Epitranscriptomics in parasitic protists: Role of RNA chemical modifications in posttranscriptional gene regulation

Penguin: A tool for predicting pseudouridine sites in direct RNA nanopore sequencing data

(2022) Doaa Hassan et al.   METHODS

scDART-seq reveals distinct m6A signatures and mRNA methylation heterogeneity in single cells

(2022) Matthew Tegowski et al.   MOLECULAR CELL

RNA polyadenylation patterns in the human transcriptome

(2022) Si-Mei Xu et al.   GENE

N6-methyladenosine in poly(A) tails stabilize VSG transcripts

(2022) Idálio J. Viegas et al.   NATURE

m6A and YTHDF proteins contribute to the localization of select neuronal mRNAs

(2022) Mathieu N Flamand et al.   NUCLEIC ACIDS RESEARCH

Nanopore-Based Detection of Viral RNA Modifications

(2022) Jonathan S. Abebe et al.   mBio

Developmental mRNA m5C landscape and regulatory innovations of massive m5C modification of maternal mRNAs in animals

(2022) Jianheng Liu et al.   Nature Communications

Experimental evolution links post-transcriptional regulation to Leishmania fitness gain

(2022) Laura Piel et al.   PLoS Pathogens

Improved Methods for Deamination-Based m6A Detection

(2022) Huanyu Zhu et al.   Frontiers in Cell and Developmental Biology

The first apicoplast tRNA thiouridylase plays a vital role in the growth of Toxoplasma gondii

(2022) Yimin Yang et al.   Frontiers in Cellular and Infection Microbiology

A long noncoding RNA promotes parasite differentiation in African trypanosomes

(2022) Fabien Guegan et al.   Science Advances

TERRA G-quadruplex RNA interaction with TRF2 GAR domain is required for telomere integrity

(2021) Yang Mei et al.   Scientific Reports

CPSF30-L: A direct connection between mRNA polyadenylation and m6A RNA modification in plants

(2021) Arthur G. Hunt   Molecular Plant

Functional Characterization of the m6A-Dependent Translational Modulator PfYTH.2 in the Human Malaria Parasite

(2021) Ameya Sinha et al.   mBio

In Vivo and In Vitro Genome-Wide Profiling of RNA Secondary Structures Reveals Key Regulatory Features in Plasmodium falciparum

(2021) Yanwei Qi et al.   Frontiers in Cellular and Infection Microbiology

Deciphering Epitranscriptome: Modification of mRNA Bases Provides a New Perspective for Post-transcriptional Regulation of Gene Expression

(2021) Suresh Kumar et al.   Frontiers in Cell and Developmental Biology

Saccharomyces cerevisiae, a Powerful Model for Studying rRNA Modifications and Their Effects on Translation Fidelity

(2021) Agnès Baudin-Baillieu et al.   INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

Enhancer RNA m6A methylation facilitates transcriptional condensate formation and gene activation

(2021) Joo-Hyung Lee et al.   MOLECULAR CELL

Pseudouridines on Trypanosoma brucei mRNAs are developmentally regulated: Implications to mRNA stability and protein binding

(2021) K. Shanmugha Rajan et al.   MOLECULAR MICROBIOLOGY

Identification of differential RNA modifications from nanopore direct RNA sequencing with xPore

(2021) Ploy N. Pratanwanich et al.   NATURE BIOTECHNOLOGY

TbTRF suppresses the TERRA level and regulates the cell cycle-dependent TERRA foci number with a TERRA binding activity in its C-terminal Myb domain

(2021) Arpita Saha et al.   NUCLEIC ACIDS RESEARCH

The role of upstream open reading frames in translation regulation in the apicomplexan parasites Plasmodium falciparum and Toxoplasma gondii

(2021) Chhaminder Kaur et al.   PARASITOLOGY

m6A RNA methylation facilitates pre-mRNA 3’-end formation and is essential for viability of Toxoplasma gondii

(2021) Michael J. Holmes et al.   PLoS Pathogens

Computational identification of Plasmodium falciparum RNA pseudouridylate synthase as a viable drug target, its physicochemical properties, 3D structure prediction and prediction of potential inhibitors

(2021) Rufus Afolabi et al.   INFECTION GENETICS AND EVOLUTION

DNA methylation atlas of the mouse brain at single-cell resolution

(2021) Hanqing Liu et al.   NATURE

In vivo architecture of the telomerase RNA catalytic core in Trypanosoma brucei

(2021) Abhishek Dey et al.   NUCLEIC ACIDS RESEARCH

Recognition of G-quadruplex RNA by a crucial RNA methyltransferase component, METTL14

(2021) Atsuhiro Yoshida et al.   NUCLEIC ACIDS RESEARCH

Plasmodium falciparum YTH2 Domain Binds to m6A-Containing mRNA and Regulates Translation

(2021) Gayathri Govindaraju et al.   mBio

Malaria Parasite Stress Tolerance Is Regulated by DNMT2-Mediated tRNA Cytosine Methylation

(2021) Elie Hammam et al.   mBio

RNA modifications detection by comparative Nanopore direct RNA sequencing

(2021) Adrien Leger et al.   Nature Communications

Staem5: A novel computational approach for accurate prediction of m5C site

(2021) Di Chai et al.   Molecular Therapy-Nucleic Acids

N6-methyladenosine of chromosome-associated regulatory RNA regulates chromatin state and transcription

(2020) Jun Liu et al.   SCIENCE

Molecular Mechanisms Driving mRNA Degradation by m6A Modification

(2020) Yujin Lee et al.   TRENDS IN GENETICS

YTHDF2 promotes spermagonial adhesion through modulating MMPs decay via m6A/mRNA pathway

(2020) Tao Huang et al.   Cell Death & Disease

GC bias affects genomic and metagenomic reconstructions, underrepresenting GC-poor organisms

(2020) Patrick Denis Browne et al.   GigaScience

DeepNano-blitz: A Fast Base Caller for MinION Nanopore Sequencers

(2020) Vladimír Boža et al.   BIOINFORMATICS

m6A Modification in Coding and Non-coding RNAs: Roles and Therapeutic Implications in Cancer

(2020) Huilin Huang et al.   CANCER CELL

The emerging role of RNA modifications in the regulation of mRNA stability

(2020) Sung Ho Boo et al.   EXPERIMENTAL AND MOLECULAR MEDICINE

Limits in the detection of m6A changes using MeRIP/m6A-seq

(2020) Alexa B. R. McIntyre et al.   Scientific Reports

A Unified Model for the Function of YTHDF Proteins in Regulating m6A-Modified mRNA

(2020) Sara Zaccara et al.   CELL

N6-Methyladenosine co-transcriptionally directs the demethylation of histone H3K9me2

(2020) Yuan Li et al.   NATURE GENETICS

Decoding the epitranscriptional landscape from native RNA sequences

(2020) Piroon Jenjaroenpun et al.   NUCLEIC ACIDS RESEARCH

Lamin A safeguards the m 6 A methylase METTL14 nuclear speckle reservoir to prevent cellular senescence

(2020) Jie Zhang et al.   AGING CELL

N6-Adenosine methylation on mRNA is recognized by YTH2 domain protein of human malaria parasite Plasmodium falciparum

(2020) Gayathri Govindaraju et al.   Epigenetics & Chromatin

The Mammalian Cap-Specific m6Am RNA Methyltransferase PCIF1 Regulates Transcript Levels in Mouse Tissues

(2020) Radha Raman Pandey et al.   Cell Reports

Advances in RNA 3D Structure Modeling Using Experimental Data

(2020) Bing Li et al.   Frontiers in Genetics

Ythdf m6A Readers Function Redundantly during Zebrafish Development

(2020) Cassandra Kontur et al.   Cell Reports

EPAI-NC: Enhanced prediction of adenosine to inosine RNA editing sites using nucleotide compositions

(2019) Ahsan Ahmad et al.   ANALYTICAL BIOCHEMISTRY

Single-molecule sequencing detection of N6-methyladenine in microbial reference materials

(2019) Alexa B. R. McIntyre et al.   Nature Communications

Using long-read sequencing to detect imprinted DNA methylation

(2019) Scott Gigante et al.   NUCLEIC ACIDS RESEARCH

Increasing the accuracy of nanopore DNA sequencing using a time-varying cross membrane voltage

(2019) Matthew T. Noakes et al.   NATURE BIOTECHNOLOGY

PCIF1 Catalyzes m6Am mRNA Methylation to Regulate Gene Expression

(2019) Erdem Sendinc et al.   MOLECULAR CELL

Single-base mapping of m6A by an antibody-independent method

(2019) Zhang Zhang et al.   Science Advances

DART-seq: an antibody-free method for global m6A detection

(2019) Kate D. Meyer   NATURE METHODS

Transcriptome-wide dynamics of extensive m6A mRNA methylation during Plasmodium falciparum blood-stage development

(2019) Sebastian Baumgarten et al.   Nature Microbiology

Direct RNA sequencing enables m6A detection in endogenous transcript isoforms at base-specific resolution

(2019) Daniel A. Lorenz et al.   RNA

Accurate detection of m6A RNA modifications in native RNA sequences

(2019) Huanle Liu et al.   Nature Communications

m6A in mRNA coding regions promotes translation via the RNA helicase-containing YTHDC2

(2019) Yuanhui Mao et al.   Nature Communications

NMR Chemical Exchange Measurements Reveal That N6-Methyladenosine Slows RNA Annealing

(2019) Honglue Shi et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

m6A minimally impacts the structure, dynamics, and Rev ARM binding properties of HIV-1 RRE stem IIB

(2019) Chia-Chieh Chu et al.   PLoS One

A Completely Reimplemented MPI Bioinformatics Toolkit with a New HHpred Server at its Core

(2018) Lukas Zimmermann et al.   JOURNAL OF MOLECULAR BIOLOGY

Characterization of a Plasmodium falciparum rRNA methyltransferase

(2018) Kirti Gupta et al.   MOLECULAR AND BIOCHEMICAL PARASITOLOGY

Zc3h13 Regulates Nuclear RNA m 6 A Methylation and Mouse Embryonic Stem Cell Self-Renewal

(2018) Jing Wen et al.   MOLECULAR CELL

Nanopore sequencing and assembly of a human genome with ultra-long reads

(2018) Miten Jain et al.   NATURE BIOTECHNOLOGY

Recognition of RNA N6-methyladenosine by IGF2BP proteins enhances mRNA stability and translation

(2018) Huilin Huang et al.   NATURE CELL BIOLOGY

Reading m 6 A in the Transcriptome: m 6 A-Binding Proteins

(2018) Deepak P. Patil et al.   TRENDS IN CELL BIOLOGY

A potentially abundant junctional RNA motif stabilized by m6A and Mg2+

(2018) Bei Liu et al.   Nature Communications

Genome-wide real-time in vivo transcriptional dynamics during Plasmodium falciparum blood-stage development

(2018) Heather J. Painter et al.   Nature Communications

Systematic and stochastic influences on the performance of the MinION nanopore sequencer across a range of nucleotide bias

(2018) Raga Krishnakumar et al.   Scientific Reports

Nuclear m6A reader YTHDC1 regulates alternative polyadenylation and splicing during mouse oocyte development

(2018) Seth D. Kasowitz et al.   PLoS Genetics

RNA methylation in nuclear pre-mRNA processing

(2018) Helena Covelo-Molares et al.   Wiley Interdisciplinary Reviews-RNA

YTH Domain: A Family of N 6 -methyladenosine (m 6 A) Readers

(2018) Shanhui Liao et al.   GENOMICS PROTEOMICS & BIOINFORMATICS

VIRMA mediates preferential m6A mRNA methylation in 3′UTR and near stop codon and associates with alternative polyadenylation

(2018) Yanan Yue et al.   Cell Discovery

Differential m6A, m6Am, and m1A Demethylation Mediated by FTO in the Cell Nucleus and Cytoplasm

(2018) Jiangbo Wei et al.   MOLECULAR CELL

Characterization of mRNA polyadenylation in the apicomplexa

(2018) Ashley T. Stevens et al.   PLoS One

The Epitranscriptome in Translation Regulation

(2018) Eyal Peer et al.   Cold Spring Harbor Perspectives in Biology

Refined RIP-seq protocol for epitranscriptome analysis with low input materials

(2018) Yong Zeng et al.   PLOS BIOLOGY

Differential m6A methylomes between two major life stages allows potential regulations in Trypanosoma brucei

(2018) Luogen Liu et al.   BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS

The m6A Writer: Rise of a Machine for Growing Tasks

(2018) Dario L. Balacco et al.   BIOCHEMISTRY

m6A-mediated translation regulation

(2018) Kate D. Meyer   Biochimica et Biophysica Acta-Gene Regulatory Mechanisms

m6A facilitates hippocampus-dependent learning and memory through YTHDF1

(2018) Hailing Shi et al.   NATURE

m 6 A mRNA modifications are deposited in nascent pre-mRNA and are not required for splicing but do specify cytoplasmic turnover

(2017) Shengdong Ke et al.   GENES & DEVELOPMENT

Regulation of m 6 A Transcripts by the 3ʹ→5ʹ RNA Helicase YTHDC2 Is Essential for a Successful Meiotic Program in the Mammalian Germline

(2017) Magdalena Natalia Wojtas et al.   MOLECULAR CELL

Detecting DNA cytosine methylation using nanopore sequencing

(2017) Jared T Simpson et al.   NATURE METHODS

N6-methyladenosine (m6A) recruits and repels proteins to regulate mRNA homeostasis

(2017) Raghu R Edupuganti et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

N 6-methyladenosine alters RNA structure to regulate binding of a low-complexity protein

(2017) Nian Liu et al.   NUCLEIC ACIDS RESEARCH

ALKBH5-dependent m6A demethylation controls splicing and stability of long 3′-UTR mRNAs in male germ cells

(2017) Chong Tang et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

mRNA pseudouridylation affects RNA metabolism in the parasite Toxoplasma gondii

(2017) Margaret A. Nakamoto et al.   RNA

N6-methyladenosine (m6A) recruits and repels proteins to regulate mRNA homeostasis

(2017) Raghu R Edupuganti et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Frequent GU wobble pairings reduce translation efficiency in Plasmodium falciparum

(2017) Sherwin Chan et al.   Scientific Reports

DeepNano: Deep recurrent neural networks for base calling in MinION nanopore reads

(2017) Vladimír Boža et al.   PLoS One

Nuclear m 6 A Reader YTHDC1 Regulates mRNA Splicing

(2016) Wen Xiao et al.   MOLECULAR CELL

Reversible methylation of m6Am in the 5′ cap controls mRNA stability

(2016) Jan Mauer et al.   NATURE

N6-methyladenosine–encoded epitranscriptomics

(2016) Nian Liu et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Circular RNA Expression: Its Potential Regulation and Function

(2016) Julia Salzman   TRENDS IN GENETICS

N6-methyladenosine–encoded epitranscriptomics

(2016) Nian Liu et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

The AMPKα1 Pathway Positively Regulates the Developmental Transition from Proliferation to Quiescence in Trypanosoma brucei

(2016) Manuel Saldivia et al.   Cell Reports

Translational regulation in blood stages of the malaria parasite Plasmodium spp. : systems-wide studies pave the way

(2016) Shruthi Sridhar Vembar et al.   Wiley Interdisciplinary Reviews-RNA

A bioinformatic survey of RNA-binding proteins in Plasmodium

(2015) BP Niranjan Reddy et al.   BMC GENOMICS

5′ UTR m6A Promotes Cap-Independent Translation

(2015) Kate D. Meyer et al.   CELL

N6-methyladenosine Modulates Messenger RNA Translation Efficiency

(2015) Xiao Wang et al.   CELL

Processing of Plasmodium falciparum Merozoite Surface Protein MSP1 Activates a Spectrin-Binding Function Enabling Parasite Egress from RBCs

(2015) Sujaan Das et al.   Cell Host & Microbe

A majority of m6A residues are in the last exons, allowing the potential for 3′ UTR regulation

(2015) Shengdong Ke et al.   GENES & DEVELOPMENT

Structure and Thermodynamics of N6-Methyladenosine in RNA: A Spring-Loaded Base Modification

(2015) Caroline Roost et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

N6-methyladenosine marks primary microRNAs for processing

(2015) Claudio R. Alarcón et al.   NATURE

Dynamic m6A mRNA methylation directs translational control of heat shock response

(2015) Jun Zhou et al.   NATURE

N6-methyladenosine-dependent RNA structural switches regulate RNA–protein interactions

(2015) Nian Liu et al.   NATURE

A novel RNA-binding mode of the YTH domain reveals the mechanism for recognition of determinant of selective removal by Mmi1

(2015) Chongyuan Wang et al.   NUCLEIC ACIDS RESEARCH

Widespread occurrence ofN6-methyladenosine in bacterial mRNA

(2015) Xin Deng et al.   NUCLEIC ACIDS RESEARCH

Noncoding RNAs as emerging regulators of Plasmodium falciparum virulence gene expression

(2014) Shruthi S Vembar et al.   CURRENT OPINION IN MICROBIOLOGY

Capturing the variant surface glycoprotein repertoire (the VSGnome) of Trypanosoma brucei Lister 427

(2014) George A.M. Cross et al.   MOLECULAR AND BIOCHEMICAL PARASITOLOGY

N6-methyladenosine modification destabilizes developmental regulators in embryonic stem cells

(2014) Yang Wang et al.   NATURE CELL BIOLOGY

The dynamic epitranscriptome: N6-methyladenosine and gene expression control

(2014) Kate D. Meyer et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Generation of Antigenic Diversity in Plasmodium falciparum by Structured Rearrangement of Var Genes During Mitosis

(2014) Antoine Claessens et al.   PLoS Genetics

A trans-spliced telomerase RNA dictates telomere synthesis in Trypanosoma brucei

(2013) Ranjodh Sandhu et al.   CELL RESEARCH

Global Analysis of Protein Expression and Phosphorylation of Three Stages of Plasmodium falciparum Intraerythrocytic Development

(2013) Brittany N. Pease et al.   JOURNAL OF PROTEOME RESEARCH

N6-methyladenosine-dependent regulation of messenger RNA stability

(2013) Xiao Wang et al.   NATURE

A METTL3–METTL14 complex mediates mammalian nuclear RNA N6-adenosine methylation

(2013) Jianzhao Liu et al.   Nature Chemical Biology

The hnRNP F/H homologue of Trypanosoma brucei is differentially expressed in the two life cycle stages of the parasite and regulates splicing and mRNA stability

(2013) Sachin Kumar Gupta et al.   NUCLEIC ACIDS RESEARCH

Comprehensive Analysis of mRNA Methylation Reveals Enrichment in 3′ UTRs and near Stop Codons

(2012) Kate D. Meyer et al.   CELL

Characterization of a Trypanosoma brucei Alkb homolog capable of repairing alkylated DNA

(2012) Jana M. Simmons et al.   EXPERIMENTAL PARASITOLOGY

ALKBH5 Is a Mammalian RNA Demethylase that Impacts RNA Metabolism and Mouse Fertility

(2012) Guanqun Zheng et al.   MOLECULAR CELL

Topology of the human and mouse m6A RNA methylomes revealed by m6A-seq

(2012) Dan Dominissini et al.   NATURE

Directional gene expression and antisense transcripts in sexual and asexual stages of Plasmodium falciparum

(2011) María J López-Barragán et al.   BMC GENOMICS

N6-Methyladenosine in nuclear RNA is a major substrate of the obesity-associated FTO

(2011) Guifang Jia et al.   Nature Chemical Biology

RNA-Seq analysis of splicing in Plasmodium falciparum uncovers new splice junctions, alternative splicing and splicing of antisense transcripts

(2011) K. Sorber et al.   NUCLEIC ACIDS RESEARCH

Analyzing and minimizing PCR amplification bias in Illumina sequencing libraries

(2011) Daniel Aird et al.   GENOME BIOLOGY

Low-complexity regions within protein sequences have position-dependent roles

(2010) Alain Coletta et al.   BMC Systems Biology

New insights into the blood-stage transcriptome ofPlasmodium falciparumusing RNA-Seq

(2010) Thomas D. Otto et al.   MOLECULAR MICROBIOLOGY

Analysis of small nucleolar RNAs reveals unique genetic features in malaria parasites

(2009) Prakash Mishra et al.   BMC GENOMICS

A Pseudouridine Synthase Homologue Is Critical to Cellular Differentiation inToxoplasma gondii

(2009) Matthew Z. Anderson et al.   EUKARYOTIC CELL

Phylogenetic analysis of the eukaryotic RNA (cytosine-5)-methyltransferases

(2009) Athanasia Pavlopoulou et al.   GENOMICS

Telomeric Expression Sites Are Highly Conserved in Trypanosoma brucei

(2008) Christiane Hertz-Fowler et al.   PLoS One