Probing Xist RNA Structure in Cells Using Targeted Structure-Seq

HOTAIR Forms an Intricate and Modular Secondary Structure

(2015) Srinivas Somarowthu et al.   MOLECULAR CELL

Noncoding RNAs and Epigenetic Mechanisms During X-Chromosome Inactivation

(2014) Anne-Valerie Gendrel et al.   Annual Review of Cell and Developmental Biology

Standardization of RNA Chemical Mapping Experiments

(2014) Wipapat Kladwang et al.   BIOCHEMISTRY

ATRX Directs Binding of PRC2 to Xist RNA and Polycomb Targets

(2014) Kavitha Sarma et al.   CELL

The Noncoding RNA Revolution—Trashing Old Rules to Forge New Ones

(2014) Thomas R. Cech et al.   CELL

Regulatory Interactions between RNA and Polycomb Repressive Complex 2

(2014) Catherine Cifuentes-Rojas et al.   MOLECULAR CELL

Jarid2 Is Implicated in the Initial Xist-Induced Targeting of PRC2 to the Inactive X Chromosome

(2014) Simão Teixeira da Rocha et al.   MOLECULAR CELL

RNA motif discovery by SHAPE and mutational profiling (SHAPE-MaP)

(2014) Nathan A Siegfried et al.   NATURE METHODS

Snapshots of pre-rRNA structural flexibility reveal eukaryotic 40S assembly dynamics at nucleotide resolution

(2014) Ralph D. Hector et al.   NUCLEIC ACIDS RESEARCH

Massive parallel-sequencing-based hydroxyl radical probing of RNA accessibility

(2014) Lukasz Jan Kielpinski et al.   NUCLEIC ACIDS RESEARCH

GenBank

(2014) Dennis A. Benson et al.   NUCLEIC ACIDS RESEARCH

Genetic and pharmacological reactivation of the mammalian inactive X chromosome

(2014) S. Bhatnagar et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

RNA structural analysis by evolving SHAPE chemistry

(2014) Robert C. Spitale et al.   Wiley Interdisciplinary Reviews-RNA

Rise of the RNA Machines: Exploring the Structure of Long Non-Coding RNAs

(2013) Irina V. Novikova et al.   JOURNAL OF MOLECULAR BIOLOGY

High-resolution Xist binding maps reveal two-step spreading during X-chromosome inactivation

(2013) Matthew D. Simon et al.   NATURE

In vivo genome-wide profiling of RNA secondary structure reveals novel regulatory features

(2013) Yiliang Ding et al.   NATURE

Genome-wide probing of RNA structure reveals active unfolding of mRNA structures in vivo

(2013) Silvi Rouskin et al.   NATURE

Genome-wide mapping of RNA structure using nuclease digestion and high-throughput sequencing

(2013) Yue Wan et al.   Nature Protocols

Noncoding RNA and Polycomb recruitment

(2013) N. Brockdorff   RNA

The Xist lncRNA Exploits Three-Dimensional Genome Architecture to Spread Across the X Chromosome

(2013) J. M. Engreitz et al.   SCIENCE

XIST-induced silencing of flanking genes is achieved by additive action of repeat a monomers in human somatic cells

(2013) Jakub Minks et al.   Epigenetics & Chromatin

Analysis of energy-based algorithms for RNA secondary structure prediction

(2012) Monir Hajiaghayi et al.   BMC BIOINFORMATICS

Recent advances in X-chromosome inactivation research

(2012) Tim Pollex et al.   CURRENT OPINION IN CELL BIOLOGY

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

Structural architecture of the human long non-coding RNA, steroid receptor RNA activator

(2012) Irina V. Novikova et al.   NUCLEIC ACIDS RESEARCH

QuShape: Rapid, accurate, and best-practices quantification of nucleic acid probing information, resolved by capillary electrophoresis

(2012) F. Karabiber et al.   RNA

ViennaRNA Package 2.0

(2011) Ronny Lorenz et al.   Algorithms for Molecular Biology

YY1 Tethers Xist RNA to the Inactive X Nucleation Center

(2011) Yesu Jeon et al.   CELL

Chromosome silencing mechanisms in X-chromosome inactivation: unknown unknowns

(2011) N. Brockdorff   DEVELOPMENT

X-chromosome hyperactivation in mammals via nonlinear relationships between chromatin states and transcription

(2011) Eda Yildirim et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Modeling and automation of sequencing-based characterization of RNA structure

(2011) S. Aviran et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The Xist RNA A-repeat comprises a novel AUCG tetraloop fold and a platform for multimerization

(2011) M. M. Duszczyk et al.   RNA

RNAstructure: software for RNA secondary structure prediction and analysis

(2010) Jessica S Reuter et al.   BMC BIOINFORMATICS

SHAPE-directed RNA secondary structure prediction

(2010) Justin T. Low et al.   METHODS

The A-repeat links ASF/SF2-dependent Xist RNA processing with random choice during X inactivation

(2010) Morgan E Royce-Tolland et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Locked nucleic acids (LNAs) reveal sequence requirements and kinetics of Xist RNA localization to the X chromosome

(2010) K. Sarma et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Folding and Finding RNA Secondary Structure

(2010) D. H. Mathews et al.   Cold Spring Harbor Perspectives in Biology

2-D Structure of the A Region of Xist RNA and Its Implication for PRC2 Association

(2010) Sylvain Maenner et al.   PLOS BIOLOGY

VARNA: Interactive drawing and editing of the RNA secondary structure

(2009) Kévin Darty et al.   BIOINFORMATICS

Jalview Version 2--a multiple sequence alignment editor and analysis workbench

(2009) A. M. Waterhouse et al.   BIOINFORMATICS

Lessons from X-chromosome inactivation: long ncRNA as guides and tethers to the epigenome

(2009) J. T. Lee   GENES & DEVELOPMENT

Architecture and secondary structure of an entire HIV-1 RNA genome

(2009) Joseph M. Watts et al.   NATURE

High-throughput single-nucleotide structural mapping by capillary automated footprinting analysis

(2008) Somdeb Mitra et al.   NUCLEIC ACIDS RESEARCH

A NMR strategy to unambiguously distinguish nucleic acid hairpin and duplex conformations applied to a Xist RNA A-repeat

(2008) Malgorzata M. Duszczyk et al.   NUCLEIC ACIDS RESEARCH

Accurate SHAPE-directed RNA structure determination

(2008) K. E. Deigan et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Polycomb Proteins Targeted by a Short Repeat RNA to the Mouse X Chromosome

(2008) J. Zhao et al.   SCIENCE