Beyond ribosome biogenesis: noncoding nucleolar RNAs in physiology and tumor biology

Precise transcript targeting by CRISPR-Csm complexes

(2023) David Colognori et al.   NATURE BIOTECHNOLOGY

Long non-coding RNAs: definitions, functions, challenges and recommendations

(2023) John S. Mattick et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Regulation of ribosomal RNA gene copy number, transcription and nucleolus organization in eukaryotes

(2023) Yutaro Hori et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

The p-Arms of Human Acrocentric Chromosomes Play by a Different Set of Rules

(2023) Brian McStay   Annual Review of Genomics and Human Genetics

SnapShot: Eukaryotic ribosome biogenesis I

(2023) Ed Hurt et al.   CELL

Methods and applications for single-cell and spatial multi-omics

(2023) Katy Vandereyken et al.   NATURE REVIEWS GENETICS

The technological landscape and applications of single-cell multi-omics

(2023) Alev Baysoy et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Nucleolus assembly impairment leads to two-cell transcriptional repression via NPM1-mediated PRC2 recruitment

(2023) Dingfeng Li et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

LncRNA miR663AHG represses the development of colon cancer in a miR663a-dependent manner

(2023) Hongfan Yuan et al.   Cell Death Discovery

Ribosome biogenesis: a central player in cancer metastasis and therapeutic resistance

(2022) Amr R. Elhamamsy et al.   CANCER RESEARCH

Exploring the expanding universe of small RNAs

(2022) Junchao Shi et al.   NATURE CELL BIOLOGY

The complete sequence of a human genome

(2022) Sergey Nurk et al.   SCIENCE

snoRNAs: functions and mechanisms in biological processes, and roles in tumor pathophysiology

(2022) Zheng-hao Huang et al.   Cell Death Discovery

Beyond rRNA: nucleolar transcription generates a complex network of RNAs with multiple roles in maintaining cellular homeostasis

(2022) Shuang Feng et al.   GENES & DEVELOPMENT

snoDB 2.0: an enhanced interactive database, specializing in human snoRNAs

(2022) Danny Bergeron et al.   NUCLEIC ACIDS RESEARCH

RNADisease v4.0: an updated resource of RNA-associated diseases, providing RNA-disease analysis, enrichment and prediction

(2022) Jia Chen et al.   NUCLEIC ACIDS RESEARCH

Targeting the nucleolus as a therapeutic strategy in human disease

(2022) Alba Corman et al.   TRENDS IN BIOCHEMICAL SCIENCES

The nucleolus is the site for inflammatory RNA decay during infection

(2022) Taeyun A. Lee et al.   Nature Communications

The snoRNA-like lncRNA LNC-SNO49AB drives leukemia by activating the RNA-editing enzyme ADAR1

(2022) Wei Huang et al.   Cell Discovery

Emerging roles and mechanisms of miR-206 in human disorders: a comprehensive review

(2022) Sheyda Khalilian et al.   Cancer Cell International

LncBook 2.0: integrating human long non-coding RNAs with multi-omics annotations

(2022) Zhao Li et al.   NUCLEIC ACIDS RESEARCH

Mutual dependency between lncRNA LETN and protein NPM1 in controlling the nucleolar structure and functions sustaining cell proliferation

(2021) Xianteng Wang et al.   CELL RESEARCH

Ectopic expression of pericentric HSATII RNA results in nuclear RNA accumulation, MeCP2 recruitment, and cell division defects

(2021) Catherine C. Landers et al.   CHROMOSOMA

RNALocate v2.0: an updated resource for RNA subcellular localization with increased coverage and annotation

(2021) Tianyu Cui et al.   NUCLEIC ACIDS RESEARCH

lncRNA SLERT controls phase separation of FC/DFCs to facilitate Pol I transcription

(2021) Man Wu et al.   SCIENCE

A novel lncRNA Discn fine-tunes replication protein A (RPA) availability to promote genomic stability

(2021) Lin Wang et al.   Nature Communications

RNA promotes the formation of spatial compartments in the nucleus

(2021) Sofia A. Quinodoz et al.   CELL

Hybridization-proximity labeling reveals spatially ordered interactions of nuclear RNA compartments

(2021) Karen Yap et al.   MOLECULAR CELL

MirGeneDB 2.1: toward a complete sampling of all major animal phyla

(2021) Bastian Fromm et al.   NUCLEIC ACIDS RESEARCH

MicroRNAs and long non-coding RNAs as novel regulators of ribosome biogenesis

(2020) Mason A. McCool et al.   BIOCHEMICAL SOCIETY TRANSACTIONS

The EZH2-PHACTR2-AS1-ribosome axis induces genomic instability and promotes growth and metastasis in breast cancer

(2020) Wenhui Chu et al.   CANCER RESEARCH

Repetitive RNAs as Regulators of Chromatin-Associated Subcompartment Formation by Phase Separation

(2020) Lukas Frank et al.   JOURNAL OF MOLECULAR BIOLOGY

Super-resolution in situ analysis of active ribosomal DNA chromatin organization in the nucleolus

(2020) Andreas Maiser et al.   Scientific Reports

The nucleolus as a multiphase liquid condensate

(2020) Denis L. J. Lafontaine et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

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

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

LncRNA EPB41L4A-AS1 regulates glycolysis and glutaminolysis by mediating nucleolar translocation of HDAC2

(2019) Meijian Liao et al.   EBioMedicine

An estimate of the total number of true human miRNAs

(2019) Julia Alles et al.   NUCLEIC ACIDS RESEARCH

Lnc-TALC promotes O6-methylguanine-DNA methyltransferase expression via regulating the c-Met pathway by competitively binding with miR-20b-3p

(2019) Pengfei Wu et al.   Nature Communications

Nascent Pre-rRNA Sorting via Phase Separation Drives the Assembly of Dense Fibrillar Components in the Human Nucleolus

(2019) Run-Wen Yao et al.   MOLECULAR CELL

Cancer‑related long noncoding RNAs show aberrant expression profiles and competing endogenous RNA potential in esophageal adenocarcinoma

(2019) Yang Yu et al.   Oncology Letters

The long non-coding RNA HOXB-AS3 regulates ribosomal RNA transcription in NPM1-mutated acute myeloid leukemia

(2019) Dimitrios Papaioannou et al.   Nature Communications

Metazoan MicroRNAs

(2018) David P. Bartel   CELL

Dynamic regulation of nucleolar architecture

(2018) Attila Németh et al.   CURRENT OPINION IN CELL BIOLOGY

MiCEE is a ncRNA-protein complex that mediates epigenetic silencing and nucleolar organization

(2018) Indrabahadur Singh et al.   NATURE GENETICS

Variation in human chromosome 21 ribosomal RNA genes characterized by TAR cloning and long-read sequencing

(2018) Jung-Hyun Kim et al.   NUCLEIC ACIDS RESEARCH

Activity dependent LoNA regulates translation by coordinating rRNA transcription and methylation

(2018) Dingfeng Li et al.   Nature Communications

Identification of differential expressed lncRNAs in human thyroid cancer by a genome-wide analyses

(2018) Wei Lu et al.   Cancer Medicine

A genome-wide analysis of long noncoding RNA profile identifies differentially expressed lncRNAs associated with Esophageal cancer

(2018) Wenjia Liu et al.   Cancer Medicine

Regulation of microRNA biogenesis and its crosstalk with other cellular pathways

(2018) Thomas Treiber et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

A Short Tandem Repeat-Enriched RNA Assembles a Nuclear Compartment to Control Alternative Splicing and Promote Cell Survival

(2018) Karen Yap et al.   MOLECULAR CELL

HMDD v3.0: a database for experimentally supported human microRNA–disease associations

(2018) Zhou Huang et al.   NUCLEIC ACIDS RESEARCH

LNCipedia 5: towards a reference set of human long non-coding RNAs

(2018) Pieter-Jan Volders et al.   NUCLEIC ACIDS RESEARCH

Small Nucleolar RNAs Tell a Different Tale

(2018) Joanna Kufel et al.   TRENDS IN GENETICS

Targeted CRISPR disruption reveals a role for RNase MRP RNA in human preribosomal RNA processing

(2017) Katherine C. Goldfarb et al.   GENES & DEVELOPMENT

LncATLAS database for subcellular localization of long noncoding RNAs

(2017) David Mas-Ponte et al.   RNA

Demethylated HSATII DNA and HSATII RNA Foci Sequester PRC1 and MeCP2 into Cancer-Specific Nuclear Bodies

(2017) Lisa L. Hall et al.   Cell Reports

MicroRNA in Control of Gene Expression: An Overview of Nuclear Functions

(2016) Caterina Catalanotto et al.   INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

Unusual Processing Generates SPA LncRNAs that Sequester Multiple RNA Binding Proteins

(2016) Huang Wu et al.   MOLECULAR CELL

Circular non-coding RNA ANRIL modulates ribosomal RNA maturation and atherosclerosis in humans

(2016) Lesca M. Holdt et al.   Nature Communications

Human Ribosomal RNA-Derived Resident MicroRNAs as the Transmitter of Information upon the Cytoplasmic Cancer Stress

(2016) Masaru Yoshikawa et al.   Biomed Research International

Alu element-containing RNAs maintain nucleolar structure and function

(2015) M. Caudron-Herger et al.   EMBO JOURNAL

Quiescence-Induced LncRNAs Trigger H4K20 Trimethylation and Transcriptional Silencing

(2014) Holger Bierhoff et al.   MOLECULAR CELL

7SL RNA represses p53 translation by competing with HuR

(2014) Kotb Abdelmohsen et al.   NUCLEIC ACIDS RESEARCH

RNA-Seq of the Nucleolus Reveals Abundant SNORD44-Derived Small RNAs

(2014) Baoyan Bai et al.   PLoS One

pRNA

(2014) Stefanie Wehner et al.   RNA Biology

A mRNA and Cognate MicroRNAs Localize in the Nucleolus

(2014) Pablo Reyes-Gutierrez et al.   Nucleus

Small RNA expression and deep sequencing analyses of the nucleolus reveal the presence of nucleolus-associated microRNAs

(2014) Baoyan Bai et al.   FEBS Open Bio

The shared genomic architecture of human nucleolar organizer regions

(2013) I. Floutsakou et al.   GENOME RESEARCH

The Cancer Genome Atlas Pan-Cancer analysis project

(2013) John N Weinstein et al.   NATURE GENETICS

Profiling and Identification of Small rDNA-Derived RNAs and Their Potential Biological Functions

(2013) Haibin Wei et al.   PLoS One

Dynamic Localisation of Mature MicroRNAs in Human Nucleoli is Influenced by Exogenous Genetic Materials

(2013) Zhou Fang Li et al.   PLoS One

Deep sequencing of subcellular RNA fractions shows splicing to be predominantly co-transcriptional in the human genome but inefficient for lncRNAs

(2012) H. Tilgner et al.   GENOME RESEARCH

Long Noncoding RNAs with snoRNA Ends

(2012) Qing-Fei Yin et al.   MOLECULAR CELL

Immobilization of Proteins in the Nucleolus by Ribosomal Intergenic Spacer Noncoding RNA

(2012) Timothy E. Audas et al.   MOLECULAR CELL

Landscape of transcription in human cells

(2012) Sarah Djebali et al.   NATURE

The liquid drop nature of nucleoli

(2012) John F. Marko   Nucleus

Identification of piRNAs in Hela cells by massive parallel sequencing

(2011) Yilu Lu et al.   BMB Reports

Aberrant Overexpression of Satellite Repeats in Pancreatic and Other Epithelial Cancers

(2011) D. T. Ting et al.   SCIENCE

Genome organization in and around the nucleolus

(2011) Attila Németh et al.   TRENDS IN GENETICS

Chemotherapeutic Drugs Inhibit Ribosome Biogenesis at Various Levels

(2010) Kaspar Burger et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

International network of cancer genome projects

(2010) Thomas J. Hudson (Chairperson) et al.   NATURE

Human box C/D snoRNAs with miRNA like functions: expanding the range of regulatory RNAs

(2010) Markus Brameier et al.   NUCLEIC ACIDS RESEARCH

Initial Genomics of the Human Nucleolus

(2010) Attila Németh et al.   PLoS Genetics

BioNumbers—the database of key numbers in molecular and cell biology

(2009) Ron Milo et al.   NUCLEIC ACIDS RESEARCH

Small RNAs derived from snoRNAs

(2009) R. J. Taft et al.   RNA

MicroRNAs with a nucleolar location

(2009) J. C. Ritland Politz et al.   RNA

A Human snoRNA with MicroRNA-Like Functions

(2008) Christine Ender et al.   MOLECULAR CELL

miChip: an array-based method for microRNA expression profiling using locked nucleic acid capture probes

(2008) Mirco Castoldi et al.   Nature Protocols