1
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Bedois AMH, Parker HJ, Price AJ, Morrison JA, Bronner ME, Krumlauf R. Sea lamprey enlightens the origin of the coupling of retinoic acid signaling to vertebrate hindbrain segmentation. Nat Commun 2024; 15:1538. [PMID: 38378737 PMCID: PMC10879103 DOI: 10.1038/s41467-024-45911-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2023] [Accepted: 02/06/2024] [Indexed: 02/22/2024] Open
Abstract
Retinoic acid (RA) is involved in antero-posterior patterning of the chordate body axis and, in jawed vertebrates, has been shown to play a major role at multiple levels of the gene regulatory network (GRN) regulating hindbrain segmentation. Knowing when and how RA became coupled to the core hindbrain GRN is important for understanding how ancient signaling pathways and patterning genes can evolve and generate diversity. Hence, we investigated the link between RA signaling and hindbrain segmentation in the sea lamprey Petromyzon marinus, an important jawless vertebrate model providing clues to decipher ancestral vertebrate features. Combining genomics, gene expression, and functional analyses of major components involved in RA synthesis (Aldh1as) and degradation (Cyp26s), we demonstrate that RA signaling is coupled to hindbrain segmentation in lamprey. Thus, the link between RA signaling and hindbrain segmentation is a pan vertebrate feature of the hindbrain and likely evolved at the base of vertebrates.
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Affiliation(s)
- Alice M H Bedois
- Stowers Institute for Medical Research, Kansas City, MO, 64110, USA
| | - Hugo J Parker
- Stowers Institute for Medical Research, Kansas City, MO, 64110, USA
| | - Andrew J Price
- Stowers Institute for Medical Research, Kansas City, MO, 64110, USA
| | - Jason A Morrison
- Stowers Institute for Medical Research, Kansas City, MO, 64110, USA
| | - Marianne E Bronner
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, 91125, USA
| | - Robb Krumlauf
- Stowers Institute for Medical Research, Kansas City, MO, 64110, USA.
- Department of Anatomy and Cell Biology, Kansas University Medical Center, Kansas City, MO, 66160, USA.
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2
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Bedois AMH, Parker HJ, Bronner ME, Krumlauf R. Sea lamprey enlightens the origin of the coupling of retinoic acid signaling to vertebrate hindbrain segmentation. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.07.07.548143. [PMID: 37461675 PMCID: PMC10350081 DOI: 10.1101/2023.07.07.548143] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 07/29/2023]
Abstract
Retinoic acid (RA) is involved in antero-posterior patterning of the chordate body axis and, in jawed vertebrates, has been shown to play a major role at multiple levels of the gene regulatory network (GRN) regulating hindbrain segmentation. Knowing when and how RA became coupled to the core hindbrain GRN is important for understanding how ancient signaling pathways and patterning genes can evolve and generate diversity. Hence, we investigated the link between RA signaling and hindbrain segmentation in the sea lamprey Petromyzon marinus, an important jawless vertebrate model providing clues to decipher ancestral vertebrate features. Combining genomics, gene expression, and functional analyses of major components involved in RA synthesis (Aldh1as) and degradation (Cyp26s), we demonstrate that RA signaling is coupled to hindbrain segmentation in lamprey. Thus, the link between RA signaling and hindbrain segmentation is a pan vertebrate feature of the hindbrain and likely evolved at the base of vertebrates.
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Affiliation(s)
- Alice M. H. Bedois
- Stowers Institute for Medical Research, Kansas City, Missouri 64110, USA
| | - Hugo J. Parker
- Stowers Institute for Medical Research, Kansas City, Missouri 64110, USA
| | - Marianne E. Bronner
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, 91125, USA
| | - Robb Krumlauf
- Stowers Institute for Medical Research, Kansas City, Missouri 64110, USA
- Department of Anatomy and Cell Biology, Kansas University Medical Center, Kansas City, Kansas 66160, USA
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3
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Abstract
During early development, the hindbrain is sub-divided into rhombomeres that underlie the organisation of neurons and adjacent craniofacial tissues. A gene regulatory network of signals and transcription factors establish and pattern segments with a distinct anteroposterior identity. Initially, the borders of segmental gene expression are imprecise, but then become sharply defined, and specialised boundary cells form. In this Review, we summarise key aspects of the conserved regulatory cascade that underlies the formation of hindbrain segments. We describe how the pattern is sharpened and stabilised through the dynamic regulation of cell identity, acting in parallel with cell segregation. Finally, we discuss evidence that boundary cells have roles in local patterning, and act as a site of neurogenesis within the hindbrain.
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Affiliation(s)
- Robb Krumlauf
- Stowers Institute for Medical Research, Kansas City, MO 64110, USA.,Dept of Anatomy and Cell Biology, Kansas University Medical School, Kansas City, KS 66160, USA
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4
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Yasuoka Y. Enhancer evolution in chordates: Lessons from functional analyses of cephalochordate cis‐regulatory modules. Dev Growth Differ 2020; 62:279-300. [DOI: 10.1111/dgd.12684] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2020] [Revised: 05/25/2020] [Accepted: 05/27/2020] [Indexed: 12/20/2022]
Affiliation(s)
- Yuuri Yasuoka
- Laboratory for Comprehensive Genomic Analysis RIKEN Center for Integrative Medical Sciences Tsurumi‐ku Japan
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5
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Parker HJ, Krumlauf R. A Hox gene regulatory network for hindbrain segmentation. Curr Top Dev Biol 2020; 139:169-203. [DOI: 10.1016/bs.ctdb.2020.03.001] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
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6
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Jackman WR, Gibert Y. Retinoic Acid Signaling and the Zebrafish Dentition During Development and Evolution. Subcell Biochem 2020; 95:175-196. [PMID: 32297300 DOI: 10.1007/978-3-030-42282-0_7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
Explaining how the extensive diversity in form of vertebrate teeth arose in evolution and the mechanisms by which teeth are made during embryogenesis are intertwined questions that can merit from a better understanding of the roles of retinoic acid (RA) in tooth development. Pioneering studies in rodents showed that dietary vitamin A (VA), and eventually RA (one of the major active metabolites of VA), are required for proper tooth formation and that dentin-forming odontoblast cells seem to be especially sensitive to changes in RA levels. Later, rodent studies further indicated that RA signaling interactions with other cell-signaling pathways are an important part of RA's actions in odontogenesis. Recent investigations employing zebrafish and other teleost fish continued this work in an evolutionary context, and specifically demonstrated that RA is required for the initiation of tooth development. RA is also sufficient in certain circumstances to induce de novo tooth formation. Both effects appear to involve cranial-neural crest cells, again suggesting that RA signaling has a particular influence on odontoblast development. These teleost studies have also highlighted both evolutionary conservation and change in how RA is employed during odontogenesis in different vertebrate lineages, and thus raises the possibility that developmental changes to RA signaling has led to some of the diversity of form seen across vertebrate dentitions. Future progress in this area will come at least in part from expanding the species examined to get a better picture of how often RA signaling has changed in evolution and how this relates to the evolution of dental form.
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Affiliation(s)
| | - Yann Gibert
- University of Mississippi Medical Center, Jackson, MS, 39216, USA
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7
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Cambronero F, Ariza‐McNaughton L, Wiedemann LM, Krumlauf R. Inter‐rhombomeric interactions reveal roles for fibroblast growth factors signaling in segmental regulation of
EphA4
expression. Dev Dyn 2019; 249:354-368. [DOI: 10.1002/dvdy.101] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2019] [Revised: 08/08/2019] [Accepted: 08/09/2019] [Indexed: 12/15/2022] Open
Affiliation(s)
| | | | - Leanne M. Wiedemann
- Stowers Institute for Medical Research Kansas City Missouri
- Department of Pathology and Laboratory MedicineKansas University Medical Center Kansas City Kansas
| | - Robb Krumlauf
- Stowers Institute for Medical Research Kansas City Missouri
- Division of Developmental NeurobiologyNational Institute for Medical Research London UK
- Department of Anatomy and Cell BiologyKansas University Medical School Kansas City Kansas
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8
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Nolte C, De Kumar B, Krumlauf R. Hox genes: Downstream "effectors" of retinoic acid signaling in vertebrate embryogenesis. Genesis 2019; 57:e23306. [PMID: 31111645 DOI: 10.1002/dvg.23306] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2019] [Revised: 05/09/2019] [Accepted: 05/10/2019] [Indexed: 12/31/2022]
Abstract
One of the major regulatory challenges of animal development is to precisely coordinate in space and time the formation, specification, and patterning of cells that underlie elaboration of the basic body plan. How does the vertebrate plan for the nervous and hematopoietic systems, heart, limbs, digestive, and reproductive organs derive from seemingly similar population of cells? These systems are initially established and patterned along the anteroposterior axis (AP) by opposing signaling gradients that lead to the activation of gene regulatory networks involved in axial specification, including the Hox genes. The retinoid signaling pathway is one of the key signaling gradients coupled to the establishment of axial patterning. The nested domains of Hox gene expression, which provide a combinatorial code for axial patterning, arise in part through a differential response to retinoic acid (RA) diffusing from anabolic centers established within the embryo during development. Hence, Hox genes are important direct effectors of retinoid signaling in embryogenesis. This review focuses on describing current knowledge on the complex mechanisms and regulatory processes, which govern the response of Hox genes to RA in several tissue contexts including the nervous system during vertebrate development.
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Affiliation(s)
- Christof Nolte
- Stowers Institute for Medical Research, Kansas City, Missouri
| | - Bony De Kumar
- Stowers Institute for Medical Research, Kansas City, Missouri
| | - Robb Krumlauf
- Stowers Institute for Medical Research, Kansas City, Missouri.,Department of Anatomy and Cell Biology, Kansas University Medical Center, Kansas City, Kansas
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9
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Parker HJ, Bronner ME, Krumlauf R. An atlas of anterior hox gene expression in the embryonic sea lamprey head: Hox-code evolution in vertebrates. Dev Biol 2019; 453:19-33. [PMID: 31071313 DOI: 10.1016/j.ydbio.2019.05.001] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2019] [Revised: 04/05/2019] [Accepted: 05/01/2019] [Indexed: 10/26/2022]
Abstract
In the hindbrain and the adjacent cranial neural crest (NC) cells of jawed vertebrates (gnathostomes), nested and segmentally-restricted domains of Hox gene expression provide a combinatorial Hox-code for specifying regional properties during head development. Extant jawless vertebrates, such as the sea lamprey (Petromyzon marinus), can provide insights into the evolution and diversification of this Hox-code in vertebrates. There is evidence for gnathostome-like spatial patterns of Hox expression in lamprey; however, the expression domains of the majority of lamprey hox genes from paralogy groups (PG) 1-4 are yet to be characterized, so it is unknown whether they are coupled to hindbrain segments (rhombomeres) and NC. In this study, we systematically describe the spatiotemporal expression of all 14 sea lamprey hox genes from PG1-PG4 in the developing hindbrain and pharynx to investigate the extent to which their expression conforms to the archetypal gnathostome hindbrain and pharyngeal hox-codes. We find many similarities in Hox expression between lamprey and gnathostome species, particularly in rhombomeric domains during hindbrain segmentation and in the cranial neural crest, enabling inference of aspects of Hox expression in the ancestral vertebrate embryonic head. These data are consistent with the idea that a Hox regulatory network underlying hindbrain segmentation is a pan vertebrate trait. We also reveal differences in hindbrain domains at later stages, as well as expression in the endostyle and in pharyngeal arch (PA) 1 mesoderm. Our analysis suggests that many Hox expression domains that are observed in extant gnathostomes were present in ancestral vertebrates but have been partitioned differently across Hox clusters in gnathostome and cyclostome lineages after duplication.
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Affiliation(s)
- Hugo J Parker
- Stowers Institute for Medical Research, Kansas City, MO 64110, USA
| | - Marianne E Bronner
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Robb Krumlauf
- Stowers Institute for Medical Research, Kansas City, MO 64110, USA; Department of Anatomy and Cell Biology, Kansas University Medical Center, Kansas City, KS 66160, USA.
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10
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A Hox-TALE regulatory circuit for neural crest patterning is conserved across vertebrates. Nat Commun 2019; 10:1189. [PMID: 30867425 PMCID: PMC6416258 DOI: 10.1038/s41467-019-09197-8] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2018] [Accepted: 02/26/2019] [Indexed: 12/13/2022] Open
Abstract
In jawed vertebrates (gnathostomes), Hox genes play an important role in patterning head and jaw formation, but mechanisms coupling Hox genes to neural crest (NC) are unknown. Here we use cross-species regulatory comparisons between gnathostomes and lamprey, a jawless extant vertebrate, to investigate conserved ancestral mechanisms regulating Hox2 genes in NC. Gnathostome Hoxa2 and Hoxb2 NC enhancers mediate equivalent NC expression in lamprey and gnathostomes, revealing ancient conservation of Hox upstream regulatory components in NC. In characterizing a lamprey hoxα2 NC/hindbrain enhancer, we identify essential Meis, Pbx, and Hox binding sites that are functionally conserved within Hoxa2/Hoxb2 NC enhancers. This suggests that the lamprey hoxα2 enhancer retains ancestral activity and that Hoxa2/Hoxb2 NC enhancers are ancient paralogues, which diverged in hindbrain and NC activities. This identifies an ancestral mechanism for Hox2 NC regulation involving a Hox-TALE regulatory circuit, potentiated by inputs from Meis and Pbx proteins and Hox auto-/cross-regulatory interactions.
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11
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Coupling the roles of Hox genes to regulatory networks patterning cranial neural crest. Dev Biol 2018; 444 Suppl 1:S67-S78. [PMID: 29571614 DOI: 10.1016/j.ydbio.2018.03.016] [Citation(s) in RCA: 44] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2018] [Revised: 03/17/2018] [Accepted: 03/17/2018] [Indexed: 11/20/2022]
Abstract
The neural crest is a transient population of cells that forms within the developing central nervous system and migrates away to generate a wide range of derivatives throughout the body during vertebrate embryogenesis. These cells are of evolutionary and clinical interest, constituting a key defining trait in the evolution of vertebrates and alterations in their development are implicated in a high proportion of birth defects and craniofacial abnormalities. In the hindbrain and the adjacent cranial neural crest cells (cNCCs), nested domains of Hox gene expression provide a combinatorial'Hox-code' for specifying regional properties in the developing head. Hox genes have been shown to play important roles at multiple stages in cNCC development, including specification, migration, and differentiation. However, relatively little is known about the underlying gene-regulatory mechanisms involved, both upstream and downstream of Hox genes. Furthermore, it is still an open question as to how the genes of the neural crest GRN are linked to Hox-dependent pathways. In this review, we describe Hox gene expression, function and regulation in cNCCs with a view to integrating these genes within the emerging gene regulatory network for cNCC development. We highlight early roles for Hox1 genes in cNCC specification, proposing that this may be achieved, in part, by regulation of the balance between pluripotency and differentiation in precursor cells within the neuro-epithelium. We then describe what is known about the regulation of Hox gene expression in cNCCs and discuss this from the perspective of early vertebrate evolution.
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12
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Wang S, Yang Q, Wang Z, Feng S, Li H, Ji D, Zhang S. Evolutionary and Expression Analyses Show Co-option of khdrbs Genes for Origin of Vertebrate Brain. Front Genet 2018; 8:225. [PMID: 29354154 PMCID: PMC5758493 DOI: 10.3389/fgene.2017.00225] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2017] [Accepted: 12/15/2017] [Indexed: 11/13/2022] Open
Abstract
Genes generated by whole genome duplications (WGD) can be co-opted by changing their regulation process or altering their coding proteins, which has been shown contributable to the emergence of vertebrate morphological novelties such as vertebrate cartilage. Mouse khdrbs genes, differing from its invertebrate orthologs, were mainly expressed in brain, hinting that khdrbs gene family as a member of genetic toolkit may be linked to vertebrate brain development. However, the evolutionary relationship between khdrbs gene family and vertebrate brain development is unclear. First, we analyzed the evolutionary history of khdrbs gene family in metazoans, and then investigated their expression patterns during early development and in adulthood of zebrafish. We found that the duplication of khdrbs gene family by WGD took place in zebrafish, and all zebrafish khdrbs genes were predominantly expressed in the substructures of brain during early development. Given the expression of invertebrate khdrbs gene in germ line, the distinct expression domains of zebrafish khdrbs genes in brain suggested that the duplicated khdrbs genes are co-opted for promoting the evolutionary origin of vertebrate brain.
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Affiliation(s)
- Su Wang
- Laboratory for Evolution and Development, Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao, China.,Laboratory for Evolution and Development, Department of Marine Biology, Ocean University of China, Qingdao, China
| | - Qingyun Yang
- Laboratory for Evolution and Development, Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao, China.,Laboratory for Evolution and Development, Department of Marine Biology, Ocean University of China, Qingdao, China
| | - Ziyue Wang
- Laboratory for Evolution and Development, Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao, China.,Laboratory for Evolution and Development, Department of Marine Biology, Ocean University of China, Qingdao, China
| | - Shuoqi Feng
- Laboratory for Evolution and Development, Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao, China.,Laboratory for Evolution and Development, Department of Marine Biology, Ocean University of China, Qingdao, China
| | - Hongyan Li
- Laboratory for Evolution and Development, Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao, China.,Laboratory for Evolution and Development, Department of Marine Biology, Ocean University of China, Qingdao, China
| | - Dongrui Ji
- Laboratory for Evolution and Development, Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao, China.,Laboratory for Evolution and Development, Department of Marine Biology, Ocean University of China, Qingdao, China
| | - Shicui Zhang
- Laboratory for Evolution and Development, Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao, China.,Laboratory for Evolution and Development, Department of Marine Biology, Ocean University of China, Qingdao, China
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13
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Parker HJ, Krumlauf R. Segmental arithmetic: summing up the Hox gene regulatory network for hindbrain development in chordates. WILEY INTERDISCIPLINARY REVIEWS-DEVELOPMENTAL BIOLOGY 2017; 6. [PMID: 28771970 DOI: 10.1002/wdev.286] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/04/2017] [Revised: 06/13/2017] [Accepted: 06/15/2017] [Indexed: 11/10/2022]
Abstract
Organization and development of the early vertebrate hindbrain are controlled by a cascade of regulatory interactions that govern the process of segmentation and patterning along the anterior-posterior axis via Hox genes. These interactions can be assembled into a gene regulatory network that provides a framework to interpret experimental data, generate hypotheses, and identify gaps in our understanding of the progressive process of hindbrain segmentation. The network can be broadly separated into a series of interconnected programs that govern early signaling, segmental subdivision, secondary signaling, segmentation, and ultimately specification of segmental identity. Hox genes play crucial roles in multiple programs within this network. Furthermore, the network reveals properties and principles that are likely to be general to other complex developmental systems. Data from vertebrate and invertebrate chordate models are shedding light on the origin and diversification of the network. Comprehensive cis-regulatory analyses of vertebrate Hox gene regulation have enabled powerful cross-species gene regulatory comparisons. Such an approach in the sea lamprey has revealed that the network mediating segmental Hox expression was present in ancestral vertebrates and has been maintained across diverse vertebrate lineages. Invertebrate chordates lack hindbrain segmentation but exhibit conservation of some aspects of the network, such as a role for retinoic acid in establishing nested Hox expression domains. These comparisons lead to a model in which early vertebrates underwent an elaboration of the network between anterior-posterior patterning and Hox gene expression, leading to the gene-regulatory programs for segmental subdivision and rhombomeric segmentation. WIREs Dev Biol 2017, 6:e286. doi: 10.1002/wdev.286 For further resources related to this article, please visit the WIREs website.
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Affiliation(s)
- Hugo J Parker
- Stowers Institute for Medical Research, Kansas City, MO, USA
| | - Robb Krumlauf
- Stowers Institute for Medical Research, Kansas City, MO, USA.,Department of Anatomy and Cell Biology, Kansas University Medical Center, Kansas City, Kansas 66160, USA
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14
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Bhatlekar S, Viswanathan V, Fields JZ, Boman BM. Overexpression of HOXA4 and HOXA9 genes promotes self-renewal and contributes to colon cancer stem cell overpopulation. J Cell Physiol 2017; 233:727-735. [PMID: 28464221 DOI: 10.1002/jcp.25981] [Citation(s) in RCA: 43] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2017] [Accepted: 05/01/2017] [Indexed: 12/30/2022]
Abstract
Because HOX genes encode master regulatory transcription factors that regulate stem cells (SCs) during development and aberrant expression of HOX genes occurs in various cancers, our goal was to determine if dysregulation of HOX genes is involved in the SC origin of colorectal cancer (CRC). We previously reported that HOXA4 and HOXD10 are expressed in the colonic SC niche and are overexpressed in CRC. HOX gene expression was studied in SCs from human colon tissue and CRC cells (CSCs) using qPCR and immunostaining. siRNA-mediated knockdown of HOX expression was used to evaluate the role of HOX genes in modulating cancer SC (CSC) phenotype at the level of proliferation, SC marker expression, and sphere formation. All-trans-retinoic-acid (ATRA), a differentiation-inducing agent was evaluated for its effects on HOX expression and CSC growth. We found that HOXA4 and HOXA9 are up-regulated in CRC SCs. siRNA knockdown of HOXA4 and HOXA9 reduced: (i) proliferation and sphere-formation and (ii) gene expression of known SC markers (ALDH1, CD166, LGR5). These results indicate that proliferation and self-renewal ability of CRC SCs are reduced in HOXA4 and HOXA9 knockdown cells. ATRA decreased HOXA4, HOXA9, and HOXD10 expression in parallel with reduction in ALDH1 expression, self-renewal, and proliferation. Overall, our findings indicate that overexpression of HOXA4 and HOXA9 contributes to self-renewal and overpopulation of SCs in CRC. Strategies designed to modulate HOX expression may provide ways to target malignant SCs and to develop more effective therapies for CRC.
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Affiliation(s)
- Seema Bhatlekar
- Center for Translational Cancer Research, Helen F. Graham Cancer Center and Research Institute, Newark, Delaware.,Department of Biological Sciences, University of Delaware, Newark, Delaware
| | - Vignesh Viswanathan
- Center for Translational Cancer Research, Helen F. Graham Cancer Center and Research Institute, Newark, Delaware.,Department of Biological Sciences, University of Delaware, Newark, Delaware
| | | | - Bruce M Boman
- Center for Translational Cancer Research, Helen F. Graham Cancer Center and Research Institute, Newark, Delaware.,Department of Biological Sciences, University of Delaware, Newark, Delaware
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15
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Pinharanda A, Martin SH, Barker SL, Davey JW, Jiggins CD. The comparative landscape of duplications in Heliconius melpomene and Heliconius cydno. Heredity (Edinb) 2017; 118:78-87. [PMID: 27925618 PMCID: PMC5176112 DOI: 10.1038/hdy.2016.107] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2016] [Revised: 08/24/2016] [Accepted: 08/25/2016] [Indexed: 01/01/2023] Open
Abstract
Gene duplications can facilitate adaptation and may lead to interpopulation divergence, causing reproductive isolation. We used whole-genome resequencing data from 34 butterflies to detect duplications in two Heliconius species, Heliconius cydno and Heliconius melpomene. Taking advantage of three distinctive signals of duplication in short-read sequencing data, we identified 744 duplicated loci in H. cydno and H. melpomene and evaluated the accuracy of our approach using single-molecule sequencing. We have found that duplications overlap genes significantly less than expected at random in H. melpomene, consistent with the action of background selection against duplicates in functional regions of the genome. Duplicate loci that are highly differentiated between H. melpomene and H. cydno map to four different chromosomes. Four duplications were identified with a strong signal of divergent selection, including an odorant binding protein and another in close proximity with a known wing colour pattern locus that differs between the two species.
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Affiliation(s)
- A Pinharanda
- Department of Zoology, University of
Cambridge, Cambridge, UK
| | - S H Martin
- Department of Zoology, University of
Cambridge, Cambridge, UK
| | - S L Barker
- Department of Zoology, University of
Cambridge, Cambridge, UK
| | - J W Davey
- Department of Zoology, University of
Cambridge, Cambridge, UK
| | - C D Jiggins
- Department of Zoology, University of
Cambridge, Cambridge, UK
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16
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Yue JX, Kozmikova I, Ono H, Nossa CW, Kozmik Z, Putnam NH, Yu JK, Holland LZ. Conserved Noncoding Elements in the Most Distant Genera of Cephalochordates: The Goldilocks Principle. Genome Biol Evol 2016; 8:2387-405. [PMID: 27412606 PMCID: PMC5010895 DOI: 10.1093/gbe/evw158] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Cephalochordates, the sister group of vertebrates + tunicates, are evolving particularly slowly. Therefore, genome comparisons between two congeners of Branchiostoma revealed so many conserved noncoding elements (CNEs), that it was not clear how many are functional regulatory elements. To more effectively identify CNEs with potential regulatory functions, we compared noncoding sequences of genomes of the most phylogenetically distant cephalochordate genera, Asymmetron and Branchiostoma, which diverged approximately 120-160 million years ago. We found 113,070 noncoding elements conserved between the two species, amounting to 3.3% of the genome. The genomic distribution, target gene ontology, and enriched motifs of these CNEs all suggest that many of them are probably cis-regulatory elements. More than 90% of previously verified amphioxus regulatory elements were re-captured in this study. A search of the cephalochordate CNEs around 50 developmental genes in several vertebrate genomes revealed eight CNEs conserved between cephalochordates and vertebrates, indicating sequence conservation over >500 million years of divergence. The function of five CNEs was tested in reporter assays in zebrafish, and one was also tested in amphioxus. All five CNEs proved to be tissue-specific enhancers. Taken together, these findings indicate that even though Branchiostoma and Asymmetron are distantly related, as they are evolving slowly, comparisons between them are likely optimal for identifying most of their tissue-specific cis-regulatory elements laying the foundation for functional characterizations and a better understanding of the evolution of developmental regulation in cephalochordates.
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Affiliation(s)
- Jia-Xing Yue
- Biosciences at Rice, Rice University, Houston, Texas Present address: Institute for Research on Cancer and Aging, Nice (IRCAN), CNRS UMR 7284, INSERM U1081, Nice 06107 France
| | - Iryna Kozmikova
- Department of Transcriptional Regulation, Institute of Molecular Genetics, Prague 14220, Czech Republic
| | - Hiroki Ono
- Marine Biology Research Division, Scripps Institution of Oceanography, UC San Diego, La Jolla, California
| | - Carlos W Nossa
- Biosciences at Rice, Rice University, Houston, Texas Present address: Gene by Gene Ltd., Houston, TX 77008
| | - Zbynek Kozmik
- Department of Transcriptional Regulation, Institute of Molecular Genetics, Prague 14220, Czech Republic
| | - Nicholas H Putnam
- Biosciences at Rice, Rice University, Houston, Texas Present address: Dovetail Genomics, Santa Cruz, CA 95060
| | - Jr-Kai Yu
- Institute of Cellular and Organismic Biology, Academia Sinica, Taipei, Taiwan
| | - Linda Z Holland
- Marine Biology Research Division, Scripps Institution of Oceanography, UC San Diego, La Jolla, California
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17
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Giunta M, Edvardson S, Xu Y, Schuelke M, Gomez-Duran A, Boczonadi V, Elpeleg O, Müller JS, Horvath R. Altered RNA metabolism due to a homozygous RBM7 mutation in a patient with spinal motor neuropathy. Hum Mol Genet 2016; 25:2985-2996. [PMID: 27193168 PMCID: PMC5181591 DOI: 10.1093/hmg/ddw149] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2016] [Revised: 05/09/2016] [Accepted: 05/10/2016] [Indexed: 12/23/2022] Open
Abstract
The exosome complex is the most important RNA processing machinery within the cell. Mutations in its subunits EXOSC8 and EXOSC3 cause pontocerebellar hypoplasia, spinal muscular atrophy (SMA) and central nervous system demyelination. We present a patient with SMA-like phenotype carrying a homozygous mutation in RBM7-a subunit of the nuclear exosome targeting (NEXT) complex-which is known to bind and carry specific subtypes of coding and non-coding RNAs to the exosome. The NEXT complex with other protein complexes is responsible for the substrate specificity of the exosome. We performed RNA-sequencing (RNA-seq) analysis on primary fibroblasts of patients with mutations in EXOSC8 and RBM7 and gene knock-down experiments using zebrafish as a model system. RNA-seq analysis identified significantly altered expression of 62 transcripts shared by the two patient cell lines. Knock-down of rbm7, exosc8 and exosc3 in zebrafish showed a common pattern of defects in motor neurons and cerebellum. Our data indicate that impaired RNA metabolism may underlie the clinical phenotype by fine tuning gene expression which is essential for correct neuronal differentiation.
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Affiliation(s)
- Michele Giunta
- Institute of Genetic Medicine, Newcastle University, Central Parkway, NE1 3BZ, Newcastle upon Tyne, UK
- Institute of Genetic Medicine, Newcastle University, Central Parkway, NE1 3BZ, Newcastle upon Tyne, UK
| | - Shimon Edvardson
- The Monique and Jacques Roboh Department of Genetic Research, Hadassah, Hebrew University Medical Center, 91120 Jerusalem, Israel
- Institute of Genetic Medicine, Newcastle University, Central Parkway, NE1 3BZ, Newcastle upon Tyne, UK
| | - Yaobo Xu
- Institute of Genetic Medicine, Newcastle University, Central Parkway, NE1 3BZ, Newcastle upon Tyne, UK
| | - Markus Schuelke
- Department of Neuropediatrics and NeuroCure Clinical Research Center, Charité-Universitätsmedizin, Charitéplatz 1, 10117 Berlin, Germany
| | - Aurora Gomez-Duran
- Institute of Genetic Medicine, Newcastle University, Central Parkway, NE1 3BZ, Newcastle upon Tyne, UK
| | - Veronika Boczonadi
- Institute of Genetic Medicine, Newcastle University, Central Parkway, NE1 3BZ, Newcastle upon Tyne, UK
| | - Orly Elpeleg
- The Monique and Jacques Roboh Department of Genetic Research, Hadassah, Hebrew University Medical Center, 91120 Jerusalem, Israel
| | - Juliane S Müller
- Institute of Genetic Medicine, Newcastle University, Central Parkway, NE1 3BZ, Newcastle upon Tyne, UK
- Institute of Genetic Medicine, Newcastle University, Central Parkway, NE1 3BZ, Newcastle upon Tyne, UK
| | - Rita Horvath
- Institute of Genetic Medicine, Newcastle University, Central Parkway, NE1 3BZ, Newcastle upon Tyne, UK
- Institute of Genetic Medicine, Newcastle University, Central Parkway, NE1 3BZ, Newcastle upon Tyne, UK
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18
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Fitness Assays Reveal Incomplete Functional Redundancy of the HoxA1 and HoxB1 Paralogs of Mice. Genetics 2016; 201:727-36. [PMID: 26447130 DOI: 10.1534/genetics.115.178079] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Gene targeting techniques have led to the phenotypic characterization of numerous genes; however, many genes show minimal to no phenotypic consequences when disrupted, despite many having highly conserved sequences. The standard explanation for these findings is functional redundancy. A competing hypothesis is that these genes have important ecological functions in natural environments that are not needed under laboratory settings. Here we discriminate between these hypotheses by competing mice (Mus musculus) whose Hoxb1 gene has been replaced by Hoxa1, its highly conserved paralog, against matched wild-type controls in seminatural enclosures. This Hoxb1(A1) swap was reported as a genetic manipulation resulting in no discernible embryonic or physiological phenotype under standard laboratory tests. We observed a transient decline in first litter size for Hoxb1(A1) homozygous mice in breeding cages, but their fitness was consistently and more dramatically reduced when competing against controls within seminatural populations. Specifically, males homozygous for the Hoxb1(A1) swap acquired 10.6% fewer territories and the frequency of the Hoxb1(A1) allele decreased from 0.500 in population founders to 0.419 in their offspring. The decrease in Hoxb1(A1) frequency corresponded with a deficiency of both Hoxb1(A1) homozygous and heterozygous offspring. These data suggest that Hoxb1 and Hoxa1 are more phenotypically divergent than previously reported and support that sub- and/or neofunctionalization has occurred in these paralogous genes leading to a divergence of gene function and incomplete redundancy. Furthermore, this study highlights the importance of obtaining fitness measures of mutants in ecologically relevant conditions to better understand gene function and evolution.
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19
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Miyashita T, Diogo R. Evolution of Serial Patterns in the Vertebrate Pharyngeal Apparatus and Paired Appendages via Assimilation of Dissimilar Units. Front Ecol Evol 2016. [DOI: 10.3389/fevo.2016.00071] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
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20
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Parker HJ, Bronner ME, Krumlauf R. The vertebrate Hox gene regulatory network for hindbrain segmentation: Evolution and diversification: Coupling of a Hox gene regulatory network to hindbrain segmentation is an ancient trait originating at the base of vertebrates. Bioessays 2016; 38:526-38. [PMID: 27027928 DOI: 10.1002/bies.201600010] [Citation(s) in RCA: 52] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Hindbrain development is orchestrated by a vertebrate gene regulatory network that generates segmental patterning along the anterior-posterior axis via Hox genes. Here, we review analyses of vertebrate and invertebrate chordate models that inform upon the evolutionary origin and diversification of this network. Evidence from the sea lamprey reveals that the hindbrain regulatory network generates rhombomeric compartments with segmental Hox expression and an underlying Hox code. We infer that this basal feature was present in ancestral vertebrates and, as an evolutionarily constrained developmental state, is fundamentally important for patterning of the vertebrate hindbrain across diverse lineages. Despite the common ground plan, vertebrates exhibit neuroanatomical diversity in lineage-specific patterns, with different vertebrates revealing variations of Hox expression in the hindbrain that could underlie this diversification. Invertebrate chordates lack hindbrain segmentation but exhibit some conserved aspects of this network, with retinoic acid signaling playing a role in establishing nested domains of Hox expression.
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Affiliation(s)
- Hugo J Parker
- Stowers Institute for Medical Research, Kansas City, MO, USA
| | - Marianne E Bronner
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Robb Krumlauf
- Stowers Institute for Medical Research, Kansas City, MO, USA.,Department of Anatomy and Cell Biology, Kansas University Medical Center, Kansas City, KS, USA
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21
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22
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Grice J, Noyvert B, Doglio L, Elgar G. A Simple Predictive Enhancer Syntax for Hindbrain Patterning Is Conserved in Vertebrate Genomes. PLoS One 2015; 10:e0130413. [PMID: 26131856 PMCID: PMC4489388 DOI: 10.1371/journal.pone.0130413] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2015] [Accepted: 05/19/2015] [Indexed: 12/17/2022] Open
Abstract
Background Determining the function of regulatory elements is fundamental for our understanding of development, disease and evolution. However, the sequence features that mediate these functions are often unclear and the prediction of tissue-specific expression patterns from sequence alone is non-trivial. Previous functional studies have demonstrated a link between PBX-HOX and MEIS/PREP binding interactions and hindbrain enhancer activity, but the defining grammar of these sites, if any exists, has remained elusive. Results Here, we identify a shared sequence signature (syntax) within a heterogeneous set of conserved vertebrate hindbrain enhancers composed of spatially co-occurring PBX-HOX and MEIS/PREP transcription factor binding motifs. We use this syntax to accurately predict hindbrain enhancers in 89% of cases (67/75 predicted elements) from a set of conserved non-coding elements (CNEs). Furthermore, mutagenesis of the sites abolishes activity or generates ectopic expression, demonstrating their requirement for segmentally restricted enhancer activity in the hindbrain. We refine and use our syntax to predict over 3,000 hindbrain enhancers across the human genome. These sequences tend to be located near developmental transcription factors and are enriched in known hindbrain activating elements, demonstrating the predictive power of this simple model. Conclusion Our findings support the theory that hundreds of CNEs, and perhaps thousands of regions across the human genome, function to coordinate gene expression in the developing hindbrain. We speculate that deeply conserved sequences of this kind contributed to the co-option of new genes into the hindbrain gene regulatory network during early vertebrate evolution by linking patterns of hox expression to downstream genes involved in segmentation and patterning, and evolutionarily newer instances may have continued to contribute to lineage-specific elaboration of the hindbrain.
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Affiliation(s)
- Joseph Grice
- The Francis Crick Institute Mill Hill Laboratory, The Ridgeway, Mill Hill, London, NW7 1AA, United Kingdom
| | - Boris Noyvert
- The Francis Crick Institute Mill Hill Laboratory, The Ridgeway, Mill Hill, London, NW7 1AA, United Kingdom
| | - Laura Doglio
- The Francis Crick Institute Mill Hill Laboratory, The Ridgeway, Mill Hill, London, NW7 1AA, United Kingdom
| | - Greg Elgar
- The Francis Crick Institute Mill Hill Laboratory, The Ridgeway, Mill Hill, London, NW7 1AA, United Kingdom
- * E-mail:
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23
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Kozmikova I, Kozmik Z. Gene regulation in amphioxus: An insight from transgenic studies in amphioxus and vertebrates. Mar Genomics 2015; 24 Pt 2:159-66. [PMID: 26094865 DOI: 10.1016/j.margen.2015.06.003] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2015] [Revised: 06/10/2015] [Accepted: 06/10/2015] [Indexed: 01/07/2023]
Abstract
Cephalochordates, commonly known as amphioxus or lancelets, are the most basal subphylum of chordates. Cephalochordates are thus key to understanding the origin of vertebrates and molecular mechanisms underlying vertebrate evolution. The evolution of developmental control mechanisms during invertebrate-to-vertebrate transition involved not only gene duplication events, but also specific changes in spatial and temporal expression of many genes. To get insight into the spatiotemporal regulation of gene expression during invertebrate-to-vertebrate transition, functional studies of amphioxus gene regulatory elements are highly warranted. Here, we review transgenic studies performed in amphioxus and vertebrates using promoters and enhancers derived from the genome of Branchiostoma floridae. We describe the current methods of transgenesis in amphioxus, provide evidence of Tol2 transposon-generated transgenic embryos of Branchiostoma lanceolatum and discuss possible future directions. We envision that comparative transgenic analysis of gene regulatory sequences in the context of amphioxus and vertebrate embryos will likely provide an important mechanistic insight into the evolution of vertebrate body plan.
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Affiliation(s)
- Iryna Kozmikova
- Institute of Molecular Genetics of the Academy of Sciences, Videnska 1083, 142 20 Prague 4, Czech Republic
| | - Zbynek Kozmik
- Institute of Molecular Genetics of the Academy of Sciences, Videnska 1083, 142 20 Prague 4, Czech Republic.
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24
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De Kumar B, Parrish ME, Slaughter BD, Unruh JR, Gogol M, Seidel C, Paulson A, Li H, Gaudenz K, Peak A, McDowell W, Fleharty B, Ahn Y, Lin C, Smith E, Shilatifard A, Krumlauf R. Analysis of dynamic changes in retinoid-induced transcription and epigenetic profiles of murine Hox clusters in ES cells. Genome Res 2015; 25:1229-43. [PMID: 26025802 PMCID: PMC4510006 DOI: 10.1101/gr.184978.114] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2014] [Accepted: 05/28/2015] [Indexed: 11/24/2022]
Abstract
The clustered Hox genes, which are highly conserved across metazoans, encode homeodomain-containing transcription factors that provide a blueprint for segmental identity along the body axis. Recent studies have underscored that in addition to encoding Hox genes, the homeotic clusters contain key noncoding RNA genes that play a central role in development. In this study, we have taken advantage of genome-wide approaches to provide a detailed analysis of retinoic acid (RA)-induced transcriptional and epigenetic changes within the homeotic clusters of mouse embryonic stem cells. Although there is a general colinear response, our analyses suggest a lack of strict colinearity for several genes in the HoxA and HoxB clusters. We have identified transcribed novel noncoding RNAs (ncRNAs) and their cis-regulatory elements that function in response to RA and demonstrated that the expression of these ncRNAs from both strands represent some of the most rapidly induced transcripts in ES cells. Finally, we have provided dynamic analyses of chromatin modifications for the coding and noncoding genes expressed upon activation and suggest that active transcription can occur in the presence of chromatin modifications and machineries associated with repressed transcription state over the clusters. Overall, our data provide a resource for a better understanding of the dynamic nature of the coding and noncoding transcripts and their associated chromatin marks in the regulation of homeotic gene transcription during development.
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Affiliation(s)
- Bony De Kumar
- Stowers Institute for Medical Research, Kansas City, Missouri 64110, USA
| | - Mark E Parrish
- Stowers Institute for Medical Research, Kansas City, Missouri 64110, USA
| | - Brian D Slaughter
- Stowers Institute for Medical Research, Kansas City, Missouri 64110, USA
| | - Jay R Unruh
- Stowers Institute for Medical Research, Kansas City, Missouri 64110, USA
| | - Madelaine Gogol
- Stowers Institute for Medical Research, Kansas City, Missouri 64110, USA
| | - Christopher Seidel
- Stowers Institute for Medical Research, Kansas City, Missouri 64110, USA
| | - Ariel Paulson
- Stowers Institute for Medical Research, Kansas City, Missouri 64110, USA
| | - Hua Li
- Stowers Institute for Medical Research, Kansas City, Missouri 64110, USA
| | - Karin Gaudenz
- Stowers Institute for Medical Research, Kansas City, Missouri 64110, USA
| | - Allison Peak
- Stowers Institute for Medical Research, Kansas City, Missouri 64110, USA
| | - William McDowell
- Stowers Institute for Medical Research, Kansas City, Missouri 64110, USA
| | - Brian Fleharty
- Stowers Institute for Medical Research, Kansas City, Missouri 64110, USA
| | - Youngwook Ahn
- Stowers Institute for Medical Research, Kansas City, Missouri 64110, USA
| | - Chengqi Lin
- Stowers Institute for Medical Research, Kansas City, Missouri 64110, USA
| | - Edwin Smith
- Stowers Institute for Medical Research, Kansas City, Missouri 64110, USA
| | - Ali Shilatifard
- Stowers Institute for Medical Research, Kansas City, Missouri 64110, USA
| | - Robb Krumlauf
- Stowers Institute for Medical Research, Kansas City, Missouri 64110, USA; Department of Anatomy and Cell Biology, Kansas University Medical Center, Kansas City, Kansas 66160, USA
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25
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Richards EJ, Zhang G, Li ZP, Permuth-Wey J, Challa S, Li Y, Kong W, Dan S, Bui MM, Coppola D, Mao WM, Sellers TA, Cheng JQ. Long non-coding RNAs (LncRNA) regulated by transforming growth factor (TGF) β: LncRNA-hit-mediated TGFβ-induced epithelial to mesenchymal transition in mammary epithelia. J Biol Chem 2015; 290:6857-67. [PMID: 25605728 DOI: 10.1074/jbc.m114.610915] [Citation(s) in RCA: 118] [Impact Index Per Article: 13.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
Long noncoding RNAs (lncRNAs) are emerging as key regulators in various biological processes. Epithelial-to-mesenchymal transition (EMT) is a developmental process hijacked by tumor cells to depart from the primary tumor site, invade surrounding tissue, and establish distant metastases. Transforming growth factor β (TGFβ) signaling has been shown to be a major inducer of EMT and to facilitate breast cancer metastasis. However, the role of lncRNAs in this process remains largely unknown. Here we report a genome-wide lncRNA profile in mouse mammary epithelial NMuMG cells upon TGFβ induction of EMT. Among 10,802 lncRNAs profiled, over 600 were up-regulated and down-regulated during the EMT, respectively. Furthermore, we identify that lncRNA-HIT (HOXA transcript induced by TGFβ) mediates TGFβ function, i.e. depletion of lncRNA-HIT inhibits TGFβ-induced migration, invasion, and EMT in NMuMG. LncRNA-HIT is also significantly elevated in the highly metastatic 4T1 cells. Knockdown of lncRNA-HIT in 4T1 results in decrease of cell migration, invasion, tumor growth, and metastasis. E-cadherin was identified as a major target of lncRNA-HIT. Moreover, lncRNA-HIT is conserved in humans and elevated expression associates with more invasive human primary breast carcinoma. Collectively, these data suggest that a subset of lncRNAs such as lncRNA-HIT play a significant role in regulation of EMT and breast cancer invasion and metastasis, and could be potential therapeutic targets in breast cancers.
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Affiliation(s)
| | - Gu Zhang
- the Zhejiang Cancer Hospital & Zhejiang Cancer Research Institute, Zhejiang 310022, China
| | - Zhu-Peng Li
- the Zhejiang Cancer Hospital & Zhejiang Cancer Research Institute, Zhejiang 310022, China
| | | | | | - Yajuan Li
- From the Departments of Molecular Oncology
| | | | - Su Dan
- the Zhejiang Cancer Hospital & Zhejiang Cancer Research Institute, Zhejiang 310022, China
| | - Marilyn M Bui
- Anatomic Pathology, Lee Moffitt Cancer Center and Research Institute, Tampa, Florida 33612 and
| | - Domenico Coppola
- Anatomic Pathology, Lee Moffitt Cancer Center and Research Institute, Tampa, Florida 33612 and
| | - Wei-Min Mao
- the Zhejiang Cancer Hospital & Zhejiang Cancer Research Institute, Zhejiang 310022, China
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26
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Jandzik D, Garnett AT, Square TA, Cattell MV, Yu JK, Medeiros DM. Evolution of the new vertebrate head by co-option of an ancient chordate skeletal tissue. Nature 2014; 518:534-7. [PMID: 25487155 DOI: 10.1038/nature14000] [Citation(s) in RCA: 69] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2014] [Accepted: 10/24/2014] [Indexed: 02/01/2023]
Abstract
A defining feature of vertebrates (craniates) is a pronounced head that is supported and protected by a robust cellular endoskeleton. In the first vertebrates, this skeleton probably consisted of collagenous cellular cartilage, which forms the embryonic skeleton of all vertebrates and the adult skeleton of modern jawless and cartilaginous fish. In the head, most cellular cartilage is derived from a migratory cell population called the neural crest, which arises from the edges of the central nervous system. Because collagenous cellular cartilage and neural crest cells have not been described in invertebrates, the appearance of cellular cartilage derived from neural crest cells is considered a turning point in vertebrate evolution. Here we show that a tissue with many of the defining features of vertebrate cellular cartilage transiently forms in the larvae of the invertebrate chordate Branchiostoma floridae (Florida amphioxus). We also present evidence that during evolution, a key regulator of vertebrate cartilage development, SoxE, gained new cis-regulatory sequences that subsequently directed its novel expression in neural crest cells. Together, these results suggest that the origin of the vertebrate head skeleton did not depend on the evolution of a new skeletal tissue, as is commonly thought, but on the spread of this tissue throughout the head. We further propose that the evolution of cis-regulatory elements near an ancient regulator of cartilage differentiation was a major factor in the evolution of the vertebrate head skeleton.
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Affiliation(s)
- David Jandzik
- 1] Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, Colorado 80309, USA [2] Department of Zoology, Comenius University, Bratislava 84215, Slovakia
| | - Aaron T Garnett
- Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, Colorado 80309, USA
| | - Tyler A Square
- Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, Colorado 80309, USA
| | - Maria V Cattell
- Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, Colorado 80309, USA
| | - Jr-Kai Yu
- Institute of Cellular and Organismic Biology, Academia Sinica, Taipei 11529, Taiwan
| | - Daniel M Medeiros
- Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, Colorado 80309, USA
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27
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Vassalli QA, Anishchenko E, Caputi L, Sordino P, D'Aniello S, Locascio A. Regulatory elements retained during chordate evolution: Coming across tunicates. Genesis 2014; 53:66-81. [DOI: 10.1002/dvg.22838] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2014] [Revised: 11/06/2014] [Accepted: 11/11/2014] [Indexed: 12/22/2022]
Affiliation(s)
- Quirino Attilio Vassalli
- Cellular and Developmental Biology Laboratory; Stazione Zoologica Anton Dohrn; Villa Comunale Naples Italy
| | - Evgeniya Anishchenko
- Cellular and Developmental Biology Laboratory; Stazione Zoologica Anton Dohrn; Villa Comunale Naples Italy
| | - Luigi Caputi
- Cellular and Developmental Biology Laboratory; Stazione Zoologica Anton Dohrn; Villa Comunale Naples Italy
| | - Paolo Sordino
- Cellular and Developmental Biology Laboratory; Stazione Zoologica Anton Dohrn; Villa Comunale Naples Italy
- CNR ISAFOM, Institute for Agricultural and Forest Systems in the Mediterranean, Unitá organizzativa di supporto; Catania Italy
| | - Salvatore D'Aniello
- Cellular and Developmental Biology Laboratory; Stazione Zoologica Anton Dohrn; Villa Comunale Naples Italy
| | - Annamaria Locascio
- Cellular and Developmental Biology Laboratory; Stazione Zoologica Anton Dohrn; Villa Comunale Naples Italy
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28
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A Hox regulatory network of hindbrain segmentation is conserved to the base of vertebrates. Nature 2014; 514:490-3. [PMID: 25219855 PMCID: PMC4209185 DOI: 10.1038/nature13723] [Citation(s) in RCA: 67] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2014] [Accepted: 07/31/2014] [Indexed: 11/08/2022]
Abstract
A defining feature governing head patterning of jawed vertebrates is a highly conserved gene regulatory network that integrates hindbrain segmentation with segmentally restricted domains of Hox gene expression. Although non-vertebrate chordates display nested domains of axial Hox expression, they lack hindbrain segmentation. The sea lamprey, a jawless fish, can provide unique insights into vertebrate origins owing to its phylogenetic position at the base of the vertebrate tree. It has been suggested that lamprey may represent an intermediate state where nested Hox expression has not been coupled to the process of hindbrain segmentation. However, little is known about the regulatory network underlying Hox expression in lamprey or its relationship to hindbrain segmentation. Here, using a novel tool that allows cross-species comparisons of regulatory elements between jawed and jawless vertebrates, we report deep conservation of both upstream regulators and segmental activity of enhancer elements across these distant species. Regulatory regions from diverse gnathostomes drive segmental reporter expression in the lamprey hindbrain and require the same transcriptional inputs (for example, Kreisler (also known as Mafba), Krox20 (also known as Egr2a)) in both lamprey and zebrafish. We find that lamprey hox genes display dynamic segmentally restricted domains of expression; we also isolated a conserved exonic hox2 enhancer from lamprey that drives segmental expression in rhombomeres 2 and 4. Our results show that coupling of Hox gene expression to segmentation of the hindbrain is an ancient trait with origin at the base of vertebrates that probably led to the formation of rhombomeric compartments with an underlying Hox code.
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29
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Parker HJ, Sauka-Spengler T, Bronner M, Elgar G. A reporter assay in lamprey embryos reveals both functional conservation and elaboration of vertebrate enhancers. PLoS One 2014; 9:e85492. [PMID: 24416417 PMCID: PMC3887057 DOI: 10.1371/journal.pone.0085492] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2013] [Accepted: 12/05/2013] [Indexed: 11/27/2022] Open
Abstract
The sea lamprey is an important model organism for investigating the evolutionary origins of vertebrates. As more vertebrate genome sequences are obtained, evolutionary developmental biologists are becoming increasingly able to identify putative gene regulatory elements across the breadth of the vertebrate taxa. The identification of these regions makes it possible to address how changes at the genomic level have led to changes in developmental gene regulatory networks and ultimately to the evolution of morphological diversity. Comparative genomics approaches using sea lamprey have already predicted a number of such regulatory elements in the lamprey genome. Functional characterisation of these sequences and other similar elements requires efficient reporter assays in lamprey. In this report, we describe the development of a transient transgenesis method for lamprey embryos. Focusing on conserved non-coding elements (CNEs), we use this method to investigate their functional conservation across the vertebrate subphylum. We find instances of both functional conservation and lineage-specific functional evolution of CNEs across vertebrates, emphasising the utility of functionally testing homologous CNEs in their host species.
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Affiliation(s)
- Hugo J. Parker
- Division of Systems Biology, Medical Research Council National Institute for Medical Research, London, United Kingdom
| | - Tatjana Sauka-Spengler
- Division of Biology, California Institute of Technology, Pasadena, California, United States of America
| | - Marianne Bronner
- Division of Biology, California Institute of Technology, Pasadena, California, United States of America
| | - Greg Elgar
- Division of Systems Biology, Medical Research Council National Institute for Medical Research, London, United Kingdom
- * E-mail:
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30
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Parallel evolution of chordate cis-regulatory code for development. PLoS Genet 2013; 9:e1003904. [PMID: 24282393 PMCID: PMC3836708 DOI: 10.1371/journal.pgen.1003904] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2013] [Accepted: 09/09/2013] [Indexed: 12/17/2022] Open
Abstract
Urochordates are the closest relatives of vertebrates and at the larval stage, possess a characteristic bilateral chordate body plan. In vertebrates, the genes that orchestrate embryonic patterning are in part regulated by highly conserved non-coding elements (CNEs), yet these elements have not been identified in urochordate genomes. Consequently the evolution of the cis-regulatory code for urochordate development remains largely uncharacterised. Here, we use genome-wide comparisons between C. intestinalis and C. savignyi to identify putative urochordate cis-regulatory sequences. Ciona conserved non-coding elements (ciCNEs) are associated with largely the same key regulatory genes as vertebrate CNEs. Furthermore, some of the tested ciCNEs are able to activate reporter gene expression in both zebrafish and Ciona embryos, in a pattern that at least partially overlaps that of the gene they associate with, despite the absence of sequence identity. We also show that the ability of a ciCNE to up-regulate gene expression in vertebrate embryos can in some cases be localised to short sub-sequences, suggesting that functional cross-talk may be defined by small regions of ancestral regulatory logic, although functional sub-sequences may also be dispersed across the whole element. We conclude that the structure and organisation of cis-regulatory modules is very different between vertebrates and urochordates, reflecting their separate evolutionary histories. However, functional cross-talk still exists because the same repertoire of transcription factors has likely guided their parallel evolution, exploiting similar sets of binding sites but in different combinations. Vertebrates share many aspects of early development with our closest chordate ancestors, the tunicates. However, whilst the repertoire of genes that orchestrate development is essentially the same in the two lineages, the genomic code that regulates these genes appears to be very different, even though it is highly conserved within vertebrates themselves. Using comparative genomics, we have identified a parallel developmental code in tunicates and confirmed that this code, despite a lack of sequence conservation, associates with a similar repertoire of genes. However, the organisation of the code spatially is very different in the two lineages, strongly suggesting that most of it arose independently in vertebrates and tunicates, and in most cases lacking any direct sequence ancestry. We have assayed elements of the tunicate code, and found that at least some of them can regulate gene expression in zebrafish embryos. Our results suggest that regulatory code has arisen independently in different animal lineages but possesses some common functionality because its evolution has been driven by a similar cohort of developmental transcription factors. Our work helps illuminate how complex, stable gene regulatory networks evolve and become fixed within lineages.
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Harmston N, Baresic A, Lenhard B. The mystery of extreme non-coding conservation. Philos Trans R Soc Lond B Biol Sci 2013; 368:20130021. [PMID: 24218634 PMCID: PMC3826495 DOI: 10.1098/rstb.2013.0021] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Regions of several dozen to several hundred base pairs of extreme conservation have been found in non-coding regions in all metazoan genomes. The distribution of these elements within and across genomes has suggested that many have roles as transcriptional regulatory elements in multi-cellular organization, differentiation and development. Currently, there is no known mechanism or function that would account for this level of conservation at the observed evolutionary distances. Previous studies have found that, while these regions are under strong purifying selection, and not mutational coldspots, deletion of entire regions in mice does not necessarily lead to identifiable changes in phenotype during development. These opposing findings lead to several questions regarding their functional importance and why they are under strong selection in the first place. In this perspective, we discuss the methods and techniques used in identifying and dissecting these regions, their observed patterns of conservation, and review the current hypotheses on their functional significance.
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Affiliation(s)
- Nathan Harmston
- Institute of Clinical Sciences, Faculty of Medicine, Imperial College London and MRC Clinical Sciences Centre, , Hammersmith Hospital Campus, Du Cane Road, London W12 0NN, UK
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Simões-Costa M, Bronner ME. Insights into neural crest development and evolution from genomic analysis. Genome Res 2013; 23:1069-80. [PMID: 23817048 PMCID: PMC3698500 DOI: 10.1101/gr.157586.113] [Citation(s) in RCA: 93] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
The neural crest is an excellent model system for the study of cell type diversification during embryonic development due to its multipotency, motility, and ability to form a broad array of derivatives ranging from neurons and glia, to cartilage, bone, and melanocytes. As a uniquely vertebrate cell population, it also offers important clues regarding vertebrate origins. In the past 30 yr, introduction of recombinant DNA technology has facilitated the dissection of the genetic program controlling neural crest development and has provided important insights into gene regulatory mechanisms underlying cell migration and differentiation. More recently, new genomic approaches have provided a platform and tools that are changing the depth and breadth of our understanding of neural crest development at a “systems” level. Such advances provide an insightful view of the regulatory landscape of neural crest cells and offer a new perspective on developmental as well as stem cell and cancer biology.
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Affiliation(s)
- Marcos Simões-Costa
- Division of Biology, California Institute of Technology, Pasadena, California 91125, USA
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Sanges R, Hadzhiev Y, Gueroult-Bellone M, Roure A, Ferg M, Meola N, Amore G, Basu S, Brown ER, De Simone M, Petrera F, Licastro D, Strähle U, Banfi S, Lemaire P, Birney E, Müller F, Stupka E. Highly conserved elements discovered in vertebrates are present in non-syntenic loci of tunicates, act as enhancers and can be transcribed during development. Nucleic Acids Res 2013; 41:3600-18. [PMID: 23393190 PMCID: PMC3616699 DOI: 10.1093/nar/gkt030] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2012] [Revised: 12/21/2012] [Accepted: 01/03/2013] [Indexed: 01/17/2023] Open
Abstract
Co-option of cis-regulatory modules has been suggested as a mechanism for the evolution of expression sites during development. However, the extent and mechanisms involved in mobilization of cis-regulatory modules remains elusive. To trace the history of non-coding elements, which may represent candidate ancestral cis-regulatory modules affirmed during chordate evolution, we have searched for conserved elements in tunicate and vertebrate (Olfactores) genomes. We identified, for the first time, 183 non-coding sequences that are highly conserved between the two groups. Our results show that all but one element are conserved in non-syntenic regions between vertebrate and tunicate genomes, while being syntenic among vertebrates. Nevertheless, in all the groups, they are significantly associated with transcription factors showing specific functions fundamental to animal development, such as multicellular organism development and sequence-specific DNA binding. The majority of these regions map onto ultraconserved elements and we demonstrate that they can act as functional enhancers within the organism of origin, as well as in cross-transgenesis experiments, and that they are transcribed in extant species of Olfactores. We refer to the elements as 'Olfactores conserved non-coding elements'.
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Affiliation(s)
- Remo Sanges
- Laboratory of Animal Physiology and Evolution, Stazione Zoologica Anton Dohrn, Villa Comunale, 80121 Naples, Italy, Centre for Rare Diseases and Personalised Medicine, School of Clinical and Experimental Medicine, College of Medical and Dental Sciences, University of Birmingham, Birmingham B15 2TT, UK, Institut de Biologie du Développement de Marseille Luminy, UMR 6216 CNRS/Université de la Méditerranée, F-13288 Marseille cedex 9, France, Centre de Recherche de Biochimie Macromoléculaire (CRBM), UMR5237 CNRS/Universités Montpellier 1, 2, 1919 route de Mende, F-34293 Montpellier cedex 5, France, Karlsruhe Institute of Technology (KIT), Institute of Toxicology and Genetics and University of Heidelberg, Hermann-von-Helmholtz-Platz 1, 76344 Eggenstein-Leopoldshafen, Germany, Telethon Institute of Genetics and Medicine, 80131 Naples, Italy, School of Engineering and Physical Sciences, Heriot Watt University, Edinburgh EH14 4AS, UK, CBM Scrl, AREA Science Park, Basovizza, 34149 Trieste, Italy, Medical Genetics, Department of Biochemistry, Biophysics and General Pathology, Second University of Naples, 80138 Naples, Italy, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK and Center for Translational Genomics and Bioinformatics, San Raffaele Scientific Institute, Via Olgettina 58, 20132 Milano, Italy
| | - Yavor Hadzhiev
- Laboratory of Animal Physiology and Evolution, Stazione Zoologica Anton Dohrn, Villa Comunale, 80121 Naples, Italy, Centre for Rare Diseases and Personalised Medicine, School of Clinical and Experimental Medicine, College of Medical and Dental Sciences, University of Birmingham, Birmingham B15 2TT, UK, Institut de Biologie du Développement de Marseille Luminy, UMR 6216 CNRS/Université de la Méditerranée, F-13288 Marseille cedex 9, France, Centre de Recherche de Biochimie Macromoléculaire (CRBM), UMR5237 CNRS/Universités Montpellier 1, 2, 1919 route de Mende, F-34293 Montpellier cedex 5, France, Karlsruhe Institute of Technology (KIT), Institute of Toxicology and Genetics and University of Heidelberg, Hermann-von-Helmholtz-Platz 1, 76344 Eggenstein-Leopoldshafen, Germany, Telethon Institute of Genetics and Medicine, 80131 Naples, Italy, School of Engineering and Physical Sciences, Heriot Watt University, Edinburgh EH14 4AS, UK, CBM Scrl, AREA Science Park, Basovizza, 34149 Trieste, Italy, Medical Genetics, Department of Biochemistry, Biophysics and General Pathology, Second University of Naples, 80138 Naples, Italy, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK and Center for Translational Genomics and Bioinformatics, San Raffaele Scientific Institute, Via Olgettina 58, 20132 Milano, Italy
| | - Marion Gueroult-Bellone
- Laboratory of Animal Physiology and Evolution, Stazione Zoologica Anton Dohrn, Villa Comunale, 80121 Naples, Italy, Centre for Rare Diseases and Personalised Medicine, School of Clinical and Experimental Medicine, College of Medical and Dental Sciences, University of Birmingham, Birmingham B15 2TT, UK, Institut de Biologie du Développement de Marseille Luminy, UMR 6216 CNRS/Université de la Méditerranée, F-13288 Marseille cedex 9, France, Centre de Recherche de Biochimie Macromoléculaire (CRBM), UMR5237 CNRS/Universités Montpellier 1, 2, 1919 route de Mende, F-34293 Montpellier cedex 5, France, Karlsruhe Institute of Technology (KIT), Institute of Toxicology and Genetics and University of Heidelberg, Hermann-von-Helmholtz-Platz 1, 76344 Eggenstein-Leopoldshafen, Germany, Telethon Institute of Genetics and Medicine, 80131 Naples, Italy, School of Engineering and Physical Sciences, Heriot Watt University, Edinburgh EH14 4AS, UK, CBM Scrl, AREA Science Park, Basovizza, 34149 Trieste, Italy, Medical Genetics, Department of Biochemistry, Biophysics and General Pathology, Second University of Naples, 80138 Naples, Italy, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK and Center for Translational Genomics and Bioinformatics, San Raffaele Scientific Institute, Via Olgettina 58, 20132 Milano, Italy
| | - Agnes Roure
- Laboratory of Animal Physiology and Evolution, Stazione Zoologica Anton Dohrn, Villa Comunale, 80121 Naples, Italy, Centre for Rare Diseases and Personalised Medicine, School of Clinical and Experimental Medicine, College of Medical and Dental Sciences, University of Birmingham, Birmingham B15 2TT, UK, Institut de Biologie du Développement de Marseille Luminy, UMR 6216 CNRS/Université de la Méditerranée, F-13288 Marseille cedex 9, France, Centre de Recherche de Biochimie Macromoléculaire (CRBM), UMR5237 CNRS/Universités Montpellier 1, 2, 1919 route de Mende, F-34293 Montpellier cedex 5, France, Karlsruhe Institute of Technology (KIT), Institute of Toxicology and Genetics and University of Heidelberg, Hermann-von-Helmholtz-Platz 1, 76344 Eggenstein-Leopoldshafen, Germany, Telethon Institute of Genetics and Medicine, 80131 Naples, Italy, School of Engineering and Physical Sciences, Heriot Watt University, Edinburgh EH14 4AS, UK, CBM Scrl, AREA Science Park, Basovizza, 34149 Trieste, Italy, Medical Genetics, Department of Biochemistry, Biophysics and General Pathology, Second University of Naples, 80138 Naples, Italy, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK and Center for Translational Genomics and Bioinformatics, San Raffaele Scientific Institute, Via Olgettina 58, 20132 Milano, Italy
| | - Marco Ferg
- Laboratory of Animal Physiology and Evolution, Stazione Zoologica Anton Dohrn, Villa Comunale, 80121 Naples, Italy, Centre for Rare Diseases and Personalised Medicine, School of Clinical and Experimental Medicine, College of Medical and Dental Sciences, University of Birmingham, Birmingham B15 2TT, UK, Institut de Biologie du Développement de Marseille Luminy, UMR 6216 CNRS/Université de la Méditerranée, F-13288 Marseille cedex 9, France, Centre de Recherche de Biochimie Macromoléculaire (CRBM), UMR5237 CNRS/Universités Montpellier 1, 2, 1919 route de Mende, F-34293 Montpellier cedex 5, France, Karlsruhe Institute of Technology (KIT), Institute of Toxicology and Genetics and University of Heidelberg, Hermann-von-Helmholtz-Platz 1, 76344 Eggenstein-Leopoldshafen, Germany, Telethon Institute of Genetics and Medicine, 80131 Naples, Italy, School of Engineering and Physical Sciences, Heriot Watt University, Edinburgh EH14 4AS, UK, CBM Scrl, AREA Science Park, Basovizza, 34149 Trieste, Italy, Medical Genetics, Department of Biochemistry, Biophysics and General Pathology, Second University of Naples, 80138 Naples, Italy, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK and Center for Translational Genomics and Bioinformatics, San Raffaele Scientific Institute, Via Olgettina 58, 20132 Milano, Italy
| | - Nicola Meola
- Laboratory of Animal Physiology and Evolution, Stazione Zoologica Anton Dohrn, Villa Comunale, 80121 Naples, Italy, Centre for Rare Diseases and Personalised Medicine, School of Clinical and Experimental Medicine, College of Medical and Dental Sciences, University of Birmingham, Birmingham B15 2TT, UK, Institut de Biologie du Développement de Marseille Luminy, UMR 6216 CNRS/Université de la Méditerranée, F-13288 Marseille cedex 9, France, Centre de Recherche de Biochimie Macromoléculaire (CRBM), UMR5237 CNRS/Universités Montpellier 1, 2, 1919 route de Mende, F-34293 Montpellier cedex 5, France, Karlsruhe Institute of Technology (KIT), Institute of Toxicology and Genetics and University of Heidelberg, Hermann-von-Helmholtz-Platz 1, 76344 Eggenstein-Leopoldshafen, Germany, Telethon Institute of Genetics and Medicine, 80131 Naples, Italy, School of Engineering and Physical Sciences, Heriot Watt University, Edinburgh EH14 4AS, UK, CBM Scrl, AREA Science Park, Basovizza, 34149 Trieste, Italy, Medical Genetics, Department of Biochemistry, Biophysics and General Pathology, Second University of Naples, 80138 Naples, Italy, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK and Center for Translational Genomics and Bioinformatics, San Raffaele Scientific Institute, Via Olgettina 58, 20132 Milano, Italy
| | - Gabriele Amore
- Laboratory of Animal Physiology and Evolution, Stazione Zoologica Anton Dohrn, Villa Comunale, 80121 Naples, Italy, Centre for Rare Diseases and Personalised Medicine, School of Clinical and Experimental Medicine, College of Medical and Dental Sciences, University of Birmingham, Birmingham B15 2TT, UK, Institut de Biologie du Développement de Marseille Luminy, UMR 6216 CNRS/Université de la Méditerranée, F-13288 Marseille cedex 9, France, Centre de Recherche de Biochimie Macromoléculaire (CRBM), UMR5237 CNRS/Universités Montpellier 1, 2, 1919 route de Mende, F-34293 Montpellier cedex 5, France, Karlsruhe Institute of Technology (KIT), Institute of Toxicology and Genetics and University of Heidelberg, Hermann-von-Helmholtz-Platz 1, 76344 Eggenstein-Leopoldshafen, Germany, Telethon Institute of Genetics and Medicine, 80131 Naples, Italy, School of Engineering and Physical Sciences, Heriot Watt University, Edinburgh EH14 4AS, UK, CBM Scrl, AREA Science Park, Basovizza, 34149 Trieste, Italy, Medical Genetics, Department of Biochemistry, Biophysics and General Pathology, Second University of Naples, 80138 Naples, Italy, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK and Center for Translational Genomics and Bioinformatics, San Raffaele Scientific Institute, Via Olgettina 58, 20132 Milano, Italy
| | - Swaraj Basu
- Laboratory of Animal Physiology and Evolution, Stazione Zoologica Anton Dohrn, Villa Comunale, 80121 Naples, Italy, Centre for Rare Diseases and Personalised Medicine, School of Clinical and Experimental Medicine, College of Medical and Dental Sciences, University of Birmingham, Birmingham B15 2TT, UK, Institut de Biologie du Développement de Marseille Luminy, UMR 6216 CNRS/Université de la Méditerranée, F-13288 Marseille cedex 9, France, Centre de Recherche de Biochimie Macromoléculaire (CRBM), UMR5237 CNRS/Universités Montpellier 1, 2, 1919 route de Mende, F-34293 Montpellier cedex 5, France, Karlsruhe Institute of Technology (KIT), Institute of Toxicology and Genetics and University of Heidelberg, Hermann-von-Helmholtz-Platz 1, 76344 Eggenstein-Leopoldshafen, Germany, Telethon Institute of Genetics and Medicine, 80131 Naples, Italy, School of Engineering and Physical Sciences, Heriot Watt University, Edinburgh EH14 4AS, UK, CBM Scrl, AREA Science Park, Basovizza, 34149 Trieste, Italy, Medical Genetics, Department of Biochemistry, Biophysics and General Pathology, Second University of Naples, 80138 Naples, Italy, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK and Center for Translational Genomics and Bioinformatics, San Raffaele Scientific Institute, Via Olgettina 58, 20132 Milano, Italy
| | - Euan R. Brown
- Laboratory of Animal Physiology and Evolution, Stazione Zoologica Anton Dohrn, Villa Comunale, 80121 Naples, Italy, Centre for Rare Diseases and Personalised Medicine, School of Clinical and Experimental Medicine, College of Medical and Dental Sciences, University of Birmingham, Birmingham B15 2TT, UK, Institut de Biologie du Développement de Marseille Luminy, UMR 6216 CNRS/Université de la Méditerranée, F-13288 Marseille cedex 9, France, Centre de Recherche de Biochimie Macromoléculaire (CRBM), UMR5237 CNRS/Universités Montpellier 1, 2, 1919 route de Mende, F-34293 Montpellier cedex 5, France, Karlsruhe Institute of Technology (KIT), Institute of Toxicology and Genetics and University of Heidelberg, Hermann-von-Helmholtz-Platz 1, 76344 Eggenstein-Leopoldshafen, Germany, Telethon Institute of Genetics and Medicine, 80131 Naples, Italy, School of Engineering and Physical Sciences, Heriot Watt University, Edinburgh EH14 4AS, UK, CBM Scrl, AREA Science Park, Basovizza, 34149 Trieste, Italy, Medical Genetics, Department of Biochemistry, Biophysics and General Pathology, Second University of Naples, 80138 Naples, Italy, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK and Center for Translational Genomics and Bioinformatics, San Raffaele Scientific Institute, Via Olgettina 58, 20132 Milano, Italy
| | - Marco De Simone
- Laboratory of Animal Physiology and Evolution, Stazione Zoologica Anton Dohrn, Villa Comunale, 80121 Naples, Italy, Centre for Rare Diseases and Personalised Medicine, School of Clinical and Experimental Medicine, College of Medical and Dental Sciences, University of Birmingham, Birmingham B15 2TT, UK, Institut de Biologie du Développement de Marseille Luminy, UMR 6216 CNRS/Université de la Méditerranée, F-13288 Marseille cedex 9, France, Centre de Recherche de Biochimie Macromoléculaire (CRBM), UMR5237 CNRS/Universités Montpellier 1, 2, 1919 route de Mende, F-34293 Montpellier cedex 5, France, Karlsruhe Institute of Technology (KIT), Institute of Toxicology and Genetics and University of Heidelberg, Hermann-von-Helmholtz-Platz 1, 76344 Eggenstein-Leopoldshafen, Germany, Telethon Institute of Genetics and Medicine, 80131 Naples, Italy, School of Engineering and Physical Sciences, Heriot Watt University, Edinburgh EH14 4AS, UK, CBM Scrl, AREA Science Park, Basovizza, 34149 Trieste, Italy, Medical Genetics, Department of Biochemistry, Biophysics and General Pathology, Second University of Naples, 80138 Naples, Italy, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK and Center for Translational Genomics and Bioinformatics, San Raffaele Scientific Institute, Via Olgettina 58, 20132 Milano, Italy
| | - Francesca Petrera
- Laboratory of Animal Physiology and Evolution, Stazione Zoologica Anton Dohrn, Villa Comunale, 80121 Naples, Italy, Centre for Rare Diseases and Personalised Medicine, School of Clinical and Experimental Medicine, College of Medical and Dental Sciences, University of Birmingham, Birmingham B15 2TT, UK, Institut de Biologie du Développement de Marseille Luminy, UMR 6216 CNRS/Université de la Méditerranée, F-13288 Marseille cedex 9, France, Centre de Recherche de Biochimie Macromoléculaire (CRBM), UMR5237 CNRS/Universités Montpellier 1, 2, 1919 route de Mende, F-34293 Montpellier cedex 5, France, Karlsruhe Institute of Technology (KIT), Institute of Toxicology and Genetics and University of Heidelberg, Hermann-von-Helmholtz-Platz 1, 76344 Eggenstein-Leopoldshafen, Germany, Telethon Institute of Genetics and Medicine, 80131 Naples, Italy, School of Engineering and Physical Sciences, Heriot Watt University, Edinburgh EH14 4AS, UK, CBM Scrl, AREA Science Park, Basovizza, 34149 Trieste, Italy, Medical Genetics, Department of Biochemistry, Biophysics and General Pathology, Second University of Naples, 80138 Naples, Italy, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK and Center for Translational Genomics and Bioinformatics, San Raffaele Scientific Institute, Via Olgettina 58, 20132 Milano, Italy
| | - Danilo Licastro
- Laboratory of Animal Physiology and Evolution, Stazione Zoologica Anton Dohrn, Villa Comunale, 80121 Naples, Italy, Centre for Rare Diseases and Personalised Medicine, School of Clinical and Experimental Medicine, College of Medical and Dental Sciences, University of Birmingham, Birmingham B15 2TT, UK, Institut de Biologie du Développement de Marseille Luminy, UMR 6216 CNRS/Université de la Méditerranée, F-13288 Marseille cedex 9, France, Centre de Recherche de Biochimie Macromoléculaire (CRBM), UMR5237 CNRS/Universités Montpellier 1, 2, 1919 route de Mende, F-34293 Montpellier cedex 5, France, Karlsruhe Institute of Technology (KIT), Institute of Toxicology and Genetics and University of Heidelberg, Hermann-von-Helmholtz-Platz 1, 76344 Eggenstein-Leopoldshafen, Germany, Telethon Institute of Genetics and Medicine, 80131 Naples, Italy, School of Engineering and Physical Sciences, Heriot Watt University, Edinburgh EH14 4AS, UK, CBM Scrl, AREA Science Park, Basovizza, 34149 Trieste, Italy, Medical Genetics, Department of Biochemistry, Biophysics and General Pathology, Second University of Naples, 80138 Naples, Italy, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK and Center for Translational Genomics and Bioinformatics, San Raffaele Scientific Institute, Via Olgettina 58, 20132 Milano, Italy
| | - Uwe Strähle
- Laboratory of Animal Physiology and Evolution, Stazione Zoologica Anton Dohrn, Villa Comunale, 80121 Naples, Italy, Centre for Rare Diseases and Personalised Medicine, School of Clinical and Experimental Medicine, College of Medical and Dental Sciences, University of Birmingham, Birmingham B15 2TT, UK, Institut de Biologie du Développement de Marseille Luminy, UMR 6216 CNRS/Université de la Méditerranée, F-13288 Marseille cedex 9, France, Centre de Recherche de Biochimie Macromoléculaire (CRBM), UMR5237 CNRS/Universités Montpellier 1, 2, 1919 route de Mende, F-34293 Montpellier cedex 5, France, Karlsruhe Institute of Technology (KIT), Institute of Toxicology and Genetics and University of Heidelberg, Hermann-von-Helmholtz-Platz 1, 76344 Eggenstein-Leopoldshafen, Germany, Telethon Institute of Genetics and Medicine, 80131 Naples, Italy, School of Engineering and Physical Sciences, Heriot Watt University, Edinburgh EH14 4AS, UK, CBM Scrl, AREA Science Park, Basovizza, 34149 Trieste, Italy, Medical Genetics, Department of Biochemistry, Biophysics and General Pathology, Second University of Naples, 80138 Naples, Italy, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK and Center for Translational Genomics and Bioinformatics, San Raffaele Scientific Institute, Via Olgettina 58, 20132 Milano, Italy
| | - Sandro Banfi
- Laboratory of Animal Physiology and Evolution, Stazione Zoologica Anton Dohrn, Villa Comunale, 80121 Naples, Italy, Centre for Rare Diseases and Personalised Medicine, School of Clinical and Experimental Medicine, College of Medical and Dental Sciences, University of Birmingham, Birmingham B15 2TT, UK, Institut de Biologie du Développement de Marseille Luminy, UMR 6216 CNRS/Université de la Méditerranée, F-13288 Marseille cedex 9, France, Centre de Recherche de Biochimie Macromoléculaire (CRBM), UMR5237 CNRS/Universités Montpellier 1, 2, 1919 route de Mende, F-34293 Montpellier cedex 5, France, Karlsruhe Institute of Technology (KIT), Institute of Toxicology and Genetics and University of Heidelberg, Hermann-von-Helmholtz-Platz 1, 76344 Eggenstein-Leopoldshafen, Germany, Telethon Institute of Genetics and Medicine, 80131 Naples, Italy, School of Engineering and Physical Sciences, Heriot Watt University, Edinburgh EH14 4AS, UK, CBM Scrl, AREA Science Park, Basovizza, 34149 Trieste, Italy, Medical Genetics, Department of Biochemistry, Biophysics and General Pathology, Second University of Naples, 80138 Naples, Italy, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK and Center for Translational Genomics and Bioinformatics, San Raffaele Scientific Institute, Via Olgettina 58, 20132 Milano, Italy
| | - Patrick Lemaire
- Laboratory of Animal Physiology and Evolution, Stazione Zoologica Anton Dohrn, Villa Comunale, 80121 Naples, Italy, Centre for Rare Diseases and Personalised Medicine, School of Clinical and Experimental Medicine, College of Medical and Dental Sciences, University of Birmingham, Birmingham B15 2TT, UK, Institut de Biologie du Développement de Marseille Luminy, UMR 6216 CNRS/Université de la Méditerranée, F-13288 Marseille cedex 9, France, Centre de Recherche de Biochimie Macromoléculaire (CRBM), UMR5237 CNRS/Universités Montpellier 1, 2, 1919 route de Mende, F-34293 Montpellier cedex 5, France, Karlsruhe Institute of Technology (KIT), Institute of Toxicology and Genetics and University of Heidelberg, Hermann-von-Helmholtz-Platz 1, 76344 Eggenstein-Leopoldshafen, Germany, Telethon Institute of Genetics and Medicine, 80131 Naples, Italy, School of Engineering and Physical Sciences, Heriot Watt University, Edinburgh EH14 4AS, UK, CBM Scrl, AREA Science Park, Basovizza, 34149 Trieste, Italy, Medical Genetics, Department of Biochemistry, Biophysics and General Pathology, Second University of Naples, 80138 Naples, Italy, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK and Center for Translational Genomics and Bioinformatics, San Raffaele Scientific Institute, Via Olgettina 58, 20132 Milano, Italy
| | - Ewan Birney
- Laboratory of Animal Physiology and Evolution, Stazione Zoologica Anton Dohrn, Villa Comunale, 80121 Naples, Italy, Centre for Rare Diseases and Personalised Medicine, School of Clinical and Experimental Medicine, College of Medical and Dental Sciences, University of Birmingham, Birmingham B15 2TT, UK, Institut de Biologie du Développement de Marseille Luminy, UMR 6216 CNRS/Université de la Méditerranée, F-13288 Marseille cedex 9, France, Centre de Recherche de Biochimie Macromoléculaire (CRBM), UMR5237 CNRS/Universités Montpellier 1, 2, 1919 route de Mende, F-34293 Montpellier cedex 5, France, Karlsruhe Institute of Technology (KIT), Institute of Toxicology and Genetics and University of Heidelberg, Hermann-von-Helmholtz-Platz 1, 76344 Eggenstein-Leopoldshafen, Germany, Telethon Institute of Genetics and Medicine, 80131 Naples, Italy, School of Engineering and Physical Sciences, Heriot Watt University, Edinburgh EH14 4AS, UK, CBM Scrl, AREA Science Park, Basovizza, 34149 Trieste, Italy, Medical Genetics, Department of Biochemistry, Biophysics and General Pathology, Second University of Naples, 80138 Naples, Italy, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK and Center for Translational Genomics and Bioinformatics, San Raffaele Scientific Institute, Via Olgettina 58, 20132 Milano, Italy
| | - Ferenc Müller
- Laboratory of Animal Physiology and Evolution, Stazione Zoologica Anton Dohrn, Villa Comunale, 80121 Naples, Italy, Centre for Rare Diseases and Personalised Medicine, School of Clinical and Experimental Medicine, College of Medical and Dental Sciences, University of Birmingham, Birmingham B15 2TT, UK, Institut de Biologie du Développement de Marseille Luminy, UMR 6216 CNRS/Université de la Méditerranée, F-13288 Marseille cedex 9, France, Centre de Recherche de Biochimie Macromoléculaire (CRBM), UMR5237 CNRS/Universités Montpellier 1, 2, 1919 route de Mende, F-34293 Montpellier cedex 5, France, Karlsruhe Institute of Technology (KIT), Institute of Toxicology and Genetics and University of Heidelberg, Hermann-von-Helmholtz-Platz 1, 76344 Eggenstein-Leopoldshafen, Germany, Telethon Institute of Genetics and Medicine, 80131 Naples, Italy, School of Engineering and Physical Sciences, Heriot Watt University, Edinburgh EH14 4AS, UK, CBM Scrl, AREA Science Park, Basovizza, 34149 Trieste, Italy, Medical Genetics, Department of Biochemistry, Biophysics and General Pathology, Second University of Naples, 80138 Naples, Italy, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK and Center for Translational Genomics and Bioinformatics, San Raffaele Scientific Institute, Via Olgettina 58, 20132 Milano, Italy
| | - Elia Stupka
- Laboratory of Animal Physiology and Evolution, Stazione Zoologica Anton Dohrn, Villa Comunale, 80121 Naples, Italy, Centre for Rare Diseases and Personalised Medicine, School of Clinical and Experimental Medicine, College of Medical and Dental Sciences, University of Birmingham, Birmingham B15 2TT, UK, Institut de Biologie du Développement de Marseille Luminy, UMR 6216 CNRS/Université de la Méditerranée, F-13288 Marseille cedex 9, France, Centre de Recherche de Biochimie Macromoléculaire (CRBM), UMR5237 CNRS/Universités Montpellier 1, 2, 1919 route de Mende, F-34293 Montpellier cedex 5, France, Karlsruhe Institute of Technology (KIT), Institute of Toxicology and Genetics and University of Heidelberg, Hermann-von-Helmholtz-Platz 1, 76344 Eggenstein-Leopoldshafen, Germany, Telethon Institute of Genetics and Medicine, 80131 Naples, Italy, School of Engineering and Physical Sciences, Heriot Watt University, Edinburgh EH14 4AS, UK, CBM Scrl, AREA Science Park, Basovizza, 34149 Trieste, Italy, Medical Genetics, Department of Biochemistry, Biophysics and General Pathology, Second University of Naples, 80138 Naples, Italy, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK and Center for Translational Genomics and Bioinformatics, San Raffaele Scientific Institute, Via Olgettina 58, 20132 Milano, Italy
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Lee Y, Collier TC, Sanford MR, Marsden CD, Fofana A, Cornel AJ, Lanzaro GC. Chromosome inversions, genomic differentiation and speciation in the African malaria mosquito Anopheles gambiae. PLoS One 2013; 8:e57887. [PMID: 23526957 PMCID: PMC3603965 DOI: 10.1371/journal.pone.0057887] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2012] [Accepted: 01/28/2013] [Indexed: 01/13/2023] Open
Abstract
The African malaria vector, Anopheles gambiae, is characterized by multiple polymorphic chromosomal inversions and has become widely studied as a system for exploring models of speciation. Near complete reproductive isolation between different inversion types, known as chromosomal forms, has led to the suggestion that A. gambiae is in early stages of speciation, with divergence evolving in the face of considerable gene flow. We compared the standard chromosomal arrangement (Savanna form) with genomes homozygous for j, b, c, and u inversions (Bamako form) in order to identify regions of genomic divergence with respect to inversion polymorphism. We found levels of divergence between the two sub-taxa within some of these inversions (2Rj and 2Rb), but at a level lower than expected and confined near the inversion breakpoints, consistent with a gene flux model. Unexpectedly, we found that the majority of diverged regions were located on the X chromosome, which contained half of all significantly diverged regions, with much of this divergence located within exons. This is surprising given that the Bamako and Savanna chromosomal forms are both within the S molecular form that is defined by a locus near centromere of X chromosome. Two X-linked genes (a heat shock protein and P450 encoding genes) involved in reproductive isolation between the M and S molecular forms of A. gambiae were also significantly diverged between the two chromosomal forms. These results suggest that genes mediating reproductive isolation are likely located on the X chromosome, as is thought to be the case for the M and S molecular forms. We conclude that genes located on the sex chromosome may be the major force driving speciation between these chromosomal forms of A. gambiae.
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Affiliation(s)
- Yoosook Lee
- Vector Genetics Laboratory, Department of Pathology, Microbiology and Immunology, School of Veterinary Medicine, University of California Davis, Davis, California, United States of America.
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Kanda M, Ikeda T, Fujiwara S. Identification of a retinoic acid-responsive neural enhancer in the Ciona intestinalis Hox1 gene. Dev Growth Differ 2013; 55:260-9. [PMID: 23302037 DOI: 10.1111/dgd.12033] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2012] [Revised: 12/06/2012] [Accepted: 12/06/2012] [Indexed: 12/16/2022]
Abstract
The Hox1 gene in the urochordate ascidian Ciona intestinalis (Ci-Hox1) is expressed in the nerve cord and epidermis. We identified a nerve cord enhancer in the second intron of Ci-Hox1, and demonstrated that retinoic acid (RA) plays a major role in activating this enhancer. The enhancer contained a putative retinoic acid-response element (RARE). Mutation of the RARE in the Ci-Hox1 nerve cord enhancer only partially abolished the enhancer activity. Genes encoding RA synthase and the RA receptor were knocked down using specific antisense morpholino oligos (MOs), and injection of embryos with these MOs resulted in the complete disappearance of epidermal expression of Ci-Hox1 and reduction of neural expression. However, nerve cord expression was not completely repressed. These results suggest that the nerve cord enhancer is activated by two partially redundant pathways; one RA-dependent and one RA-independent.
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Affiliation(s)
- Miyuki Kanda
- Department of Applied Science, Kochi University, 2-5-1 Akebono-cho, Kochi, 780-8520, Japan.
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Pascual-Anaya J, Adachi N, Alvarez S, Kuratani S, D'Aniello S, Garcia-Fernàndez J. Broken colinearity of the amphioxus Hox cluster. EvoDevo 2012. [PMID: 23198682 PMCID: PMC3534614 DOI: 10.1186/2041-9139-3-28] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
Background In most eumetazoans studied so far, Hox genes determine the identity of structures along the main body axis. They are usually linked in genomic clusters and, in the case of the vertebrate embryo, are expressed with spatial and temporal colinearity. Outside vertebrates, temporal colinearity has been reported in the cephalochordate amphioxus (the least derived living relative of the chordate ancestor) but only for anterior and central genes, namely Hox1 to Hox4 and Hox6. However, most of the Hox gene expression patterns in amphioxus have not been reported. To gain global insights into the evolution of Hox clusters in chordates, we investigated a more extended expression profile of amphioxus Hox genes. Results Here we report an extended expression profile of the European amphioxus Branchiostoma lanceolatum Hox genes and describe that all Hox genes, except Hox13, are expressed during development. Interestingly, we report the breaking of both spatial and temporal colinearity for at least Hox6 and Hox14, which thus have escaped from the classical Hox code concept. We show a previously unidentified Hox6 expression pattern and a faint expression for posterior Hox genes in structures such as the posterior mesoderm, notochord, and hindgut. Unexpectedly, we found that amphioxus Hox14 had the most divergent expression pattern. This gene is expressed in the anterior cerebral vesicle and pharyngeal endoderm. Amphioxus Hox14 expression represents the first report of Hox gene expression in the most anterior part of the central nervous system. Nevertheless, despite these divergent expression patterns, amphioxus Hox6 and Hox14 seem to be still regulated by retinoic acid. Conclusions Escape from colinearity by Hox genes is not unusual in either vertebrates or amphioxus and we suggest that those genes escaping from it are probably associated with the patterning of lineage-specific morphological traits, requiring the loss of those developmental constraints that kept them colinear.
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Affiliation(s)
- Juan Pascual-Anaya
- Departament de Genètica and Institut de Biomedicina (IBUB), University of Barcelona, Av, Diagonal, 643, Barcelona, 08028, Spain.
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Seritrakul P, Samarut E, Lama TTS, Gibert Y, Laudet V, Jackman WR. Retinoic acid expands the evolutionarily reduced dentition of zebrafish. FASEB J 2012; 26:5014-24. [PMID: 22942074 DOI: 10.1096/fj.12-209304] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Zebrafish lost anterior teeth during evolution but retain a posterior pharyngeal dentition that requires retinoic acid (RA) cell-cell signaling for its development. The purposes of this study were to test the sufficiency of RA to induce tooth development and to assess its role in evolution. We found that exposure of embryos to exogenous RA induces a dramatic anterior expansion of the number of pharyngeal teeth that later form and shifts anteriorly the expression patterns of genes normally expressed in the posterior tooth-forming region, such as pitx2 and dlx2b. After RA exposure, we also observed a correlation between cartilage malformations and ectopic tooth induction, as well as abnormal cranial neural crest marker gene expression. Additionally, we observed that the RA-induced zebrafish anterior teeth resemble in pattern and number the dentition of fish species that retain anterior pharyngeal teeth such as medaka but that medaka do not express the aldh1a2 RA-synthesizing enzyme in tooth-forming regions. We conclude that RA is sufficient to induce anterior ectopic tooth development in zebrafish where teeth were lost in evolution, potentially by altering neural crest cell development, and that changes in the location of RA synthesis correlate with evolutionary changes in vertebrate dentitions.
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Affiliation(s)
- Pawat Seritrakul
- Department of Biology, Bowdoin College, 6500 College Station, Brunswick, ME 04011, USA
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Comparative genomics of the Hedgehog loci in chordates and the origins of Shh regulatory novelties. Sci Rep 2012; 2:433. [PMID: 22666536 PMCID: PMC3364491 DOI: 10.1038/srep00433] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2012] [Accepted: 05/15/2012] [Indexed: 12/04/2022] Open
Abstract
The origin and evolution of the complex regulatory landscapes of some vertebrate developmental genes, often spanning hundreds of Kbp and including neighboring genes, remain poorly understood. The Sonic Hedgehog (Shh) genomic regulatory block (GRB) is one of the best functionally characterized examples, with several discrete enhancers reported within its introns, vast upstream gene-free region and neighboring genes (Lmbr1 and Rnf32). To investigate the origin and evolution of this GRB, we sequenced and characterized the Hedgehog (Hh) loci from three invertebrate chordate amphioxus species, which share several early expression domains with Shh. Using phylogenetic footprinting within and between chordate lineages, and reporter assays in zebrafish probing >30 Kbp of amphioxus Hh, we report large sequence and functional divergence between both groups. In addition, we show that the linkage of Shh to Lmbr1 and Rnf32, necessary for the unique gnatostomate-specific Shh limb expression, is a vertebrate novelty occurred between the two whole-genome duplications.
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Beaster-Jones L. Cis-regulation and conserved non-coding elements in amphioxus. Brief Funct Genomics 2012; 11:118-30. [DOI: 10.1093/bfgp/els006] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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Xu W, Yang N, Pan L, Fu J, Xue X. The expression of HoxB5 and its role in neonatal rats with chronic lung disease. Fetal Pediatr Pathol 2012; 31:11-20. [PMID: 22233504 DOI: 10.3109/15513815.2011.618867] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
The purpose of this investigation is to research the expression and effect of HoxB5 during pulmonary injury and to investigate the repairing ability of alveolar epithelial cells in such processes. Eighty neonatal rats were randomly divided into two groups: a group of high concentration of oxygen and the control group. The high oxygen group would inhale 85 to 90% oxygen and the control group would inhale air. The lung tissues on the 1(st), 3(rd), 7(th), 14(th), and 21(st) days would be obtained, in which immunohistochemical assay and Reverse Transcription Polymerase Chain Reaction (RT-PCR) would be performed to test the expressions of proteins and mRNAs of surfactant protein C (SPC) and AQP5. For expression of HoxB5 protein and its mRNA, immunohistochemical assay, western blot, in-situ hybridization, and RT-PCR would be run. The expression of SPC in the group of high concentration of oxygen was significantly reduced on day 3. Its expressions on day 14 and day 21 were significantly higher than those of the control group (p < 0.05). The expression of AQP5 in the group of high concentration of oxygen progressively decreased and such difference with the control group was significant (p < 0.05). The four experimental methods all showed the expression of HoxB5 in the group with high concentration of oxygen gradually decreased since day 7 (p < 0.05). High concentration of oxygen is damaging to alveolar epithelial cells. Although the number of type II alveolar epithelial cells (AECII) increases, its ability to differentiate and transform is significantly reduced and the reduced expression level of HoxB5 is possibly the reason for AECII to lose differentiation function to AECI.
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Affiliation(s)
- Wei Xu
- Department of Pediatrics, Shengjing Hospital, China Medical University, Shenyang, Liaoning, China
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41
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Lee JH, Silhavy JL, Lee JE, Al-Gazali L, Thomas S, Davis EE, Bielas SL, Hill KJ, Iannicelli M, Brancati F, Gabriel SB, Russ C, Logan CV, Sharif SM, Bennett CP, Abe M, Hildebrandt F, Diplas BH, Attié-Bitach T, Katsanis N, Rajab A, Koul R, Sztriha L, Waters ER, Ferro-Novick S, Woods CG, Johnson CA, Valente EM, Zaki MS, Gleeson JG. Evolutionarily assembled cis-regulatory module at a human ciliopathy locus. Science 2012; 335:966-9. [PMID: 22282472 DOI: 10.1126/science.1213506] [Citation(s) in RCA: 64] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Abstract
Neighboring genes are often coordinately expressed within cis-regulatory modules, but evidence that nonparalogous genes share functions in mammals is lacking. Here, we report that mutation of either TMEM138 or TMEM216 causes a phenotypically indistinguishable human ciliopathy, Joubert syndrome. Despite a lack of sequence homology, the genes are aligned in a head-to-tail configuration and joined by chromosomal rearrangement at the amphibian-to-reptile evolutionary transition. Expression of the two genes is mediated by a conserved regulatory element in the noncoding intergenic region. Coordinated expression is important for their interdependent cellular role in vesicular transport to primary cilia. Hence, during vertebrate evolution of genes involved in ciliogenesis, nonparalogous genes were arranged to a functional gene cluster with shared regulatory elements.
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Affiliation(s)
- Jeong Ho Lee
- Neurogenetics Laboratory, Howard Hughes Medical Institute (HHMI), Department of Neurosciences, University of California, San Diego, CA, USA
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Natale A, Sims C, Chiusano ML, Amoroso A, D'Aniello E, Fucci L, Krumlauf R, Branno M, Locascio A. Evolution of anterior Hox regulatory elements among chordates. BMC Evol Biol 2011; 11:330. [PMID: 22085760 PMCID: PMC3227721 DOI: 10.1186/1471-2148-11-330] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2011] [Accepted: 11/15/2011] [Indexed: 11/10/2022] Open
Abstract
Background The Hox family of transcription factors has a fundamental role in segmentation pathways and axial patterning of embryonic development and their clustered organization is linked with the regulatory mechanisms governing their coordinated expression along embryonic axes. Among chordates, of particular interest are the Hox paralogous genes in groups 1-4 since their expression is coupled to the control of regional identity in the anterior nervous system, where the highest structural diversity is observed. Results To investigate the degree of conservation in cis-regulatory components that form the basis of Hox expression in the anterior nervous system, we have used assays for transcriptional activity in ascidians and vertebrates to compare and contrast regulatory potential. We identified four regulatory sequences located near the CiHox1, CiHox2 and CiHox4 genes of the ascidian Ciona intestinalis which direct neural specific domains of expression. Using functional assays in Ciona and vertebrate embryos in combination with sequence analyses of enhancer fragments located in similar positions adjacent to Hox paralogy group genes, we compared the activity of these four Ciona cis-elements with a series of neural specific enhancers from the amphioxus Hox1-3 genes and from mouse Hox paralogous groups 1-4. Conclusions This analysis revealed that Kreisler and Krox20 dependent enhancers critical in segmental regulation of the hindbrain appear to be specific for the vertebrate lineage. In contrast, neural enhancers that function as Hox response elements through the action of Hox/Pbx binding motifs have been conserved during chordate evolution. The functional assays reveal that these Hox response cis-elements are recognized by the regulatory components of different and extant species. Together, our results indicate that during chordate evolution, cis-elements dependent upon Hox/Pbx regulatory complexes, are responsible for key aspects of segmental Hox expression in neural tissue and appeared with urochordates after cephalochordate divergence.
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Affiliation(s)
- Alfonso Natale
- Laboratory of Cellular and Developmental Biology, Stazione Zoologica Anton Dohrn, Villa Comunale, Naples, Italy
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43
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Bertrand S, Escriva H. Evolutionary crossroads in developmental biology: amphioxus. Development 2011; 138:4819-30. [DOI: 10.1242/dev.066720] [Citation(s) in RCA: 105] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
The phylogenetic position of amphioxus, together with its relatively simple and evolutionarily conserved morphology and genome structure, has led to its use as a model for studies of vertebrate evolution. In particular, the recent development of technical approaches, as well as access to the complete amphioxus genome sequence, has provided the community with tools with which to study the invertebrate-chordate to vertebrate transition. Here, we present this animal model, discussing its life cycle, the model species studied and the experimental techniques that it is amenable to. We also summarize the major findings made using amphioxus that have informed us about the evolution of vertebrate traits.
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Affiliation(s)
- Stephanie Bertrand
- CNRS UMR7232, UPMC Université Paris 06, Observatoire océanologique, F-66651 Banyuls-sur-Mer, France
| | - Hector Escriva
- CNRS UMR7232, UPMC Université Paris 06, Observatoire océanologique, F-66651 Banyuls-sur-Mer, France
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Kim ES, Kim GH, Kang ML, Kang YM, Kang KN, Hwang KC, Min BH, Kim JH, Kim MS. Potential induction of rat muscle-derived stem cells to neural-like cells by retinoic acid. J Tissue Eng Regen Med 2010; 5:410-4. [DOI: 10.1002/term.328] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2009] [Accepted: 04/27/2010] [Indexed: 12/29/2022]
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Theodosiou M, Laudet V, Schubert M. From carrot to clinic: an overview of the retinoic acid signaling pathway. Cell Mol Life Sci 2010; 67:1423-45. [PMID: 20140749 PMCID: PMC11115864 DOI: 10.1007/s00018-010-0268-z] [Citation(s) in RCA: 229] [Impact Index Per Article: 16.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2009] [Revised: 01/06/2010] [Accepted: 01/11/2010] [Indexed: 01/23/2023]
Abstract
Vitamin A is essential for the formation and maintenance of many body tissues. It is also important for embryonic growth and development and can act as a teratogen at critical periods of development. Retinoic acid (RA) is the biologically active form of vitamin A and its signaling is mediated by the RA and retinoid X receptors. In addition to its role as an important molecule during development, RA has also been implicated in clinical applications, both as a potential anti-tumor agent as well as for the treatment of skin diseases. This review presents an overview of how dietary retinoids are converted to RA, hence presenting the major players in RA metabolism and signaling, and highlights examples of treatment applications of retinoids. Moreover, we discuss the origin and diversification of the retinoid pathway, which are important factors for understanding the evolution of ligand-specificity among retinoid receptors.
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Affiliation(s)
- Maria Theodosiou
- Institut de Génomique Fonctionnelle de Lyon, Université de Lyon (Université Lyon 1, CNRS, INRA, Ecole Normale Supérieure de Lyon), 46 allée d'Italie, 69364 Lyon Cedex 07, France.
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46
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Retinoic acid signaling targets Hox genes during the amphioxus gastrula stage: Insights into early anterior–posterior patterning of the chordate body plan. Dev Biol 2010; 338:98-106. [DOI: 10.1016/j.ydbio.2009.11.016] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2009] [Revised: 11/06/2009] [Accepted: 11/06/2009] [Indexed: 01/08/2023]
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Yu JKS. The evolutionary origin of the vertebrate neural crest and its developmental gene regulatory network – insights from amphioxus. ZOOLOGY 2010; 113:1-9. [DOI: 10.1016/j.zool.2009.06.001] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2009] [Revised: 06/08/2009] [Accepted: 06/16/2009] [Indexed: 01/26/2023]
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Spitz F. Control of vertebrate Hox clusters by remote and global cis-acting regulatory sequences. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2010; 689:63-78. [PMID: 20795322 DOI: 10.1007/978-1-4419-6673-5_4] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Despite apparently shared structural organisation and functional roles, vertebrate Hox genes are controlled by regulatory mechanisms rather distinct from those of the prototypic Drosophila Antennapedia (ANT-C) and Bithorax (BX-C) Complexes. If individual regulatory modules have been shown to recapitulate specific Hox expression patterns, other experimental studies underscore that vertebrate Hox clusters are controlled in many of their functions in a global manner, through distinct mechanisms. We will discuss the different models that have been proposed to account for these global regulatory modes. In this context, the studies of the regulation of the HoxD complex during limb development highlighted the role of global regulatory elements and the different mechanisms associated to transform a structural organisation into distinct temporal and spatial expression domains. We will further discuss how these mechanisms may have benefited from the structure of the vertebrate homeotic clusters and reciprocally contribute to shape their evolution towards an increased level of organisation and compaction.
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Affiliation(s)
- François Spitz
- Developmental Biology Unit, European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117 Heidelberg, Germany.
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49
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Kanda M, Wada H, Fujiwara S. Epidermal expression of Hox1 is directly activated by retinoic acid in the Ciona intestinalis embryo. Dev Biol 2009; 335:454-63. [PMID: 19782671 DOI: 10.1016/j.ydbio.2009.09.027] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2009] [Revised: 09/01/2009] [Accepted: 09/18/2009] [Indexed: 11/30/2022]
Abstract
Hox genes play important roles in the specification of spatial identity during development of vertebrate embryos. Retinoic acid regulates the transcription of Hox genes in vertebrates. We identified an epidermal enhancer in the 5' flanking region of an ortholog of Hox1 (Ci-Hox1) in the ascidian Ciona intestinalis. This enhancer element drives the transcription of a lacZ reporter gene in the epidermis in the posterior trunk and the anterior tail region of tailbud-stage embryos. Inhibition of retinoic acid synthesis resulted in inactivation of the expression of the reporter gene. The enhancer contains a putative retinoic acid response element. When this element was mutagenized, the expression of the reporter gene disappeared from the epidermis. This sequence was also required for the response to exogenously administered retinoic acid. A heterodimeric nuclear receptor, consisting of the retinoic acid receptor and retinoid X receptor, bound to this sequence. These results indicate that retinoic acid directly activates the epidermal enhancer of Ci-Hox1. This is the first demonstration that retinoic acid is necessary for endogenous gene expression in ascidian embryos.
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Affiliation(s)
- Miyuki Kanda
- Department of Applied Science, Kochi University, Akebono-cho, Kochi-shi, Japan.
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50
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Bessa J, Tena JJ, de la Calle-Mustienes E, Fernández-Miñán A, Naranjo S, Fernández A, Montoliu L, Akalin A, Lenhard B, Casares F, Gómez-Skarmeta JL. Zebrafish enhancer detection (ZED) vector: A new tool to facilitate transgenesis and the functional analysis ofcis-regulatory regions in zebrafish. Dev Dyn 2009; 238:2409-17. [PMID: 19653328 DOI: 10.1002/dvdy.22051] [Citation(s) in RCA: 114] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Affiliation(s)
- José Bessa
- Centro Andaluz de Biología del Desarrollo, CSIC-Universidad Pablo de Olavide, Campus UPO, Seville, Spain.
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