GC-AG Introns Features in Long Non-coding and Protein-Coding Genes Suggest Their Role in Gene Expression Regulation

Introns as Gene Regulators: A Brick on the Accelerator

(2019) Alan B. Rose   Frontiers in Genetics

Repression of long non-coding RNA MEG3 restores nerve growth and alleviates neurological impairment after cerebral ischemia-reperfusion injury in a rat model

(2019) Dong You et al.   BIOMEDICINE & PHARMACOTHERAPY

A novel role of U1 snRNP: Splice site selection from a distance

(2019) Ravindra N. Singh et al.   Biochimica et Biophysica Acta-Gene Regulatory Mechanisms

Targeting the MALAT1/PARP1/LIG3 complex induces DNA damage and apoptosis in multiple myeloma

(2018) Yi Hu et al.   LEUKEMIA

The evolution of posttranscriptional regulation

(2018) Bernhard Schaefke et al.   Wiley Interdisciplinary Reviews-RNA

LncRNA MEG3 impacts proliferation, invasion, and migration of ovarian cancer cells through regulating PTEN

(2018) Juelan Wang et al.   INFLAMMATION RESEARCH

Long noncoding RNA MEG3 inhibits proliferation and migration but induces autophagy by regulation of Sirt7 and PI3K/AKT/mTOR pathway in glioma cells

(2018) Dong-Hui Xu et al.   JOURNAL OF CELLULAR BIOCHEMISTRY

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

(2018) Lina Ma et al.   NUCLEIC ACIDS RESEARCH

PANTHER version 14: more genomes, a new PANTHER GO-slim and improvements in enrichment analysis tools

(2018) Huaiyu Mi et al.   NUCLEIC ACIDS RESEARCH

GENCODE reference annotation for the human and mouse genomes

(2018) Adam Frankish et al.   NUCLEIC ACIDS RESEARCH

The Gene Ontology Resource: 20 years and still GOing strong

(2018)   NUCLEIC ACIDS RESEARCH

Splicing of long non-coding RNAs primarily depends on polypyrimidine tract and 5′ splice-site sequences due to weak interactions with SR proteins

(2018) Zuzana Krchňáková et al.   NUCLEIC ACIDS RESEARCH

High-confidence coding and noncoding transcriptome maps

(2017) Bo-Hyun You et al.   GENOME RESEARCH

LncRNA SOX2-OT is a novel prognostic biomarker for osteosarcoma patients and regulates osteosarcoma cells proliferation and motility through modulating SOX2

(2017) Zhi Wang et al.   IUBMB LIFE

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

(2017) Chung-Chau Hon et al.   NATURE

High-throughput annotation of full-length long noncoding RNAs with capture long-read sequencing

(2017) Julien Lagarde et al.   NATURE GENETICS

Salmon provides fast and bias-aware quantification of transcript expression

(2017) Rob Patro et al.   NATURE METHODS

NONCODEV5: a comprehensive annotation database for long non-coding RNAs

(2017) ShuangSang Fang et al.   NUCLEIC ACIDS RESEARCH

The Dimensions, Dynamics, and Relevance of the Mammalian Noncoding Transcriptome

(2017) Ira W. Deveson et al.   TRENDS IN GENETICS

The New RNA World: Growing Evidence for Long Noncoding RNA Functionality

(2017) Allison Jandura et al.   TRENDS IN GENETICS

The long non-coding RNA NEAT1 is responsive to neuronal activity and is associated with hyperexcitability states

(2017) Guy Barry et al.   Scientific Reports

How do lncRNAs regulate transcription?

(2017) Yicheng Long et al.   Science Advances

Divergent lncRNAs Regulate Gene Expression and Lineage Differentiation in Pluripotent Cells

(2016) Sai Luo et al.   Cell Stem Cell

Chromatin environment, transcriptional regulation, and splicing distinguish lincRNAs and mRNAs

(2016) Marta Melé et al.   GENOME RESEARCH

Transcription of the non-coding RNA upperhand controls Hand2 expression and heart development

(2016) Kelly M. Anderson et al.   NATURE

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

(2016) Jesse M. Engreitz et al.   NATURE

p53 induces formation of NEAT1 lncRNA-containing paraspeckles that modulate replication stress response and chemosensitivity

(2016) Carmen Adriaens et al.   NATURE MEDICINE

Alternative splicing and the evolution of phenotypic novelty

(2016) Stephen J. Bush et al.   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

The Spliceosome: The Ultimate RNA Chaperone and Sculptor

(2016) Panagiotis Papasaikas et al.   TRENDS IN BIOCHEMICAL SCIENCES

Extension of human lncRNA transcripts by RACE coupled with long-read high-throughput sequencing (RACE-Seq)

(2016) Julien Lagarde et al.   Nature Communications

Evolutionary clues in lncRNAs

(2016) Anne Nitsche et al.   Wiley Interdisciplinary Reviews-RNA

The landscape of long noncoding RNAs in the human transcriptome

(2015) Matthew K Iyer et al.   NATURE GENETICS

The BioMart community portal: an innovative alternative to large, centralized data repositories

(2015) Damian Smedley et al.   NUCLEIC ACIDS RESEARCH

Comparison of splice sites reveals that long noncoding RNAs are evolutionarily well conserved

(2015) Anne Nitsche et al.   RNA

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

(2015) et al.   SCIENCE

Principles of Long Noncoding RNA Evolution Derived from Direct Comparison of Transcriptomes in 17 Species

(2015) Hadas Hezroni et al.   Cell Reports

Bidirectional promoters are the major source of gene activation-associated non-coding RNAs in mammals

(2014) Masahiro Uesaka et al.   BMC GENOMICS

Conservation in first introns is positively associated with the number of exons within genes and the presence of regulatory epigenetic signals

(2014) Seung Park et al.   BMC GENOMICS

Purifying Selection on Splice-Related Motifs, Not Expression Level nor RNA Folding, Explains Nearly All Constraint on Human lincRNAs

(2014) Andreas Schüler et al.   MOLECULAR BIOLOGY AND EVOLUTION

A comprehensive survey of non-canonical splice sites in the human transcriptome

(2014) Guillermo E. Parada et al.   NUCLEIC ACIDS RESEARCH

Long non-coding RNA-dependent transcriptional regulation in neuronal development and disease

(2014) Brian S. Clark et al.   Frontiers in Genetics

A meta-analysis of the genomic and transcriptomic composition of complex life

(2013) Gangiang Liu et al.   CELL CYCLE

Promoter directionality is controlled by U1 snRNP and polyadenylation signals

(2013) Albert E. Almada et al.   NATURE

Long non-coding RNAs: new players in cell differentiation and development

(2013) Alessandro Fatica et al.   NATURE REVIEWS GENETICS

Divergent transcription of long noncoding RNA/mRNA gene pairs in embryonic stem cells

(2013) A. A. Sigova et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

U1 snRNP Determines mRNA Length and Regulates Isoform Expression

(2012) Michael G. Berg et al.   CELL

Deep sequencing of subcellular RNA fractions shows splicing to be predominantly co-transcriptional in the human genome but inefficient for lncRNAs

(2012) H. Tilgner et al.   GENOME RESEARCH

The GENCODE v7 catalog of human long noncoding RNAs: Analysis of their gene structure, evolution, and expression

(2012) T. Derrien et al.   GENOME RESEARCH

LNCipedia: a database for annotated human lncRNA transcript sequences and structures

(2012) Pieter-Jan Volders et al.   NUCLEIC ACIDS RESEARCH

Airn Transcriptional Overlap, But Not Its lncRNA Products, Induces Imprinted Igf2r Silencing

(2012) P. A. Latos et al.   SCIENCE

First Exon Length Controls Active Chromatin Signatures and Transcription

(2012) Nicole I. Bieberstein et al.   Cell Reports

Integrative annotation of human large intergenic noncoding RNAs reveals global properties and specific subclasses

(2011) M. N. Cabili et al.   GENES & DEVELOPMENT

Compensatory signals associated with the activation of human GC 5′ splice sites

(2011) Jana Kralovicova et al.   NUCLEIC ACIDS RESEARCH

Genetic variations regulate alternative splicing in the 5' untranslated regions of the mouse glioma-associated oncogene 1, Gli1

(2010) Ramesh Palaniswamy et al.   BMC MOLECULAR BIOLOGY

Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources

(2009) Da Wei Huang et al.   Nature Protocols

To localize or not to localize: mRNA fate is in 3′UTR ends

(2009) Catia Andreassi et al.   TRENDS IN CELL BIOLOGY

Accumulation of GC donor splice signals in mammals

(2008) Alexander Churbanov et al.   Biology Direct

Two wobble-splicing events affect ING4 protein subnuclear localization and degradation

(2008) K TSAI et al.   EXPERIMENTAL CELL RESEARCH