Chromatin-sensitive cryptic promoters putatively drive expression of alternative protein isoforms in yeast

Gcn4 Binding in Coding Regions Can Activate Internal and Canonical 5′ Promoters in Yeast

(2018) Yashpal Rawal et al.   MOLECULAR CELL

Antisense transcription‐dependent chromatin signature modulates sense transcript dynamics

(2018) Thomas Brown et al.   Molecular Systems Biology

Emerging Roles of Non-Coding RNA Transcription

(2018) Minna U. Kaikkonen et al.   TRENDS IN BIOCHEMICAL SCIENCES

N-terminal acetylation levels are maintained during acetyl-CoA deficiency in Saccharomyces cerevisiae

(2018) Sylvia Varland et al.   MOLECULAR & CELLULAR PROTEOMICS

Spt6 Is Required for the Fidelity of Promoter Selection

(2018) Stephen M. Doris et al.   MOLECULAR CELL

UMI-tools: modeling sequencing errors in Unique Molecular Identifiers to improve quantification accuracy

(2017) Tom Smith et al.   GENOME RESEARCH

Discovery of noncanonical translation initiation sites through mass spectrometric analysis of protein N termini

(2017) Chan Hyun Na et al.   GENOME RESEARCH

DNMT and HDAC inhibitors induce cryptic transcription start sites encoded in long terminal repeats

(2017) David Brocks et al.   NATURE GENETICS

Alternative start and termination sites of transcription drive most transcript isoform differences across human tissues

(2017) Alejandro Reyes et al.   NUCLEIC ACIDS RESEARCH

eIF5A facilitates translation termination globally and promotes the elongation of many non polyproline-specific tripeptide sequences

(2017) Vicent Pelechano et al.   NUCLEIC ACIDS RESEARCH

From transcriptional complexity to cellular phenotypes: Lessons from yeast

(2017) Vicent Pelechano   YEAST

The Gcn4 transcription factor reduces protein synthesis capacity and extends yeast lifespan

(2017) Nitish Mittal et al.   Nature Communications

Transcription of a 5' extended mRNA isoform directs dynamic chromatin changes and interference of a downstream promoter

(2017) Minghao Chia et al.   eLife

N-Terminal Peptide Detection with Optimized Peptide-Spectrum Matching and Streamlined Sequence Libraries

(2016) Brynne E. Lycette et al.   JOURNAL OF PROTEOME RESEARCH

Positional proteomics reveals differences in N-terminal proteoform stability

(2016) D. Gawron et al.   Molecular Systems Biology

Genome-wide quantification of 5′-phosphorylated mRNA degradation intermediates for analysis of ribosome dynamics

(2016) Vicent Pelechano et al.   Nature Protocols

Selective suppression of antisense transcription by Set2-mediated H3K36 methylation

(2016) Swaminathan Venkatesh et al.   Nature Communications

Modulation of mRNA and lncRNA expression dynamics by the Set2–Rpd3S pathway

(2016) Ji Hyun Kim et al.   Nature Communications

Widespread Co-translational RNA Decay Reveals Ribosome Dynamics

(2015) Vicent Pelechano et al.   CELL

A high-throughput ChIP-Seq for large-scale chromatin studies

(2015) C. D. Chabbert et al.   Molecular Systems Biology

CAGEr: precise TSS data retrieval and high-resolution promoterome mining for integrative analyses

(2015) Vanja Haberle et al.   NUCLEIC ACIDS RESEARCH

Quality control of transcription start site selection by nonsense-mediated-mRNA decay

(2015) Christophe Malabat et al.   eLife

Alternative polyadenylation diversifies post-transcriptional regulation by selective RNA-protein interactions

(2014) I. Gupta et al.   Molecular Systems Biology

Promoter sequences direct cytoplasmic localization and translation of mRNAs during starvation in yeast

(2014) Brian M. Zid et al.   NATURE

featureCounts: an efficient general purpose program for assigning sequence reads to genomic features

(2013) Y. Liao et al.   BIOINFORMATICS

Roles for transcript leaders in translation and mRNA decay revealed by transcript leader sequencing

(2013) J. A. Arribere et al.   GENOME RESEARCH

Dealing with Pervasive Transcription

(2013) Torben Heick Jensen et al.   MOLECULAR CELL

Extensive transcriptional heterogeneity revealed by isoform profiling

(2013) Vicent Pelechano et al.   NATURE

Gene regulation by antisense transcription

(2013) Vicent Pelechano et al.   NATURE REVIEWS GENETICS

STAR: ultrafast universal RNA-seq aligner

(2012) Alexander Dobin et al.   BIOINFORMATICS

Transcription of Two Long Noncoding RNAs Mediates Mating-Type Control of Gametogenesis in Budding Yeast

(2012) Folkert J. van Werven et al.   CELL

Set3 HDAC Mediates Effects of Overlapping Noncoding Transcription on Gene Induction Kinetics

(2012) TaeSoo Kim et al.   CELL

Amino Termini of Many Yeast Proteins Map to Downstream Start Codons

(2012) Claire T. Fournier et al.   JOURNAL OF PROTEOME RESEARCH

Antisense expression increases gene expression variability and locus interdependency

(2011) Z. Xu et al.   Molecular Systems Biology

Nascent transcript sequencing visualizes transcription at nucleotide resolution

(2011) L. Stirling Churchman et al.   NATURE

Selecting protein N-terminal peptides by combined fractional diagonal chromatography

(2011) An Staes et al.   Nature Protocols

Epigenome characterization at single base-pair resolution

(2011) J. G. Henikoff et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Functional consequences of bidirectional promoters

(2011) Wu Wei et al.   TRENDS IN GENETICS

Intergenic transcription causes repression by directing nucleosome assembly

(2010) S. J. Hainer et al.   GENES & DEVELOPMENT

 40p53 controls the switch from pluripotency to differentiation by regulating IGF signaling in ESCs

(2010) E. Ungewitter et al.   GENES & DEVELOPMENT

A canonical promoter organization of the transcription machinery and its regulators in the Saccharomyces genome

(2009) B. J. Venters et al.   GENOME RESEARCH

Bidirectional promoters generate pervasive transcription in yeast

(2009) Zhenyu Xu et al.   NATURE

Widespread bidirectional promoters are the major source of cryptic transcripts in yeast

(2009) Helen Neil et al.   NATURE

The Set2/Rpd3S Pathway Suppresses Cryptic Transcription without Regard to Gene Length or Transcription Frequency

(2009) Colin R. Lickwar et al.   PLoS One

Chromatin- and Transcription-Related Factors Repress Transcription from within Coding Regions throughout the Saccharomyces cerevisiae Genome

(2008) Vanessa Cheung et al.   PLOS BIOLOGY