Nature Search

Epitranscriptome regulation

Dan Dominissini
Gideon Rechavi
Multimedia28 Sept 2018
Nature Structural & Molecular Biology

P: 1
A chromatin-regulated biphasic circuit coordinates IL-1β-mediated inflammation

The long noncoding RNA AMANZI downregulates IL-1β expression and trained immunity by inducing IL-37 transcription via long-range chromatin contacts. The common variant rs16944 present in AMANZI modulates proinflammation or immunosuppression risk.

Ezio T. Fok
Simone J. C. F. M. Moorlag
Musa M. Mhlanga
Research13 Dec 2023
Nature Genetics

Volume: 56, P: 85-99
N⁶-methyladenosine mRNA marking promotes selective translation of regulons required for human erythropoiesis

Erythropoiesis can be regulated by transcriptional, epigenetic, and post-transcriptional mechanisms. Here the authors report that N⁶-methyladenosine mRNA methyltransferase complex stimulates erythropoiesis by promoting translation of specific mRNAs.

Daniel A. Kuppers
Sonali Arora
Patrick J. Paddison
ResearchOpen Access10 Oct 2019
Nature Communications

Volume: 10, P: 1-17
The dynamic N¹-methyladenosine methylome in eukaryotic messenger RNA

Here the m¹A modification is discovered in messenger RNA and mapped at the transcriptome-wide level; the modification is conserved, dynamic, accumulates in structured regions around translation initiation sites upstream of the first splice site, and correlates with higher protein expression.

Dan Dominissini
Sigrid Nachtergaele
Chuan He
Research10 Feb 2016
Nature

Volume: 530, P: 441-446
RNA editing by ADAR1 leads to context-dependent transcriptome-wide changes in RNA secondary structure

Adenosine deaminase acting on RNA 1 (ADAR1) edits adenosine to inosine. Here the authors, using parallel analysis of RNA secondary structure sequencing, provide evidence that ADAR1 induces sequence-context-dependent RNA secondary structures changes, often leading to stabilization of the RNA duplex.

Oz Solomon
Ayelet Di Segni
Gidi Rechavi
ResearchOpen Access13 Nov 2017
Nature Communications

Volume: 8, P: 1-14
Topology of the human and mouse m⁶A RNA methylomes revealed by m⁶A-seq

N⁶-methyladenosine (m⁶A) is the most prevalent internal modification in messenger RNA; here the human and mouse m⁶A modification landscape is presented in a transcriptome-wide manner, providing insights into this epigenetic modification.

Dan Dominissini
Sharon Moshitch-Moshkovitz
Gideon Rechavi
Research29 Apr 2012
Nature

Volume: 485, P: 201-206
The m⁶A epitranscriptome: transcriptome plasticity in brain development and function

The impact of RNA modifications, such as RNA methylation, on gene expression and cellular function has been the subject of recent intense investigations. Here Dominissini and colleagues provide an overview of the mechanisms of such epitranscriptomic regulation and their functional consequences in the nervous system.

Ido Livneh
Sharon Moshitch-Moshkovitz
Dan Dominissini
Reviews05 Dec 2019
Nature Reviews Neuroscience

Volume: 21, P: 36-51
Nm-seq maps 2′-O-methylation sites in human mRNA with base precision

Iterative oxidation, elimination and dephosphorylation steps remove nucleotides from the 3′ end of RNA until a 2′-O-methylated ribose that cannot be oxidized is encountered and brings the process to a stop. High-throughput sequencing of these fragments exposes 2′-O-methyl sites at base resolution.

Qing Dai
Sharon Moshitch-Moshkovitz
Chuan He
Research15 May 2017
Nature Methods

Volume: 14, P: 695-698
Mammalian WTAP is a regulatory subunit of the RNA N6-methyladenosine methyltransferase

Xiao-Li Ping
Bao-Fa Sun
Yun-Gui Yang
ResearchOpen Access10 Jan 2014
Cell Research

Volume: 24, P: 177-189
2′-O-methylation in mRNA disrupts tRNA decoding during translation elongation

2′-O-methylation within mRNA coding regions sterically perturbs interactions of ribosomal-monitoring bases with cognate codon–anticodon helices, leading to excessive rejection of cognate aminoacylated tRNAs during initial selection and proofreading.

Junhong Choi
Gabriele Indrisiunaite
Joseph D. Puglisi
Research19 Feb 2018
Nature Structural & Molecular Biology

Volume: 25, P: 208-216
N⁶-methyladenosine in mRNA disrupts tRNA selection and translation-elongation dynamics

Methylation of adenosine within mRNA coding regions delays tRNA accommodation during translation and thus changes translation dynamics, which might influence protein folding.

Junhong Choi
Ka-Weng Ieong
Joseph D Puglisi
Research11 Jan 2016
Nature Structural & Molecular Biology

Volume: 23, P: 110-115
mRNA m⁶A plays opposite role in regulating UCP2 and PNPLA2 protein expression in adipocytes

Xinxia Wang
Baofa Sun
Yizhen Wang
Research27 Feb 2018
International Journal of Obesity

Volume: 42, P: 1912-1924
mRNA m⁶A detection

N⁶-methyladenosine (m⁶A) is an mRNA modification influencing gene expression. Advanced methodologies for mapping m⁶A enhance understanding of its dynamic roles and interactions. In this Primer, Moshitch-Moshkovitz et al. discuss various detection tools and analysis techniques facilitating insights into RNA epitranscriptomics.

Sharon Moshitch-Moshkovitz
Michal Sevilla-Sharon
Dan Dominissini
Reviews12 Dec 2024
Nature Reviews Methods Primers

Volume: 4, P: 1-20
FTO levels affect RNA modification and the transcriptome

Tea Berulava
Matthias Ziehe
Bernhard Horsthemke
Research08 Aug 2012
European Journal of Human Genetics

Volume: 21, P: 317-323
Gene expression regulation mediated through reversible m⁶A RNA methylation

Diverse types of RNA in various species are modified by methylation to formN⁶-methyladenosine (m⁶A). This Review describes how progress in the characterization of m⁶A distributions and of proteins that 'write', 'erase' and 'read' this mark is revealing roles for reversible m⁶A methylation in dynamic gene expression control.

Ye Fu
Dan Dominissini
Chuan He
Reviews25 Mar 2014
Nature Reviews Genetics

Volume: 15, P: 293-306
Transcriptome-wide mapping of N⁶-methyladenosine by m⁶A-seq based on immunocapturing and massively parallel sequencing

Dan Dominissini
Sharon Moshitch-Moshkovitz
Gideon Rechavi
Protocols03 Jan 2013
Nature Protocols

Volume: 8, P: 176-189
A single center experience with publicly funded clinical exome sequencing for neurodevelopmental disorders or multiple congenital anomalies

Ben Pode-Shakked
Ortal Barel
Lior Greenbaum
ResearchOpen Access27 Sept 2021
Scientific Reports

Volume: 11, P: 1-8
Splicing mutations in glycogen-storage disease type II: evaluation of the full spectrum of mutations and their relation to patients’ phenotypes

Stefania Zampieri
Emanuele Buratti
Andrea Dardis
Research22 Dec 2010
European Journal of Human Genetics

Volume: 19, P: 422-431
RNA modifications: what have we learned and where are we headed?

Five experts discuss topical aspects of RNA modifications, highlighting where the research field stands, recommendations for best practices and visions for the future of epitranscriptomics studies.

Michaela Frye
Samie R. Jaffrey
Tsutomu Suzuki
Reviews03 May 2016
Nature Reviews Genetics

Volume: 17, P: 365-372
The presence of a single PML-RARA isoform lacking exon 5 in FISH-negative APL samples

O Ashur-Fabian
L Trakhtenbrot
N Amariglio
Correspondence25 Oct 2007
Leukemia

Volume: 22, P: 200-203
5-methylcytosine mediates nuclear export of mRNA

5-methylcytosine was shown before to be an epitranscriptomic mark. Yang et al. now explored the unique topology of this mRNA modification, identified its writer and demonstrated its involvement in nuclear-cytoplasmic shuttling mediated by a specific reader.

Dan Dominissini
Gideon Rechavi
Research Highlights23 May 2017
Cell Research

Volume: 27, P: 717-719
Opposing actions of environmental enrichment and Alzheimer’s disease on the expression of hippocampal microRNAs in mouse models

B Barak
I Shvarts-Serebro
U Ashery
ResearchOpen Access10 Sept 2013
Translational Psychiatry

Volume: 3, P: e304

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