4.6 Article

Retrotransposon LINE-1 bodies in the cytoplasm of piRNA-deficient mouse spermatocytes: Ribonucleoproteins overcoming the integrated stress response

Related references

Note: Only part of the references are listed.
Review Biochemistry & Molecular Biology

An update on post-transcriptional regulation of retrotransposons

Zbigniew Warkocki

Summary: This article summarizes the current understanding of retrotransposon biology, with a focus on LINE-1. By studying the involvement of post-transcriptional factors, it has been found that retrotransposon expression is tightly regulated to prevent harmful effects. Additionally, this paper discusses the roles of retrotransposons in RNA metabolism, cellular innate immunity, and cellular enzymes.

FEBS LETTERS (2023)

Article Multidisciplinary Sciences

The interferon stimulated gene-encoded protein HELZ2 inhibits human LINE-1 retrotransposition and LINE-1 RNA-mediated type I interferon induction

Ahmad Luqman-Fatah et al.

Summary: Proteins encoded by interferon stimulated genes (ISGs) can inhibit LINE-1 retrotransposition. In this study, proteins that interact with the L1 ORF1-encoded protein (ORF1p) were identified using immunoprecipitation and mass spectrometry. Three ISG proteins were found to inhibit retrotransposition by interacting with ORF1p.

NATURE COMMUNICATIONS (2023)

Article Genetics & Heredity

MxB inhibits long interspersed element type 1 retrotransposition

Yu Huang et al.

Summary: This study reveals that MxB protein effectively restricts LINE-1 retrotransposition by sequestering LINE-1 ribonucleoprotein within the cytoplasmic stress granules. This finding is significant for understanding the mechanisms of cellular control over retrotransposable element activity.

PLOS GENETICS (2022)

Article Multidisciplinary Sciences

LINE-1 expression in cancer correlates with p53 mutation, copy number alteration, and S phase checkpoint

Wilson McKerrow et al.

Summary: LINE-1, an active retrotransposon, is derepressed in many cancers and is correlated with p53 mutation and copy number alteration. It induces replication stress and is associated with the DNA damage response pathway in endometrial cancer.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2022)

Article Biochemistry & Molecular Biology

Neuronal RNA granules are ribosome complexes stalled at the pre-translocation state

Kalle Kipper et al.

Summary: The polarized cell morphology of neurons plays a crucial role in various neuronal processes, including the transport and translation of specific mRNAs. Localized protein synthesis in neurons is essential for memory formation and neurodegeneration. Through proteomics and electron microscopy, the structure of neuronal RNA granules has been characterized.

JOURNAL OF MOLECULAR BIOLOGY (2022)

Article Biochemistry & Molecular Biology

Novel FMRP interaction networks linked to cellular stress

Mohamed S. Taha et al.

Summary: The study found that FMRP interacts with a wide range of proteins, suggesting its involvement in multiple cellular processes, particularly under stress conditions. This indicates the important role of FMRP in cells, especially during stress.

FEBS JOURNAL (2021)

Article Biochemistry & Molecular Biology

The STRING database in 2021: customizable protein-protein networks, and functional characterization of user-uploaded gene/measurement sets

Damian Szklarczyk et al.

Summary: The STRING database integrates various associations between proteins, including physical interactions and functional associations, by collecting evidence from sources such as literature, databases, computational predictions, and systematic transfers. STRING aims for wide coverage and provides extensive user interface features and querying methods for experimental data.

NUCLEIC ACIDS RESEARCH (2021)

Article Biochemistry & Molecular Biology

Activation of endogenous retroviruses during brain development causes an inflammatory response

Marie E. Jonsson et al.

Summary: The study demonstrates that silencing of ERVs during brain development is critical, and that transcriptional activation of ERVs in neurons results in an inflammatory response.

EMBO JOURNAL (2021)

Article Biochemistry & Molecular Biology

Integrated multi-omics reveals common properties underlying stress granule and P-body formation

Christopher J. Kershaw et al.

Summary: This study systematically determined the protein and mRNA composition of P-bodies and stress granules before and after nutrient stress, revealing the existence of high molecular weight complexes as potential seeds for mature condensates. Shared proteins and RNA components between these biological condensates were identified, highlighting a complex interaction profile during their maturation process. The interaction networks represent a tunable response to stress, showcasing previously unrecognized condensate heterogeneity.

RNA BIOLOGY (2021)

Article Genetics & Heredity

RIP-seq reveals LINE-1 ORF1p association with p-body enriched mRNAs

Erica M. Briggs et al.

Summary: The study reveals higher levels of LINE-1 RNA and non-LINE-1 mRNAs bound by ORF1p in prostate cancer cells, suggesting biological relevance to prostate cancer.

MOBILE DNA (2021)

Article Multidisciplinary Sciences

RNF219 attenuates global mRNA decay through inhibition of CCR4-NOT complex-mediated deadenylation

Fabian Poetz et al.

Summary: The study identified RNF219 as an acetylation-regulated cofactor of the CCR4-NOT complex, which inhibits mRNA degradation mediated by the complex through interaction with NOT9. RNF219 attenuates global mRNA turnover in cells with a differential requirement of its RING domain.

NATURE COMMUNICATIONS (2021)

Article Biophysics

Phase separation of the LINE-1 ORF1 protein is mediated by the N-terminus and coiled-coil domain

Jocelyn C. Newton et al.

Summary: L1 element autonomously replicates in the human genome, causing DNA damage and genomic instability. Activation of L1 triggers interferon response and age-associated inflammation. ORF1 protein forms liquid droplets in a salt-dependent manner, with interactions between its N-terminal and coiled-coil domain being necessary for phase separation.

BIOPHYSICAL JOURNAL (2021)

Article Multidisciplinary Sciences

Evolutionary history of the vertebrate Piwi gene family

Javier Gutierrez et al.

Summary: PIWIs are regulatory proteins that protect germline against transposable elements and are primarily expressed in gonads in vertebrates. The duplication history of Piwi genes is complex, with some genes being retained in all members, while others being derived from duplication events in common ancestors and subsequently lost in certain lineages. Despite two rounds of whole genome duplication in vertebrate evolution, Piwi expansion seems to have occurred independently of these events.

PEERJ (2021)

Review Genetics & Heredity

Transposable elements shape the evolution of mammalian development

Anna D. Senft et al.

Summary: Transposable elements (TEs) play a significant role in mammalian development and evolution by directly contributing genetic materials and indirectly affecting the evolution of TE repression systems such as KRAB-ZFPs. Despite the threats to genome stability, TEs actively shape mammalian-specific developmental processes and continue to impact mammalian development through ongoing co-evolution.

NATURE REVIEWS GENETICS (2021)

Review Genetics & Heredity

The Structural, Functional and Evolutionary Impact of Transposable Elements in Eukaryotes

Dareen Almojil et al.

Summary: Transposable elements (TEs) are widespread in eukaryotes and have had a significant impact on genome organization and evolution, playing roles in regulating genes and providing a source for genetic novelties. This impact is now being more fully appreciated and their role in various biological processes, such as speciation and adaptation, is still being deciphered.

GENES (2021)

Article Multidisciplinary Sciences

Maximizing the ovarian reserve in mice by evading LINE-1 genotoxicity

Marla E. Tharp et al.

NATURE COMMUNICATIONS (2020)

Review Genetics & Heredity

A Field Guide to Eukaryotic Transposable Elements

Jonathan N. Wells et al.

ANNUAL REVIEW OF GENETICS, VOL 54, 2020 (2020)

Article Cell Biology

Mammalian stress granules and P bodies at a glance

Claire L. Riggs et al.

JOURNAL OF CELL SCIENCE (2020)

Article Multidisciplinary Sciences

L1 drives IFN in senescent cells and promotes age-associated inflammation

Marco De Cecco et al.

NATURE (2019)

Review Genetics & Heredity

Regulation of transposable elements by DNA modifications

Ozgen Deniz et al.

NATURE REVIEWS GENETICS (2019)

Article Biochemistry & Molecular Biology

Co-translational assembly of proteasome subunits in NOT1-containing assemblysomes

Olesya O. Panasenko et al.

NATURE STRUCTURAL & MOLECULAR BIOLOGY (2019)

Article Biochemistry & Molecular Biology

Cycloheximide can distort measurements of mRNA levels and translation efficiency

Daniel A. Santos et al.

NUCLEIC ACIDS RESEARCH (2019)

Article Cell Biology

Stress Granules and Processing Bodies in Translational Control

Pavel Ivanov et al.

COLD SPRING HARBOR PERSPECTIVES IN BIOLOGY (2019)

Article Genetics & Heredity

The Arms Race Between KRAB–Zinc Finger Proteins and Endogenous Retroelements and Its Impact on Mammals

Melania Bruno et al.

Annual Review of Genetics (2019)

Review Cell Biology

Host-transposon interactions: conflict, cooperation, and cooption

Rachel L. Cosby et al.

GENES & DEVELOPMENT (2019)

Article Biochemical Research Methods

Telescope: Characterization of the retrotranscriptome by accurate estimation of transposable element expression

Matthew L. Bendall et al.

PLOS COMPUTATIONAL BIOLOGY (2019)

Review Biochemistry & Molecular Biology

Structural and sequence diversity of eukaryotic transposable elements

Kenji K. Kojima

GENES & GENETIC SYSTEMS (2019)

Review Biochemistry & Molecular Biology

Mammalian transposable elements and their impacts on genome evolution

Roy N. Platt et al.

CHROMOSOME RESEARCH (2018)

Review Biochemistry & Molecular Biology

Battling for Ribosomes: Translational Control at the Forefront of the Antiviral Response

Huy-Dung Hoang et al.

JOURNAL OF MOLECULAR BIOLOGY (2018)

Article Biochemistry & Molecular Biology

The TIA1 RNA-Binding Protein Family Regulates EIF2AK2-Mediated Stress Response and Cell Cycle Progression

Cindy Meyer et al.

MOLECULAR CELL (2018)

Article Biotechnology & Applied Microbiology

Improving cytidine and adenine base editors by expression optimization and ancestral reconstruction

Luke W. Koblan et al.

NATURE BIOTECHNOLOGY (2018)

Review Genetics & Heredity

P-Bodies: Cytosolic Droplets for Coordinated mRNA Storage

Nancy Standart et al.

TRENDS IN GENETICS (2018)

Article Genetics & Heredity

Transient reduction of DNA methylation at the onset of meiosis in male mice

Valeriya Gaysinskaya et al.

EPIGENETICS & CHROMATIN (2018)

Article Biochemical Research Methods

Transcriptome-wide measurement of translation by ribosome profiling

Nicholas J. McGlincy et al.

METHODS (2017)

Article Biochemistry & Molecular Biology

The Stress Granule Transcriptome Reveals Principles of mRNA Accumulation in Stress Granules

Anthony Khong et al.

MOLECULAR CELL (2017)

Article Cell Biology

Hide and seek: how chromatin-based pathways silence retroelements in the mammalian germline

Antoine Molaro et al.

CURRENT OPINION IN GENETICS & DEVELOPMENT (2016)

Review Cell Biology

The Ccr4-Not complex is a key regulator of eukaryotic gene expression

Martine A. Collart

WILEY INTERDISCIPLINARY REVIEWS-RNA (2016)

Review Genetics & Heredity

Roles for retrotransposon insertions in human disease

Dustin C. Hancks et al.

MOBILE DNA (2016)

Review Biochemistry & Molecular Biology

PIWI-Interacting RNA: Its Biogenesis and Functions

Yuka W. Iwasaki et al.

ANNUAL REVIEW OF BIOCHEMISTRY, VOL 84 (2015)

Review Biochemistry & Molecular Biology

Functional and structural insights into the piRNA factor Maelstrom

Kaoru Sato et al.

FEBS LETTERS (2015)

Article Cell Biology

P-body assembly requires DDX6 repression complexes rather than decay or Ataxin2/2L complexes

Jessica Ayache et al.

MOLECULAR BIOLOGY OF THE CELL (2015)

Article Biotechnology & Applied Microbiology

Inducible in vivo genome editing with CRISPR-Cas9

Lukas E. Dow et al.

NATURE BIOTECHNOLOGY (2015)

Article Genetics & Heredity

The Zinc-Finger Antiviral Protein ZAP Inhibits LINE and Alu Retrotransposition

John B. Moldovan et al.

PLOS GENETICS (2015)

Article Genetics & Heredity

The Broad-Spectrum Antiviral Protein ZAP Restricts Human Retrotransposition

John L. Goodier et al.

PLOS GENETICS (2015)

Article Microbiology

The Influence of LINE-1 and SINE Retrotransposons on Mammalian Genomes

Sandra R. Richardson et al.

MICROBIOLOGY SPECTRUM (2015)

Article Cell Biology

A Role for Retrotransposon LINE-1 in Fetal Oocyte Attrition in Mice

Safia Malki et al.

DEVELOPMENTAL CELL (2014)

Article Biochemistry & Molecular Biology

Reduced pachytene piRNAs and translation underlie spermiogenic arrest in Maelstrom mutant mice

Julio Castaneda et al.

EMBO JOURNAL (2014)

Article Multidisciplinary Sciences

An evolutionary arms race between KRAB zinc-finger genes ZNF91/93 and SVA/L1 retrotransposons

Frank M. J. Jacobs et al.

NATURE (2014)

Article Multidisciplinary Sciences

Autophagy supports genomic stability by degrading retrotransposon RNA

Huishan Guo et al.

NATURE COMMUNICATIONS (2014)

Article Genetics & Heredity

The Not5 Subunit of the Ccr4-Not Complex Connects Transcription and Translation

Zoltan Villanyi et al.

PLOS GENETICS (2014)

Article Biotechnology & Applied Microbiology

Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2

Michael I. Love et al.

GENOME BIOLOGY (2014)

Article Biochemical Research Methods

STAR: ultrafast universal RNA-seq aligner

Alexander Dobin et al.

BIOINFORMATICS (2013)

Article Biochemical Research Methods

EBSeq: an empirical Bayes hierarchical model for inference in RNA-seq experiments

Ning Leng et al.

BIOINFORMATICS (2013)

Article Biochemistry & Molecular Biology

Enrichment of processed pseudogene transcripts in L1-ribonucleoprotein particles

Prabhat K. Mandal et al.

HUMAN MOLECULAR GENETICS (2013)

Article Biochemistry & Molecular Biology

Mapping the LINE1 ORF1 protein interactome reveals associated inhibitors of human retrotransposition

John L. Goodier et al.

NUCLEIC ACIDS RESEARCH (2013)

Article Virology

The PKR activator, PACT, becomes a PKR inhibitor during HIV-1 replication

Guerline Clerzius et al.

RETROVIROLOGY (2013)

Review Genetics & Heredity

Long Interspersed Element-1 (LINE-1): Passenger or Driver in Human Neoplasms?

Nemanja Rodic et al.

PLOS GENETICS (2013)

Article Biochemistry & Molecular Biology

LINEs, SINEs and other retroelements: do birds of a feather flock together?

Astrid M. Roy-Engel

FRONTIERS IN BIOSCIENCE-LANDMARK (2012)

Article Biochemistry & Molecular Biology

Not4 E3 Ligase Contributes to Proteasome Assembly and Functional Integrity in Part through Ecm29

Olesya O. Panasenko et al.

MOLECULAR AND CELLULAR BIOLOGY (2011)

Review Biotechnology & Applied Microbiology

piRNAs, transposon silencing, and germline genome integrity

Julio Castaneda et al.

MUTATION RESEARCH-FUNDAMENTAL AND MOLECULAR MECHANISMS OF MUTAGENESIS (2011)

Review Microbiology

Viral subversion of the host protein synthesis machinery

Derek Walsh et al.

NATURE REVIEWS MICROBIOLOGY (2011)

Article Biochemistry & Molecular Biology

LINE-1 Retrotransposition Activity in Human Genomes

Christine R. Beck et al.

Review Biochemistry & Molecular Biology

Evolution of Eukaryotic DNA Methylation and the Pursuit of Safer Sex

Assaf Zemach et al.

CURRENT BIOLOGY (2010)

Article Biochemistry & Molecular Biology

Discrete subcellular partitioning of human retrotransposon RNAs despite a common mechanism of genome insertion

John L. Goodier et al.

HUMAN MOLECULAR GENETICS (2010)

Article Genetics & Heredity

Characterization of LINE-1 Ribonucleoprotein Particles

Aurelien J. Doucet et al.

PLOS GENETICS (2010)

Editorial Material Biochemistry & Molecular Biology

Stress granules

Paul Anderson et al.

CURRENT BIOLOGY (2009)

Article Biochemistry & Molecular Biology

Ror2 Receptor Requires Tyrosine Kinase Activity to Mediate Wnt5A Signaling

Amanda Mikels et al.

JOURNAL OF BIOLOGICAL CHEMISTRY (2009)

Article Biochemistry & Molecular Biology

TRBP Control of PACT-Induced Phosphorylation of Protein Kinase R Is Reversed by Stress

Aicha Daher et al.

MOLECULAR AND CELLULAR BIOLOGY (2009)

Article Biochemical Research Methods

Enzymatic assembly of DNA molecules up to several hundred kilobases

Daniel G. Gibson et al.

NATURE METHODS (2009)

Article Genetics & Heredity

Cytoplasmic Compartmentalization of the Fetal piRNA Pathway in Mice

Alexei A. Aravin et al.

PLOS GENETICS (2009)

Article Biotechnology & Applied Microbiology

Ultrafast and memory-efficient alignment of short DNA sequences to the human genome

Ben Langmead et al.

GENOME BIOLOGY (2009)

Review Biochemistry & Molecular Biology

Retrotransposons revisited: The restraint and rehabilitation of parasites

John L. Goodier et al.

Article Genetics & Heredity

LINE-1 ORF1 protein enhances Alu SINE retrotransposition

Nicholas Wallace et al.

Article Biochemistry & Molecular Biology

Cis-preferential LINE-1 reverse transcriptase activity in ribonucleoprotein particles

Deanna A. Kulpa et al.

NATURE STRUCTURAL & MOLECULAR BIOLOGY (2006)

Review Genetics & Heredity

Retroviral elements and their hosts: Insertional mutagenesis in the mouse germ line

Irina A. Maksakova et al.

PLOS GENETICS (2006)

Article Biochemistry & Molecular Biology

Ribonucleoprotein particle formation is necessary but not sufficient for LINE-1 retrotransposition

DA Kulpa et al.

HUMAN MOLECULAR GENETICS (2005)

Review Cell Biology

LINEs, SINEs and processed pseudogenes: parasitic strategies for genome modeling

M Dewannieux et al.

CYTOGENETIC AND GENOME RESEARCH (2005)

Review Multidisciplinary Sciences

Mobile elements: Drivers of genome evolution

HH Kazazian

SCIENCE (2004)

Article Cell Biology

Stress granule assembly is mediated by prion-like aggregation of TIA-1

N Gilks et al.

MOLECULAR BIOLOGY OF THE CELL (2004)

Article Multidisciplinary Sciences

A highly active synthetic mammalian retrotransposon

JS Han et al.

NATURE (2004)

Article Genetics & Heredity

LINE-mediated retrotransposition of marked Alu sequences

M Dewannieux et al.

NATURE GENETICS (2003)

Article Biochemistry & Molecular Biology

PACT-mediated enhancement of reporter gene expression at the translational level

SD Li et al.

JOURNAL OF INTERFERON AND CYTOKINE RESEARCH (2003)

Review Multidisciplinary Sciences

Initial sequencing and comparative analysis of the mouse genome

RH Waterston et al.

NATURE (2002)

Article Biochemistry & Molecular Biology

Human L1 element target-primed reverse transcription in vitro

GJ Cost et al.

EMBO JOURNAL (2002)

Review Multidisciplinary Sciences

Initial sequencing and analysis of the human genome

ES Lander et al.

NATURE (2001)

Article Biochemistry & Molecular Biology

Human L1 retrotransposition:: cis preference versus trans complementation

W Wei et al.

MOLECULAR AND CELLULAR BIOLOGY (2001)

Article Biochemistry & Molecular Biology

Determination of L1 retrotransposition kinetics in cultured cells

EM Ostertag et al.

NUCLEIC ACIDS RESEARCH (2000)

Article Genetics & Heredity

Human LINE retrotransposons generate processed pseudogenes

C Esnault et al.

NATURE GENETICS (2000)