scholarly journals 5-Hydroxymethylcytosine in E-box motifs ACAT|GTG and ACAC|GTG increases DNA-binding of the B-HLH transcription factor TCF4

2016 ◽  
Vol 8 (9) ◽  
pp. 936-945 ◽  
Author(s):  
Syed Khund-Sayeed ◽  
Ximiao He ◽  
Timothy Holzberg ◽  
Jun Wang ◽  
Divya Rajagopal ◽  
...  

We designed a novel method to double-strand Agilent microarrays such that 5mC and 5hmC are incorporated on one DNA strand. Using protein binding microarrays we demonstrate the utility of this method in exploring how cytosine modification outside of CG dinucleotide alter the DNA binding of sequence-specific transcription factors.

1992 ◽  
Vol 103 (1) ◽  
pp. 9-14 ◽  
Author(s):  
K.A. Lee

Dimeric transcription factors that bind to DNA are often grouped into families on the basis of dimerization and DNA-binding specificities. cDNA cloning studies have established that members of the same family have structurally related dimerisation and DNA-binding domains but diverge in other regions that are important for transcriptional activation. These features lead to the straightforward suggestion that although all members of a family bind to similar DNA elements, individual members exhibit distinct transcriptional effector functions. This simple view is now supported by experimental evidence from those systems that have proved amenable to study. There are however some largely unaddressed questions that concern the mechanisms that allow family members to go about their business without interference from their highly related siblings. Here I will discuss some insights from studies of the bZIP class of transcription factors.


1992 ◽  
Vol 146 (1) ◽  
pp. 25-28 ◽  
Author(s):  
Xiao-Bing Wang ◽  
Yasuhiro Watanabe ◽  
Takesi Osugi ◽  
Mitsushi Ikemoto ◽  
Masayuki Hirata ◽  
...  

1998 ◽  
Vol 18 (7) ◽  
pp. 4089-4096 ◽  
Author(s):  
Benjamin L. Ebert ◽  
H. Franklin Bunn

ABSTRACT Molecular adaptation to hypoxia depends on the binding of hypoxia-inducible factor 1 (HIF-1) to cognate response elements in oxygen-regulated genes. In addition, adjacent sequences are required for hypoxia-inducible transcription. To investigate the mechanism of interaction between these cis-acting sequences, the multiprotein complex binding to the lactate dehydrogenase A (LDH-A) promoter was characterized. The involvement of HIF-1, CREB-1/ATF-1, and p300/CREB binding protein (CBP) was demonstrated by techniques documenting in vitro binding, in combination with transient transfections that test the in vivo functional importance of each protein. In both the LDH-A promoter and the erythropoietin 3′ enhancer, formation of multiprotein complexes was analyzed by using biotinylated probes encompassing functionally critical cis-acting sequences. Strong binding of p300/CBP required interactions with multiple DNA binding proteins. Thus, the necessity of transcription factor binding sites adjacent to a HIF-1 site for hypoxically inducible transcription may be due to the requirement of p300 to interact with multiple transcription factors for high-affinity binding and activation of transcription. Since it has been found to interact with a wide range of transcription factors, p300 is likely to play a similar role in other genes, mediating interactions between DNA binding proteins, thereby activating stimulus-specific and tissue-specific gene transcription.


2004 ◽  
Vol 24 (21) ◽  
pp. 9517-9526 ◽  
Author(s):  
Lynn M. Powell ◽  
Petra I. zur Lage ◽  
David R. A. Prentice ◽  
Biruntha Senthinathan ◽  
Andrew P. Jarman

ABSTRACT For a particular functional family of basic helix-loop-helix (bHLH) transcription factors, there is ample evidence that different factors regulate different target genes but little idea of how these different target genes are distinguished. We investigated the contribution of DNA binding site differences to the specificities of two functionally related proneural bHLH transcription factors required for the genesis of Drosophila sense organ precursors (Atonal and Scute). We show that the proneural target gene, Bearded, is regulated by both Scute and Atonal via distinct E-box consensus binding sites. By comparing with other Ato-dependent enhancer sequences, we define an Ato-specific binding consensus that differs from the previously defined Scute-specific E-box consensus, thereby defining distinct EAto and ESc sites. These E-box variants are crucial for function. First, tandem repeats of 20-bp sequences containing EAto and ESc sites are sufficient to confer Atonal- and Scute-specific expression patterns, respectively, on a reporter gene in vivo. Second, interchanging EAto and ESc sites within enhancers almost abolishes enhancer activity. While the latter finding shows that enhancer context is also important in defining how proneural proteins interact with these sites, it is clear that differential utilization of DNA binding sites underlies proneural protein specificity.


1998 ◽  
Vol 62 (3) ◽  
pp. 586-596 ◽  
Author(s):  
Richard A. Wilson ◽  
Herbert N. Arst

SUMMARY The transcriptional activator AREA is a member of the GATA family of transcription factors and mediates nitrogen metabolite repression in the fungus Aspergillus nidulans. The nutritional versatility of A. nidulans and its amenability to classical and reverse genetic manipulations make the AREA DNA binding domain (DBD) a useful model for analyzing GATA family DBDs, particularly as structures of two AREA-DNA complexes have been determined. The 109 extant mutant forms of the AREA DBD surveyed here constitute one of the highest totals of eukaryotic transcription factor DBD mutants, are discussed in light of the roles of individual residues, and are compared to corresponding mutant sequence changes in other fungal GATA factor DBDs. Other topics include delineation of the DBD using both homology and mutational truncation, use of frameshift reversion to detect regions of tolerance to mutational change, the finding that duplication of the DBD can apparently enhance AREA function, and use of the AREA system to analyze a vertebrate GATA factor DBD. Some major points to emerge from work on the AREA DBD are (i) tolerance to sequence change (with retention of function) is surprisingly great, (ii) mutational changes in a transcription factor can have widely differing, even opposing, effects on expression of different structural genes so that monitoring expression of one or even several structural genes can be insufficient and possibly misleading, and (iii) a mutational change altering local hydrophobic packing and DNA binding target specificity can markedly influence the behavior of mutational changes elsewhere in the DBD.


1992 ◽  
Vol 12 (8) ◽  
pp. 3449-3459
Author(s):  
A L Nielsen ◽  
N Pallisgaard ◽  
F S Pedersen ◽  
P Jørgensen

The enhancer region of Akv murine leukemia virus contains the sequence motif ACAGATGG. This sequence is homologous to the E-box motif originally defined as a regulatory element in the enhancers of immunoglobulin mu and kappa genes. We have used double-stranded oligonucleotide probes, corresponding to the E box of the murine leukemia virus Akv, to screen a randomly primed lambda gt11 cDNA expression library made from mouse NIH 3T3 fibroblast RNA. We have identified seven lambda clones expressing DNA-binding proteins representing two different genes termed ALF1 and ALF2. The results of sequencing ALF2 cDNA suggests that we have recovered the gene for the basic-helix-loop-helix transcription factor A1, the murine analog of the human transcription factor E47. The cDNA sequence of ALF1 codes for a new member of the basic-helix-loop-helix protein family. Two splice variants of ALF1 cDNA have been found, differing by a 72-bp insertion, coding for putative proteins of 682 and 706 amino acids. The two ALF1 mRNAs are expressed at various levels in mouse tissues. In vitro DNA binding assays, using prokaryotically expressed ALF1 proteins, demonstrated specific binding of the ALF1 proteins to the Akv murine leukemia virus E-box motif ACAGATGG. Expression in NIH 3T3 fibroblasts of GAL4-ALF1 chimeric protein stimulated expression from a minimal promoter linked to a GAL4 binding site, indicating the existence of a transcriptional activator domain in ALF1.


Blood ◽  
2007 ◽  
Vol 110 (11) ◽  
pp. 56-56
Author(s):  
Irene Riz ◽  
Kristin K. Baxter ◽  
Hyo Jung Lee ◽  
Reza Behnam ◽  
Teresa S. Hawley ◽  
...  

Abstract Homeodomain proteins (homeoproteins) have long been recognized as powerful transcriptional regulators. Inappropriate expression of these transcription factors often leads to major developmental malformations or malignant transformation. The in vitro DNA binding sites of homeoproteins are short sequences that are widely distributed throughout the genome and some canonical binding sites have been shown to be functionally important at distances >20 kb away from the nearest transcription start site. In addition to DNA-binding activity, several homeoproteins have been demonstrated to interact with chromatin-modifying enzymes. For example, we and others have reported that the TLX1 homeoprotein of T-cell acute lymphoblastic leukemia (T-ALL) inhibits the PP1/PP2A serine/threonine phosphatases (I. Riz and R.G. Hawley, Oncogene 24: 5561–5575, 2005) and more recently have found that TLX1 modulates histone/transcription factor acetyltransferase CBP activity (I. Riz et al., Oncogene 26: 4115–4123, 2007). PP1/PP2A and CBP are complex molecular machines integrating diverse regulatory pathways that impact on cell survival, proliferation and differentiation outcomes. Organogenesis and malignant transformation - despite obvious differences - share a common requirement for high-order cooperativity of transcription factors and transcriptional cofactors in regulating the expression of multiple sets of genes executing cell fate shifts. Targeting key regulatory nodes in order to coordinately regulate multiple genes is a common strategy of virus induced cell-transformation: accordingly, PP1/PP2A and CBP are targeted by transforming viral proteins. The Groucho/TLE (transducin-like Enhancer-of-split) family of corepressors are another example of master regulators of cell fate; for instance, it was reported that triggering the MAPK signaling cascade inactivates TLE corepressors leading to coordinated derepression of a large number of genes involved in cell proliferation. We now demonstrate that TLX1 interferes with TLE1 repressive function. By streptavidin affinity-based precipitation of biotinylated recombinant TLX1 protein (TLX1 fused to a biotinylation peptide) we show in vivo interaction of TLX1 and TLE1 in several different cell types, including human T-ALL and neuroblastoma cells. Interaction of TLX1 with TLE1 occurs via an Engrailed homology 1 (Eh1)-like domain as documented by GST pull-down assays and laser scanning confocal microscopy. Transient transfection experiments indicate that TLX1 prevents TLE1-mediated repression of reporter genes. Furthermore, in the context of endogenous chromatin structure, TLX1 derepresses the bHLH transcription factor gene, ACSL1(HASH1), a well characterized target of the HES1/TLE1 repressor complex. The process requires direct interaction of TLX1 with TLE1 and binding of TLX1 to DNA, since a point mutation in the Eh1-like motif or deletion of the third helix of the TLX1 homeodomain abrogated the effect. Additional data to be presented suggest a long-range mechanism of transcriptional regulation by TLX1: we propose that “transcriptional activation” by TLX1 (and, by analogy, other homeoproteins that interact with TLE corepressors) results in part from the chaperoned redistribution of TLE corepressors from proximal promoter regions of target genes to distal chromatin regulatory sites.


2003 ◽  
Vol 23 (21) ◽  
pp. 7585-7599 ◽  
Author(s):  
Zhixiong Xu ◽  
Suming Huang ◽  
Long-Sheng Chang ◽  
Alan D. Agulnick ◽  
Stephen J. Brandt

ABSTRACT The TAL1 (or SCL) gene, originally identified from its involvement by a recurrent chromosomal translocation, encodes a basic helix-loop-helix transcription factor essential for erythropoiesis. Although presumed to regulate transcription, its target genes are largely unknown. We show here that a nuclear complex containing TAL1, its DNA-binding partner E47, zinc finger transcription factor GATA-1, LIM domain protein LMO2, and LIM domain-binding protein Ldb1 transactivates the protein 4.2 (P4.2) gene through two E box GATA elements in its proximal promoter. Binding of this complex to DNA was dependent on the integrity of both E box and GATA sites and was demonstrated to occur on the P4.2 promoter in cells. Maximal transcription in transiently transfected cells required both E box GATA elements and expression of all five components of the complex. This complex was shown, in addition, to be capable of linking in solution double-stranded oligonucleotides corresponding to the two P4.2 E box GATA elements. This DNA-linking activity required Ldb1 and increased with dimethyl sulfoxide-induced differentiation of murine erythroleukemia (MEL) cells. In contrast, enforced expression in MEL cells of dimerization-defective mutant Ldb1, as well as wild-type Ldb1, significantly decreased E box GATA DNA-binding activities, P4.2 promoter activity, and accumulation of P4.2 and β-globin mRNAs. These studies define a physiologic target for a TAL1- and GATA-1-containing ternary complex and reveal a positive role for Ldb1 in erythroid gene expression and differentiation.


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