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Divergence of cis-regulatory elements drives species-specific traits1, but how this manifests in the evolution of the neocortex at the molecular and cellular level remains unclear. Here we investigated the gene regulatory programs in the primary motor cortex of human, macaque, marmoset and mouse using single-cell multiomics assays, generating gene expression, chromatin accessibility, DNA methylome and chromosomal conformation profiles from a total of over 200,000 cells. From these data, we show evidence that divergence of transcription factor expression corresponds to species-specific epigenome landscapes. We find that conserved and divergent gene regulatory features are reflected in the evolution of the three-dimensional genome. Transposable elements contribute to nearly 80% of the human-specific candidate cis-regulatory elements in cortical cells. Through machine learning, we develop sequence-based predictors of candidate cis-regulatory elements in different species and demonstrate that the genomic regulatory syntax is highly preserved from rodents to primates. Finally, we show that epigenetic conservation combined with sequence similarity helps to uncover functional cis-regulatory elements and enhances our ability to interpret genetic variants contributing to neurological disease and traits.A single-cell multiomics analysis of over 200,000 cells of the primary motor cortex of human, macaque, marmoset and mouse shows that divergence of transcription factor expression corresponds to species-specific epigenome landscapes, and conserved and divergent gene regulatory features are reflected in the evolution of the three-dimensional genome. [ABSTRACT FROM AUTHOR]

This paper presents the Edge-Based Privacy Preserving Approach (EBPPA) for healthcare applications that store private user data on cloud servers, and perform computation operations for patient diagnoses. The increasing cyber-attacks on hospital systems and the exposure of mathematical operations on cloud-stored data to untrusted entities pose significant data privacy and security risks. To address these challenges, our proposed approach incorporates two key components such as Homomorphic Encryption and the XGBoost algorithm. Homomorphic Encryption protects medical plaintext data, by enabling computations on encrypted data without decryption. This ensures that sensitive patient data remains secure even if attackers access it. Additionally, we employ Secret Sharing, which distributes computations to multiple virtual nodes located on edge. By doing so, all arithmetic operations are masked, preventing untrusted cloud servers from gaining knowledge about the specific tasks performed on the encrypted patient data. This enhances the confidentiality of the data and safeguards against potential privacy breaches. The virtual edge nodes (VENs) in our approach leverage the computational resources of the cloud to handle computationally intensive mathematical functions efficiently. This enables accurate and efficient healthcare data processing and reduces latency in data transmission between devices and edge nodes. To validate the effectiveness of our approach, we conducted a comparative analysis with existing studies. The results demonstrate that storing homomorphically encrypted data at the edge preserves data privacy and integrity while ensuring the confidentiality of the data through secret sharing-based multi-node computation. This approach offers a robust solution for protecting sensitive patient data from unauthorized access and maintaining data confidentiality in untrusted cloud networks. Our proposed Edge Based Privacy Preserving Approach (EBPPA) combines Homomorphic Encryption, which secures medical data, and the XGBoost algorithm, which enables accurate computations, to address healthcare applications’ challenges. By leveraging secret sharing and virtual edge nodes, our approach provides enhanced data privacy, integrity, and confidentiality, making it a promising solution for securing sensitive patient data in the healthcare domain. [ABSTRACT FROM AUTHOR]

Environmental factors may alter the fetal genome to cause metabolic diseases. It is unknown whether embryonic immune cell programming impacts the risk of type 2 diabetes in later life. We demonstrate that transplantation of fetal hematopoietic stem cells (HSCs) made vitamin D deficient in utero induce diabetes in vitamin D-sufficient mice. Vitamin D deficiency epigenetically suppresses Jarid2 expression and activates the Mef2/PGC1a pathway in HSCs, which persists in recipient bone marrow, resulting in adipose macrophage infiltration. These macrophages secrete miR106-5p, which promotes adipose insulin resistance by repressing PIK3 catalytic and regulatory subunits and down-regulating AKT signaling. Vitamin D-deficient monocytes from human cord blood have comparable Jarid2/Mef2/PGC1a expression changes and secrete miR-106b-5p, causing adipocyte insulin resistance. These findings suggest that vitamin D deficiency during development has epigenetic consequences impacting the systemic metabolic milieu. Environmental conditions during pregnancy contribute to offspring metabolic disease. Here, the authors show that immune cells reprogrammed in utero by maternal vitamin D deficiency increase lifetime diabetes risk in the offspring and are sufficient to transplant diabetes. [ABSTRACT FROM AUTHOR]

The zebrafish (Danio rerio) has been widely used in the study of human disease and development, and about 70% of the protein-coding genes are conserved between the two species1. However, studies in zebrafish remain constrained by the sparse annotation of functional control elements in the zebrafish genome. Here we performed RNA sequencing, assay for transposase-accessible chromatin using sequencing (ATAC-seq), chromatin immunoprecipitation with sequencing, whole-genome bisulfite sequencing, and chromosome conformation capture (Hi-C) experiments in up to eleven adult and two embryonic tissues to generate a comprehensive map of transcriptomes, cis-regulatory elements, heterochromatin, methylomes and 3D genome organization in the zebrafish Tübingen reference strain. A comparison of zebrafish, human and mouse regulatory elements enabled the identification of both evolutionarily conserved and species-specific regulatory sequences and networks. We observed enrichment of evolutionary breakpoints at topologically associating domain boundaries, which were correlated with strong histone H3 lysine 4 trimethylation (H3K4me3) and CCCTC-binding factor (CTCF) signals. We performed single-cell ATAC-seq in zebrafish brain, which delineated 25 different clusters of cell types. By combining long-read DNA sequencing and Hi-C, we assembled the sex-determining chromosome 4 de novo. Overall, our work provides an additional epigenomic anchor for the functional annotation of vertebrate genomes and the study of evolutionarily conserved elements of 3D genome organization. A comprehensive map of transcriptomes, cis-regulatory elements, heterochromatin structure, the methylome and 3D genome organization in the zebrafish (Danio rerio) enables identification of species-specific and evolutionarily conserved regulatory features, and provides a foundation for modelling studies on human disease and development. [ABSTRACT FROM AUTHOR]

Smart mobile devices are critical component in the mobile communication, it has been acted as various services with the development of the mobile internet. For example, mobile payment has become universal in the mobile e-commerce, and it is widely attracting attention by most people. However, the extensive application of the mobile e-commerce would increase the security issue for mobile users who use the smart mobile devices, such as integrity and authentication protection for the transaction data and the user privacy. Furthermore, most smart mobile devices are designed with low power and resource constrained systems, it is not suitable for providing competent security levels through higher complexity cryptographic algorithms to resolve the above security issues. In this paper, we propose a new self-certified digital signature scheme based on NTRUSign which builded in the complexity of approximating the closest vector in NTRU lattices without certification for the smart mobile communication. In contrast to previous research, the result shows that the new scheme achieve such as efficiency that it may overcome the space obstacles and provide a real-world practical solution for some security issues in the smart mobile communication. [ABSTRACT FROM AUTHOR]

Transposable element (TE)-derived sequences comprise half of the human genome and DNA methylome and are presumed to be densely methylated and inactive. Examination of genome-wide DNA methylation status within 928 TE subfamilies in human embryonic and adult tissues identified unexpected tissue-specific and subfamily-specific hypomethylation signatures. Genes proximal to tissue-specific hypomethylated TE sequences were enriched for functions important for the relevant tissue type, and their expression correlated strongly with hypomethylation within the TEs. When hypomethylated, these TE sequences gained tissue-specific enhancer marks, including monomethylation of histone H3 at lysine 4 (H3K4me1) and occupancy by p300, and a majority exhibited enhancer activity in reporter gene assays. Many such TEs also harbored binding sites for transcription factors that are important for tissue-specific functions and showed evidence of evolutionary selection. These data suggest that sequences derived from TEs may be responsible for wiring tissue type-specific regulatory networks and may have acquired tissue-specific epigenetic regulation. [ABSTRACT FROM AUTHOR]

The article offers information on the Roadmap Epigenome Browser which is based on the Human Epigenome Browser from the Washington University and integrates data from the U.S. National Institute of Health Roadmap Epigenomics Consortium and ENCODE list of functional elements in the human genome. It informs that Roadmap Epigenome Brower enables researchers to explore the tissue-specific regulatory roles of genetic variants in the context of disease. It discusses single nucleotide polymorphism.

The authors focus on a research related to the genome interactions in eukaryotes performed using the WashU Epigenome Browser located at http://epigenomegateway.wustl.edu. They state that they have tried to explore the histone modification profile of human cells and long-range interaction data of human genome. They also mention that human genomes can show similar interaction pattern despite they have different histone modifications.

The article offers information on the Human Epigenome Browser, which was developed to host Human Epigenome Atlas data produced by the Roadmap Epigenomics Project. It mentions that the browser is a web-based browser which extends the concept introduced by University of California, Santa Cruz Cancer Genomics Browser. It says that the browser hosts epigenome datasets which include data on the number of full base-resolution DNA methylomes, locations of open chromatin, and RNA splicing profiles.