Retrotransposon expression profiling: Unveiling the hidden SINE transcriptome through Next-Generation Sequencing data analysis

Of the ~1.7 million SINE elements in the human genome, only a tiny number are estimated to be active in transcription by RNA polymerase (Pol) III. Tracing the individual loci from which SINE transcripts originate is complicated by their highly repetitive nature. By exploiting RNA-Seq datasets and unique SINE DNA sequences, we devised a bioinformatic pipeline allowing us to identify Pol III-dependent transcripts of individual SINE elements. When applied to ENCODE transcriptomes of seven human cell lines, this search strategy identified ~1300 Alu loci and ~1100 MIR loci corresponding to detectable transcripts, with ~120 and ~60 respectively Alu and MIR loci expressed in at least three cell lines. In vitro transcription of selected SINEs did not reflect their in vivo expression properties, and required the native 5’-flanking region in addition to internal promoter. We also identified a cluster of expressed AluYa5-derived transcription units, juxtaposed to snaR genes on chromosome 19, formed by a promoter-containing left monomer fused to an Alu-unrelated downstream moiety. Autonomous Pol III transcription was also revealed for SINEs nested within Pol II-transcribed genes raising the possibility of an underlying mechanism for Pol II gene regulation by SINE transcriptional units. Moreover the application of our bioinformatic pipeline to both RNA-seq data of cells subjected to an in vitro pro-oncogenic stimulus and of in vivo matched tumor and non-tumor samples allowed us to detect increased Alu RNA expression as well as the source loci of such deregulation. The ability to investigate SINE transcriptomes at single-locus resolution will facilitate both the identification of novel biologically relevant SINE RNAs and the assessment of SINE expression alteration under pathological conditions.

Physical and MAC layer techniques for next generation satellite communications

In this thesis, we consider four different scenarios of interest in modern satellite communications. For each scenario, we will propose the use of advanced solutions aimed at increasing the spectral efficiency of the communication links. First, we will investigate the optimization of the current standard for digital video broadcasting. We will increase the symbol rate of the signal and determine the optimal signal bandwidth. We will apply the time packing technique and propose a specifically design constellation. We will then compare some receiver architectures with different performance and complexity. The second scenario still addresses broadcast transmissions, but in a network composed of two satellites. We will compare three alternative transceiver strategies, namely, signals completely overlapped in frequency, frequency division multiplexing, and the Alamouti space-time block code, and, for each technique, we will derive theoretical results on the achievable rates. We will also evaluate the performance of said techniques in three different channel models. The third scenario deals with the application of multiuser detection in multibeam satellite systems. We will analyze a case in which the users are near the edge of the coverage area and, hence, they experience a high level of interference from adjacent cells. Also in this case, three different approaches will be compared. A classical approach in which each beam carries information for a user, a cooperative solution based on time division multiplexing, and the Alamouti scheme. The information theoretical analysis will be followed by the study of practical coded schemes. We will show that the theoretical bounds can be approached by a properly designed code or bit mapping. Finally, we will consider an Earth observation scenario, in which data is generated on the satellite and then transmitted to the ground. We will study two channel models, taking into account one or two transmit antennas, and apply techniques such as time and frequency packing, signal predistortion, multiuser detection and the Alamouti scheme.