Extrachromosomal circular DNA (eccDNA) is a class of double-stranded circular DNA molecules present outside of regular chromosomal DNA. eccDNA is widely found in human normal and cancer tissues, body fluids, and other eukaryotic cells. According to the lengths, eccDNA can be classified into two main categories : eccDNA (<10 kb) and ecDNA (>=10 kb)[1]. eccDNAs […]
Article Arg-tRNA synthetase links inflammatory metabolism to RNA splicing and nuclear trafficking via SRRM2 Published in Nature Cell Biology Abstract This study revealed a noncanonical role of arginyl-tRNA synthetase (ArgRS), a key enzyme in the tRNA charging machinery, in linking inflammatory metabolism to RNA processing. Under inflammatory conditions, extracellular arginine depletion reduced nuclear
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Article Restoration of N-glycosylation via leucine-activated leucyl-tRNA synthetase 1 overcomes chemoresistance in intrahepatic cholangiocarcinoma Published in Journal of Hepatology Abstract This study demonstrated that leucyl-tRNA synthetase 1 (LARS1), a key enzyme in tRNA charging, regulates chemotherapy response in intrahepatic cholangiocarcinoma (ICC). Loss of LARS1 impaired leucyl-tRNA charging, selectively reducing translation of leucine codon–enriched transcripts
TRAC-seq and HAC-seq are designed for precise detection of individual RNA modifications at single-nucleotide resolution. By combining selective chemical/enzymatic treatment with next-generation sequencing, these methods convert specific RNA modifications into characteristic reverse transcription signatures, enabling accurate identification and site-specific mapping of target modifications across the transcriptome. Their high sensitivity and nucleotide-level precision make them powerful
tRNAs are abundant small RNAs essential for delivering amino acids and decoding genetic codons during protein translation. Beyond this canonical role, tRNAs actively regulate translation and disease processes through changes in tRNA expression, modification, and charging, three key determinants of tRNA function. Altered tRNA expression can reshape codon-dependent translation, while tRNA modifications (e.g., m7G, m1A)
What is RNA G-Quadruplex (rG4)? RNA G-quadruplexes (rG4s) are non-canonical secondary structures originated from guanine-rich RNA sequences, where four guanines are arranged together by Hoogsteen hydrogen bonding in a planar G-quartet and the quartets are stacked forming a stable four-stranded conformation. Monovalent cations, particularly K⁺, greatly enhance the rG4 stability (Fig. 1). rG4s are evolutionarily
RNA G-Quadruplex (rG4) – What it is, why it matters, how to study it Read More »
Introduction Circular RNA (circRNA) is a novel type of RNA that, unlike linear RNA, forms a covalently closed continuous loop, and is highly represented in the eukaryotic transcriptome. Most of these circRNAs are generated from exonic sequences, are conserved across species, and often show tissue/developmental-stage-specific expression. Circular RNAs are more stable than linear RNAs
Dysregulation of H3K36 tri-methylation In clear cell renal cell carcinoma (ccRCC), read-through transcription and DoG formation are extensive due to defective transcription termination and consequent aberrant splicing [1]. Notably, H3K36 methyl transferase gene SETD2 is frequently mutated. SETD2 knockout in ccRCC cells induced read-through transcription[1]. Read-through transcription has also been observed in a variety of cancers, underlining this transcription
Epigenetic and Epitranscriptomic Regulation of DoG RNAs Read More »
The functional roles of read-through transcription and DoG RNAs are currently the focus of active research, with several proposed mechanisms highlighting their involvement in gene regulation. DoG RNAs mediate transcriptional interference in cell senescence DoGs can act as antisense RNAs to control the gene expression of convergent protein-coding genes. In senescent cells, a family of
DoG RNAs Modulate Gene Transcription in Diseases Read More »
Downstream-of-gene (DoG) RNAs are RNA transcripts that arise downstream of ~10% of host genes and are continuous with their upstream RNAs [1]. DoGs are defined as having a minimal length of 5 kb beyond the polyadenylation signal (PAS) at transcription end site (TES), with maximal length up to 200 kb in mammalian cells [1]. Due