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Tong, Yong-Guang
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Publications (7 of 7) Show all publications
Hench, J., Henriksson, J., Abou-Zied, A. M., Lüppert, M., Dethlefsen, J., Mukherjee, K., . . . Bürglin, T. R. (2015). The Homeobox Genes of Caenorhabditis elegans and Insights into Their Spatio-Temporal Expression Dynamics during Embryogenesis. PLoS ONE, 10(5), Article ID e0126947.
Open this publication in new window or tab >>The Homeobox Genes of Caenorhabditis elegans and Insights into Their Spatio-Temporal Expression Dynamics during Embryogenesis
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2015 (English)In: PLoS ONE, ISSN 1932-6203, E-ISSN 1932-6203, Vol. 10, no 5, article id e0126947Article in journal (Refereed) Published
Abstract [en]

Homeobox genes play crucial roles for the development of multicellular eukaryotes. We have generated a revised list of all homeobox genes for Caenorhabditis elegans and provide a nomenclature for the previously unnamed ones. We show that, out of 103 homeobox genes, 70 are co-orthologous to human homeobox genes. 14 are highly divergent, lacking an obvious ortholog even in other Caenorhabditis species. One of these homeobox genes encodes 12 homeodomains, while three other highly divergent homeobox genes encode a novel type of double homeodomain, termed HOCHOB. To understand how transcription factors regulate cell fate during development, precise spatio-temporal expression data need to be obtained. Using a new imaging framework that we developed, Endrov, we have generated spatio-temporal expression profiles during embryogenesis of over 60 homeobox genes, as well as a number of other developmental control genes using GFP reporters. We used dynamic feedback during recording to automatically adjust the camera exposure time in order to increase the dynamic range beyond the limitations of the camera. We have applied the new framework to examine homeobox gene expression patterns and provide an analysis of these patterns. The methods we developed to analyze and quantify expression data are not only suitable for C. elegans, but can be applied to other model systems or even to tissue culture systems.

National Category
Biological Sciences
Identifiers
urn:nbn:se:sh:diva-27668 (URN)10.1371/journal.pone.0126947 (DOI)000355319400026 ()26024448 (PubMedID)2-s2.0-84932606751 (Scopus ID)
Funder
Swedish Research Council, 621-2010-5634Swedish Foundation for Strategic Research Wenner-Gren Foundations
Available from: 2015-06-08 Created: 2015-06-08 Last updated: 2018-11-13Bibliographically approved
Henriksson, J., Hench, J., Tong, Y. G., Johansson, A., Johansson, D. & Bürglin, T. R. (2013). Endrov: an integrated platform for image analysis. Nature Methods, 10(6), 454-456
Open this publication in new window or tab >>Endrov: an integrated platform for image analysis
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2013 (English)In: Nature Methods, ISSN 1548-7091, E-ISSN 1548-7105, Vol. 10, no 6, p. 454-456Article in journal (Refereed) Published
National Category
Biochemistry and Molecular Biology
Identifiers
urn:nbn:se:sh:diva-19422 (URN)10.1038/nmeth.2478 (DOI)000319668700005 ()2-s2.0-84880784676 (Scopus ID)
Available from: 2013-07-11 Created: 2013-07-11 Last updated: 2017-12-06Bibliographically approved
Kagoshima, H., Cassata, G., Tong, Y. G., Pujol, N., Niklaus, G. & Bürglin, T. R. (2013). The LIM homeobox gene ceh-14 is required for phasmid function and neurite outgrowth. Developmental Biology, 380(2), 314-323
Open this publication in new window or tab >>The LIM homeobox gene ceh-14 is required for phasmid function and neurite outgrowth
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2013 (English)In: Developmental Biology, ISSN 0012-1606, E-ISSN 1095-564X, Vol. 380, no 2, p. 314-323Article in journal (Refereed) Published
Abstract [en]

Transcription factors play key roles in cell fate specification and cell differentiation. Previously, we showed that the LIM homeodomain factor CEH-14 is expressed in the AFD neurons where it is required for thermotaxis behavior in Caenorhabditis elegans. Here, we show that ceh-14 is expressed in the phasmid sensory neurons, PHA and PHB, a number of neurons in the tail, i.e., PHC, DVC, PVC, PVN, PVQ PVT, PVW and PVR, as well as the touch neurons. Analysis of the promoter region shows that important regulatory elements for the expression in most neurons reside from -4 kb to -1.65 kb upstream of the start codon. Further, within the first introns are elements for expression in the hypodermis. Phylogenetic footprinting revealed numerous conserved motifs in these regions. In addition to the existing deletion mutation ceh-14(ch3), we isolated a new allele, ceh-14(ch2), in which only one LIM domain is disrupted. The latter mutant allele is partially defective for thermosensation. Analysis of both mutant alleles showed that they are defective in phasmid dye-filling. However, the cell body, dendritic outgrowth and ciliated endings of PHA and PHB appear normal, indicating that ceh-14 is not required for growth. The loss of a LIM domain in the ceh-14(ch2) allele causes a partial loss-of-function phenotype. Examination of the neurites of ALA and tail neurons using a ceh-14::GFP reporter shows abnormal axonal outgrowth and pathfinding.

National Category
Biological Sciences
Identifiers
urn:nbn:se:sh:diva-19637 (URN)10.1016/j.ydbio.2013.04.009 (DOI)000322297900015 ()23608457 (PubMedID)2-s2.0-84879881843 (Scopus ID)
Note

Som manuskript i avhandling. As manuscript in dissertation.

Available from: 2013-09-02 Created: 2013-09-02 Last updated: 2017-12-06Bibliographically approved
Tong, Y.-G. & Bürglin, T. R. (2010). Conditions for dye-filling of sensory neurons in Caenorhabditis elegans. Journal of Neuroscience Methods, 188(1), 58-61
Open this publication in new window or tab >>Conditions for dye-filling of sensory neurons in Caenorhabditis elegans
2010 (English)In: Journal of Neuroscience Methods, ISSN 0165-0270, E-ISSN 1872-678X, Vol. 188, no 1, p. 58-61Article in journal (Refereed) Published
Abstract [en]

Dye-filling is a common method used to stain Caenorhabditis elegans ensory neurons in vivo. While the amphids and phasmids are easy to tain, a subset of sensory neurons, the IL2 neurons, are difficult to tain reproducibly. Here we examined the conditions under which the IL2 eurons take up the lipophilic fluorescent dye DiI. We find that IL2 ye-filling depends on salt concentration, but not osmolarity. Low salt rior and during incubation is important for efficient dye uptake. dditional parameters that affect dye-filling are the speed of shaking uring incubation and the addition of detergents. Our modified ye-filling procedure provides a reliable method to distinguish mutant lleles that stain amphids and phasmids, IL2 neurons, or both. An dditional benefit is that it can also stain the excretory duct. The ethod allows genetic screens to be performed to identify mutants that electively affect only one of the sensory structures or the excretory uct.

National Category
Neurology
Identifiers
urn:nbn:se:sh:diva-13709 (URN)10.1016/j.jneumeth.2010.02.003 (DOI)000276866400009 ()20149821 (PubMedID)2-s2.0-77950460160 (Scopus ID)
Available from: 2011-12-06 Created: 2011-12-06 Last updated: 2017-12-08Bibliographically approved
Tong, Y.-G. (2010). Regulatory function of homeobox genes in the development of Caenorhabditis elegans. (Doctoral dissertation). Stockholm: Karolinska Institutet
Open this publication in new window or tab >>Regulatory function of homeobox genes in the development of Caenorhabditis elegans
2010 (English)Doctoral thesis, comprehensive summary (Other academic)
Abstract [en]

The nematode worm Caenorhabditis elegans has been widely used as a genetic model for over 40 years to investigate developmental control genes. In this thesis, I studied the roles of several homeobox genes and a novel RNA binding protein (RBD) in the development of C. elegans to understand the function of these genes in higher organisms. Homeobox genes are transcriptional regulators that are highly conserved in evolution and play important domains in eukaryotes, and genes encoding this domain play roles in a wide variety of post-transcriptional gene regulation processes. In paper I, we characterized a novel protein, RNA binding domain-1 (RBD-1), which is involved in ribosome biogenesis. This protein contains six consensus RNA-binding domains and is conserved as to sequence, domain organization, and subcellular localization from yeast to human. RBD-1 is essential for the development of C. elegans. The RNAi experiments using the cDNA of RBD-1 demonstrated various abnormalities in the C. elegans development, such as defects in morphology (dumpy), incomplete molting, and defective gonadal and vulval development. Animals depleted for RBD-1 arrested mainly at the L1 larval stage. In the course of studying the homeobox genes, we often used the dye-filling assay. It is the simplest method presently used to assay the structural integrity of sensory cilia. In paper II, we optimized conditions, in which reliable staining of the inner labial (IL2) neurons could be obtained, namely in low salt conditions, in the presence of determethod to distinguish mutant alleles that stain amphids and phasmids, and IL2 neurons. Using this assay, we found that a mutation in the POU homeobox gene unc-86 abolished dye-filling in IL2 neurons but not amphids and phasmids. mids. In Paper III, we showed that the LIM homeobox gene ceh-14 was expressed in other sensory neurons and interneurons, including the phasmid neurons and the ALA interneuron, while previously it was shown that ceh-14 is expressed in the AFD neurons and required for thermotaxis behavior in C. elegans. ceh-14 mutant animals displayed defects in dendrite outgrowth of the phasmid neurons, while the ALA interneuron and some tail neurons showed ceh-14 and the paired-like homeobox gene ceh-17 act in the separate pathway to control normal axonal outgrowth of ALA neuron. Overexpression of CEH-14 in the nervous system may titrate out interacting factors, such as LDB-1, which caused developmental defects In paper IV, we investigated the function of four homeobox genes, ceh-6, ceh-26, ttx-1 and ceh-37, in the excretory cell development. We showed that the POU-III class homeobox gene ceh-6, the Prospero class homeobox gene ceh-26, and two otd/Otx family homeobox genes, ceh-37 and ttx-1 formed a regulatory hierarchy required for the development and function of the excretory cell in C. elegans. The excretory cell is required for maintaining osmotic balance and excreting waste products. While ceh-6 has previously been demonstrated to play a role in the excretory cell patterning, we showed here that ceh-26 and ceh-37 are expressed in the excretory cell. ceh-26 mutants arrested in early larval development with defects characteristic for a lack of excretory cell function. Double mutant of the otd/Otx genes ceh-37 and ttx-1 was displaying larval arrest, consistent with the excretory cell dysfunction, which indicates that there is functional redundancy between these two genes. Using mutant alleles and RNAi, we showed that ceh-26::GFP and ceh-37::GFP was down-regulated in ceh-6 mutants. Further, we found that ceh-37::GFP was down-regulated in the ceh-26 genes, such as channel proteins (the target genes ) that are expressed in the excretory cell and found that only a subset of the genes regulated by ceh-6 was also regulated by ceh-37/ttx-1. We mapped the promoter regions of ceh-26 and of the target gene clh-4 to identify putative homeodomain proteins binding sites. Given that these homeobox genes are well conserved in evolution, we may expect that parts of this cascade are also conserved in other organisms.

Place, publisher, year, edition, pages
Stockholm: Karolinska Institutet, 2010. p. 47
National Category
Biochemistry and Molecular Biology
Identifiers
urn:nbn:se:sh:diva-29738 (URN)978-91-7457-018-2 (ISBN)
Available from: 2016-03-14 Created: 2016-03-14 Last updated: 2016-03-14Bibliographically approved
Björk, P., Baurén, G., Jin, S., Tong, Y.-G., Bürglin, T. R., Hellman, U. & Wieslander, L. (2002). A novel conserved RNA-binding domain protein, RBD-1, is essential for ribosome biogenesis. Molecular Biology of the Cell, 13(10), 3683-3695
Open this publication in new window or tab >>A novel conserved RNA-binding domain protein, RBD-1, is essential for ribosome biogenesis
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2002 (English)In: Molecular Biology of the Cell, ISSN 1059-1524, E-ISSN 1939-4586, Vol. 13, no 10, p. 3683-3695Article in journal (Refereed) Published
Abstract [en]

Synthesis of the ribosomal subunits from pre-rRNA requires a large number of trans-acting proteins and small nucleolar ribonucleoprotein particles to execute base modifications, RNA cleavages, and structural rearrangements. We have characterized a novel protein, RNA-binding domain-1 (RBD-1), that is involved in ribosome biogenesis. This protein contains six consensus RNA-binding domains and is conserved as to sequence, domain organization, and cellular location from yeast to human. RBD-1 is essential in Caenorhabditis elegans. In the dipteran Chironomus tentans, RBD-1 (Ct-RBD-1) binds pre-rRNA in vitro and anti-Ct-RBD-1 antibodies repress pre-rRNA processing in vivo. Ct-RBD-1 is mainly located in the nucleolus in an RNA polymerase I transcription-dependent manner, but it is also present in discrete foci in the interchromatin and in the cytoplasm. In cytoplasmic extracts, 20-30% of Ct-RBD-1 is associated with ribosomes and, preferentially, with the 40S ribosomal subunit. Our data suggest that RBD-1 plays a role in structurally coordinating pre-rRNA during ribosome biogenesis and that this function is conserved in all eukaryotes.

National Category
Biochemistry and Molecular Biology
Identifiers
urn:nbn:se:sh:diva-29737 (URN)10.1091/mbc.E02-03-0138 (DOI)12388766 (PubMedID)
Available from: 2016-03-14 Created: 2016-03-14 Last updated: 2017-07-19Bibliographically approved
Tong, Y.-G., Meenon, K., Meenon, K., Prétôt, R., Viktorin-Aspöck, G. & Bürglin, T. R.A regulatory network of homeobox genes is required for the function of the Caenorhabditis elegans excretory cell.
Open this publication in new window or tab >>A regulatory network of homeobox genes is required for the function of the Caenorhabditis elegans excretory cell
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(English)Manuscript (preprint) (Other academic)
National Category
Biochemistry and Molecular Biology
Identifiers
urn:nbn:se:sh:diva-29736 (URN)
Note

Som manuskript i avhandling. As manuscript in dissertation.

Available from: 2016-03-14 Created: 2016-03-14 Last updated: 2016-03-14Bibliographically approved
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