Pseudogenes as Functionally Significant Elements of the Genome

Functional Classification and Experimental Dissection of Long Noncoding RNAs

(2018) Florian Kopp et al.   CELL

Nuclear functions of mammalian MicroRNAs in gene regulation, immunity and cancer

(2018) Hongyu Liu et al.   Molecular Cancer

Congenital Adrenal Hyperplasia (CAH) due to 21-Hydroxylase Deficiency: A Comprehensive Focus on 233 Pathogenic Variants of CYP21A2 Gene

(2018) Paola Concolino et al.   Molecular Diagnosis & Therapy

Classifying BRAF alterations in cancer: new rational therapeutic strategies for actionable mutations

(2018) Matthew Dankner et al.   ONCOGENE

Nuclear Long Noncoding RNAs: Key Regulators of Gene Expression

(2018) Qinyu Sun et al.   TRENDS IN GENETICS

Natural antisense transcripts in diseases: From modes of action to targeted therapies

(2018) Elżbieta Wanowska et al.   Wiley Interdisciplinary Reviews-RNA

The competing endogenous RNA network of CYP4Z1 and pseudogene CYP4Z2P exerts an anti-apoptotic function in breast cancer

(2017) Cheng Li et al.   FEBS LETTERS

LncRNA Structural Characteristics in Epigenetic Regulation

(2017) Chenguang Wang et al.   INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

Transposable Elements in Human Cancer: Causes and Consequences of Deregulation

(2017) Sumadi Anwar et al.   INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

Gene regulation of mammalian long non-coding RNA

(2017) Heeyoun Bunch   MOLECULAR GENETICS AND GENOMICS

The Pseudogene DUXAP8 Promotes Non-small-cell Lung Cancer Cell Proliferation and Invasion by Epigenetically Silencing EGR1 and RHOB

(2017) Ming Sun et al.   MOLECULAR THERAPY

Transcription start site-associated small RNAs in thePTENgene

(2017) Ji-Long Liu et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The molecular dynamics of long noncoding RNA control of transcription in PTEN and its pseudogene

(2017) Nicholas Lister et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Numtogenesis as a mechanism for development of cancer

(2017) Keshav K. Singh et al.   SEMINARS IN CANCER BIOLOGY

Protein-Coding Genes’ Retrocopies and Their Functions

(2017) Magdalena Regina Kubiak et al.   Viruses-Basel

Decreased expression of pseudogene PTENP1 promotes malignant behaviours and is associated with the poor survival of patients with HNSCC

(2017) Jiannan Liu et al.   Scientific Reports

Neuronal-expressed microRNA-targeted pseudogenes compete with coding genes in the human brain

(2017) S Barbash et al.   Translational Psychiatry

The GBAP1 pseudogene acts as a ceRNA for the glucocerebrosidase gene GBA by sponging miR-22-3p

(2017) Letizia Straniero et al.   Scientific Reports

NumtS colonization in mammalian genomes

(2017) F. M. Calabrese et al.   Scientific Reports

CircRNA-derived pseudogenes

(2016) Rui Dong et al.   CELL RESEARCH

Comparative genomics of the human, macaque and mouse major histocompatibility complex

(2016) Takashi Shiina et al.   IMMUNOLOGY

Pseudogenes regulate parental gene expressionviaceRNA network

(2016) Yang An et al.   JOURNAL OF CELLULAR AND MOLECULAR MEDICINE

Competing endogenous RNA networks of CYP4Z1 and pseudogene CYP4Z2P confer tamoxifen resistance in breast cancer

(2016) Lufeng Zheng et al.   MOLECULAR AND CELLULAR ENDOCRINOLOGY

Olfactory receptor pseudo-pseudogenes

(2016) Lucia L. Prieto-Godino et al.   NATURE

Transcription of the non-coding RNA upperhand controls Hand2 expression and heart development

(2016) Kelly M. Anderson et al.   NATURE

Endogenous microRNA sponges: evidence and controversy

(2016) Daniel W. Thomson et al.   NATURE REVIEWS GENETICS

A double-strand break can trigger immunoglobulin gene conversion

(2016) Giulia Bastianello et al.   NUCLEIC ACIDS RESEARCH

Non-coding RNAs as regulators in epigenetics

(2016) Jian-Wei Wei et al.   ONCOLOGY REPORTS

Molecular Evolution of PTEN Pseudogenes in Mammals

(2016) Jingsi Tang et al.   PLoS One

One Loop to Rule Them All: The Ping-Pong Cycle and piRNA-Guided Silencing

(2016) Benjamin Czech et al.   TRENDS IN BIOCHEMICAL SCIENCES

Inhibitory effect of RNA-mediated knockdown of zinc finger protein 91 pseudogene on pancreatic cancer cell growth and invasion

(2016) Weiyi Huang et al.   Oncology Letters

HMGA1-pseudogenes and cancer

(2016) Marco De Martino et al.   Oncotarget

PIWI-Interacting RNA: Its Biogenesis and Functions

(2015) Yuka W. Iwasaki et al.   Annual Review of Biochemistry

Pseudogenes transcribed in breast invasive carcinoma show subtype-specific expression and ceRNA potential

(2015) Joshua D Welch et al.   BMC GENOMICS

The 3′UTR of the pseudogene CYP4Z2P promotes tumor angiogenesis in breast cancer by acting as a ceRNA for CYP4Z1

(2015) Lufeng Zheng et al.   BREAST CANCER RESEARCH AND TREATMENT

The role of NANOG transcriptional factor in the development of malignant phenotype of cancer cells

(2015) Natalia Gawlik-Rzemieniewska et al.   CANCER BIOLOGY & THERAPY

The BRAF Pseudogene Functions as a Competitive Endogenous RNA and Induces Lymphoma In Vivo

(2015) Florian A. Karreth et al.   CELL

Gene Conversion Between Cationic Trypsinogen (PRSS1 ) and the Pseudogene Trypsinogen 6 (PRSS3P2 ) in Patients with Chronic Pancreatitis

(2015) Agnieszka Magdalena Rygiel et al.   HUMAN MUTATION

Circulating CUDR, LSINCT-5 and PTENP1 long noncoding RNAs in sera distinguish patients with gastric cancer from healthy controls

(2015) Lei Dong et al.   INTERNATIONAL JOURNAL OF CANCER

Are Human Translated Pseudogenes Functional?

(2015) Jinrui Xu et al.   MOLECULAR BIOLOGY AND EVOLUTION

VEGFR-1 Pseudogene Expression and Regulatory Function in Human Colorectal Cancer Cells

(2015) X. Ye et al.   MOLECULAR CANCER RESEARCH

The landscape of long noncoding RNAs in the human transcriptome

(2015) Matthew K Iyer et al.   NATURE GENETICS

From guide to target: molecular insights into eukaryotic RNA-interference machinery

(2015) Jonathan J Ipsaro et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Interaction of long noncoding RNAs and microRNAs in the pathogenesis of idiopathic pulmonary fibrosis

(2015) Chaoqun Huang et al.   PHYSIOLOGICAL GENOMICS

The small RNA content of human sperm reveals pseudogene-derived piRNAs complementary to protein-coding genes

(2015) Lorena Pantano et al.   RNA

Pseudogene-expressed RNAs: a new frontier in cancers

(2015) Xuefei Shi et al.   TUMOR BIOLOGY

Oncocers: ceRNA-mediated cross-talk by sponging miRNAs in oncogenic pathways

(2015) Sercan Ergun et al.   TUMOR BIOLOGY

Differentially-Expressed Pseudogenes in HIV-1 Infection

(2015) Aditi Gupta et al.   Viruses-Basel

From guide to target: molecular insights into eukaryotic RNA-interference machinery

(2015) Jonathan J Ipsaro et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Many lncRNAs, 5’UTRs, and pseudogenes are translated and some are likely to express functional proteins

(2015) Zhe Ji et al.   eLife

siRNA Versus miRNA as Therapeutics for Gene Silencing

(2015) Jenny K W Lam et al.   Molecular Therapy-Nucleic Acids

Functions of noncoding sequences in mammalian genomes

(2015) L. I. Patrushev et al.   BIOCHEMISTRY-MOSCOW

Retrotransposons and pseudogenes regulate mRNAs and lncRNAs via the piRNA pathway in the germline

(2014) Toshiaki Watanabe et al.   GENOME RESEARCH

Posttranscriptional Regulation of Gene Expression by Piwi Proteins and piRNAs

(2014) Toshiaki Watanabe et al.   MOLECULAR CELL

A draft map of the human proteome

(2014) Min-Sik Kim et al.   NATURE

The multilayered complexity of ceRNA crosstalk and competition

(2014) Yvonne Tay et al.   NATURE

The Pan-Cancer analysis of pseudogene expression reveals biologically and clinically relevant tumour subtypes

(2014) Leng Han et al.   Nature Communications

Processed pseudogenes acquired somatically during cancer development

(2014) Susanna L. Cooke et al.   Nature Communications

Ribosome Profiling Reveals Pervasive Translation Outside of Annotated Protein-Coding Genes

(2014) Nicholas T. Ingolia et al.   Cell Reports

Processed pseudogene insertions in somatic cells

(2014) Haig H Kazazian   Mobile DNA

Pseudogene OCT4-pg4 functions as a natural micro RNA sponge to regulate OCT4 expression by competing for miR-145 in hepatocellular carcinoma

(2013) Lei Wang et al.   CARCINOGENESIS

Pseudogenes: Pseudo or Real Functional Elements?

(2013) Wen Li et al.   Journal of Genetics and Genomics

Gene regulation by antisense transcription

(2013) Vicent Pelechano et al.   NATURE REVIEWS GENETICS

A pseudogene long-noncoding-RNA network regulates PTEN transcription and translation in human cells

(2013) Per Johnsson et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

A mammalian pseudogene lncRNA at the interface of inflammation and anti-inflammatory therapeutics

(2013) Nicole A Rapicavoli et al.   eLife

Retrotransposition of gene transcripts leads to structural variation in mammalian genomes

(2013) Adam D Ewing et al.   GENOME BIOLOGY

Mass Spectrometry–Based Proteomics and Network Biology

(2012) Ariel Bensimon et al.   Annual Review of Biochemistry

Expressed Pseudogenes in the Transcriptional Landscape of Human Cancers

(2012) Shanker Kalyana-Sundaram et al.   CELL

Olfactory Receptor Multigene Family in Vertebrates: From the Viewpoint of Evolutionary Genomics

(2012) Yoshihito Niimura   CURRENT GENOMICS

Human Nanog pseudogene8 promotes the proliferation of gastrointestinal cancer cells

(2012) Keita Uchino et al.   EXPERIMENTAL CELL RESEARCH

"Orphan" Retrogenes in the Human Genome

(2012) J. Ciomborowska et al.   MOLECULAR BIOLOGY AND EVOLUTION

Landscape of transcription in human cells

(2012) Sarah Djebali et al.   NATURE

Pseudogenes: Newly Discovered Players in Human Cancer

(2012) L. Poliseno   Science Signaling

Role of BMI1, a Stem Cell Factor, in Cancer Recurrence and Chemoresistance: Preclinical and Clinical Evidences

(2012) Hifzur Rahman Siddique et al.   STEM CELLS

Increased expression of CYP4Z1 promotes tumor angiogenesis and growth in human breast cancer

(2012) Wei Yu et al.   TOXICOLOGY AND APPLIED PHARMACOLOGY

The GENCODE pseudogene resource

(2012) Baikang Pei et al.   GENOME BIOLOGY

Identification of Hydroxysteroid (17β) dehydrogenase type 12 (HSD17B12) as a CD8+ T-cell-defined human tumor antigen of human carcinomas

(2011) Carmen Visus et al.   CANCER IMMUNOLOGY IMMUNOTHERAPY

A ceRNA Hypothesis: The Rosetta Stone of a Hidden RNA Language?

(2011) Leonardo Salmena et al.   CELL

Polymorphic NumtS trace human population relationships

(2011) Martin Lang et al.   HUMAN GENETICS

Deletion of PTENP1 Pseudogene in Human Melanoma

(2011) Laura Poliseno et al.   JOURNAL OF INVESTIGATIVE DERMATOLOGY

Genetic Diversification by Somatic Gene Conversion

(2011) Kohei Kurosawa et al.   Genes

Expression of OCT4 pseudogenes in human tumours: lessons from glioma and breast carcinoma

(2010) Shidou Zhao et al.   JOURNAL OF PATHOLOGY

Nuclear mitochondrial pseudogenes

(2010) A. I. Gaziev et al.   MOLECULAR BIOLOGY

A coding-independent function of gene and pseudogene mRNAs regulates tumour biology

(2010) Laura Poliseno et al.   NATURE

RNAi Screen Indicates Widespread Biological Function for Human Natural Antisense Transcripts

(2010) Mohammad Ali Faghihi et al.   PLoS One

Pseudogene-mediated posttranscriptional silencing of HMGA1 can result in insulin resistance and type 2 diabetes

(2010) Eusebio Chiefari et al.   Nature Communications

Identification of a 17β-hydroxysteroid dehydrogenase type 12 pseudogene as the source of a highly restricted BALB/c Meth A tumor rejection peptide

(2009) Ronald C. Hendrickson et al.   CANCER IMMUNOLOGY IMMUNOTHERAPY

MicroRNAs: Target Recognition and Regulatory Functions

(2009) David P. Bartel   CELL

Origins and Mechanisms of miRNAs and siRNAs

(2009) Richard W. Carthew et al.   CELL

Current Trends in Pseudogene Detection and Characterization

(2009) Eric Rouchka et al.   Current Bioinformatics

Connexin43 pseudogene in breast cancer cells offers a novel therapeutic target

(2009) A. Bier et al.   MOLECULAR CANCER THERAPEUTICS

Endogenous siRNAs from naturally formed dsRNAs regulate transcripts in mouse oocytes

(2008) Toshiaki Watanabe et al.   NATURE

Pseudogene-derived small interfering RNAs regulate gene expression in mouse oocytes

(2008) Oliver H. Tam et al.   NATURE

RNA-based gene duplication: mechanistic and evolutionary insights

(2008) Henrik Kaessmann et al.   NATURE REVIEWS GENETICS

Numt-Mediated Double-Strand Break Repair Mitigates Deletions during Primate Genome Evolution

(2008) Einat Hazkani-Covo et al.   PLoS Genetics