Interaction of regulator proteins with recognition sequences of DNA

Noncanonical binding of transcription factors: time to revisit specificity?

Transcription factors (TFs) are one of the most studied classes of DNA-binding proteins that have a direct functional impact on gene transcription and thus, on human physiology and disease. The mechanisms that TFs use for recognizing target DNA binding sites have been studied for nearly five decades, yet they remain poorly understood. It is classically assumed that a TF recognizes a specific sequence pattern, or motif, as its binding sites. However, recent studies are consistently finding examples of noncanonical binding, that is, TFs binding at sites that do not resemble their sequence motifs. Here we review the current literature on four major types of noncanonical TF binding, namely binding based on DNA shape readout, at Guanine-quadruplex structures, at repeat sequences, and bispecific binding. These examples point to a critical need for studies to unify our current observations, many of which are at odds with the "one TF, one motif" view, into a more comprehensive definition of the DNA-binding specificity of TFs.

Repair-modification and evolution of the eukaryotic genome organization

For a complete reconstruction of the damaged unmethylated islands, in theory, the conventional excision-repair is sufficient. For a complete reconstruction of the damaged methylated domains, a coupling has to take place involving the excision-repair (able to reestablish their ATGC-language) plus the DNA-methylase (able to reestablish their modified ATGC5mC-language). This coupling, defined as "repair-modification," is essentially functioning during the S-phase, because the DNA-polymerase beta (pol beta) is active during the whole cell cycle, whereas the DNA-methylase (met) is active in S and appears to be repressed or inactive during the major part of G1 and during the phases G2 and M. Consequently, after damage, some silent genes might become expressed during these phases, if it is true that DNA methylation is inversely proportional to transcription. Repair-modification should, therefore, exert a continuous differential pressure on evolution of given parts of the genome, when they are methylated to a different extent. According to Darwinian concepts, repair-modification would lead to a high variability, especially of uncoding DNA sequences (if hypermethylated), whereas on the basis of this variability, selection might favor transposition of specific regulatory elements into given transcriptional units. In these, the conservative nature of the coding elements (if unmethylated) would obviously be ensured by the conventional excision-repair.

Organization, replication and modification of the human genome: synthesis and methylation of palindromic, repeated and unique HeLa nDNA sequences during the S-phase

At least five supermethylated nDNA families have been found in HeLa cells. The concentration of 5-methylcytosine increases on palindromes from 1 to 5 hours during the nDNA duplicative phase, decreasing again at the 6th hour of S. The early S-phase involves the accumulation of 5-methylcytosines on the nDNA sequences reassociating near a Cot = 3 x 10(-1). Late S involves increment of this base on the sequences which reassociate near a Cot = 9 x 10(-1) and Cot = 7 x 10(1). The unique sequences show a moderate methylation from 3 to 6 hours of S. This information shows that genes are methylated with an order during the S-phase in a system in which nDNA organization, modification and replication appear to be severely subordinated one to another. The possible role of methylation of foldback nDNA in regulation of transcription during the eukaryotic cell life cycle is discussed.

The diverse effects of 5'-bromodeoxyuridine on enzyme activities in cultured H35 hepatoma cells

Reuber (H35) hepatoma cells were grown in medium containing 10(-5)M bromodeoxyuridine (BrdU), which was incorporated into their DNA. Cell growth rate was unaffected by BrdU for the first two generations, after which it was reduced by about 50%. The effect of BrdU incorporation on the activities of several enzymes with rapid turnover rates was examined to test the hypothesis that the synthesis of such enzymes will be preferentially inhibited by BrdU. Tyrosine amino-transferase (TAT) activity decreased by 70% within two generations whereas thymidine kinase activity remained at control values. PEP carboxykinase activity was unchanged during the first generation in BrdU-containing medium but, during the second, its activity increased by at least 30%. Ornithine decarboxylase levels decreased by about 50% only after two generations in the presence of BrdU. There appeared to be no simple relationship between turnover rates and the effect of BrdU on enzyme activity. Incorporation of BrdU was found to inhibit the induction of both TAT and PEP carboxykinase by dexamethasone and to enhance the inhibition of cell growth by this steroid. These results are discussed with respect to possible mechanisms of gene expression and development in both normal and neoplastic cells.

Inverted repetitious sequences in the macronuclear DNA of hypotrichous ciliates

The low-molecular-weight macronuclear DNA of the hypotrichous ciliates Oxytricha, Euplotes, and Paraurostyla contains inverted repetitious sequences. Up to 89% of the denatured macronuclear DNA molecules form single-stranded circles due to intramolecular renaturation of complementary sequences at or near the ends of the same polynucleotide chain. Other ciliated protozoans, such as Tetrahymena, with high-molecular-weight macronuclear DNA and an alternative mode of macronuclear development, appear to lack these selfcomplementary sequences. The denatured macronuclear molecules of hypotrichs are held in the circular conformation by a hydrogen-bonded duplex region, which is probably less than 50 base pairs in length, since the duplex regions are not visible by electron microscopy and since the circles in 0.12 M phosphate buffer are not retained during hydroxylapatite chromatography at 60 degrees. The existence of extremely small circles, with contour lengths shorter than the smallest pieces of native DNA, suggests that inverted repetitions containing nicks (broken phosphodiester bonds in duplex DNA) or gaps (interruptions with missing nucleotides) are present at internal positions as well as at the ends of native molecules. Estimates from length measurements of native and denatured Oxytricha macronuclear DNA indicate an average of 1.7 nicks per duplex molecule. Thus, in order to account for the high frequency of circle formation, a restriction-type enzyme(s) must exist which inserts single-strand, site-specific nicks or gaps at internal positions in the macronuclear DNA of Oxytricha.