4.8 Article

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

Related references

Note: Only part of the references are listed.
Article Biochemistry & Molecular Biology

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

Francesco Neri et al.

MOLECULAR AND CELLULAR BIOLOGY (2012)

Article Biochemistry & Molecular Biology

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

Hadas Hezroni et al.

JOURNAL OF BIOLOGICAL CHEMISTRY (2011)

Article Multidisciplinary Sciences

lincRNAs act in the circuitry controlling pluripotency and differentiation

Mitchell Guttman et al.

NATURE (2011)

Article Multidisciplinary Sciences

Global quantification of mammalian gene expression control

Bjoern Schwanhaeusser et al.

NATURE (2011)

Review Cell Biology

Open chromatin in pluripotency and reprogramming

Alexandre Gaspar-Maia et al.

NATURE REVIEWS MOLECULAR CELL BIOLOGY (2011)

Article Biochemistry & Molecular Biology

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

Sergio Fernandes de Almeida et al.

NATURE STRUCTURAL & MOLECULAR BIOLOGY (2011)

Article Biochemistry & Molecular Biology

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

Xue-hai Liang et al.

NUCLEIC ACIDS RESEARCH (2011)

Article Biochemistry & Molecular Biology

seqMINER: an integrated ChIP-seq data interpretation platform

Tao Ye et al.

NUCLEIC ACIDS RESEARCH (2011)

Article Genetics & Heredity

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

Christine M. Williamson et al.

PLOS GENETICS (2011)

Article Biotechnology & Applied Microbiology

Genomewide characterization of non-polyadenylated RNAs

Li Yang et al.

GENOME BIOLOGY (2011)

Article Biochemistry & Molecular Biology

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

Shivendra Kishore et al.

HUMAN MOLECULAR GENETICS (2010)

Article Biochemistry & Molecular Biology

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

Andrew J. Oler et al.

NATURE STRUCTURAL & MOLECULAR BIOLOGY (2010)

Article Multidisciplinary Sciences

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

Jia Qian Wu et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2010)

Article Multidisciplinary Sciences

Long Noncoding RNA as Modular Scaffold of Histone Modification Complexes

Miao-Chih Tsai et al.

SCIENCE (2010)

Article Biochemical Research Methods

Infernal 1.0: inference of RNA alignments

Eric P. Nawrocki et al.

BIOINFORMATICS (2009)

Review Biochemistry & Molecular Biology

Pre-mRNA Processing Reaches Back to Transcription and Ahead to Translation

Melissa J. Moore et al.

Article Biochemical Research Methods

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

Da Wei Huang et al.

NATURE PROTOCOLS (2009)

Article Biochemistry & Molecular Biology

Nucleosome positioning as a determinant of exon recognition

Hagen Tilgner et al.

NATURE STRUCTURAL & MOLECULAR BIOLOGY (2009)

Article Biochemistry & Molecular Biology

Chromatin organization marks exon-intron structure

Schraga Schwartz et al.

NATURE STRUCTURAL & MOLECULAR BIOLOGY (2009)

Article Biochemistry & Molecular Biology

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

Toutai Mituyama et al.

NUCLEIC ACIDS RESEARCH (2009)

Article Multidisciplinary Sciences

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

Ahmad M. Khalil et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2009)

Article Biotechnology & Applied Microbiology

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

Arun K. Ramani et al.

GENOME BIOLOGY (2009)

Article Biotechnology & Applied Microbiology

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

Ben Langmead et al.

GENOME BIOLOGY (2009)

Article Biotechnology & Applied Microbiology

Genome-wide analysis of antisense transcription with Affymetrix exon array

Xijin Ge et al.

BMC GENOMICS (2008)

Article Biochemistry & Molecular Biology

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

Jeremy E. Wilusz et al.

Review Biochemistry & Molecular Biology

Stem cells, the molecular circuitry of pluripotency and nuclear reprogramming

Rudolf Jaenisch et al.

News Item Cell & Tissue Engineering

Global transcription in pluripotent embryonic stem cells

Sol Efroni et al.

CELL STEM CELL (2008)

Article Cell Biology

Functional integration of transcriptional and RNA processing machineries

Shatakshi Pandit et al.

CURRENT OPINION IN CELL BIOLOGY (2008)

Article Biochemical Research Methods

Stem cell transcriptome profiling via massive-scale mRNA sequencing

Nicole Cloonan et al.

NATURE METHODS (2008)

Review Genetics & Heredity

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

William F. Marzluff et al.

NATURE REVIEWS GENETICS (2008)

Article Multidisciplinary Sciences

Poly A- Transcripts Expressed in HeLa Cells

Qingfa Wu et al.

PLOS ONE (2008)

Article Multidisciplinary Sciences

The Antisense Transcriptomes of Human Cells

Yiping He et al.

SCIENCE (2008)

Review Genetics & Heredity

The expanding RNA polymerase III transcriptome

Giorgio Dieci et al.

TRENDS IN GENETICS (2007)

Article Biochemistry & Molecular Biology

Mapping the C-elegans noncoding transcriptome with a whole-genome tiling microarray

Housheng He et al.

GENOME RESEARCH (2007)

Article Multidisciplinary Sciences

Genome-wide maps of chromatin state in pluripotent and lineage-committed cells

Tarjei S. Mikkelsen et al.

NATURE (2007)

Article Biochemistry & Molecular Biology

U12DB: a database of orthologous U12-type spliceosomal introns

Tyler S. Alioto

NUCLEIC ACIDS RESEARCH (2007)

Review Biochemistry & Molecular Biology

The relationship between non-protein-coding DNA and eukaryotic complexity

Ryan J. Taft et al.

BIOESSAYS (2007)

Article Biochemistry & Molecular Biology

Distinct pathways for snoRNA and mRNA termination

Minkyu Kim et al.

MOLECULAR CELL (2006)

Article Biochemistry & Molecular Biology

The abundance of the spliceosomal snRNPs is not limiting the splicing of U12-type introns

Heli K. J. Pessa et al.

Article Biochemistry & Molecular Biology

Comprehensive splice-site analysis using comparative genomics

Nihar Sheth et al.

NUCLEIC ACIDS RESEARCH (2006)

Article Multidisciplinary Sciences

The transcriptional landscape of the mammalian genome

P Carninci et al.

SCIENCE (2005)

Article Multidisciplinary Sciences

Antisense transcription in the mammalian transcriptome

S Katayama et al.

SCIENCE (2005)

Article Biochemistry & Molecular Biology

Splicing of a rare class of introns by the U12-dependent spliceosome

CL Will et al.

BIOLOGICAL CHEMISTRY (2005)

Article Biochemistry & Molecular Biology

Evolutionarily conserved elements in vertebrate, insect, worm, and yeast genomes

A Siepel et al.

GENOME RESEARCH (2005)

Article Biochemistry & Molecular Biology

Kinefold web server for RNA/DNA folding path and structure prediction including pseudoknots and knots

A Xayaphoummine et al.

NUCLEIC ACIDS RESEARCH (2005)

Article Multidisciplinary Sciences

Transcriptional maps of 10 human chromosomes at 5-nucleotide resolution

J Cheng et al.

SCIENCE (2005)

Article Biochemistry & Molecular Biology

Applications of DNA tiling arrays to experimental genome annotation and regulatory pathway discovery

P Bertone et al.

CHROMOSOME RESEARCH (2005)

Article Biochemistry & Molecular Biology

Novel RNAs identified from an in-depth analysis of the transcriptome of human chromosomes 21 and 22

D Kampa et al.

GENOME RESEARCH (2004)

Article Multidisciplinary Sciences

Global identification of human transcribed sequences with genome tiling arrays

P Bertone et al.

SCIENCE (2004)

Article Biochemistry & Molecular Biology

Identification of putative noncoding RNAs among the RIKEN mouse full-length cDNA collection

K Numata et al.

GENOME RESEARCH (2003)

Article Biotechnology & Applied Microbiology

Widespread occurrence of antisense transcription in the human genome

R Yelin et al.

NATURE BIOTECHNOLOGY (2003)

Article Biochemistry & Molecular Biology

Rfam: an RNA family database

S Griffiths-Jones et al.

NUCLEIC ACIDS RESEARCH (2003)

Article Biochemistry & Molecular Biology

The splicing of U12-type introns can be a rate-limiting step in gene expression

AA Patel et al.

EMBO JOURNAL (2002)

Review Biochemistry & Molecular Biology

Antisense-RNA regulation and RNA interference

S Brantl

BIOCHIMICA ET BIOPHYSICA ACTA-GENE STRUCTURE AND EXPRESSION (2002)

Article Multidisciplinary Sciences

Large-scale transcriptional activity in chromosomes 21 and 22

P Kapranov et al.

SCIENCE (2002)

Article Biotechnology & Applied Microbiology

Efficient generation of midbrain and hindbrain neurons from mouse embryonic stem cells

SH Lee et al.

NATURE BIOTECHNOLOGY (2000)