Studying RNA–DNA interactome by Red-C identifies noncoding RNAs associated with various chromatin types and reveals transcription dynamics

RADICL-seq identifies general and cell type–specific principles of genome-wide RNA-chromatin interactions

(2020) Alessandro Bonetti et al.   Nature Communications

RNA: Nuclear Glue for Folding the Genome

(2019) Ryu-Suke Nozawa et al.   TRENDS IN CELL BIOLOGY

Genome-wide colocalization of RNA–DNA interactions and fusion RNA pairs

(2019) Zhangming Yan et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

C-TALE, a new cost-effective method for targeted enrichment of Hi-C/3C-seq libraries

(2019) Arkadiy K. Golov et al.   METHODS

Chromatin-associated RNAs as facilitators of functional genomic interactions

(2019) Xiao Li et al.   NATURE REVIEWS GENETICS

Genome Organization in and around the Nucleolus

(2019) Cristiana Bersaglieri et al.   Cells

Non-coding RNAs as Regulators of Lymphangiogenesis in Lymphatic Development, Inflammation, and Cancer Metastasis

(2019) Ming-xin Cao et al.   Frontiers in Oncology

Dosage Compensation of the X Chromosome: A Complex Epigenetic Assignment Involving Chromatin Regulators and Long Noncoding RNAs

(2018) Maria Samata et al.   Annual Review of Biochemistry

Nuclear Long Noncoding RNAs: Key Regulators of Gene Expression

(2018) Qinyu Sun et al.   TRENDS IN GENETICS

Chromatin-associated RNA sequencing (ChAR-seq) maps genome-wide RNA-to-DNA contacts

(2018) Jason C Bell et al.   eLife

Primary transcripts: from the discovery of RNA processing to current concepts of gene expression - Review

(2018) Klaus Scherrer   EXPERIMENTAL CELL RESEARCH

The Biogenesis, Functions, and Challenges of Circular RNAs

(2018) Xiang Li et al.   MOLECULAR CELL

X-Chromosome Inactivation: A Crossroads Between Chromosome Architecture and Gene Regulation

(2018) Rafael Galupa et al.   Annual Review of Genetics

GRID-seq reveals the global RNA–chromatin interactome

(2017) Xiao Li et al.   NATURE BIOTECHNOLOGY

Mapping 3D genome architecture through in situ DNase Hi-C

(2016) Vijay Ramani et al.   Nature Protocols

Enhancers as non-coding RNA transcription units: recent insights and future perspectives

(2016) Wenbo Li et al.   NATURE REVIEWS GENETICS

Unique features of long non-coding RNA biogenesis and function

(2016) Jeffrey J. Quinn et al.   NATURE REVIEWS GENETICS

Long non-coding RNAs: spatial amplifiers that control nuclear structure and gene expression

(2016) Jesse M. Engreitz et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Human Ribosomal RNA-Derived Resident MicroRNAs as the Transmitter of Information upon the Cytoplasmic Cancer Stress

(2016) Masaru Yoshikawa et al.   Biomed Research International

Locus-Specific Targeting to the X Chromosome Revealed by the RNA Interactome of CTCF

(2015) Johnny T. Kung et al.   MOLECULAR CELL

RNA-mediated epigenetic regulation of gene expression

(2015) Daniel Holoch et al.   NATURE REVIEWS GENETICS

Control of Chromatin Structure by Long Noncoding RNA

(2015) Gudrun Böhmdorfer et al.   TRENDS IN CELL BIOLOGY

A 3D Map of the Human Genome at Kilobase Resolution Reveals Principles of Chromatin Looping

(2014) Suhas S.P. Rao et al.   CELL

Long Noncoding RNAs in Cell-Fate Programming and Reprogramming

(2014) Ryan A. Flynn et al.   Cell Stem Cell

CTCF regulates the human p53 gene through direct interaction with its natural antisense transcript, Wrap53

(2014) R. Saldana-Meyer et al.   GENES & DEVELOPMENT

Coupling mRNA processing with transcription in time and space

(2014) David L. Bentley   NATURE REVIEWS GENETICS

Topological organization of multichromosomal regions by the long intergenic noncoding RNA Firre

(2014) Ezgi Hacisuleyman et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Discovering the complexity of the metazoan transcriptome

(2014) Matthew J Hangauer et al.   GENOME BIOLOGY

The MicroRNA Biology of the Mammalian Nucleus

(2014) Thomas C Roberts   Molecular Therapy-Nucleic Acids

Long non-coding RNAs: modulators of nuclear structure and function

(2013) Jan H Bergmann et al.   CURRENT OPINION IN CELL BIOLOGY

RNA in unexpected places: long non-coding RNA functions in diverse cellular contexts

(2013) Sarah Geisler et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

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

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

VlincRNAs controlled by retroviral elements are a hallmark of pluripotency and cancer

(2013) Georges St Laurent et al.   GENOME BIOLOGY

Formation of nuclear heterochromatin

(2012) Claudio Guetg et al.   Epigenetics

Cis-acting noncoding RNAs: friends and foes

(2012) Sònia Guil et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Mapping and analysis of chromatin state dynamics in nine human cell types

(2011) Jason Ernst et al.   NATURE

Non-coding RNAs in human disease

(2011) Manel Esteller   NATURE REVIEWS GENETICS

Incorporation of non-natural nucleotides into template-switching oligonucleotides reduces background and improves cDNA synthesis from very small RNA samples

(2010) Jeremy Kapteyn et al.   BMC GENOMICS

High-Resolution Whole-Genome Sequencing Reveals That Specific Chromatin Domains from Most Human Chromosomes Associate with Nucleoli

(2010) Silvana van Koningsbruggen et al.   MOLECULAR BIOLOGY OF THE CELL

The Nuclear-Retained Noncoding RNA MALAT1 Regulates Alternative Splicing by Modulating SR Splicing Factor Phosphorylation

(2010) Vidisha Tripathi et al.   MOLECULAR CELL

Apparent Non-Canonical Trans-Splicing Is Generated by Reverse Transcriptase In Vitro

(2010) Jonathan Houseley et al.   PLoS One

Initial Genomics of the Human Nucleolus

(2010) Attila Németh et al.   PLoS Genetics

Intergenic transcripts originating from a subclass of ribosomal DNA repeats silence ribosomal RNA genes in trans

(2009) Raffaella Santoro et al.   EMBO REPORTS

Sequencing newly replicated DNA reveals widespread plasticity in human replication timing

(2009) R. S. Hansen et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Comprehensive Mapping of Long-Range Interactions Reveals Folding Principles of the Human Genome

(2009) E. Lieberman-Aiden et al.   SCIENCE

Kcnq1ot1 Antisense Noncoding RNA Mediates Lineage-Specific Transcriptional Silencing through Chromatin-Level Regulation

(2008) Radha Raman Pandey et al.   MOLECULAR CELL

MmeI: a minimal Type II restriction-modification system that only modifies one DNA strand for host protection

(2008) Richard D. Morgan et al.   NUCLEIC ACIDS RESEARCH