Epigenomic and Epitranscriptomic Basis of Development and Human Disease

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Background

Gene expression is regulated genetically and epigenetically in accordance with the programmed developmental process starting from embryogenesis. Any aberrant micro-cytological or epigenetic events could cause devastating change in gene expression, leading to developmental abnormality this may lead to the initiation or the intensification of many diseases such as neurological disorders, cardiological diseases, cancers, and immunological disorders. The epigenetic mechanisms such as: dynamic modification of DNA and histone, nucleosome location, and noncoding RNA are all involved in the regulation of all the biological process. In addition to this base modifications in RNA have been identified to play a pivotal role as well.
Within the DNA base modifications in epigenome, methylation of 5-cytosine (5-mC) is believed to be the most abundant and best characterized epigenetic marker., At the same time, 5-hydroxycytosine (5-hmC), the sixth modified DNA base and the derivative of 5-mC, has also been characterized as an important epigenetic marker in mammalian epigenome. In contrast, studies on the N6-methyladenosine modification in DNA (6mdA) in mammals and insects requires more comprehension. On the other hand, N6-methyladenosine modification in RNA (m6A) has been acknowledged as the most abundant epitranscriptomic marker in mammals, and the extensive studies in recent years have made significant contribution to uncover the regulation mechanisms of this marker.

Functionally, epigenomic and epitranscriptomic markers continue to be highlighted to play an essential elemental role in embryogenesis, cell reprogramming, stem cell self-renewal, proliferation and differentiation, central nerve system (CNS), immune system development, aging, and so on. Furthermore, these modifications in DNA and RNA have been characterized at a biochemical, molecular, and phenotypical level including elucidation of their methyltransferase complexes (writers), demethylases (eraser), and direct interaction proteins (readers).
DNMTs serve as writers for 5-mC, while ten-eleven-translocation proteins (TETs) family including the three paralogs Tet1, Tet2 and Tet3 behave as the erasers for 5-mC, each harboring a catalytic core domain at the carboxyl terminal side. Tet1 catalyzes mainly the demethylation of promoters and transcription start sites and bears dual functions in tumoriogenesis and neuronal development. Tet2 primarily regulates the demethylation of enhancers and gene bodies, and inactivating mutations in the Tet2 gene account for almost 30% of all myeloid malignancies, while Tet3 has an essential role in embryonic development.
METTL3–METTL14 complex linked with WTAP and KIAA1429 has been characterized as main writers for m6A, while FTO and ALKBH5 have been identified as the main m6A erasers. Several protein families have been acknowledged as the m6A readers, including the YTH domain, hnRNP family including hnRNP-A2/B1, hnRNP-C, hnRNP-G, hnRNP-F, hnRNP-H1 and hnRNP-H2, as well as the KH domain, zf-CCHC domain, RBD, RRM, and zinc knuckle domain protein families.
The identified writers and erasers of the methylation modifications exhibit tissue-specific and delicate spatiotemporal expression patterns. More importantly, some writers, erasers, and / or the readers have been identified as the promising biomarkers that could be potentially translated to the clinical applications for therapy.
The levels and the landscapes of 5-mC, 5-hmC, 6mdA in the epigenome and m6A in the epitranscriptome are precisely and dynamically regulated by the fine-tuned orchestration of the writers, erasers, and readers in accordance with stages of the growth, development, and reproduction as naturally programmed during the lifespan. More interestingly, the emerging discoveries appreciate the link between aberrant modifications and pathogenesis of diseases, like cancers, neurodegenerative disorders, and so on.
Thus further investigation of the epigenetic mechanisms for regulation of biological process could accelerate dissection of the pathogenesis for the multiple human diseases caused by aberrant epigenomic and epitranscriptomic modifications.
This research topic will specifically focus on the research advances in the epigenomic and epitranscriptomic regulation of organs and systems development as well as the link between the epigenetic alteration and pathogenesis of human diseases.
Contributors are invited to submit original research articles as well as review articles, with focus on epigenomic and epitranscriptomic study. The collected manuscripts should address the functions of base modifications in epigenome and epitranscriptome, non-coding RNAs, as well as chromatin remodeling in the development of organs /systems and pathogenesis of human diseases. Potential topics include but not limited to:
 Identification of new epigenetic / epitranscriptomic marker(s), new writers / erasers / readers.
 Advancements in technology / bioinformatic methodology for analysis of the DNA and RNA modification markers.
 Application of high throughput sequencing in genome-wide mapping of epigenetic markers, and transcriptomes and proteomics in pathogenesis study of human diseases.
 Small molecule drug screening to identify the enhancers / repressors of the epigenetic modifications involved in embryogenesis, development of CNS, stem cells fate, and pathogenesis of diseases.
 Dynamic alteration of base modification markers and epigenetic landscapes during mammal development and in response to environment stimuli such as natural toxicity and artificial stress.
 Epigenomic and epitranscriptomic alteration in response to Coronal virus (including Cov-19) infection
 In vitro human organoids and in vivo animal models for epigenetic / epitranscriptomic study on development and diseases.
 Study on the link between aberrant modifications and disease using clinical patient samples
 Small RNAs and other non-coding RNAs such as miRNA, piRNA, LncRNA and

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