4.8 Article

HIF1α-AS1 is a DNA:DNA:RNA triplex-forming lncRNA interacting with the HUSH complex

Related references

Note: Only part of the references are listed.
Review Cell Biology

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

Luisa Statello et al.

Summary: Recent studies have shed new light on the biogenesis and functions of long non-coding RNAs (lncRNAs), showcasing their diverse roles in gene regulation and signaling pathways, particularly in the contexts of neuronal disorders, immune responses, and cancer. The discovery of unique biogenesis pathways and subcellular localizations of lncRNAs has opened up potential therapeutic avenues for targeting lncRNAs in various biological and pathophysiological conditions.

NATURE REVIEWS MOLECULAR CELL BIOLOGY (2021)

Article Biochemistry & Molecular Biology

UniProt: the universal protein knowledgebase in 2021

Alex Bateman et al.

Summary: The UniProt Knowledgebase aims to provide users with a comprehensive, high-quality set of protein sequences annotated with functional information. Updates over the past two years have increased the number of sequences to approximately 190 million, with new methods to assess proteome completeness and quality. UniProtKB has responded to the COVID-19 pandemic by expertly curating relevant entries and making them rapidly available through a dedicated portal.

NUCLEIC ACIDS RESEARCH (2021)

Article Multidisciplinary Sciences

MPP8 is essential for sustaining self-renewal of ground-state pluripotent stem cells

Iris Muller et al.

Summary: Deciphering the mechanisms controlling pluripotent ground state is crucial in understanding embryonic development. MPP8, an epigenetic protein, has been identified as essential for maintaining ground-state pluripotency through repression of LINE1 elements, independent of chromatin binding or H3K9me3 levels.

NATURE COMMUNICATIONS (2021)

Article Multidisciplinary Sciences

Aging-regulated anti-apoptotic long non-coding RNA Sarrah augments recovery from acute myocardial infarction

D. Julia Trembinski et al.

NATURE COMMUNICATIONS (2020)

Article Multidisciplinary Sciences

TASOR is a pseudo-PARP that directs HUSH complex assembly and epigenetic transposon control

Christopher H. Douse et al.

NATURE COMMUNICATIONS (2020)

Review Biochemistry & Molecular Biology

The role of disorder in RNA binding affinity and specificity

Diana S. M. Ottoz et al.

OPEN BIOLOGY (2020)

Article Multidisciplinary Sciences

The HUSH complex is a gatekeeper of type I interferon through epigenetic regulation of LINE-1s

Hale Tunbak et al.

NATURE COMMUNICATIONS (2020)

Article Biochemistry & Molecular Biology

Detection of RNA-DNA binding sites in long noncoding RNAs

Chao-Chung Kuo et al.

NUCLEIC ACIDS RESEARCH (2019)

Article Multidisciplinary Sciences

DNA•RNA triple helix formation can function as a cis-acting regulatory mechanism at the human β-globin locus

Zhuo Zhou et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2019)

Article Multidisciplinary Sciences

Deciphering the complex role of thrombospondin-1 in glioblastoma development

Thomas Daubon et al.

NATURE COMMUNICATIONS (2019)

Article Biochemical Research Methods

PhenoScanner V2: an expanded tool for searching human genotype-phenotype associations

Mihir A. Kamat et al.

BIOINFORMATICS (2019)

Article Cardiac & Cardiovascular Systems

Pleiotropic effects of laminar flow and statins depend on the Kruppel-like factor-induced lncRNA MANTIS

Matthias S. Leisegang et al.

EUROPEAN HEART JOURNAL (2019)

Article Multidisciplinary Sciences

A RASSF1A-HIF1α loop drives Warburg effect in cancer and pulmonary hypertension

Swati Dabral et al.

NATURE COMMUNICATIONS (2019)

Article Biotechnology & Applied Microbiology

Long Noncoding RNA-Maternally Expressed Gene 3 Contributes to Hypoxic Pulmonary Hypertension

Yan Xing et al.

MOLECULAR THERAPY (2019)

Article Biochemistry & Molecular Biology

The PRIDE database and related tools and resources in 2019: improving support for quantification data

Yasset Perez-Riverol et al.

NUCLEIC ACIDS RESEARCH (2019)

Article Biochemistry & Molecular Biology

Isolation and genome-wide characterization of cellular DNA:RNA triplex structures

Nevcin Sentuerk Cetin et al.

NUCLEIC ACIDS RESEARCH (2019)

Article Multidisciplinary Sciences

NP220 mediates silencing of unintegrated retroviral DNA

Yiping Zhu et al.

NATURE (2018)

Article Medicine, Research & Experimental

Genome-wide computational analysis of potential long noncoding RNA mediated DNA: DNA:RNA triplexes in the human genome

Saakshi Jalali et al.

JOURNAL OF TRANSLATIONAL MEDICINE (2017)

Article Biochemical Research Methods

An improved ATAC-seq protocol reduces background and enables interrogation of frozen tissues

M. Ryan Corces et al.

NATURE METHODS (2017)

Article Biochemistry & Molecular Biology

CPC2: a fast and accurate coding potential calculator based on sequence intrinsic features

Yu-Jian Kang et al.

NUCLEIC ACIDS RESEARCH (2017)

Article Multidisciplinary Sciences

Data Descriptor: FANTOM5 CAGE profiles of human and mouse samples

Shuhei Noguchi et al.

SCIENTIFIC DATA (2017)

Article Multidisciplinary Sciences

PARTICLE triplexes cluster in the tumor suppressor WWOX and may extend throughout the human genome

Valerie Brid O'Leary et al.

SCIENTIFIC REPORTS (2017)

Review Biochemistry & Molecular Biology

Endothelial cell metabolism in health and disease: impact of hypoxia

Brian W. Wong et al.

EMBO JOURNAL (2017)

Article Cardiac & Cardiovascular Systems

Long Noncoding RNA MANTIS Facilitates Endothelial Angiogenic Function

Matthias S. Leisegang et al.

CIRCULATION (2017)

Article Biochemistry & Molecular Biology

The lncRNA HOTAIR impacts on mesenchymal stem cells via triple helix formation

Marie Kalwa et al.

NUCLEIC ACIDS RESEARCH (2016)

Review Biochemistry & Molecular Biology

RNA-DNA Triplex Formation by Long Noncoding RNAs

Yue Li et al.

CELL CHEMICAL BIOLOGY (2016)

Article Biotechnology & Applied Microbiology

Evaluation of off-target and on-target scoring algorithms and integration into the guide RNA selection tool CRISPOR

Maximilian Haeussler et al.

GENOME BIOLOGY (2016)

Review Pharmacology & Pharmacy

Eph Receptors and Ephrins: Therapeutic Opportunities

Antonio Barquilla et al.

ANNUAL REVIEW OF PHARMACOLOGY AND TOXICOLOGY, VOL 55 (2015)

Article Biochemistry & Molecular Biology

LncRNA Khps1 Regulates Expression of the Proto-oncogene SPHK1 via Triplex-Mediated Changes in Chromatin Structure

Anna Postepska-Igielska et al.

MOLECULAR CELL (2015)

Article Multidisciplinary Sciences

Genome-scale transcriptional activation by an engineered CRISPR-Cas9 complex

Silvana Konermann et al.

NATURE (2015)

Article Multidisciplinary Sciences

Epigenetic silencing by the HUSH complex mediates position-effect variegation in human cells

Iva A. Tchasovnikarova et al.

SCIENCE (2015)

Article Multidisciplinary Sciences

MEG3 long noncoding RNA regulates the TGF-β pathway genes through formation of RNA-DNA triplex structures

Tanmoy Mondal et al.

NATURE COMMUNICATIONS (2015)

Article Biotechnology & Applied Microbiology

Gateways to the FANTOM5 promoter level mammalian expression atlas

Marina Lizio et al.

GENOME BIOLOGY (2015)

Article Biochemical Research Methods

NMRFAM-SPARKY: enhanced software for biomolecular NMR spectroscopy

Woonghee Lee et al.

BIOINFORMATICS (2015)

Article Multidisciplinary Sciences

A promoter-level mammalian expression atlas

Alistair R. R. Forrest et al.

NATURE (2014)

Article Biochemistry & Molecular Biology

Pro-proliferative and inflammatory signaling converge on FoxO1 transcription factor in pulmonary hypertension

Rajkumar Savai et al.

NATURE MEDICINE (2014)

Letter Biochemical Research Methods

Improved vectors and genome-wide libraries for CRISPR screening

Neville E. Sanjana et al.

NATURE METHODS (2014)

Review Biotechnology & Applied Microbiology

Therapeutic targeting of EPH receptors and their ligands

Andrew W. Boyd et al.

NATURE REVIEWS DRUG DISCOVERY (2014)

Article Biochemistry & Molecular Biology

deepTools: a flexible platform for exploring deep-sequencing data

Fidel Ramirez et al.

NUCLEIC ACIDS RESEARCH (2014)

Article Biochemical Research Methods

STAR: ultrafast universal RNA-seq aligner

Alexander Dobin et al.

BIOINFORMATICS (2013)

Article Biochemical Research Methods

Integrative Genomics Viewer (IGV): high-performance genomics data visualization and exploration

Helga Thorvaldsdottir et al.

BRIEFINGS IN BIOINFORMATICS (2013)

Article Respiratory System

Risk factors and basic mechanisms of chronic thromboembolic pulmonary hypertension: a current understanding

Irene M. Lang et al.

EUROPEAN RESPIRATORY JOURNAL (2013)

Article Biochemical Research Methods

Kraken: A set of tools for quality control and analysis Of high-throughput sequence data

Matthew P. A. Davis et al.

METHODS (2013)

Article Biochemistry & Molecular Biology

CPAT: Coding-Potential Assessment Tool using an alignment-free logistic regression model

Liguo Wang et al.

NUCLEIC ACIDS RESEARCH (2013)

Article Biochemistry & Molecular Biology

Neurodegenerative diseases: Quantitative predictions of protein-RNA interactions

Davide Cirillo et al.

Article Biochemistry & Molecular Biology

Overexpression of the long non-coding RNA MEG3 impairs in vitro glioma cell proliferation

Pengjun Wang et al.

JOURNAL OF CELLULAR BIOCHEMISTRY (2012)

Review Cardiac & Cardiovascular Systems

Conditioning the whole heart-not just the cardiomyocyte

Robert M. Bell et al.

JOURNAL OF MOLECULAR AND CELLULAR CARDIOLOGY (2012)

Review Biochemistry & Molecular Biology

R Loops: From Transcription Byproducts to Threats to Genome Stability

Andres Aguilera et al.

MOLECULAR CELL (2012)

Article Multidisciplinary Sciences

An integrated encyclopedia of DNA elements in the human genome

Ian Dunham et al.

NATURE (2012)

Article Biochemical Research Methods

Fast gapped-read alignment with Bowtie 2

Ben Langmead et al.

NATURE METHODS (2012)

Article Biochemistry & Molecular Biology

Genomic Maps of Long Noncoding RNA Occupancy Reveal Principles of RNA-Chromatin Interactions

Ci Chu et al.

MOLECULAR CELL (2011)

Article Multidisciplinary Sciences

MPP8 mediates the interactions between DNA methyltransferase Dnmt3a and H3K9 methyltransferase GLP/G9a

Yanqi Chang et al.

NATURE COMMUNICATIONS (2011)

Article Biochemistry & Molecular Biology

High-resolution NMR structure of an RNA model system: the 14-mer cUUCGg tetraloop hairpin RNA

Senada Nozinovic et al.

NUCLEIC ACIDS RESEARCH (2010)

Article Biotechnology & Applied Microbiology

Differential expression analysis for sequence count data

Simon Anders et al.

GENOME BIOLOGY (2010)

Review Biochemistry & Molecular Biology

Ribonuclease H: the enzymes in eukaryotes

Susana M. Cerritelli et al.

FEBS JOURNAL (2009)

Article Biotechnology & Applied Microbiology

Model-based Analysis of ChIP-Seq (MACS)

Yong Zhang et al.

GENOME BIOLOGY (2008)

Article Physiology

Hyperproliferative apoptosis-resistant endothelial cells in idiopathic pulmonary arterial hypertension

Fares A. Masri et al.

AMERICAN JOURNAL OF PHYSIOLOGY-LUNG CELLULAR AND MOLECULAR PHYSIOLOGY (2007)

Review Neurosciences

Angiogenesis in brain tumours

Rakesh K. Jain et al.

NATURE REVIEWS NEUROSCIENCE (2007)

Article Biochemical Research Methods

ARIA: automated NOE assignment and NMR structure calculation

JP Linge et al.

BIOINFORMATICS (2003)

Review Biochemical Research Methods

Automated assignment of ambiguous nuclear overhauser effects with ARIA

JP Linge et al.

NUCLEAR MAGNETIC RESONANCE OF BIOLOGICAL MACROMOLECULES, PT B (2001)