SUMMARY It is now established that Bcl11b specifies T cell fate. Here we show that in developing T-cells the Bcl11b enhancer repositioned from the lamina to the nuclear interior. Our search for factors that relocalized the Bcl11b enhancer identified a non-coding RNA named ThymoD (Thymocyte Differentiation Factor). ThymoD-deficient mice displayed a block at the onset of T cell development and developed lymphoid malignancies. We found that ThymoD transcription promoted demethylation at CTCF bound sites and activated cohesin-dependent looping to reposition the Bcl11b enhancer from the lamina to the nuclear interior and to juxtapose the Bcl11b enhancer and promoter into a single loop domain. These large-scale changes in nuclear architecture were associated with the deposition of activating epigenetic marks across the loop domain, plausibly facilitating phase separation. These data indicate how during developmental progression and tumor suppression non-coding transcription orchestrates chromatin folding and compartmentalization to direct with high precision enhancer-promoter communication.

B-cell fate is orchestrated by a series of well-characterized developmental regulators. Here, we found that the onset of B-cell development was accompanied by large-scale changes in DNA cytosine modifications associated with promoters, enhancers, and anchors. These changes were tightly linked to alterations in transcription factor occupancy and nascent RNA (eRNA) transcription. We found that the prepro-B to the pro-B-cell transition was associated with a global exchange of DNA cytosine modifications for polycomb-mediated repression at CpG islands. Hypomethylated regions were found exclusively in the active/permissive compartment of the nucleus and were predominantly associated with regulatory elements or anchors that orchestrate the folding patterns of the genome. We identified superanchors, characterized by clusters of hypomethylated CCCTC-binding factor (CTCF)-bound elements, which were predominantly located at boundaries that define topological associated domains. A particularly prominent hypomethylated superanchor was positioned down-stream of the Ig heavy chain (Igh) locus. Analysis of global formaldehyde-cross-linking studies indicated that the Igh locus superanchor interacts with the V H region repertoire across vast genomic distances. We propose that the Igh locus superanchor sequesters the V H and D H J H regions into a spatial confined geometric environment to promote rapid first-passage times. Collectively, these studies demonstrate how, in developing B cells, DNA cytosine modifications associated with regulatory and architectural elements affect patterns of gene expression, folding patterns of the genome, and antigen receptor assembly.DNA modification | superanchor | nuclear architecture | immunoglobulin heavy chain locus | superinsulator T he onset of B-cell development is initiated in the fetal liver or adult bone marrow at the common lymphoid progenitor cell (CLP) cell stage (1, 2). Specification to the B-cell lineage is established by a spectrum of transcriptional regulators that act collaboratively to prime and ultimately activate a B-lineagespecific program of gene expression (3, 4). Conspicuous among the activators that establish B-cell identity are the E2A, EBF1, and FOXO1 proteins (5-8). In CLPs, the E2A proteins induce the expression of FOXO1, which, in turn, activates EBF1 transcription (6). EBF1 and FOXO1 subsequently act in a regulatory feedback loop to induce an active enhancer repertoire and activate a B-lineage specific program of gene expression (9, 10).It is now well established that the chromatin fiber is marked by DNA methylation (11-13). Methylation of cytosines primarily occurs at CpG residues, although methylation in CHG and CHH nucleotides has also been observed (14). The vast majority of CpG nucleotides are methylated. Unmethylated CpG residues and CpG islands are closely associated with transcriptionally active promoters. Other demethylated regions, found distal to gene promoters, tend to be cell-type specific, with changes in DNA methylation state often correlating with alt...

Rare cases of possible materno-fetal transmission of cancer have been recorded over the past 100 years but evidence for a shared cancer clone has been very limited. We provide genetic evidence for mother to offspring transmission, in utero, of a leukemic cell clone. Maternal and infant cancer clones shared the same unique BCR-ABL1 genomic fusion sequence, indicating a shared, single-cell origin. Microsatellite markers in the infant cancer were all of maternal origin. Additionally, the infant, maternally-derived cancer cells had a major deletion on one copy of chromosome 6p that included deletion of HLA alleles that were not inherited by the infant (i.e., foreign to the infant), suggesting a possible mechanism for immune evasion.fetus ͉ fusion gene ͉ leukemia

Novel penem molecules with heterocycle substitutions at the 6 position via a methylidene linkage were investigated for their activities and efficacy as ␤-lactamase inhibitors. The concentrations of these molecules that resulted in 50% inhibition of enzyme activity were 0.4 to 3.1 nM for the TEM-1 enzyme, 7.8 to 72 nM for Imi-1, 1.5 to 4.8 nM for AmpC, and 14 to 260 nM for a CcrA metalloenzyme. All the inhibitors were more stable than imipenem against hydrolysis by hog and human dehydropeptidases. Piperacillin was combined with a constant 4-g/ml concentration of each inhibitor for MIC determinations. The combinations reduced piperacillin MICs by 2-to 32-fold for extended-spectrum ␤-lactamase (ESBL)-producing Escherichia coli and Klebsiella pneumoniae strains. The MICs for piperacillin-resistant (MIC of piperacillin, >64 g/ml) strains of Enterobacter spp., Citrobacter spp., and Serratia spp. were reduced to the level of susceptibility (MIC of piperacillin, <16 g/ml) when the drug was combined with 4, 2, or 1 g of these penem inhibitors/ml. Protection against acute lethal bacterial infections with class A and C ␤-lactamase-and ESBL-producing organisms in mice was also demonstrated with piperacillin plus inhibitor. Median effective doses were reduced by approximately two-to eightfold compared to those of piperacillin alone when the drug was combined with the various inhibitors at a 4:1 ratio. Pharmacokinetic analysis after intravenous administration of the various inhibitors showed mean residence times of 0.1 to 0.5 h, clearance rates of 15 to 81 ml/min/kg, and volumes of distribution between 0.4 and 2.5 liters/kg. The novel methylidene penem molecules inhibit both class A and class C enzymes and warrant further investigation for potential as therapeutic agents when used in combination with a ␤-lactam antibiotic.

A novel polyborosilazane was synthesized by reacting perhydropolysilazane with trimethyl borate. The chemical structure of this polymer was investigated by the techniques of infrared spectroscopy and nuclear magnetic resonance measurements. Amorphous silicon nitride was obtained by pyrolysis of this polymer in a stream of anhydrous ammonia to 1000°C with high ceramic yield. The pyrolysis product remained amorphous after additional heating to 1700°C under N,. Crystallization to cu-Si,N4 and p-Si,N4 proceeded with heat treatment at 1800°C under N2. These results indicate that polyborosilazane is a good precursor for amorphous silicon nitride based materials.

By changing the packing rate of metallic spheres inside a pipe, we experimentally investigated a density fluctuation of metallic spheres that fall through a vertical glass pipe filled with liquid. We found that only at the intermediate packing rate pϳ0.18 the power spectrum of the density fluctuation of falling metallic spheres P( f ) obeys a power law as P( f )ϳ1/f ␣ , where f is a frequency and ␣ is a positive constant. This intermediate packing rate corresponds to a slugging transition point from the low-packing-rate region where metallic spheres fall almost freely to the high-packing-rate region where density waves ͑slugs of granular materials͒ emerge and so metallic spheres fall in a group very slowly. We also compare our experimental results with the jamming transition and the 1/f noise that appear in a crowded traffic flow.

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Differentiating neutrophils undergo large-scale changes in nuclear morphology. How such alterations in structure are established and modulated upon exposure to microbial agents is largely unknown. Here, we found that prior to encounter with bacteria, an armamentarium of inflammatory genes was positioned in a transcriptionally passive environment suppressing premature transcriptional activation. Upon microbial exposure, however, human neutrophils rapidly (<3 h) repositioned the ensemble of proinflammatory genes toward the transcriptionally permissive compartment. We show that the repositioning of genes was closely associated with the swift recruitment of cohesin across the inflammatory enhancer landscape, permitting an immediate transcriptional response upon bacterial exposure. We found that activated enhancers, marked by increased deposition of H3K27Ac, were highly enriched for cistromic elements associated with PU.1, CEBPB, TFE3, JUN, and FOSL2 occupancy. These data reveal how upon microbial challenge the cohesin machinery is recruited to an activated enhancer repertoire to instruct changes in chromatin folding, nuclear architecture, and to activate an inflammatory gene program.