CRITERIA FOR AN UPDATED CLASSIFICATION OF HUMAN TRANSCRIPTION FACTOR DNA-BINDING DOMAINS

2013 ◽  
Vol 11 (01) ◽  
pp. 1340007 ◽  
Author(s):  
EDGAR WINGENDER
Keyword(s):  
Dna Binding ◽  
Leucine Zipper ◽  
Regulatory Elements ◽  
Biological Species ◽  
Basic Leucine Zipper ◽  
Dna Binding Domains ◽  
Binding Domains ◽  
Comprehensive Classification ◽  
Human Transcription Factor

By binding to cis-regulatory elements in a sequence-specific manner, transcription factors regulate the activity of nearby genes. Here, we discuss the criteria for a comprehensive classification of human TFs based on their DNA-binding domains. In particular, classification of basic leucine zipper (bZIP) and zinc finger factors is exemplarily discussed. The resulting classification can be used as a template for TFs of other biological species.

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.

scholarly journals B-Cell Coactivator OBF-1 Exhibits Unusual Transcriptional Properties and Functions in a DNA-Bound Oct-1-Dependent Fashion

1999 ◽  
Vol 19 (6) ◽  
pp. 4247-4254 ◽  
Author(s):  
Andrea Krapp ◽  
Michel Strubin
Keyword(s):  
Dna Binding ◽  
B Cell ◽  
Target Genes ◽  
Regulatory Elements ◽  
Binding Domain ◽  
Dna Binding Domain ◽  
Activation Domain ◽  
Activation Domains ◽  
Dna Binding Domains ◽  
Binding Domains

ABSTRACT Eukaryotic transcriptional activators generally comprise both a DNA-binding domain that recognizes specific cis-regulatory elements in the target genes and an activation domain which is essential for transcriptional stimulation. Activation domains typically behave as structurally and functionally autonomous modules that retain their intrinsic activities when directed to a promoter by a variety of heterologous DNA-binding domains. Here we report that OBF-1, a B-cell-specific coactivator for transcription factor Oct-1, challenges this traditional view in that it contains an atypical activation domain that exhibits two unexpected functional properties when tested in the yeast Saccharomyces cerevisiae. First, OBF-1 by itself has essentially no intrinsic activation potential, yet it strongly synergizes with other activation domains such as VP16 and Gal4. Second, OBF-1 exerts its effect in association with DNA-bound Oct-1 but is inactive when attached to a heterologous DNA-binding domain. These findings suggest that activation by OBF-1 is not obtained by simple recruitment of the coactivator to the promoter but requires interaction with DNA-bound Oct-1 to stimulate a step distinct from those regulated by classical activation domains.

scholarly journals Diverse Eukaryotic CGG-Binding Proteins Produced by Independent Domestications of hAT Transposons

2021 ◽  
Author(s):  
Isaac Yellan ◽  
Ally W H Yang ◽  
Timothy R Hughes
Keyword(s):  
Dna Binding ◽  
Binding Proteins ◽  
Sequence Specificity ◽  
Binding Motifs ◽  
Dna Binding Domains ◽  
Binding Domains ◽  
Dna Binding Motifs ◽  
Wide Range ◽  
Human Transcription Factor ◽  
Hat Transposons

Abstract The human transcription factor (TF) CGGBP1 (CGG-binding protein) is conserved only in amniotes and is believed to derive from the zf-BED and Hermes transposase DNA-binding domains (DBDs) of a hAT DNA transposon. Here, we show that sequence-specific DNA-binding proteins with this bipartite domain structure have resulted from dozens of independent hAT domestications in different eukaryotic lineages. CGGBPs display a wide range of sequence specificity, usually including preferences for CGG or CGC trinucleotides, whereas some bind AT-rich motifs. The CGGBPs are almost entirely nonsyntenic, and their protein sequences, DNA-binding motifs, and patterns of presence or absence in genomes are uncharacteristic of ancestry via speciation. At least eight CGGBPs in the coelacanth Latimeria chalumnae bind distinct motifs, and the expression of the corresponding genes varies considerably across tissues, suggesting tissue-restricted function.

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