Circular RNAs drive oncogenic chromosomal translocations within the MLL recombinome in leukemia

The RNA interactome in the Hallmarks of Cancer

(2023) Marta M. Gabryelska et al.   Wiley Interdisciplinary Reviews-RNA

Best practice standards for circular RNA research

(2022) Anne F. Nielsen et al.   NATURE METHODS

Subtype-specific 3D genome alteration in acute myeloid leukaemia

(2022) Jie Xu et al.   NATURE

Linking circular intronic RNA degradation and function in transcription by RNase H1

(2021) Xiang Li et al.   Science China-Life Sciences

Proteasome Inhibition Attenuates Self-Renewal in Human Acute Myeloid Leukemia By Targeting NF-Kappa B in Leukemia Stem Cells

(2021) Marie Lue Antony et al.   BLOOD

Targeting Mitochondria-Located circRNA SCAR Alleviates NASH via Reducing mROS Output

(2020) Qiyi Zhao et al.   CELL

CircRNA inhibits DNA damage repair by interacting with host gene

(2020) Xiaolong Xu et al.   Molecular Cancer

IL-13 secreted by ILC2s promotes the self-renewal of intestinal stem cells through circular RNA circPan3

(2019) Pingping Zhu et al.   NATURE IMMUNOLOGY

CircRNAs Are Here to Stay: A Perspective on the MLL Recombinome

(2019) Anna Dal Molin et al.   Frontiers in Genetics

Tyrosine kinase c-Abl couples RNA polymerase II transcription to DNA double-strand breaks

(2019) Kaspar Burger et al.   NUCLEIC ACIDS RESEARCH

The Landscape of Circular RNA in Cancer

(2019) Josh N. Vo et al.   CELL

Widespread and Functional RNA Circularization in Localized Prostate Cancer

(2019) Sujun Chen et al.   CELL

Release of paused RNA polymerase II at specific loci favors DNA double-strand-break formation and promotes cancer translocations

(2019) Gaetano Ivan Dellino et al.   NATURE GENETICS

SplintQuant: A method for accurately quantifying circular RNA transcript abundance without reverse transcription bias

(2019) Vanessa M. Conn et al.   RNA

Developing novel methods to image and visualize 3D genomes

(2018) Tszshan Ma et al.   CELL BIOLOGY AND TOXICOLOGY

miR‐200/375 control epithelial plasticity‐associated alternative splicing by repressing the RNA‐binding protein Quaking

(2018) Katherine A Pillman et al.   EMBO JOURNAL

A length-dependent evolutionarily conserved pathway controls nuclear export of circular RNAs

(2018) Chuan Huang et al.   GENES & DEVELOPMENT

3D FISH to analyse gene domain-specific chromatin re-modeling in human cancer cell lines

(2018) Silvia Kocanova et al.   METHODS

Profiling and functional analysis of circular RNAs in acute promyelocytic leukemia and their dynamic regulation during all-trans retinoic acid treatment

(2018) Shufen Li et al.   Cell Death & Disease

Clinker: visualizing fusion genes detected in RNA-seq data

(2018) Breon M Schmidt et al.   GigaScience

The emerging role of circular RNAs in transcriptome regulation

(2017) S. Huang et al.   GENOMICS

Wanted DEAD/H or Alive: Helicases Winding Up in Cancers

(2017) Wanpei Cai et al.   JNCI-Journal of the National Cancer Institute

The MLL recombinome of acute leukemias in 2017

(2017) C Meyer et al.   LEUKEMIA

R-ChIP Using Inactive RNase H Reveals Dynamic Coupling of R-loops with Transcriptional Pausing at Gene Promoters

(2017) Liang Chen et al.   MOLECULAR CELL

WebGestalt 2017: a more comprehensive, powerful, flexible and interactive gene set enrichment analysis toolkit

(2017) Jing Wang et al.   NUCLEIC ACIDS RESEARCH

Circular RNAs in cancer: opportunities and challenges in the field

(2017) L S Kristensen et al.   ONCOGENE

Proteasome expression and activity in cancer and cancer stem cells

(2017) Ioannis A Voutsadakis   TUMOR BIOLOGY

BLISS is a versatile and quantitative method for genome-wide profiling of DNA double-strand breaks

(2017) Winston X. Yan et al.   Nature Communications

Defining the location of promoter-associated R-loops at near-nucleotide resolution using bisDRIP-seq

(2017) Jason G Dumelie et al.   eLife

Wanted DEAD/H or Alive: Helicases Winding Up in Cancers

(2017) Wanpei Cai et al.   JNCI-Journal of the National Cancer Institute

Oncogenic Role of Fusion-circRNAs Derived from Cancer-Associated Chromosomal Translocations

(2016) Jlenia Guarnerio et al.   CELL

Diverse alternative back-splicing and alternative splicing landscape of circular RNAs

(2016) Xiao-Ou Zhang et al.   GENOME RESEARCH

Prevalent, Dynamic, and Conserved R-Loop Structures Associate with Specific Epigenomic Signatures in Mammals

(2016) Lionel A. Sanz et al.   MOLECULAR CELL

Organization and function of the 3D genome

(2016) Boyan Bonev et al.   NATURE REVIEWS GENETICS

COSMIC: somatic cancer genetics at high-resolution

(2016) Simon A. Forbes et al.   NUCLEIC ACIDS RESEARCH

The role of the proteasome in AML

(2016) C M Csizmar et al.   Blood Cancer Journal

Systematic Classification of Mixed-Lineage Leukemia Fusion Partners Predicts Additional Cancer Pathways

(2016) Rolf Marschalek   Annals of Laboratory Medicine

Native Elongating Transcript Sequencing Reveals Human Transcriptional Activity at Nucleotide Resolution

(2015) Andreas Mayer et al.   CELL

The RNA Binding Protein Quaking Regulates Formation of circRNAs

(2015) Simon J. Conn et al.   CELL

The Yin and Yang of R-loop biology

(2015) Lorenzo Costantino et al.   CURRENT OPINION IN CELL BIOLOGY

The Fanconi Anemia Pathway Maintains Genome Stability by Coordinating Replication and Transcription

(2015) Rebekka A. Schwab et al.   MOLECULAR CELL

In vivo genome editing using Staphylococcus aureus Cas9

(2015) F. Ann Ran et al.   NATURE

R loops: new modulators of genome dynamics and function

(2015) José M. Santos-Pereira et al.   NATURE REVIEWS GENETICS

Exon-intron circular RNAs regulate transcription in the nucleus

(2015) Zhaoyong Li et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Clustering of mammalianHoxgenes with other H3K27me3 targets within an active nuclear domain

(2015) Maxence Vieux-Rochas et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Somatic mutation in cancer and normal cells

(2015) I. Martincorena et al.   SCIENCE

Breaking bad: R-loops and genome integrity

(2015) Julie Sollier et al.   TRENDS IN CELL BIOLOGY

Exon-intron circular RNAs regulate transcription in the nucleus

(2015) Zhaoyong Li et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Mutagenesis by AID: Being in the Right Place at the Right Time

(2015) Cristina Rada   PLoS Genetics

Fanconi anemia and the development of leukemia

(2014) Blanche P. Alter   BEST PRACTICE & RESEARCH CLINICAL HAEMATOLOGY

Sushi.R: flexible, quantitative and integrative genomic visualizations for publication-quality multi-panel figures

(2014) D. H. Phanstiel et al.   BIOINFORMATICS

RNA Clamping by Vasa Assembles a piRNA Amplifier Complex on Transposon Transcripts

(2014) Jordi Xiol et al.   CELL

A double-edged sword: R loops as threats to genome integrity and powerful regulators of gene expression

(2014) K. Skourti-Stathaki et al.   GENES & DEVELOPMENT

circRNA Biogenesis Competes with Pre-mRNA Splicing

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

R-loops induce repressive chromatin marks over mammalian gene terminators

(2014) Konstantina Skourti-Stathaki et al.   NATURE

Mechanisms underlying mutational signatures in human cancers

(2014) Thomas Helleday et al.   NATURE REVIEWS GENETICS

Genome-Wide Distribution of RNA-DNA Hybrids Identifies RNase H Targets in tRNA Genes, Retrotransposons and Mitochondria

(2014) Aziz El Hage et al.   PLoS Genetics

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

(2013) Y. Liao et al.   BIOINFORMATICS

Acquired Mutations That Affect Pre-mRNA Splicing in Hematologic Malignancies and Solid Tumors

(2013) L. M. Scott et al.   JNCI-Journal of the National Cancer Institute

R Loops Are Linked to Histone H3 S10 Phosphorylation and Chromatin Condensation

(2013) Maikel Castellano-Pozo et al.   MOLECULAR CELL

APOBEC3B is an enzymatic source of mutation in breast cancer

(2013) Michael B. Burns et al.   NATURE

Natural RNA circles function as efficient microRNA sponges

(2013) Thomas B. Hansen et al.   NATURE

Circular RNAs are a large class of animal RNAs with regulatory potency

(2013) Sebastian Memczak et al.   NATURE

Nucleotide-resolution DNA double-strand break mapping by next-generation sequencing

(2013) Nicola Crosetto et al.   NATURE METHODS

From pseudo-ceRNAs to circ-ceRNAs: a tale of cross-talk and competition

(2013) Riccardo Taulli et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

WEB-based GEne SeT AnaLysis Toolkit (WebGestalt): update 2013

(2013) Jing Wang et al.   NUCLEIC ACIDS RESEARCH

Identification of an Enhancer That Increases miR-200b~200a~429 Gene Expression in Breast Cancer Cells

(2013) Joanne L. Attema et al.   PLoS One

Etoposide Induces Nuclear Re-Localisation of AID

(2013) Laurens J. Lambert et al.   PLoS One

R-loop formation atSnord116mediates topotecan inhibition ofUbe3a-antisenseand allele-specific chromatin decondensation

(2013) Weston T. Powell et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

A Circuitous Route to Noncoding RNA

(2013) J. E. Wilusz et al.   SCIENCE

R-Loop Stabilization Represses Antisense Transcription at the Arabidopsis FLC Locus

(2013) Q. Sun et al.   SCIENCE

STAR: ultrafast universal RNA-seq aligner

(2012) Alexander Dobin et al.   BIOINFORMATICS

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

(2012) H. Thorvaldsdottir et al.   BRIEFINGS IN BIOINFORMATICS

Prognostic significance of 11q23 aberrations in adult acute myeloid leukemia and the role of allogeneic stem cell transplantation

(2012) Y Chen et al.   LEUKEMIA

R-Loop Formation Is a Distinctive Characteristic of Unmethylated Human CpG Island Promoters

(2012) Paul A. Ginno et al.   MOLECULAR CELL

Circular RNAs Are the Predominant Transcript Isoform from Hundreds of Human Genes in Diverse Cell Types

(2012) Julia Salzman et al.   PLoS One

Model for MLL translocations in therapy-related leukemia involving topoisomerase II -mediated DNA strand breaks and gene proximity

(2012) I. G. Cowell et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Circular RNAs are abundant, conserved, and associated with ALU repeats

(2012) W. R. Jeck et al.   RNA

Requirement of DDX39 DEAD box RNA helicase for genome integrity and telomere protection

(2011) Hyun Hee Yoo et al.   AGING CELL

Cdc48/p97 Mediates UV-Dependent Turnover of RNA Pol II

(2011) Rati Verma et al.   MOLECULAR CELL

Pre-mRNA splicing: where and when in the nucleus

(2011) Joonhee Han et al.   TRENDS IN CELL BIOLOGY

The mechanisms regulating the subcellular localization of AID

(2011) Anne-Marie Patenaude et al.   Nucleus

BEDTools: a flexible suite of utilities for comparing genomic features

(2010) Aaron R. Quinlan et al.   BIOINFORMATICS

Activation-Induced Cytidine Deaminase Targets DNA at Sites of RNA Polymerase II Stalling by Interaction with Spt5

(2010) Rushad Pavri et al.   CELL

The molecular signature of oncofusion proteins in acute myeloid leukemia

(2010) Joost H.A. Martens et al.   FEBS LETTERS

Ubiquitin–proteasome system profiling in acute leukemias and its clinical relevance

(2010) Wanlong Ma et al.   LEUKEMIA RESEARCH

H3K79 Methylation Profiles Define Murine and Human MLL-AF4 Leukemias

(2008) Andrei V. Krivtsov et al.   CANCER CELL

Chromosomal Rearrangements Leading to MLL Gene Fusions: Clinical and Biological Aspects

(2008) D. P. Harper et al.   CANCER RESEARCH

Model-based Analysis of ChIP-Seq (MACS)

(2008) Yong Zhang et al.   GENOME BIOLOGY