Shui Ye

By Dan Wu, Dilyara Cheranova, Daniel P. Heruth, Li Qin Zhang and Shui Qing Ye

Part of the book: Chemical Biology

By Ding-You Li, Min Yang, Sitang Gong and Shui Qing Ye

Nonalcoholic fatty liver disease (NAFLD) has emerged as the most common cause of liver disease among children and adolescents in industrialized countries due to increasing prevalence of obesity. It is generally recognized that both genetic and environmental risk factors contribute to the pathogenesis of NAFLD. Convincing evidences have shown that gut microbiota alteration is associated with NAFLD pathogenesis both in patients and animal models. Bacterial overgrowth and increased intestinal permeability are evident in NAFLD patients and lead to increased delivery of gut-derived bacterial products, such as lipopolysaccharide and bacterial DNA, to the liver through portal vein and then activation of toll-like receptors (TLRs), mainly TLR4 and TLR9, and their downstream cytokines and chemokines, resulting in hepatic inflammation. Currently, the role of gut microbiota in the pathogenesis of NAFLD is still the focus of many active clinical/basic researches. Modulation of gut microbiota with probiotics or prebiotics has been targeted as a preventive or therapeutic strategy on this pathological condition. Their beneficial effects on the NAFLD have been demonstrated in animal models and limited human studies.

Part of the book: The Gut Microbiome

By Min Xiong, Daniel P. Heruth, Xun Jiang, Shamima Islam, Li Qin Zhang, Ding‐You Li and Shui Q. Ye

Epitranscriptomics is a newly burgeoning field pertaining to the complete delineation and elucidation of chemical modifications of nucleotides found within all classes of RNA that do not involve a change in the ribonucleotide sequence. More than 140 diverse and distinct nucleotide modifications have been identified in RNA, dwarfing the number of nucleotide modifications found in DNA. The majority of epitranscriptomic modifications have been identified in ribosomal RNA (rRNA), transfer RNA (tRNA), and small nuclear RNA (snRNA). However, in total, the knowledge of the occurrence, and specifically the function, of RNA modifications remains scarce. Recently, the rapid advancement of next‐generation sequencing and mass spectrometry technologies have allowed for the identification and functional characterization of nucleotide modifications in both protein‐coding and non‐coding RNA on a global, transcriptome scale. In this chapter, we will introduce the concepts of nucleotide modification, summarize transcriptome‐wide RNA modification mapping techniques, highlight recent studies exploring the functions of RNA modifications and their association to disease, and finally offer insight into the future progression of epitranscriptomics.

Part of the book: Applications of RNA-Seq and Omics Strategies