scholarly journals Roles of Transcription Factor Mot3 and Chromatin in Repression of the Hypoxic Gene ANB1 in Yeast

2000 ◽  
Vol 20 (19) ◽  
pp. 7088-7098 ◽  
Author(s):  
Alexander J. Kastaniotis ◽  
Thomas A. Mennella ◽  
Christian Konrad ◽  
Ana M. Rodriguez Torres ◽  
Richard S. Zitomer
Keyword(s):  
Binding Site ◽  
Regulatory Region ◽  
Direct Interaction ◽  
Minor Effect ◽  
Histone H4 ◽  
Coding Region ◽  
Basal Transcriptional Machinery ◽  
In The Wild ◽  
A Minor

ABSTRACT The hypoxic genes of Saccharomyces cerevisiae are repressed by a complex consisting of the aerobically expressed, sequence-specific DNA-binding protein Rox1 and the Tup1-Ssn6 general repressors. The regulatory region of one well-studied hypoxic gene,ANB1, is comprised of two operators, OpA and OpB, each of which has two strong Rox1 binding sites, yet OpA represses transcription almost 10 times more effectively than OpB. We show here that this difference is due to the presence of a Mot3 binding site in OpA. Mutations in this site reduced OpA repression to OpB levels, and the addition of a Mot3 binding site to OpB enhanced repression. Deletion of the mot3 gene also resulted in reduced repression of ANB1. Repression of two other hypoxic genes in which Mot3 sites were associated with Rox1 sites was reduced in the deletion strain, but other hypoxic genes were unaffected. In addition, the mot3Δ mutation caused a partial derepression of the Mig1–Tup1-Ssn6-repressed SUC2 gene, but not the α2–Mcm1–Tup1-Ssn6-repressed STE2 gene. The Mot3 protein was demonstrated to bind to the ANB1 OpA in vitro. Competition experiments indicated that there was no interaction between Rox1 and Mot3, indicating that Mot3 functions either in Tup1-Ssn6 recruitment or directly in repression. A great deal of evidence has accumulated suggesting that the Tup1-Ssn6 complex represses transcription through both nucleosome positioning and a direct interaction with the basal transcriptional machinery. We demonstrate here that under repressed conditions a nucleosome is positioned over the TATA box in the wild-type ANB1promoter. This nucleosome was absent in cells carrying arox1, tup1, or mot3 deletion, all of which cause some degree of derepression. Interestingly, however, this positioned nucleosome was also lost in a cell carrying a deletion of the N-terminal coding region of histone H4, yet ANB1expression remained fully repressed. A similar deletion in the gene for histone H3, which had no effect on repression, had only a minor effect on the positioned nucleosome. These results indicate that the nucleosome phasing on the ANB1 promoter caused by the Rox1–Mot3–Tup1-Ssn6 complex is either completely redundant with a chromatin-independent repression mechanism or, less likely, plays no role in repression at all.

UHF-1, a factor required for maximal transcription of early and late sea urchin histone H4 genes: analysis of promoter-binding sites

1991 ◽  
Vol 11 (2) ◽  
pp. 1048-1061
Author(s):  
I J Lee ◽  
L Tung ◽  
D A Bumcrot ◽  
E S Weinberg
Keyword(s):  
Binding Site ◽  
Sea Urchin ◽  
Transcriptional Start Site ◽  
Sodium Dodecyl ◽  
Nuclear Extract ◽  
Dnase I ◽  
Histone H4 ◽  
Band Shift

A protein, denoted UHF-1, was found to bind upstream of the transcriptional start site of both the early and late H4 (EH4 and LH4) histone genes of the sea urchin Strongylocentrotus purpuratus. A nuclear extract from hatching blastulae contained proteins that bind to EH4 and LH4 promoter fragments in a band shift assay and produced sharp DNase I footprints upstream of the EH4 gene (from -133 to -106) and the LH4 gene (from -94 to -66). DNase I footprinting performed in the presence of EH4 and LH4 promoter competitor DNAs indicated that UHF-1 binds more strongly to the EH4 site. A sequence match of 11 of 13 nucleotides was found within the two footprinted regions: [sequence: see text]. Methylation interference and footprinting experiments showed that UHF-1 bound to the two sites somewhat differently. DNA-protein UV cross-linking studies indicated that UHF-1 has an electrophoretic mobility on sodium dodecyl sulfate-acrylamide gels of approximately 85 kDa and suggested that additional proteins, specific to each promoter, bind to each site. In vitro and in vivo assays were used to demonstrate that the UHF-1-binding site is essential for maximal transcription of the H4 genes. Deletion of the EH4 footprinted region resulted in a 3-fold decrease in transcription in a nuclear extract and a 2.6-fold decrease in expression in morulae from templates that had been injected into eggs. In the latter case, deletion of the binding site did not grossly disrupt the temporal program of expression from the injected EH4 genes. LH4 templates containing a 10-bp deletion in the consensus region or base substitutions in the footprinted region were transcribed at 14 to 58% of the level of the wild-type LH4 template. UHF-1 is therefore essential for maximal expression of the early and late H4 genes.

scholarly journals Synergistic activation of ADH2 expression is sensitive to upstream activation sequence 2 (UAS2) orientation, copy number and UAS1-UAS2 helical phasing.

1995 ◽  
Vol 15 (6) ◽  
pp. 3442-3449 ◽  
Author(s):  
M S Donoviel ◽  
N Kacherovsky ◽  
E T Young
Keyword(s):  
Gene Expression ◽  
Binding Site ◽  
Reporter Gene ◽  
Copy Number ◽  
Glucose Repression ◽  
Regulatory Protein ◽  
Regulatory Region ◽  
Upstream Regulatory Region ◽  
Specific Sequence

The alcohol dehydrogenase 2 (ADH2) gene of Saccharomyces cerevisiae is under stringent glucose repression. Two cis-acting upstream activation sequences (UAS) that function synergistically in the derepression of ADH2 gene expression have been identified. UAS1 is the binding site for the transcriptional regulator Adr1p. UAS2 has been shown to be important for ADH2 expression and confers glucose-regulated, ADR1-independent activity to a heterologous reporter gene. An analysis of point mutations within UAS2, in the context of the entire ADH2 upstream regulatory region, showed that the specific sequence of UAS2 is important for efficient derepression of ADH2, as would be expected if UAS2 were the binding site for a transcriptional regulatory protein. In the context of the ADH2 upstream regulatory region, including UAS1, working in concert with the ADH2 basal promoter elements, UAS2-dependent gene activation was dependent on orientation, copy number, and helix phase. Multimerization of UAS2, or its presence in reversed orientation, resulted in a decrease in ADH2 expression. In contrast, UAS2-dependent expression of a reporter gene containing the ADH2 basal promoter and coding sequence was enhanced by multimerization of UAS2 and was independent of UAS2 orientation. The reduced expression caused by multimerization of UAS2 in the native promoter was observed only in the presence of ADR1. Inhibition of UAS2-dependent gene expression by Adr1p was also observed with a UAS2-dependent ADH2 reporter gene. This inhibition increased with ADR1 copy number and required the DNA-binding activity of Adr1p. Specific but low-affinity binding of Adr1p to UAS2 in vitro was demonstrated, suggesting that the inhibition of UAS2-dependent gene expression observed in vivo could be a direct effect due to Adr1p binding to UAS2.

scholarly journals Neurokinin B regulates reproduction via inhibition of kisspeptin in a teleost, the striped bass

2017 ◽  
Vol 233 (2) ◽  
pp. 159-174 ◽  
Author(s):  
Nilli Zmora ◽  
Ten-Tsao Wong ◽  
John Stubblefield ◽  
Berta Levavi-Sivan ◽  
Yonathan Zohar
Keyword(s):  
Striped Bass ◽  
Brain Slices ◽  
Neuronal Population ◽  
Minor Effect ◽  
Pituitary Cells ◽  
Neurokinin B ◽  
A Minor ◽  
Lh Secretion

Kisspeptin and neurokinin B (NKB) are neuropeptides co-expressed in the mammalian hypothalamus and coordinately control GnRH signaling. We have found that Nkb and kisspeptin neurons are distinct in the teleost, striped bass (STB) and capitalized on this phenomenon to study the mode of action of Nkb and its related neuropeptide-F (Nkf), both of which are encoded by the tac3 gene. In vitro brain slices and in vivo administration studies revealed that Nkb/f consistently downregulated kiss2, whereas antagonist (AntD) administration restored this effect. Overall, a minor effect was noted on gnrh1 expression, whereas Gnrh1 content in the pituitaries was reduced after Nkb/f treatment and increased with AntD. Concomitantly, immunostaining demonstrated that hypothalamic Nkb neurons border and densely innervate the largest kiss2 neuronal population in the hypothalamus, which also coexpresses Nkb receptor. No expression of Nkb receptor or Nkb neuronal projections was detected near/in Gnrh1 soma in the preoptic area. At the level of the pituitary, however, the picture was more complex: both Nkb/f and AntD upregulated lhb and fshb expression and Lh secretion in vivo. Together with the stimulatory effect of Nkb/f on Lh/Fsh secretion from pituitary cells, in vitro, this may indicate an additional independent action of Nkb/f within the pituitary, in which the hypothalamic pathway is more dominant. The current study demonstrates that Nkb/f utilizes multiple pathways to regulate reproduction in the STB and that in the brain, Nkb mainly acts as a negative modulator of kiss2 to regulate the release of Gnrh1.

scholarly journals U2 small nuclear RNA 3' end formation is directed by a critical internal structure distinct from the processing site.

1993 ◽  
Vol 13 (2) ◽  
pp. 1119-1129 ◽  
Author(s):  
M R Jacobson ◽  
M Rhoadhouse ◽  
T Pederson
Keyword(s):  
Rna Processing ◽  
Minor Effect ◽  
Small Nuclear Rna ◽  
Recognition Sequence ◽  
Stem Loop ◽  
Branch Site ◽  
Nuclear Rna ◽  
A Minor ◽  
Site Recognition

Mature U2 small nuclear RNA is generated by the removal of 11 to 12 nucleotides from the 3' end of the primary transcript. This pre-U2 RNA processing reaction takes place in the cytoplasm. In this study, the sequences and/or structures of pre-U2 RNA that are important for 3' processing have been examined in an in vitro system. The 7-methylguanosine cap, stem-loops I and II, the lariat branch site recognition sequence, the conserved Sm domain, and several other regions throughout the 5' end of U2 RNA have no apparent role in the 3' processing reaction. In fact, deletion of the entire first 104 nucleotides resulted in mini-pre-U2 RNAs which were efficiently processed. Similarly, deletion of the top two-thirds of stem-loop III or mutation of nucleotides in the loop of stem-loop IV had little effect on 3' processing. Most surprisingly, the precursor's 11- to 12-nucleotide 3' extension itself was of relatively little importance, since this sequence could be replaced with completely different sequences with only a minor effect on the 3' processing reaction. In contrast, we have defined a critical structure consisting of the bottom of stem III and the stem of stem-loop IV that is essential for 3' processing of pre-U2 RNA. Compensatory mutations which restore base pairing in this region resulted in normal 3' processing. Thus, although the U2 RNA processing activity recognizes the bottom of stem III and stem IV, the sequence of this critical region is much less important than its structure. These results, together with the surprising observation that the reaction is relatively indifferent to the sequence of the 11- to 12-nucleotide 3' extension itself, point to a 3' processing reaction of pre-U2 RNA that has sequence and structure requirements significantly different from those previously identified for pre-mRNA 3' processing.

scholarly journals cis-Acting Sequences Required for NtcB-Dependent, Nitrite-Responsive Positive Regulation of the Nitrate Assimilation Operon in the Cyanobacterium Synechococcus sp. Strain PCC 7942

1998 ◽  
Vol 180 (16) ◽  
pp. 4080-4088 ◽  
Author(s):  
Shin-Ichi Maeda ◽  
Yuriko Kawaguchi ◽  
Taka-Aki Ohe ◽  
Tatsuo Omata
Keyword(s):  
Binding Site ◽  
Consensus Sequence ◽  
Regulatory Region ◽  
Nitrate Assimilation ◽  
Reporter System ◽  
Positive Regulation ◽  
Cis Acting ◽  
Type Protein ◽  
Pcc 7942

ABSTRACT There are three binding sites for NtcA (nirI,nirII, and nirIII), the global nitrogen regulator of cyanobacteria, in the DNA region between the two divergently transcribed operons (nirA andnirB operons) involved in nitrate assimilation inSynechococcus sp. strain PCC 7942. Using theluxAB reporter system, we showed that nirI andnirIII, which are located 23 bp upstream from the −10 promoter element of nirA and nirB, respectively, are required for induction by nitrogen depletion of thenirA and nirB operons, respectively. The induction of nirA operon transcription was a prerequisite for the nitrite-responsive positive regulation of the transcription by NtcB, a LysR-type protein. The NtcA-binding sitenirII, located in the middle of the nirA-nirBintergenic region, and a potential binding site for a LysR-type protein (TGCAN5TGCA; designated L1), located betweennirI and nirII, were required for the nitrite-responsive, NtcB-dependent enhancement of nirAoperon transcription. Although the requirement for the L1 site was consistent with the involvement of the LysR family protein NtcB in transcriptional regulation, NtcB did not bind to the nirAregulatory region in vitro in the presence of nitrite and NtcA, suggesting the involvement of some additional factor(s) in the regulation. An L1-like inverted repeat with the consensus sequence TGCN7GCA was conserved in the nirA promoter region of cyanobacteria, being centered at position −23 with respect to the NtcA-binding site corresponding to nirI, which suggested the common occurrence of nitrite-responsive regulation of the nitrate assimilation operon among cyanobacteria.

DN.9693 COMPARED WITH PROSTACYCLIN AND PROSTAGLANDIN E1 IN SEVEN PLATELET TESTS

1987 ◽  
Author(s):  
J R O'Brien ◽  
M D Etherington ◽  
G P Salmon
Keyword(s):  
Bleeding Time ◽  
Prostaglandin E ◽  
Minor Effect ◽  
Membrane Glycoproteins ◽  
Clot Retraction ◽  
Platelet Factor ◽  
Active Concentration ◽  
A Minor ◽  
Induced Aggregation

A new drug, DN.9693, has low Km phosphodiesterase inhibitory properties. Its effect on seven broad spectrum platelet "function" tests has been compared with the effects of prostacyclin E1 (PGI1) and prostaglandin E (PGE ). The tests were (1) platelet aggregation induced by ADP, collagen, adrenaline, thrombin, arachidonic acid and ristocetin; (2) a new test in which platelets aggregate after adding distilled water to cause osmotic stress; (3) the loss of platelets washed in buffered saline; (4) clot retraction; (5) the glass bead column platelet retention test; (6) the in vitro filter "bleeding time" (see two other submitted abstracts); (7) the amount of platelet factor 4 (PF4) which "leaks" from platelets at room temperature.PGI2 inhibited all seven tests, 50% inhibition of the various tests required from 0.1 to 44ng/ml of PGI2. PGE1 also inhibited in all tests but on average required 18 times higher concentrations. Thus an increase in cAMP may be relevant to all these tests, but an understanding of the mechanisms involved is incomplete. DN.9693 inhibited only the first four tests; the equi-active concentration was about 600 times that of PGI2. DN.9693, 2.5μg/ml, caused 50% inhibition of ristocetin induced aggregation and at 4μg/ml had a minor effect on the filter bleeding time. Thus DN.9693 may affect the platelet membrane glycoproteins. In conclusion it is confirmed that PGE1 is less active than PGI^ but has similar activities. DN.9693 whenstudied in these tests has many, but notall, of the prostaglandin-like properties.

Identification of HeLa cell nuclear factors that bind to and activate the early promoter of human polyomavirus BK in vitro

1989 ◽  
Vol 9 (9) ◽  
pp. 3821-3828
Author(s):  
T Chakraborty ◽  
G C Das
Keyword(s):  
Hela Cell ◽  
Binding Site ◽  
Regulatory Region ◽  
Human Polyomavirus ◽  
Early Promoter ◽  
Nuclear Factors ◽  
Cellular Factors ◽  
Polyomavirus Bk ◽  
Late Side

Human polyomavirus BK (BKV), an oncogenic DNA virus, differs from other papovaviruses in the organization of the regulatory region and in tissue tropism for kidney cells. The noncoding regulatory region of the viral genome in prototype strains includes three 68-base-pair (bp) repeats, each containing a number of potential regulatory elements. Some of these signals are unique to human papovaviruses, and others are homologous to those identified in many viral and cellular genes. We evaluated the contribution of individual 68-bp repeats to the initiation of transcription from the early promoter in a HeLa cell extract and identified cis-acting elements to which human cellular factors bind to activate transcription. The early promoter with only one copy of the 68-bp repeat could accurately initiate transcription in vitro, but additional copies were required for its stimulation. DNA-binding assays and DNase I protection experiments identified six domains in the regulatory region protected by human cellular factors. Two of these footprints were located within the proximal and distal 68-bp repeats, and one was located at the late side of the repeats. These footprints were centered over a TGGA(N)5-6GCCA core and were produced by a protein of the nuclear factor 1 (NF-1) family. This protein is either identical or similar to that which binds to the high-affinity site at the origin of adenovirus DNA replication. Three other domains, two at the junctions of the 68-bp repeats and one in the late side of the repeats, were partially protected by proteins with AP-1- and Sp-1-like activities. Transcription initiation from the early promoter was drastically reduced when a complete 68-bp repeat or the NF-1 binding site was used as a competitor in the in vitro assay. However, a point mutation within the NF-1 binding site, which reduced NF-1 binding in vitro to a level comparable to that of nonspecific DNA, also eliminated its ability to compete with early transcription. The murine homolog of the AP-1 binding site had a modest effect on in vitro transcription. Our results suggest that, among the multiple HeLa cell nuclear factors, NF-1 acts as a major activator of the early promoter in vitro.

U2 small nuclear RNA 3' end formation is directed by a critical internal structure distinct from the processing site

1993 ◽  
Vol 13 (2) ◽  
pp. 1119-1129
Author(s):  
M R Jacobson ◽  
M Rhoadhouse ◽  
T Pederson
Keyword(s):  
Rna Processing ◽  
Minor Effect ◽  
Small Nuclear Rna ◽  
Recognition Sequence ◽  
Stem Loop ◽  
Branch Site ◽  
Nuclear Rna ◽  
A Minor ◽  
Site Recognition

Mature U2 small nuclear RNA is generated by the removal of 11 to 12 nucleotides from the 3' end of the primary transcript. This pre-U2 RNA processing reaction takes place in the cytoplasm. In this study, the sequences and/or structures of pre-U2 RNA that are important for 3' processing have been examined in an in vitro system. The 7-methylguanosine cap, stem-loops I and II, the lariat branch site recognition sequence, the conserved Sm domain, and several other regions throughout the 5' end of U2 RNA have no apparent role in the 3' processing reaction. In fact, deletion of the entire first 104 nucleotides resulted in mini-pre-U2 RNAs which were efficiently processed. Similarly, deletion of the top two-thirds of stem-loop III or mutation of nucleotides in the loop of stem-loop IV had little effect on 3' processing. Most surprisingly, the precursor's 11- to 12-nucleotide 3' extension itself was of relatively little importance, since this sequence could be replaced with completely different sequences with only a minor effect on the 3' processing reaction. In contrast, we have defined a critical structure consisting of the bottom of stem III and the stem of stem-loop IV that is essential for 3' processing of pre-U2 RNA. Compensatory mutations which restore base pairing in this region resulted in normal 3' processing. Thus, although the U2 RNA processing activity recognizes the bottom of stem III and stem IV, the sequence of this critical region is much less important than its structure. These results, together with the surprising observation that the reaction is relatively indifferent to the sequence of the 11- to 12-nucleotide 3' extension itself, point to a 3' processing reaction of pre-U2 RNA that has sequence and structure requirements significantly different from those previously identified for pre-mRNA 3' processing.

scholarly journals Analysis of the subcellular localization of huntingtin with a set of rabbit polyclonal antibodies in cultured mammalian cells of neuronal origin: comparison with the distribution of huntingtin in Huntington'sdisease autopsy brain

1999 ◽  
Vol 354 (1386) ◽  
pp. 1061-1067 ◽  
Author(s):  
J. C. Dorsman ◽  
M. A. Smoor ◽  
M. L. C. Maat Schieman ◽  
M. Bout ◽  
S. Siesling ◽  
...  
Keyword(s):  
Subcellular Localization ◽  
Mammalian Cells ◽  
Neurodegenerative Disorder ◽  
Polyclonal Antibodies ◽  
Coding Region ◽  
Human Proteins ◽  
Functional Consequences ◽  
Glutamine Repeat ◽  
A Minor

Huntington'sdisease (HD) is a neurodegenerative disorder with a midlife onset. The disease is caused by expansion of a CAG (glutamine) repeat within the coding region of the HD gene. The molecular mechanism by which the mutated protein causes this disease is still unclear. To study the protein we have generated a set of rabbit polyclonal antibodies raised against different segments of the N–terminal, central and C–terminal parts of the protein. The polyclonal antibodies were affinity purified and characterized in ELISA and Western blotting experiments. All antibodies can react with the mouse and human proteins. The specificity of these antibodies is underscored by their recognition of huntingtin with different repeat sizes in extracts prepared from patient–derived lymphoblasts. The antibodies were used in immunofluorescence experiments to study the subcellular localization of huntingtin in mouse neuroblastoma N1E–115 cells. The results indicate that most huntingtin is present in the cytoplasm, whereas a minor fraction is present in the nucleus. On differentiation of the N1E–115 cells in vitro , the subcellular distribution of huntingtin does not change significantly. These results suggest that full–length huntingtin with a normal repeat length can be detected in the nucleus of cycling and non–cycling cultured mammalian cells of neuronal origin. However, in HD autopsy brain the huntingtin–containing neuronal intranuclear inclusions can be detected only with antibodies raised against the N–terminus of huntingtin. Thus several forms of huntingtin display the propensity for nuclear localization, possibly with different functional consequences.

scholarly journals CRISPR/Cas9 Deletion of SOX2 Regulatory Region 2 (SRR2) Decreases SOX2 Malignant Activity in Glioblastoma

Cancers ◽  
2021 ◽  
Vol 13 (7) ◽  
pp. 1574
Author(s):  
Ander Saenz-Antoñanzas ◽  
Veronica Moncho-Amor ◽  
Jaione Auzmendi-Iriarte ◽  
Alejandro Elua-Pinin ◽  
Karine Rizzoti ◽  
...  
Keyword(s):  
Adult Stem Cells ◽  
Regulatory Region ◽  
Cell Activity ◽  
Coding Region ◽  
Glioblastoma Cells ◽  
Tumor Initiating Cells ◽  
Sox2 Expression ◽  
Stem Cell Activity

SOX2 is a transcription factor associated with stem cell activity in several tissues. In cancer, SOX2 expression is increased in samples from several malignancies, including glioblastoma, and high SOX2 levels are associated with the population of tumor-initiating cells and with poor patient outcome. Therefore, understanding how SOX2 is regulated in cancer cells is relevant to tackle tumorigenesis. The SOX2 regulatory region 2(SRR2) is located downstream of the SOX2 coding region and mediates SOX2 expression in embryonic and adult stem cells. In this study, we deleted SRR2 using CRISPR/Cas9 in glioblastoma cells. Importantly, SRR2-deleted glioblastoma cells presented reduced SOX2 expression and decreased proliferative activity and self-renewal capacity in vitro. In line with these results, SRR2-deleted glioblastoma cells displayed decreased tumor initiation and growth in vivo. These effects correlated with an elevation of p21CIP1 cell cycle and p27KIP1 quiescence regulators. In conclusion, our data reveal that SRR2 deletion halts malignant activity of SOX2 and confirms that the SRR2 enhancer regulates SOX2 expression in cancer.

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