The Remarkably Diverse Family of T-Box Factors in Caenorhabditis elegans

2017 ◽  
pp. 27-54 ◽  
Author(s):  
P.G. Okkema
Keyword(s):  
Caenorhabditis Elegans ◽  
T Box

scholarly journals Mapping and analysis of Caenorhabditis elegans transcription factor sequence specificities

eLife ◽  
2015 ◽  
Vol 4 ◽  
Author(s):  
Kamesh Narasimhan ◽  
Samuel A Lambert ◽  
Ally WH Yang ◽  
Jeremy Riddell ◽  
Sanie Mnaimneh ◽  
...  
Keyword(s):  
Caenorhabditis Elegans ◽  
Dna Binding ◽  
Regulatory Elements ◽  
Nuclear Hormone Receptor ◽  
Binding Motifs ◽  
T Box ◽  
C Elegans ◽  
Dna Binding Domains ◽  
Binding Domains ◽  
Protein Binding Microarray

Caenorhabditis elegans is a powerful model for studying gene regulation, as it has a compact genome and a wealth of genomic tools. However, identification of regulatory elements has been limited, as DNA-binding motifs are known for only 71 of the estimated 763 sequence-specific transcription factors (TFs). To address this problem, we performed protein binding microarray experiments on representatives of canonical TF families in C. elegans, obtaining motifs for 129 TFs. Additionally, we predict motifs for many TFs that have DNA-binding domains similar to those already characterized, increasing coverage of binding specificities to 292 C. elegans TFs (∼40%). These data highlight the diversification of binding motifs for the nuclear hormone receptor and C2H2 zinc finger families and reveal unexpected diversity of motifs for T-box and DM families. Motif enrichment in promoters of functionally related genes is consistent with known biology and also identifies putative regulatory roles for unstudied TFs.

SUMOylation-dependent function of a T-box transcriptional repressor in Caenorhabditis elegans

2007 ◽  
Vol 35 (6) ◽  
pp. 1424-1426 ◽  
Author(s):  
T.L. Crum ◽  
P.G. Okkema
Keyword(s):  
Transcription Factors ◽  
Caenorhabditis Elegans ◽  
Muscle Development ◽  
Transcriptional Repressor ◽  
Transcriptional Repressors ◽  
Pharyngeal Muscle ◽  
T Box ◽  
Subfamily Member ◽  
Dependent Function

T-box transcription factors are crucial developmental regulators, and they have not previously been associated with SUMOylation. In Caenorhabditis elegans, the Tbx2 subfamily member TBX-2 (T-box protein 2) is required for anterior pharyngeal muscle development. TBX-2 interacts with SUMOylation pathway enzymes, and loss of these enzymes phenocopies tbx-2 mutants. We hypothesize that TBX-2 functions as a SUMOylation-dependent transcriptional repressor. TBX-2 contains two consensus SUMOylation sites conserved in many T-box transcriptional repressors, and we suggest that the function of these T-box factors may similarly involve SUMOylation.

scholarly journals The Caenorhabditis elegans fate-determining gene mab-9 encodes a T-box protein required to pattern the posterior hindgut

2000 ◽  
Vol 14 (5) ◽  
pp. 596-603 ◽  
Author(s):  
Alison Woollard ◽  
Jonathan Hodgkin
Keyword(s):  
Caenorhabditis Elegans ◽  
Cell Fate ◽  
Transcriptional Regulators ◽  
Male Tail ◽  
T Box ◽  
Tail Development ◽  
Blast Cells ◽  
Direct Cell

Caenorhabditis elegans mab-9 mutants are defective in hindgut and male tail development because of cell fate transformations in two posterior blast cells, B and F. We have cloned mab-9 and show that it encodes a member of the T-box family of transcriptional regulators. MAB-9 localizes to the nucleus of B and F and their descendents during development, suggesting that it acts cell autonomously in the posterior hindgut to direct cell fate. T-box genes related to brachyury have also been implicated in hindgut patterning, and our results support models for an evolutionarily ancient role for these genes in hindgut formation.

Three novel T-box genes in Caenorhabditis elegans

Genome ◽  
1997 ◽  
Vol 40 (4) ◽  
pp. 458-464 ◽  
Author(s):  
Sergei I. Agulnik ◽  
Ilya Ruvinsky ◽  
Lee M. Silver
Keyword(s):  
Transcription Factor ◽  
Caenorhabditis Elegans ◽  
Genome Project ◽  
Pcr Analysis ◽  
Vertebrate Development ◽  
T Box ◽  
C Elegans ◽  
Close Proximity ◽  
Chromosome Iii ◽  
Chromosome Ii

The T-box gene family consists of members that share a unique DNA binding domain. The best characterized T-box gene, Brachyury or T, encodes a transcription factor that plays an important role in early vertebrate development. Seven other recently described mouse T-box genes are also expressed during development. In the nematode Caenorhabditis elegans, four T-box genes have been characterized to date. In this study, we describe three new C. elegans T-box genes, named Ce-tbx-11, Ce-tbx-12, and Ce-tbx-17. Ce-tbx-11 and Ce-tbx-17 were uncovered through the sequencing efforts of the C. elegans Genome Project. Ce-tbx-12 was uncovered through degenerate PCR analysis of C. elegans genomic DNA. Ce-tbx-11 and Ce-tbx-17 are located in close proximity to the four other previously described T-box genes in the central region of chromosome III. In contrast, Ce-tbx-12 maps alone to chromosome II. Phylogenetic analysis of all known T-box domain sequences provides evidence of an ancient origin for this gene family.Key words: transcription factor, T-box genes, evolution, Brachyury.

Conservation of the T-box gene family from Mus musculus to Caenorhabditis elegans

Genomics ◽  
1995 ◽  
Vol 25 (1) ◽  
pp. 214-219 ◽  
Author(s):  
Sergei I. Agulnik ◽  
Roni J. Bollag ◽  
Lee M. Silver
Keyword(s):  
Caenorhabditis Elegans ◽  
Gene Family ◽  
Mus Musculus ◽  
T Box

The glycomes of Caenorhabditis elegans and other model organisms

2002 ◽  
Vol 69 ◽  
pp. 117-134 ◽  
Author(s):  
Stuart M. Haslam ◽  
David Gems ◽  
Howard R. Morris ◽  
Anne Dell
Keyword(s):  
Caenorhabditis Elegans ◽  
Current Knowledge ◽  
Structural Data ◽  
Model Organisms ◽  
Entire Genome ◽  
C Elegans ◽  
The Face ◽  
Area Of Concern ◽  
Nematode Worm

There is no doubt that the immense amount of information that is being generated by the initial sequencing and secondary interrogation of various genomes will change the face of glycobiological research. However, a major area of concern is that detailed structural knowledge of the ultimate products of genes that are identified as being involved in glycoconjugate biosynthesis is still limited. This is illustrated clearly by the nematode worm Caenorhabditis elegans, which was the first multicellular organism to have its entire genome sequenced. To date, only limited structural data on the glycosylated molecules of this organism have been reported. Our laboratory is addressing this problem by performing detailed MS structural characterization of the N-linked glycans of C. elegans; high-mannose structures dominate, with only minor amounts of complex-type structures. Novel, highly fucosylated truncated structures are also present which are difucosylated on the proximal N-acetylglucosamine of the chitobiose core as well as containing unusual Fucα1–2Gal1–2Man as peripheral structures. The implications of these results in terms of the identification of ligands for genomically predicted lectins and potential glycosyltransferases are discussed in this chapter. Current knowledge on the glycomes of other model organisms such as Dictyostelium discoideum, Saccharomyces cerevisiae and Drosophila melanogaster is also discussed briefly.

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