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1

The application of FPLC chromatography [Mono Q] for the purification of wheat RNA polymerases II and III

100%

Glanc P., Galbas M., Dullin P., Szalata M., Slomski R.

Cellular and Molecular Biology Letters

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2003

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tom 08

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nr 3

Transcription is the main step in the regulation of gene expression. To study this process in vitro, it is necessary to obtain highly purified RNA polymerases. Here, we describe a method of RNA polymerase purification using a Mono Q FPLC column. Using Mono Q column chromatography accelerates the purification process and separates RNA polymerase II from RNA polymerase III with good yield.

2

The relation of transcription to memory formation

100%

Korzus E.

Acta Biochimica Polonica

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2003

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tom 50

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nr 3

A distinction between short-term memories lasting minutes to hours and long-term memories lasting for many days is that the formation of long-term memories requires new gene expression. In this review, the focus is on the current understanding of the relation of transcription to memory consolidation based on the data collected from behavioral studies performed primarily on genetically altered animals. Studies in Drosophila and Aplysia indicate that the transcription factor cAMP/Ca2+ response element binding protein (CREB) is critical in mediating the conversion from short- to long-term memory. More recent genetic studies in mice also demonstrated CREB and inducible transcription factor Zif268 involvement in information storage processes. Transcription seems to play essential role in memory formation but the mechanisms for activation of transcription and downstream processes during memory consolidation remain unclear.

3

Properties of Escherichia coli RNA polymerase from a strain devoid of the stringent response alarmone ppGpp

75%

Szalewska-Palasz A.

Acta Biochimica Polonica

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2008

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tom 55

|

nr 2

317-323

The stringent response alarmone guanosine tetraphosphate (ppGpp) affects transcription from many promoters. ppGpp binds directly to the transcription enzyme of Escherichia coli, RNA polymerase. Analysis of the crystal structure of RNA polymerase with ppGpp suggested that binding of this nucleotide may result in some conformational or post-translational alterations to the enzyme. These changes might affect in vitroperformance of the enzyme. Here, a comparison of the in vitroproperties of RNA polymerases isolated from wild type and ppGpp-deficient bacteria shows that both enzymes do not differ in i) transcription activity of various promoters (e.g. σ70rrnBP1, λpL, T7A1), ii) response to ppGpp, iii) promoter-RNA polymerase open complex stability. Thus, it may be concluded that ppGpp present in the bacterial cell prior to purification of the RNA polymerase does not result in the alterations to the enzyme that could be permanent and affect its in vitrotranscription capacity.

4

A transcriptionally active copia-like retroelement in Citrus limon

75%

De F. B., Wilson R. R., Argenziano C., Kafantaris I., Conicella C.

Cellular and Molecular Biology Letters

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2009

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tom 14

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nr 2

289-304

The plant nuclear genome is largely composed of mobile DNA, which can rearrange genomes and other individual gene structure and also affect gene regulation through various promoted activities: transposition, insertion, excision, chromosome breakage, and ectopic recombination. Ty1-copia-like retrotransposon is a widespread class of transposable elements in the plant kingdom, representing a large part of the total DNA content. Here, a novel retrotransposon-like sequence was isolated and identified as the Ty1-copia-like reverse transcriptase domain (named here CLCoy1), based on the homology of known elements. Fluorescence in situ hybridization, revealed that CLCoy1 was mainly located in telomeric and sub-telomeric regions along the Citrus chromosomes. CLCoy1 composes 3.6% of the genome and, interestingly, while transposons are mostly specific to a species, this element was identified in other Citrus species such as Citrus aurantium, Fortunella margarita and Citrus paradisi, but undetected in Poncirus trifoliata. We also determined that wounding, salt and cell culture stress produced transcriptional activation of this novel retroelement in Citrus limon. The novel Ty1-copia-like element CLCoy1 may have played a major role in shaping genome structure and size during Citrus species evolution.

5

Redox state of plastoquionone pool regulates expression of Arabidopsis thaliana genes in response to elevated irradiance

75%

Adamiec M., Drath M., Jackowski G.

Acta Biochimica Polonica

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2008

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tom 55

|

nr 1

DNA microarray technology was applied to gain insight into the role of the redox state of PQ pool as a retrograde factor mediating differential expression of Arabidopsis nuclear genes during the acclimation to changing irradiance. DNA microarray chips containing probes corresponding to 24000 Arabidopsis nuclear genes were screened with cRNA samples prepared from leaves of plants exposed for 5 h to low irradiance (control) vs. medium, high and excessive irradiances (MI, HI and EI, respectively). Six hundred and sixty three genes were differentially expressed as a result of an exposure to at least one elevated irradiance. Among 663 differentially expressed genes a total of 50 were reverted by DCMU - 24 ones modulated at medium irradiance, 32 ones modulated at high irradiance and a single one modulated at excessive irradiance. We postulate that their expression is regulated by redox state of plastoquinone (PQ) pool. Thus the PQ-mediated redox regulation of expression of Arabidopsis nuclear genes is probably limited to the irradiance window representing non-stressing conditions. We found that the promoter regions of the PQ-regulated genes contained conserved elements, suggesting transcriptional control by a shared set of trans-acting factors which participate in signal transduction from the redox state of the PQ pool.

6

In vitro transcription of class III genes

75%

Glanc P., Galbas M., Dullin P.

Cellular and Molecular Biology Letters

|

2002

|

tom 07

|

nr Suppl.

7

Effect of proflavine and its 2,7-dialkyl substituted derivatives upon initiation of transcription

75%

Piestrzeniewicz M. K., Szemraj J., Gniazdowski M.

Acta Biochimica Polonica

|

1993

|

tom 40

|

nr 1

8

Pharmacological inhibitors of cyclin-dependent kinases [CDKs] and glycogen synthase kinase-3 [GSK-3]

75%

Meijer L.

Cellular and Molecular Biology Letters

|

2003

|

tom 08

|

nr 2A

9

The Escherichia coli RNA polymerase alpha subunit and transcriptional activation by bacteriophage lambda CII protein

75%

Gabig M., Obuchowski M., Ciesielska A., Latala B., Wegrzyn A., Thomas M. S., Wegrzyn G.

Acta Biochimica Polonica

|

1998

|

tom 45

|

nr 1

Bacteriophage λ is not able to lysogenise the Escherichia coli rpoA341 mutant. This mutation causes a single amino acid substitution Lys271Glu in the C-terminal domain of the RNA polymerase α subunit (αCTD). Our previous studies indicated that the impaired lysogenisation of the rpoA341 host is due to a defect in transcriptional activation by the phage CII protein and suggested a role for αCTD in this process. Here we used a series of truncation and point mutants in the rpoA gene placed on a plasmid to investigate the process of transcriptional activation by the CII gene product. Our results indicate that amino-acid residues 265, 268 and 271 in the α subunit may play an important role in the CII-mediated activation of the pE promoter (most probably residue 271) or may be involved in putative interactions between αCTD and an UP-like element near pE (most probably residues 265 and 268). Measurement of the activity of pE-lacZ, pI-lacZ and paQ-lacZ fusions in the rpoA+ and rpoA341 hosts demonstrated that the mechanism of activation of these CII-dependent promoters may be in each case different.

10

The center of accessibility: D beta control of V[D]J recombination

63%

Sikes M. L., McMillan R. E., Bradshaw J. M.

Archivum Immunologiae et Therapiae Experimentalis

|

2010

|

tom 58

|

nr 6

427-433

11

Two pathogenic mutations located within the 5'-regulatory sequence of the GJB1 gene affecting initiation of transcription and translation

63%

Kabzinska D., Kotruchow K., Ryniewicz B., Kochanski A.

Acta Biochimica Polonica

|

2011

|

tom 58

|

nr 3

In contrast to mutations in the coding sequences of a genes involved in the pathogenesis of Charcot-Marie-Tooth disease (CMT), little is known about CMT phenotypes resulting from a DNA variants located in regulatory sequences of a given " CMT gene". Charcot-Marie-Tooth type X1 disease (CMTX1) is caused by mutations in the GJB1 gene coding for an ion channel known as connexin, with a molecular mass of 32 kDa (Cx32). Only 0.01% of the GJB1 gene mutations have been reported in its 5' regulatory sequence. Pathogenic mutations occured in the internal ribosome entry site (IRES) are extremely rarely reported in human genetic disorders. To the best of our knowledge, in this study we report for the first time in an Eastern European population, two CMTX1 families in which two pathogenic mutations in the 5' regulatory sequence of the GJB1 gene (c.-529T>C and -459C>T) have been found. The two mutations identified in our study disturb the 5' UTR sequence in two different ways, by affecting the transcription factor SOX10 binding site (c.-529T>C) and by the disrupting IRES element of GJB1 gene (c.-459C>T). These regions are responsible for transcription (SOX10) and initiation of translation (IRES), respectively. On the basis of our findings that, in contrast to the most DNA sequence variants reported in untranslated regulatory regions of genes, the c.-459C>T and c.-529T>C mutations remain pathogenic in the context of different ethnic background.

12

F-actin distribution pattern in the nuclei of early mouse embryos

63%

Bogolyubova I.

Folia Histochemica et Cytobiologica

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2009

|

tom 47

|

nr 3

13

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The expression of UVR3 and two putative photolyases, PHR2 and At4g25290, is regulated by light

63%

Sztatelman O., Labuz J., Banas A. K.

BioTechnologia. Journal of Biotechnology Computational Biology and Bionanotechnology

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2013

|

tom 94

|

nr 3

14

Cohesin Irr1/Scc3 is likely to influence transcription in Saccharomyces cerevisiae via interaction with Mediator complex

63%

Cena A., Skoneczny M., Chelstowska A., Kowalec P., Natorff R., Kurlandzka A.

Acta Biochimica Polonica

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2013

|

tom 60

|

nr 2

The evolutionarily conserved proteins forming sister chromatid cohesion complex are also involved in the regulation of gene transcription. The participation of SA2p (mammalian ortholog of yeast Irr1p, associated with the core of the complex) in the regulation of transcription is already described. Here we analyzed microarray profiles of gene expression of a Saccharomyces cerevisiae irr1-1/IRR1 heterozygous diploid strain. We report that expression of 33 genes is affected by the presence of the mutated Irr1-1p and identify those genes. This supports the suggested role of Irr1p in the regulation of transcription. We also indicate that Irr1p may interact with elements of transcriptional coactivator Mediator.

15

Sirt7 an emerging sirtuin: deciphering newer roles

63%

Kim W., Kim J. E.

Journal of Physiology and Pharmacology

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2013

|

tom 64

|

nr 5

16

The transcriptional regulation of podocin [NPHS2] by Lmx1b and a promoter single nucleotide polymorphism

63%

Harendza S., Stahl R. A. K., Schneider A.

Cellular and Molecular Biology Letters

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2009

|

tom 14

|

nr 4

679-691

Podocin (NPHS2) is a component of the glomerular slit membrane with major regulatory functions in the renal permeability of proteins. A loss of podocin and a decrease in its resynthesis can influence the outcome of renal diseases with nephrotic syndrome, such as minimal change glomerulonephritis, focal segmental glomerulosclerosis (FSGS) and membranous nephropathy. The transcriptional regulation of podocin may play a major role in these processes. We defined the transcriptional regulation of the human podocin gene and the influence of single nucleotide polymorphisms (SNPs) within its promoter region in the podocytes using reporter gene constructs and gel shift analysis. In addition, we took genomic DNA from healthy Caucasian blood donors and from biopsies of kidneys with defined renal diseases and screened it for podocin promoter SNPs. Our data shows that the transcription of podocin is mainly regulated by the transcription factor Lmx1b, which binds to a FLAT-F element and displays enhancer function. With the SNP variant −116T, there was a significant reduction in luciferase activity, and nuclear protein binding was observed, while the SNP −670C/T did not display functionality. The allelic distribution of −116C/T in patients with kidney diseases leading to nephrotic syndrome was not significantly different from that in the control group. Our data indicates that among other factors, podocin is specifically regulated by the transcription factor Lmx1b and by the functional polymorphism -116C/T. However, there is no association between −116C/T and susceptibility to minimal change glomerulonephritis, focal segmental glomerulosclerosis or membranous nephropathy.

17

Transcriptional activity of a complex of wheat RNA polymerase II and nonhistone chromosomal protein (NHCP)

63%

Dullin P., Galbas M., Chodynicka-Kordus G., Fabisz-Kijowska A., Walerych W.

Acta Biochimica Polonica

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1989

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tom 36

|

nr 3-4

18

Localization of the calreticulin gene mRNA in unpollinated and pollinated styles of Petunia hybrida Hort.

63%

Lenartowska M., Lenartowski R., Bednarska E.

Journal of Applied Genetics

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2001

|

tom 42

|

nr 1

19

Functional and physical interactions of Krr1p, a Saccharomyces cerevisiae nucleolar protein

63%

Gromadka R., Karkusiewicz I., Rempola B., Rytka J.

Acta Biochimica Polonica

|

2004

|

tom 51

|

nr 1

The Krr1 protein of Saccharomyces cerevisiae is involved in processing of pre-rRNA and assembly of pre-ribosomal 40S subunits. To further investigate the function of Krr1p we constructed a conditional cold sensitive mutant krrl-21, and isolated seven genes from Schizosaccharomyces pombe whose products suppressed the cold sensitive phenotype of krrl-21 cells. Among the multicopy suppressors we found genes coding for translation elongation factor EF-1a, a putative ribose methyltransferase and five genes encoding ribosomal proteins. Using the tandem affinity purification (TAP) method we identified thirteen S. cerevisiae ribosomal proteins interacting with Krr1p. Taken together, these results indicate that Krr1p interacts functionally as well as physically with ribosomal proteins. Northern blot analysis revealed that changes in the level of krrl-21 mRNA were accompanied by similar changes in the level of mRNAs of genes encoding ribosomal proteins. Thus, Krr1p and the genes encoding ribosomal proteins it interacts with seem to be coordinately regulated at the level of transcription.

20

The effect of protein phosphorylation on in vitro class III gene transcription

63%

Glanc P., Galbas M., Dullin P.

Cellular and Molecular Biology Letters

|

2002

|

tom 07

|

nr Suppl.

Ograniczanie wyników

The application of FPLC chromatography [Mono Q] for the purification of wheat RNA polymerases II and III

The relation of transcription to memory formation

Properties of Escherichia coli RNA polymerase from a strain devoid of the stringent response alarmone ppGpp

A transcriptionally active copia-like retroelement in Citrus limon

Redox state of plastoquionone pool regulates expression of Arabidopsis thaliana genes in response to elevated irradiance

In vitro transcription of class III genes

Effect of proflavine and its 2,7-dialkyl substituted derivatives upon initiation of transcription

Pharmacological inhibitors of cyclin-dependent kinases [CDKs] and glycogen synthase kinase-3 [GSK-3]

The Escherichia coli RNA polymerase alpha subunit and transcriptional activation by bacteriophage lambda CII protein

The center of accessibility: D beta control of V[D]J recombination

Two pathogenic mutations located within the 5'-regulatory sequence of the GJB1 gene affecting initiation of transcription and translation

F-actin distribution pattern in the nuclei of early mouse embryos

The expression of UVR3 and two putative photolyases, PHR2 and At4g25290, is regulated by light

Cohesin Irr1/Scc3 is likely to influence transcription in Saccharomyces cerevisiae via interaction with Mediator complex

Sirt7 an emerging sirtuin: deciphering newer roles

The transcriptional regulation of podocin [NPHS2] by Lmx1b and a promoter single nucleotide polymorphism

Transcriptional activity of a complex of wheat RNA polymerase II and nonhistone chromosomal protein (NHCP)

Localization of the calreticulin gene mRNA in unpollinated and pollinated styles of Petunia hybrida Hort.

Functional and physical interactions of Krr1p, a Saccharomyces cerevisiae nucleolar protein

The effect of protein phosphorylation on in vitro class III gene transcription