Protein-Coding Genes’ Retrocopies and Their Functions

Retroposition as a source of antisense long non-coding RNAs with possible regulatory functions

(2016) Oleksii Bryzghalov et al.   ACTA BIOCHIMICA POLONICA

Comparative genomic analysis of retrogene repertoire in two green algae Volvox carteri and Chlamydomonas reinhardtii

(2016) Marcin Jąkalski et al.   Biology Direct

CircRNA-derived pseudogenes

(2016) Rui Dong et al.   CELL RESEARCH

Genome-wide methylation analysis of retrocopy-associated CpG islands and their genomic environment

(2016) Katrin Grothaus et al.   Epigenetics

Identification of Multiple Forms of RNA Transcripts Associated with Human-Specific Retrotransposed Gene Copies

(2016) Saori Mori et al.   Genome Biology and Evolution

LTR-mediated retroposition as a mechanism of RNA-based duplication in metazoans

(2016) Shengjun Tan et al.   GENOME RESEARCH

The life history of retrocopies illuminates the evolution of new mammalian genes

(2016) Francesco Nicola Carelli et al.   GENOME RESEARCH

Engineered LINE-1 retrotransposition in nondividing human neurons

(2016) Angela Macia et al.   GENOME RESEARCH

Pseudogene transcripts: Participants in tumorigenicity and promising therapeutic targets

(2016) Xin Zhang et al.   LEUKEMIA RESEARCH

Retrotransposons as regulators of gene expression

(2016) R. A. Elbarbary et al.   SCIENCE

Distinct temporal changes in host cell lncRNA expression during the course of an adenovirus infection

(2016) Hongxing Zhao et al.   VIROLOGY

Evolutionary interplay between sister cytochrome P450 genes shapes plasticity in plant metabolism

(2016) Zhenhua Liu et al.   Nature Communications

SinEx DB: a database for single exon coding sequences in mammalian genomes

(2016) Roddy Jorquera et al.   Database-The Journal of Biological Databases and Curation

The Ensembl gene annotation system

(2016) Bronwen L. Aken et al.   Database-The Journal of Biological Databases and Curation

LINE-1-like retrotransposons contribute to RNA-based gene duplication in dicots

(2016) Zhenglin Zhu et al.   Scientific Reports

Expression of evolutionarily novel genes in tumors

(2016) A. P. Kozlov   Infectious Agents and Cancer

Global Intersection of Long Non-Coding RNAs with Processed and Unprocessed Pseudogenes in the Human Genome

(2016) Michael J. Milligan et al.   Frontiers in Genetics

FTH1P3, a Novel H-Ferritin Pseudogene Transcriptionally Active, Is Ubiquitously Expressed and Regulated during Cell Differentiation

(2016) Maddalena Di Sanzo et al.   PLoS One

Emergence and evolution of inter-specific segregating retrocopies in cynomolgus monkey (Macaca fascicularis) and rhesus macaque (Macaca mulatta)

(2016) Xu Zhang et al.   Scientific Reports

HMGA1P7-pseudogene regulates H19 and Igf2 expression by a competitive endogenous RNA mechanism

(2016) Marco De Martino et al.   Scientific Reports

Suppression of hepatocellular carcinoma by baculovirus-mediated expression of long non-coding RNA PTENP1 and MicroRNA regulation

(2015) Chiu-Ling Chen et al.   BIOMATERIALS

microRNA-622 acts as a tumor suppressor in hepatocellular carcinoma

(2015) Wei-Hua Song et al.   CANCER BIOLOGY & THERAPY

Primate-Specific ORF0 Contributes to Retrotransposon-Mediated Diversity

(2015) Ahmet M. Denli et al.   CELL

U6 snRNA Pseudogenes: Markers of Retrotransposition Dynamics in Mammals

(2015) Aurélien J. Doucet 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

A 3′ Poly(A) Tract Is Required for LINE-1 Retrotransposition

(2015) Aurélien J. Doucet et al.   MOLECULAR CELL

The UCSC Genome Browser database: 2016 update

(2015) Matthew L. Speir et al.   NUCLEIC ACIDS RESEARCH

Allele-Selective Transcriptome Recruitment to Polysomes Primed for Translation: Protein-Coding and Noncoding RNAs, and RNA Isoforms

(2015) Roshan Mascarenhas et al.   PLoS One

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

(2015) Lorena Pantano et al.   RNA

Pseudogene integrator complex subunit 6 pseudogene 1 (INTS6P1) as a novel plasma-based biomarker for hepatocellular carcinoma screening

(2015) Ka Yin Lui et al.   TUMOR BIOLOGY

Pseudogene-expressed RNAs: a new frontier in cancers

(2015) Xuefei Shi et al.   TUMOR BIOLOGY

Differentially-Expressed Pseudogenes in HIV-1 Infection

(2015) Aditi Gupta et al.   Viruses-Basel

Pseudogene INTS6P1 regulates its cognate gene INTS6 through competitive binding of miR-17-5p in hepatocellular carcinoma

(2015) Haoran Peng et al.   Oncotarget

Inter-population Differences in Retrogene Loss and Expression in Humans

(2015) Michał Kabza et al.   PLoS Genetics

A feedback loop between nonsense-mediated decay and the retrogene DUX4 in facioscapulohumeral muscular dystrophy

(2015) Qing Feng et al.   eLife

piRNAs from Pig Testis Provide Evidence for a Conserved Role of the Piwi Pathway in Post-Transcriptional Gene Regulation in Mammals

(2015) Daniel Gebert et al.   PLoS One

HMGA1 pseudogenes as candidate proto-oncogenic competitive endogenous RNAs

(2015) Francesco Esposito et al.   Oncotarget

Diversity through duplication: Whole-genome sequencing reveals novel gene retrocopies in the human population

(2014) Sandra R. Richardson et al.   BIOESSAYS

Retroduplication and loss of parental genes is a mechanism for the generation of intronless genes in Ciona intestinalis and Ciona savignyi

(2014) Dong Seon Kim et al.   DEVELOPMENT GENES AND EVOLUTION

The Imprinted NPAP1 Gene in the Prader–Willi Syndrome Region Belongs to a POM121-Related Family of Retrogenes

(2014) Lisa C. Neumann et al.   Genome Biology and Evolution

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

(2014) Toshiaki Watanabe et al.   GENOME RESEARCH

Primary Immunodeficiency Caused by an Exonized Retroposed Gene Copy Inserted in theCYBBGene

(2014) Martin de Boer et al.   HUMAN MUTATION

Pseudogene PTENP1 Functions as a Competing Endogenous RNA to Suppress Clear-Cell Renal Cell Carcinoma Progression

(2014) G. Yu et al.   MOLECULAR CANCER THERAPEUTICS

A draft map of the human proteome

(2014) Min-Sik Kim et al.   NATURE

Pollen-Specific Activation of Arabidopsis Retrogenes Is Associated with Global Transcriptional Reprogramming

(2014) A. Abdelsamad et al.   PLANT CELL

Profiling of extensively diversified plant LINEs reveals distinct plant-specific subclades

(2014) Tony Heitkam et al.   PLANT JOURNAL

Characterization of Human Pseudogene-Derived Non-Coding RNAs for Functional Potential

(2014) Xingyi Guo et al.   PLoS One

Small RNA profiling and characterization of piRNA clusters in the adult testes of the common marmoset, a model primate

(2014) Takamasa Hirano et al.   RNA

MiR-492 contributes to cell proliferation and cell cycle of human breast cancer cells by suppressing SOX7 expression

(2014) Fei Shen et al.   TUMOR BIOLOGY

Processed pseudogenes acquired somatically during cancer development

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

Young, intact and nested retrotransposons are abundant in the onion and asparagus genomes

(2013) C. Vitte et al.   ANNALS OF BOTANY

RCPedia: a database of retrocopied genes

(2013) Fábio C. P. Navarro et al.   BIOINFORMATICS

Frequency of intron loss correlates with processed pseudogene abundance: a novel strategy to test the reverse transcriptase model of intron loss

(2013) Tao Zhu et al.   BMC BIOLOGY

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

Defending the genome from the enemy within: mechanisms of retrotransposon suppression in the mouse germline

(2013) James H. Crichton et al.   CELLULAR AND MOLECULAR LIFE SCIENCES

Analysis of variable retroduplications in human populations suggests coupling of retrotransposition to cell division

(2013) A. Abyzov et al.   GENOME RESEARCH

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

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

Transcribed pseudogene ψPPM1K generates endogenous siRNA to suppress oncogenic cell growth in hepatocellular carcinoma

(2013) Wen-Ling Chan et al.   NUCLEIC ACIDS RESEARCH

Retrotransposon replication in plants

(2013) Alan H Schulman   Current Opinion in Virology

Gene Copy-Number Polymorphism Caused by Retrotransposition in Humans

(2013) Daniel R. Schrider et al.   PLoS Genetics

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

Expressed Pseudogenes in the Transcriptional Landscape of Human Cancers

(2012) Shanker Kalyana-Sundaram et al.   CELL

Does expression of the retrogene UTP14c in the ovary pre-dispose women to ovarian cancer?

(2012) Jan Rohozinski et al.   MEDICAL HYPOTHESES

"Orphan" Retrogenes in the Human Genome

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

A physical, genetic and functional sequence assembly of the barley genome

(2012)   NATURE

An integrated map of genetic variation from 1,092 human genomes

(2012)   NATURE

Epigenetic control of alternative mRNA processing at the imprinted Herc3/Nap1l5 locus

(2012) Michael Cowley et al.   NUCLEIC ACIDS RESEARCH

The GENCODE pseudogene resource

(2012) Baikang Pei et al.   GENOME BIOLOGY

Non-coding RNA and pseudogenes in neurodegenerative diseases: “The (un)Usual Suspects”

(2012) Valerio Costa et al.   Frontiers in Genetics

IGD: A resource for intronless genes in the human genome

(2011) Amel Louhichi et al.   GENE

Retrogenes in Rice (Oryza sativa L. ssp. japonica) Exhibit Correlated Expression with Their Source Genes

(2011) Hiroaki Sakai et al.   Genome Biology and Evolution

Adaptive seeds tame genomic sequence comparison

(2011) S. M. Kielbasa et al.   GENOME RESEARCH

Shotgun proteomics aids discovery of novel protein-coding genes, alternative splicing, and "resurrected" pseudogenes in the mouse genome

(2011) M. Brosch et al.   GENOME RESEARCH

Retrotransposition of marked SVA elements by human L1s in cultured cells

(2011) Dustin C. Hancks et al.   HUMAN MOLECULAR GENETICS

Deletion of PTENP1 Pseudogene in Human Melanoma

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

Trimeric structure and flexibility of the L1ORF1 protein in human L1 retrotransposition

(2011) Elena Khazina et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

The non-autonomous retrotransposon SVA is trans -mobilized by the human LINE-1 protein machinery

(2011) Julija Raiz et al.   NUCLEIC ACIDS RESEARCH

Intronic L1 Retrotransposons and Nested Genes Cause Transcriptional Interference by Inducing Intron Retention, Exonization and Cryptic Polyadenylation

(2011) Kristel Kaer et al.   PLoS One

Pseudogene-derived small interference RNAs regulate gene expression in African Trypanosoma brucei

(2011) Y.-Z. Wen et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Pseudogenes as an alternative source of natural antisense transcripts

(2010) Enrique M Muro et al.   BMC EVOLUTIONARY BIOLOGY

LINE-1 Retrotransposition Activity in Human Genomes

(2010) Christine R. Beck et al.   CELL

Unwitting hosts fall victim to imprinting

(2010) Ruth B. McCole et al.   Epigenetics

High-throughput sequencing reveals extensive variation in human-specific L1 content in individual human genomes

(2010) A. D. Ewing et al.   GENOME RESEARCH

MicroRNA-492 is processed from the keratin 19 gene and up-regulated in metastatic hepatoblastoma

(2010) Julia von Frowein et al.   HEPATOLOGY

RAB6C Is a Retrogene that Encodes a Centrosomal Protein Involved in Cell Cycle Progression

(2010) Joanne Young et al.   JOURNAL OF MOLECULAR BIOLOGY

Primate and Rodent Specific Intron Gains and the Origin of Retrogenes with Splice Variants

(2010) Michał W Szcześniak et al.   MOLECULAR BIOLOGY AND EVOLUTION

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

(2010) Laura Poliseno et al.   NATURE

A mobile threat to genome stability: The impact of non-LTR retrotransposons upon the human genome

(2010) Miriam K. Konkel et al.   SEMINARS IN CANCER BIOLOGY

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

(2010) Eusebio Chiefari et al.   Nature Communications

Connexin43 pseudogene in breast cancer cells offers a novel therapeutic target

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

A Functional Mouse Retroposed Gene Rps23r1 Reduces Alzheimer's β-Amyloid Levels and Tau Phosphorylation

(2009) Yun-wu Zhang et al.   NEURON

An Expressed Fgf4 Retrogene Is Associated with Breed-Defining Chondrodysplasia in Domestic Dogs

(2009) H. G. Parker et al.   SCIENCE

Small RNAs Originated from Pseudogenes: cis- or trans-Acting?

(2009) Xingyi Guo et al.   PLoS Computational Biology

Retrocopy contributions to the evolution of the human genome

(2008) Robert Baertsch et al.   BMC GENOMICS

Retrotransposons Revisited: The Restraint and Rehabilitation of Parasites

(2008) John L. Goodier et al.   CELL

Regulation of alternative polyadenylation by genomic imprinting

(2008) A. J. Wood et al.   GENES & DEVELOPMENT

Retrotransposition as a Source of New Promoters

(2008) K. Okamura et al.   MOLECULAR BIOLOGY AND EVOLUTION

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

The diversity of retrotransposons and the properties of their reverse transcriptases

(2008) Thomas H. Eickbush et al.   VIRUS RESEARCH

Birth and Rapid Subcellular Adaptation of a Hominoid-Specific CDC14 Protein

(2008) Lia Rosso et al.   PLOS BIOLOGY