Human Cytomegalovirus Infection Elicits Global Changes in Host Transcription by RNA Polymerases I, II, and III

Manipulation of RNA polymerase III by Herpes Simplex Virus-1

(2022) Sarah E. Dremel et al.   Nature Communications

Differences in RNA polymerase II complexes and their interactions with surrounding chromatin on human and cytomegalovirus genomes

(2022) Benjamin M. Spector et al.   Nature Communications

tRNA-derived fragments (tRFs): establishing their turf in post-transcriptional gene regulation

(2021) Srikar Krishna et al.   CELLULAR AND MOLECULAR LIFE SCIENCES

High-resolution quantitative profiling of tRNA abundance and modification status in eukaryotes by mim-tRNAseq

(2021) Andrew Behrens et al.   MOLECULAR CELL

Inhibition of Host Gene Expression by KSHV: Sabotaging mRNA Stability and Nuclear Export

(2021) Carissa Ikka Pardamean et al.   Frontiers in Cellular and Infection Microbiology

Two distinct mechanisms of RNA polymerase II elongation stimulation in vivo

(2021) Kristina Žumer et al.   MOLECULAR CELL

Cytomegalovirus late transcription factor target sequence diversity orchestrates viral early to late transcription

(2021) Ming Li et al.   PLoS Pathogens

RNA decay during gammaherpesvirus infection reduces RNA polymerase II occupancy of host promoters but spares viral promoters

(2020) Ella Hartenian et al.   PLoS Pathogens

Evaluating Enhancer Function and Transcription

(2020) Andrew Field et al.   Annual Review of Biochemistry

Gene-Specific Control of tRNA Expression by RNA Polymerase II

(2020) Alan Gerber et al.   MOLECULAR CELL

Human cytomegalovirus IE2 drives transcription initiation from a select subset of late infection viral promoters by host RNA polymerase II

(2020) Ming Li et al.   PLoS Pathogens

A unified view of the sequence and functional organization of the human RNA polymerase II promoter

(2020) Donal S Luse et al.   NUCLEIC ACIDS RESEARCH

Quantitative tRNA-sequencing uncovers metazoan tissue-specific tRNA regulation

(2020) Otis Pinkard et al.   Nature Communications

Alteration of the Premature tRNA Landscape by Gammaherpesvirus Infection

(2020) Jessica M. Tucker et al.   mBio

The chromatin landscape of the ribosomal RNA genes in mouse and human

(2019) Tom Moss et al.   CHROMOSOME RESEARCH

Nucleotide Resolution Comparison of Transcription of Human Cytomegalovirus and Host Genomes Reveals Universal Use of RNA Polymerase II Elongation Control Driven by Dissimilar Core Promoter Elements

(2019) Mrutyunjaya Parida et al.   mBio

Use of the nuclear walk-on methodology to determine sites of RNA polymerase II initiation and pausing and quantify nascent RNAs in cells

(2019) Christopher B. Ball et al.   METHODS

A key anti-viral protein, RSAD2/VIPERIN, restricts the release of measles virus from infected cells

(2019) Cheyne Kurokawa et al.   VIRUS RESEARCH

How to Recruit the Correct RNA Polymerase? Lessons from snRNA Genes

(2019) Oleksandr Dergai et al.   TRENDS IN GENETICS

Interferon-Stimulated Genes: What Do They All Do?

(2019) John W. Schoggins   Annual Review of Virology

Human cytomegalovirus induces and exploits Roquin to counteract the IRF1-mediated antiviral state

(2019) Jaewon Song et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Herpes simplex viral nucleoprotein creates a competitive transcriptional environment facilitating robust viral transcription and host shut off

(2019) Sarah E Dremel et al.   eLife

RNA Polymerase II Promoter-Proximal Pausing and Release to Elongation Are Key Steps Regulating Herpes Simplex Virus 1 Transcription

(2019) Claire H. Birkenheuer et al.   JOURNAL OF VIROLOGY

Signaling to and from the RNA Polymerase III Transcription and Processing Machinery

(2018) Ian M. Willis et al.   Annual Review of Biochemistry

Modifications and functional genomics of human transfer RNA

(2018) Tao Pan   CELL RESEARCH

Born to run: control of transcription elongation by RNA polymerase II

(2018) Fei Xavier Chen et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Remodeling mTORC1 Responsiveness to Amino Acids by the Herpes Simplex Virus UL46 and Us3 Gene Products Supports Replication during Nutrient Insufficiency

(2018) Elizabeth I. Vink et al.   JOURNAL OF VIROLOGY

Regulatory Networks Involving STATs, IRFs, and NFκB in Inflammation

(2018) Ekaterini Platanitis et al.   Frontiers in Immunology

CDK9 and SPT5 proteins are specifically required for expression of herpes simplex virus 1 replication-dependent late genes

(2017) Zhiyuan Zhao et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Determinants of Histone H3K4 Methylation Patterns

(2017) Luis M. Soares et al.   MOLECULAR CELL

Oxidative stress rapidly stabilizes promoter-proximal paused Pol II across the human genome

(2017) Kyle A. Nilson et al.   NUCLEIC ACIDS RESEARCH

YAMAT-seq: an efficient method for high-throughput sequencing of mature transfer RNAs

(2017) Megumi Shigematsu et al.   NUCLEIC ACIDS RESEARCH

Transcriptional Regulation of Antiviral Interferon-Stimulated Genes

(2017) Wenshi Wang et al.   TRENDS IN MICROBIOLOGY

Characterizing Expression and Processing of Precursor and Mature Human tRNAs by Hydro-tRNAseq and PAR-CLIP

(2017) Tasos Gogakos et al.   Cell Reports

A Deconvolution Protocol for ChIP-Seq Reveals Analogous Enhancer Structures on the Mouse and Human Ribosomal RNA Genes

(2017) Jean-Clement Mars et al.   G3-Genes Genomes Genetics

A unique enhancer boundary complex on the mouse ribosomal RNA genes persists after loss of Rrn3 or UBF and the inactivation of RNA polymerase I transcription

(2017) Chelsea Herdman et al.   PLoS Genetics

Transcription by RNA polymerase III: insights into mechanism and regulation

(2016) Tomasz W. Turowski et al.   BIOCHEMICAL SOCIETY TRANSACTIONS

Human Cytomegalovirus pTRS1 and pIRS1 Antagonize Protein Kinase R To Facilitate Virus Replication

(2016) Benjamin Ziehr et al.   JOURNAL OF VIROLOGY

Analysis of computational footprinting methods for DNase sequencing experiments

(2016) Eduardo G Gusmao et al.   NATURE METHODS

Base-pair-resolution genome-wide mapping of active RNA polymerases using precision nuclear run-on (PRO-seq)

(2016) Dig Bijay Mahat et al.   Nature Protocols

Tuberous Sclerosis Complex Protein 2-Independent Activation of mTORC1 by Human Cytomegalovirus pUL38

(2015) Yadan Bai et al.   JOURNAL OF VIROLOGY

Broad H3K4me3 is associated with increased transcription elongation and enhancer activity at tumor-suppressor genes

(2015) Kaifu Chen et al.   NATURE GENETICS

Efficient and quantitative high-throughput tRNA sequencing

(2015) Guanqun Zheng et al.   NATURE METHODS

Getting up to speed with transcription elongation by RNA polymerase II

(2015) Iris Jonkers et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Selective Recruitment of Nuclear Factors to Productively Replicating Herpes Simplex Virus Genomes

(2015) Jill A. Dembowski et al.   PLoS Pathogens

Enrichr: interactive and collaborative HTML5 gene list enrichment analysis tool

(2013) Edward Y Chen et al.   BMC BIOINFORMATICS

A unique nucleosome arrangement, maintained actively by chromatin remodelers facilitates transcription of yeast tRNA genes

(2013) Yatendra Kumar et al.   BMC GENOMICS

H3K4me3 Interactions with TAF3 Regulate Preinitiation Complex Assembly and Selective Gene Activation

(2013) Shannon M. Lauberth et al.   CELL

Nucleosome maps of the human cytomegalovirus genome reveal a temporal switch in chromatin organization linked to a major IE protein

(2013) E. Zalckvar et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Selective degradation of mRNAs by the HSV host shutoff RNase is regulated by the UL47 tegument protein

(2013) M. Shu et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Precise Maps of RNA Polymerase Reveal How Promoters Direct Initiation and Pausing

(2013) H. Kwak et al.   SCIENCE

Transcription termination by the eukaryotic RNA polymerase III

(2012) Aneeshkumar G. Arimbasseri et al.   Biochimica et Biophysica Acta-Gene Regulatory Mechanisms

Coordination of late gene transcription of human cytomegalovirus with viral DNA synthesis: recombinant viruses as potential therapeutic vaccine candidates

(2012) Hiroki Isomura et al.   EXPERT OPINION ON THERAPEUTIC TARGETS

INTERFEROME v2.0: an updated database of annotated interferon-regulated genes

(2012) Irina Rusinova et al.   NUCLEIC ACIDS RESEARCH

The Battle over mTOR: An Emerging Theatre in Host–Pathogen Immunity

(2012) Sunil Martin et al.   PLoS Pathogens

Transcription by RNA polymerase III: more complex than we thought

(2011) Robert J. White   NATURE REVIEWS GENETICS

BEDTools: a flexible suite of utilities for comparing genomic features

(2010) Aaron R. Quinlan et al.   BIOINFORMATICS

Constitutive mTORC1 activation by a herpesvirus Akt surrogate stimulates mRNA translation and viral replication

(2010) U. Chuluunbaatar et al.   GENES & DEVELOPMENT

mTORC1 Directly Phosphorylates and Regulates Human MAF1

(2010) A. A. Michels et al.   MOLECULAR AND CELLULAR BIOLOGY

mTOR associates with TFIIIC, is found at tRNA and 5S rRNA genes, and targets their repressor Maf1

(2010) T. Kantidakis et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Human Cytomegalovirus Protein UL38 Inhibits Host Cell Stress Responses by Antagonizing the Tuberous Sclerosis Protein Complex

(2008) Nathaniel J. Moorman et al.   Cell Host & Microbe

Regulation of RNA Polymerase III Transcription by Maf1 in Mammalian Cells

(2008) Sarah J. Goodfellow et al.   JOURNAL OF MOLECULAR BIOLOGY

Role of cdk9 in the Optimization of Expression of the Genes Regulated by ICP22 of Herpes Simplex Virus 1

(2008) L. O. Durand et al.   JOURNAL OF VIROLOGY