Related references
Note: Only part of the references are listed.Long non-coding RNAs: definitions, functions, challenges and recommendations
John S. S. Mattick et al.
NATURE REVIEWS MOLECULAR CELL BIOLOGY (2023)
Linking discoveries, mechanisms, and technologies to develop a clearer perspective on plant long noncoding RNAs
Kyle Palos et al.
PLANT CELL (2023)
An antisense intragenic lncRNA SEAIRa mediates transcriptional and epigenetic repression of SERRATE in Arabidopsis
Wei Chen et al.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2023)
Epigenetic modifications: Allusive clues of lncRNA functions in plants
Wenjing Yang et al.
COMPUTATIONAL AND STRUCTURAL BIOTECHNOLOGY JOURNAL (2023)
GreeNC 2.0: a comprehensive database of plant long non-coding RNAs
Marco Di Marsico et al.
NUCLEIC ACIDS RESEARCH (2022)
Revealing the novel complexity of plant long non-coding RNA by strand-specific and whole transcriptome sequencing for evolutionarily representative plant species
Yan Zhu et al.
BMC GENOMICS (2022)
DNA methylation-free Arabidopsis reveals crucial roles of DNA methylation in regulating gene expression and development
Li He et al.
NATURE COMMUNICATIONS (2022)
Epigenetic variation: A major player in facilitating plant fitness under changing environmental conditions
Vijay Rani Rajpal et al.
FRONTIERS IN CELL AND DEVELOPMENTAL BIOLOGY (2022)
DNA methylation underpins the epigenomic landscape regulating genome transcription in Arabidopsis
Lun Zhao et al.
GENOME BIOLOGY (2022)
Transcriptome-guided annotation and functional classification of long non-coding RNAs in Arabidopsis thaliana
Jose Antonio Corona-Gomez et al.
SCIENTIFIC REPORTS (2022)
Identification and functional annotation of long intergenic non-coding RNAs in Brassicaceae
Kyle Palos et al.
PLANT CELL (2022)
PLncDB V2.0: a comprehensive encyclopedia of plant long noncoding RNAs
Jingjing Jin et al.
NUCLEIC ACIDS RESEARCH (2021)
Gene regulation by long non-coding RNAs and its biological functions
Luisa Statello et al.
NATURE REVIEWS MOLECULAR CELL BIOLOGY (2021)
Role of Polycomb in the control of transposable elements
Angelique Deleris et al.
TRENDS IN GENETICS (2021)
The chromatin remodeler DDM1 prevents transposon mobility through deposition of histone variant H2A.W
Akihisa Osakabe et al.
NATURE CELL BIOLOGY (2021)
TrancriptomeReconstructoR: data-driven annotation of complex transcriptomes
Maxim Ivanov et al.
BMC BIOINFORMATICS (2021)
Identification of long noncoding natural antisense transcripts (lncNATs) correlated with drought stress response in wild rice (Oryza nivara)
Yong-Chao Xu et al.
BMC GENOMICS (2021)
DNA Methylation and Histone H1 Jointly Repress Transposable Elements and Aberrant Intragenic Transcripts
Jaemyung Choi et al.
MOLECULAR CELL (2020)
Identification and comprehensive characterization of lncRNAs with copy number variations and their driving transcriptional perturbed subpathways reveal functional significance for cancer
Yanjun Xu et al.
BRIEFINGS IN BIOINFORMATICS (2020)
Native elongation transcript sequencing reveals temperature dependent dynamics of nascent RNAPII transcription in Arabidopsis
Peter Kindgren et al.
NUCLEIC ACIDS RESEARCH (2020)
Arabidopsis RNA Polymerase IV generates 21-22 nucleotide small RNAs that can participate in RNA-directed DNA methylation and may regulate genes
Kaushik Panda et al.
PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES (2020)
Transposable elements as a potent source of diverse cis-regulatory sequences in mammalian genomes
Vasavi Sundaram et al.
PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES (2020)
Landscape of the Noncoding Transcriptome Response of Two Arabidopsis Ecotypes to Phosphate Starvation1
Thomas Blein et al.
PLANT PHYSIOLOGY (2020)
Transcript isoform sequencing reveals widespread promoter-proximal transcriptional termination in Arabidopsis
Quentin Angelo Thomas et al.
NATURE COMMUNICATIONS (2020)
Long Non-coding RNA in Plants in the Era of Reference Sequences
Hikmet Budak et al.
FRONTIERS IN PLANT SCIENCE (2020)
Long Noncoding RNAs: Molecular Modalities to Organismal Functions
John L. Rinn et al.
ANNUAL REVIEW OF BIOCHEMISTRY, VOL 89 (2020)
Xist Repeats A and B Account for Two Distinct Phases of X Inactivation Establishment
David Colognori et al.
DEVELOPMENTAL CELL (2020)
Twenty years of transposable element analysis in theArabidopsis thalianagenome
Hadi Quesneville
MOBILE DNA (2020)
Analysis of copy number alterations reveals the lncRNA ALAL-1 as a regulator of lung cancer immune evasion
Alejandro Athie et al.
JOURNAL OF CELL BIOLOGY (2020)
Chromatin regulates expression of small RNAs to help maintain transposon methylome homeostasis in Arabidopsis
Ranjith K. Papareddy et al.
GENOME BIOLOGY (2020)
Widespread inter-individual gene expression variability in Arabidopsis thaliana
Sandra Cortijo et al.
MOLECULAR SYSTEMS BIOLOGY (2019)
LNCipedia 5: towards a reference set of human long non-coding RNAs
Pieter-Jan Volders et al.
NUCLEIC ACIDS RESEARCH (2019)
Common alleles of CMT2 and NRPE1 are major determinants of CHH methylation variation in Arabidopsis thaliana
Eriko Sasaki et al.
PLOS GENETICS (2019)
Population-level analysis reveals the widespread occurrence and phenotypic consequence of DNA methylation variation not tagged by genetic variation in maize
Jing Xu et al.
GENOME BIOLOGY (2019)
Sequences enriched in Alu repeats drive nuclear localization of long RNAs in human cells
Yoav Lubelsky et al.
NATURE (2018)
Transcriptional read-through of the long non-coding RNA SVALKA governs plant cold acclimation
Peter Kindgren et al.
NATURE COMMUNICATIONS (2018)
Global identification of Arabidopsis lncRNAs reveals the regulation of MAF4 by a natural antisense RNA
Xinyue Zhao et al.
NATURE COMMUNICATIONS (2018)
CPC2: a fast and accurate coding potential calculator based on sequence intrinsic features
Yu-Jian Kang et al.
NUCLEIC ACIDS RESEARCH (2017)
Araport11: a complete reannotation of the Arabidopsis thaliana reference genome
Chia-Yi Cheng et al.
PLANT JOURNAL (2017)
The Role of KRAB-ZFPs in Transposable Element Repression and Mammalian Evolution
Peng Yang et al.
TRENDS IN GENETICS (2017)
Mapping the mouse Allelome reveals tissue-specific regulation of allelic expression
Daniel Andergassen et al.
ELIFE (2017)
Evolinc:A Tool for the Identification and Evolutionary Comparison of Long Intergenic Non-coding RNAs
Andrew D. L. Nelson et al.
FRONTIERS IN GENETICS (2017)
Non-coding RNAs and Their Roles in Stress Response in Plants
Jingjing Wang et al.
GENOMICS PROTEOMICS & BIOINFORMATICS (2017)
Gene body DNA methylation in plants
Adam J. Bewick et al.
CURRENT OPINION IN PLANT BIOLOGY (2017)
Systematic characterization of novel lncRNAs responding to phosphate starvation in Arabidopsis thaliana
Jiapei Yuan et al.
BMC GENOMICS (2016)
Epigenomic Diversity in a Global Collection of Arabidopsis thaliana Accessions
Taiji Kawakatsu et al.
CELL (2016)
1,135 Genomes Reveal the Global Pattern of Polymorphism in Arabidopsis thaliana
Carlos Alonso-Blanco et al.
CELL (2016)
Challenges in the analysis of long noncoding RNA functionality
Sergio Leone et al.
FEBS LETTERS (2016)
deepTools2: a next generation web server for deep-sequencing data analysis
Fidel Ramirez et al.
NUCLEIC ACIDS RESEARCH (2016)
The First Rule of Plant Transposable Element Silencing: Location, Location, Location
Meredith J. Sigman et al.
PLANT CELL (2016)
Nascent RNA sequencing reveals distinct features in plant transcription
Jonathan Hetzel et al.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2016)
Control of seed dormancy in Arabidopsis by a cis-acting noncoding antisense transcript
Halina Fedak et al.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2016)
Long non-coding RNAs display higher natural expression variation than protein-coding genes in healthy humans
Aleksandra E. Kornienko et al.
GENOME BIOLOGY (2016)
Global identification and analysis of long non-coding RNAs in diploid strawberry Fragaria vesca during flower and fruit development
Chunying Kang et al.
BMC GENOMICS (2015)
Silencing of active transposable elements in plants
Dalen Fultz et al.
CURRENT OPINION IN PLANT BIOLOGY (2015)
Genome-wide view of natural antisense transcripts in Arabidopsis thaliana
Chunhui Yuan et al.
DNA RESEARCH (2015)
StringTie enables improved reconstruction of a transcriptome from RNA-seq reads
Mihaela Pertea et al.
NATURE BIOTECHNOLOGY (2015)
Discovery and annotation of long noncoding RNAs
John S. Mattick et al.
NATURE STRUCTURAL & MOLECULAR BIOLOGY (2015)
The human transcriptome across tissues and individuals
Marta Mele et al.
SCIENCE (2015)
Discovery and annotation of long noncoding RNAs
John S. Mattick et al.
NATURE STRUCTURAL & MOLECULAR BIOLOGY (2015)
Long Non-coding RNAs and Their Biological Roles in Plants
Xue Liu et al.
GENOMICS PROTEOMICS & BIOINFORMATICS (2015)
Evolutionary conservation of long non-coding RNAs; sequence, structure, function
Per Johnsson et al.
BIOCHIMICA ET BIOPHYSICA ACTA-GENERAL SUBJECTS (2014)
featureCounts: an efficient general purpose program for assigning sequence reads to genomic features
Yang Liao et al.
BIOINFORMATICS (2014)
The Histone Variant H2A. W Defines Heterochromatin and Promotes Chromatin Condensation in Arabidopsis
Ramesh Yelagandula et al.
CELL (2014)
Evolutionary dynamics of coding and non-coding transcriptomes
Anamaria Necsulea et al.
NATURE REVIEWS GENETICS (2014)
RNA-directed DNA methylation: an epigenetic pathway of increasing complexity
Marjori A. Matzke et al.
NATURE REVIEWS GENETICS (2014)
Antisense COOLAIR mediates the coordinated switching of chromatin states at FLC during vernalization
Tibor Csorba et al.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2014)
The RIDL hypothesis: transposable elements as functional domains of long noncoding RNAs
Rory Johnson et al.
RNA (2014)
Volatile evolution of long noncoding RNA repertoires: mechanisms and biological implications
Aurelie Kapusta et al.
TRENDS IN GENETICS (2014)
Genome-wide discovery and characterization of maize long non-coding RNAs
Lin Li et al.
GENOME BIOLOGY (2014)
STAR: ultrafast universal RNA-seq aligner
Alexander Dobin et al.
BIOINFORMATICS (2013)
The Arabidopsis Nucleosome Remodeler DDM1 Allows DNA Methyltransferases to Access H1-Containing Heterochromatin
Assaf Zemach et al.
CELL (2013)
Long Noncoding RNAs: Cellular Address Codes in Development and Disease
Pedro J. Batista et al.
CELL (2013)
Integrated detection of natural antisense transcripts using strand-specific RNA sequencing data
Song Li et al.
GENOME RESEARCH (2013)
Tagmentation-based whole-genome bisulfite sequencing
Qi Wang et al.
NATURE PROTOCOLS (2013)
Targeting long non-coding RNA to therapeutically upregulate gene expression
Claes Wahlestedt
NATURE REVIEWS DRUG DISCOVERY (2013)
The Initiation of Epigenetic Silencing of Active Transposable Elements Is Triggered by RDR6 and 21-22 Nucleotide Small Interfering RNAs
Saivageethi Nuthikattu et al.
PLANT PHYSIOLOGY (2013)
Transposable Elements Are Major Contributors to the Origin, Diversification, and Regulation of Vertebrate Long Noncoding RNAs
Aurelie Kapusta et al.
PLOS GENETICS (2013)
Multiple knockout mouse models reveal lincRNAs are required for life and brain development
Martin Sauvageau et al.
ELIFE (2013)
NERD, a Plant-Specific GW Protein, Defines an Additional RNAi-Dependent Chromatin-Based Pathway in Arabidopsis
Dominique Pontier et al.
MOLECULAR CELL (2012)
Genome-Wide Analysis Uncovers Regulation of Long Intergenic Noncoding RNAs in Arabidopsis
Jun Liu et al.
PLANT CELL (2012)
Flowering time control: another window to the connection between antisense RNA and chromatin
Robert Ietswaart et al.
TRENDS IN GENETICS (2012)
Rapid Turnover of Long Noncoding RNAs and the Evolution of Gene Expression
Claudia Kutter et al.
PLOS GENETICS (2012)
Identification and characterization of wheat long non-protein coding RNAs responsive to powdery mildew infection and heat stress by using microarray analysis and SBS sequencing
Mingming Xin et al.
BMC PLANT BIOLOGY (2011)
Epigenetic modifications in plants: an evolutionary perspective
Suhua Feng et al.
CURRENT OPINION IN PLANT BIOLOGY (2011)
Integrative annotation of human large intergenic noncoding RNAs reveals global properties and specific subclasses
Moran N. Cabili et al.
GENES & DEVELOPMENT (2011)
Long noncoding RNAs and human disease
Orly Wapinski et al.
TRENDS IN CELL BIOLOGY (2011)
Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation
Cole Trapnell et al.
NATURE BIOTECHNOLOGY (2010)
Epigenetic Reprogramming and Small RNA Silencing of Transposable Elements in Pollen
R. Keith Slotkin et al.
CELL (2009)
A genome-wide view of miniature inverted-repeat transposable elements (MITEs) in rice, Oryza sativa ssp japonica
Nobuhiko Oki et al.
GENES & GENETIC SYSTEMS (2008)
A model for transmission of the H3K27me3 epigenetic mark
Klaus H. Hansen et al.
NATURE CELL BIOLOGY (2008)
Plant nuclear RNA polymerase IV mediates siRNA and DNA methylation-dependent heterochromatin formation
Y Onodera et al.
CELL (2005)
A compendium of methods useful for characterizing Arabidopsis pollen mutants and gametophytically-expressed genes
SA Johnson-Brousseau et al.
PLANT JOURNAL (2004)
Share Paper
