Mapping epigenetic modifications by sequencing technologies

X Chen, H Xu, X Shu, CX Song - Cell Death & Differentiation, 2023 - nature.com
The “epigenetics” concept was first described in 1942. Thus far, chemical modifications on
histones, DNA, and RNA have emerged as three important building blocks of epigenetic …

Interconnections between m6A RNA modification, RNA structure, and protein–RNA complex assembly

S Höfler, O Duss - Life Science Alliance, 2024 - life-science-alliance.org
Protein–RNA complexes exist in many forms within the cell, from stable machines such as
the ribosome to transient assemblies like the spliceosome. All protein–RNA assemblies rely …

LSA-ac4C: a hybrid neural network incorporating double-layer LSTM and self-attention mechanism for the prediction of N4-acetylcytidine sites in human mRNA

FL Lai, F Gao - International Journal of Biological Macromolecules, 2023 - Elsevier
Abstract N4-acetylcytidine (ac4C) is a vital constituent of the epitranscriptome and plays a
crucial role in the regulation of mRNA expression. Numerous studies have established …

Workability of mRNA sequencing for predicting protein abundance

EA Ponomarenko, GS Krasnov, OI Kiseleva… - Genes, 2023 - mdpi.com
Transcriptomics methods (RNA-Seq, PCR) today are more routine and reproducible than
proteomics methods, ie, both mass spectrometry and immunochemical analysis. For this …

Pitfalls of using sequence databases for heterologous expression studies–a technical review

S Maxeiner, G Krasteva‐Christ… - The Journal of …, 2023 - Wiley Online Library
Synthesis of DNA fragments based on gene sequences that are available in public
resources has become an efficient and affordable method that has gradually replaced …

Meta-2OM: A multi-classifier meta-model for the accurate prediction of RNA 2′-O-methylation sites in human RNA

M Harun-Or-Roshid, NT Pham, B Manavalan, H Kurata - Plos one, 2024 - journals.plos.org
2′-O-methylation (2-OM or Nm) is a widespread RNA modification observed in various
RNA types like tRNA, mRNA, rRNA, miRNA, piRNA, and snRNA, which plays a crucial role …

Decoding epitranscriptomic regulation of viral infection: mapping of RNA N6-methyladenosine by advanced sequencing technologies

X Fan, Y Zhang, R Guo, K Yue, G Smagghe… - Cellular & Molecular …, 2024 - Springer
Elucidating the intricate interactions between viral pathogens and host cellular machinery
during infection is paramount for understanding pathogenic mechanisms and identifying …

Genetic regulation of m6A RNA methylation and its contribution in human complex diseases

K Chen, J Nan, X Xiong - Science China Life Sciences, 2024 - Springer
Abstract N 6-methyladenosine (m6A) has been established as the most prevalent chemical
modification in message RNA (mRNA), playing an essential role in determining the fate of …

Adenine Methylation Enhances the Conformational Flexibility of an RNA Hairpin Tetraloop

L Levintov, H Vashisth - The Journal of Physical Chemistry B, 2024 - ACS Publications
The N6-methyladenosine modification is one of the most abundant post-transcriptional
modifications in ribonucleic acid (RNA) molecules. Using molecular dynamics simulations …

A role for a Trypanosoma brucei cytosine RNA methyltransferase homolog in ribosomal RNA processing

KT Militello, J Leigh, M Pusateri, LK Read, D Vogler - Plos one, 2024 - journals.plos.org
In Trypanosoma brucei, gene expression is primarily regulated posttranscriptionally making
RNA metabolism critical. T. brucei has an epitranscriptome containing modified RNA bases …