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Article: Homeodomain subtypes and functional diversity.

Bürglin, Thomas R

2011 Volume 52, Page(s) 95–122

Abstract: The homeodomain is a protein domain of about 60 amino acids that is encoded by homeobox genes. The homeodomain is a DNA binding domain, and hence homeodomain proteins are essentially transcription factors (TFs). They have been shown to play major roles ... ...

Abstract	The homeodomain is a protein domain of about 60 amino acids that is encoded by homeobox genes. The homeodomain is a DNA binding domain, and hence homeodomain proteins are essentially transcription factors (TFs). They have been shown to play major roles in many developmental processes of animals, as well as fungi and plants. A primary function of homeodomain proteins is to regulate the expression of other genes in development and differentiation. Thousands of homeobox genes have been identified, and they can be grouped into many different classes. Often other conserved protein domains are found linked to a homeodomain. Several particular types of homeobox genes are organized into chromosomal clusters. The best-known cluster, the HOX cluster, is found in all bilaterian animals. Tetrapods contain four HOX clusters that arose through duplication in early vertebrate evolution. The genes in these clusters are called Hox genes. Lower chordates, insects and nematodes tend to have only one HOX cluster. Of particular interest is that many of the HOX cluster genes function in the process of pattern formation along the anterior-posterior body axis. Many other types of homeodomain proteins play roles in the determination of cell fates and cell differentiation. Homeobox genes thus perform key roles for all aspects of the development of an organism.
MeSH term(s)	Amino Acid Motifs ; Animals ; Biological Evolution ; Evolution, Molecular ; Genes, Homeobox ; Homeodomain Proteins ; Molecular Sequence Data ; Multigene Family ; Transcription Factors/genetics
Chemical Substances	Homeodomain Proteins ; Transcription Factors
Language	English
Publishing date	2011
Publishing country	United States
Document type	Journal Article
ISSN	0306-0225 ; 0096-8757
ISSN	0306-0225 ; 0096-8757
DOI	10.1007/978-90-481-9069-0_5
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Article ; Online: Homeodomain proteins: an update.

Bürglin, Thomas R / Affolter, Markus

Chromosoma

2016 Volume 125, Issue 3, Page(s) 497–521

Abstract: Here, we provide an update of our review on homeobox genes that we wrote together with Walter Gehring in 1994. Since then, comprehensive surveys of homeobox genes have become possible due to genome sequencing projects. Using the 103 Drosophila homeobox ... ...

Abstract	Here, we provide an update of our review on homeobox genes that we wrote together with Walter Gehring in 1994. Since then, comprehensive surveys of homeobox genes have become possible due to genome sequencing projects. Using the 103 Drosophila homeobox genes as example, we present an updated classification. In animals, there are 16 major classes, ANTP, PRD, PRD-LIKE, POU, HNF, CUT (with four subclasses: ONECUT, CUX, SATB, and CMP), LIM, ZF, CERS, PROS, SIX/SO, plus the TALE superclass with the classes IRO, MKX, TGIF, PBC, and MEIS. In plants, there are 11 major classes, i.e., HD-ZIP (with four subclasses: I to IV), WOX, NDX, PHD, PLINC, LD, DDT, SAWADEE, PINTOX, and the two TALE classes KNOX and BEL. Most of these classes encode additional domains apart from the homeodomain. Numerous insights have been obtained in the last two decades into how homeodomain proteins bind to DNA and increase their specificity by interacting with other proteins to regulate cell- and tissue-specific gene expression. Not only protein-DNA base pair contacts are important for proper target selection; recent experiments also reveal that the shape of the DNA plays a role in specificity. Using selected examples, we highlight different mechanisms of homeodomain protein-DNA interaction. The PRD class of homeobox genes was of special interest to Walter Gehring in the last two decades. The PRD class comprises six families in Bilateria, and tinkers with four different motifs, i.e., the PAIRED domain, the Groucho-interacting motif EH1 (aka Octapeptide or TN), the homeodomain, and the OAR motif. Homologs of the co-repressor protein Groucho are also present in plants (TOPLESS), where they have been shown to interact with small amphipathic motives (EAR), and in yeast (TUP1), where we find an EH1-like motif in MATα2.
MeSH term(s)	Amino Acid Sequence ; Animals ; Base Sequence ; Drosophila melanogaster/genetics ; Gene Expression Regulation/genetics ; Genes, Homeobox/genetics ; Homeodomain Proteins/classification ; Homeodomain Proteins/genetics ; Transcription Factors/genetics
Chemical Substances	Homeodomain Proteins ; Transcription Factors
Language	English
Publishing date	2016
Publishing country	Austria
Document type	Journal Article ; Research Support, Non-U.S. Gov't ; Review
ZDB-ID	203083-4
ISSN	1432-0886 ; 0009-5915
ISSN (online)	1432-0886
ISSN	0009-5915
DOI	10.1007/s00412-015-0543-8
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Article ; Online: Tracking and characterization of partial and full epithelial-mesenchymal transition cells in a mouse model of metastatic breast cancer.

Lüönd, Fabiana / Santacroce, Natascha / Beisel, Christian / Guérard, Laurent / Bürglin, Thomas R / Christofori, Gerhard / Sugiyama, Nami

STAR protocols

2022 Volume 3, Issue 2, Page(s) 101438

Abstract: The various stages of epithelial-mesenchymal transition (EMT) generate phenotypically heterogeneous populations of cells. Here, we detail a dual recombinase lineage tracing system using a transgenic mouse model of metastatic breast cancer to trace and ... ...

Abstract	The various stages of epithelial-mesenchymal transition (EMT) generate phenotypically heterogeneous populations of cells. Here, we detail a dual recombinase lineage tracing system using a transgenic mouse model of metastatic breast cancer to trace and characterize breast cancer cells at different EMT stages. We describe analytical steps to label cancer cells at an early partial or a late full EMT state, followed by tracking their behavior in tumor slice cultures. We then characterize their transcriptome by five-cell RNA sequencing. For complete details on the use and execution of this protocol, please refer to Luond et al. (2021).
MeSH term(s)	Animals ; Cell Line, Tumor ; Disease Models, Animal ; Epithelial-Mesenchymal Transition/genetics ; Mice ; Mice, Transgenic ; Neoplasms ; Transcriptome
Language	English
Publishing date	2022-06-10
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ISSN	2666-1667
ISSN (online)	2666-1667
DOI	10.1016/j.xpro.2022.101438
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Article ; Online: The Hedgehog protein family.

Bürglin, Thomas R

Genome biology

2008 Volume 9, Issue 11, Page(s) 241

Abstract: The Hedgehog (Hh) pathway is one of the fundamental signal transduction pathways in animal development and is also involved in stem-cell maintenance and carcinogenesis. The hedgehog (hh) gene was first discovered in Drosophila, and members of the family ... ...

Abstract	The Hedgehog (Hh) pathway is one of the fundamental signal transduction pathways in animal development and is also involved in stem-cell maintenance and carcinogenesis. The hedgehog (hh) gene was first discovered in Drosophila, and members of the family have since been found in most metazoa. Hh proteins are composed of two domains, an amino-terminal domain HhN, which has the biological signal activity, and a carboxy-terminal autocatalytic domain HhC, which cleaves Hh into two parts in an intramolecular reaction and adds a cholesterol moiety to HhN. HhC has sequence similarity to the self-splicing inteins, and the shared region is termed Hint. New classes of proteins containing the Hint domain have been discovered recently in bacteria and eukaryotes, and the Hog class, of which Hh proteins comprise one family, is widespread throughout eukaryotes. The non-Hh Hog proteins have carboxy-terminal domains (the Hog domain) highly similar to HhC, although they lack the HhN domain, and instead have other amino-terminal domains. Hog proteins are found in many protists, but the Hh family emerged only in early metazoan evolution. HhN is modified by cholesterol at its carboxyl terminus and by palmitate at its amino terminus in both flies and mammals. The modified HhN is released from the cell and travels through the extracellular space. On binding its receptor Patched, it relieves the inhibition that Patched exerts on Smoothened, a G-protein-coupled receptor. The resulting signaling cascade converges on the transcription factor Cubitus interruptus (Ci), or its mammalian counterparts, the Gli proteins, which activate or repress target genes.
MeSH term(s)	Animals ; Eukaryotic Cells/metabolism ; Hedgehog Proteins/chemistry ; Hedgehog Proteins/genetics ; Hedgehog Proteins/metabolism ; Humans ; Signal Transduction
Chemical Substances	Hedgehog Proteins
Language	English
Publishing date	2008-11-19
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't ; Review
ZDB-ID	2040529-7
ISSN	1474-760X ; 1474-760X
ISSN (online)	1474-760X
ISSN	1474-760X
DOI	10.1186/gb-2008-9-11-241
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Article ; Online: Evolution of hedgehog and hedgehog-related genes, their origin from Hog proteins in ancestral eukaryotes and discovery of a novel Hint motif.

Bürglin, Thomas R

BMC genomics

2008 Volume 9, Page(s) 127

Abstract: Background: The Hedgehog (Hh) signaling pathway plays important roles in human and animal development as well as in carcinogenesis. Hh molecules have been found in both protostomes and deuterostomes, but curiously the nematode Caenorhabditis elegans ... ...

Abstract	Background: The Hedgehog (Hh) signaling pathway plays important roles in human and animal development as well as in carcinogenesis. Hh molecules have been found in both protostomes and deuterostomes, but curiously the nematode Caenorhabditis elegans lacks a bona-fide Hh. Instead a series of Hh-related proteins are found, which share the Hint/Hog domain with Hh, but have distinct N-termini. Results: We performed extensive genome searches such as the cnidarian Nematostella vectensis and several nematodes to gain further insights into Hh evolution. We found six genes in N. vectensis with a relationship to Hh: two Hh genes, one gene with a Hh N-terminal domain fused to a Willebrand factor type A domain (VWA), and three genes containing Hint/Hog domains with distinct novel N-termini. In the nematode Brugia malayi we find the same types of hh-related genes as in C. elegans. In the more distantly related Enoplea nematodes Xiphinema and Trichinella spiralis we find a bona-fide Hh. In addition, T. spiralis also has a quahog gene like C. elegans, and there are several additional hh-related genes, some of which have secreted N-terminal domains of only 15 to 25 residues. Examination of other Hh pathway components revealed that T. spiralis - like C. elegans - lacks some of these components. Extending our search to all eukaryotes, we recovered genes containing a Hog domain similar to Hh from many different groups of protists. In addition, we identified a novel Hint gene family present in many eukaryote groups that encodes a VWA domain fused to a distinct Hint domain we call Vint. Further members of a poorly characterized Hint family were also retrieved from bacteria. Conclusion: In Cnidaria and nematodes the evolution of hh genes occurred in parallel to the evolution of other genes that contain a Hog domain but have different N-termini. The fact that Hog genes comprising a secreted N-terminus and a Hog domain are found in many protists indicates that this gene family must have arisen in very early eukaryotic evolution, and gave rise eventually to hh and hh-related genes in animals. The results indicate a hitherto unsuspected ability of Hog domain encoding genes to evolve new N-termini. In one instance in Cnidaria, the Hh N-terminal signaling domain is associated with a VWA domain and lacks a Hog domain, suggesting a modular mode of evolution also for the N-terminal domain. The Hog domain proteins, the inteins and VWA-Vint proteins are three families of Hint domain proteins that evolved in parallel in eukaryotes.
MeSH term(s)	Amino Acid Motifs/genetics ; Amino Acid Sequence ; Animals ; Base Sequence ; Computational Biology ; Evolution, Molecular ; Genomics ; Hedgehog Proteins/genetics ; Likelihood Functions ; Models, Genetic ; Molecular Sequence Data ; Nematoda/genetics ; Phylogeny ; Protein Structure, Tertiary ; Sea Anemones/genetics ; Sequence Alignment ; Signal Transduction/genetics ; Species Specificity
Chemical Substances	Hedgehog Proteins
Language	English
Publishing date	2008-03-11
Publishing country	England
Document type	Comparative Study ; Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
ZDB-ID	2041499-7
ISSN	1471-2164 ; 1471-2164
ISSN (online)	1471-2164
ISSN	1471-2164
DOI	10.1186/1471-2164-9-127
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Article ; Online: Tracking and characterization of partial and full epithelial-mesenchymal transition cells in a mouse model of metastatic breast cancer

Fabiana Lüönd / Natascha Santacroce / Christian Beisel / Laurent Guérard / Thomas R. Bürglin / Gerhard Christofori / Nami Sugiyama

STAR Protocols, Vol 3, Iss 2, Pp 101438- (2022)

2022

Abstract: Summary: The various stages of epithelial-mesenchymal transition (EMT) generate phenotypically heterogeneous populations of cells. Here, we detail a dual recombinase lineage tracing system using a transgenic mouse model of metastatic breast cancer to ... ...

Abstract	Summary: The various stages of epithelial-mesenchymal transition (EMT) generate phenotypically heterogeneous populations of cells. Here, we detail a dual recombinase lineage tracing system using a transgenic mouse model of metastatic breast cancer to trace and characterize breast cancer cells at different EMT stages. We describe analytical steps to label cancer cells at an early partial or a late full EMT state, followed by tracking their behavior in tumor slice cultures. We then characterize their transcriptome by five-cell RNA sequencing.For complete details on the use and execution of this protocol, please refer to Luond et al. (2021). : Publisher’s note: Undertaking any experimental protocol requires adherence to local institutional guidelines for laboratory safety and ethics.
Keywords	Cell Biology ; Single Cell ; Flow Cytometry/Mass Cytometry ; Cancer ; RNAseq ; Microscopy ; Science (General) ; Q1-390
Language	English
Publishing date	2022-06-01T00:00:00Z
Publisher	Elsevier
Document type	Article ; Online
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Article ; Online: Tracking and characterization of partial and full epithelial-mesenchymal transition cells in a mouse model of metastatic breast cancer

Lüönd, Fabiana / Santacroce, Natascha / Beisel, Christian / Guérard, Laurent / Bürglin, Thomas R. / Christofori, Gerhard / Sugiyama, Nami

STAR Protocols, 3 (2)

2022

Abstract	The various stages of epithelial-mesenchymal transition (EMT) generate phenotypically heterogeneous populations of cells. Here, we detail a dual recombinase lineage tracing system using a transgenic mouse model of metastatic breast cancer to trace and characterize breast cancer cells at different EMT stages. We describe analytical steps to label cancer cells at an early partial or a late full EMT state, followed by tracking their behavior in tumor slice cultures. We then characterize their transcriptome by five-cell RNA sequencing. For complete details on the use and execution of this protocol, please refer to Luond et al. (2021). ISSN:2666-1667
Keywords	Cell Biology ; Single Cell ; Flow Cytometry/Mass Cytometry ; Cancer ; RNAseq ; Microscopy ; Molecular Biology ; Cell Differentiation
Language	English
Publishing date	2022-06-17
Publisher	Elsevier
Publishing country	ch
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Dye-filling of the amphid sheath glia: implications for the functional relationship between sensory neurons and glia in Caenorhabditis elegans.

Ohkura, Kiyotaka / Bürglin, Thomas R

Biochemical and biophysical research communications

2011 Volume 406, Issue 2, Page(s) 188–193

Abstract: The nervous system is composed of cells including neurons and glia. It has been believed that the former cells play central roles in various neural functions while the latter ones have only supportive functions for neurons. However, recent findings ... ...

Abstract	The nervous system is composed of cells including neurons and glia. It has been believed that the former cells play central roles in various neural functions while the latter ones have only supportive functions for neurons. However, recent findings suggest that glial cells actively participate in neural activities, and the cooperation between neurons and glia is important for nervous system functions. In Caenorhabditis elegans, amphid sensory organs in the head also consist of sensory neurons and glia-like support cells (amphid socket and amphid sheath cells). Ciliary endings of some sensory neurons exposed to the environment detect various chemicals, molecules and signals, and the cilia of some neurons can also take up fluorescent dyes such as DiI. Here, we show that the amphid sheath glia are also stained with DiI and that its uptake by the amphid sheath cells correlates with DiI-filling of sensory neurons, suggesting that the amphid sheath glia might interact with sensory neurons. Furthermore, the localization of the amphid sheath cell reporter F52E1.2SP::YFP is abnormal in che-2 mutants, which have defective cilia. These findings imply that sensory neurons might affect amphid sheath glia functions in the amphid sensory organ of C. elegans.
MeSH term(s)	Animals ; Caenorhabditis elegans/cytology ; Caenorhabditis elegans/metabolism ; Caenorhabditis elegans/physiology ; Fluorescent Dyes/chemistry ; Fluorescent Dyes/metabolism ; Myelin Sheath/metabolism ; Myelin Sheath/physiology ; Sensory Receptor Cells/metabolism ; Sensory Receptor Cells/physiology ; Staining and Labeling
Chemical Substances	Fluorescent Dyes
Language	English
Publishing date	2011-03-11
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	205723-2
ISSN	1090-2104 ; 0006-291X ; 0006-291X
ISSN (online)	1090-2104 ; 0006-291X
ISSN	0006-291X
DOI	10.1016/j.bbrc.2011.02.003
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Article: The homeobox genes of Encephalitozoon cuniculi (Microsporidia) reveal a putative mating-type locus.

Bürglin, Thomas R

Development genes and evolution

2003 Volume 213, Issue 1, Page(s) 50–52

Abstract: Homeobox genes have been found in animals, fungi, and plants. Recently, the complete genomic sequence of Encephalitozoon cuniculi has become available and it was shown that this Microsporida species is related to fungi. Given this close relatedness to ... ...

Abstract	Homeobox genes have been found in animals, fungi, and plants. Recently, the complete genomic sequence of Encephalitozoon cuniculi has become available and it was shown that this Microsporida species is related to fungi. Given this close relatedness to fungi, I have searched the genome of E. cuniculifor homeobox genes. There are 12 homeobox genes as well as one STE12 orthologue. The large number of homeobox genes when compared to the annotations, which only list one, suggests that possibly other smaller genes may have been overlooked in the published analysis and E. cuniculi may have more than 1,997 genes. Sequence and phylogenetic analyses show that the E. cuniculi homeobox genes also fall into two distinct groups, with two TALE and ten typical homeobox genes being present. Like in the mating-type locus of yeast and other fungi, one TALE and one typical homeobox are found in close proximity of each other on the chromosome, suggesting that Microsporidia also contain a mating-type locus.
MeSH term(s)	Amino Acid Sequence ; Animals ; Cluster Analysis ; Encephalitozoon cuniculi/genetics ; Genes, Fungal/genetics ; Genes, Homeobox/genetics ; Genes, Mating Type, Fungal ; Molecular Sequence Data ; Phylogeny ; Sequence Alignment
Language	English
Publishing date	2003-02
Publishing country	Germany
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	1327962-2
ISSN	1432-041X ; 0949-944X
ISSN (online)	1432-041X
ISSN	0949-944X
DOI	10.1007/s00427-002-0287-3
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Article ; Online: Comprehensive characterization of the embryonic factor LEUTX.

iScience

2023 Volume 26, Issue 3, Page(s) 106172

Abstract: The paired-like homeobox transcription factor LEUTX is expressed in human preimplantation embryos between the 4- and 8-cell stages, and then silenced in somatic tissues. To characterize the function of LEUTX, we performed a multiomic characterization of ... ...

Abstract	The paired-like homeobox transcription factor LEUTX is expressed in human preimplantation embryos between the 4- and 8-cell stages, and then silenced in somatic tissues. To characterize the function of LEUTX, we performed a multiomic characterization of LEUTX using two proteomics methods and three genome-wide sequencing approaches. Our results show that LEUTX stably interacts with the EP300 and CBP histone acetyltransferases through its 9 amino acid transactivation domain (9aaTAD), as mutation of this domain abolishes the interactions. LEUTX targets genomic cis-regulatory sequences that overlap with repetitive elements, and through these elements it is suggested to regulate the expression of its downstream genes. We find LEUTX to be a transcriptional activator, upregulating several genes linked to preimplantation development as well as 8-cell-like markers, such as DPPA3 and ZNF280A. Our results support a role for LEUTX in preimplantation development as an enhancer binding protein and as a potent transcriptional activator.
Language	English
Publishing date	2023-02-09
Publishing country	United States
Document type	Journal Article
ISSN	2589-0042
ISSN (online)	2589-0042
DOI	10.1016/j.isci.2023.106172
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