Stanley M. Gartler

Sequencing newly replicated DNA reveals widespread plasticity in human replication timing

Faithful transmission of genetic material to daughter cells involves a characteristic temporal order of DNA replication, which may play a significant role in the inheritance of epigenetic states. We developed a genome-scale approach—Repli Seq—to map temporally ordered replicating DNA using massively parallel sequencing and applied it to study regional variation in human DNA replication time across multiple human cell types. The method requires as few as 8,000 cytometry-fractionated cells for a single analysis, and provides high-resolution DNA replication patterns with respect to both cell-cycle time and genomic position. We find that different cell types exhibit characteristic replication signatures that reveal striking plasticity in regional replication time patterns covering at least 50% of the human genome. We also identified autosomal regions with marked biphasic replication timing that include known regions of monoallelic expression as well as many previously uncharacterized domains. Comparison with high-resolution genome-wide profiles of DNaseI sensitivity revealed that DNA replication typically initiates within foci of accessible chromatin comprising clustered DNaseI hypersensitive sites, and that replication time is better correlated with chromatin accessibility than with gene expression. The data collectively provide a unique, genome-wide picture of the epigenetic compartmentalization of the human genome and suggest that cell-lineage specification involves extensive reprogramming of replication timing patterns.

Glucose-6-Phosphate Dehydrogenase Mosaicism: Utilization as a Cell Marker in the Study of Leiomyomas

The sex-linked electrophoretic variants A and B of glucose-6-phosphate dehydrogenase were studied in 86 samples of myometrium and 27 leiomyomas from five heterozygous women. All but one sample of myometrium had both A and B bands in equal or nearly equal amounts. In contrast to this, all of the leiomyomas had either an A band or a B band. Both A and B tumors were found in all uteri. These findings are consistent with the hypothesis that these tumors arose from single cells.

Histone deacetylase inhibition elicits an evolutionarily conserved self-renewal program in embryonic stem cells.

Recent evidence indicates that mouse and human embryonic stem cells (ESCs) are fixed at different developmental stages, with the former positioned earlier. We show that a narrow concentration of the naturally occurring short-chain fatty acid, sodium butyrate, supports the extensive self-renewal of mouse and human ESCs, while promoting their convergence toward an intermediate stem cell state. In response to butyrate, human ESCs regress to an earlier developmental stage characterized by a gene expression profile resembling that of mouse ESCs, preventing precocious Xist expression while retaining the ability to form complex teratomas in vivo. Other histone deacetylase inhibitors (HDACi) also support human ESC self-renewal. Our results indicate that HDACi can promote ESC self-renewal across species, and demonstrate that ESCs can toggle between alternative states in response to environmental factors.

Lesch-Nyhan Syndrome: Rapid Detection of Heterozygotes by Use of Hair Follicles

A method is described which permits rapid phenotypic diagnosis of the Lesch-Nyhan heterozygote by direct assay of hypoxanthine guanine phosphori-bosyltransferase activity in single hair follicles obtained from the scalp.

Multiple Cell Origin of Hereditary Neurofibromas

Abstract In a female heterozygous for the A and B genes at the X-linked glucose-6-phosphate dehydrogenase (G-6-PD) locus, single cells express the activity of only one or the other gene. Thus, this...

Evidence for two functional X chromosomes in human oocytes

Abstract Oocytes from individuals heterozygous for the X-linked glucose-6-phosphate dehydrogenase (G6PD) electrophoretic variants, types A and B, were examined for their G6PD pattern. Three bands were observed, A, B, and AB; the presence of the AB (hybrid) band demonstrates that both X-linked G6PD alleles are functional in the maturing human oocyte.

Ontogeny of X-chromosome inactivation in the female germ line☆

Abstract Data are presented on G6PD electrophoretic patterns in fetal ovarian preparations of G6PD heterozygotes. The results indicate that in the early or mitotic period of female germ cell development, only a single X chromosome is active in each oogonium just as is the case for X inactivated somatic tissue. However, in the later or meiotic stage, reactivation of the inactive X chromosome in each oocyte occurs so that two functional X chromosomes are present in each oocyte.

Cystathionine Synthase Activity in Human Lymphocytes: Induction by Phytohemagglutinin

Uncultured human leukocytes contain no detectable cystathionine synthase activity. A method is described in which the addition of phytohemagglutinin (PHA) to short-term lymphocyte cultures results in a significant induction of enzymatic activity. This PHA-stimulated activity has characteristics that resemble those previously described for cystathionine synthase of normal liver and cultured fibroblasts. Lymphocyte cystathionine synthase activity is completely dependent on the presence of homocysteine and is absent or severely deficient in extracts from individuals with the syndrome of homocystinuria. This system for induction of cystathionine synthase in lymphocytes thus provides a simple in vitro technique for (a) diagnosing homocystinuria, (b) studying the mechanism of enzyme regulation and differentiation, and (c) examining the nutritional and hormonal control of cystathionine synthase activity both in normal subjects and homocystinuric patients.

Mammalian X chromosome inactivation: testing the hypothesis of transcriptional control

Mammalian X chromosome inactivation is generally considered to be a good example of stable transcriptional repression; however, there has been no satisfactory evidence for transcriptional control. We have made a test of the hypothesis of transcriptional control by Northern blot analysis of RNA from a woman heterozygous for a mutant Hpt allele which shows no detectable transcription of wildtype mRNA. Cells from this Hpt+ Hpt− woman were separated into HPRT+ and HPRT− subpopulations by selection in HAT or thioguanine. The HPRT+ population (in which the Hpt+ is on the active X) transcribed normal Hpt mRNA, while the HPRT− population (in which the Hpt+ allele is on the inactive X) did not. These results provide strong support for the hypothesis of transcriptional control.

Hemimethylation and Non-CpG Methylation Levels in a Promoter Region of Human LINE-1 (L1) Repeated Elements

DNA methylation within the promoter region of human LINE1 (L1) transposable elements is important for maintaining transcriptional inactivation and for inhibiting L1 transposition. Determining methylation patterns on the complementary strands of repeated sequences is difficult using standard bisulfite methylation analysis. Evolutionary changes in each repeat and the variations between cells or alleles of the same repeat lead to a heterogeneous population of sequences. Potential sequence biases can arise during analyses that are different for the converted sense and antisense strands. These problems can be avoided with hairpin-bisulfite PCR, a double-stranded PCR method in which complementary strands of individual molecules are attached by a hairpin linker ligated to genomic DNA. Using human L1 elements to study methylation of repeated sequences, (i) we distinguish valid L1 sequences from redundant and contaminant sequences by applying the powerful new method of molecular barcodes, (ii) we resolve a controversy on the level of hemimethylation of L1 sequences in fetal fibroblasts in favor of relatively little hemimethylation, (iii) we report that human L1 sequences in different cell types also have primarily concordant CpG methylation patterns on complementary strands, and (iv) we provide evidence that non-CpG cytosines within the regions analyzed are rarely methylated.