Functional annotation of human long noncoding RNAs via molecular phenotyping

Recounting the FANTOM CAGE–Associated Transcriptome

(2020) Eddie Luidy Imada et al.   GENOME RESEARCH

Targeted, High-Resolution RNA Sequencing of Non-coding Genomic Regions Associated With Neuropsychiatric Functions

(2019) Simon A. Hardwick et al.   Frontiers in Genetics

ilastik: interactive machine learning for (bio)image analysis

(2019) Stuart Berg et al.   NATURE METHODS

Functional Classification and Experimental Dissection of Long Noncoding RNAs

(2018) Florian Kopp et al.   CELL

Promoter of lncRNA Gene PVT1 Is a Tumor-Suppressor DNA Boundary Element

(2018) Seung Woo Cho et al.   CELL

Specificity of RNAi, LNA and CRISPRi as loss-of-function methods in transcriptional analysis

(2018) Lovorka Stojic et al.   NUCLEIC ACIDS RESEARCH

Nuclear Long Noncoding RNAs: Key Regulators of Gene Expression

(2018) Qinyu Sun et al.   TRENDS IN GENETICS

lncRNA A1BG‐AS1 suppresses proliferation and invasion of hepatocellular carcinoma cells by targeting miR‐216a‐5p

(2018) Jigang Bai et al.   JOURNAL OF CELLULAR BIOCHEMISTRY

Genome-wide screening for functional long noncoding RNAs in human cells by Cas9 targeting of splice sites

(2018) Ying Liu et al.   NATURE BIOTECHNOLOGY

LncBook: a curated knowledgebase of human long non-coding RNAs

(2018) Lina Ma et al.   NUCLEIC ACIDS RESEARCH

Sequence Determinants for Nuclear Retention and Cytoplasmic Export of mRNAs and lncRNAs

(2018) Alexander F. Palazzo et al.   Frontiers in Genetics

An atlas of human long non-coding RNAs with accurate 5′ ends

(2017) Chung-Chau Hon et al.   NATURE

Genome-scale activation screen identifies a lncRNA locus regulating a gene neighbourhood

(2017) Julia Joung et al.   NATURE

Reproducible RNA-seq analysis using recount2

(2017) Leonardo Collado-Torres et al.   NATURE BIOTECHNOLOGY

GRID-seq reveals the global RNA–chromatin interactome

(2017) Xiao Li et al.   NATURE BIOTECHNOLOGY

The functions and unique features of long intergenic non-coding RNA

(2017) Julia D. Ransohoff et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

RNA Duplex Map in Living Cells Reveals Higher-Order Transcriptome Structure

(2016) Zhipeng Lu et al.   CELL

Genome-wide screen of cell-cycle regulators in normal and tumor cells identifies a differential response to nucleosome depletion

(2016) Maria Sokolova et al.   CELL CYCLE

Divergent lncRNAs Regulate Gene Expression and Lineage Differentiation in Pluripotent Cells

(2016) Sai Luo et al.   Cell Stem Cell

A G-Rich Motif in the lncRNA Braveheart Interacts with a Zinc-Finger Transcription Factor to Specify the Cardiovascular Lineage

(2016) Zhihong Xue et al.   MOLECULAR CELL

Local regulation of gene expression by lncRNA promoters, transcription and splicing

(2016) Jesse M. Engreitz et al.   NATURE

Evolution to the rescue: using comparative genomics to understand long non-coding RNAs

(2016) Igor Ulitsky   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

Transcriptional termination in mammals: Stopping the RNA polymerase II juggernaut

(2016) N. J. Proudfoot   SCIENCE

CRISPRi-based genome-scale identification of functional long noncoding RNA loci in human cells

(2016) S. John Liu et al.   SCIENCE

Linking Long Noncoding RNA Localization and Function

(2016) Ling-Ling Chen   TRENDS IN BIOCHEMICAL SCIENCES

A conserved abundant cytoplasmic long noncoding RNA modulates repression by Pumilio proteins in human cells

(2016) Ailone Tichon et al.   Nature Communications

Systematic Discovery of Xist RNA Binding Proteins

(2015) Ci Chu et al.   CELL

Paradigm shifts in genomics through the FANTOM projects

(2015) Michiel de Hoon et al.   MAMMALIAN GENOME

An Overview of Genome Organization and How We Got There: from FISH to Hi-C

(2015) James Fraser et al.   MICROBIOLOGY AND MOLECULAR BIOLOGY REVIEWS

Hierarchical folding and reorganization of chromosomes are linked to transcriptional changes in cellular differentiation

(2015) J. Fraser et al.   Molecular Systems Biology

Integrative analysis of 111 reference human epigenomes

(2015) Anshul Kundaje et al.   NATURE

The landscape of long noncoding RNAs in the human transcriptome

(2015) Matthew K Iyer et al.   NATURE GENETICS

The Genotype-Tissue Expression (GTEx) pilot analysis: Multitissue gene regulation in humans

(2015) et al.   SCIENCE

MEG3 long noncoding RNA regulates the TGF-β pathway genes through formation of RNA–DNA triplex structures

(2015) Tanmoy Mondal et al.   Nature Communications

lncRNAdb v2.0: expanding the reference database for functional long noncoding RNAs

(2014) Xiu Cheng Quek et al.   NUCLEIC ACIDS RESEARCH

An update on LNCipedia: a database for annotated human lncRNA sequences

(2014) Pieter-Jan Volders et al.   NUCLEIC ACIDS RESEARCH

Physiological roles of long noncoding RNAs: insight from knockout mice

(2014) Lingjie Li et al.   TRENDS IN CELL BIOLOGY

Fibroblasts in fibrosis: novel roles and mediators

(2014) Ryan T. Kendall et al.   Frontiers in Pharmacology

DNMT1-interacting RNAs block gene-specific DNA methylation

(2013) Annalisa Di Ruscio et al.   NATURE

A pseudogene long-noncoding-RNA network regulates PTEN transcription and translation in human cells

(2013) Per Johnsson et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Long non-coding antisense RNA controls Uchl1 translation through an embedded SINEB2 repeat

(2012) Claudia Carrieri et al.   NATURE

Modular regulatory principles of large non-coding RNAs

(2012) Mitchell Guttman et al.   NATURE

Direct Reprogramming of Adult Human Fibroblasts to Functional Neurons under Defined Conditions

(2011) Rajesh Ambasudhan et al.   Cell Stem Cell

lincRNAs act in the circuitry controlling pluripotency and differentiation

(2011) Mitchell Guttman et al.   NATURE

Long non-coding RNA HOTAIR reprograms chromatin state to promote cancer metastasis

(2010) Rajnish A. Gupta et al.   NATURE

The transcriptional network that controls growth arrest and differentiation in a human myeloid leukemia cell line

(2009) Harukazu Suzuki et al.   NATURE GENETICS

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

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

Fibroblasts and myofibroblasts in wound healing: Force generation and measurement

(2009) Bin Li et al.   Journal of Tissue Viability