of Pathology, Shantou University Medical College, Shantou, Guangdong, China
- Department of Radiotherapy, Cancer Hospital of Shantou University Medical College, Shantou, Guangdong, China
| | - Lan Hu
- Department of Pathology, Shantou University Medical College, Shantou, Guangdong, China
- Department of Radiotherapy, Cancer Hospital of Shantou University Medical College, Shantou, Guangdong, China
| | - Jinghao Zhang
- Department of Orthopaedics, First Affiliated Hospital of Shantou University Medical College, Shantou, China
- Department of Pathology, Shantou University Medical College, Shantou, Guangdong, China
| | - Lei Xie
- Department of Orthopaedics, First Affiliated Hospital of Shantou University Medical College, Shantou, China
- Sport Medicine Centre, First Affiliated Hospital of Shantou University Medical College, Shantou, Guangdong, China
| | - Shubiao Chen
- Department of Orthopaedics, First Affiliated Hospital of Shantou University Medical College, Shantou, China
- Sport Medicine Centre, First Affiliated Hospital of Shantou University Medical College, Shantou, Guangdong, China
- Department of General Surgery, First Affiliated Hospital of Shantou University Medical College, Shantou, China
| |
Collapse
|
2
|
Zhang Z, Liu Y, Liang N, Yu Z, Deme L, Xu D, Liu J, Ren W, Xu S, Yang G. Functional evidence supports the potential role of Tbx4-HLEA in the hindlimb degeneration of cetaceans. EvoDevo 2025; 16:3. [PMID: 40121501 PMCID: PMC11929173 DOI: 10.1186/s13227-025-00239-5] [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: 09/18/2024] [Accepted: 03/13/2025] [Indexed: 03/25/2025] Open
Abstract
The evolution of limb morphology plays an important role in animal adaptation to different ecological niches. To fully adapt to aquatic life, cetaceans underwent hindlimb degeneration and forelimb transformed into flipper; however, the molecular mechanisms underlying the limb changes in cetaceans remain unclear. We previous study had shown that the Tbx4 hindlimb enhancer A (Tbx4-HLEA) in cetaceans exhibited specific deletions and nucleotide substitutions, with significantly reduced regulatory activity. To further investigate whether cetacean HLEA has a potential impact on hindlimb development in vivo, a knock-in mouse model was generated by knocking in the homologous cetacean HLEA in the present study. Phenotypic analysis showed a significant reduction in hindlimb bud development in homozygous knock-in mice at embryonic day (E)10.5; however, the phenotypic difference was rescued after E11.5. Transcriptomic and epigenetic analyses indicated that the cetacean HLEA acts as an enhancer in the mouse embryos and significantly reduces the transcriptional expression levels of Tbx4 at E10.5, supporting that downregulation of cetaceans HLEA regulatory activity reduces the expression of Tbx4. Additionally, both the number of activated non-coding elements and chromatin accessibility near Tbx4 were increased in homozygous knock-in mice at E11.5. The functional redundancy of enhancers compensated for the functional defect of cetacean HLEA, rescuing the expression level of Tbx4, and may account for the phenotype restoration after E11.5. In conclusion, our study suggested that the evolution of cetacean HLEA may be an important link with relevant molecular mechanism for the hindlimb degeneration.
Collapse
Affiliation(s)
- Zhenhua Zhang
- Jiangsu Key Laboratory for the Conservation and Utilization of Biodiversity in the Middle and Lower Reaches of the Yangtze River, College of Life Sciences, Nanjing Normal University, Nanjing, 210023, China
| | - Yao Liu
- Jiangsu Key Laboratory for the Conservation and Utilization of Biodiversity in the Middle and Lower Reaches of the Yangtze River, College of Life Sciences, Nanjing Normal University, Nanjing, 210023, China
| | - Na Liang
- Jiangsu Key Laboratory for the Conservation and Utilization of Biodiversity in the Middle and Lower Reaches of the Yangtze River, College of Life Sciences, Nanjing Normal University, Nanjing, 210023, China
| | - Zhenpeng Yu
- Jiangsu Key Laboratory for the Conservation and Utilization of Biodiversity in the Middle and Lower Reaches of the Yangtze River, College of Life Sciences, Nanjing Normal University, Nanjing, 210023, China
| | - Luoying Deme
- Jiangsu Key Laboratory for the Conservation and Utilization of Biodiversity in the Middle and Lower Reaches of the Yangtze River, College of Life Sciences, Nanjing Normal University, Nanjing, 210023, China
| | - Duo Xu
- Jiangsu Key Laboratory for the Conservation and Utilization of Biodiversity in the Middle and Lower Reaches of the Yangtze River, College of Life Sciences, Nanjing Normal University, Nanjing, 210023, China
| | - Jia Liu
- Jiangsu Key Laboratory for the Conservation and Utilization of Biodiversity in the Middle and Lower Reaches of the Yangtze River, College of Life Sciences, Nanjing Normal University, Nanjing, 210023, China
| | - Wenhua Ren
- Jiangsu Key Laboratory for the Conservation and Utilization of Biodiversity in the Middle and Lower Reaches of the Yangtze River, College of Life Sciences, Nanjing Normal University, Nanjing, 210023, China
| | - Shixia Xu
- Jiangsu Key Laboratory for the Conservation and Utilization of Biodiversity in the Middle and Lower Reaches of the Yangtze River, College of Life Sciences, Nanjing Normal University, Nanjing, 210023, China.
| | - Guang Yang
- Jiangsu Key Laboratory for the Conservation and Utilization of Biodiversity in the Middle and Lower Reaches of the Yangtze River, College of Life Sciences, Nanjing Normal University, Nanjing, 210023, China.
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, 511458, China.
| |
Collapse
|
3
|
Wang Z, Peng C, Wu W, Yan C, Lv Y, Li JT. Developmental regulation of conserved non-coding element evolution provides insights into limb loss in squamates. SCIENCE CHINA. LIFE SCIENCES 2023; 66:2399-2414. [PMID: 37256419 DOI: 10.1007/s11427-023-2362-5] [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: 04/14/2023] [Accepted: 05/09/2023] [Indexed: 06/01/2023]
Abstract
Limb loss shows recurrent phenotypic evolution across squamate lineages. Here, based on three de novo-assembled genomes of limbless lizards from different lineages, we showed that divergence of conserved non-coding elements (CNEs) played an important role in limb development. These CNEs were associated with genes required for limb initiation and outgrowth, and with regulatory signals in the early stage of limb development. Importantly, we identified the extensive existence of insertions and deletions (InDels) in the CNEs, with the numbers ranging from 111 to 756. Most of these CNEs with InDels were lineage-specific in the limbless squamates. Nearby genes of these InDel CNEs were important to early limb formation, such as Tbx4, Fgf10, and Gli3. Based on functional experiments, we found that nucleotide mutations and InDels both affected the regulatory function of the CNEs. Our study provides molecular evidence underlying limb loss in squamate reptiles from a developmental perspective and sheds light on the importance of regulatory element InDels in phenotypic evolution.
Collapse
Affiliation(s)
- Zeng Wang
- CAS Key Laboratory of Mountain Ecological Restoration and Bioresource Utilization & h Ecological Restoration and Biodiversity Conservation Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, 610041, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Changjun Peng
- CAS Key Laboratory of Mountain Ecological Restoration and Bioresource Utilization & h Ecological Restoration and Biodiversity Conservation Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, 610041, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Wei Wu
- CAS Key Laboratory of Mountain Ecological Restoration and Bioresource Utilization & h Ecological Restoration and Biodiversity Conservation Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, 610041, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Chaochao Yan
- CAS Key Laboratory of Mountain Ecological Restoration and Bioresource Utilization & h Ecological Restoration and Biodiversity Conservation Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, 610041, China
| | - Yunyun Lv
- CAS Key Laboratory of Mountain Ecological Restoration and Bioresource Utilization & h Ecological Restoration and Biodiversity Conservation Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, 610041, China
- College of Life Science, Neijiang Normal University, Neijiang, 641100, China
| | - Jia-Tang Li
- CAS Key Laboratory of Mountain Ecological Restoration and Bioresource Utilization & h Ecological Restoration and Biodiversity Conservation Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, 610041, China.
- University of Chinese Academy of Sciences, Beijing, 100049, China.
- Southeast Asia Biodiversity Research Institute, Chinese Academy of Sciences, Yezin Nay Pyi Taw, 05282, Myanmar.
| |
Collapse
|
4
|
Identification of candidate enhancers controlling the transcriptome during the formation of interphalangeal joints. Sci Rep 2022; 12:12835. [PMID: 35896673 PMCID: PMC9329285 DOI: 10.1038/s41598-022-16951-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2022] [Accepted: 07/19/2022] [Indexed: 11/09/2022] Open
Abstract
The formation of the synovial joint begins with the visible emergence of a stripe of densely packed mesenchymal cells located between distal ends of the developing skeletal anlagen called the interzone. Recently the transcriptome of the early synovial joint was reported. Knowledge about enhancers would complement these data and lead to a better understanding of the control of gene transcription at the onset of joint development. Using ChIP-sequencing we have mapped the H3-signatures H3K27ac and H3K4me1 to locate regulatory elements specific for the interzone and adjacent phalange, respectively. This one-stage atlas of candidate enhancers (CEs) was used to map the association between these respective joint tissue specific CEs and biological processes. Subsequently, integrative analysis of transcriptomic data and CEs identified new putative regulatory elements of genes expressed in interzone (e.g., GDF5, BMP2 and DACT2) and phalange (e.g., MATN1, HAPLN1 and SNAI1). We also linked such CEs to genes known as crucial in synovial joint hypermobility and osteoarthritis, as well as phalange malformations. These analyses show that the CE atlas can serve as resource for identifying, and as starting point for experimentally validating, putative disease-causing genomic regulatory regions in patients with synovial joint dysfunctions and/or phalange disorders, and enhancer-controlled synovial joint and phalange formation.
Collapse
|
5
|
Liang N, Deme L, Kong Q, Sun L, Cao Y, Wu T, Huang X, Xu S, Yang G. Divergence of Tbx4 hindlimb enhancer HLEA underlies the hindlimb loss during cetacean evolution. Genomics 2022; 114:110292. [DOI: 10.1016/j.ygeno.2022.110292] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2020] [Revised: 01/13/2022] [Accepted: 02/01/2022] [Indexed: 11/04/2022]
|
6
|
Roscito JG, Sameith K, Kirilenko BM, Hecker N, Winkler S, Dahl A, Rodrigues MT, Hiller M. Convergent and lineage-specific genomic differences in limb regulatory elements in limbless reptile lineages. Cell Rep 2022; 38:110280. [DOI: 10.1016/j.celrep.2021.110280] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2021] [Revised: 11/24/2021] [Accepted: 12/27/2021] [Indexed: 01/02/2023] Open
|
7
|
Cell-specific alterations in Pitx1 regulatory landscape activation caused by the loss of a single enhancer. Nat Commun 2021; 12:7235. [PMID: 34903763 PMCID: PMC8668926 DOI: 10.1038/s41467-021-27492-1] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2021] [Accepted: 11/24/2021] [Indexed: 11/17/2022] Open
Abstract
Developmental genes are frequently controlled by multiple enhancers sharing similar specificities. As a result, deletions of such regulatory elements have often failed to reveal their full function. Here, we use the Pitx1 testbed locus to characterize in detail the regulatory and cellular identity alterations following the deletion of one of its enhancers (Pen). By combining single cell transcriptomics and an in-embryo cell tracing approach, we observe an increased fraction of Pitx1 non/low-expressing cells and a decreased fraction of Pitx1 high-expressing cells. We find that the over-representation of Pitx1 non/low-expressing cells originates from a failure of the Pitx1 locus to coordinate enhancer activities and 3D chromatin changes. This locus mis-activation induces a localized heterochrony and a concurrent loss of irregular connective tissue, eventually leading to a clubfoot phenotype. This data suggests that, in some cases, redundant enhancers may be used to locally enforce a robust activation of their host regulatory landscapes.
Collapse
|
8
|
Wang JS, Kamath T, Mazur CM, Mirzamohammadi F, Rotter D, Hojo H, Castro CD, Tokavanich N, Patel R, Govea N, Enishi T, Wu Y, da Silva Martins J, Bruce M, Brooks DJ, Bouxsein ML, Tokarz D, Lin CP, Abdul A, Macosko EZ, Fiscaletti M, Munns CF, Ryder P, Kost-Alimova M, Byrne P, Cimini B, Fujiwara M, Kronenberg HM, Wein MN. Control of osteocyte dendrite formation by Sp7 and its target gene osteocrin. Nat Commun 2021; 12:6271. [PMID: 34725346 PMCID: PMC8560803 DOI: 10.1038/s41467-021-26571-7] [Citation(s) in RCA: 49] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2021] [Accepted: 10/12/2021] [Indexed: 02/05/2023] Open
Abstract
Some osteoblasts embed within bone matrix, change shape, and become dendrite-bearing osteocytes. The circuitry that drives dendrite formation during "osteocytogenesis" is poorly understood. Here we show that deletion of Sp7 in osteoblasts and osteocytes causes defects in osteocyte dendrites. Profiling of Sp7 target genes and binding sites reveals unexpected repurposing of this transcription factor to drive dendrite formation. Osteocrin is a Sp7 target gene that promotes osteocyte dendrite formation and rescues defects in Sp7-deficient mice. Single-cell RNA-sequencing demonstrates defects in osteocyte maturation in the absence of Sp7. Sp7-dependent osteocyte gene networks are associated with human skeletal diseases. Moreover, humans with a SP7R316C mutation show defective osteocyte morphology. Sp7-dependent genes that mark osteocytes are enriched in neurons, highlighting shared features between osteocytic and neuronal connectivity. These findings reveal a role for Sp7 and its target gene Osteocrin in osteocytogenesis, revealing that pathways that control osteocyte development influence human bone diseases.
Collapse
Affiliation(s)
- Jialiang S Wang
- Endocrine Unit, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Tushar Kamath
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Stanley Center for Psychiatric Research, Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Courtney M Mazur
- Endocrine Unit, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Fatemeh Mirzamohammadi
- Endocrine Unit, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
- Department of Plastic and Reconstructive Surgery, Wright State University, Dayton, OH, USA
| | - Daniel Rotter
- Endocrine Unit, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
- University of Applied Sciences Technikum Wien, Vienna, Austria
| | - Hironori Hojo
- Center for Disease Biology and Integrative Medicine, The University of Tokyo Graduate School of Medicine, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-8656, Japan
| | - Christian D Castro
- Endocrine Unit, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Nicha Tokavanich
- Endocrine Unit, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Rushi Patel
- Endocrine Unit, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Nicolas Govea
- Endocrine Unit, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
- Department of Anesthesiology, Weill Cornell Medical School, New York, NY, USA
| | - Tetsuya Enishi
- Endocrine Unit, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
- Department of Orthopedic Surgery, Tokushima Municipal Hospital, Tokushima, Japan
| | - Yunshu Wu
- Endocrine Unit, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, China
| | | | - Michael Bruce
- Endocrine Unit, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Daniel J Brooks
- Endocrine Unit, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
- Center for Advanced Orthopedic Studies, Department of Orthopedic Surgery, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MaA, USA
| | - Mary L Bouxsein
- Endocrine Unit, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
- Center for Advanced Orthopedic Studies, Department of Orthopedic Surgery, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MaA, USA
| | - Danielle Tokarz
- Advanced Microscopy Program, Center for Systems Biology and Wellman Center for Photomedicine, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
- Department of Chemistry, Saint Mary's University, Halifax, Canada
| | - Charles P Lin
- Advanced Microscopy Program, Center for Systems Biology and Wellman Center for Photomedicine, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Abdul Abdul
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Stanley Center for Psychiatric Research, Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Evan Z Macosko
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Stanley Center for Psychiatric Research, Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Department of Psychiatry, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Melissa Fiscaletti
- Pediatric Department, Sainte-Justine University Hospital Centre, Montreal, Canada
| | - Craig F Munns
- Institute of Endocrinology and Diabetes, The Children's Hospital at Westmead, Sydney, NSW, Australia
- Discipline of Paediatrics & Child Health, University of Sydney, Sydney, 2006, Australia
| | - Pearl Ryder
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Broad Institute of Harvard and MIT, Imaging Platform, Cambridge, MA, USA
| | - Maria Kost-Alimova
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Broad Institute of Harvard and MIT, Center for the Development of Therapeutics, Cambridge, MA, USA
| | - Patrick Byrne
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Broad Institute of Harvard and MIT, Center for the Development of Therapeutics, Cambridge, MA, USA
| | - Beth Cimini
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Broad Institute of Harvard and MIT, Imaging Platform, Cambridge, MA, USA
| | - Makoto Fujiwara
- Department of Pediatrics, Osaka University Graduate School of Medicine, Osaka, Japan
| | - Henry M Kronenberg
- Endocrine Unit, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Marc N Wein
- Endocrine Unit, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA.
- Broad Institute of Harvard and MIT, Cambridge, MA, USA.
- Harvard Stem Cell Institute, Cambridge, MA, USA.
| |
Collapse
|
9
|
Swank S, Sanger TJ, Stuart YE. (Non)Parallel developmental mechanisms in vertebrate appendage reduction and loss. Ecol Evol 2021; 11:15484-15497. [PMID: 34824770 PMCID: PMC8601893 DOI: 10.1002/ece3.8226] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2021] [Revised: 08/31/2021] [Accepted: 09/21/2021] [Indexed: 01/16/2023] Open
Abstract
Appendages have been reduced or lost hundreds of times during vertebrate evolution. This phenotypic convergence may be underlain by shared or different molecular mechanisms in distantly related vertebrate clades. To investigate, we reviewed the developmental and evolutionary literature of appendage reduction and loss in more than a dozen vertebrate genera from fish to mammals. We found that appendage reduction and loss was nearly always driven by modified gene expression as opposed to changes in coding sequences. Moreover, expression of the same genes was repeatedly modified across vertebrate taxa. However, the specific mechanisms by which expression was modified were rarely shared. The multiple routes to appendage reduction and loss suggest that adaptive loss of function phenotypes might arise routinely through changes in expression of key developmental genes.
Collapse
Affiliation(s)
- Samantha Swank
- Department of BiologyLoyola University ChicagoChicagoIllinoisUSA
| | - Thomas J. Sanger
- Department of BiologyLoyola University ChicagoChicagoIllinoisUSA
| | - Yoel E. Stuart
- Department of BiologyLoyola University ChicagoChicagoIllinoisUSA
| |
Collapse
|
10
|
Duboc V, Sulaiman FA, Feneck E, Kucharska A, Bell D, Holder-Espinasse M, Logan MPO. Tbx4 function during hindlimb development reveals a mechanism that explains the origins of proximal limb defects. Development 2021; 148:271903. [PMID: 34423345 PMCID: PMC8497778 DOI: 10.1242/dev.199580] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2021] [Accepted: 08/02/2021] [Indexed: 11/20/2022]
Abstract
We dissect genetically a gene regulatory network that involves the transcription factors Tbx4, Pitx1 and Isl1 acting cooperatively to establish the hindlimb bud, and identify key differences in the pathways that initiate formation of the hindlimb and forelimb. Using live image analysis of murine limb mesenchyme cells undergoing chondrogenesis in micromass culture, we distinguish a series of changes in cellular behaviours and cohesiveness that are required for chondrogenic precursors to undergo differentiation. Furthermore, we provide evidence that the proximal hindlimb defects observed in Tbx4 mutant mice result from a failure in the early differentiation step of chondroprogenitors into chondrocytes, providing an explanation for the origins of proximally biased limb defects.
Collapse
Affiliation(s)
- Veronique Duboc
- Randall Centre for Cell and Molecular Biophysics, King's College London, Guy's Campus, London SE1 1UL, UK
| | - Fatima A Sulaiman
- Randall Centre for Cell and Molecular Biophysics, King's College London, Guy's Campus, London SE1 1UL, UK
| | - Eleanor Feneck
- Randall Centre for Cell and Molecular Biophysics, King's College London, Guy's Campus, London SE1 1UL, UK
| | - Anna Kucharska
- Randall Centre for Cell and Molecular Biophysics, King's College London, Guy's Campus, London SE1 1UL, UK
| | - Donald Bell
- Light Microscopy, Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | | | - Malcolm P O Logan
- Randall Centre for Cell and Molecular Biophysics, King's College London, Guy's Campus, London SE1 1UL, UK
| |
Collapse
|
11
|
Johnstone CP, Wang NB, Sevier SA, Galloway KE. Understanding and Engineering Chromatin as a Dynamical System across Length and Timescales. Cell Syst 2020; 11:424-448. [PMID: 33212016 DOI: 10.1016/j.cels.2020.09.011] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2020] [Revised: 09/22/2020] [Accepted: 09/29/2020] [Indexed: 12/20/2022]
Abstract
Connecting the molecular structure and function of chromatin across length and timescales remains a grand challenge to understanding and engineering cellular behaviors. Across five orders of magnitude, dynamic processes constantly reshape chromatin structures, driving spaciotemporal patterns of gene expression and cell fate. Through the interplay of structure and function, the genome operates as a highly dynamic feedback control system. Recent experimental techniques have provided increasingly detailed data that revise and augment the relatively static, hierarchical view of genomic architecture with an understanding of how dynamic processes drive organization. Here, we review how novel technologies from sequencing, imaging, and synthetic biology refine our understanding of chromatin structure and function and enable chromatin engineering. Finally, we discuss opportunities to use these tools to enhance understanding of the dynamic interrelationship of chromatin structure and function.
Collapse
Affiliation(s)
| | - Nathan B Wang
- Department of Chemical Engineering, MIT, 25 Ames St., Cambridge, MA 02139, USA
| | - Stuart A Sevier
- Department of Systems Biology, Harvard Medical School, Boston, MA, USA; Department of Data Sciences, Dana-Farber Cancer Institute, Boston, MA, USA.
| | - Kate E Galloway
- Department of Chemical Engineering, MIT, 25 Ames St., Cambridge, MA 02139, USA.
| |
Collapse
|
12
|
Byun JS, Oh M, Lee S, Gil JE, Mo Y, Ku B, Kim WK, Oh KJ, Lee EW, Bae KH, Lee SC, Han BS. The transcription factor PITX1 drives astrocyte differentiation by regulating the SOX9 gene. J Biol Chem 2020; 295:13677-13690. [PMID: 32759168 DOI: 10.1074/jbc.ra120.013352] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2020] [Revised: 08/03/2020] [Indexed: 12/13/2022] Open
Abstract
Astrocytes perform multiple essential functions in the developing and mature brain, including regulation of synapse formation, control of neurotransmitter release and uptake, and maintenance of extracellular ion balance. As a result, astrocytes have been implicated in the progression of neurodegenerative disorders such as Alzheimer's disease, Huntington's disease, and Parkinson's disease. Despite these critical functions, the study of human astrocytes can be difficult because standard differentiation protocols are time-consuming and technically challenging, but a differentiation protocol recently developed in our laboratory enables the efficient derivation of astrocytes from human embryonic stem cells. We used this protocol along with microarrays, luciferase assays, electrophoretic mobility shift assays, and ChIP assays to explore the genes involved in astrocyte differentiation. We demonstrate that paired-like homeodomain transcription factor 1 (PITX1) is critical for astrocyte differentiation. PITX1 overexpression induced early differentiation of astrocytes, and its knockdown blocked astrocyte differentiation. PITX1 overexpression also increased and PITX1 knockdown decreased expression of sex-determining region Y box 9 (SOX9), known initiator of gliogenesis, during early astrocyte differentiation. Moreover, we determined that PITX1 activates the SOX9 promoter through a unique binding motif. Taken together, these findings indicate that PITX1 drives astrocyte differentiation by sustaining activation of the SOX9 promoter.
Collapse
Affiliation(s)
- Jeong Su Byun
- Biodefence Research Center, Korea Research Institute of Bioscience and Biotechnology, Gwahak-ro, Yuseong-gu, Daejeon, Republic of Korea
| | - Mihee Oh
- Biodefence Research Center, Korea Research Institute of Bioscience and Biotechnology, Gwahak-ro, Yuseong-gu, Daejeon, Republic of Korea
| | - Seonha Lee
- Biodefence Research Center, Korea Research Institute of Bioscience and Biotechnology, Gwahak-ro, Yuseong-gu, Daejeon, Republic of Korea; Department of Functional Genomics, University of Science and Technology of Korea, Gajeong-ro, Yuseong-gu, Daejeon, Republic of Korea
| | - Jung-Eun Gil
- Biodefence Research Center, Korea Research Institute of Bioscience and Biotechnology, Gwahak-ro, Yuseong-gu, Daejeon, Republic of Korea
| | - Yeajin Mo
- Disease Target Structure Research Center, Korea Research Institute of Bioscience and Biotechnology, Gwahak-ro, Yuseong-gu, Daejeon, Republic of Korea
| | - Bonsu Ku
- Disease Target Structure Research Center, Korea Research Institute of Bioscience and Biotechnology, Gwahak-ro, Yuseong-gu, Daejeon, Republic of Korea
| | - Won-Kon Kim
- Department of Functional Genomics, University of Science and Technology of Korea, Gajeong-ro, Yuseong-gu, Daejeon, Republic of Korea; Metabolic Regulation Research Center, Korea Research Institute of Bioscience and Biotechnology, Gwahak-ro, Yuseong-gu, Daejeon, Republic of Korea
| | - Kyoung-Jin Oh
- Department of Functional Genomics, University of Science and Technology of Korea, Gajeong-ro, Yuseong-gu, Daejeon, Republic of Korea; Metabolic Regulation Research Center, Korea Research Institute of Bioscience and Biotechnology, Gwahak-ro, Yuseong-gu, Daejeon, Republic of Korea
| | - Eun-Woo Lee
- Metabolic Regulation Research Center, Korea Research Institute of Bioscience and Biotechnology, Gwahak-ro, Yuseong-gu, Daejeon, Republic of Korea
| | - Kwang-Hee Bae
- Department of Functional Genomics, University of Science and Technology of Korea, Gajeong-ro, Yuseong-gu, Daejeon, Republic of Korea; Metabolic Regulation Research Center, Korea Research Institute of Bioscience and Biotechnology, Gwahak-ro, Yuseong-gu, Daejeon, Republic of Korea
| | - Sang Chul Lee
- Department of Functional Genomics, University of Science and Technology of Korea, Gajeong-ro, Yuseong-gu, Daejeon, Republic of Korea; Metabolic Regulation Research Center, Korea Research Institute of Bioscience and Biotechnology, Gwahak-ro, Yuseong-gu, Daejeon, Republic of Korea
| | - Baek-Soo Han
- Biodefence Research Center, Korea Research Institute of Bioscience and Biotechnology, Gwahak-ro, Yuseong-gu, Daejeon, Republic of Korea; Department of Functional Genomics, University of Science and Technology of Korea, Gajeong-ro, Yuseong-gu, Daejeon, Republic of Korea.
| |
Collapse
|
13
|
Vea IM, Shingleton AW. Network-regulated organ allometry: The developmental regulation of morphological scaling. WILEY INTERDISCIPLINARY REVIEWS-DEVELOPMENTAL BIOLOGY 2020; 10:e391. [PMID: 32567243 DOI: 10.1002/wdev.391] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/31/2019] [Revised: 04/30/2020] [Accepted: 05/23/2020] [Indexed: 12/11/2022]
Abstract
Morphological scaling relationships, or allometries, describe how traits grow coordinately and covary among individuals in a population. The developmental regulation of scaling is essential to generate correctly proportioned adults across a range of body sizes, while the mis-regulation of scaling may result in congenital birth defects. Research over several decades has identified the developmental mechanisms that regulate the size of individual traits. Nevertheless, we still have poor understanding of how these mechanisms work together to generate correlated size variation among traits in response to environmental and genetic variation. Conceptually, morphological scaling can be generated by size-regulatory factors that act directly on multiple growing traits (trait-autonomous scaling), or indirectly via hormones produced by central endocrine organs (systemically regulated scaling), and there are a number of well-established examples of such mechanisms. There is much less evidence, however, that genetic and environmental variation actually acts on these mechanisms to generate morphological scaling in natural populations. More recent studies indicate that growing organs can themselves regulate the growth of other organs in the body. This suggests that covariation in trait size can be generated by network-regulated scaling mechanisms that respond to changes in the growth of individual traits. Testing this hypothesis, and one of the main challenges of understanding morphological scaling, requires connecting mechanisms elucidated in the laboratory with patterns of scaling observed in the natural world. This article is categorized under: Establishment of Spatial and Temporal Patterns > Regulation of Size, Proportion, and Timing Comparative Development and Evolution > Organ System Comparisons Between Species.
Collapse
Affiliation(s)
- Isabelle M Vea
- Department of Biological Sciences, University of Illinois at Chicago, Chicago, Illinois, USA
| | - Alexander W Shingleton
- Department of Biological Sciences, University of Illinois at Chicago, Chicago, Illinois, USA
| |
Collapse
|
14
|
Richard D, Liu Z, Cao J, Kiapour AM, Willen J, Yarlagadda S, Jagoda E, Kolachalama VB, Sieker JT, Chang GH, Muthuirulan P, Young M, Masson A, Konrad J, Hosseinzadeh S, Maridas DE, Rosen V, Krawetz R, Roach N, Capellini TD. Evolutionary Selection and Constraint on Human Knee Chondrocyte Regulation Impacts Osteoarthritis Risk. Cell 2020; 181:362-381.e28. [PMID: 32220312 PMCID: PMC7179902 DOI: 10.1016/j.cell.2020.02.057] [Citation(s) in RCA: 77] [Impact Index Per Article: 15.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2019] [Revised: 12/10/2019] [Accepted: 02/26/2020] [Indexed: 02/06/2023]
Abstract
During human evolution, the knee adapted to the biomechanical demands of bipedalism by altering chondrocyte developmental programs. This adaptive process was likely not without deleterious consequences to health. Today, osteoarthritis occurs in 250 million people, with risk variants enriched in non-coding sequences near chondrocyte genes, loci that likely became optimized during knee evolution. We explore this relationship by epigenetically profiling joint chondrocytes, revealing ancient selection and recent constraint and drift on knee regulatory elements, which also overlap osteoarthritis variants that contribute to disease heritability by tending to modify constrained functional sequence. We propose a model whereby genetic violations to regulatory constraint, tolerated during knee development, lead to adult pathology. In support, we discover a causal enhancer variant (rs6060369) present in billions of people at a risk locus (GDF5-UQCC1), showing how it impacts mouse knee-shape and osteoarthritis. Overall, our methods link an evolutionarily novel aspect of human anatomy to its pathogenesis.
Collapse
Affiliation(s)
- Daniel Richard
- Human Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA
| | - Zun Liu
- Human Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA
| | - Jiaxue Cao
- Human Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA; Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, China
| | - Ata M Kiapour
- Orthopaedic Surgery, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Jessica Willen
- Human Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA
| | | | - Evelyn Jagoda
- Human Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA
| | - Vijaya B Kolachalama
- Department of Medicine, Boston University School of Medicine, Boston, MA 02115, USA; Whitaker Cardiovascular Institute, Boston University School of Medicine, Boston, MA 02115, USA; Hariri Institute for Computing and Computational Science and Engineering, Boston University, Boston, MA 02115, USA
| | - Jakob T Sieker
- Orthopaedic Surgery, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA; Pathology and Laboratory Medicine, Tufts Medical Center, Boston, MA 02111, USA
| | - Gary H Chang
- Department of Medicine, Boston University School of Medicine, Boston, MA 02115, USA
| | | | - Mariel Young
- Human Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA
| | - Anand Masson
- McCaig Institute for Bone and Joint Health, University of Calgary, Calgary, AB T2N 1N4, Canada
| | - Johannes Konrad
- Orthopaedic Surgery, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Shayan Hosseinzadeh
- Orthopaedic Surgery, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - David E Maridas
- Developmental Biology, Harvard School of Dental Medicine, Boston, MA 02115, USA
| | - Vicki Rosen
- Developmental Biology, Harvard School of Dental Medicine, Boston, MA 02115, USA
| | - Roman Krawetz
- McCaig Institute for Bone and Joint Health, University of Calgary, Calgary, AB T2N 1N4, Canada
| | - Neil Roach
- Human Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA
| | - Terence D Capellini
- Human Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA.
| |
Collapse
|
15
|
Cooper KL. Developmental and Evolutionary Allometry of the Mammalian Limb Skeleton. Integr Comp Biol 2020; 59:1356-1368. [PMID: 31180500 DOI: 10.1093/icb/icz082] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The variety of limb skeletal proportions enables a remarkable diversity of behaviors that include powered flight in bats and flipper-propelled swimming in whales using extremes of a range of homologous limb architectures. Even within human limbs, bone lengths span more than an order of magnitude from the short finger and toe bones to the long arm and leg bones. Yet all of this diversity arises from embryonic skeletal elements that are each a very similar size at formation. In this review article, I survey what is and is not yet known of the development and evolution of skeletal proportion at multiple hierarchical levels of biological organization. These include the cellular parameters of skeletal elongation in the cartilage growth plate, genes associated with differential growth, and putative gene regulatory mechanisms that would allow both covariant and independent evolution of the forelimbs and hindlimbs and of individual limb segments. Although the genetic mechanisms that shape skeletal proportion are still largely unknown, and most of what is known is limited to mammals, it is becoming increasingly apparent that the diversity of bone lengths is an emergent property of a complex system that controls elongation of individual skeletal elements using a genetic toolkit shared by all.
Collapse
Affiliation(s)
- Kimberly L Cooper
- Division of Biological Sciences, University of California San Diego, La Jolla, CA 92093-0377, USA
| |
Collapse
|
16
|
Roseman CC, Capellini TD, Jagoda E, Williams SA, Grabowski M, O'Connor C, Polk JD, Cheverud JM. Variation in mouse pelvic morphology maps to locations enriched in Sox9 Class II and Pitx1 regulatory features. JOURNAL OF EXPERIMENTAL ZOOLOGY PART B-MOLECULAR AND DEVELOPMENTAL EVOLUTION 2020; 334:100-112. [PMID: 32017444 DOI: 10.1002/jez.b.22926] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/02/2019] [Revised: 11/12/2019] [Accepted: 12/21/2019] [Indexed: 11/10/2022]
Abstract
Variation in pelvic morphology has a complex genetic basis and its patterning and specification is governed by conserved developmental pathways. Whether the mechanisms underlying the differentiation and specification of the pelvis also produce the morphological covariation on which natural selection may act, is still an open question in evolutionary developmental biology. We use high-resolution quantitative trait locus (QTL) mapping in the F34 generation of an advanced intercross experiment (LG,SM-G34 ) to characterize the genetic architecture of the mouse pelvis. We test the prediction that genomic features linked to developmental patterning and differentiation of the hind limb and pelvis and the regulation of chondrogenesis are overrepresented in QTL. We find 31 single QTL trait associations at the genome- or chromosome-wise significance level coalescing to 27 pleiotropic loci. We recover further QTL at a more relaxed significance threshold replicating locations found in a previous experiment in an earlier generation of the same population. QTL were more likely than chance to harbor Pitx1 and Sox9 Class II chromatin immunoprecipitation-seq features active during development of skeletal features. There was weak or no support for the enrichment of seven more categories of developmental features drawn from the literature. Our results suggest that genotypic variation is channeled through a subset of developmental processes involved in the generation of phenotypic variation in the pelvis. This finding indicates that the evolvability of complex traits may be subject to biases not evident from patterns of covariance among morphological features or developmental patterning when either is considered in isolation.
Collapse
Affiliation(s)
- Charles C Roseman
- Victor E. Shelford Vivarium, Department of Animal Biology, School of Integrative Biology, University of Illinois, Urbana-Champaign, Illinois
| | - Terence D Capellini
- Department of Human Evolutionary Biology, Harvard University, Cambridge, Massachusetts
| | - Evelyn Jagoda
- Department of Human Evolutionary Biology, Harvard University, Cambridge, Massachusetts
| | - Scott A Williams
- Department of Anthropology, Center for the Study of Human Origins, New York University, New York, New York.,New York Consortium in Evolutionary Primatology, New York, New York
| | - Mark Grabowski
- Research Centre in Evolutionary Anthropology and Palaeoecology, Liverpool John Moores University, Liverpool, UK
| | - Christine O'Connor
- Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, Minnesota.,Department of Ecology, Evolution and Behavior, University of Minnesota, St. Paul, Minnesota
| | - John D Polk
- Department of Anthropology, University of Illinois, Urbana-Champaign, Illinois.,Department of Biomedical and Translational Sciences, Carle-Illinois College of Medicine, Urbana, Illinois
| | | |
Collapse
|
17
|
Kjosness KM, Reno PL. Identifying the homology of the short human pisiform and its lost ossification center. EvoDevo 2019; 10:32. [PMID: 31788181 PMCID: PMC6876086 DOI: 10.1186/s13227-019-0145-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2019] [Accepted: 11/05/2019] [Indexed: 01/14/2023] Open
Abstract
Background The pisiform and calcaneus are paralogous bones of the wrist and ankle and are the only carpal and tarsal, respectively, to develop from two ossification centers with an associated growth plate in mammals. Human pisiforms and calcanei have undergone drastic evolutionary changes since our last common ancestor with chimpanzees and bonobos. The human pisiform is truncated and has lost an ossification center with the associated growth plate, while the human calcaneus has expanded and retained two ossification centers and a growth plate. Mammalian pisiforms represent a wide range of morphologies but extremely short pisiforms are rare and ossification center loss is even rarer. This raises the question of whether the sole human pisiform ossification center is homologous to the primary center or the secondary center of other species. We performed an ontogenetic study of pisiform and calcaneus ossification patterns and timing in macaques, apes, and humans (n = 907) from museum skeletal collections to address this question. Results Human pisiforms ossify irregularly and lack characteristic features of other primates while they develop. Pisiform primary and secondary center ossification timing typically matches that of the calcaneus of non-human primates, while the human pisiform corresponds with calcaneal secondary center ossification. Finally, human pisiforms ossify at the same dental stages as pisiform and calcaneal secondary centers in other hominoids. Conclusions These data indicate that the human pisiform is homologous to the pisiform epiphysis of other species, and that humans have lost a primary ossification center and associated growth plate while retaining ossification timing of the secondary center. This represents an exceptional evolutionary event and demonstrates a profound developmental change in the human wrist that is unusual not only among primates, but among mammals.
Collapse
Affiliation(s)
- Kelsey M Kjosness
- Department of Bio-Medical Sciences, Philadelphia College of Osteopathic Medicine, 4170 City Avenue, Philadelphia, PA 19131 USA
| | - Philip L Reno
- Department of Bio-Medical Sciences, Philadelphia College of Osteopathic Medicine, 4170 City Avenue, Philadelphia, PA 19131 USA
| |
Collapse
|
18
|
Genome Sequencing of the Japanese Eel ( Anguilla japonica) for Comparative Genomic Studies on tbx4 and a tbx4 Gene Cluster in Teleost Fishes. Mar Drugs 2019; 17:md17070426. [PMID: 31330852 PMCID: PMC6669545 DOI: 10.3390/md17070426] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2019] [Revised: 07/17/2019] [Accepted: 07/18/2019] [Indexed: 01/08/2023] Open
Abstract
Limbs originated from paired fish fins are an important innovation in Gnathostomata. Many studies have focused on limb development-related genes, of which the T-box transcription factor 4 gene (tbx4) has been considered as one of the most essential factors in the regulation of the hindlimb development. We previously confirmed pelvic fin loss in tbx4-knockout zebrafish. Here, we report a high-quality genome assembly of the Japanese eel (Anguilla japonica), which is an economically important fish without pelvic fins. The assembled genome is 1.13 Gb in size, with a scaffold N50 of 1.03 Mb. In addition, we collected 24 tbx4 sequences from 22 teleost fishes to explore the correlation between tbx4 and pelvic fin evolution. However, we observed complete exon structures of tbx4 in several pelvic-fin-loss species such as Ocean sunfish (Mola mola) and ricefield eel (Monopterus albus). More interestingly, an inversion of a special tbx4 gene cluster (brip1-tbx4-tbx2b- bcas3) occurred twice independently, which coincides with the presence of fin spines. A nonsynonymous mutation (M82L) was identified in the nuclear localization sequence (NLS) of the Japanese eel tbx4. We also examined variation and loss of hindlimb enhancer B (HLEB), which may account for pelvic fin loss in Tetraodontidae and Diodontidae. In summary, we generated a genome assembly of the Japanese eel, which provides a valuable genomic resource to study the evolution of fish tbx4 and helps elucidate the mechanism of pelvic fin loss in teleost fishes. Our comparative genomic studies, revealed for the first time a potential correlation between the tbx4 gene cluster and the evolutionary development of toxic fin spines. Because fin spines in teleosts are usually venoms, this tbx4 gene cluster may facilitate the genetic engineering of toxin-related marine drugs.
Collapse
|
19
|
Pigeon foot feathering reveals conserved limb identity networks. Dev Biol 2019; 454:128-144. [PMID: 31247188 DOI: 10.1016/j.ydbio.2019.06.015] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2019] [Revised: 06/19/2019] [Accepted: 06/20/2019] [Indexed: 12/15/2022]
Abstract
The tetrapod limb is a stunning example of evolutionary diversity, with dramatic variation not only among distantly related species, but also between the serially homologous forelimbs (FLs) and hindlimbs (HLs) within species. Despite this variation, highly conserved genetic and developmental programs underlie limb development and identity in all tetrapods, raising the question of how limb diversification is generated from a conserved toolkit. In some breeds of domestic pigeon, shifts in the expression of two conserved limb identity transcription factors, PITX1 and TBX5, are associated with the formation of feathered HLs with partial FL identity. To determine how modulation of PITX1 and TBX5 expression affects downstream gene expression, we compared the transcriptomes of embryonic limb buds from pigeons with scaled and feathered HLs. We identified a set of differentially expressed genes enriched for genes encoding transcription factors, extracellular matrix proteins, and components of developmental signaling pathways with important roles in limb development. A subset of the genes that distinguish scaled and feathered HLs are also differentially expressed between FL and scaled HL buds in pigeons, pinpointing a set of gene expression changes downstream of PITX1 and TBX5 in the partial transformation from HL to FL identity. We extended our analyses by comparing pigeon limb bud transcriptomes to chicken, anole lizard, and mammalian datasets to identify deeply conserved PITX1- and TBX5-responsive components of the limb identity program. Our analyses reveal a suite of predominantly low-level gene expression changes that are conserved across amniotes to regulate the identity of morphologically distinct limbs.
Collapse
|
20
|
Shen X, Gu Y, Yu S, Gong P, Mao Y, Li Y, Zheng Y, Qiao F, Zhao Z, Fan H. Silenced PITX1 promotes chemotherapeutic resistance to 5-fluorocytosine and cisplatin in gastric cancer cells. Exp Ther Med 2019; 17:4046-4054. [PMID: 31007741 PMCID: PMC6468935 DOI: 10.3892/etm.2019.7459] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2018] [Accepted: 01/31/2019] [Indexed: 12/11/2022] Open
Abstract
Resistance to chemotherapeutic drugs leads to a poor prognosis in gastric cancer (GC). The present study aimed to assess the association between pituitary homeobox paired homeodomain transcription 1 (PITX1) expression and the sensitivity of GC cells to the chemotherapeutic drugs 5-fluorouracil (5-FU) and cisplatin (CDDP). In the present study, the gastric cancer cell lines GES-1, AGS, BGC-823, MCG-803 and SGC-7901 were used. The expression of PITX1 was determined via reverse transcription-quantitative polymerase chain reaction in GC cell lines. AGS and BGC-823 cells, which exhibit a decreased PITX1 expression, were transfected with a PITX1 cDNA construct and its control vector. MCG-803 and SGC-7901 cells, which exhibit an increased PITX1 expression, were transfected with siRNA against PITX1 and its control scramble sequence. A Cell Counting kit-8 assay was performed to determine the impact of PITX1 expression on the sensitivity of GC cells to 5-FU and CDDP. The Cancer Genome Atlas database was used to analyze the expression of PITX1 with GC prognosis in the Asian population and to assess the potential mechanism of PITX1 in 5-FU and CDDP resistance. The results revealed that the overexpression of PIXT1 increased the sensitivity of GC cells to 5-FU/CDDP. The combination of 5-FU/CDDP and PITX1 overexpression also reduced the proliferation of GC cells. Additionally, PIXT1 knockdown decreased the sensitivity of GC cells to 5-FU/CDDP. TCGA data revealed that a lower expression of PITX1 is exhibited in Asian GC patients than in normal individuals. GC patients with a lower expression of PITX1 had a poor prognosis. The expression of PITX1 affected the sensitivity of GC cells to 5-FU/CDDP, indicating that PITX1 may increase the efficacy of treatment in GC patients.
Collapse
Affiliation(s)
- Xiaohui Shen
- Department of Medical Genetics and Developmental Biology, Medical School of Southeast University, The Key Laboratory of Developmental Genes and Human Diseases, Ministry of Education, Southeast University, Nanjing, Jiangsu 210009, P.R. China
| | - Yuejun Gu
- Department of Medical Genetics and Developmental Biology, Medical School of Southeast University, The Key Laboratory of Developmental Genes and Human Diseases, Ministry of Education, Southeast University, Nanjing, Jiangsu 210009, P.R. China
| | - Shengling Yu
- Department of Medical Genetics and Developmental Biology, Medical School of Southeast University, The Key Laboratory of Developmental Genes and Human Diseases, Ministry of Education, Southeast University, Nanjing, Jiangsu 210009, P.R. China
| | - Pihai Gong
- Department of Medical Genetics and Developmental Biology, Medical School of Southeast University, The Key Laboratory of Developmental Genes and Human Diseases, Ministry of Education, Southeast University, Nanjing, Jiangsu 210009, P.R. China
| | - Yuhang Mao
- Department of Medical Genetics and Developmental Biology, Medical School of Southeast University, The Key Laboratory of Developmental Genes and Human Diseases, Ministry of Education, Southeast University, Nanjing, Jiangsu 210009, P.R. China
| | - Yiping Li
- Department of Pathology, Medical School of Southeast University, Nanjing, Jiangsu 210009, P.R. China
| | - Ying Zheng
- Department of Medical Genetics and Developmental Biology, Medical School of Southeast University, The Key Laboratory of Developmental Genes and Human Diseases, Ministry of Education, Southeast University, Nanjing, Jiangsu 210009, P.R. China
| | - Fengchang Qiao
- Department of Medical Genetics and Developmental Biology, Medical School of Southeast University, The Key Laboratory of Developmental Genes and Human Diseases, Ministry of Education, Southeast University, Nanjing, Jiangsu 210009, P.R. China
| | - Zhujiang Zhao
- Department of Medical Genetics and Developmental Biology, Medical School of Southeast University, The Key Laboratory of Developmental Genes and Human Diseases, Ministry of Education, Southeast University, Nanjing, Jiangsu 210009, P.R. China
| | - Hong Fan
- Department of Medical Genetics and Developmental Biology, Medical School of Southeast University, The Key Laboratory of Developmental Genes and Human Diseases, Ministry of Education, Southeast University, Nanjing, Jiangsu 210009, P.R. China
| |
Collapse
|
21
|
Fu S, Wang Q, Moore JE, Purcaro MJ, Pratt HE, Fan K, Gu C, Jiang C, Zhu R, Kundaje A, Lu A, Weng Z. Differential analysis of chromatin accessibility and histone modifications for predicting mouse developmental enhancers. Nucleic Acids Res 2018; 46:11184-11201. [PMID: 30137428 PMCID: PMC6265487 DOI: 10.1093/nar/gky753] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2018] [Revised: 07/15/2018] [Accepted: 08/08/2018] [Indexed: 12/11/2022] Open
Abstract
Enhancers are distal cis-regulatory elements that modulate gene expression. They are depleted of nucleosomes and enriched in specific histone modifications; thus, calling DNase-seq and histone mark ChIP-seq peaks can predict enhancers. We evaluated nine peak-calling algorithms for predicting enhancers validated by transgenic mouse assays. DNase and H3K27ac peaks were consistently more predictive than H3K4me1/2/3 and H3K9ac peaks. DFilter and Hotspot2 were the best DNase peak callers, while HOMER, MUSIC, MACS2, DFilter and F-seq were the best H3K27ac peak callers. We observed that the differential DNase or H3K27ac signals between two distant tissues increased the area under the precision-recall curve (PR-AUC) of DNase peaks by 17.5-166.7% and that of H3K27ac peaks by 7.1-22.2%. We further improved this differential signal method using multiple contrast tissues. Evaluated using a blind test, the differential H3K27ac signal method substantially improved PR-AUC from 0.48 to 0.75 for predicting heart enhancers. We further validated our approach using postnatal retina and cerebral cortex enhancers identified by massively parallel reporter assays, and observed improvements for both tissues. In summary, we compared nine peak callers and devised a superior method for predicting tissue-specific mouse developmental enhancers by reranking the called peaks.
Collapse
Affiliation(s)
- Shaliu Fu
- Clinical Translational Research Center, Shanghai Pulmonary Hospital, School of Life Sciences and Technology, Tongji University, Shanghai 200092, China
| | - Qin Wang
- Clinical Translational Research Center, Shanghai Pulmonary Hospital, School of Life Sciences and Technology, Tongji University, Shanghai 200092, China
| | - Jill E Moore
- Program in Bioinformatics and Integrative Biology, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Michael J Purcaro
- Program in Bioinformatics and Integrative Biology, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Henry E Pratt
- Program in Bioinformatics and Integrative Biology, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Kaili Fan
- Clinical Translational Research Center, Shanghai Pulmonary Hospital, School of Life Sciences and Technology, Tongji University, Shanghai 200092, China
| | - Cuihua Gu
- Clinical Translational Research Center, Shanghai Pulmonary Hospital, School of Life Sciences and Technology, Tongji University, Shanghai 200092, China
| | - Cizhong Jiang
- Clinical Translational Research Center, Shanghai Pulmonary Hospital, School of Life Sciences and Technology, Tongji University, Shanghai 200092, China
| | - Ruixin Zhu
- Clinical Translational Research Center, Shanghai Pulmonary Hospital, School of Life Sciences and Technology, Tongji University, Shanghai 200092, China
| | - Anshul Kundaje
- Department of Genetics, School of Medicine, Department of Computer Science, Stanford University, Stanford, CA 94305, USA
| | - Aiping Lu
- Clinical Translational Research Center, Shanghai Pulmonary Hospital, School of Life Sciences and Technology, Tongji University, Shanghai 200092, China
| | - Zhiping Weng
- Clinical Translational Research Center, Shanghai Pulmonary Hospital, School of Life Sciences and Technology, Tongji University, Shanghai 200092, China
- Program in Bioinformatics and Integrative Biology, University of Massachusetts Medical School, Worcester, MA 01605, USA
| |
Collapse
|
22
|
Roscito JG, Sameith K, Parra G, Langer BE, Petzold A, Moebius C, Bickle M, Rodrigues MT, Hiller M. Phenotype loss is associated with widespread divergence of the gene regulatory landscape in evolution. Nat Commun 2018; 9:4737. [PMID: 30413698 PMCID: PMC6226452 DOI: 10.1038/s41467-018-07122-z] [Citation(s) in RCA: 47] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2018] [Accepted: 10/15/2018] [Indexed: 02/07/2023] Open
Abstract
Detecting the genomic changes underlying phenotypic changes between species is a main goal of evolutionary biology and genomics. Evolutionary theory predicts that changes in cis-regulatory elements are important for morphological changes. We combined genome sequencing, functional genomics and genome-wide comparative analyses to investigate regulatory elements in lineages that lost morphological traits. We first show that limb loss in snakes is associated with widespread divergence of limb regulatory elements. We next show that eye degeneration in subterranean mammals is associated with widespread divergence of eye regulatory elements. In both cases, sequence divergence results in an extensive loss of transcription factor binding sites. Importantly, diverged regulatory elements are associated with genes required for normal limb patterning or normal eye development and function, suggesting that regulatory divergence contributed to the loss of these phenotypes. Together, our results show that genome-wide decay of the phenotype-specific cis-regulatory landscape is a hallmark of lost morphological traits. Cis-regulatory elements are important factors for morphological changes. Here, the authors show widespread divergence of limb and eye regulatory elements in limb loss in snakes and eye degeneration in subterranean mammals respectively.
Collapse
Affiliation(s)
- Juliana G Roscito
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, 01307, Germany.,Max Planck Institute for the Physics of Complex Systems, Dresden, 01187, Germany.,Center for Systems Biology Dresden, Dresden, 01307, Germany.,Instituto de Biociências, Universidade de São Paulo, São Paulo, 05508-090, Brazil
| | - Katrin Sameith
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, 01307, Germany.,Max Planck Institute for the Physics of Complex Systems, Dresden, 01187, Germany.,Center for Systems Biology Dresden, Dresden, 01307, Germany
| | - Genis Parra
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, 01307, Germany.,Max Planck Institute for the Physics of Complex Systems, Dresden, 01187, Germany.,Center for Systems Biology Dresden, Dresden, 01307, Germany
| | - Bjoern E Langer
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, 01307, Germany.,Max Planck Institute for the Physics of Complex Systems, Dresden, 01187, Germany.,Center for Systems Biology Dresden, Dresden, 01307, Germany
| | - Andreas Petzold
- Center for Regenerative Therapies TU Dresden, Dresden, 01307, Germany
| | - Claudia Moebius
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, 01307, Germany
| | - Marc Bickle
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, 01307, Germany
| | | | - Michael Hiller
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, 01307, Germany. .,Max Planck Institute for the Physics of Complex Systems, Dresden, 01187, Germany. .,Center for Systems Biology Dresden, Dresden, 01307, Germany.
| |
Collapse
|
23
|
Morioka S, Mohanty-Hejmadi P, Yaoita Y, Tazawa I. Homeotic transformation of tails into limbs in anurans. Dev Growth Differ 2018; 60:365-376. [PMID: 30133711 DOI: 10.1111/dgd.12547] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2018] [Revised: 05/25/2018] [Accepted: 06/06/2018] [Indexed: 12/18/2022]
Abstract
Anuran tadpoles can regenerate their tails after amputation. However, they occasionally form ectopic limbs instead of the lost tail part after vitamin A treatment. This is regarded as an example of a homeotic transformation. In this phenomenon, the developmental fate of the tail blastema is apparently altered from that of a tail to that of limbs, indicating a realignment of positional information in the blastema. Morphological observations and analyses of the development of skeletal elements during the process suggest that positional information in the blastema is rewritten from tail to trunk specification under the influence of vitamin A, resulting in limb formation. Despite the extensive information gained from morphological observations, a comprehensive understanding of this phenomenon also requires molecular data. We review previous studies related to anuran homeotic transformation. The findings of these studies provide a basis for evaluating major hypotheses and identifying molecular data that should be prioritized in future studies. Finally, we argue that positional information for the tail blastema changes to that for a part of the trunk, leading to homeotic transformations. To suggest this hypothesis, we present published data that favor the rewriting of positional information.
Collapse
Affiliation(s)
- Sho Morioka
- Amphibian Research Center, Graduate School of Science, Hiroshima University, Higashihiroshima, Hiroshima, Japan
| | | | - Yoshio Yaoita
- Division of Embryology, Amphibian Research Center, Hiroshima University, Higashihiroshima, Hiroshima, Japan
| | - Ichiro Tazawa
- Division of Embryology, Amphibian Research Center, Hiroshima University, Higashihiroshima, Hiroshima, Japan
| |
Collapse
|
24
|
Tollis M, Hutchins ED, Stapley J, Rupp SM, Eckalbar WL, Maayan I, Lasku E, Infante CR, Dennis SR, Robertson JA, May CM, Crusoe MR, Bermingham E, DeNardo DF, Hsieh STT, Kulathinal RJ, McMillan WO, Menke DB, Pratt SC, Rawls JA, Sanjur O, Wilson-Rawls J, Wilson Sayres MA, Fisher RE, Kusumi K. Comparative Genomics Reveals Accelerated Evolution in Conserved Pathways during the Diversification of Anole Lizards. Genome Biol Evol 2018; 10:489-506. [PMID: 29360978 PMCID: PMC5798147 DOI: 10.1093/gbe/evy013] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/17/2018] [Indexed: 11/21/2022] Open
Abstract
Squamates include all lizards and snakes, and display some of the most diverse and extreme morphological adaptations among vertebrates. However, compared with birds and mammals, relatively few resources exist for comparative genomic analyses of squamates, hampering efforts to understand the molecular bases of phenotypic diversification in such a speciose clade. In particular, the ∼400 species of anole lizard represent an extensive squamate radiation. Here, we sequence and assemble the draft genomes of three anole species-Anolis frenatus, Anolis auratus, and Anolis apletophallus-for comparison with the available reference genome of Anolis carolinensis. Comparative analyses reveal a rapid background rate of molecular evolution consistent with a model of punctuated equilibrium, and strong purifying selection on functional genomic elements in anoles. We find evidence for accelerated evolution in genes involved in behavior, sensory perception, and reproduction, as well as in genes regulating limb bud development and hindlimb specification. Morphometric analyses of anole fore and hindlimbs corroborated these findings. We detect signatures of positive selection across several genes related to the development and regulation of the forebrain, hormones, and the iguanian lizard dewlap, suggesting molecular changes underlying behavioral adaptations known to reinforce species boundaries were a key component in the diversification of anole lizards.
Collapse
Affiliation(s)
- Marc Tollis
- School of Life Sciences, Arizona State University
- Virginia G. Piper Center for Personalized Diagnostics, The Biodesign Institute at Arizona State University
| | - Elizabeth D Hutchins
- School of Life Sciences, Arizona State University
- Neurogenomics Division, Translational Genomics Research Institute, Phoenix, Arizona
| | - Jessica Stapley
- Smithsonian Tropical Research Institute, Panamá, República de Panamá
| | - Shawn M Rupp
- School of Life Sciences, Arizona State University
| | | | - Inbar Maayan
- School of Life Sciences, Arizona State University
| | - Eris Lasku
- School of Life Sciences, Arizona State University
| | - Carlos R Infante
- Department of Genetics, University of Georgia
- Department of Molecular and Cellular Biology, University of Arizona
| | - Stuart R Dennis
- Smithsonian Tropical Research Institute, Panamá, República de Panamá
| | | | | | | | - Eldredge Bermingham
- Smithsonian Tropical Research Institute, Panamá, República de Panamá
- Patricia and Phillip Frost Museum of Science, Miami, Florida
| | | | | | | | | | | | | | | | - Oris Sanjur
- Smithsonian Tropical Research Institute, Panamá, República de Panamá
| | | | - Melissa A Wilson Sayres
- School of Life Sciences, Arizona State University
- The Center for Evolution and Medicine, Arizona State University
| | - Rebecca E Fisher
- School of Life Sciences, Arizona State University
- Department of Basic Medical Sciences, University of Arizona College of Medicine–Phoenix
| | - Kenro Kusumi
- School of Life Sciences, Arizona State University
- Neurogenomics Division, Translational Genomics Research Institute, Phoenix, Arizona
- Department of Basic Medical Sciences, University of Arizona College of Medicine–Phoenix
| |
Collapse
|
25
|
Wang JS, Infante CR, Park S, Menke DB. PITX1 promotes chondrogenesis and myogenesis in mouse hindlimbs through conserved regulatory targets. Dev Biol 2017; 434:186-195. [PMID: 29273440 DOI: 10.1016/j.ydbio.2017.12.013] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2017] [Revised: 12/05/2017] [Accepted: 12/18/2017] [Indexed: 10/18/2022]
Abstract
The PITX1 transcription factor is expressed during hindlimb development, where it plays a critical role in directing hindlimb growth and the specification of hindlimb morphology. While it is known that PITX1 regulates hindlimb formation, in part, through activation of the Tbx4 gene, other transcriptional targets remain to be elucidated. We have used a combination of ChIP-seq and RNA-seq to investigate enhancer regions and target genes that are directly regulated by PITX1 in embryonic mouse hindlimbs. In addition, we have analyzed PITX1 binding sites in hindlimbs of Anolis lizards to identify ancient PITX1 regulatory targets. We find that PITX1-bound regions in both mouse and Anolis hindlimbs are strongly associated with genes implicated in limb and skeletal system development. Gene expression analyses reveal a large number of misexpressed genes in the hindlimbs of Pitx1-/- mouse embryos. By intersecting misexpressed genes with genes that have neighboring mouse PITX1 binding sites, we identified 440 candidate targets of PITX1. Of these candidates, 68 exhibit ultra-conserved PITX1 binding events that are shared between mouse and Anolis hindlimbs. Among the ancient targets of PITX1 are important regulators of cartilage and skeletal muscle development, including Sox9 and Six1. Our data suggest that PITX1 promotes chondrogenesis and myogenesis in the hindlimb by direct regulation of several key members of the cartilage and muscle transcriptional networks.
Collapse
Affiliation(s)
- Jialiang S Wang
- Department of Genetics, University of Georgia, Athens, GA 30602, USA
| | - Carlos R Infante
- Department of Genetics, University of Georgia, Athens, GA 30602, USA; Department of Molecular and Cellular Biology, University of Arizona, Tucson, AZ 85721, USA
| | - Sungdae Park
- Department of Genetics, University of Georgia, Athens, GA 30602, USA
| | - Douglas B Menke
- Department of Genetics, University of Georgia, Athens, GA 30602, USA.
| |
Collapse
|
26
|
Melville J, Hunjan S, McLean F, Mantziou G, Boysen K, Parry LJ. Expression of a hindlimb-determining factor Pitx1 in the forelimb of the lizard Pogona vitticeps during morphogenesis. Open Biol 2017; 6:rsob.160252. [PMID: 27784790 PMCID: PMC5090065 DOI: 10.1098/rsob.160252] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2016] [Accepted: 09/29/2016] [Indexed: 11/24/2022] Open
Abstract
With over 9000 species, squamates, which include lizards and snakes, are the largest group of reptiles and second-largest order of vertebrates, spanning a vast array of appendicular skeletal morphology. As such, they provide a promising system for examining developmental and molecular processes underlying limb morphology. Using the central bearded dragon (Pogona vitticeps) as the primary study model, we examined limb morphometry throughout embryonic development and characterized the expression of three known developmental genes (GHR, Pitx1 and Shh) from early embryonic stage through to hatchling stage via reverse transcription quantitative polymerase chain reaction (RT-qPCR) and immunohistochemistry (IHC). In this study, all genes were found to be transcribed in both the forelimbs and hindlimbs of P. vitticeps. While the highest level of GHR expression occurred at the hatchling stage, Pitx1 and Shh expression was greatest earlier during embryogenesis, which coincides with the onset of the differentiation between forelimb and hindlimb length. We compared our finding of Pitx1 expression—a hindlimb-determining gene—in the forelimbs of P. vitticeps to that in a closely related Australian agamid lizard, Ctenophorus pictus, where we found Pitx1 expression to be more highly expressed in the hindlimb compared with the forelimb during early and late morphogenesis—a result consistent with that found across other tetrapods. Expression of Pitx1 in forelimbs has only rarely been documented, including via in situ hybridization in a chicken and a frog. Our findings from both RT-qPCR and IHC indicate that further research across a wider range of tetrapods is needed to more fully understand evolutionary variation in molecular processes underlying limb morphology.
Collapse
Affiliation(s)
| | | | | | | | - Katja Boysen
- Museum Victoria, Carlton, Victoria 3001, Australia
| | - Laura J Parry
- School of Biosciences, University of Melbourne, Parkville, Victoria 3010, Australia
| |
Collapse
|
27
|
Ferrai C, Torlai Triglia E, Risner-Janiczek JR, Rito T, Rackham OJ, de Santiago I, Kukalev A, Nicodemi M, Akalin A, Li M, Ungless MA, Pombo A. RNA polymerase II primes Polycomb-repressed developmental genes throughout terminal neuronal differentiation. Mol Syst Biol 2017; 13:946. [PMID: 29038337 PMCID: PMC5658700 DOI: 10.15252/msb.20177754] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
Polycomb repression in mouse embryonic stem cells (ESCs) is tightly associated with promoter co‐occupancy of RNA polymerase II (RNAPII) which is thought to prime genes for activation during early development. However, it is unknown whether RNAPII poising is a general feature of Polycomb repression, or is lost during differentiation. Here, we map the genome‐wide occupancy of RNAPII and Polycomb from pluripotent ESCs to non‐dividing functional dopaminergic neurons. We find that poised RNAPII complexes are ubiquitously present at Polycomb‐repressed genes at all stages of neuronal differentiation. We observe both loss and acquisition of RNAPII and Polycomb at specific groups of genes reflecting their silencing or activation. Strikingly, RNAPII remains poised at transcription factor genes which are silenced in neurons through Polycomb repression, and have major roles in specifying other, non‐neuronal lineages. We conclude that RNAPII poising is intrinsically associated with Polycomb repression throughout differentiation. Our work suggests that the tight interplay between RNAPII poising and Polycomb repression not only instructs promoter state transitions, but also may enable promoter plasticity in differentiated cells.
Collapse
Affiliation(s)
- Carmelo Ferrai
- Epigenetic Regulation and Chromatin Architecture, Max Delbrück Center for Molecular Medicine, Berlin, Germany .,Genome Function, MRC London Institute of Medical Sciences (previously MRC Clinical Sciences Centre), London, UK.,Institute of Clinical Sciences (ICS), Faculty of Medicine, Imperial College London, London, UK
| | - Elena Torlai Triglia
- Epigenetic Regulation and Chromatin Architecture, Max Delbrück Center for Molecular Medicine, Berlin, Germany
| | - Jessica R Risner-Janiczek
- Institute of Clinical Sciences (ICS), Faculty of Medicine, Imperial College London, London, UK.,Stem Cell Neurogenesis, MRC London Institute of Medical Sciences (previously MRC Clinical Sciences Centre), London, UK.,Neurophysiology Group, MRC London Institute of Medical Sciences (previously MRC Clinical Sciences Centre), London, UK
| | - Tiago Rito
- Epigenetic Regulation and Chromatin Architecture, Max Delbrück Center for Molecular Medicine, Berlin, Germany
| | | | - Inês de Santiago
- Genome Function, MRC London Institute of Medical Sciences (previously MRC Clinical Sciences Centre), London, UK.,Institute of Clinical Sciences (ICS), Faculty of Medicine, Imperial College London, London, UK
| | - Alexander Kukalev
- Epigenetic Regulation and Chromatin Architecture, Max Delbrück Center for Molecular Medicine, Berlin, Germany
| | - Mario Nicodemi
- Dipartimento di Fisica, Università di Napoli Federico II and INFN Napoli, Complesso Universitario di Monte Sant'Angelo, Naples, Italy
| | - Altuna Akalin
- Scientific Bioinformatics Platform, Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine, Berlin, Germany
| | - Meng Li
- Institute of Clinical Sciences (ICS), Faculty of Medicine, Imperial College London, London, UK.,Stem Cell Neurogenesis, MRC London Institute of Medical Sciences (previously MRC Clinical Sciences Centre), London, UK
| | - Mark A Ungless
- Institute of Clinical Sciences (ICS), Faculty of Medicine, Imperial College London, London, UK .,Neurophysiology Group, MRC London Institute of Medical Sciences (previously MRC Clinical Sciences Centre), London, UK
| | - Ana Pombo
- Epigenetic Regulation and Chromatin Architecture, Max Delbrück Center for Molecular Medicine, Berlin, Germany .,Genome Function, MRC London Institute of Medical Sciences (previously MRC Clinical Sciences Centre), London, UK.,Institute of Clinical Sciences (ICS), Faculty of Medicine, Imperial College London, London, UK.,Institute for Biology, Humboldt-Universität zu Berlin, Berlin Germany
| |
Collapse
|
28
|
Nemec S, Luxey M, Jain D, Huang Sung A, Pastinen T, Drouin J. Pitx1 directly modulates the core limb development program to implement hindlimb identity. Development 2017; 144:3325-3335. [PMID: 28807899 DOI: 10.1242/dev.154864] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2017] [Accepted: 08/04/2017] [Indexed: 01/24/2023]
Abstract
Forelimbs (FLs) and hindlimbs (HLs) develop complex musculoskeletal structures that rely on the deployment of a conserved developmental program. Pitx1, a transcription factor gene with expression restricted to HL and absent from FL, plays an important role in generating HL features. The genomic mechanisms by which Pitx1 effects HL identity remain poorly understood. Here, we use expression profiling and analysis of direct Pitx1 targets to characterize the HL- and FL-restricted genetic programs in mouse and situate the Pitx1-dependent gene network within the context of limb-specific gene regulation. We show that Pitx1 is a crucial component of a narrow network of HL-restricted regulators, acting on a developmental program that is shared between FL and HL. Pitx1 targets sites that are in a similar chromatin state in FL and HL and controls expression of patterning genes as well as the chondrogenic program, consistent with impaired chondrogenesis in Pitx1-/- HL. These findings support a model in which multifactorial actions of a limited number of HL regulators redirect the generic limb development program in order to generate the unique structural features of the limb.
Collapse
Affiliation(s)
- Stephen Nemec
- Institut de Recherches Cliniques de Montréal, Montréal, QC, H2W 1R7 Canada.,Department of Experimental Medicine, McGill University, Montreal, QC, H4A 3J1 Canada
| | - Maëva Luxey
- Institut de Recherches Cliniques de Montréal, Montréal, QC, H2W 1R7 Canada
| | - Deepak Jain
- Institut de Recherches Cliniques de Montréal, Montréal, QC, H2W 1R7 Canada.,Department of Biochemistry, McGill University, Montreal, QC, H3G 1Y6 Canada
| | - Aurélie Huang Sung
- Institut de Recherches Cliniques de Montréal, Montréal, QC, H2W 1R7 Canada
| | - Tomi Pastinen
- Department of Human Genetics, McGill University and Genome Quebec Innovation Centre, Montreal, QC, H3A 0G1 Canada
| | - Jacques Drouin
- Institut de Recherches Cliniques de Montréal, Montréal, QC, H2W 1R7 Canada .,Department of Experimental Medicine, McGill University, Montreal, QC, H4A 3J1 Canada.,Department of Biochemistry, McGill University, Montreal, QC, H3G 1Y6 Canada
| |
Collapse
|
29
|
Abstract
The limb is a commonly used model system for developmental biology. Given the need for precise control of complex signalling pathways to achieve proper patterning, the limb is also becoming a model system for gene regulation studies. Recent developments in genomic technologies have enabled the genome-wide identification of regulatory elements that control limb development, yielding insights into the determination of limb morphology and forelimb versus hindlimb identity. The modulation of regulatory interactions - for example, through the modification of regulatory sequences or chromatin architecture - can lead to morphological evolution, acquired regeneration capacity or limb malformations in diverse species, including humans.
Collapse
Affiliation(s)
- Florence Petit
- Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, California 94158, USA.,University of Lille, CHU Lille, EA 7364-RADEME, F-59000 Lille, France
| | - Karen E Sears
- School of Integrative Biology, Institute for Genomic Biology, University of Illinois, Urbana, Illinois 61801, USA
| | - Nadav Ahituv
- Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, California 94158, USA.,Institute for Human Genetics, University of California San Francisco, California 94158, USA
| |
Collapse
|
30
|
Melamed P, Yosefzon Y, Rudnizky S, Pnueli L. Transcriptional enhancers: Transcription, function and flexibility. Transcription 2016; 7:26-31. [PMID: 26934309 DOI: 10.1080/21541264.2015.1128517] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Active transcriptional enhancers are often transcribed to eRNAs, whose changing levels mirror those of the target gene mRNA. We discuss some of the reported functions of these eRNAs and their likely diversity to allow utilization of distinct cis regulatory regions to enhance transcription in diverse developmental and cellular contexts.
Collapse
Affiliation(s)
- Philippa Melamed
- a Faculty of Biology, Technion-Israel Institute of Technology , Haifa , Israel
| | - Yahav Yosefzon
- a Faculty of Biology, Technion-Israel Institute of Technology , Haifa , Israel
| | - Sergei Rudnizky
- a Faculty of Biology, Technion-Israel Institute of Technology , Haifa , Israel
| | - Lilach Pnueli
- a Faculty of Biology, Technion-Israel Institute of Technology , Haifa , Israel
| |
Collapse
|
31
|
Ye W, Song Y, Huang Z, Osterwalder M, Ljubojevic A, Xu J, Bobick B, Abassah-Oppong S, Ruan N, Shamby R, Yu D, Zhang L, Cai CL, Visel A, Zhang Y, Cobb J, Chen Y. A unique stylopod patterning mechanism by Shox2-controlled osteogenesis. Development 2016; 143:2548-2560. [PMID: 27287812 PMCID: PMC4958343 DOI: 10.1242/dev.138750] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2016] [Accepted: 05/31/2016] [Indexed: 02/05/2023]
Abstract
Vertebrate appendage patterning is programmed by Hox-TALE factor-bound regulatory elements. However, it remains unclear which cell lineages are commissioned by Hox-TALE factors to generate regional specific patterns and whether other Hox-TALE co-factors exist. In this study, we investigated the transcriptional mechanisms controlled by the Shox2 transcriptional regulator in limb patterning. Harnessing an osteogenic lineage-specific Shox2 inactivation approach we show that despite widespread Shox2 expression in multiple cell lineages, lack of the stylopod observed upon Shox2 deficiency is a specific result of Shox2 loss of function in the osteogenic lineage. ChIP-Seq revealed robust interaction of Shox2 with cis-regulatory enhancers clustering around skeletogenic genes that are also bound by Hox-TALE factors, supporting a lineage autonomous function of Shox2 in osteogenic lineage fate determination and skeleton patterning. Pbx ChIP-Seq further allowed the genome-wide identification of cis-regulatory modules exhibiting co-occupancy of Pbx, Meis and Shox2 transcriptional regulators. Integrative analysis of ChIP-Seq and RNA-Seq data and transgenic enhancer assays indicate that Shox2 patterns the stylopod as a repressor via interaction with enhancers active in the proximal limb mesenchyme and antagonizes the repressive function of TALE factors in osteogenesis.
Collapse
Affiliation(s)
- Wenduo Ye
- Department of Cell and Molecular Biology, Tulane University, New Orleans, LA 70118, USA
| | - Yingnan Song
- Department of Cell and Molecular Biology, Tulane University, New Orleans, LA 70118, USA Southern Center for Biomedical Research and Fujian Key Laboratory of Developmental and Neural Biology, College of Life Sciences, Fujian Normal University, Fuzhou, Fujian 350108, People's Republic of China
| | - Zhen Huang
- Department of Cell and Molecular Biology, Tulane University, New Orleans, LA 70118, USA Southern Center for Biomedical Research and Fujian Key Laboratory of Developmental and Neural Biology, College of Life Sciences, Fujian Normal University, Fuzhou, Fujian 350108, People's Republic of China
| | | | - Anja Ljubojevic
- Department of Biological Sciences, University of Calgary, Calgary, Alberta, Canada T2N 1N4
| | - Jue Xu
- Department of Cell and Molecular Biology, Tulane University, New Orleans, LA 70118, USA State Key Laboratory of Oral Disease, West China Hospital of Stomatology, Sichuan University, Chengdu, Sichuan 610041, People's Republic of China
| | - Brent Bobick
- Department of Biological Sciences, University of Calgary, Calgary, Alberta, Canada T2N 1N4
| | - Samuel Abassah-Oppong
- Department of Biological Sciences, University of Calgary, Calgary, Alberta, Canada T2N 1N4
| | - Ningsheng Ruan
- Department of Cell and Molecular Biology, Tulane University, New Orleans, LA 70118, USA Southern Center for Biomedical Research and Fujian Key Laboratory of Developmental and Neural Biology, College of Life Sciences, Fujian Normal University, Fuzhou, Fujian 350108, People's Republic of China
| | - Ross Shamby
- Department of Cell and Molecular Biology, Tulane University, New Orleans, LA 70118, USA
| | - Diankun Yu
- Department of Cell and Molecular Biology, Tulane University, New Orleans, LA 70118, USA
| | - Lu Zhang
- Department of Developmental and Regenerative Biology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Chen-Leng Cai
- Department of Developmental and Regenerative Biology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Axel Visel
- Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA U.S. Department of Energy Joint Genome Institute, Walnut Creek, CA 94598, USA School of Natural Sciences, University of California at Merced, Merced, CA 95343, USA
| | - Yanding Zhang
- Southern Center for Biomedical Research and Fujian Key Laboratory of Developmental and Neural Biology, College of Life Sciences, Fujian Normal University, Fuzhou, Fujian 350108, People's Republic of China
| | - John Cobb
- Department of Biological Sciences, University of Calgary, Calgary, Alberta, Canada T2N 1N4
| | - YiPing Chen
- Department of Cell and Molecular Biology, Tulane University, New Orleans, LA 70118, USA Southern Center for Biomedical Research and Fujian Key Laboratory of Developmental and Neural Biology, College of Life Sciences, Fujian Normal University, Fuzhou, Fujian 350108, People's Republic of China
| |
Collapse
|
32
|
Yamamizu K, Sharov AA, Piao Y, Amano M, Yu H, Nishiyama A, Dudekula DB, Schlessinger D, Ko MSH. Generation and gene expression profiling of 48 transcription-factor-inducible mouse embryonic stem cell lines. Sci Rep 2016; 6:25667. [PMID: 27150017 PMCID: PMC4858678 DOI: 10.1038/srep25667] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2015] [Accepted: 04/21/2016] [Indexed: 11/22/2022] Open
Abstract
Mouse embryonic stem cells (ESCs) can differentiate into a wide range – and possibly all cell types in vitro, and thus provide an ideal platform to study systematically the action of transcription factors (TFs) in cell differentiation. Previously, we have generated and analyzed 137 TF-inducible mouse ESC lines. As an extension of this “NIA Mouse ESC Bank,” we generated and characterized 48 additional mouse ESC lines, in which single TFs in each line could be induced in a doxycycline-controllable manner. Together, with the previous ESC lines, the bank now comprises 185 TF-manipulable ESC lines (>10% of all mouse TFs). Global gene expression (transcriptome) profiling revealed that the induction of individual TFs in mouse ESCs for 48 hours shifts their transcriptomes toward specific differentiation fates (e.g., neural lineages by Myt1 Isl1, and St18; mesodermal lineages by Pitx1, Pitx2, Barhl2, and Lmx1a; white blood cells by Myb, Etv2, and Tbx6, and ovary by Pitx1, Pitx2, and Dmrtc2). These data also provide and lists of inferred target genes of each TF and possible functions of these TFs. The results demonstrate the utility of mouse ESC lines and their transcriptome data for understanding the mechanism of cell differentiation and the function of TFs.
Collapse
Affiliation(s)
- Kohei Yamamizu
- Laboratory of Genetics, National Institute on Aging, National Institutes of Health, Baltimore, MD 21224, USA
| | - Alexei A Sharov
- Laboratory of Genetics, National Institute on Aging, National Institutes of Health, Baltimore, MD 21224, USA
| | - Yulan Piao
- Laboratory of Genetics, National Institute on Aging, National Institutes of Health, Baltimore, MD 21224, USA
| | - Misa Amano
- Laboratory of Genetics, National Institute on Aging, National Institutes of Health, Baltimore, MD 21224, USA
| | - Hong Yu
- Laboratory of Genetics, National Institute on Aging, National Institutes of Health, Baltimore, MD 21224, USA
| | - Akira Nishiyama
- Laboratory of Genetics, National Institute on Aging, National Institutes of Health, Baltimore, MD 21224, USA
| | - Dawood B Dudekula
- Laboratory of Genetics, National Institute on Aging, National Institutes of Health, Baltimore, MD 21224, USA
| | - David Schlessinger
- Laboratory of Genetics, National Institute on Aging, National Institutes of Health, Baltimore, MD 21224, USA
| | - Minoru S H Ko
- Laboratory of Genetics, National Institute on Aging, National Institutes of Health, Baltimore, MD 21224, USA.,Department of Systems Medicine, Keio University School of Medicine, Tokyo 160-8582, Japan
| |
Collapse
|
33
|
Domyan ET, Kronenberg Z, Infante CR, Vickrey AI, Stringham SA, Bruders R, Guernsey MW, Park S, Payne J, Beckstead RB, Kardon G, Menke DB, Yandell M, Shapiro MD. Molecular shifts in limb identity underlie development of feathered feet in two domestic avian species. eLife 2016; 5:e12115. [PMID: 26977633 PMCID: PMC4805547 DOI: 10.7554/elife.12115] [Citation(s) in RCA: 65] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2015] [Accepted: 02/19/2016] [Indexed: 12/15/2022] Open
Abstract
Birds display remarkable diversity in the distribution and morphology of scales and feathers on their feet, yet the genetic and developmental mechanisms governing this diversity remain unknown. Domestic pigeons have striking variation in foot feathering within a single species, providing a tractable model to investigate the molecular basis of skin appendage differences. We found that feathered feet in pigeons result from a partial transformation from hindlimb to forelimb identity mediated by cis-regulatory changes in the genes encoding the hindlimb-specific transcription factor Pitx1 and forelimb-specific transcription factor Tbx5. We also found that ectopic expression of Tbx5 is associated with foot feathers in chickens, suggesting similar molecular pathways underlie phenotypic convergence between these two species. These results show how changes in expression of regional patterning genes can generate localized changes in organ fate and morphology, and provide viable molecular mechanisms for diversity in hindlimb scale and feather distribution.
Collapse
Affiliation(s)
- Eric T Domyan
- Department of Biology, University of Utah, Salt Lake City, United States
| | - Zev Kronenberg
- Department of Human Genetics, University of Utah, Salt Lake City, United States
| | - Carlos R Infante
- Department of Genetics, University of Georgia, Athens, United States
| | - Anna I Vickrey
- Department of Biology, University of Utah, Salt Lake City, United States
| | - Sydney A Stringham
- Department of Biology, University of Utah, Salt Lake City, United States
| | - Rebecca Bruders
- Department of Biology, University of Utah, Salt Lake City, United States
| | - Michael W Guernsey
- Department of Biology, University of Utah, Salt Lake City, United States
| | - Sungdae Park
- Department of Genetics, University of Georgia, Athens, United States
| | - Jason Payne
- Poultry Science Department, University of Georgia, Athens, United States
| | - Robert B Beckstead
- Poultry Science Department, University of Georgia, Athens, United States
| | - Gabrielle Kardon
- Department of Human Genetics, University of Utah, Salt Lake City, United States
| | - Douglas B Menke
- Department of Genetics, University of Georgia, Athens, United States
| | - Mark Yandell
- Department of Human Genetics, University of Utah, Salt Lake City, United States
- Utah Center for Genetic Discovery, University of Utah, Salt Lake City, United States
| | - Michael D Shapiro
- Department of Biology, University of Utah, Salt Lake City, United States
| |
Collapse
|
34
|
Alvarado DM, McCall K, Hecht JT, Dobbs MB, Gurnett CA. Deletions of 5' HOXC genes are associated with lower extremity malformations, including clubfoot and vertical talus. J Med Genet 2016; 53:250-5. [PMID: 26729820 DOI: 10.1136/jmedgenet-2015-103505] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2015] [Accepted: 11/29/2015] [Indexed: 01/07/2023]
Abstract
BACKGROUND Deletions of the HOXC gene cluster result in variable phenotypes in mice, but have been rarely described in humans. OBJECTIVE To report chromosome 12q13.13 microdeletions ranging from 13 to 175 kb and involving the 5' HOXC genes in four families, segregating congenital lower limb malformations, including clubfoot, vertical talus and hip dysplasia. METHODS Probands (N=253) with clubfoot or vertical talus were screened for point mutations and copy number variants using multiplexed direct genomic selection, a pooled BAC targeted capture approach. SNP genotyping included 1178 probands with clubfoot or vertical talus and 1775 controls. RESULTS The microdeletions share a minimal non-coding region overlap upstream of HOXC13, with variable phenotypes depending upon HOXC13, HOXC12 or the HOTAIR lncRNA inclusion. SNP analysis revealed HOXC11 p.Ser191Phe segregating with clubfoot in a small family and enrichment of HOXC12 p.Asn176Lys in patients with clubfoot or vertical talus (rs189468720, p=0.0057, OR=3.8). Defects in limb morphogenesis include shortened and overlapping toes, as well as peroneus muscle hypoplasia. Finally, HOXC and HOXD gene expression is reduced in fibroblasts from a patient with a 5' HOXC deletion, consistent with previous studies demonstrating that dosage of lncRNAs alters expression of HOXD genes in trans. CONCLUSIONS Because HOXD10 has been implicated in the aetiology of congenital vertical talus, variation in its expression may contribute to the lower limb phenotypes occurring with 5' HOXC microdeletions. Identification of 5' HOXC microdeletions highlights the importance of transcriptional regulators in the aetiology of severe lower limb malformations and will improve their diagnosis and management.
Collapse
Affiliation(s)
- David M Alvarado
- Department of Orthopedic Surgery, Washington University, St. Louis, Missouri, USA
| | - Kevin McCall
- Department of Orthopedic Surgery, Washington University, St. Louis, Missouri, USA
| | - Jacqueline T Hecht
- Department of Pediatrics, University of Texas Medical School, Houston, Texas, USA
| | - Matthew B Dobbs
- Department of Orthopedic Surgery, Washington University, St. Louis, Missouri, USA Shriners Hospital for Children, St Louis, Missouri, USA
| | - Christina A Gurnett
- Department of Orthopedic Surgery, Washington University, St. Louis, Missouri, USA Department of Neurology, Washington University, St. Louis, Missouri, USA Department of Pediatrics, Washington University, St. Louis, Missouri, USA
| |
Collapse
|
35
|
Yang S, Oksenberg N, Takayama S, Heo SJ, Poliakov A, Ahituv N, Dubchak I, Boffelli D. Functionally conserved enhancers with divergent sequences in distant vertebrates. BMC Genomics 2015; 16:882. [PMID: 26519295 PMCID: PMC4628251 DOI: 10.1186/s12864-015-2070-7] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2015] [Accepted: 10/13/2015] [Indexed: 02/08/2023] Open
Abstract
BACKGROUND To examine the contributions of sequence and function conservation in the evolution of enhancers, we systematically identified enhancers whose sequences are not conserved among distant groups of vertebrate species, but have homologous function and are likely to be derived from a common ancestral sequence. Our approach combined comparative genomics and epigenomics to identify potential enhancer sequences in the genomes of three groups of distantly related vertebrate species. RESULTS We searched for sequences that were conserved within groups of closely related species but not between groups of more distant species, and were associated with an epigenetic mark of enhancer activity. To facilitate inferring orthology between non-conserved sequences, we limited our search to introns whose orthology could be unambiguously established by mapping the bracketing exons. We show that a subset of these non-conserved but syntenic sequences from the mouse and zebrafish genomes have homologous functions in a zebrafish transgenic enhancer assay. The conserved expression patterns driven by these enhancers are probably associated with short transcription factor-binding motifs present in the divergent sequences. CONCLUSIONS We have identified numerous potential enhancers with divergent sequences but a conserved function. These results indicate that selection on function, rather than sequence, may be a common mode of enhancer evolution; evidence for selection at the sequence level is not a necessary criterion to define a gene regulatory element.
Collapse
Affiliation(s)
- Song Yang
- Genomics Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA.
| | - Nir Oksenberg
- Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, CA, 94158, USA.
- Institute for Human Genetics, University of California San Francisco, San Francisco, CA, 94158, USA.
| | - Sachiko Takayama
- Children's Hospital Oakland Research Institute, Oakland, CA, 94609, USA.
| | - Seok-Jin Heo
- Children's Hospital Oakland Research Institute, Oakland, CA, 94609, USA.
| | - Alexander Poliakov
- US Department of Energy Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, CA, 94598, USA.
| | - Nadav Ahituv
- Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, CA, 94158, USA.
- Institute for Human Genetics, University of California San Francisco, San Francisco, CA, 94158, USA.
| | - Inna Dubchak
- Genomics Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA.
- US Department of Energy Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, CA, 94598, USA.
| | - Dario Boffelli
- Children's Hospital Oakland Research Institute, Oakland, CA, 94609, USA.
| |
Collapse
|
36
|
Infante CR, Mihala AG, Park S, Wang JS, Johnson KK, Lauderdale JD, Menke DB. Shared Enhancer Activity in the Limbs and Phallus and Functional Divergence of a Limb-Genital cis-Regulatory Element in Snakes. Dev Cell 2015; 35:107-19. [PMID: 26439399 DOI: 10.1016/j.devcel.2015.09.003] [Citation(s) in RCA: 64] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2014] [Revised: 07/24/2015] [Accepted: 09/09/2015] [Indexed: 11/18/2022]
Abstract
The amniote phallus and limbs differ dramatically in their morphologies but share patterns of signaling and gene expression in early development. Thus far, the extent to which genital and limb transcriptional networks also share cis-regulatory elements has remained unexplored. We show that many limb enhancers are retained in snake genomes, suggesting that these elements may function in non-limb tissues. Consistent with this, our analysis of cis-regulatory activity in mice and Anolis lizards reveals that patterns of enhancer activity in embryonic limbs and genitalia overlap heavily. In mice, deletion of HLEB, an enhancer of Tbx4, produces defects in hindlimbs and genitalia, establishing the importance of this limb-genital enhancer for development of these different appendages. Further analyses demonstrate that the HLEB of snakes has lost hindlimb enhancer function while retaining genital activity. Our findings identify roles for Tbx4 in genital development and highlight deep similarities in cis-regulatory activity between limbs and genitalia.
Collapse
Affiliation(s)
- Carlos R Infante
- Department of Genetics, University of Georgia, Athens, GA 30602, USA
| | | | - Sungdae Park
- Department of Genetics, University of Georgia, Athens, GA 30602, USA
| | - Jialiang S Wang
- Department of Genetics, University of Georgia, Athens, GA 30602, USA
| | - Kenji K Johnson
- Department of Cellular Biology, University of Georgia, Athens, GA 30602, USA
| | - James D Lauderdale
- Department of Genetics, University of Georgia, Athens, GA 30602, USA; Department of Cellular Biology, University of Georgia, Athens, GA 30602, USA
| | - Douglas B Menke
- Department of Genetics, University of Georgia, Athens, GA 30602, USA.
| |
Collapse
|
37
|
Kong G, Liu Z, Wu K, Zhang Y, Deng Z, Feng W, Chen S, Wang H. Strong expression of paired-like homeodomain transcription factor 1 (PITX1) is associated with a favorable outcome in human osteosarcoma. Tumour Biol 2015; 36:7735-41. [PMID: 25936343 DOI: 10.1007/s13277-015-3512-1] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2015] [Accepted: 04/27/2015] [Indexed: 02/05/2023] Open
Abstract
Paired-like homeodomain transcription factor 1 (PITX1) has been implicated as a tumor suppressor in various cancers. However, the biological and clinical significance of PITX1 in osteosarcoma has not been fully elucidated. Here, we studied the expression and clinical significance of PITX1 in 6 normal lower limb bone tissue specimens and 35 osteosarcoma tissue samples by immunohistochemistry. PITX1 was expressed in all normal tissues (6/6, 100 %) and in 85.7 % (30/35) of tumor tissues (P > 0.05). In addition, all normal tissue specimens showed high PITX1 expression (6/6, 100 %) while only 23.3 % (7/30) osteosarcoma tissue specimens had high PITX1 expression (P < 0.05). Patients with median overall survival (OS) >12 months had significantly higher PITX1 levels compared with those whose median OS was less than or equal to 12 months (P < 0.05 or 0.001). Furthermore, patients with lung metastasis had significantly lower PITX1 levels than patients without lung metastasis. In conclusion, PITX1 expression is downregulated in osteosarcoma and correlates with patient survival and lung metastasis.
Collapse
Affiliation(s)
- Gengbin Kong
- Department of Orthopaedics, First Affiliated Hospital of Shantou University Medical College, No.57 Changping Road, Shantou, Guangdong, 515041, People's Republic of China
| | - Zhaoyong Liu
- Department of Orthopaedics, First Affiliated Hospital of Shantou University Medical College, No.57 Changping Road, Shantou, Guangdong, 515041, People's Republic of China
| | - Kezhou Wu
- Department of Orthopaedics, First Affiliated Hospital of Shantou University Medical College, No.57 Changping Road, Shantou, Guangdong, 515041, People's Republic of China
| | - Ying Zhang
- Department of Pathology, Shantou University Medical College, No.22 Xinling Road, Shantou, Guangdong, 515041, People's Republic of China
| | - Zhihua Deng
- Department of Orthopaedics, First Affiliated Hospital of Shantou University Medical College, No.57 Changping Road, Shantou, Guangdong, 515041, People's Republic of China
| | - Weili Feng
- Department of Orthopaedics, First Affiliated Hospital of Shantou University Medical College, No.57 Changping Road, Shantou, Guangdong, 515041, People's Republic of China
| | - Shubiao Chen
- Department of Orthopaedics, First Affiliated Hospital of Shantou University Medical College, No.57 Changping Road, Shantou, Guangdong, 515041, People's Republic of China
| | - Hu Wang
- Department of Orthopaedics, First Affiliated Hospital of Shantou University Medical College, No.57 Changping Road, Shantou, Guangdong, 515041, People's Republic of China.
| |
Collapse
|
38
|
Tickle C. How the embryo makes a limb: determination, polarity and identity. J Anat 2015; 227:418-30. [PMID: 26249743 DOI: 10.1111/joa.12361] [Citation(s) in RCA: 83] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/02/2015] [Indexed: 12/11/2022] Open
Abstract
The vertebrate limb with its complex anatomy develops from a small bud of undifferentiated mesoderm cells encased in ectoderm. The bud has its own intrinsic polarity and can develop autonomously into a limb without reference to the rest of the embryo. In this review, recent advances are integrated with classical embryology, carried out mainly in chick embryos, to present an overview of how the embryo makes a limb bud. We will focus on how mesoderm cells in precise locations in the embryo become determined to form a limb and express the key transcription factors Tbx4 (leg/hindlimb) or Tbx5 (wing/forelimb). These Tbx transcription factors have equivalent functions in the control of bud formation by initiating a signalling cascade involving Wnts and fibroblast growth factors (FGFs) and by regulating recruitment of mesenchymal cells from the coelomic epithelium into the bud. The mesoderm that will form limb buds and the polarity of the buds is determined with respect to both antero-posterior and dorso-ventral axes of the body. The position in which a bud develops along the antero-posterior axis of the body will also determine its identity - wing/forelimb or leg/hindlimb. Hox gene activity, under the influence of retinoic acid signalling, is directly linked with the initiation of Tbx5 gene expression in the region along the antero-posterior axis of the body that will form wings/forelimbs and determines antero-posterior polarity of the buds. In contrast, Tbx4 expression in the regions that will form legs/hindlimbs is regulated by the homeoprotein Pitx1 and there is no evidence that Hox genes determine antero-posterior polarity of the buds. Bone morphogenetic protein (BMP) signalling determines the region along the dorso-ventral axis of the body in which both wings/forelimbs and legs/hindlimbs develop and dorso-ventral polarity of the buds. The polarity of the buds leads to the establishment of signalling regions - the dorsal and ventral ectoderm, producing Wnts and BMPs, respectively, the apical ectodermal ridge producing fibroblast growth factors and the polarizing region, Sonic hedgehog (Shh). These signals are the same in both wings/forelimbs and legs/hindlimbs and control growth and pattern formation by providing the mesoderm cells of the limb bud as it develops with positional information. The precise anatomy of the limb depends on the mesoderm cells in the developing bud interpreting positional information according to their identity - determined by Pitx1 in hindlimbs - and genotype. The competence to form a limb extends along the entire antero-posterior axis of the trunk - with Hox gene activity inhibiting the formation of forelimbs in the interlimb region - and also along the dorso-ventral axis.
Collapse
Affiliation(s)
- Cheryll Tickle
- Department of Biology and Biochemistry, University of Bath, Bath, UK
| |
Collapse
|
39
|
Lewandowski JP, Du F, Zhang S, Powell MB, Falkenstein KN, Ji H, Vokes SA. Spatiotemporal regulation of GLI target genes in the mammalian limb bud. Dev Biol 2015; 406:92-103. [PMID: 26238476 DOI: 10.1016/j.ydbio.2015.07.022] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2015] [Revised: 07/22/2015] [Accepted: 07/28/2015] [Indexed: 11/19/2022]
Abstract
GLI proteins convert Sonic hedgehog (Shh) signaling into a transcriptional output in a tissue-specific fashion. The Shh pathway has been extensively studied in the limb bud, where it helps regulate growth through a SHH-FGF feedback loop. However, the transcriptional response is still poorly understood. We addressed this by determining the gene expression patterns of approximately 200 candidate GLI-target genes and identified three discrete SHH-responsive expression domains. GLI-target genes expressed in the three domains are predominately regulated by derepression of GLI3 but have different temporal requirements for SHH. The GLI binding regions associated with these genes harbor both distinct and common DNA motifs. Given the potential for interaction between the SHH and FGF pathways, we also measured the response of GLI-target genes to inhibition of FGF signaling and found the majority were either unaffected or upregulated. These results provide the first characterization of the spatiotemporal response of a large group of GLI-target genes and lay the foundation for a systems-level understanding of the gene regulatory networks underlying SHH-mediated limb patterning.
Collapse
Affiliation(s)
- Jordan P Lewandowski
- Department of Molecular Biosciences, Institute for Cellular and Molecular Biology, University of Texas at Austin, 2500 Speedway Stop A4800, Austin, TX 78712, USA
| | - Fang Du
- Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, 615 North Wolfe Street, Room E3638, Baltimore, MD 21205, USA
| | - Shilu Zhang
- Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, 615 North Wolfe Street, Room E3638, Baltimore, MD 21205, USA
| | - Marian B Powell
- Department of Molecular Biosciences, Institute for Cellular and Molecular Biology, University of Texas at Austin, 2500 Speedway Stop A4800, Austin, TX 78712, USA
| | - Kristin N Falkenstein
- Department of Molecular Biosciences, Institute for Cellular and Molecular Biology, University of Texas at Austin, 2500 Speedway Stop A4800, Austin, TX 78712, USA
| | - Hongkai Ji
- Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, 615 North Wolfe Street, Room E3638, Baltimore, MD 21205, USA
| | - Steven A Vokes
- Department of Molecular Biosciences, Institute for Cellular and Molecular Biology, University of Texas at Austin, 2500 Speedway Stop A4800, Austin, TX 78712, USA.
| |
Collapse
|
40
|
Wei G, Luo H, Sun Y, Li J, Tian L, Liu W, Liu L, Luo J, He J, Chen R. Transcriptome profiling of esophageal squamous cell carcinoma reveals a long noncoding RNA acting as a tumor suppressor. Oncotarget 2015; 6:17065-80. [PMID: 26158411 PMCID: PMC4627292 DOI: 10.18632/oncotarget.4185] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2015] [Accepted: 05/02/2015] [Indexed: 12/23/2022] Open
Abstract
Esophageal Squamous Cell Carcinoma (ESCC) is among the most common malignant cancers worldwide. In the past, extensive efforts have been made to characterize the involvement of protein-coding genes in ESCC tumorigenesis but few for long noncoding RNAs (lncRNAs). To investigate the transcriptome profile and functional relevance of lncRNAs, we performed an integrative analysis of a customized combined lncRNA-mRNA microarray and RNA-seq data on ESCCs and matched normal tissues. We identified numerous lncRNAs that were differentially expressed between the normal and tumor tissues, termed "ESCC-associated lncRNAs (ESCALs)", of which, the majority displayed restricted expression pattern. Also, a subset of ESCALs appeared to be associated with ESCC patient survival. Gene set enrichment analysis (GSEA) further suggested that over half of the ESCALs were positively-or negatively-associated with metastasis. Among these, we identified a novel nuclear-retained lncRNA, named Epist, which is generally highly expressed in esophagus, and which is down-regulated during ESCC progression. Epist over-expression and knockdown studies further suggest that Epist inhibits the metastasis, acting as a tumor suppressor in ESCC. Collectively, our analysis of the ESCC transcriptome identified the potential tumor suppressing lncRNA Epist, and provided a foundation for future efforts to identify functional lncRNAs for cancerous therapeutic targeting.
Collapse
Affiliation(s)
- Guifeng Wei
- Bioinformatics Laboratory and CAS Key Laboratory of RNA Biology, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Huaxia Luo
- Bioinformatics Laboratory and CAS Key Laboratory of RNA Biology, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Yu Sun
- Bioinformatics Laboratory and CAS Key Laboratory of RNA Biology, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Jiagen Li
- Department of Thoracic Surgery, Cancer Institute and Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Liqing Tian
- Bioinformatics Laboratory and CAS Key Laboratory of RNA Biology, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
| | - Wei Liu
- Bioinformatics Laboratory and CAS Key Laboratory of RNA Biology, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Lihui Liu
- Bioinformatics Laboratory and CAS Key Laboratory of RNA Biology, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Jianjun Luo
- Bioinformatics Laboratory and CAS Key Laboratory of RNA Biology, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
| | - Jie He
- Department of Thoracic Surgery, Cancer Institute and Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Runsheng Chen
- Bioinformatics Laboratory and CAS Key Laboratory of RNA Biology, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
- Research Network of Computational Biology, RNCB, Beijing, China
| |
Collapse
|
41
|
RNA transcribed from a distal enhancer is required for activating the chromatin at the promoter of the gonadotropin α-subunit gene. Proc Natl Acad Sci U S A 2015; 112:4369-74. [PMID: 25810254 DOI: 10.1073/pnas.1414841112] [Citation(s) in RCA: 76] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Since the discovery that many transcriptional enhancers are transcribed into long noncoding RNAs termed "enhancer RNAs" (eRNAs), their putative role in enhancer function has been debated. Very recent evidence has indicted that some eRNAs play a role in initiating or activating transcription, possibly by helping recruit and/or stabilize binding of the general transcription machinery to the proximal promoter of their target genes. The distal enhancer of the gonadotropin hormone α-subunit gene, chorionic gonadotropin alpha (Cga), is responsible for Cga cell-specific expression in gonadotropes and thyrotropes, and we show here that it encodes two bidirectional nonpolyadenylated RNAs whose levels are increased somewhat by exposure to gonadotropin-releasing hormone but are not necessarily linked to Cga transcriptional activity. Knockdown of the more distal eRNA led to a drop in Cga mRNA levels, initially without effect on the forward eRNA levels. With time, however, the repression on the Cga increased, and the forward eRNA levels were suppressed also. We demonstrate that the interaction of the enhancer with the promoter is lost after eRNA knockdown. Dramatic changes also were seen in the chromatin, with an increase in total histone H3 occupancy throughout this region and a virtual loss of histone H3 Lys 4 trimethylation at the promoter following the eRNA knockdown. Moreover, histone H3 Lys 27 (H3K27) acetylation, which was found at both enhancer and promoter in wild-type cells, appeared to have been replaced by H3K27 trimethylation at the enhancer. Thus, the Cga eRNA mediates the physical interaction between these genomic regions and determines the chromatin structure of the proximal promoter to allow gene expression.
Collapse
|
42
|
Dubchak I, Balasubramanian S, Wang S, Meyden C, Sulakhe D, Poliakov A, Börnigen D, Xie B, Taylor A, Ma J, Paciorkowski AR, Mirzaa GM, Dave P, Agam G, Xu J, Al-Gazali L, Mason CE, Ross ME, Maltsev N, Gilliam TC. An integrative computational approach for prioritization of genomic variants. PLoS One 2014; 9:e114903. [PMID: 25506935 PMCID: PMC4266634 DOI: 10.1371/journal.pone.0114903] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2014] [Accepted: 11/15/2014] [Indexed: 12/27/2022] Open
Abstract
An essential step in the discovery of molecular mechanisms contributing to disease phenotypes and efficient experimental planning is the development of weighted hypotheses that estimate the functional effects of sequence variants discovered by high-throughput genomics. With the increasing specialization of the bioinformatics resources, creating analytical workflows that seamlessly integrate data and bioinformatics tools developed by multiple groups becomes inevitable. Here we present a case study of a use of the distributed analytical environment integrating four complementary specialized resources, namely the Lynx platform, VISTA RViewer, the Developmental Brain Disorders Database (DBDB), and the RaptorX server, for the identification of high-confidence candidate genes contributing to pathogenesis of spina bifida. The analysis resulted in prediction and validation of deleterious mutations in the SLC19A placental transporter in mothers of the affected children that causes narrowing of the outlet channel and therefore leads to the reduced folate permeation rate. The described approach also enabled correct identification of several genes, previously shown to contribute to pathogenesis of spina bifida, and suggestion of additional genes for experimental validations. The study demonstrates that the seamless integration of bioinformatics resources enables fast and efficient prioritization and characterization of genomic factors and molecular networks contributing to the phenotypes of interest.
Collapse
Affiliation(s)
- Inna Dubchak
- Genomics Division, Lawrence Berkeley National Laboratory, Berkeley, California, United States of America
- Department of Energy Joint Genome Institute, Walnut Creek, California, United States of America
- * E-mail: (ID); (NM)
| | - Sandhya Balasubramanian
- Department of Human Genetics, University of Chicago, Chicago, Illinois, United States of America
| | - Sheng Wang
- Toyota Technological Institute at Chicago, Chicago, Illinois, United States of America
| | - Cem Meyden
- Department of Physiology and Biophysics, Weill Cornell Medical College, New York, New York, United States of America
- The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medical College, New York, New York, United States of America
- Feil Family Brain and Mind Research Institute, Weill Cornell Medical College, New York, New York, United States of America
| | - Dinanath Sulakhe
- Department of Human Genetics, University of Chicago, Chicago, Illinois, United States of America
- Computation Institute, University of Chicago/Argonne National Laboratory, Chicago, Illinois, United States of America
| | - Alexander Poliakov
- Department of Energy Joint Genome Institute, Walnut Creek, California, United States of America
| | - Daniela Börnigen
- Department of Human Genetics, University of Chicago, Chicago, Illinois, United States of America
- Toyota Technological Institute at Chicago, Chicago, Illinois, United States of America
| | - Bingqing Xie
- Department of Human Genetics, University of Chicago, Chicago, Illinois, United States of America
- Department of Computer Science, Illinois Institute of Technology, Chicago, Illinois, United States of America
| | - Andrew Taylor
- Department of Human Genetics, University of Chicago, Chicago, Illinois, United States of America
| | - Jianzhu Ma
- Toyota Technological Institute at Chicago, Chicago, Illinois, United States of America
| | - Alex R. Paciorkowski
- Departments of Neurology, Pediatrics, and Biomedical Genetics and Center for Neural Development and Disease, University of Rochester Medical Center, Rochester, New York, United States of America
| | - Ghayda M. Mirzaa
- Seattle Children's Research Institute and Department of Pediatrics, University of Washington, Seattle, Washington, United States of America
| | - Paul Dave
- Computation Institute, University of Chicago/Argonne National Laboratory, Chicago, Illinois, United States of America
| | - Gady Agam
- Department of Computer Science, Illinois Institute of Technology, Chicago, Illinois, United States of America
| | - Jinbo Xu
- Toyota Technological Institute at Chicago, Chicago, Illinois, United States of America
| | - Lihadh Al-Gazali
- Department of Pediatrics, Faculty of Medicine and Health Sciences, United Arab Emirates University, Al-Ain, UAE
| | - Christopher E. Mason
- Department of Physiology and Biophysics, Weill Cornell Medical College, New York, New York, United States of America
- The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medical College, New York, New York, United States of America
- Feil Family Brain and Mind Research Institute, Weill Cornell Medical College, New York, New York, United States of America
| | - M. Elizabeth Ross
- Laboratory of Neurogenetics and Development, Weill Cornell Medical College, New York, New York, United States of America
| | - Natalia Maltsev
- Department of Human Genetics, University of Chicago, Chicago, Illinois, United States of America
- Computation Institute, University of Chicago/Argonne National Laboratory, Chicago, Illinois, United States of America
- * E-mail: (ID); (NM)
| | - T. Conrad Gilliam
- Department of Human Genetics, University of Chicago, Chicago, Illinois, United States of America
- Computation Institute, University of Chicago/Argonne National Laboratory, Chicago, Illinois, United States of America
| |
Collapse
|
43
|
Gallagher JEG, Zheng W, Rong X, Miranda N, Lin Z, Dunn B, Zhao H, Snyder MP. Divergence in a master variator generates distinct phenotypes and transcriptional responses. Genes Dev 2014; 28:409-21. [PMID: 24532717 PMCID: PMC3937518 DOI: 10.1101/gad.228940.113] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
Genetic basis of phenotypic differences in individuals is an important area in biology and personalized medicine. Analysis of divergent Saccharomyces cerevisiae strains grown under different conditions revealed extensive variation in response to both drugs (e.g., 4-nitroquinoline 1-oxide [4NQO]) and different carbon sources. Differences in 4NQO resistance were due to amino acid variation in the transcription factor Yrr1. Yrr1(YJM789) conferred 4NQO resistance but caused slower growth on glycerol, and vice versa with Yrr1(S96), indicating that alleles of Yrr1 confer distinct phenotypes. The binding targets of Yrr1 alleles from diverse yeast strains varied considerably among different strains grown under the same conditions as well as for the same strain under different conditions, indicating that distinct molecular programs are conferred by the different Yrr1 alleles. Our results demonstrate that genetic variations in one important control gene (YRR1), lead to distinct regulatory programs and phenotypes in individuals. We term these polymorphic control genes "master variators."
Collapse
|
44
|
Ricardi MM, González RM, Zhong S, Domínguez PG, Duffy T, Turjanski PG, Salgado Salter JD, Alleva K, Carrari F, Giovannoni JJ, Estévez JM, Iusem ND. Genome-wide data (ChIP-seq) enabled identification of cell wall-related and aquaporin genes as targets of tomato ASR1, a drought stress-responsive transcription factor. BMC PLANT BIOLOGY 2014; 14:29. [PMID: 24423251 PMCID: PMC3923394 DOI: 10.1186/1471-2229-14-29] [Citation(s) in RCA: 63] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/11/2013] [Accepted: 01/10/2014] [Indexed: 05/20/2023]
Abstract
BACKGROUND Identifying the target genes of transcription factors is important for unraveling regulatory networks in all types of organisms. Our interest was precisely to uncover the spectrum of loci regulated by a widespread plant transcription factor involved in physiological adaptation to drought, a type of stress that plants have encountered since the colonization of land habitats 400 MYA. The regulator under study, named ASR1, is exclusive to the plant kingdom (albeit absent in Arabidopsis) and known to alleviate the stress caused by restricted water availability. As its target genes are still unknown despite the original cloning of Asr1 cDNA 20 years ago, we examined the tomato genome for specific loci interacting in vivo with this conspicuous protein. RESULTS We performed ChIP followed by high throughput DNA sequencing (ChIP-seq) on leaves from stressed tomato plants, using a high-quality anti-ASR1 antibody. In this way, we unraveled a novel repertoire of target genes, some of which are clearly involved in the response to drought stress. Many of the ASR1-enriched genomic loci we found encode enzymes involved in cell wall synthesis and remodeling as well as channels implicated in water and solute flux, such as aquaporins. In addition, we were able to determine a robust consensus ASR1-binding DNA motif. CONCLUSIONS The finding of cell wall synthesis and aquaporin genes as targets of ASR1 is consistent with their suggested role in the physiological adaptation of plants to water loss. The results gain insight into the environmental stress-sensing pathways leading to plant tolerance of drought.
Collapse
Affiliation(s)
- Martiniano M Ricardi
- Instituto de Fisiología, Biología Molecular y Neurociencias (IFIByNE)-CONICET, Buenos Aires, Argentina
| | - Rodrigo M González
- Instituto de Fisiología, Biología Molecular y Neurociencias (IFIByNE)-CONICET, Buenos Aires, Argentina
| | - Silin Zhong
- Boyce Thompson Institute for Plant Research, Tower Road, Cornell University, Ithaca, NY, USA
| | - Pía G Domínguez
- Instituto de Biotecnología – INTA, Hurlingham, Provincia de Buenos Aires, Argentina
| | - Tomas Duffy
- Instituto de Biotecnología – INTA, Hurlingham, Provincia de Buenos Aires, Argentina
| | - Pablo G Turjanski
- Departamento de Computación, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Juan D Salgado Salter
- Instituto de Fisiología, Biología Molecular y Neurociencias (IFIByNE)-CONICET, Buenos Aires, Argentina
| | - Karina Alleva
- Instituto de Biodiversidad y Biología Experimental (IBBEA, CONICET-UBA), Buenos Aires, Argentina
| | - Fernando Carrari
- Instituto de Biotecnología – INTA, Hurlingham, Provincia de Buenos Aires, Argentina
| | | | - José M Estévez
- Instituto de Fisiología, Biología Molecular y Neurociencias (IFIByNE)-CONICET, Buenos Aires, Argentina
| | - Norberto D Iusem
- Instituto de Fisiología, Biología Molecular y Neurociencias (IFIByNE)-CONICET, Buenos Aires, Argentina
- Departamento de Fisiología, Biología Molecular y Celular, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires, Argentina
| |
Collapse
|
45
|
Park S, Infante CR, Rivera-Davila LC, Menke DB. Conserved regulation ofhoxc11by pitx1 inAnolislizards. JOURNAL OF EXPERIMENTAL ZOOLOGY PART B-MOLECULAR AND DEVELOPMENTAL EVOLUTION 2013; 322:156-65. [DOI: 10.1002/jez.b.22554] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/24/2013] [Accepted: 11/26/2013] [Indexed: 11/12/2022]
Affiliation(s)
- Sungdae Park
- Department of Genetics; University of Georgia; Athens Georgia
| | | | - Laura C. Rivera-Davila
- Department of Genetics; University of Georgia; Athens Georgia
- Department of Biology; University of Puerto Rico at Cayey; RISE Program; Cayey Puerto Rico
| | | |
Collapse
|