Non-polyadenylated transcription in embryonic stem cells reveals novel non-coding RNA related to pluripotency and differentiation

Regulating RNA polymerase pausing and transcription elongation in embryonic stem cells

(2011) I. M. Min et al.   GENES & DEVELOPMENT

Pluripotency-related, Valproic Acid (VPA)-induced Genome-wide Histone H3 Lysine 9 (H3K9) Acetylation Patterns in Embryonic Stem Cells

(2011) Hadas Hezroni et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Myc Regulates the Transcription of the PRC2 Gene To Control the Expression of Developmental Genes in Embryonic Stem Cells

(2011) F. Neri et al.   MOLECULAR AND CELLULAR BIOLOGY

lincRNAs act in the circuitry controlling pluripotency and differentiation

(2011) Mitchell Guttman et al.   NATURE

Global quantification of mammalian gene expression control

(2011) Björn Schwanhäusser et al.   NATURE

Splicing enhances recruitment of methyltransferase HYPB/Setd2 and methylation of histone H3 Lys36

(2011) Sérgio Fernandes de Almeida et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Genomic binding of Pol III transcription machinery and relationship with TFIIS transcription factor distribution in mouse embryonic stem cells

(2011) Lucie Carrière et al.   NUCLEIC ACIDS RESEARCH

Association of TALS Developmental Disorder with Defect in Minor Splicing Component U4atac snRNA

(2011) P. Edery et al.   SCIENCE

Mutations in U4atac snRNA, a Component of the Minor Spliceosome, in the Developmental Disorder MOPD I

(2011) H. He et al.   SCIENCE

Genomic Prevalence of Heterochromatic H3K9me2 and Transcription Do Not Discriminate Pluripotent from Terminally Differentiated Cells

(2011) Florian Lienert et al.   PLoS Genetics

Uncoupling Antisense-Mediated Silencing and DNA Methylation in the Imprinted Gnas Cluster

(2011) Christine M. Williamson et al.   PLoS Genetics

Genomewide characterization of non-polyadenylated RNAs

(2011) Li Yang et al.   GENOME BIOLOGY

A Large Intergenic Noncoding RNA Induced by p53 Mediates Global Gene Repression in the p53 Response

(2010) Maite Huarte et al.   CELL

The snoRNA MBII-52 (SNORD 115) is processed into smaller RNAs and regulates alternative splicing

(2010) Shivendra Kishore et al.   HUMAN MOLECULAR GENETICS

Large intergenic non-coding RNA-RoR modulates reprogramming of human induced pluripotent stem cells

(2010) Sabine Loewer et al.   NATURE GENETICS

Open chromatin in pluripotency and reprogramming

(2010) Alexandre Gaspar-Maia et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Human RNA polymerase III transcriptomes and relationships to Pol II promoter chromatin and enhancer-binding factors

(2010) Andrew J Oler et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Efficient and specific knockdown of small non-coding RNAs in mammalian cells and in mice

(2010) Xue-hai Liang et al.   NUCLEIC ACIDS RESEARCH

seqMINER: an integrated ChIP-seq data interpretation platform

(2010) Tao Ye et al.   NUCLEIC ACIDS RESEARCH

Digital Genome-Wide ncRNA Expression, Including SnoRNAs, across 11 Human Tissues Using PolyA-Neutral Amplification

(2010) John C. Castle et al.   PLoS One

Dynamic transcriptomes during neural differentiation of human embryonic stem cells revealed by short, long, and paired-end sequencing

(2010) J. Q. Wu et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Long Noncoding RNA as Modular Scaffold of Histone Modification Complexes

(2010) M.-C. Tsai et al.   SCIENCE

Infernal 1.0: inference of RNA alignments

(2009) E. P. Nawrocki et al.   BIOINFORMATICS

Pre-mRNA Processing Reaches Back toTranscription and Ahead to Translation

(2009) Melissa J. Moore et al.   CELL

Chromatin signature reveals over a thousand highly conserved large non-coding RNAs in mammals

(2009) Mitchell Guttman et al.   NATURE

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

(2009) Da Wei Huang et al.   Nature Protocols

Nucleosome positioning as a determinant of exon recognition

(2009) Hagen Tilgner et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Chromatin organization marks exon-intron structure

(2009) Schraga Schwartz et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Many human large intergenic noncoding RNAs associate with chromatin-modifying complexes and affect gene expression

(2009) Ahmad M. Khalil et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

High resolution transcriptome maps for wild-type and nonsense-mediated decay-defective Caenorhabditis elegans

(2009) Arun K Ramani et al.   GENOME BIOLOGY

Ultrafast and memory-efficient alignment of short DNA sequences to the human genome

(2009) Ben Langmead et al.   GENOME BIOLOGY

Profiling the HeLa S3 transcriptome using randomly primed cDNA and massively parallel short-read sequencing

(2008) Ryan D. Morin et al.   BIOTECHNIQUES

Genome-wide analysis of antisense transcription with Affymetrix exon array

(2008) Xijin Ge et al.   BMC GENOMICS

3′ End Processing of a Long Nuclear-Retained Noncoding RNA Yields a tRNA-like Cytoplasmic RNA

(2008) Jeremy E. Wilusz et al.   CELL

Stem Cells, the Molecular Circuitry of Pluripotency and Nuclear Reprogramming

(2008) Rudolf Jaenisch et al.   CELL

Global Transcription in Pluripotent Embryonic Stem Cells

(2008) Sol Efroni et al.   Cell Stem Cell

Functional integration of transcriptional and RNA processing machineries

(2008) Shatakshi Pandit et al.   CURRENT OPINION IN CELL BIOLOGY

Stem cell transcriptome profiling via massive-scale mRNA sequencing

(2008) Nicole Cloonan et al.   NATURE METHODS

Metabolism and regulation of canonical histone mRNAs: life without a poly(A) tail

(2008) William F. Marzluff et al.   NATURE REVIEWS GENETICS

The Functional RNA Database 3.0: databases to support mining and annotation of functional RNAs

(2008) T. Mituyama et al.   NUCLEIC ACIDS RESEARCH

Poly A- Transcripts Expressed in HeLa Cells

(2008) Qingfa Wu et al.   PLoS One

The Antisense Transcriptomes of Human Cells

(2008) Yiping He et al.   SCIENCE