1
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Pollex T, Marco-Ferreres R, Ciglar L, Ghavi-Helm Y, Rabinowitz A, Viales RR, Schaub C, Jankowski A, Girardot C, Furlong EEM. Chromatin gene-gene loops support the cross-regulation of genes with related function. Mol Cell 2024; 84:822-838.e8. [PMID: 38157845 DOI: 10.1016/j.molcel.2023.12.023] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2023] [Revised: 10/31/2023] [Accepted: 12/14/2023] [Indexed: 01/03/2024]
Abstract
Chromatin loops between gene pairs have been observed in diverse contexts in both flies and vertebrates. Combining high-resolution Capture-C, DNA fluorescence in situ hybridization, and genetic perturbations, we dissect the functional role of three loops between genes with related function during Drosophila embryogenesis. By mutating the loop anchor (but not the gene) or the gene (but not loop anchor), we disentangle loop formation and gene expression and show that the 3D proximity of paralogous gene loci supports their co-regulation. Breaking the loop leads to either an attenuation or enhancement of expression and perturbs their relative levels of expression and cross-regulation. Although many loops appear constitutive across embryogenesis, their function can change in different developmental contexts. Taken together, our results indicate that chromatin gene-gene loops act as architectural scaffolds that can be used in different ways in different contexts to fine-tune the coordinated expression of genes with related functions and sustain their cross-regulation.
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Affiliation(s)
- Tim Pollex
- European Molecular Biology Laboratory (EMBL), Genome Biology Unit, 69117 Heidelberg, Germany
| | - Raquel Marco-Ferreres
- European Molecular Biology Laboratory (EMBL), Genome Biology Unit, 69117 Heidelberg, Germany
| | - Lucia Ciglar
- European Molecular Biology Laboratory (EMBL), Genome Biology Unit, 69117 Heidelberg, Germany
| | - Yad Ghavi-Helm
- European Molecular Biology Laboratory (EMBL), Genome Biology Unit, 69117 Heidelberg, Germany
| | - Adam Rabinowitz
- European Molecular Biology Laboratory (EMBL), Genome Biology Unit, 69117 Heidelberg, Germany
| | | | - Christoph Schaub
- European Molecular Biology Laboratory (EMBL), Genome Biology Unit, 69117 Heidelberg, Germany
| | - Aleksander Jankowski
- European Molecular Biology Laboratory (EMBL), Genome Biology Unit, 69117 Heidelberg, Germany
| | - Charles Girardot
- European Molecular Biology Laboratory (EMBL), Genome Biology Unit, 69117 Heidelberg, Germany
| | - Eileen E M Furlong
- European Molecular Biology Laboratory (EMBL), Genome Biology Unit, 69117 Heidelberg, Germany.
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2
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Afzal Z, Lange JJ, Nolte C, McKinney S, Wood C, Paulson A, De Kumar B, Unruh J, Slaughter BD, Krumlauf R. Shared retinoic acid responsive enhancers coordinately regulate nascent transcription of Hoxb coding and non-coding RNAs in the developing mouse neural tube. Development 2023; 150:dev201259. [PMID: 37102683 PMCID: PMC10233718 DOI: 10.1242/dev.201259] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2022] [Accepted: 04/19/2023] [Indexed: 04/28/2023]
Abstract
Signaling pathways regulate the patterns of Hox gene expression that underlie their functions in the specification of axial identity. Little is known about the properties of cis-regulatory elements and underlying transcriptional mechanisms that integrate graded signaling inputs to coordinately control Hox expression. Here, we optimized a single molecule fluorescent in situ hybridization (smFISH) technique with probes spanning introns to evaluate how three shared retinoic acid response element (RARE)-dependent enhancers in the Hoxb cluster regulate patterns of nascent transcription in vivo at the level of single cells in wild-type and mutant embryos. We predominately detect nascent transcription of only a single Hoxb gene in each cell, with no evidence for simultaneous co-transcriptional coupling of all or specific subsets of genes. Single and/or compound RARE mutations indicate that each enhancer differentially impacts global and local patterns of nascent transcription, suggesting that selectivity and competitive interactions between these enhancers is important to robustly maintain the proper levels and patterns of nascent Hoxb transcription. This implies that rapid and dynamic regulatory interactions potentiate transcription of genes through combined inputs from these enhancers in coordinating the retinoic acid response.
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Affiliation(s)
- Zainab Afzal
- Stowers Institute for Medical Research, Kansas City, MO 64110, USA
- Anatomy and Cell Biology Department, Kansas University Medical Center, Kansas City, KS 66160, USA
| | - Jeffrey J. Lange
- Stowers Institute for Medical Research, Kansas City, MO 64110, USA
| | - Christof Nolte
- Stowers Institute for Medical Research, Kansas City, MO 64110, USA
| | - Sean McKinney
- Stowers Institute for Medical Research, Kansas City, MO 64110, USA
| | - Christopher Wood
- Stowers Institute for Medical Research, Kansas City, MO 64110, USA
| | - Ariel Paulson
- Stowers Institute for Medical Research, Kansas City, MO 64110, USA
| | - Bony De Kumar
- Stowers Institute for Medical Research, Kansas City, MO 64110, USA
| | - Jay Unruh
- Stowers Institute for Medical Research, Kansas City, MO 64110, USA
| | | | - Robb Krumlauf
- Stowers Institute for Medical Research, Kansas City, MO 64110, USA
- Anatomy and Cell Biology Department, Kansas University Medical Center, Kansas City, KS 66160, USA
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3
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Brent AE, Buchholtz EA, Mansfield JH. Evolutionary assembly and disassembly of the mammalian sternum. Curr Biol 2023; 33:197-205.e2. [PMID: 36563692 DOI: 10.1016/j.cub.2022.11.055] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2022] [Revised: 10/15/2022] [Accepted: 11/23/2022] [Indexed: 12/24/2022]
Abstract
Evolutionary transitions are frequently associated with novel anatomical structures,1 but the origins of the structures themselves are often poorly known. We use developmental, genetic, and paleontological data to demonstrate that the therian sternum was assembled from pre-existing elements. Imaging of the perinatal mouse reveals two paired sternal elements, both composed primarily of cells with lateral plate mesoderm origin. Location, articulations, and development identify them as homologs of the interclavicle and the sternal bands of synapsid outgroups. The interclavicle, not previously recognized in therians,2 articulates with the clavicle and differs from the sternal bands in both embryonic HOX expression and pattern of skeletal maturation. The sternal bands articulate with the ribs in two styles, most clearly differentiated by their association with sternebrae. Evolutionary trait mapping indicates that the interclavicle and sternal bands were independent elements throughout most of synapsid history. The differentiation of rib articulation styles and the subdivision of the sternal bands into sternebrae were key innovations likely associated with transitions in locomotor and respiratory mechanics.3,4 Fusion of the interclavicle and the anterior sternal bands to form a presternum anterior to the first sternebra was a historically recent innovation unique to therians. Subsequent disassembly of the radically reduced sternum of mysticete cetaceans was element specific, reflecting the constraints that conserved developmental programs exert on composite structures.
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Affiliation(s)
- Ava E Brent
- Department of Biology, Barnard College, Columbia University, 3009 Broadway, New York, NY 10027, USA
| | - Emily A Buchholtz
- Department of Biological Sciences, Wellesley College, 106 Central Street, Wellesley, MA 02481, USA.
| | - Jennifer H Mansfield
- Department of Biology, Barnard College, Columbia University, 3009 Broadway, New York, NY 10027, USA
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4
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Abstract
Hox genes encode evolutionarily conserved transcription factors that are essential for the proper development of bilaterian organisms. Hox genes are unique because they are spatially and temporally regulated during development in a manner that is dictated by their tightly linked genomic organization. Although their genetic function during embryonic development has been interrogated, less is known about how these transcription factors regulate downstream genes to direct morphogenetic events. Moreover, the continued expression and function of Hox genes at postnatal and adult stages highlights crucial roles for these genes throughout the life of an organism. Here, we provide an overview of Hox genes, highlighting their evolutionary history, their unique genomic organization and how this impacts the regulation of their expression, what is known about their protein structure, and their deployment in development and beyond.
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Affiliation(s)
- Katharine A. Hubert
- Program in Genetics, University of Wisconsin School of Medicine and Public Health, Madison, WI 53705, USA
- Department of Cell and Regenerative Biology, University of Wisconsin School of Medicine and Public Health, Madison, WI 53705, USA
| | - Deneen M. Wellik
- Department of Cell and Regenerative Biology, University of Wisconsin School of Medicine and Public Health, Madison, WI 53705, USA
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5
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Gaunt SJ. Seeking Sense in the Hox Gene Cluster. J Dev Biol 2022; 10:jdb10040048. [PMID: 36412642 PMCID: PMC9680502 DOI: 10.3390/jdb10040048] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2022] [Revised: 10/31/2022] [Accepted: 11/09/2022] [Indexed: 11/18/2022] Open
Abstract
The Hox gene cluster, responsible for patterning of the head-tail axis, is an ancestral feature of all bilaterally symmetrical animals (the Bilateria) that remains intact in a wide range of species. We can say that the Hox cluster evolved successfully only once since it is commonly the same in all groups, with labial-like genes at one end of the cluster expressed in the anterior embryo, and Abd-B-like genes at the other end of the cluster expressed posteriorly. This review attempts to make sense of the Hox gene cluster and to address the following questions. How did the Hox cluster form in the protostome-deuterostome last common ancestor, and why was this with a particular head-tail polarity? Why is gene clustering usually maintained? Why is there collinearity between the order of genes along the cluster and the positions of their expressions along the embryo? Why do the Hox gene expression domains overlap along the embryo? Why have vertebrates duplicated the Hox cluster? Why do Hox gene knockouts typically result in anterior homeotic transformations? How do animals adapt their Hox clusters to evolve new structural patterns along the head-tail axis?
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Affiliation(s)
- Stephen J Gaunt
- Department of Zoology, University of Cambridge, Downing Street, Cambridge CB2 3EJ, UK
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6
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Loker R, Mann RS. Divergent expression of paralogous genes by modification of shared enhancer activity through a promoter-proximal silencer. Curr Biol 2022; 32:3545-3555.e4. [PMID: 35853455 PMCID: PMC9398998 DOI: 10.1016/j.cub.2022.06.069] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2022] [Revised: 05/18/2022] [Accepted: 06/22/2022] [Indexed: 11/16/2022]
Abstract
The duplication of genes and their associated cis-regulatory elements, or enhancers, is a key contributor to genome evolution and biological complexity. Moreover, many paralogs, particularly tandem duplicates, are fixed for long periods of time under the control of shared enhancers. However, in most cases, the mechanism by which gene expression and function diverge following duplication is not known. Here, we dissect the regulation and function of the paralogous nubbin/pdm2 genes during wing development in Drosophila melanogaster. We show that these paralogs play a redundant role in the wing and that their expression relies on a single shared wing enhancer. However, the two genes differ in their ability to respond to this enhancer, with nub responding in all wing progenitor cells and pdm2 only in a small subset. This divergence is a result of a pdm2-specific silencer element at the pdm2 promoter that receives repressive input from the transcription factor Rotund. Repression through this silencer also depends on nub, allowing pdm2 to fully respond to the wing enhancer when nub expression is perturbed and functional compensation to occur. Thus, expression divergence downstream of a shared enhancer arises as a consequence of silencing the promoter of one paralog.
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Affiliation(s)
- Ryan Loker
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY, USA
| | - Richard S Mann
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY, USA; Department of Neuroscience, Department of Systems Biology, Mortimer B. Zuckerman Mind Brain Behavior Institute, Columbia University, New York, NY, USA.
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7
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Chen CH, Behringer RR. Transgenic human HOXB1-9 directs anterior-posterior axial skeleton pattern in Hoxb1-9 deficient mice. Differentiation 2022; 127:1-11. [DOI: 10.1016/j.diff.2022.07.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2022] [Accepted: 07/25/2022] [Indexed: 11/03/2022]
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8
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Transcriptional Regulation and Implications for Controlling Hox Gene Expression. J Dev Biol 2022; 10:jdb10010004. [PMID: 35076545 PMCID: PMC8788451 DOI: 10.3390/jdb10010004] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2021] [Revised: 01/04/2022] [Accepted: 01/06/2022] [Indexed: 02/06/2023] Open
Abstract
Hox genes play key roles in axial patterning and regulating the regional identity of cells and tissues in a wide variety of animals from invertebrates to vertebrates. Nested domains of Hox expression generate a combinatorial code that provides a molecular framework for specifying the properties of tissues along the A–P axis. Hence, it is important to understand the regulatory mechanisms that coordinately control the precise patterns of the transcription of clustered Hox genes required for their roles in development. New insights are emerging about the dynamics and molecular mechanisms governing transcriptional regulation, and there is interest in understanding how these may play a role in contributing to the regulation of the expression of the clustered Hox genes. In this review, we summarize some of the recent findings, ideas and emerging mechanisms underlying the regulation of transcription in general and consider how they may be relevant to understanding the transcriptional regulation of Hox genes.
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9
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OUP accepted manuscript. Stem Cells 2022; 40:175-189. [DOI: 10.1093/stmcls/sxab014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2021] [Accepted: 10/28/2021] [Indexed: 11/14/2022]
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10
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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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11
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The Hox protein conundrum: The "specifics" of DNA binding for Hox proteins and their partners. Dev Biol 2021; 477:284-292. [PMID: 34102167 PMCID: PMC8846413 DOI: 10.1016/j.ydbio.2021.06.002] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2020] [Revised: 06/01/2021] [Accepted: 06/02/2021] [Indexed: 11/25/2022]
Abstract
Homeotic genes (Hox genes) are homeodomain-transcription factors involved in conferring segmental identity along the anterior-posterior body axis. Molecular characterization of HOX protein function raises some interesting questions regarding the source of the binding specificity of the HOX proteins. How do HOX proteins regulate common and unique target specificity across space and time? This review attempts to summarize and interpret findings in this area, largely focused on results from in vitro and in vivo studies in Drosophila and mouse systems. Recent studies related to HOX protein binding specificity compel us to reconsider some of our current models for transcription factor-DNA interactions. It is crucial to study transcription factor binding by incorporating components of more complex, multi-protein interactions in concert with small changes in binding motifs that can significantly impact DNA binding specificity and subsequent alterations in gene expression. To incorporate the multiple elements that can determine HOX protein binding specificity, we propose a more integrative Cooperative Binding model.
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12
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Gonçalves CS, Le Boiteux E, Arnaud P, Costa BM. HOX gene cluster (de)regulation in brain: from neurodevelopment to malignant glial tumours. Cell Mol Life Sci 2020; 77:3797-3821. [PMID: 32239260 PMCID: PMC11105007 DOI: 10.1007/s00018-020-03508-9] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2019] [Revised: 03/10/2020] [Accepted: 03/17/2020] [Indexed: 12/19/2022]
Abstract
HOX genes encode a family of evolutionarily conserved homeodomain transcription factors that are crucial both during development and adult life. In humans, 39 HOX genes are arranged in four clusters (HOXA, B, C, and D) in chromosomes 7, 17, 12, and 2, respectively. During embryonic development, particular epigenetic states accompany their expression along the anterior-posterior body axis. This tightly regulated temporal-spatial expression pattern reflects their relative chromosomal localization, and is critical for normal embryonic brain development when HOX genes are mainly expressed in the hindbrain and mostly absent in the forebrain region. Epigenetic marks, mostly polycomb-associated, are dynamically regulated at HOX loci and regulatory regions to ensure the finely tuned HOX activation and repression, highlighting a crucial epigenetic plasticity necessary for homeostatic development. HOX genes are essentially absent in healthy adult brain, whereas they are detected in malignant brain tumours, namely gliomas, where HOX genes display critical roles by regulating several hallmarks of cancer. Here, we review the major mechanisms involved in HOX genes (de)regulation in the brain, from embryonic to adult stages, in physiological and oncologic conditions. We focus particularly on the emerging causes of HOX gene deregulation in glioma, as well as on their functional and clinical implications.
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Affiliation(s)
- Céline S Gonçalves
- Life and Health Sciences Research Institute (ICVS), School of Medicine, University of Minho, Campus de Gualtar, 4710-057, Braga, Portugal
- ICVS/3B's - PT Government Associate Laboratory, Braga/Guimarães, Portugal
| | - Elisa Le Boiteux
- Université Clermont Auvergne, CNRS, INSERM-iGReD, Clermont-Ferrand, France
| | - Philippe Arnaud
- Université Clermont Auvergne, CNRS, INSERM-iGReD, Clermont-Ferrand, France
| | - Bruno M Costa
- Life and Health Sciences Research Institute (ICVS), School of Medicine, University of Minho, Campus de Gualtar, 4710-057, Braga, Portugal.
- ICVS/3B's - PT Government Associate Laboratory, Braga/Guimarães, Portugal.
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13
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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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14
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Miller SW, Posakony JW. Disparate expression specificities coded by a shared Hox-C enhancer. eLife 2020; 9:39876. [PMID: 32342858 PMCID: PMC7188484 DOI: 10.7554/elife.39876] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2018] [Accepted: 04/09/2020] [Indexed: 12/13/2022] Open
Abstract
Can a single regulatory sequence be shared by two genes undergoing functional divergence? Here we describe a single promiscuous enhancer within the Drosophila Antennapedia Complex, EO053, that directs aspects of the expression of two adjacent genes, pb (a Hox2 ortholog) and zen2 (a divergent Hox3 paralog), with disparate spatial and temporal expression patterns. We were unable to separate the pb-like and zen2-like specificities within EO053, and we identify sequences affecting both expression patterns. Importantly, genomic deletion experiments demonstrate that EO053 cooperates with additional pb- and zen2-specific enhancers to regulate the mRNA expression of both genes. We examine sequence conservation of EO053 within the Schizophora, and show that patterns of synteny between the Hox2 and Hox3 orthologs in Arthropods are consistent with a shared regulatory relationship extending prior to the Hox3/zen divergence. Thus, EO053 represents an example of two genes having evolved disparate outputs while utilizing this shared regulatory region. Editorial note: This article has been through an editorial process in which the authors decide how to respond to the issues raised during peer review. The Reviewing Editor's assessment is that all the issues have been addressed (see decision letter).
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Affiliation(s)
- Steve W Miller
- Division of Biological Sciences, Section of Cell & Developmental Biology, University of California San Diego, La Jolla, United States
| | - James W Posakony
- Division of Biological Sciences, Section of Cell & Developmental Biology, University of California San Diego, La Jolla, United States
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15
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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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16
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Rodrigo G. Insights about collective decision-making at the genetic level. Biophys Rev 2019; 12:19-24. [PMID: 31845181 DOI: 10.1007/s12551-019-00608-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2019] [Accepted: 12/05/2019] [Indexed: 01/08/2023] Open
Abstract
By living in a collective, individuals can share and aggregate information to base their decisions on the many rather than on the one, thereby increasing accuracy. But a collective can also be defined at the molecular level. In the following, we reason that genes, by working collectively, share fundamental features with social organisms, which ends, without invoking cognition, in wiser responses. For that, we compile into a single picture the terms redundancy, stochastic resonance, intrinsic and extrinsic noise, and cross-regulation.
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Affiliation(s)
- Guillermo Rodrigo
- Institute for Integrative Systems Biology (I2SysBio), CSIC - U. Valencia, 46980, Paterna, Spain.
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17
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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: 28] [Impact Index Per Article: 5.6] [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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18
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Frank D, Sela-Donenfeld D. Hindbrain induction and patterning during early vertebrate development. Cell Mol Life Sci 2019; 76:941-960. [PMID: 30519881 PMCID: PMC11105337 DOI: 10.1007/s00018-018-2974-x] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2018] [Revised: 11/19/2018] [Accepted: 11/21/2018] [Indexed: 12/28/2022]
Abstract
The hindbrain is a key relay hub of the central nervous system (CNS), linking the bilaterally symmetric half-sides of lower and upper CNS centers via an extensive network of neural pathways. Dedicated neural assemblies within the hindbrain control many physiological processes, including respiration, blood pressure, motor coordination and different sensations. During early development, the hindbrain forms metameric segmented units known as rhombomeres along the antero-posterior (AP) axis of the nervous system. These compartmentalized units are highly conserved during vertebrate evolution and act as the template for adult brainstem structure and function. TALE and HOX homeodomain family transcription factors play a key role in the initial induction of the hindbrain and its specification into rhombomeric cell fate identities along the AP axis. Signaling pathways, such as canonical-Wnt, FGF and retinoic acid, play multiple roles to initially induce the hindbrain and regulate Hox gene-family expression to control rhombomeric identity. Additional transcription factors including Krox20, Kreisler and others act both upstream and downstream to Hox genes, modulating their expression and protein activity. In this review, we will examine the earliest embryonic signaling pathways that induce the hindbrain and subsequent rhombomeric segmentation via Hox and other gene expression. We will examine how these signaling pathways and transcription factors interact to activate downstream targets that organize the segmented AP pattern of the embryonic vertebrate hindbrain.
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Affiliation(s)
- Dale Frank
- Department of Biochemistry, Faculty of Medicine, The Rappaport Family Institute for Research in the Medical Sciences, Technion-Israel Institute of Technology, 31096, Haifa, Israel.
| | - Dalit Sela-Donenfeld
- Koret School of Veterinary Medicine, The Robert H Smith Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, 76100, Rehovot, Israel.
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19
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Abstract
Collinear regulation of Hox genes in space and time has been an outstanding question ever since the initial work of Ed Lewis in 1978. Here we discuss recent advances in our understanding of this phenomenon in relation to novel concepts associated with large-scale regulation and chromatin structure during the development of both axial and limb patterns. We further discuss how this sequential transcriptional activation marks embryonic stem cell-like axial progenitors in mammals and, consequently, how a temporal genetic system is further translated into spatial coordinates via the fate of these progenitors. In this context, we argue the benefit and necessity of implementing this unique mechanism as well as the difficulty in evolving an alternative strategy to deliver this critical positional information.
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Affiliation(s)
- Jacqueline Deschamps
- Hubrecht Institute, University Medical Center Utrecht, 3584 CT Utrecht, the Netherlands
| | - Denis Duboule
- School of Life Sciences, Ecole Polytechnique Fédérale, Lausanne, 1015 Lausanne, Switzerland.,Department of Genetics and Evolution, University of Geneva, 1211 Geneva 4, Switzerland
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20
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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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Laganà AS, Vitale SG, Salmeri FM, Triolo O, Ban Frangež H, Vrtačnik-Bokal E, Stojanovska L, Apostolopoulos V, Granese R, Sofo V. Unus pro omnibus, omnes pro uno: A novel, evidence-based, unifying theory for the pathogenesis of endometriosis. Med Hypotheses 2017; 103:10-20. [DOI: 10.1016/j.mehy.2017.03.032] [Citation(s) in RCA: 131] [Impact Index Per Article: 18.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2016] [Accepted: 03/21/2017] [Indexed: 01/17/2023]
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Sagner A, Briscoe J. Morphogen interpretation: concentration, time, competence, and signaling dynamics. WILEY INTERDISCIPLINARY REVIEWS-DEVELOPMENTAL BIOLOGY 2017; 6. [PMID: 28319331 PMCID: PMC5516147 DOI: 10.1002/wdev.271] [Citation(s) in RCA: 79] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/18/2016] [Revised: 01/22/2017] [Accepted: 02/10/2017] [Indexed: 12/14/2022]
Abstract
Tissue patterning during animal development is orchestrated by a handful of inductive signals. Most of these developmental cues act as morphogens, meaning they are locally produced secreted molecules that act at a distance to govern tissue patterning. The iterative use of the same signaling molecules in different developmental contexts demands that signal interpretation occurs in a highly context‐dependent manner. Hence the interpretation of signal depends on the specific competence of the receiving cells. Moreover, it has become clear that the differential interpretation of morphogens depends not only on the level of signaling but also the signaling dynamics, particularly the duration of signaling. In this review, we outline molecular mechanisms proposed in recent studies that explain how the response to morphogens is determined by differential competence, pathway intrinsic feedback, and the interpretation of signaling dynamics by gene regulatory networks. WIREs Dev Biol 2017, 6:e271. doi: 10.1002/wdev.271 For further resources related to this article, please visit the WIREs website.
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McGuigan AP, Javaherian S. Tissue Patterning: Translating Design Principles from In Vivo to In Vitro. Annu Rev Biomed Eng 2016; 18:1-24. [DOI: 10.1146/annurev-bioeng-083115-032943] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Alison P. McGuigan
- Department of Chemical Engineering and Applied Chemistry and
- Institute of Biomaterials and Biomedical Engineering, University of Toronto, Toronto, Ontario M5S 3E5, Canada;
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Böhmer C, Rauhut OWM, Wörheide G. New insights into the vertebral Hox code of archosaurs. Evol Dev 2016; 17:258-69. [PMID: 26372060 DOI: 10.1111/ede.12136] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Variation in axial formulae (i.e., number and identity of vertebrae) is an important feature in the evolution of vertebrates. Vertebrae at different axial positions exhibit a region-specific morphology. Key determinants for the establishment of particular vertebral shapes are the highly conserved Hox genes. Here, we analyzed Hox gene expression in the presacral vertebral column in the Nile crocodile in order to complement and extend a previous examination in the alligator and thus establish a Hox code for the axial skeleton of crocodilians in general. The newly determined expression of HoxA-4, C-5, B-7, and B-8 all revealed a crocodilian-specific pattern. HoxA-4 and HoxC-5 characterize cervical morphologies and the latter furthermore is associated with the position of the forelimb relative to the axial skeleton. HoxB-7 and HoxB-8 map exclusively to the dorsal vertebral region. The resulting expression patterns of these two Hox genes is the first description of their exact expression in the archosaurian embryo. Our comparative analyses of the Hox code in several amniote taxa provide new evidence that evolutionary differences in the axial skeleton correspond to changes in Hox gene expression domains. We detect two general processes: (i) expansion of a Hox gene's expression domain as well as (ii) a shift of gene expression. We infer that the ancestral archosaur Hox code may have resembled that of the crocodile. In association with the evolution of morphological traits, it may have been modified to patterns that can be observed in birds.
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Affiliation(s)
- Christine Böhmer
- Department für Geo- und Umweltwissenschaften & GeoBio-Center, Ludwig-Maximilians-Universität München, Richard-Wagner-Str. 10, 80333 München, Germany.,SNSB - Bayerische Staatssammlung für Paläontologie und Geologie, Richard-Wagner-Str. 10, 80333 München, Germany
| | - Oliver W M Rauhut
- Department für Geo- und Umweltwissenschaften & GeoBio-Center, Ludwig-Maximilians-Universität München, Richard-Wagner-Str. 10, 80333 München, Germany.,SNSB - Bayerische Staatssammlung für Paläontologie und Geologie, Richard-Wagner-Str. 10, 80333 München, Germany
| | - Gert Wörheide
- Department für Geo- und Umweltwissenschaften & GeoBio-Center, Ludwig-Maximilians-Universität München, Richard-Wagner-Str. 10, 80333 München, Germany.,SNSB - Bayerische Staatssammlung für Paläontologie und Geologie, Richard-Wagner-Str. 10, 80333 München, Germany
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Merabet S, Mann RS. To Be Specific or Not: The Critical Relationship Between Hox And TALE Proteins. Trends Genet 2016; 32:334-347. [PMID: 27066866 DOI: 10.1016/j.tig.2016.03.004] [Citation(s) in RCA: 95] [Impact Index Per Article: 11.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2016] [Revised: 03/09/2016] [Accepted: 03/10/2016] [Indexed: 10/22/2022]
Abstract
Hox proteins are key regulatory transcription factors that act in different tissues of the embryo to provide specific spatial and temporal coordinates to each cell. These patterning functions often depend on the presence of the TALE-homeodomain class cofactors, which form cooperative DNA-binding complexes with all Hox proteins. How this family of cofactors contributes to the highly diverse and specific functions of Hox proteins in vivo remains an important unsolved question. We review here the most recent advances in understanding the molecular mechanisms underlying Hox-TALE function. In particular, we discuss the role of DNA shape, DNA-binding affinity, and protein-protein interaction flexibility in dictating Hox-TALE specificity. We propose several models to explain how these mechanisms are integrated with each other in the context of the many distinct functions that Hox and TALE factors carry out in vivo.
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Affiliation(s)
- Samir Merabet
- Institut de Génomique Fonctionnelle de Lyon, Centre National de Recherche Scientifique, Ecole Normale Supérieure de Lyon, France.
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26
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Hoxa cluster genes determine the proliferative activity of adult mouse hematopoietic stem and progenitor cells. Blood 2016; 127:87-90. [DOI: 10.1182/blood-2015-02-626390] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2015] [Accepted: 10/26/2015] [Indexed: 11/20/2022] Open
Abstract
Key Points
Deletion of Hoxa genes reduces the engraftment potential of adult hematopoietic stem cells. Ectopic overexpression of Hoxa9 partially restores Hoxa−/− hematopoietic stem cell activity.
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Comelli P, Glowa D, Chandler JW, Werr W. Founder-cell-specific transcription of the DORNRÖSCHEN-LIKE promoter and integration of the auxin response. JOURNAL OF EXPERIMENTAL BOTANY 2016; 67:143-155. [PMID: 26428063 DOI: 10.1093/jxb/erv442] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
Transcription of the DORNRÖSCHEN (DRNL) promoter marks lateral-organ founder cells throughout Arabidopsis development, from cotyledons to flowers or floral organs. In the inflorescence apex, DRNL::GFP depicts incipient floral phyllotaxy, and organs in the four floral whorls are differentially prepatterned: the sepals unidirectionally along an abaxial-adaxial axis, the four petals and two lateral stamens in two putative morphogenetic fields, and the medial stamens subsequently in a ring-shaped domain, before two groups of carpel founder cells are specified. The dynamic DRNL transcription pattern is controlled by three enhancer elements, which redundantly and synergistically control qualitative or quantitative aspects of expression, and differentially integrate the auxin response in Arabidopsis inflorescence and floral meristems. The high sequence conservation of all three enhancer elements among the Brassicaceae is striking, which suggests that densely packed cis-regulatory elements are conserved to recruit multiple transcription factors, including auxin response factors, into higher-order enhanceosome complexes. The spatial organization of the enhancers is also conserved, by a microsynteny that extends beyond the Brassicaceae, which relates to enhancer sharing, as the distal element En1 bidirectionally serves DRNL and the upstream At1g24600 gene; the genes are transcribed in opposite directions and possibly comprise a conserved functional chromatin domain.
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Affiliation(s)
- Petra Comelli
- Institute of Developmental Biology, Biocenter Cologne, University of Cologne, Zuelpicher Str. 47b, 50674 Cologne, Germany
| | - Dorothea Glowa
- Institute of Developmental Biology, Biocenter Cologne, University of Cologne, Zuelpicher Str. 47b, 50674 Cologne, Germany
| | - John W Chandler
- Institute of Developmental Biology, Biocenter Cologne, University of Cologne, Zuelpicher Str. 47b, 50674 Cologne, Germany
| | - Wolfgang Werr
- Institute of Developmental Biology, Biocenter Cologne, University of Cologne, Zuelpicher Str. 47b, 50674 Cologne, Germany
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29
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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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Housden BE, Perrimon N. Spatial and temporal organization of signaling pathways. Trends Biochem Sci 2014; 39:457-64. [PMID: 25155749 DOI: 10.1016/j.tibs.2014.07.008] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2014] [Revised: 07/23/2014] [Accepted: 07/24/2014] [Indexed: 12/14/2022]
Abstract
The development and maintenance of the many different cell types in metazoan organisms requires robust and diverse intercellular communication mechanisms. Relatively few such signaling pathways have been identified, leading to the question of how such a broad diversity of output is generated from relatively simple signals. Recent studies have revealed complex mechanisms integrating temporal and spatial information to generate diversity in signaling pathway output. We review some general principles of signaling pathways, focusing on transcriptional outputs in Drosophila. We consider the role of spatial and temporal aspects of different transduction pathways and then discuss how recently developed tools and approaches are helping to dissect the complex mechanisms linking pathway stimulation to output.
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Affiliation(s)
| | - Norbert Perrimon
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA; Howard Hughes Medical Institute, Harvard Medical School, Boston, MA 02115, USA.
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Prin F, Serpente P, Itasaki N, Gould AP. Hox proteins drive cell segregation and non-autonomous apical remodelling during hindbrain segmentation. Development 2014; 141:1492-502. [PMID: 24574009 PMCID: PMC3957373 DOI: 10.1242/dev.098954] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2013] [Accepted: 01/22/2014] [Indexed: 01/26/2023]
Abstract
Hox genes encode a conserved family of homeodomain transcription factors regulating development along the major body axis. During embryogenesis, Hox proteins are expressed in segment-specific patterns and control numerous different segment-specific cell fates. It has been unclear, however, whether Hox proteins drive the epithelial cell segregation mechanism that is thought to initiate the segmentation process. Here, we investigate the role of vertebrate Hox proteins during the partitioning of the developing hindbrain into lineage-restricted units called rhombomeres. Loss-of-function mutants and ectopic expression assays reveal that Hoxb4 and its paralogue Hoxd4 are necessary and sufficient for cell segregation, and for the most caudal rhombomere boundary (r6/r7). Hox4 proteins regulate Eph/ephrins and other cell-surface proteins, and can function in a non-cell-autonomous manner to induce apical cell enlargement on both sides of their expression border. Similarly, other Hox proteins expressed at more rostral rhombomere interfaces can also regulate Eph/ephrins, induce apical remodelling and drive cell segregation in ectopic expression assays. However, Krox20, a key segmentation factor expressed in odd rhombomeres (r3 and r5), can largely override Hox proteins at the level of regulation of a cell surface target, Epha4. This study suggests that most, if not all, Hox proteins share a common potential to induce cell segregation but in some contexts this is masked or modulated by other transcription factors.
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Affiliation(s)
- Fabrice Prin
- Division of Physiology and Metabolism, Medical Research Council, National Institute for Medical Research, The Ridgeway, Mill Hill, London, NW7 1AA, UK
| | - Patricia Serpente
- Division of Physiology and Metabolism, Medical Research Council, National Institute for Medical Research, The Ridgeway, Mill Hill, London, NW7 1AA, UK
| | - Nobue Itasaki
- Division of Developmental Neurobiology, Medical Research Council, National Institute for Medical Research, The Ridgeway, Mill Hill, London, NW7 1AA, UK
| | - Alex P. Gould
- Division of Physiology and Metabolism, Medical Research Council, National Institute for Medical Research, The Ridgeway, Mill Hill, London, NW7 1AA, UK
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Homeotic gene regulation: a paradigm for epigenetic mechanisms underlying organismal development. Subcell Biochem 2014; 61:177-207. [PMID: 23150252 DOI: 10.1007/978-94-007-4525-4_9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
The organization of eukaryotic genome into chromatin within the nucleus eventually dictates the cell type specific expression pattern of genes. This higher order of chromatin organization is established during development and dynamically maintained throughout the life span. Developmental mechanisms are conserved in bilaterians and hence they have body plan in common, which is achieved by regulatory networks controlling cell type specific gene expression. Homeotic genes are conserved in metazoans and are crucial for animal development as they specify cell type identity along the anterior-posterior body axis. Hox genes are the best studied in the context of epigenetic regulation that has led to significant understanding of the organismal development. Epigenome specific regulation is brought about by conserved chromatin modulating factors like PcG/trxG proteins during development and differentiation. Here we discuss the conserved epigenetic mechanisms relevant to homeotic gene regulation in metazoans.
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Ahn Y, Mullan HE, Krumlauf R. Long-range regulation by shared retinoic acid response elements modulates dynamic expression of posterior Hoxb genes in CNS development. Dev Biol 2014; 388:134-44. [PMID: 24525295 DOI: 10.1016/j.ydbio.2014.01.027] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2013] [Revised: 01/13/2014] [Accepted: 01/31/2014] [Indexed: 10/25/2022]
Abstract
Retinoic acid (RA) signaling plays an important role in determining the anterior boundary of Hox gene expression in the neural tube during embryogenesis. In particular, RA signaling is implicated in a rostral expansion of the neural expression domain of 5׳ Hoxb genes (Hoxb9-Hoxb5) in mice. However, underlying mechanisms for this gene regulation have remained elusive due to the lack of RA responsive element (RARE) in the 5׳ half of the HoxB cluster. To identify cis-regulatory elements required for the rostral expansion, we developed a recombineering technology to serially label multiple genes with different reporters in a single bacterial artificial chromosome (BAC) vector containing the mouse HoxB cluster. This allowed us to simultaneously monitor the expression of multiple genes. In contrast to plasmid-based reporters, transgenic BAC reporters faithfully recapitulated endogenous gene expression patterns of the Hoxb genes including the rostral expansion. Combined inactivation of two RAREs, DE-RARE and ENE-RARE, in the BAC completely abolished the rostral expansion of the 5׳ Hoxb genes. Knock-out of endogenous DE-RARE lead to significantly reduced expression of multiple Hoxb genes and attenuated Hox gene response to exogenous RA treatment in utero. Regulatory potential of DE-RARE was further demonstrated by its ability to anteriorize 5׳ Hoxa gene expression in the neural tube when inserted into a HoxA BAC reporter. Our data demonstrate that multiple RAREs cooperate to remotely regulate 5׳ Hoxb genes during CNS development, providing a new insight into the mechanisms for gene regulation within the Hox clusters.
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Affiliation(s)
- Youngwook Ahn
- Stowers Institute for Medical Research, Kansas City, MO 64110, USA
| | - Hillary E Mullan
- Stowers Institute for Medical Research, Kansas City, MO 64110, 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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Longobardi E, Penkov D, Mateos D, De Florian G, Torres M, Blasi F. Biochemistry of the tale transcription factors PREP, MEIS, and PBX in vertebrates. Dev Dyn 2014; 243:59-75. [PMID: 23873833 PMCID: PMC4232920 DOI: 10.1002/dvdy.24016] [Citation(s) in RCA: 103] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2013] [Revised: 06/19/2013] [Accepted: 07/05/2013] [Indexed: 12/22/2022] Open
Abstract
TALE (three amino acids loop extension) homeodomain transcription factors are required in various steps of embryo development, in many adult physiological functions, and are involved in important pathologies. This review focuses on the PREP, MEIS, and PBX sub-families of TALE factors and aims at giving information on their biochemical properties, i.e., structure, interactors, and interaction surfaces. Members of the three sets of protein form dimers in which the common partner is PBX but they can also directly interact with other proteins forming higher-order complexes, in particular HOX. Finally, recent advances in determining the genome-wide DNA-binding sites of PREP1, MEIS1, and PBX1, and their partial correspondence with the binding sites of some HOX proteins, are reviewed. These studies have generated a few general rules that can be applied to all members of the three gene families. PREP and MEIS recognize slightly different consensus sequences: PREP prefers to bind to promoters and to have PBX as a DNA-binding partner; MEIS prefers HOX as partner, and both PREP and MEIS drive PBX to their own binding sites. This outlines the clear individuality of the PREP and MEIS proteins, the former mostly devoted to basic cellular functions, the latter more to developmental functions.
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Affiliation(s)
- E Longobardi
- Fondazione Istituto FIRC di Oncologia Molecolare (IFOM), Milano, Italy
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Schulte D, Frank D. TALE transcription factors during early development of the vertebrate brain and eye. Dev Dyn 2013; 243:99-116. [DOI: 10.1002/dvdy.24030] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2013] [Revised: 07/11/2013] [Accepted: 07/13/2013] [Indexed: 12/25/2022] Open
Affiliation(s)
- Dorothea Schulte
- Institute of Neurology (Edinger Institute); University Hospital Frankfurt, J.W. Goethe University; Frankfurt Germany
| | - Dale Frank
- Department of Biochemistry; The Rappaport Family Institute for Research in the Medical Sciences, Faculty of Medicine, Technion-Israel Institute of Technology; Haifa Israel
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Soshnikova N. Hox genes regulation in vertebrates. Dev Dyn 2013; 243:49-58. [PMID: 23832853 DOI: 10.1002/dvdy.24014] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2013] [Revised: 06/30/2013] [Accepted: 07/01/2013] [Indexed: 12/16/2022] Open
Abstract
Hox genes encode transcription factors defining cellular identities along the major and secondary body axes. Their coordinated expression in both space and time is critical for embryonic patterning. Accordingly, Hox genes transcription is tightly controlled at multiple levels, and involves an intricate combination of local and long-range cis-regulatory elements. Recent studies revealed that in addition to transcription factors, dynamic patterns of histone marks and higher-order chromatin structure are important determinants of Hox gene regulation. Furthermore, the emerging picture suggests an involvement of various species of non-coding RNA in targeting activating and repressive complexes to Hox clusters. I review these recent developments and discuss their relevance to the control of Hox gene expression in vivo, as well as to our understanding of transcriptional regulatory mechanisms.
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Drummond DL, Cheng CS, Selland LG, Hocking JC, Prichard LB, Waskiewicz AJ. The role of Zic transcription factors in regulating hindbrain retinoic acid signaling. BMC DEVELOPMENTAL BIOLOGY 2013; 13:31. [PMID: 23937294 PMCID: PMC3751700 DOI: 10.1186/1471-213x-13-31] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/15/2013] [Accepted: 08/05/2013] [Indexed: 01/05/2023]
Abstract
Background The reiterated architecture of cranial motor neurons aligns with the segmented structure of the embryonic vertebrate hindbrain. Anterior-posterior identity of cranial motor neurons depends, in part, on retinoic acid signaling levels. The early vertebrate embryo maintains a balance between retinoic acid synthetic and degradative zones on the basis of reciprocal expression domains of the retinoic acid synthesis gene aldhehyde dehydrogenase 1a2 (aldh1a2) posteriorly and the oxidative gene cytochrome p450 type 26a1 (cyp26a1) in the forebrain, midbrain, and anterior hindbrain. Results This manuscript investigates the role of zinc finger of the cerebellum (zic) transcription factors in regulating levels of retinoic acid and differentiation of cranial motor neurons. Depletion of zebrafish Zic2a and Zic2b results in a strong downregulation of aldh1a2 expression and a concomitant reduction in activity of a retinoid-dependent transgene. The vagal motor neuron phenotype caused by loss of Zic2a/2b mimics a depletion of Aldh1a2 and is rescued by exogenously supplied retinoic acid. Conclusion Zic transcription factors function in patterning hindbrain motor neurons through their regulation of embryonic retinoic acid signaling.
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Affiliation(s)
- Danna L Drummond
- Department of Biological Sciences, University of Alberta, CW405, Edmonton, AB T6G 2E9, Canada
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Penkov D, Mateos San Martín D, Fernandez-Díaz LC, Rosselló CA, Torroja C, Sánchez-Cabo F, Warnatz HJ, Sultan M, Yaspo ML, Gabrieli A, Tkachuk V, Brendolan A, Blasi F, Torres M. Analysis of the DNA-binding profile and function of TALE homeoproteins reveals their specialization and specific interactions with Hox genes/proteins. Cell Rep 2013; 3:1321-33. [PMID: 23602564 DOI: 10.1016/j.celrep.2013.03.029] [Citation(s) in RCA: 99] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2012] [Revised: 02/19/2013] [Accepted: 03/20/2013] [Indexed: 11/28/2022] Open
Abstract
The interactions of Meis, Prep, and Pbx1 TALE homeoproteins with Hox proteins are essential for development and disease. Although Meis and Prep behave similarly in vitro, their in vivo activities remain largely unexplored. We show that Prep and Meis interact with largely independent sets of genomic sites and select different DNA-binding sequences, Prep associating mostly with promoters and housekeeping genes and Meis with promoter-remote regions and developmental genes. Hox target sequences associate strongly with Meis but not with Prep binding sites, while Pbx1 cooperates with both Prep and Meis. Accordingly, Meis1 shows strong genetic interaction with Pbx1 but not with Prep1. Meis1 and Prep1 nonetheless coregulate a subset of genes, predominantly through opposing effects. Notably, the TALE homeoprotein binding profile subdivides Hox clusters into two domains differentially regulated by Meis1 and Prep1. During evolution, Meis and Prep thus specialized their interactions but maintained significant regulatory coordination.
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Affiliation(s)
- Dmitry Penkov
- Foundation FIRC Institute of Molecular Oncology at the IFOM-IEO Campus, via Adamello 16, 20139 Milan, Italy
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Scmh1 has E3 ubiquitin ligase activity for geminin and histone H2A and regulates geminin stability directly or indirectly via transcriptional repression of Hoxa9 and Hoxb4. Mol Cell Biol 2012. [PMID: 23207902 DOI: 10.1128/mcb.00974-12] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
Polycomb-group (PcG) complex 1 acts as an E3 ubiquitin ligase both for histone H2A to silence transcription and for geminin to regulate its stability. Scmh1 is a substoichiometric component of PcG complex 1 that provides the complex with an interaction domain for geminin. Scmh1 is unstable and regulated through the ubiquitin-proteasome system, but its molecular roles are unknown, so we generated Scmh1-deficient mice to elucidate its function. Loss of Scmh1 caused derepression of Hoxb4 and Hoxa9, direct targets of PcG complex 1-mediated transcriptional silencing in hematopoietic cells. Double knockdown of Hoxb4 and Hoxa9 or transduction of a dominant-negative Hoxb4N→A mutant caused geminin accumulation. Age-related transcriptional downregulation of derepressed Hoxa9 also leads to geminin accumulation. Transduction of Scmh1 lacking a geminin-binding domain restored derepressed expression of Hoxb4 and Hoxa9 but did not downregulate geminin like full-length Scmh1. Each of Hoxb4 and Hoxa9 can form a complex with Roc1-Ddb1-Cul4a to act as an E3 ubiquitin ligase for geminin. We suggest that geminin dysregulation may be restored by derepressed Hoxb4 and Hoxa9 in Scmh1-deficient mice. These findings suggest that PcG and a subset of Hox genes compose a homeostatic regulatory system for determining expression level of geminin.
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Minguillon C, Nishimoto S, Wood S, Vendrell E, Gibson-Brown JJ, Logan MPO. Hox genes regulate the onset of Tbx5 expression in the forelimb. Development 2012; 139:3180-8. [PMID: 22872086 DOI: 10.1242/dev.084814] [Citation(s) in RCA: 59] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Tbx4 and Tbx5 are two closely related T-box genes that encode transcription factors expressed in the prospective hindlimb and forelimb territories, respectively, of all jawed vertebrates. Despite their striking limb type-restricted expression pattern, we have shown that these genes do not participate in the acquisition of limb type-specific morphologies. Instead, Tbx4 and Tbx5 play similar roles in the initiation of hindlimb and forelimb outgrowth, respectively. We hypothesized that different combinations of Hox proteins expressed in different rostral and caudal domains of the lateral plate mesoderm, where limb induction occurs, might be involved in regulating the limb type-restricted expression of Tbx4 and Tbx5 and in the later determination of limb type-specific morphologies. Here, we identify the minimal regulatory element sufficient for the earliest forelimb-restricted expression of the mouse Tbx5 gene and show that this sequence is Hox responsive. Our results support a mechanism in which Hox genes act upstream of Tbx5 to control the axial position of forelimb formation.
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Affiliation(s)
- Carolina Minguillon
- Division of Developmental Biology, MRC National Institute for Medical Research, Mill Hill, London NW7 1AA, UK.
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41
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Tschopp P, Duboule D. A genetic approach to the transcriptional regulation of Hox gene clusters. Annu Rev Genet 2012; 45:145-66. [PMID: 22060042 DOI: 10.1146/annurev-genet-102209-163429] [Citation(s) in RCA: 60] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
The evolution of vertebrate genomes was accompanied by an astounding increase in the complexity of their regulatory modalities. Genetic redundancy resulting from large-scale genome duplications at the base of the chordate tree was repeatedly exploited by the functional redeployment of paralogous genes via innovations in their regulatory circuits. As a paradigm of such regulatory evolution, we have extensively studied those control mechanisms at work in-cis over vertebrate Hox gene clusters. Here, we review the portfolio of genetic strategies that have been developed to tackle the intricate relationship between genomic topography and the transcriptional activities in this gene family, and we describe some of the mechanistic insights we gained by using the HoxD cluster as an example. We discuss the high heuristic value of this system in our general understanding of how changes in transcriptional regulation can diversify gene function and thereby fuel morphological evolution.
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Affiliation(s)
- Patrick Tschopp
- National Center of Competence in Research, Frontiers in Genetics, Department of Genetics and Evolution, University of Geneva, 1211 Geneva 4, Switzerland
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42
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Rhee JM, Iannaccone PM. Mapping mouse hemangioblast maturation from headfold stages. Dev Biol 2012; 365:1-13. [PMID: 22426104 DOI: 10.1016/j.ydbio.2012.02.023] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2011] [Revised: 02/14/2012] [Accepted: 02/15/2012] [Indexed: 11/18/2022]
Abstract
The mouse posterior primitive streak at neural plate/headfold stages (NP/HF, ~7.5 dpc-8 dpc) represents an optimal window from which hemangioblasts can be isolated. We performed immunohistochemistry on this domain using established monoclonal antibodies for proteins that affect blood and endothelial fates. We demonstrate that HoxB4 and GATA1 are the first set of markers that segregate independently to endothelial or blood populations during NP/HF stages of mouse embryonic development. In a subset of cells, both proteins are co-expressed and immunoreactivities appear mutually excluded within nuclear spaces. We searched for this particular state at later sites of hematopoietic stem cell emergence, viz., the aorta-gonad-mesonephros (AGM) and the fetal liver at 10.5-11.5 dpc, and found that only a rare number of cells displayed this character. Based on this spatial-temporal argument, we propose that the earliest blood progenitors emerge either directly from the epiblast or through segregation within the allantoic core domain (ACD) through reduction of cell adhesion and pSmad1/5 nuclear signaling, followed by a stochastic decision toward a blood or endothelial fate that involves GATA1 and HoxB4, respectively. A third form in which binding distributions are balanced may represent a common condition shared by hemangioblasts and HSCs. We developed a heuristic model of hemangioblast maturation, in part, to be explicit about our assumptions.
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Affiliation(s)
- Jerry M Rhee
- Children's Memorial Research Center, Department of Pediatrics, Developmental Biology Program, Northwestern University Feinberg School of Medicine, Chicago, IL, USA.
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Tschopp P, Christen AJ, Duboule D. Bimodal control of Hoxd gene transcription in the spinal cord defines two regulatory subclusters. Development 2012; 139:929-39. [PMID: 22278926 DOI: 10.1242/dev.076794] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
The importance of Hox genes in the specification of neuronal fates in the spinal cord has long been recognized. However, the transcriptional controls underlying their collinear expression domains remain largely unknown. Here we show in mice that the correspondence between the physical order of Hoxd genes and their rostral expression boundaries, although respecting spatial collinearity, does not display a fully progressive distribution. Instead, two major anteroposterior boundaries are detected, coinciding with the functional subdivision of the spinal cord. Tiling array analyses reveal two distinct blocks of transcription, regulated independently from one another, that define the observed expression boundaries. Targeted deletions in vivo that remove the genomic fragments separating the two blocks induce ectopic expression of posterior genes. We further evaluate the independent regulatory potential and transcription profile of each gene locus by a tiling array approach using a contiguous series of transgenes combined with locus-specific deletions. Our work uncovers a bimodal type of HoxD spatial collinearity in the developing spinal cord that relies on two separate 'enhancer mini-hubs' to ensure correct Hoxd gene expression levels while maintaining their appropriate anteroposterior boundaries.
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Affiliation(s)
- Patrick Tschopp
- National Research Centre Frontiers in Genetics at Department of Genetics and Evolution, University of Geneva, Sciences III, Quai Ernest-Ansermet 30, Geneva 4, Switzerland
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Mansfield JH, McGlinn E. Evolution, Expression, and Developmental Function of Hox-Embedded miRNAs. Curr Top Dev Biol 2012; 99:31-57. [DOI: 10.1016/b978-0-12-387038-4.00002-1] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
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Fournier M, Lebert-Ghali CÉ, Krosl G, Bijl JJ. HOXA4 induces expansion of hematopoietic stem cells in vitro and confers enhancement of pro-B-cells in vivo. Stem Cells Dev 2011; 21:133-42. [PMID: 21749220 DOI: 10.1089/scd.2011.0259] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Members of the homeobox (Hox) gene family are known to mediate expansion of hematopoietic stem cells (HSCs) and progenitors. The absence of oncogenic properties promoted HOXB4 as prime candidate in the quest to expand HSCs for clinical purposes. Despite its potential to expand HSCs, studies with mutant mice showed that Hoxb4 is not essential for HSC generation and function under physiological conditions. Expression studies and the existence of functional redundancy in particular between paralog Hox genes suggest that HOXA4 might have potent properties to expand HSCs. Here we measured the ability of HOXA4 to promote ex vivo expansion of HSCs and progenitors using retrovirus-mediated overexpression. Our results provide evidence that HOXA4-transduced HSCs and primitive progenitors expand in culture conditions and demonstrate that the potential of expanded HOXA4 HSCs to give rise to mature myeloid and lymphoid progeny in normal proportions remained intact. Interestingly, constitutive overexpression of HOXA4 resulted in an unbalanced expansion of lymphoid/myeloid progenitors in bone marrow chimeras favorable to B-cell progenitors responsive to interleukin-7. This expansion was specific for these progenitors and not for the more primitive Whitlock-Witte-initiating cells. These data indicate that early stages of B-cell development associated with proliferation are in particular sensitive to HOXA4. Thus, this study supports the potential use of HOXA4 to expand both HSCs and B-cell progenitor populations for therapeutic strategies.
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Bhattacharyya S, Tian J, Bouhassira EE, Locker J. Systematic targeted integration to study Albumin gene control elements. PLoS One 2011; 6:e23234. [PMID: 21858039 PMCID: PMC3155544 DOI: 10.1371/journal.pone.0023234] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2011] [Accepted: 07/12/2011] [Indexed: 11/18/2022] Open
Abstract
To study transcriptional regulation by distant enhancers, we devised a system of easily modified reporter plasmids for integration into single-copy targeting cassettes in clones of HuH7, a human hepatocellular carcinoma. The plasmid constructs tested transcriptional function of a 35-kb region that contained the rat albumin gene and its upstream flanking region. Expression of integrants was analyzed in two orientations, and compared to transient expression of non-integrated plasmids. Enhancers were studied in their natural positions relative to the promoter and localized by deletion. All constructs were also analyzed by transient transfection assays. In addition to the known albumin gene enhancer (E1 at -10 kb), we demonstrated two new enhancers, E2 at -13, and E4 at +1.2 kb. All three enhancers functioned in both transient assays and integrated constructs. However, chromosomal integration demonstrated several differences from transient expression. For example, analysis of E2 showed that enhancer function within the chromosome required a larger gene region than in transient assays. Another conserved region, E3 at -0.7 kb, functioned as an enhancer in transient assays but inhibited the function of E1 and E2 when chromosomally integrated. The enhancers did not show additive or synergistic behavior,an effect consistent with competition for the promoter or inhibitory interactions among enhancers. Growth arrest by serum starvation strongly stimulated the function of some integrated enhancers, consistent with the expected disruption of enhancer-promoter looping during the cell cycle.
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Affiliation(s)
- Sanchari Bhattacharyya
- Department of Pathology, Albert Einstein College of Medicine, Bronx, New York, United States of America
| | - Jianmin Tian
- Department of Pathology, Albert Einstein College of Medicine, Bronx, New York, United States of America
- The Marion Bessin Liver Center, Albert Einstein College of Medicine, Bronx, New York, United States of America
| | - Eric E. Bouhassira
- Department of Medicine, Albert Einstein College of Medicine, Bronx, New York, United States of America
| | - Joseph Locker
- Department of Pathology, Albert Einstein College of Medicine, Bronx, New York, United States of America
- The Marion Bessin Liver Center, Albert Einstein College of Medicine, Bronx, New York, United States of America
- * E-mail:
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miRNA-mediated feedback inhibition of JAK/STAT morphogen signalling establishes a cell fate threshold. Nat Cell Biol 2011; 13:1062-9. [PMID: 21857668 PMCID: PMC3167036 DOI: 10.1038/ncb2316] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2010] [Accepted: 06/24/2011] [Indexed: 12/20/2022]
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McDougall C, Korchagina N, Tobin JL, Ferrier DE. Annelid Distal-less/Dlx duplications reveal varied post-duplication fates. BMC Evol Biol 2011; 11:241. [PMID: 21846345 PMCID: PMC3199776 DOI: 10.1186/1471-2148-11-241] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2011] [Accepted: 08/16/2011] [Indexed: 11/24/2022] Open
Abstract
Background Dlx (Distal-less) genes have various developmental roles and are widespread throughout the animal kingdom, usually occurring as single copy genes in non-chordates and as multiple copies in most chordate genomes. While the genomic arrangement and function of these genes is well known in vertebrates and arthropods, information about Dlx genes in other organisms is scarce. We investigate the presence of Dlx genes in several annelid species and examine Dlx gene expression in the polychaete Pomatoceros lamarckii. Results Two Dlx genes are present in P. lamarckii, Capitella teleta and Helobdella robusta. The C. teleta Dlx genes are closely linked in an inverted tail-to-tail orientation, reminiscent of the arrangement of vertebrate Dlx pairs, and gene conversion appears to have had a role in their evolution. The H. robusta Dlx genes, however, are not on the same genomic scaffold and display divergent sequences, while, if the P. lamarckii genes are linked in a tail-to-tail orientation they are a minimum of 41 kilobases apart and show no sign of gene conversion. No expression in P. lamarckii appendage development has been observed, which conflicts with the supposed conserved role of these genes in animal appendage development. These Dlx duplications do not appear to be annelid-wide, as the polychaete Platynereis dumerilii likely possesses only one Dlx gene. Conclusions On the basis of the currently accepted annelid phylogeny, we hypothesise that one Dlx duplication occurred in the annelid lineage after the divergence of P. dumerilii from the other lineages and these duplicates then had varied evolutionary fates in different species. We also propose that the ancestral role of Dlx genes is not related to appendage development.
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Affiliation(s)
- Carmel McDougall
- The Scottish Oceans Institute, University of St Andrews, East Sands, St Andrews KY168LB, UK.
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Directed neural differentiation of mouse embryonic stem cells is a sensitive system for the identification of novel Hox gene effectors. PLoS One 2011; 6:e20197. [PMID: 21637844 PMCID: PMC3102681 DOI: 10.1371/journal.pone.0020197] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2011] [Accepted: 04/20/2011] [Indexed: 12/19/2022] Open
Abstract
The evolutionarily conserved Hox family of homeodomain transcription factors
plays fundamental roles in regulating cell specification along the anterior
posterior axis during development of all bilaterian animals by controlling cell
fate choices in a highly localized, extracellular signal and cell context
dependent manner. Some studies have established downstream target genes in
specific systems but their identification is insufficient to explain either the
ability of Hox genes to direct homeotic transformations or the
breadth of their patterning potential. To begin delineating Hox
gene function in neural development we used a mouse ES cell based system that
combines efficient neural differentiation with inducible Hoxb1 expression. Gene
expression profiling suggested that Hoxb1 acted as both
activator and repressor in the short term but predominantly as a repressor in
the long run. Activated and repressed genes segregated in distinct processes
suggesting that, in the context examined, Hoxb1 blocked
differentiation while activating genes related to early developmental processes,
wnt and cell surface receptor linked signal transduction and cell-to-cell
communication. To further elucidate aspects of Hoxb1 function
we used loss and gain of function approaches in the mouse and chick embryos. We
show that Hoxb1 acts as an activator to establish the full expression domain of
CRABPI and II in rhombomere 4 and as a
repressor to restrict expression of Lhx5 and
Lhx9. Thus the Hoxb1 patterning activity
includes the regulation of the cellular response to retinoic acid and the delay
of the expression of genes that commit cells to neural differentiation. The
results of this study show that ES neural differentiation and inducible
Hox gene expression can be used as a sensitive model system
to systematically identify Hox novel target genes, delineate
their interactions with signaling pathways in dictating cell fate and define the
extent of functional overlap among different Hox genes.
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50
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In der Rieden PMJ, Jansen HJ, Durston AJ. XMeis3 is necessary for mesodermal Hox gene expression and function. PLoS One 2011; 6:e18010. [PMID: 21464931 PMCID: PMC3065463 DOI: 10.1371/journal.pone.0018010] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2010] [Accepted: 02/21/2011] [Indexed: 12/13/2022] Open
Abstract
Hox transcription factors provide positional information during patterning of the anteroposterior axis. Hox transcription factors can co-operatively bind with PBC-class co-factors, enhancing specificity and affinity for their appropriate binding sites. The nuclear localisation of these co-factors is regulated by the Meis-class of homeodomain proteins. During development of the zebrafish hindbrain, Meis3 has previously been shown to synergise with Hoxb1 in the autoregulation of Hoxb1. In Xenopus XMeis3 posteriorises the embryo upon ectopic expression. Recently, an early temporally collinear expression sequence of Hox genes was detected in Xenopus gastrula mesoderm (see intro. P3). There is evidence that this sequence sets up the embryo's later axial Hox expression pattern by time-space translation. We investigated whether XMeis3 is involved in regulation of this early mesodermal Hox gene expression. Here, we present evidence that XMeis3 is necessary for expression of Hoxd1, Hoxb4 and Hoxc6 in mesoderm during gastrulation. In addition, we show that XMeis3 function is necessary for the progression of gastrulation. Finally, we present evidence for synergy between XMeis3 and Hoxd1 in Hoxd1 autoregulation in mesoderm during gastrulation.
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