Novel physical phenomena can emerge in low-dimensional nanomaterials. Bulk MoS(2), a prototypical metal dichalcogenide, is an indirect bandgap semiconductor with negligible photoluminescence. When the MoS(2) crystal is thinned to monolayer, however, a strong photoluminescence emerges, indicating an indirect to direct bandgap transition in this d-electron system. This observation shows that quantum confinement in layered d-electron materials like MoS(2) provides new opportunities for engineering the electronic structure of matter at the nanoscale.

We report the generation and analysis of functional data from multiple, diverse experiments performed on a targeted 1% of the human genome as part of the pilot phase of the ENCODE Project. These data have been further integrated and augmented by a number of evolutionary and computational analyses. Together, our results advance the collective knowledge about human genome function in several major areas. First, our studies provide convincing evidence that the genome is pervasively transcribed, such that the majority of its bases can be found in primary transcripts, including non-protein-coding transcripts, and those that extensively overlap one another. Second, systematic examination of transcriptional regulation has yielded new understanding about transcription start sites, including their relationship to specific regulatory sequences and features of chromatin accessibility and histone modification. Third, a more sophisticated view of chromatin structure has emerged, including its inter-relationship with DNA replication and transcriptional regulation. Finally, integration of these new sources of information, in particular with respect to mammalian evolution based on inter- and intra-species sequence comparisons, has yielded new mechanistic and evolutionary insights concerning the functional landscape of the human genome. Together, these studies are defining a path for pursuit of a more comprehensive characterization of human genome function.

Van der Waals heterostructures have recently emerged as a new class of materials, where quantum coupling between stacked atomically thin two-dimensional layers, including graphene, hexagonal-boron nitride and transition-metal dichalcogenides (MX2), give rise to fascinating new phenomena. MX2 heterostructures are particularly exciting for novel optoelectronic and photovoltaic applications, because two-dimensional MX2 monolayers can have an optical bandgap in the near-infrared to visible spectral range and exhibit extremely strong light-matter interactions. Theory predicts that many stacked MX2 heterostructures form type II semiconductor heterojunctions that facilitate efficient electron-hole separation for light detection and harvesting. Here, we report the first experimental observation of ultrafast charge transfer in photoexcited MoS2/WS2 heterostructures using both photoluminescence mapping and femtosecond pump-probe spectroscopy. We show that hole transfer from the MoS2 layer to the WS2 layer takes place within 50 fs after optical excitation, a remarkable rate for van der Waals coupled two-dimensional layers. Such ultrafast charge transfer in van der Waals heterostructures can enable novel two-dimensional devices for optoelectronics and light harvesting.

Much attention has focused on a small set of transcription factors that maintain human or mouse embryonic stem (ES) cells in a pluripotent state. To gain a more complete understanding of the regulatory network that maintains this state, we identified target promoters of nine transcription factors, including somatic cell reprogramming factors (Oct4, Sox2, Klf4, and c-Myc) and others (Nanog, Dax1, Rex1, Zpf281, and Nac1), on a global scale in mouse ES cells. We found that target genes fall into two classes: promoters bound by few factors tend to be inactive or repressed, whereas promoters bound by more than four factors are largely active in the pluripotent state and become repressed upon differentiation. Furthermore, we propose a transcriptional hierarchy for reprogramming factors and broadly distinguish targets of c-Myc versus other factors. Our data provide a resource for exploration of the complex network maintaining pluripotency.

Trimethylation on H3K27 (H3K27me3) mediated by Polycomb repressive complex 2 (PRC2) has been linked to embryonic stem cell (ESC) identity and pluripotency. EZH2, the catalytic subunit of PRC2, has been reported as the sole histone methyltransferase that methylates H3K27 and mediates transcriptional silencing. Analysis of Ezh2(-/-) ESCs suggests existence of an additional enzyme(s) catalyzing H3K27 methylation. We have identified EZH1, a homolog of EZH2 that is physically present in a noncanonical PRC2 complex, as an H3K27 methyltransferase in vivo and in vitro. EZH1 colocalizes with the H3K27me3 mark on chromatin and preferentially preserves this mark on development-related genes in Ezh2(-/-) ESCs. Depletion of Ezh1 in cells lacking Ezh2 abolishes residual methylation on H3K27 and derepresses H3K27me3 target genes, demonstrating a role of EZH1 in safeguarding ESC identity. Ezh1 partially complements Ezh2 in executing pluripotency during ESC differentiation, suggesting that cell-fate transitions require epigenetic specificity.

SUMMARY c-Myc (Myc) is an important transcriptional regulator in embryonic stem (ES) cells, somatic cell reprogramming, and cancer. Here, we identify a Myc-centered regulatory network in ES cells by combining protein-protein and protein-DNA interaction studies, and show that Myc interacts with the NuA4 complex, a regulator of ES cell identity. In combination with regulatory network information, we define three ES cell modules (Core, Polycomb, and Myc), and show that the modules are functionally separable, illustrating that the overall ES cell transcription program is comprised of distinct units. With these modules as an analytical tool, we have reassessed the hypothesis linking an ES cell signature with cancer or cancer stem cells. We find that the Myc module, independent of the Core module, is active in various cancers and predicts cancer outcome. The apparent similarity of cancer and ES cell signatures reflects in large part the pervasive nature of Myc regulatory network.

DNA segments that actively regulate transcription in vivo are typically characterized by eviction of nucleosomes from chromatin and are experimentally identified by their hypersensitivity to nucleases. Here we demonstrate a simple procedure for the isolation of nucleosome-depleted DNA from human chromatin, termed FAIRE (Formaldehyde-Assisted Isolation of Regulatory Elements). To perform FAIRE, chromatin is crosslinked with formaldehyde in vivo, sheared by sonication, and phenol-chloroform extracted. The DNA recovered in the aqueous phase is fluorescently labeled and hybridized to a DNA microarray. FAIRE performed in human cells strongly enriches DNA coincident with the location of DNaseI hypersensitive sites, transcriptional start sites, and active promoters. Evidence for cell-type-specific patterns of FAIRE enrichment is also presented. FAIRE has utility as a positive selection for genomic regions associated with regulatory activity, including regions traditionally detected by nuclease hypersensitivity assays.

Abstract:Phosphorene, a single atomic layer of black phosphorus, has recently emerged as a new twodimensional (2D) material that holds promise for electronic and photonic technology. Here we experimentally demonstrate that the electronic structure of few-layer phosphorene varies significantly with the number of layers, in good agreement with theoretical predictions. The interband optical transitions cover a wide, technologically important spectrum range from visible to mid-infrared. In addition, we observe strong photoluminescence in few-layer phosphorene at energies that match well with the absorption edge, indicating they are direct bandgap semiconductors. The strongly layer-dependent electronic structure of phosphorene, in combination with its high electrical mobility, gives it distinct advantages over other twodimensional materials in electronic and opto-electronic applications.Page 3 of 17! ! Atomically thin 2D crystals have emerged as a new class of materials with unique material properties that are potentially important for electronic and photonic technologies [1][2][3][4][5][6][7][8][9][10] . Various 2D crystals have been uncovered, ranging from metallic (and superconducting) NbSe 2 and semimetallic graphene to semiconducting MoS 2 and insulating hexagonal boron nitride (hBN).The energy bandgap, a defining characteristic of an electronic material, varies correspondingly from 0 (in metals and graphene) to 5.8 eV (in hBN) in these 2D crystals. Despite the rich variety currently available, 2D materials with a bandgap in the range from 0.3 eV to 1.5 eV are notably missing 11 . Such a bandgap corresponds to a spectral range from mid-infrared to near-infrared that is important for optoelectronic technologies such as telecommunication and solar energy harvesting. It is therefore desirable to have 2D materials with a bandgap that falls in this range, and in particular, matches that of the technologically important silicon (bandgap = 1.1 eV) and III-V semiconductors like InGaAs, without compromising sample mobility 12 .Monolayer and few-layer phosphorene are predicted to bridge the much needed bandgap range from 0.3 to 2 eV (Refs. 13-17). Inside monolayer phosphorene, each phosphorus atom is covalently bonded with three adjacent phosphorus atoms to form a puckered honeycomb structure 18 . The three near sp 3 bonds together with the lone-pair orbital take up all five valence electrons of phosphorus, so monolayer phosphorene is a semiconductor with a predicted direct optical bandgap of ~ 1.5 eV at the Γ point of the Brillouin zone. The bandgap in few-layer phosphorene can be strongly modified by interlayer interactions, which leads to a bandgap that decreases with phosphorene film thickness, eventually reaching 0.3 eV in the bulk limit.Experimental observations of layer-dependent band structure in phosphorene, on the other hand, have been rather limited. Previously, photoluminescence (PL) spectroscopy has been used to probe the bandgap of monolayer and few-layer phosphorene 8,[19][20][21][22] . Such studies, howeve...