Change point analysis of histone modifications reveals epigenetic blocks linking to physical domains

Histone modification is a vital epigenetic mechanism for transcriptional control in eukaryotes. High-throughput techniques have enabled whole-genome analysis of histone modifications in recent years. However, most studies assume one combination of histone modification invariantly translates to one transcriptional output regardless of local chromatin environment. In this study we hypothesize that, the genome is organized into local domains that manifest similar enrichment pattern of histone modification, which leads to orchestrated regulation of expression of genes with relevant biological functions. We propose a multivariate Bayesian Change Point (BCP) model to segment the Drosophila melanogaster genome into consecutive blocks on the basis of combinatorial patterns of histone marks. By modeling the sparse distribution of histone marks with a zero-inflated Gaussian mixture, our partitions capture local BLOCKs that manifest relatively homogeneous enrichment pattern of histone marks. We further characterized BLOCKs by their transcription levels, distribution of genes, degree of co-regulation and GO enrichment. Our results demonstrate that these BLOCKs, although inferred merely from histone modifications, reveal strong relevance with physical domains, which suggests their important roles in chromatin organization and coordinated gene regulation

The Yb protein defines a novel organelle and regulates male germline stem cell self-renewal in Drosophila melanogaster

Yb regulates the proliferation of both germline and somatic stem cells in the Drosophila melanogaster ovary by activating piwi and hh expression in niche cells. In this study, we show that Yb protein is localized as discrete cytoplasmic spots exclusively in the somatic cells of the ovary and testis. These spots, which are different from all known cytoplasmic structures in D. melanogaster, are evenly electron-dense spheres 1.5 µm in diameter (herein termed the Yb body). The Yb body is frequently associated with mitochondria and a less electron-dense sphere of similar size that appears to be RNA rich. There are one to two Yb bodies/cell, often located close to germline cells. The N-terminal region of Yb is required for hh expression in niche cells, whereas the C-terminal region is required for localization to Yb bodies. The entire Yb protein is necessary for piwi expression in niche cells. A double mutant of Yb and a novel locus show male germline loss, revealing a function for Yb in male germline stem cell maintenance

Deciphering the role of RNA structure in translation efficiency.

BACKGROUND: RNA secondary structure has broad impact on the fate of RNA metabolism. The reduced stability of secondary structures near the translation initiation site/start codon of the coding region promotes the efficiency of translation in both prokaryotic and eukaryotic species. However, the inaccuracy of in silico folding and the focus on the coding region limit our understanding of the global relationship between the whole mRNA structure and translation efficiency. Leveraging high-throughput RNA structure probing data in the transcriptome, we aim to systematically investigate the role of RNA structure in regulating translation efficiency. RESULTS: Here, we analyze the influences of hundreds of sequence and structural features on translation efficiency in the mouse embryonic stem cells (mESCs) and zebrafish developmental stages. Our findings reveal that overall in vivo RNA structure has a higher relative importance in predicting translation efficiency than in vitro RNA structure in both mESCs and zebrafish. Also, RNA structures in 3\u27 untranslated region (UTR) have much stronger influence on translation efficiency compared to those in coding regions or 5\u27 UTR. Furthermore, strong alternation between in vitro and in vivo structures in 3\u27 UTR are detected in highly translated mRNAs in mESCs but not zebrafish. Instead, moderate alteration between in vitro and in vivo RNA structures in the 5\u27 UTR and proximal coding regions are detected in highly translated mRNAs in zebrafish. CONCLUSIONS: Our results suggest the openness of the 3\u27 UTR promotes the translation efficiency in both mice and zebrafish, with the in vivo structure in 3\u27 UTR more important in mice than in zebrafish. This reveals a novel role of RNA secondary structure on translational regulation

Enhancing LTE with Cloud-RAN and Load-Controlled Parasitic Antenna Arrays

Cloud radio access network systems, consisting of remote radio heads densely distributed in a coverage area and connected by optical fibers to a cloud infrastructure with large computational capabilities, have the potential to meet the ambitious objectives of next generation mobile networks. Actual implementations of C-RANs tackle fundamental technical and economic challenges. In this article, we present an end-to-end solution for practically implementable C-RANs by providing innovative solutions to key issues such as the design of cost-effective hardware and power-effective signals for RRHs, efficient design and distribution of data and control traffic for coordinated communications, and conception of a flexible and elastic architecture supporting dynamic allocation of both the densely distributed RRHs and the centralized processing resources in the cloud to create virtual base stations. More specifically, we propose a novel antenna array architecture called load-controlled parasitic antenna array (LCPAA) where multiple antennas are fed by a single RF chain. Energy- and spectral-efficient modulation as well as signaling schemes that are easy to implement are also provided. Additionally, the design presented for the fronthaul enables flexibility and elasticity in resource allocation to support BS virtualization. A layered design of information control for the proposed end-to-end solution is presented. The feasibility and effectiveness of such an LCPAA-enabled C-RAN system setup has been validated through an over-the-air demonstration

RIS-Aided Wireless Communications: Prototyping, Adaptive Beamforming, and Indoor/Outdoor Field Trials

The prospects of using a Reconfigurable Intelligent Surface (RIS) to aid wireless communication systems have recently received much attention from academia and industry. Most papers make theoretical studies based on elementary models, while the prototyping of RIS-aided wireless communication and real-world field trials are scarce. In this paper, we describe a new RIS prototype consisting of 1100 controllable elements working at 5.8 GHz band. We propose an efficient algorithm for configuring the RIS over the air by exploiting the geometrical array properties and a practical receiver-RIS feedback link. In our indoor test, where the transmitter and receiver are separated by a 30 cm thick concrete wall, our RIS prototype provides a 26 dB power gain compared to the baseline case where the RIS is replaced by a copper plate. A 27 dB power gain was observed in the short-distance outdoor measurement. We also carried out long-distance measurements and successfully transmitted a 32 Mbps data stream over 500 m. A 1080p video was live-streamed and it only played smoothly when the RIS was utilized. The power consumption of the RIS is around 1 W. Our paper is vivid proof that the RIS is a very promising technology for future wireless communications.Comment: 13 pages, 18 figures, submitte

A High-Resolution Whole-Genome Map of Key Chromatin Modifications in the Adult Drosophila melanogaster

Epigenetic research has been focused on cell-type-specific regulation; less is known about common features of epigenetic programming shared by diverse cell types within an organism. Here, we report a modified method for chromatin immunoprecipitation and deep sequencing (ChIP–Seq) and its use to construct a high-resolution map of the Drosophila melanogaster key histone marks, heterochromatin protein 1a (HP1a) and RNA polymerase II (polII). These factors are mapped at 50-bp resolution genome-wide and at 5-bp resolution for regulatory sequences of genes, which reveals fundamental features of chromatin modification landscape shared by major adult Drosophila cell types: the enrichment of both heterochromatic and euchromatic marks in transposons and repetitive sequences, the accumulation of HP1a at transcription start sites with stalled polII, the signatures of histone code and polII level/position around the transcriptional start sites that predict both the mRNA level and functionality of genes, and the enrichment of elongating polII within exons at splicing junctions. These features, likely conserved among diverse epigenomes, reveal general strategies for chromatin modifications

Precancerous Stem Cells Have the Potential for both Benign and Malignant Differentiation

Cancer stem cells (CSCs) have been identified in hematopoietic and solid tumors. However, their precursors—namely, precancerous stem cells (pCSCs) —have not been characterized. Here we experimentally define the pCSCs that have the potential for both benign and malignant differentiation, depending on environmental cues. While clonal pCSCs can develop into various types of tissue cells in immunocompetent mice without developing into cancer, they often develop, however, into leukemic or solid cancers composed of various types of cancer cells in immunodeficient mice. The progress of the pCSCs to cancers is associated with the up-regulation of c-kit and Sca-1, as well as with lineage markers. Mechanistically, the pCSCs are regulated by the PIWI/AGO family gene called piwil2. Our results provide clear evidence that a single clone of pCSCs has the potential for both benign and malignant differentiation, depending on the environmental cues. We anticipate pCSCs to be a novel target for the early detection, prevention, and therapy of cancers