scholarly journals Long-range interactions at the HO promoter.

1997 ◽  
Vol 17 (5) ◽  
pp. 2669-2678 ◽  
Author(s):  
H J McBride ◽  
R M Brazas ◽  
Y Yu ◽  
K Nasmyth ◽  
D J Stillman
Keyword(s):  
Binding Site ◽  
Long Range ◽  
Transcriptional Activation ◽  
Binding Sites ◽  
Point Mutations ◽  
Dna Binding Protein ◽  
Physical Interaction ◽  
Homeodomain Protein ◽  
Long Range Interactions ◽  
Ho Gene

The SWI5 gene encodes a zinc finger DNA-binding protein required for the transcriptional activation of the yeast HO gene. There are two Swi5p binding sites in the HO promoter, site A at -1800 and site B at -1300. Swi5p binding at site B has been investigated in some detail, and we have shown that Swi5p binds site B in a mutually cooperative fashion with Pho2p, a homeodomain protein. In this report, we demonstrate that Swi5p and Pho2p bind cooperatively to both sites A and B but that there are differences in binding to these two promoter sites. It has been shown previously that point mutations in either Swi5p binding site only modestly reduce HO expression in a PHO2 strain. We show that these mutant promoters are completely inactive in a pho2 mutant. We have created stronger point mutations at the two Swi5p binding sites within the HO promoter, and we show that the two binding sites, separated by 500 bp, are both absolutely required for HO expression, independent of PHO2. These results create an apparent dilemma, as the strong mutations at the Swi5p binding sites show that both binding sites are required for HO expression, but the earlier binding site mutations allow Swi5p to activate HO, but only in the presence of Pho2p. To explain these results, a model is proposed in which physical interaction between Swi5p proteins bound to these two sites separated by 500 bp is required for activation of the HO promoter. Experimental evidence is presented that supports the model. In addition, through deletion analysis we have identified a region near the amino terminus of Swi5p that is required for PHO2-independent activation of HO, suggesting that this region mediates the long-range interactions between Swi5p molecules bound at the distant sites.

DNA-binding and transcriptional regulatory properties of hepatic leukemia factor (HLF) and the t(17;19) acute lymphoblastic leukemia chimera E2A-HLF

1994 ◽  
Vol 14 (9) ◽  
pp. 5986-5996
Author(s):  
S P Hunger ◽  
R Brown ◽  
M L Cleary
Keyword(s):  
Dna Binding ◽  
Binding Site ◽  
Dna Sequences ◽  
Transcriptional Activation ◽  
Binding Sites ◽  
Lymphoblastic Leukemia ◽  
Consensus Sequence ◽  
Reporter Genes ◽  
Wild Type ◽  
Basic Leucine Zipper

The t(17;19) translocation in acute lymphoblastic leukemias results in creation of E2A-hepatic leukemia factor (HLF) chimeric proteins that contain the DNA-binding and protein dimerization domains of the basic leucine zipper (bZIP) protein HLF fused to a portion of E2A proteins with transcriptional activation properties. An in vitro binding site selection procedure was used to determine DNA sequences preferentially bound by wild-type HLF and chimeric E2A-HLF proteins isolated from various t(17;19)-bearing leukemias. All were found to selectively bind the consensus sequence 5'-GTTACGTAAT-3' with high affinity. Wild-type and chimeric HLF proteins also bound closely related sites identified previously for bZIP proteins of both the proline- and acidic amino acid-rich (PAR) and C/EBP subfamilies; however, E2A-HLF proteins were significantly less tolerant of certain deviations from the HLF consensus binding site. These differences were directly attributable to loss of an HLF ancillary DNA-binding domain in all E2A-HLF chimeras and were further exacerbated by a zipper mutation in one isolate. Both wild-type and chimeric HLF proteins displayed transcriptional activator properties in lymphoid and nonlymphoid cells on reporter genes containing HLF or C/EBP consensus binding sites. But on reporter genes with nonoptimal binding sites, their transcriptional properties diverged and E2A-HLF competitively inhibited activation by wild-type PAR proteins. These findings establish a spectrum of binding site-specific transcriptional properties for E2A-HLF which may preferentially activate expression of select subordinate genes as a homodimer and potentially antagonize expression of others through heteromeric interactions.

scholarly journals Dissection of a carboxy-terminal region of the yeast regulatory protein RAP1 with effects on both transcriptional activation and silencing

1992 ◽  
Vol 12 (3) ◽  
pp. 1209-1217
Author(s):  
C F Hardy ◽  
D Balderes ◽  
D Shore
Keyword(s):  
Dna Binding ◽  
Binding Site ◽  
Transcriptional Activation ◽  
Binding Sites ◽  
Binding Protein ◽  
Binding Domain ◽  
Dominant Negative Effect ◽  
Dna Binding Domain ◽  
Wild Type ◽  
Carboxy Terminal

RAP1 is an essential sequence-specific DNA-binding protein in Saccharomyces cerevisiae whose binding sites are found in a large number of promoters, where they function as upstream activation sites, and at the silencer elements of the HMR and HML mating-type loci, where they are important for repression. We have examined the involvement of specific regions of the RAP1 protein in both repression and activation of transcription by studying the properties of a series of hybrid proteins containing RAP1 sequences fused to the DNA-binding domain of the yeast protein GAL4 (amino acids 1 to 147). GAL4 DNA-binding domain/RAP1 hybrids containing only the carboxy-terminal third of the RAP1 protein (which lacks the RAP1 DNA-binding domain) function as transcriptional activators of a reporter gene containing upstream GAL4 binding sites. Expression of some hybrids from the strong ADH1 promoter on multicopy plasmids has a dominant negative effect on silencers, leading to either partial or complete derepression of normally silenced genes. The GAL4/RAP1 hybrids have different effects on wild-type and several mutated but functional silencers. Silencers lacking either an autonomously replicating sequence consensus element or the RAP1 binding site are strongly derepressed, whereas the wild-type silencer or a silencer containing a deletion of the binding site for another silencer-binding protein, ABF1, are only weakly affected by hybrid expression. By examining a series of GAL4 DNA-binding domain/RAP1 hybrids, we have mapped the transcriptional activation and derepression functions to specific parts of the RAP1 carboxy terminus.(ABSTRACT TRUNCATED AT 250 WORDS)

scholarly journals DNA-binding and transcriptional regulatory properties of hepatic leukemia factor (HLF) and the t(17;19) acute lymphoblastic leukemia chimera E2A-HLF.

1994 ◽  
Vol 14 (9) ◽  
pp. 5986-5996 ◽  
Author(s):  
S P Hunger ◽  
R Brown ◽  
M L Cleary
Keyword(s):  
Dna Binding ◽  
Binding Site ◽  
Dna Sequences ◽  
Transcriptional Activation ◽  
Binding Sites ◽  
Lymphoblastic Leukemia ◽  
Consensus Sequence ◽  
Reporter Genes ◽  
Wild Type ◽  
Basic Leucine Zipper

The t(17;19) translocation in acute lymphoblastic leukemias results in creation of E2A-hepatic leukemia factor (HLF) chimeric proteins that contain the DNA-binding and protein dimerization domains of the basic leucine zipper (bZIP) protein HLF fused to a portion of E2A proteins with transcriptional activation properties. An in vitro binding site selection procedure was used to determine DNA sequences preferentially bound by wild-type HLF and chimeric E2A-HLF proteins isolated from various t(17;19)-bearing leukemias. All were found to selectively bind the consensus sequence 5'-GTTACGTAAT-3' with high affinity. Wild-type and chimeric HLF proteins also bound closely related sites identified previously for bZIP proteins of both the proline- and acidic amino acid-rich (PAR) and C/EBP subfamilies; however, E2A-HLF proteins were significantly less tolerant of certain deviations from the HLF consensus binding site. These differences were directly attributable to loss of an HLF ancillary DNA-binding domain in all E2A-HLF chimeras and were further exacerbated by a zipper mutation in one isolate. Both wild-type and chimeric HLF proteins displayed transcriptional activator properties in lymphoid and nonlymphoid cells on reporter genes containing HLF or C/EBP consensus binding sites. But on reporter genes with nonoptimal binding sites, their transcriptional properties diverged and E2A-HLF competitively inhibited activation by wild-type PAR proteins. These findings establish a spectrum of binding site-specific transcriptional properties for E2A-HLF which may preferentially activate expression of select subordinate genes as a homodimer and potentially antagonize expression of others through heteromeric interactions.

scholarly journals A yeast ARS-binding protein activates transcription synergistically in combination with other weak activating factors.

1990 ◽  
Vol 10 (3) ◽  
pp. 887-897 ◽  
Author(s):  
A R Buchman ◽  
R D Kornberg
Keyword(s):  
Dna Sequences ◽  
Transcriptional Activation ◽  
Binding Sites ◽  
Essential Gene ◽  
Specific Binding ◽  
Binding Protein ◽  
Point Mutations ◽  
Yeast Genes

ABFI (ARS-binding protein I) is a yeast protein that binds specific DNA sequences associated with several autonomously replicating sequences (ARSs). ABFI also binds sequences located in promoter regions of some yeast genes, including DED1, an essential gene of unknown function that is transcribed constitutively at a high level. ABFI was purified by specific binding to the DED1 upstream activating sequence (UAS) and was found to recognize related sequences at several other promoters, at an ARS (ARS1), and at a transcriptional silencer (HMR E). All ABFI-binding sites, regardless of origin, provided weak UAS function in vivo when examined in test plasmids. UAS function was abolished by point mutations that reduced ABFI binding in vitro. Analysis of the DED1 promoter showed that two ABFI-binding sites combine synergistically with an adjacent T-rich sequence to form a strong constitutive activator. The DED1 T-rich element acted synergistically with all other ABFI-binding sites and with binding sites for other multifunctional yeast activators. An examination of the properties of sequences surrounding ARS1 left open the possibility that ABFI enhances the initiation of DNA replication at ARS1 by transcriptional activation.

scholarly journals Dissection of a carboxy-terminal region of the yeast regulatory protein RAP1 with effects on both transcriptional activation and silencing.

1992 ◽  
Vol 12 (3) ◽  
pp. 1209-1217 ◽  
Author(s):  
C F Hardy ◽  
D Balderes ◽  
D Shore
Keyword(s):  
Dna Binding ◽  
Binding Site ◽  
Transcriptional Activation ◽  
Binding Sites ◽  
Binding Protein ◽  
Binding Domain ◽  
Dominant Negative Effect ◽  
Dna Binding Domain ◽  
Wild Type ◽  
Carboxy Terminal

RAP1 is an essential sequence-specific DNA-binding protein in Saccharomyces cerevisiae whose binding sites are found in a large number of promoters, where they function as upstream activation sites, and at the silencer elements of the HMR and HML mating-type loci, where they are important for repression. We have examined the involvement of specific regions of the RAP1 protein in both repression and activation of transcription by studying the properties of a series of hybrid proteins containing RAP1 sequences fused to the DNA-binding domain of the yeast protein GAL4 (amino acids 1 to 147). GAL4 DNA-binding domain/RAP1 hybrids containing only the carboxy-terminal third of the RAP1 protein (which lacks the RAP1 DNA-binding domain) function as transcriptional activators of a reporter gene containing upstream GAL4 binding sites. Expression of some hybrids from the strong ADH1 promoter on multicopy plasmids has a dominant negative effect on silencers, leading to either partial or complete derepression of normally silenced genes. The GAL4/RAP1 hybrids have different effects on wild-type and several mutated but functional silencers. Silencers lacking either an autonomously replicating sequence consensus element or the RAP1 binding site are strongly derepressed, whereas the wild-type silencer or a silencer containing a deletion of the binding site for another silencer-binding protein, ABF1, are only weakly affected by hybrid expression. By examining a series of GAL4 DNA-binding domain/RAP1 hybrids, we have mapped the transcriptional activation and derepression functions to specific parts of the RAP1 carboxy terminus.(ABSTRACT TRUNCATED AT 250 WORDS)

Modulation of Compactness and Long-Range Interactions of Unfolded Lysozyme by Single Point Mutations

2004 ◽  
Vol 116 (43) ◽  
pp. 5904-5909 ◽  
Author(s):  
Julia Wirmer ◽  
Christian Schlörb ◽  
Judith Klein-Seetharaman ◽  
Ryoma Hirano ◽  
Tadashi Ueda ◽  
...  
Keyword(s):  
Long Range ◽  
Single Point ◽  
Point Mutations ◽  
Long Range Interactions ◽  
Single Point Mutations

scholarly journals Vibrio cholerae ToxT Independently Activates the Divergently Transcribed aldA and tagA Genes

2005 ◽  
Vol 187 (23) ◽  
pp. 7890-7900 ◽  
Author(s):  
Jeffrey H. Withey ◽  
Victor J. DiRita
Keyword(s):  
Small Intestine ◽  
Binding Site ◽  
Vibrio Cholerae ◽  
Virulence Factors ◽  
Transcriptional Activation ◽  
Binding Sites ◽  
Inverted Repeat ◽  
Transcriptional Regulators ◽  
Dna Binding Sites ◽  
Genes Encoding

ABSTRACT The Vibrio cholerae ToxT regulon includes the genes encoding cholera toxin (CT) and the toxin-coregulated pilus (TCP), which are the major virulence factors required for causing cholera disease and colonizing the upper small intestine of the host, respectively. The genes encoding CT, ctxAB, and the genes encoding the components of the TCP, tcpA to tcpJ, are organized within operons, upstream of which are DNA binding sites for the transcriptional activator ToxT. ToxT is a member of the large AraC/XylS family of transcriptional regulators and also activates transcription of five other genes whose roles in V. cholerae pathogenesis, if any, are poorly understood. acfA and acfD are divergently transcribed genes required for efficient colonization of the intestine. Transcriptional activation of acfA and acfD requires a pair of central ToxT binding sites in an inverted-repeat configuration for ToxT-directed transcription of both genes. tcpI has an unknown role in pathogenesis. aldA and tagA are divergently transcribed genes that also have unknown roles in pathogenesis. In this study, we map the aldA and tagA promoters and identify the ToxT binding sites upstream of each gene. Our results suggest that two ToxT binding sites in an inverted-repeat configuration are required for ToxT-directed transcription of tagA and that a single ToxT binding site is required for ToxT-directed transcription of aldA. Furthermore, to direct transcription of tagA and aldA, ToxT uses independent binding regions upstream of each gene, in contrast to what we previously found for the divergently transcribed acfA and acfD genes, which share ToxT binding sites between the two genes.

Responding to Media Inquiries about Earthquake Triggering Interactions

2021 ◽  
Author(s):  
Fang Fan ◽  
Lingling Ye ◽  
Hiroo Kanamori ◽  
Thorne Lay
Keyword(s):  
Long Range ◽  
Aftershock Sequence ◽  
Public Understanding ◽  
Physical Interaction ◽  
Earthquake Triggering ◽  
Dynamic Triggering ◽  
Long Range Interactions ◽  
The Media ◽  
To Come ◽  
Frequency Relationship

Abstract In the aftermath of a significant earthquake, seismologists are frequently asked questions by the media and public regarding possible interactions with recent prior events, including events at great distances away, along with prospects of larger events yet to come, both locally and remotely. For regions with substantial earthquake catalogs that provide information on the regional Gutenberg–Richter magnitude–frequency relationship, Omori temporal aftershock statistical behavior, and aftershock productivity parameters, probabilistic responses can be provided for likelihood of nearby future events of larger magnitude, as well as expected behavior of the overall aftershock sequence. However, such procedures generally involve uncertain extrapolations of parameterized equations to infrequent large events and do not provide answers to inquiries about long-range interactions, either retrospectively for interaction with prior remote large events or prospectively for interaction with future remote large events. Dynamic triggering that may be involved in such long-range interactions occurs, often with significant temporal delay, but is not well understood, making it difficult to respond to related inquiries. One approach to addressing such inquiries is to provide retrospective or prospective occurrence histories for large earthquakes based on global catalogs; while not providing quantitative understanding of any physical interaction, experience-based guidance on the (typically very low) chances of causal interactions can inform public understanding of likelihood of specific scenarios they are commonly very interested in.

Cooperative binding of an Ultrabithorax homeodomain protein to nearby and distant DNA sites

1993 ◽  
Vol 13 (11) ◽  
pp. 6941-6956
Author(s):  
P A Beachy ◽  
J Varkey ◽  
K E Young ◽  
D P von Kessler ◽  
B I Sun ◽  
...  
Keyword(s):  
Binding Site ◽  
Transcriptional Activation ◽  
Regulatory Protein ◽  
Transcriptional Response ◽  
Regulatory Elements ◽  
Dna Looping ◽  
Integrative Model ◽  
Cooperative Binding ◽  
Homeodomain Protein ◽  
Carboxy Terminal

Cooperativity in binding of regulatory proteins to multiple DNA sites can heighten the sensitivity and specificity of the transcriptional response. We report here the cooperative DNA-binding properties of a developmentally active regulatory protein encoded by the Drosophila homeotic gene Ultrabithorax (Ubx). We show that naturally occurring binding sites for the Ubx-encoded protein contain clusters of multiple individual binding site sequences. Such sites can form complexes containing a dozen or more Ubx-encoded protein molecules, with simultaneous cooperative interactions between adjacent and distant DNA sites. The distant mode of interaction involves a DNA looping mechanism; both modes appear to enhance transcriptional activation in a simple yeast assay system. We found that cooperative binding is dependent on sequences outside the homeodomain, and we have identified regions predicted to form coiled coils carboxy terminal to the homeodomains of the Ubx-encoded protein and several other homeotic proteins. On the basis of our findings, we propose a multisite integrative model of homeotic protein action in which functional regulatory elements can be built from a few high-affinity sites, from many lower-affinity sites, or from sites of some intermediate number and affinity. An important corollary of this model is that even small differences in binding of homeotic proteins to individual sites could be summed to yield large overall differences in binding to multiple sites. This model is consistent with reports that homeodomain protein targets contain multiple individual binding site sequences distributed throughout sizable DNA regions. Also consistent is a recent report that sequences carboxy terminal to the Ubx homeodomain can contribute to segmental specificity.

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