The proteins of mRNA modification: writers, readers, and erasers

MN Flamand, M Tegowski… - Annual review of …, 2023 - annualreviews.org
Over the past decade, mRNA modifications have emerged as important regulators of gene
expression control in cells. Fueled in large part by the development of tools for detecting …

The epitranscriptome beyond m6A

D Wiener, S Schwartz - Nature Reviews Genetics, 2021 - nature.com
Following its transcription, RNA can be modified by> 170 chemically distinct types of
modifications—the epitranscriptome. In recent years, there have been substantial efforts to …

Quantitative sequencing using BID-seq uncovers abundant pseudouridines in mammalian mRNA at base resolution

Q Dai, LS Zhang, HL Sun, K Pajdzik, L Yang… - Nature …, 2023 - nature.com
Functional characterization of pseudouridine (Ψ) in mammalian mRNA has been hampered
by the lack of a quantitative method that maps Ψ in the whole transcriptome. We report …

Exploring the expanding universe of small RNAs

J Shi, T Zhou, Q Chen - Nature cell biology, 2022 - nature.com
The world of small noncoding RNAs (sncRNAs) is ever-expanding, from small interfering
RNA, microRNA and Piwi-interacting RNA to the recently emerging non-canonical sncRNAs …

Pseudouridine synthases modify human pre-mRNA co-transcriptionally and affect pre-mRNA processing

NM Martinez, A Su, MC Burns, JK Nussbacher… - Molecular cell, 2022 - cell.com
Pseudouridine is a modified nucleotide that is prevalent in human mRNAs and is
dynamically regulated. Here, we investigate when in their life cycle mRNAs become …

Quantitative profiling of pseudouridylation landscape in the human transcriptome

M Zhang, Z Jiang, Y Ma, W Liu, Y Zhuang, B Lu… - Nature chemical …, 2023 - nature.com
Pseudouridine (Ψ) is an abundant post-transcriptional RNA modification in ncRNA and
mRNA. However, stoichiometric measurement of individual Ψ sites in human transcriptome …

Mapping the epigenetic modifications of DNA and RNA

LY Zhao, J Song, Y Liu, CX Song, C Yi - Protein & cell, 2020 - academic.oup.com
Over 17 and 160 types of chemical modifications have been identified in DNA and RNA,
respectively. The interest in understanding the various biological functions of DNA and RNA …

Deciphering epitranscriptome: modification of mRNA bases provides a new perspective for post-transcriptional regulation of gene expression

S Kumar, T Mohapatra - Frontiers in cell and developmental biology, 2021 - frontiersin.org
Gene regulation depends on dynamic and reversibly modifiable biological and chemical
information in the epigenome/epitranscriptome. Accumulating evidence suggests that …

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 …

Regulation and function of RNA pseudouridylation in human cells

EK Borchardt, NM Martinez… - Annual review of …, 2020 - annualreviews.org
Recent advances in pseudouridine detection reveal a complex pseudouridine landscape
that includes messenger RNA and diverse classes of noncoding RNA in human cells. The …