HLA-G, a nonclassical HLA molecule uniquely expressed in the placenta, is a central component of fetus-induced immune tolerance during pregnancy. The tissue-specific expression of HLA-G, however, remains poorly understood. Here, systematic interrogation of the HLA-G locus using massively parallel reporter assay (MPRA) uncovered a previously unidentified cis-regulatory element 12 kb upstream of HLA-G with enhancer activity, Enhancer L. Strikingly, clustered regularly-interspaced short palindromic repeats (CRISPR)/ Cas9-mediated deletion of this enhancer resulted in ablation of HLA-G expression in JEG3 cells and in primary human trophoblasts isolated from placenta. RNA-seq analysis demonstrated that Enhancer L specifically controls HLA-G expression. Moreover, DNase-seq and chromatin conformation capture (3C) defined Enhancer L as a cell type-specific enhancer that loops into the HLA-G promoter. Interestingly, MPRA-based saturation mutagenesis of Enhancer L identified motifs for transcription factors of the CEBP and GATA families essential for placentation. These factors associate with Enhancer L and regulate HLA-G expression. Our findings identify long-range chromatin looping mediated by core trophoblast transcription factors as the mechanism controlling tissue-specific HLA-G expression at the maternal-fetal interface. More broadly, these results establish the combination of MPRA and CRISPR/Cas9 deletion as a powerful strategy to investigate human immune gene regulation.

ENCODE 3 (2012-2017) expanded production and added new types of assays 8 (Fig. 1, Extended Data Fig. 1), which revealed landscapes of RNA binding and the 3D organization of chromatin via methods such as chromatin interaction analysis by paired-end tagging (ChIA-PET) and Hi-C chromosome conformation capture. Phases 2 and 3 delivered 9,239 experiments (7,495 in human and 1,744 in mouse) in more than 500 cell types and tissues, including mapping of transcribed regions and transcript isoforms, regions of transcripts recognized by RNA-binding proteins, transcription factor binding regions, and regions that harbour specific histone modifications, open chromatin, and 3D chromatin interactions. The results of all of these experiments are available at the ENCODE portal (http://www.encodeproject.org). These efforts, combined with those of related projects and many other laboratories, have produced a greatly enhanced view of the human genome (Fig. 2), identifying 20,225 protein-coding and 37,595 noncoding genes

Trust in remote interaction is a fundamental challenge in distributed computing environments. To obtain a remote party's trust, computing systems must be able to guarantee the privacy of intellectual property and the integrity of program execution. Unfortunately, traditional platforms cannot provide such guarantees under physical threats that exist in distributed environments.The AEGIS secure processor enables a physically secure computing platform to be built with a main processor as the only trusted hardware component. AEGIS empowers a remote party to authenticate the platform and guarantees secure execution even under physical threats. To realize the security features of AEGIS with only a single chip, this thesis presents a secure processor architecture along with its enabling security mechanisms. The architecture suggests a technique called suspended secure processing to allow a secure part of an application to be protected separately from the rest. Physical random functions provide a cheap and secure way of generating a unique secret key on each processor, which enables a remote party to authenticate the processor chip. Memory encryption and integrity verification mechanisms guarantee the privacy and the integrity of off-chip memory content, respectively.A fully-functional RTL implementation and simulation studies demonstrate that the overheads associated with this single-chip approach is reasonable. The security components in AEGIS consumes about 230K logic gates. AEGIS, with its off-chip protection mechanisms, is slower than traditional processors by 26% on average for large applications and by a few percent for embedded applications. This thesis also shows that using AEGIS requires only minor modifications to traditional operating systems and compilers.

Secure processors enable new applications by ensuring private and authentic program execution even in the face of physical attack. In this paper we present the AEGIS secure processor architecture, and evaluate its RTL implementation on FPGAs. By using Physical Random Functions, we propose a new way of reliably protecting and sharing secrets that is more secure than existing solutions based on non-volatile memory. Our architecture gives applications the flexibility of trusting and protecting only a portion of a given process, unlike prior proposals which require a process to be protected in entirety. We also put forward a specific model of how secure applications can be programmed in a high-level language and compiled to run on our system. Finally, we evaluate a fully functional FPGA implementation of our processor, assess the implementation tradeoffs, compare performance, and demonstrate the benefits of partially protecting a program.