Epigenetic regulation of human non-coding RNA gene transcription

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

(2021) Andrew Behrens et al.   MOLECULAR CELL

Splicing-associated chromatin signatures: a combinatorial and position-dependent role for histone marks in splicing definition

(2021) E. Agirre et al.   Nature Communications

Investigating the Potential Roles of SINEs in the Human Genome

(2021) Xiao-Ou Zhang et al.   Annual Review of Genomics and Human Genetics

How many tRNAs are out there?

(2021) David Wiener et al.   MOLECULAR CELL

The Ribosomal Gene Loci—The Power behind the Throne

(2021) Konstantin I. Panov et al.   Genes

Epigenetic Regulation of MicroRNA Clusters and Families during Tumor Development

(2021) Jana Gregorova et al.   Cancers

Retrotransposons as Drivers of Mammalian Brain Evolution

(2021) Roberto Ferrari et al.   Life-Basel

RNA polymerase II speed: a key player in controlling and adapting transcriptome composition

(2021) Lisa Muniz et al.   EMBO JOURNAL

DIANA-miTED: a microRNA tissue expression database

(2021) Ioannis Kavakiotis et al.   NUCLEIC ACIDS RESEARCH

Antagonising Chromatin Remodelling Activities in the Regulation of Mammalian Ribosomal Transcription

(2021) Kanwal Tariq et al.   Genes

The Role of rDNA Clusters in Global Epigenetic Gene Regulation

(2021) Nickolai A. Tchurikov et al.   Frontiers in Genetics

RNA promotes the formation of spatial compartments in the nucleus

(2021) Sofia A. Quinodoz et al.   CELL

Xist nucleates local protein gradients to propagate silencing across the X chromosome

(2021) Yolanda Markaki et al.   CELL

miRNATissueAtlas2: an update to the human miRNA tissue atlas

(2021) Andreas Keller et al.   NUCLEIC ACIDS RESEARCH

Pol3Base: a resource for decoding the interactome, expression, evolution, epitranscriptome and disease variations of Pol III-transcribed ncRNAs

(2021) Li Cai et al.   NUCLEIC ACIDS RESEARCH

Dual-initiation promoters with intertwined canonical and TCT/TOP transcription start sites diversify transcript processing

(2020) Chirag Nepal et al.   Nature Communications

Small nucleolar RNAs: continuing identification of novel members and increasing diversity of their molecular mechanisms of action

(2020) Danny Bergeron et al.   BIOCHEMICAL SOCIETY TRANSACTIONS

The expanding regulatory mechanisms and cellular functions of circular RNAs

(2020) Ling-Ling Chen   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Nucleolar RNA polymerase II drives ribosome biogenesis

(2020) Karan J. Abraham et al.   NATURE

Functional Long Non-coding RNAs Evolve from Junk Transcripts

(2020) Alexander F. Palazzo et al.   CELL

The ubiquitous transcriptional protein ZNF143 activates a diversity of genes while assisting to organize chromatin structure

(2020) Laura Huning et al.   GENE

Implication of a new function of human tDNAs in chromatin organization

(2020) Yuki Iwasaki et al.   Scientific Reports

The Crosstalk Between Epigenetic Mechanisms and Alternative RNA Processing Regulation

(2020) Jian Zhang et al.   Frontiers in Genetics

Gene regulation by long non-coding RNAs and its biological functions

(2020) Luisa Statello et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

GENCODE 2021

(2020) Adam Frankish et al.   NUCLEIC ACIDS RESEARCH

Circular RNA: an important player with multiple facets to regulate its parental gene expression

(2020) Tong Shao et al.   Molecular Therapy-Nucleic Acids

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

(2019) Tom Moss et al.   CHROMOSOME RESEARCH

Alu RNA Modulates the Expression of Cell Cycle Genes in Human Fibroblasts

(2019) Simona Cantarella et al.   INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

Nucleolus and rRNA Gene Chromatin in Early Embryo Development

(2019) Jelena Kresoja-Rakic et al.   TRENDS IN GENETICS

Genome-wide analysis of polymerase III–transcribed Alu elements suggests cell-type–specific enhancer function

(2019) Xiao-Ou Zhang et al.   GENOME RESEARCH

The biogenesis, biology and characterization of circular RNAs

(2019) Lasse S. Kristensen et al.   NATURE REVIEWS GENETICS

TFIIIC Binding to Alu Elements Controls Gene Expression via Chromatin Looping and Histone Acetylation

(2019) Roberto Ferrari et al.   MOLECULAR CELL

snoDB: an interactive database of human snoRNA sequences, abundance and interactions

(2019) Philia Bouchard-Bourelle et al.   NUCLEIC ACIDS RESEARCH

Predicting transfer RNA gene activity from sequence and genome context

(2019) Bryan P. Thornlow et al.   GENOME RESEARCH

Functional diversity of small nucleolar RNAs

(2019) Tomaž Bratkovič et al.   NUCLEIC ACIDS RESEARCH

DNA methylation directs microRNA biogenesis in mammalian cells

(2019) Ohad Glaich et al.   Nature Communications

Regulation of tRNA gene transcription by the chromatin structure and nucleosome dynamics

(2018) Ashutosh Shukla et al.   Biochimica et Biophysica Acta-Gene Regulatory Mechanisms

Non-coding RNAs, epigenetics, and cancer: tying it all together

(2018) Humberto J. Ferreira et al.   CANCER AND METASTASIS REVIEWS

Metazoan MicroRNAs

(2018) David P. Bartel   CELL

lncRNA PAPAS tethered to the rDNA enhancer recruits hypophosphorylated CHD4/NuRD to repress rRNA synthesis at elevated temperatures

(2018) Zhongliang Zhao et al.   GENES & DEVELOPMENT

nc886 is induced by TGF-β and suppresses the microRNA pathway in ovarian cancer

(2018) Ji-Hye Ahn et al.   Nature Communications

Circular RNA CpG island hypermethylation-associated silencing in human cancer

(2018) Humberto J. Ferreira et al.   Oncotarget

Human transposable elements in Repbase: genomic footprints from fish to humans

(2018) Kenji K. Kojima   Mobile DNA

Transfer RNA genes experience exceptionally elevated mutation rates

(2018) Bryan P. Thornlow et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

PIWI-interacting RNAs: small RNAs with big functions

(2018) Deniz M. Ozata et al.   NATURE REVIEWS GENETICS

miRBase: from microRNA sequences to function

(2018) Ana Kozomara et al.   NUCLEIC ACIDS RESEARCH

Host Noncoding Retrotransposons Induced by DNA Viruses: a SINE of Infection?

(2017) Jessica M. Tucker et al.   JOURNAL OF VIROLOGY

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

(2017) Julien Lagarde et al.   NATURE GENETICS

The Diversity of Long Noncoding RNAs and Their Generation

(2017) Huang Wu et al.   TRENDS IN GENETICS

Epigenetic regulation of noncoding RNA transcription by mammalian RNA polymerase III

(2017) Jong-Lyul Park et al.   Epigenomics

Enhancer SINEs Link Pol III to Pol II Transcription in Neurons

(2017) Cristina Policarpi et al.   Cell Reports

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

(2017) Tasos Gogakos et al.   Cell Reports

Regulation of expression of human RNA polymerase II-transcribed snRNA genes

(2017) Joana Guiro et al.   Open Biology

Nucleosome Positioning and NDR Structure at RNA Polymerase III Promoters

(2017) Alexandra Søgaard Helbo et al.   Scientific Reports

tRNA biology in the omics era: Stress signalling dynamics and cancer progression

(2016) Andrea Orioli   BIOESSAYS

Long Noncoding RNAs in Cancer Pathways

(2016) Adam M. Schmitt et al.   CANCER CELL

Divergent lncRNAs Regulate Gene Expression and Lineage Differentiation in Pluripotent Cells

(2016) Sai Luo et al.   Cell Stem Cell

Whole-genome expression analysis of mammalian-wide interspersed repeat elements in human cell lines

(2016) Davide Carnevali et al.   DNA RESEARCH

A Portrait of Ribosomal DNA Contacts with Hi-C Reveals 5S and 45S rDNA Anchoring Points in the Folded Human Genome

(2016) Shoukai Yu et al.   Genome Biology and Evolution

The epigenetic landscape ofAlurepeats delineates the structural and functional genomic architecture of colon cancer cells

(2016) Mireia Jordà et al.   GENOME RESEARCH

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

(2016) Marta Melé et al.   GENOME RESEARCH

Enhancers as non-coding RNA transcription units: recent insights and future perspectives

(2016) Wenbo Li et al.   NATURE REVIEWS GENETICS

The molecular hallmarks of epigenetic control

(2016) C. David Allis et al.   NATURE REVIEWS GENETICS

An updated human snoRNAome

(2016) Hadi Jorjani et al.   NUCLEIC ACIDS RESEARCH

Cajal bodies are linked to genome conformation

(2016) Qiuyan Wang et al.   Nature Communications

Identifying and functionally characterizing tissue-specific and ubiquitously expressed human lncRNAs

(2016) Chunjie Jiang et al.   Oncotarget

The Biogenesis of Nascent Circular RNAs

(2016) Yang Zhang et al.   Cell Reports

Decreased long noncoding RNA SPRY4-IT1 contributing to gastric cancer cell metastasis partly via affecting epithelial–mesenchymal transition

(2015) Min Xie et al.   Journal of Translational Medicine

U6 snRNA Pseudogenes: Markers of Retrotransposition Dynamics in Mammals

(2015) Aurélien J. Doucet et al.   MOLECULAR BIOLOGY AND EVOLUTION

Histone exchange, chromatin structure and the regulation of transcription

(2015) Swaminathan Venkatesh et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

The B-WICH chromatin-remodelling complex regulates RNA polymerase III transcription by promoting Max-dependent c-Myc binding

(2015) Fatemeh Sadeghifar et al.   NUCLEIC ACIDS RESEARCH

PRC2 regulates RNA polymerase III transcribed non-translated RNA gene transcription through EZH2 and SUZ12 interaction with TFIIIC complex

(2015) Chang Liu et al.   NUCLEIC ACIDS RESEARCH

Concerted copy number variation balances ribosomal DNA dosage in human and mouse genomes

(2015) John G. Gibbons et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The domain structure and distribution of Alu elements in long noncoding RNAs and mRNAs

(2015) Eugene Z. Kim et al.   RNA

SINE transcription by RNA polymerase III is suppressed by histone methylation but not by DNA methylation

(2015) Dhaval Varshney et al.   Nature Communications

Comprehensive analysis of human small RNA sequencing data provides insights into expression profiles and miRNA editing

(2015) Jing Gong et al.   RNA Biology

ZNF143 provides sequence specificity to secure chromatin interactions at gene promoters

(2015) Swneke D. Bailey et al.   Nature Communications

lncRNA Maturation to Initiate Heterochromatin Formation in the Nucleolus Is Required for Exit from Pluripotency in ESCs

(2014) Nataša Savić et al.   Cell Stem Cell

MeCP2 Suppresses Nuclear MicroRNA Processing and Dendritic Growth by Regulating the DGCR8/Drosha Complex

(2014) Tian-Lin Cheng et al.   DEVELOPMENTAL CELL

microRNA-34b/con chromosome 11q23 is aberrantly methylated in chronic lymphocytic leukemia

(2014) Stefan Deneberg et al.   Epigenetics

circRNA Biogenesis Competes with Pre-mRNA Splicing

(2014) Reut Ashwal-Fluss et al.   MOLECULAR CELL

Quiescence-Induced LncRNAs Trigger H4K20 Trimethylation and Transcriptional Silencing

(2014) Holger Bierhoff et al.   MOLECULAR CELL

Identification of RNA polymerase III-transcribed Alu loci by computational screening of RNA-Seq data

(2014) Anastasia Conti et al.   NUCLEIC ACIDS RESEARCH

Epigenetic regulation of transcription by RNA polymerase III

(2013) Purnima Bhargava   Biochimica et Biophysica Acta-Gene Regulatory Mechanisms

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

(2013) Yatendra Kumar et al.   BMC GENOMICS

Epigenetic modulation of the miR-200 family is associated with transition to a breast cancer stem-cell-like state

(2013) Y.-Y. Lim et al.   JOURNAL OF CELL SCIENCE

Functional roles of enhancer RNAs for oestrogen-dependent transcriptional activation

(2013) Wenbo Li et al.   NATURE

Human snRNA genes use polyadenylation factors to promote efficient transcription termination

(2013) Dawn O’Reilly et al.   NUCLEIC ACIDS RESEARCH

Regulation of several androgen-induced genes through the repression of the miR-99a/let-7c/miR-125b-2 miRNA cluster in prostate cancer cells

(2013) D Sun et al.   ONCOGENE

Identification of RNA polymerase III-transcribed genes in eukaryotic genomes

(2012) Giorgio Dieci et al.   Biochimica et Biophysica Acta-Gene Regulatory Mechanisms

Epigenetic control of RNA polymerase I transcription in mammalian cells

(2012) Ingrid Grummt et al.   Biochimica et Biophysica Acta-Gene Regulatory Mechanisms

Regulation of Human RNA Polymerase III Transcription by DNMT1 and DNMT3a DNA Methyltransferases

(2012) Tharakeswari Selvakumar et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Landscape of transcription in human cells

(2012) Sarah Djebali et al.   NATURE

Novel Insights into DNA Methylation Features in Spermatozoa: Stability and Peculiarities

(2012) Csilla Krausz et al.   PLoS One

Epigenetic Disruption of the PIWI Pathway in Human Spermatogenic Disorders

(2012) Holger Heyn et al.   PLoS One

The chromatin remodeling complex NuRD establishes the poised state of rRNA genes characterized by bivalent histone modifications and altered nucleosome positions

(2012) W. Xie et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

CpG island hypermethylation-associated silencing of small nucleolar RNAs in human cancer

(2012) Humberto J. Ferreira et al.   RNA Biology

Nucleolar Association and Transcriptional Inhibition through 5S rDNA in Mammals

(2012) Andrew M. Fedoriw et al.   PLoS Genetics

Human tRNA genes function as chromatin insulators

(2011) Jesse R Raab et al.   EMBO JOURNAL

RNA polymerase III transcription control elements: Themes and variations

(2011) Andrea Orioli et al.   GENE

Extra-transcriptional functions of RNA Polymerase III complexes: TFIIIC as a potential global chromatin bookmark

(2011) David Donze   GENE

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

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

Transcription by RNA polymerase III: more complex than we thought

(2011) Robert J. White   NATURE REVIEWS GENETICS

PIWI-interacting small RNAs: the vanguard of genome defence

(2011) Mikiko C. Siomi et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Yeast H2A.Z, FACT complex and RSC regulate transcription of tRNA gene through differential dynamics of flanking nucleosomes

(2011) Sahasransu Mahapatra et al.   NUCLEIC ACIDS RESEARCH

The Chromatin Remodelling Complex B-WICH Changes the Chromatin Structure and Recruits Histone Acetyl-Transferases to Active rRNA Genes

(2011) Anna Vintermist et al.   PLoS One

Precursor miR-886, a novel noncoding RNA repressed in cancer, associates with PKR and modulates its activity

(2011) K. Lee et al.   RNA

SINEs

(2011) Dmitri A. Kramerov et al.   Wiley Interdisciplinary Reviews-RNA

Alu elements: know the SINEs

(2011) Prescott Deininger   GENOME BIOLOGY

The NoRC complex mediates the heterochromatin formation and stability of silent rRNA genes and centromeric repeats

(2010) Claudio Guetg et al.   EMBO JOURNAL

Defining the RNA polymerase III transcriptome: Genome-wide localization of the RNA polymerase III transcription machinery in human cells

(2010) D. Canella et al.   GENOME RESEARCH

Pol II and its associated epigenetic marks are present at Pol III–transcribed noncoding RNA genes

(2010) Artem Barski et al.   NATURE STRUCTURAL & MOLECULAR 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

FACT facilitates chromatin transcription by RNA polymerases I and III

(2009) Joanna L Birch et al.   EMBO JOURNAL

Intergenic transcripts originating from a subclass of ribosomal DNA repeats silence ribosomal RNA genes in trans

(2009) Raffaella Santoro et al.   EMBO REPORTS

Eukaryotic snoRNAs: A paradigm for gene expression flexibility

(2009) Giorgio Dieci et al.   GENOMICS

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

Epigenetic Silencing of MicroRNA-34b/c and B-Cell Translocation Gene 4 Is Associated with CpG Island Methylation in Colorectal Cancer

(2008) M. Toyota et al.   CANCER RESEARCH

Dynamic Regulation of Nucleosome Positioning in the Human Genome

(2008) Dustin E. Schones et al.   CELL

The structure of NoRC-associated RNA is crucial for targeting the chromatin remodelling complex NoRC to the nucleolus

(2008) Christine Mayer et al.   EMBO REPORTS

Most mammalian mRNAs are conserved targets of microRNAs

(2008) R. C. Friedman et al.   GENOME RESEARCH

Different Functional Modes of p300 in Activation of RNA Polymerase III Transcription from Chromatin Templates

(2008) C. Mertens et al.   MOLECULAR AND CELLULAR BIOLOGY