Quantitative correlation between cellular proliferation and nuclear poly (ADP-ribose) polymerase (PARP-1).

Treatment of cells with lysophosphatidyl choline and centrifugal extraction can separate poly (ADP-ribose) synthetase (PARP-1) and DNA synthetase activities, permitting the experimental analysis and comparison of both multienzyme systems. Only PARP-1 is being assayed by our system. Ca(2+) and Mg(2+) have minor activating effects, and added histones are without activating action. Short end-blocked dsDNAs at nM concentrations and spermine at mM concentrations are maximally activating coenzymes of poly (ADP-ribose) synthesis. Comparison of non-proliferating non-malignant cells with rapidly growing cancer cells demonstrates that rates of poly (ADP-ribose) synthesis and DNA synthesis are highest in pre-confluent non-malignant cells and in proliferating cancer cells, and lowest in contact-inhibited non-malignant cells. Rates of poly (ADP-ribose) synthesis correlate with the number of enzymatically activable PARP-1 molecules per cell, determined under Vmax conditions where activity is linearly proportional to enzyme protein. Contact-inhibited non-malignant cells exhibit only trans-ADP-ribosylation that is not affected by ATP, while rapid growth, especially in cancer cells, demonstrates extensive auto-poly (ADP)-ribosylation that is strongly inhibited by ATP at concentrations present in cells exhibiting normal bioenergetics. Rates of mRNA synthesis in non-proliferating non-malignant cells and in cancer cells were indistinguishable, indicating that the differences observed between cellular phenotypes are most likely due to reassembly of PARP-1 molecules in nuclei to homo-dimers (in cancer cells) and hetero-dimers (in non-cancer cells). A specific inhibitor and an inactivator of PARP-1 each inhibit DNA synthesis when intact cancer cells are pretreated with these drugs. Direct addition of these drugs to permeabilized cells performing DNA synthesis has no effect on DNA synthesis. The most striking diagnostic signal for cancer cells is activation of PARP-1 and of DNA synthesis.

Asymmetric cell divisions are concentrated in the dermomyotome dorsomedial lip during epaxial primary myotome morphogenesis.

To determine if somitic stem cell pools could be identified by an intrinsic difference in mitotic behaviour, the orientation of mitoses in the dermomyotome epithelium was analysed. We describe a concentration of apico-basal mitoses within the dermomyotome dorsomedial lip (DML). The occurrence of apico-basal divisions is closely associated with asymmetric localisation of the notch pathway factor numb, allowing description of such divisions as asymmetric. In contrast, planar divisions, occurring in the plane of the epithelium, are symmetric. Further, we show that the DML environmental niche is sufficient to promote numb expression in epaxial dermomyotome tissue that does not normally express this factor. These data provide, for the first time, a non-retrospective tracing analysis of the mechanism by which the DML fulfils the stem-cell pool role it plays during epaxial primary myotome morphogenesis.

Activity assays for poly-ADP ribose polymerase.

Poly(ADP-ribose) polymerase (PARP-1) is a nuclear enzyme that has traditionally been thought to require discontinuous or "damaged" DNA (dcDNA) as a coenzyme, a preconception that has limited research mainly to its role in cell pathology, i.e., DNA repair and apoptosis. Recent evidence has shown that this enzyme is broadly involved in normal cell physiological functions including chromatin modeling and gene regulation when DNA strand breaks are absent. We have recently shown that double-stranded DNA (dsDNA) serves as a more efficient coenzyme for PARP-1 than dcDNA, providing a mechanistic basis for PARP-1 function in normal cell physiology. Here we provide a detailed outline of methods for analyzing PARP-1 enzymatic activity using dsDNA as a coenzyme compared with broken or damaged DNA. Two procedures are described, one for analysis of auto-, and the other for trans-ADP-ribosylation. These assays provide a means of investigating the physiological role(s) of PARP-1 in normal cells.

Somite unit chronometry to analyze teratogen phase specificity in the paraxial mesoderm.

Phase specificity, the temporal and tissue restriction of teratogen-induced defects during embryonic -development, is a poorly understood but common property of teratogens, an important source of human birth defects. Somite counting and somite units are novel chronometric tools used here to identify stages of paraxial mesoderm development that are sensitive to pulse-chase exposure (2 to >16 h) to 5-bromodeoxyuridine (BrdU). In all cases, it was the presomitic mesoderm (PSM) that was sensitive to BrdU induced segmentation anomalies. At high concentration (1.0 × 10(-2) M BrdU), PSM presegment stages ss-IV and earlier were irreversibly inhibited from completing segmentation. At low concentration (2.6 × 10(-6) M), BrdU induced periodic focal defects that predominantly trace back to PSM presegments between ss-V and ss-IX. Phase specificity is characteristic of both types of segmentation anomalies. Focal segmentation defects are phase-specific because they result from disruption of 2-3 presegments in the PSM while adjacent -rostral and caudal presegments are (apparently) unaffected. Irreversible inhibition of segmentation is also phase-specific because only PSM presegments ss-IV or earlier were affected while older segments (ss-III to ss-I) were able to complete segmentation. The presegments predominantly affected have not yet passed the determination front, the point at which the segmentation clock establishes somite rostro-caudal -polarity. Somite unit chronometry provides a means to identify specific PSM presegment stages that are susceptible to induced segmentation defects and the biological processes that underlie that vulnerability.

Somite cell cycle analysis using somite-staging to measure intrinsic developmental time.

Somite stages were employed as units of intrinsic developmental time to measure cell doubling rate and other cell cycle parameters of chick forelimb level somites. Somite cell nuclei doubled over an interval corresponding to approximately 7+ somite stages (7+ ss; approximately 11 hr) and approximately 24 new primary myotome cells are born per somite stage ( approximately 16/hr). FACS analysis of DNA content in dissociated paraxial mesoderm cells indicated that slightly more than half are in G1/G0 phase of the cell cycle and that the average combined length of the S phase and G2 phase intervals is approximately 3 ss ( approximately 4.5 hr). A wavefront of increased mitotic nuclei per segment coincident with somite budding potentially reflects a surge in the number of cells entering S phase 3 ss earlier as each PSM segment becomes unresponsive to FGF signaling as it passes through the determination front.

The pattern of MyoD and contractile protein localization in primary epaxial myotome reflects the dynamic progression of nascent myoblast differentiation.

The localization of contractile and regulatory proteins in early stages of epaxial primary myotome development was analyzed by immunofluorescence microscopy. Contractile proteins that appear in an ordered sequence in the rostro-caudal axis of somite development were found to reiterate that sequence in the dorso-medial-to-ventro-lateral axis of primary epaxial myotome development. Pair-wise localization of MyoD-titin, desmin-titin, and desmin-myosin defined three zones extending from the dermomyotome dorso-medial lip (DML) into the primary myotome layer. Zones M1 and M2, which were positive for MyoD + titin and MyoD + titin + desmin, respectively, were restricted to the dorso-medial-most extremity of the myotome layer and did not expand during the course of myotome development. Zone M3 was positive for MyoD, desmin, titin, myosin, and cardiac troponin T and was the only zone that expanded during primary myotome development. Myotome fibers in zone M3 were unit-length, spanning the full rostro-caudal axis of the myotome while fibers in zones M1 and M2 were shorter than unit length. Anti-myoD immunofluorescence, when detected in cells lacking contractile-protein-positive cytoplasm, was restricted to the DML and nascent myotome cells immediately subjacent to the DML. These results demonstrate a dynamic spatio-temporal sequence in the differentiation program of nascent myotome cells as they emerge from the DML; zones M1 and M2 reflect standing waves of sequential contractile protein activation during the maturation of nascent myotomal myoblasts, while the expanding zone M3 reflects the accumulation of mature myotome fibers expressing a full cohort contractile proteins.

Persistent myogenic capacity of the dermomyotome dorsomedial lip and restriction of myogenic competence.

The dorsomedial lip (DML) of the somite dermomyotome is the source of cells for the early growth and morphogenesis of the epaxial primary myotome and the overlying dermomyotome epithelium. We have used quail-chick transplantation to investigate the mechanistic basis for DML activity. The ablated DML of chick wing-level somites was replaced with tissue fragments from various mesoderm regions of quail embryos and their capacity to form myotomal tissue assessed by confocal microscopy. Transplanted fragments from the epithelial sheet region of the dermomyotome exhibited full DML growth and morphogenetic capacity. Ventral somite fragments (sclerotome), head paraxial mesoderm or non-paraxial (lateral plate) mesoderm tested in this assay were each able to expand mitotically in concert with the surrounding paraxial mesoderm, although no myogenic potential was evident. When ablated DMLs were replaced with fragments of the dermomyotome ventrolateral lip of wing-level somites or pre-somitic mesoderm (segmental plate), myotome development was evident but was delayed or otherwise limited in some cases. Timed DML ablation-replacement experiments demonstrate that DML activity is progressive throughout the embryonic period (to at least E7) and its continued presence is necessary for the complete patterning of each myotome segment. The results of serial transplantation and BrdU pulse-chase experiments are most consistent with the conclusion that the DML consists of a self-renewing population of progenitor cells that are the primary source of cells driving the growth and morphogenesis of the myotome and dermomyotome in the epaxial domain of the body.

Regulation of the enzymatic catalysis of poly(ADP-ribose) polymerase by dsDNA, polyamines, Mg2+, Ca2+, histones H1 and H3, and ATP.

The enzymatic mechanism of poly(ADP-ribose) polymerase (PARP-1) has been analyzed in two in vitro systems: (a) in solution and (b) when the acceptor histones were attached to a solid surface. In system (a), it was established that the coenzymatic function of dsDNAs was sequence-independent. However, it is apparent from the calculated specificity constants that the AT homopolymer is by far the most effective coenzyme and randomly damaged DNA is the poorest. Rates of auto(poly-ADP-ribosylation) with dsDNAs as coenzymes were nearly linear for 20 min, in contrast to rates with dcDNA, which showed product [(ADPR)n] inhibition. An allosteric activation of auto(poly-ADP-ribosylation) by physiologic cellular components, Mg2+, Ca2+, and polyamines, was demonstrated, with spermine as the most powerful activator. On a molar basis, histones H(1) and H(3) were the most effective PARP-1 activators, and their action was abolished by acetylation of lysine end groups. It was shown in system (b) that oligo(ADP-ribosyl) transfer to histone H(1) is 1% of that of auto(poly-ADP-ribosylation) of PARP-1, and this trans(ADP-ribosylation) is selectively regulated by putrescine (activator). Physiologic cellular concentrations of ATP inhibit PARP-1 auto(poly-ADP-ribosylation) but less so the transfer of oligo(ADP-ribose) to histones, indicating that PARP-1 auto(ADP-ribosylation) activity is dormant in bioenergetically intact cells, allowing only trans(ADP-ribosylation) to take place. The inhibitory mechanism of ATP on PARP-1 consists of a noncompetitive interaction with the NAD site and competition with the coenzymic DNA binding site. A novel regulation of PARP-1 activity and its chromatin-related functions by cellular bioenergetics is proposed that occurs in functional cells not exposed to catastrophic DNA damage.

Coenzymatic activity of randomly broken or intact double-stranded DNAs in auto and histone H1 trans-poly(ADP-ribosylation), catalyzed by poly(ADP-ribose) polymerase (PARP I).

The enzymatic transfer of ADP-ribose from NAD to histone H1 (defined as trans-poly(ADP-ribosylation)) or to PARP I (defined as auto-poly(ADP-ribosylation)) was studied with respect to the nature of the DNA required as a coenzyme. Linear double-stranded DNA (dsDNA) containing the MCAT core motif was compared with DNA containing random nicks (discontinuous or dcDNA). The dsDNAs activated trans-poly(ADP-ribosylation) about 5 times more effectively than dcDNA as measured by V(max). Activation of auto-poly(ADP-ribosylation) by dcDNA was 10 times greater than by dsDNA. The affinity of PARP I toward dcDNA or dsDNA in the auto-poly(ADP-ribosylation) was at least 100-fold lower than in trans-poly(ADP-ribosylation) (K(a) = 1400 versus 3-15, respectively). Mg2+ inhibited trans-poly(ADP-ribosylation) and so did dcDNA at concentrations required to maximally activate auto-poly(ADP-ribosylation). Mg2+ activated auto-poly(ADP-ribosylation) of PARP I. These results for the first time demonstrate that physiologically occurring dsDNAs can serve as coenzymes for PARP I and catalyze preferentially trans-poly(ADP- ribosylation), thereby opening the possibility to study the physiologic function of PARP I.

Analysis of nucleotide sequence-dependent DNA binding of poly(ADP-ribose) polymerase in a purified system.

The enzymatic transfer of ADP-ribose from NAD to histone H(1) [defined as trans(oligo-ADP-ribosylation)] or to PARP-1 [defined as auto(poly-ADP-ribosylation)] requires binding of coenzymic DNA. The preceding paper [Kun, E., et al. (2004) Biochemistry 43, 210-216] shows that oligonucleotides of dsDNA can serve as coenzymic DNA for PARP-1 trans- or auto-modification activity. Results of DNA-protein binding (EMSA) experiments reported here demonstrate that short DNA oligonucleotides containing the 5'-TGTTG-3' nucleotide sequence motif preferentially bind to cloned PARP-1 in vitro. The same nucleotide sequence motif is responsible for striated myocyte-selective transcription of a contractile protein gene encoding cardiac troponin T (cTnT). Results of experiments reported here demonstrate that mutation of this motif also abolishes the differentiation-dependent activation of the transfected cTnT promoter in myoblasts cultured in vitro, indicating that nucleotide sequence-dependent binding of PARP-1 to promoter DNA of the cTnT gene is also necessary for differentiation-dependent activation. Thus, PARP-1 has two types of dsDNA binding activity: (1) nucleotide sequence-dependent binding, analyzed here with EMSA experiments, and (2) coenzymic binding, measured catalytically, which does not depend on the nucleotide sequence of the dsDNA. We hypothesize that the well-known association of PARP-1 with chromatin can be attributed to its stable binding to chromosomal dsDNA, some portion of which is likely to be nucleotide sequence-dependent binding. According to this hypothesis, the distribution of this protein-modifying enzyme in chromatin may be targeted to specific genomic loci and vary according to cell type and developmental stage.

In vivo regulation of the chicken cardiac troponin T gene promoter in zebrafish embryos.

The chicken cardiac troponin T (cTnT) gene is representative of numerous cardiac and skeletal muscle-specific genes that contain muscle-CAT (MCAT) elements within their promoters. We examined the regulation of the chicken cTnT gene in vivo in zebrafish embryos, and in vitro in cardiomyocyte, myoblast, and fibroblast cultures. Defined regions of the cTnT promoter were linked to the green fluorescent protein (GFP) gene for in vivo analysis, and the luciferase gene for in vitro analysis. Injection of the cTnT promoter constructs into fertilized zebrafish eggs resulted in GFP expression in both heart and skeletal muscle cells reproducing the pattern of expression of the endogenous cTnT gene in the chicken embryo. Promoter deletion analysis revealed that the cis-regulatory regions responsible for cardiac and skeletal muscle-specific expression functioned in an equivalent manner in both in vitro and in vivo environments. In addition, we show that mutation of the poly-ADP ribose polymerase-I (PARP-I) binding site adjacent to the distal MCAT element in the chicken cTnT promoter produced a non-cell-specific promoter in vitro and in the zebrafish. Thus, the PARP-I transcriptional regulatory mechanism that governs muscle specificity of the chicken cTnT promoter is conserved across several chordate classes spanning at least 350 million years of evolution.

Precocious terminal differentiation of premigratory limb muscle precursor cells requires positive signalling.

The timing of myogenic differentiation of hypaxial muscle precursor cells in the somite lags behind that of epaxial precursors. Two hypotheses have been proposed to explain this delay. One attributes the delay to the presence of negative-acting signals from the lateral plate mesoderm adjacent to the hypaxial muscle precursor cells located in the ventrolateral lip of the somitic dermomyotome (Pourquié et al. [1995] Proc. Natl. Acad. Sci. USA 92:3219-3223). The second attributes the delay to an absence of positive-acting inductive signals, similar to those from the axial structures that induce epaxial myotome development (Pownall et al. [1996] Development 122:1475-1488). Because both studies relied principally upon changes in the expression pattern of mRNAs specific to early muscle precursor cell markers, we revisited these experiments using two methods to assess muscle terminal differentiation. First, injection of fluorescent dyes before surgery was used to determine whether ventrolateral lip cells transform from epithelial cells to elongated myocytes. Second, an antibody to a terminal differentiation marker and a new monoclonal antibody that recognises avian and mammalian Pax3 were used for immunohistochemistry to assess the transition from precursor cell to myocyte. The results support both hypotheses and show further that placing axial structures adjacent to the somite ventrolateral lip induces an axial pattern of myocyte terminal differentiation and elongation.