Terminal transferase-dependent PCR (TDPCR) for in vivo UV photofootprinting of vertebrate cells

Wavelength dependence of ultraviolet radiation-induced DNA damage as determined by laser irradiation suggests that cyclobutane pyrimidine dimers are the principal DNA lesions produced by terrestrial sunlight

To elucidate the involvement of specific ultraviolet (UV) wavelengths in solar mutagenesis, we used a laser system to investigate the induction of DNA damage, both in the overall genome and at the nucleotide resolution level, in the genomic DNA of transgenic Big Blue mouse fibroblasts irradiated with a series of UV wavelengths, inclusive of UVC (λ<280 nm), UVB (λ=280-320 nm), and UVA (λ>320 nm). Subsequently, we sought correlation between the locations of UV-induced DNA lesions in the cII transgene of irradiated DNA samples and the frequency distribution and codon position of the induced cII mutations in counterpart mouse cells irradiated with simulated sunlight. Using a combination of enzymatic digestion assays coupled with gel electrophoresis, immunodot blot assays, and DNA footprinting assays, we demonstrated a unique wavelength-dependent formation of photodimeric lesions, i.e., cyclobutane pyrimidine dimers (CPDs) and (6-4) photoproducts [(6-4)PPs], based on direct UV absorption of DNA, in irradiated mouse genomic DNA, which could partially explain the induction of mutations in mouse cells irradiated with simulated sunlight. Most notably, there was a divergence of CPD and (6-4)PP formation at an irradiation wavelength of 296 nm in mouse genomic DNA. Whereas substantial formation of (6-4)PPs was detectable in samples irradiated at this wavelength, which intensified as the irradiation wavelength decreased, only small quantities of these lesions were found in samples irradiated at wavelengths of 300-305 nm, with no detectable level of (6-4)PPs in samples irradiated with longer wavelengths. Although CPD formation followed the same pattern of increase with decreasing wavelengths of irradiation, there were substantial levels of CPDs in samples irradiated with UVB wavelengths borderlined with UVA, and small but detectable levels of these lesions in samples irradiated with longer wavelengths. Because the terrestrial sunlight spectrum rolls off sharply at wavelengths ~300 nm, our findings suggest that CPDs are the principal lesion responsible for most DNA damage-dependent biological effects of sunlight.

Interrogating the transgenic genome: development of an interspecies tiling array

A single expressing copy of the human protamine domain was randomly inserted into an intron of Cyp2c38. The transgenic locus was shown to recapitulate the level of expression observed in normal human testis while not perturbing endogenous protamine expression. The development of an interspecies tiling array was pursued to enable direct comparison of the orthologous protamine domains in a single experiment. Probe design was adapted to generate species-specific high resolution probe sets that would tolerate repetitive elements. Results from competitive hybridizations demonstrate that interspecies tiling arrays are a valuable tool for parallel analysis of highly similar DNA sequences. This approach provides a rapid and reliable means of interrogating samples prior to deep sequencing analysis. These arrays should readily compliment most DNA isolation and analysis techniques such as ChIP, nuclease sensitivity and nuclear matrix association assays.

Regulation of CEACAM1 transcription in human breast epithelial cells

BACKGROUND

Carcinoembryonic antigen cell adhesion molecule 1 (CEACAM1) is a transmembrane protein with multiple functions in different cell types. CEACAM1 expression is frequently mis-regulated in cancer, with down-regulation reported in several tumors of epithelial origin and de novo expression of CEACAM1 in lung cancer and malignant melanoma. In this report we analyzed the regulation of CEACAM1 expression in three breast cancer cell lines that varied in CEACAM1 expression from none (MCF7) to moderate (MDA-MB-468) to high (MCF10A, comparable to normal breast).

RESULTS

Using in vivo footprinting and chromatin immunoprecipitation experiments we show that the CEACAM1 proximal promoter in breast cells is bound in its active state by SP1, USF1/USF2, and IRF1/2. When down-regulated the CEACAM1 promoter remains accessible to USF2 and partially accessible to USF1. Interferon-γ up-regulates CEACAM1 mRNA by a mechanism involving further induction of IRF-1 and USF1 binding at the promoter. As predicted by this analysis, silencing of IRF1 and USF1 but not USF2 by RNAi resulted in a significant decrease in CEACAM1 protein expression in MDA-MB-468 cells. The inactive CEACAM1 promoter in MCF7 cells exhibits decreased histone acetylation at the promoter region, with no evidence of H3K9 or H3K27 trimethylation, histone modifications often linked to condensed chromatin structure.

CONCLUSIONS

Our data suggest that transcription activators USF1 and IRF1 interact to modulate CEACAM1 expression and that the chromatin structure of the promoter is likely maintained in a poised state that can promote rapid induction under appropriate conditions.

In vitro recapitulating of TP53 mutagenesis in hepatocellular carcinoma associated with dietary aflatoxin B1 exposure

BACKGROUND & AIMS

Dietary exposure to aflatoxin B(1) (AFB(1)), in addition to other known factors, increases risk for human hepatocellular carcinoma (HCC). HCCs from AFB(1)-exposed individuals frequently have distinct TP53 mutations, such as G to T transversions in the second guanine of codon 249 (AGG to AGT), and a characteristic mutational spectrum predominated by G:C to T:A mutations.

METHODS

To recapitulate the distinctive features of TP53 mutations in AFB(1)-associated HCC, we investigated AFB(1)-induced DNA adduction in relation to mutagenesis in transgenic mouse fibroblasts exposed to AFB(1) in vitro.

RESULTS

Immunodotblot determination of DNA adducts in the overall genome of AFB(1)-exposed cells revealed the dose-dependant formation of persistent imidazole ring-opened AFB(1)-DNA adducts. DNA footprinting analysis of the cII transgene in AFB(1)-exposed cells verified the dose-dependent and sequence-specific formation of DNA adducts. The preferential formation of AFB(1)-induced DNA adducts along the cII transgene was almost exclusively localized to guanine-containing sequences encompassing CpG dinucleotides. Mutation analysis of the cII transgene in AFB(1)-exposed cells revealed a dose-dependent induction of cII mutant frequency (P < .001) and a unique induced mutational spectrum characterized by predominant induction of G:C to T:A transversions that occurred within CpG sequence contexts. Notably, codons 42 and 45 of the cII transgene, which have identical sequence contexts to that of codon 249 of human TP53, constituted 2 frequently mutated sites in AFB(1)-exposed cells that contained the G to T transversion signature mutation at their third base positions.

CONCLUSIONS

In this model system, AFB(1)-induced DNA adduction and mutagenesis recapitulate the unique mutational features of TP53 in AFB(1)-associated human HCC.

C/EBPbeta induces chromatin opening at a cell-type-specific enhancer

We have used the chicken mim-1 gene as a model to study the mechanisms by which transcription factors gain initial access to their target sites in compacted chromatin. The expression of mim-1 is restricted to the myelomonocytic lineage of the hematopoietic system where it is regulated synergistically by the Myb and CCAAT/enhancer binding protein (C/EBP) factors. Myb and C/EBPbeta cooperate at two distinct cis elements of mim-1, the promoter and a cell-type-specific enhancer, both of which are associated with DNase I hypersensitive sites in myelomonocytic cells but not in mim-1-nonexpressing cells. Previous work has shown that ectopic expression of Myb and C/EBPbeta activates the endogenous mim-1 gene in a nonhematopoietic cell type (fibroblasts), where the gene is normally completely silent. Here, we investigated the molecular details of this finding and show that the activation of mim-1 occurs by two independent mechanisms. In the absence of Myb, C/EBPbeta triggers the initial steps of chromatin opening at the mim-1 enhancer without inducing transcription of the gene. mim-1 transcription occurs only in the presence of Myb and is associated with chromatin opening at the promoter. Our work identifies a novel function for C/EBPbeta in the initial steps of a localized chromatin opening at a specific, physiologically relevant target region.

Novel high-resolution characterization of ancient DNA reveals C > U-type base modification events as the sole cause of post mortem miscoding lesions

Ancient DNA (aDNA) research has long depended on the power of PCR to amplify trace amounts of surviving genetic material from preserved specimens. While PCR permits specific loci to be targeted and amplified, in many ways it can be intrinsically unsuited to damaged and degraded aDNA templates. PCR amplification of aDNA can produce highly-skewed distributions with significant contributions from miscoding lesion damage and non-authentic sequence artefacts. As traditional PCR-based approaches have been unable to fully resolve the molecular nature of aDNA damage over many years, we have developed a novel single primer extension (SPEX)-based approach to generate more accurate sequence information. SPEX targets selected template strands at defined loci and can generate a quantifiable redundancy of coverage; providing new insights into the molecular nature of aDNA damage and fragmentation. SPEX sequence data reveals inherent limitations in both traditional and metagenomic PCR-based approaches to aDNA, which can make current damage analyses and correct genotyping of ancient specimens problematic. In contrast to previous aDNA studies, SPEX provides strong quantitative evidence that C > U-type base modifications are the sole cause of authentic endogenous damage-derived miscoding lesions. This new approach could allow ancient specimens to be genotyped with unprecedented accuracy.

Riboflavin activated by ultraviolet A1 irradiation induces oxidative DNA damage-mediated mutations inhibited by vitamin C

An increasingly popular theory ascribes UVA (>320-400 nm) carcinogenicity to the ability of this wavelength to trigger intracellular photosensitization reactions, thereby giving rise to promutagenic oxidative DNA damage. We have tested this theory both at the genomic and nucleotide resolution level in mouse embryonic fibroblasts carrying the lambda phage cII transgene. We have also tested the hypothesis that inclusion of a cellular photosensitizer (riboflavin) can intensify UVA-induced DNA damage and mutagenesis, whereas addition of an antioxidant (vitamin C) can counteract the induced effects. Cleavage assays with formamidopyrimidine DNA glycosylase (Fpg) coupled to alkaline gel electrophoresis and ligation-mediated PCR (LM-PCR) showed that riboflavin treatment (1 microM) combined with UVA1 (340-400 nm) irradiation (7.68 J/cm(2)) or higher dose UVA1 irradiation alone induced Fpg-sensitive sites (indicative of oxidized and/or ring-opened purines) in the overall genome and in the cII transgene, respectively. Also, the combined treatment with riboflavin and UVA1 irradiation gave rise to single-strand DNA breaks in the genome and in the cII transgene determined by terminal transferase-dependent PCR (TD-PCR). A cotreatment with vitamin C (1 mM) efficiently inhibited the formation of the induced lesions. Mutagenicity analysis showed that riboflavin treatment combined with UVA1 irradiation or high-dose UVA1 irradiation alone significantly increased the relative frequency of cII mutants, both mutation spectra exhibiting significant increases in the relative frequency of G:C --> T:A transversions, the signature mutations of oxidative DNA damage. The induction of cII mutant frequency was effectively reduced consequent to a cotreatment with vitamin C. Our findings support the notion that UVA-induced photosensitization reactions are responsible for oxidative DNA damage leading to mutagenesis.

DNA lesions induced by UV A1 and B radiation in human cells: comparative analyses in the overall genome and in the p53 tumor suppressor gene

The UV components of sunlight (UVA and UVB) are implicated in the etiology of human skin cancer. The underlying mechanism of action for UVB carcinogenicity is well defined; however, the mechanistic involvement of UVA in carcinogenesis is not fully delineated. We investigated the genotoxicity of UVA1 versus UVB in the overall genome and in the p53 tumor suppressor gene in normal human skin fibroblasts. Immuno-dot blot analysis identified the cis-syn cyclobutane pyrimidine-dimer (CPD) as a distinctive UVB-induced lesion and confirmed its formation in the genomic DNA of UVA1-irradiated cells dependent on radiation dose. HPLC/tandem MS analysis showed an induction of 8-oxo-7,8-dihydro-2'-deoxyguanosine in the genomic DNA of UVA1-irradiated cells only. Mapping of DNA damages by terminal transferase-dependent PCR revealed preferential, but not identical, formation of polymerase-blocking lesions and/or strand breaks along exons 5-8 of the p53 gene in UVB- and UVA1-irradiated cells. The UVB-induced lesions detected by terminal transferase-PCR were almost exclusively mapped to pyrimidine-rich sequences; however, the UVA1-induced lesions were mapped to purine- and pyrimidine-containing sequences along the p53 gene. Cleavage assays with lesion-specific DNA repair enzymes coupled to ligation-mediated PCR showed preferential, but not identical, formation of CPDs along the p53 gene in UVB- and UVA1-irradiated cells. Additionally, dose-dependent formation of oxidized and ring-opened purines and abasic sites was established in the p53 gene in only UVA1-irradiated cells. We conclude that UVA1 induces promutagenic CPDs and oxidative DNA damage at both the genomic and nucleotide resolution level in normal human skin fibroblasts.

Rapid, solid-phase based automated analysis of chromatin structure and transcription factor occupancy in living eukaryotic cells

Transcription factors, chromatin components and chromatin modification activities are involved in many diseases including cancer. However, the means by which alterations in these factors influence the epigenotype of specific cell types is poorly understood. One problem that limits progress is that regulatory regions of eukaryotic genes sometimes extend over large regions of DNA. To improve chromatin structure–function analysis over such large regions, we have developed an automated, relatively simple procedure that uses magnetic beads and a capillary sequencer for ligation-mediated-PCR (LM-PCR). We show that the procedure can be used for the rapid examination of chromatin fine-structure, nucleosome positioning as well as changes in transcription factor binding-site occupancy during cellular differentiation.

Differential transcription factor occupancy but evolutionarily conserved chromatin features at the human and mouse M-CSF (CSF-1) receptor loci

The c-FMS gene encodes the macrophage colony-stimulating factor receptor (M-CSFR or CSF1-R), which is a tyrosine kinase growth factor receptor essential for macrophage development. We have previously characterized the chromatin features of the mouse gene; however, very little is known about chromatin structure and function of the human c-FMS locus. Here we present a side-by-side comparison of the chromatin structure, histone modification, transcription factor occupancy and cofactor recruitment of the human and the mouse c-FMS loci. We show that, similar to the mouse gene, the human c-FMS gene possesses a promoter and an intronic enhancer element (c-fms intronic regulatory element or FIRE). Both elements are evolutionarily conserved and specifically active in macrophages. However, we demonstrate by in vivo footprinting that both murine and human c-FMS cis-regulatory elements are recognised by an overlapping, but non-identical, set of transcription factors. Despite these differences, chromatin immunoprecipitation experiments show highly similar patterns of histone H3 modification and a similar distribution of chromatin modifying and remodelling activities at individual cis-regulatory elements and across the c-FMS locus. Our experiments support the hypothesis that the same regulatory principles operate at both genes via conserved cores of transcription factor binding sites.

Transcription factor complex formation and chromatin fine structure alterations at the murine c-fms (CSF-1 receptor) locus during maturation of myeloid precursor cells

Expression of the gene for the macrophage colony stimulating factor receptor (CSF-1R), c-fms, has been viewed as a hallmark of the commitment of multipotent precursor cells to macrophages. Lineage-restricted expression of the gene is controlled by conserved elements in the proximal promoter and within the first intron. To investigate the developmental regulation of c-fms at the level of chromatin structure, we developed an in vitro system to examine the maturation of multipotent myeloid precursor cells into mature macrophages. The dynamics of chromatin fine structure alterations and transcription factor occupancy at the c-fms promoter and intronic enhancer was examined by in vivo DMS and UV-footprinting. We show that the c-fms gene is already transcribed at low levels in early myeloid precursors on which no CSF-1R surface expression can be detected. At this stage of myelopoiesis, the formation of transcription factor complexes on the promoter was complete. By contrast, occupancy of the enhancer was acutely regulated during macrophage differentiation. Our data show that cell-intrinsic differentiation decisions at the c-fms locus precede the appearance of c-fms on the cell surface. They also suggest that complex lineage-specific enhancers such as the c-fms intronic enhancer regulate local chromatin structure through the coordinated assembly and disassembly of distinct transcription factor complexes.

Identification of factors mediating the developmental regulation of the early acting -3.9 kb chicken lysozyme enhancer element

The chicken lysozyme gene -3.9 kb enhancer forms a DNase I hypersensitive site (DHS) early in macrophage differentiation, but not in more primitive multipotent myeloid precursor cells. A nucleosome becomes precisely positioned across the enhancer in parallel with DHS formation. In transfection assays, the 5'-part of the -3.9 kb element has ubiquitous enhancer activity. The 3'-part has no stimulatory activity, but is necessary for enhancer repression in lysozyme non-expressing cells. Recent studies have shown that the chromatin fine structure of this region is affected by inhibition of histone deacetylase activity after Trichostatin A (TSA) treatment, but only in lysozyme non-expressing cells. These results indicated a developmental modification of chromatin structure from a dynamic, but inactive, to a stabilised, possibly hyperacetylated, active state. Here we have identified positively and negatively acting transcription factors binding to the -3.9 kb enhancer and determined their contribution to enhancer activity. Furthermore, we examined the influence of TSA treatment on enhancer activity in macrophage cells and lysozyme non-expressing cells, including multipotent macrophage precursors. Interestingly, TSA treatment was able to restore enhancer activity fully in macrophage precursor cells, but not in non-macrophage lineage cells. These results suggest (i) that the transcription factor complement of multipotent progenitor cells is similar to that of lysozyme-expressing cells and (ii) that developmental regulation of the -3.9 kb enhancer is mediated by the interplay of repressing and activating factors that respond to or initiate changes in the chromatin acetylation state.