Kunqi Chen

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Verified

Kunqi verified their affiliation via an institutional email.

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• Doctor of Philosophy
• Professor at Fujian Medical University

Angiogenesis plays a crucial role in the development of HBV‐related hepatocellular carcinoma (HCC). VEGFA is a key angiogenic factor, and while its transcriptional regulation by HBV has been extensively studied, its posttranscriptional regulation by HBV remains poorly understood. Building on our previous findings that delineated an RBM15/YTHDF2/IGF...

N⁶-methyladenosine (m6A), the most prevalent internal mRNA modification in higher eukaryotes, plays diverse roles in cellular regulation. By incorporating both sequence- and genome-derived features, Fan et al.¹ designed a novel Transformer-BiGRU framework that achieves superior performance in computational m6A identification, thus demonstrating the...

The National Genomics Data Center (NGDC), which is a part of the China National Center for Bioinformation (CNCB), offers a comprehensive suite of database resources to support the global scientific community. Amidst the unprecedented accumulation of multi-omics data, CNCB-NGDC is committed to continually evolving and updating its core database reso...

Immunotherapy research focuses on reshaping the tumor microenvironment (TME) to enhance its antitumor immune responses, with an emphasis on understanding the impact of RNA methylation in triple-negative breast cancer (TNBC) TME regulation. This study explored the influence of various RNA methyltransferases on TME cells in TNBC and their correlation...

Cancer is a complex and multifaceted group of diseases characterized by uncontrolled cell growth that leads to the formation of malignant tumors. Recent studies suggest that N6-methyladenosine (m6A) RNA methylation plays pivotal roles in cancer pathology by influencing various cellular processes. However, the degree to which these mechanisms are sh...

Protein degradation through the ubiquitin proteasome system at the spatial and temporal regulation is essential for many cellular processes. E3 ligases and degradation signals (degrons), the sequences they recognize in the target proteins, are key parts of the ubiquitin-mediated proteolysis, and their interactions determine the degradation specific...

DNA/chromatin-based functions of the DEK oncogene, a unique nucleic acid-interacting factor in metazoans, have been widely investigated, yet its role in cellular RNA biology is under-studied. Herein we employed CLIP-seq alongside mutational, biochemical, and cellular approaches to gain deeper insights into the cellular DEK-RNA interplay. We confirm...

Vascular endothelial growth factor A (VEGFA) plays a critical role as a potent angiogenesis factor and is highly expressed in hepatocellular carcinoma (HCC). Although the expression of VEGFA has been strongly linked to the aggressive nature of HCC, the specific posttranscriptional modifications that might contribute to VEGFA expression and HCC angi...

5-formylcytidine (f5C) is a unique post-transcriptional RNA modification found in mRNA and tRNA at the wobble site, playing a crucial role in mitochondrial protein synthesis and potentially contributing to the regulation of translation. Recent studies have unveiled that the f5C modifications may drive mitochondrial mRNA translation to power cancer...

Background: Mesaconitine (MA), a diester-diterpenoid alkaloid extracted from the medicinal herb Aconitum carmichaelii, is commonly used to treat various diseases. Previous studies have indicated the potent toxicity of aconitum despite its pharmacological activities, with limited understanding of its effects on the nervous system and the underlying...

Lipid metabolism participates in various physiological processes and has been shown to be connected to the development and progression of multiple diseases, especially metabolic hepatopathy. Apolipoproteins (Apos) act as vectors that combine with lipids, such as cholesterol and triglycerides (TGs). Despite being involved in lipid transportation and...

Background Mucinous colonic adenocarcinoma remains a challenging disease due to its high propensity for metastasis and recurrence. N7-methylguanosine (m7G) and long non-coding RNA (lncRNA) are closely associated with the occurrence and progression of tumors. However, research on m7G-related lncRNA in mucinous colonic adenocarcinoma is lacking. Ther...

With recent progress in mapping N7-methylguanosine (m7G) RNA methylation sites, tens of thousands of experimentally validated m7G sites have been discovered in various species, shedding light on the significant role of m7G modification in regulating numerous biological processes including disease pathogenesis. An integrated resource that enables th...

N 6-Methyladenosine (m6A) is one of the most abundant internal chemical modifications on eukaryote mRNA and is involved in numerous essential molecular functions and biological processes. To facilitate the study of this important post-transcriptional modification, we present here m6A-Atlas v2.0, an updated version of m6A-Atlas. It was expanded to i...

Pseudouridine (Ψ) is the first-discovered RNA modification abundantly present in many classes of RNAs, which plays a pivotal role in a series of biological processes. Accurately identifying the location of Ψ sites is helpful for relevant downstream researches. In this chapter, we introduce a website PIANO-for pseudouridine site (Ψ) identification a...

Epigenetic factor Brd4 has emerged as a key regulator of cancer cell proliferation. Targeted inhibition of Brd4 suppresses growth and induces apoptosis of various cancer cells. In addition to apoptosis, Brd4 has also been shown to regulate several other forms of programmed cell death (PCD), including autophagy, necroptosis, pyroptosis, and ferropto...

With advanced technologies to map RNA modifications, our understanding of them has been revolutionized, and they are seen to be far more widespread and important than previously thought. Current next-generation sequencing (NGS)-based modification profiling methods are blind to RNA modifications and thus require selective chemical treatment or antib...

As the most pervasive epigenetic mark present on mRNA and lncRNA, N6-methyladenosine (m6A) RNA methylation regulates all stages of RNA life in various biological processes and disease mechanisms. Computational methods for deciphering RNA modification have achieved great success in recent years; nevertheless, their potential remains underexploited....

Recent advances in epitranscriptomics have unveiled functional associations between RNA modifications (RMs) and multiple human diseases, but distinguishing the functional or disease-related single nucleotide variants (SNVs) from the majority of ‘silent’ variants remains a major challenge. We previously developed the RMDisease database for unveiling...

As the most pervasive epigenetic marker present on mRNA and lncRNA, N⁶-methyladenosine (m⁶A) RNA methylation has been shown to participate in essential biological processes. Recent studies revealed the distinct patterns of m⁶A methylome across human tissues, and a major challenge remains in elucidating the tissue-specific presence and circuitry of...

Traditional epitranscriptome profiling approach relies on specific antibodies or chemical treatments to capture modified RNA molecules and then applies high throughput sequencing to identify their transcriptomic locations. However, due to the lack of suitable or high-quality antibodies, only a small proportion of the 170 documented RNA modification...

As the most pervasive epigenetic marker present on mRNA and lncRNA, N6-methyladenosine (m6A) RNA methylation has been shown to participate in essential biological processes. Recent studies revealed the distinct patterns of m6A methylome across human tissues, and a major challenge remains in elucidating the tissue-specific presence and circuitry of...

5-Methylcytosine (m5C) is one of the most prevalent covalent modifications on RNA. It is known to regulate a broad variety of RNA functions, including nuclear export, RNA stability and translation. Here, we present m5C-Atlas, a database for comprehensive collection and annotation of RNA 5-methylcytosine. The database contains 166 540 m5C sites in 1...

The primary sequences of DNA, RNA and protein have been used as the dominant information source of existing machine learning tools, especially for contexts not fully explored by wet-experimental approaches. Since molecular markers are profoundly orchestrated in the living organisms, those markers that cannot be unambiguously recovered from the prim...

Recent studies suggest that epi-transcriptome regulation via post-transcriptional RNA modifications is vital for all RNA types. Precise identification of RNA modification sites is essential for understanding the functions and regulatory mechanisms of RNAs. Here, we present MultiRM, a method for the integrated prediction and interpretation of post-t...

Motivation N6-methyladenosine (m6A) is the most prevalent RNA modification on mRNAs and lncRNAs. Evidence increasingly demonstrates its crucial importance in essential molecular mechanisms and various diseases. With recent advances in sequencing techniques, tens of thousands of m6A sites are identified in a typical high-throughput experiment, posin...

N⁶-Methyladenosine (m⁶A) is the most prevalent posttranscriptional modification in eukaryotes and plays a pivotal role in various biological processes, such as splicing, RNA degradation, and RNA–protein interaction. Accurately identification of the location of m⁶A is essential for related downstream studies. In this chapter, we introduce a predicti...

N6,2’-O-dimethyladenosine (m⁶Am) is a reversible modification widely occurred on varied RNA molecules. The biological function of m⁶Am is yet to be known though recent studies have revealed its influences in cellular mRNA fate. Precise identification of m⁶Am sites on RNA is vital for the understanding of its biological functions. We present here m6...

As one of the widely occurring RNA modifications, 5-methyl-uridine (m 5 U) has recently been shown to play critical roles in various biological functions and disease pathogenesis, such as under stress response and during breast cancer development. Precise identification of m 5 U sites on RNA is vital for the understanding of the regulatory mechanis...

Motivation The distribution of biological features strongly indicates their functional relevance. Compared to DNA-related features, deciphering the distribution of mRNA-related features is non-trivial due to the existence of isoform ambiguity and compositional diversity of mRNAs. Results We propose here a rigorous statistical framework, MetaTX, fo...

Deciphering the biological impacts of millions of single nucleotide variants remains a major challenge. Recent studies suggest that RNA modifications play versatile roles in essential biological mechanisms, and are closely related to the progression of various diseases including multiple cancers. To comprehensively unveil the association between di...

N 6-Methyladenosine (m6A) is the most prevalent RNA modification on mRNAs and lncRNAs. It plays a pivotal role during various biological processes and disease pathogenesis. We present here a comprehensive knowledgebase, m6A-Atlas, for unraveling the m6A epitranscriptome. Compared to existing databases, m6A-Atlas features a high-confidence collectio...

N⁶-methyladenosine (m⁶A) is the most abundant post-transcriptional modification in mRNA, and regulates critical biological functions via m⁶A reader proteins that bind to m⁶A-containing transcripts. There exist multiple m⁶A reader proteins in the human genome, but their respective binding specificity and functional relevance under different biologic...

RNA N ⁶ -methyladenosine (m ⁶ A) has emerged as an important epigenetic modification for its role in regulating the stability, structure, processing, and translation of RNA. Instability of m ⁶ A homeostasis may result in flaws in stem cell regulation, decrease in fertility, and risk of cancer. To this day, experimental detection and quantification...

Pseudouridine (Ψ) is the first discovered and the most prevalent posttranscriptional modification, which has been widely studied during the past decades. Pseudouridine was observed in almost all kinds of RNAs and shown to have important biological functions. Currently, the time-consuming and high-cost procedures of experimental approaches limit its...

Post-transcriptional RNA modification occurs on all types of RNA and plays a vital role in regulating every aspect of RNA function. Thanks to the development of high-throughput sequencing technologies, transcriptome-wide profiling of RNA modifications has been made possible. With the accumulation of a large number of high-throughput datasets, bioin...

Known as the “fifth RNA nucleotide”, pseudouridine (Ψ or psi) is the first-discovered and most abundant RNA modification occurring at the Uridine site, and it plays a prominent role in a number of biological processes. Thousands of Ψ sites have been identified within different biological contexts thanks to the advancement in high-throughput sequenc...

Motivation: Recent progress in m7G RNA methylation studies has focused on its internal (rather than capped) presence within mRNAs. Tens of thousands of internal mRNA m7G sites have been identified within mammalian transcriptomes, and a single resource to best share, annotate and analyze the massive m7G data generated recently is sorely needed. Re...

Currently, although many successful bioinformatics efforts have been reported in the epitranscriptomics field for N ⁶ -methyladenosine (m ⁶ A) site identification, none is focused on the substrate specificity of different m ⁶ A-related enzymes, ie, the methyltransferases (writers) and demethylases (erasers). In this work, to untangle the target spe...

Over one hundred different types of post-transcriptional RNA modifications have been identified in human. Researchers discovered that RNA modifications can regulate various biological processes, and RNA methylation, especially N6-methyladenosine, has become one of the most researched topics in epigenetics. To date, the study of epitranscriptome lay...

Recent studies have revealed that the RNA N⁶-methyladenosine (m⁶A) modification plays a critical role in a variety of biological processes and associated with multiple diseases including cancers. Till this day, transcriptome-wide m⁶A RNA methylation sites have been identified by high-throughput sequencing technique combined with computational metho...

N6-methyladenosine (m6A) is the most prevalentpost-transcriptional modification in eukaryotes, andplays a pivotal role in various biological processes,such as splicing, RNA degradation and RNA–proteininteraction. We report here a prediction frame-work WHISTLE for transcriptome-wide m6A RNA-methylation site prediction. When tested on six in-dependen...

To date, with well over 100 different types of RNA modifications associated with various molecular functions identified on diverse types of RNA molecules, the epitranscriptome has emerged to be an important layer for gene expression regulation. It is of crucial importance and increasing interest to understand how the epitranscriptome is regulated t...