Overlapping genes in natural and engineered genomes

Revisiting sORFs: overcoming challenges to identify and characterize functional microproteins

(2021) Dörte Schlesinger et al.   FEBS Journal

Noncanonical open reading frames encode functional proteins essential for cancer cell survival

(2021) John R. Prensner et al.   NATURE BIOTECHNOLOGY

Targeted replacement of full-length CFTR in human airway stem cells by CRISPR-Cas9 for pan-mutation correction in the endogenous locus

(2021) Sriram Vaidyanathan et al.   MOLECULAR THERAPY

Creating custom synthetic genomes in Escherichia coli with REXER and GENESIS

(2021) Wesley E. Robertson et al.   Nature Protocols

Frameshifting preserves key physicochemical properties of proteins

(2020) Lukas Bartonek et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Pervasive functional translation of noncanonical human open reading frames

(2020) Jin Chen et al.   SCIENCE

Comprehensive annotations of human herpesvirus 6A and 6B genomes reveal novel and conserved genomic features

(2020) Yaara Finkel et al.   eLife

A Continuum of Evolving De Novo Genes Drives Protein-Coding Novelty in Drosophila

(2020) Brennen Heames et al.   JOURNAL OF MOLECULAR EVOLUTION

Advances in bacterial transcriptome understanding: From overlapping transcription to the excludon concept

(2020) Alejandro Toledo‐Arana et al.   MOLECULAR MICROBIOLOGY

Rapid discovery and evolution of orthogonal aminoacyl-tRNA synthetase–tRNA pairs

(2020) Daniele Cervettini et al.   NATURE BIOTECHNOLOGY

A fully orthogonal system for protein synthesis in bacterial cells

(2020) Nikolay A. Aleksashin et al.   Nature Communications

A Novel pH-Regulated, Unusual 603 bp Overlapping Protein Coding Gene pop Is Encoded Antisense to ompA in Escherichia coli O157:H7 (EHEC)

(2020) Barbara Zehentner et al.   Frontiers in Microbiology

Prevalence of small base-pairing RNAs derived from diverse genomic loci

(2020) Philip P. Adams et al.   Biochimica et Biophysica Acta-Gene Regulatory Mechanisms

Evolution of new proteins from translated sORFs in long non-coding RNAs

(2020) Jorge Ruiz-Orera et al.   EXPERIMENTAL CELL RESEARCH

New insights into the evolutionary features of viral overlapping genes by discriminant analysis

(2020) Angelo Pavesi   VIROLOGY

Genetic circuit design automation for yeast

(2020) Ye Chen et al.   Nature Microbiology

Unusually efficient CUG initiation of an overlapping reading frame in POLG mRNA yields novel protein POLGARF

(2020) Gary Loughran et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Genome Modularization Reveals Overlapped Gene Topology Is Necessary for Efficient Viral Reproduction

(2020) Bradley W. Wright et al.   ACS Synthetic Biology

The FUS gene is dual‐coding with both proteins contributing to FUS ‐mediated toxicity

(2020) Marie A Brunet et al.   EMBO REPORTS

Identification and analysis of small proteins and short open reading frame encoded peptides in Hep3B cell

(2020) Bing Wang et al.   Journal of Proteomics

Materials design by synthetic biology

(2020) Tzu-Chieh Tang et al.   Nature Reviews Materials

Comprehensive profiling of translation initiation in influenza virus infected cells

(2019) Heather M. Machkovech et al.   PLoS Pathogens

Hachimoji DNA and RNA: A genetic system with eight building blocks

(2019) Shuichi Hoshika et al.   SCIENCE

Retapamulin-Assisted Ribosome Profiling Reveals the Alternative Bacterial Proteome

(2019) Sezen Meydan et al.   MOLECULAR CELL

Total synthesis of Escherichia coli with a recoded genome

(2019) Julius Fredens et al.   NATURE

Chemical synthesis rewriting of a bacterial genome to achieve design flexibility and biological functionality

(2019) Jonathan E. Venetz et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

De novo gene birth

(2019) Stephen Branden Van Oss et al.   PLoS Genetics

The Translational Landscape of the Human Heart

(2019) Sebastiaan van Heesch et al.   CELL

Bicistronic Design-Based Continuous and High-Level Membrane Protein Production in Escherichia coli

(2019) Nico J. Claassens et al.   ACS Synthetic Biology

Fail-safe genetic codes designed to intrinsically contain engineered organisms

(2019) Jonathan Calles et al.   NUCLEIC ACIDS RESEARCH

Synthetic sequence entanglement augments stability and containment of genetic information in cells

(2019) Tomasz Blazejewski et al.   SCIENCE

Optimality in the standard genetic code is robust with respect to comparison code sets

(2019) Stefan Wichmann et al.   BIOSYSTEMS

Finally, a role befitting Astar: the strongly conserved, unessential microvirus A* proteins ensure the product fidelity of packaging reactions.

(2019) Aaron P. Roznowski et al.   JOURNAL OF VIROLOGY

Definitive demonstration by synthesis of genome annotation completeness

(2019) Paul R. Jaschke et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Enhancers Facilitate the Birth of De Novo Genes and Gene Integration into Regulatory Networks

(2019) Paco Majic et al.   MOLECULAR BIOLOGY AND EVOLUTION

Gene Birth Contributes to Structural Disorder Encoded by Overlapping Genes

(2018) Sara Willis et al.   GENETICS

Recognition of the polycistronic nature of human genes is critical to understanding the genotype-phenotype relationship

(2018) Marie A. Brunet et al.   GENOME RESEARCH

Transcriptional Landscape and Regulatory Roles of Small Noncoding RNAs in the Oxidative Stress Response of the Haloarchaeon Haloferax volcanii

(2018) Diego Rivera Gelsinger et al.   JOURNAL OF BACTERIOLOGY

Gene Birth Contributes to Structural Disorder Encoded by Overlapping Genes

(2018) Sara Willis et al.   GENETICS

Overlapping genes and the proteins they encode differ significantly in their sequence composition from non-overlapping genes

(2018) Angelo Pavesi et al.   PLoS One

The translation of non-canonical open reading frames controls mucosal immunity

(2018) Ruaidhrí Jackson et al.   NATURE

Designing of a single gene encoding four functional proteins

(2017) Masayori Inouye et al.   JOURNAL OF THEORETICAL BIOLOGY

Deep sequencing approaches for the analysis of prokaryotic transcriptional boundaries and dynamics

(2017) Katherine James et al.   METHODS

Measurements of translation initiation from all 64 codons in E. coli

(2017) Ariel Hecht et al.   NUCLEIC ACIDS RESEARCH

CDKN2B deletion is essential for pancreatic cancer development instead of unmeaningful co-deletion due to juxtaposition to CDKN2A

(2017) Q Tu et al.   ONCOGENE

Design of a synthetic yeast genome

(2017) Sarah M. Richardson et al.   SCIENCE

Mammalian Polycistronic mRNAs and Disease

(2017) Timofey A. Karginov et al.   TRENDS IN GENETICS

Arresting Evolution

(2017) James J. Bull et al.   TRENDS IN GENETICS

Computational design of fully overlapping coding schemes for protein pairs and triplets

(2017) Vaitea Opuu et al.   Scientific Reports

Deep transcriptome annotation enables the discovery and functional characterization of cryptic small proteins

(2017) Sondos Samandi et al.   eLife

Gene overlapping and size constraints in the viral world

(2016) Nadav Brandes et al.   Biology Direct

Functional Segregation of Overlapping Genes in HIV

(2016) Jason D. Fernandes et al.   CELL

Antisense transcription as a tool to tune gene expression

(2016) J. A. Brophy et al.   Molecular Systems Biology

Incredible RNA: Dual Functions of Coding and Noncoding

(2016)   MOLECULES AND CELLS

Synthetic biology to access and expand nature's chemical diversity

(2016) Michael J. Smanski et al.   NATURE REVIEWS MICROBIOLOGY

NCBI prokaryotic genome annotation pipeline

(2016) Tatiana Tatusova et al.   NUCLEIC ACIDS RESEARCH

Design, synthesis, and testing toward a 57-codon genome

(2016) N. Ostrov et al.   SCIENCE

Design and synthesis of a minimal bacterial genome

(2016) C. A. Hutchison et al.   SCIENCE

Translational control by 5'-untranslated regions of eukaryotic mRNAs

(2016) A. G. Hinnebusch et al.   SCIENCE

Death of a dogma: eukaryotic mRNAs can code for more than one protein

(2015) Hélène Mouilleron et al.   NUCLEIC ACIDS RESEARCH

The application of terminomics for the identification of protein start sites and proteoforms in bacteria

(2015) Iain J. Berry et al.   PROTEOMICS

Operon structure and cotranslational subunit association direct protein assembly in bacteria

(2015) Y.-W. Shieh et al.   SCIENCE

Refactoring the Six-Gene Photosystem II Core in the Chloroplast of the Green Algae Chlamydomonas reinhardtii

(2015) Javier A. Gimpel et al.   ACS Synthetic Biology

Overlapping genes: a window on gene evolvability

(2014) Maxime Huvet et al.   BMC GENOMICS

Identification of small ORFs in vertebrates using ribosome footprinting and evolutionary conservation

(2014) A. A. Bazzini et al.   EMBO JOURNAL

Overlapping genes: a new strategy of thermophilic stress tolerance in prokaryotes

(2014) Deeya Saha et al.   EXTREMOPHILES

Discovery of Human sORF-Encoded Polypeptides (SEPs) in Cell Lines and Tissue

(2014) Jiao Ma et al.   JOURNAL OF PROTEOME RESEARCH

A Comprehensive, High-Resolution Map of a Gene’s Fitness Landscape

(2014) Elad Firnberg et al.   MOLECULAR BIOLOGY AND EVOLUTION

A 'resource allocator' for transcription based on a highly fragmented T7 RNA polymerase

(2014) T. H. Segall-Shapiro et al.   Molecular Systems Biology

Biological functions of natural antisense transcripts

(2013) Andreas Werner   BMC BIOLOGY

The Evolution and Functional Significance of Nested Gene Structures in Drosophila melanogaster

(2013) Y. C. G. Lee et al.   Genome Biology and Evolution

Growth Temperature and Genome Size in Bacteria Are Negatively Correlated, Suggesting Genomic Streamlining During Thermal Adaptation

(2013) Niv Sabath et al.   Genome Biology and Evolution

The Effect of Gene Overlapping on the Rate of RNA Virus Evolution

(2013) Etienne Simon-Loriere et al.   MOLECULAR BIOLOGY AND EVOLUTION

Design of orthogonal genetic switches based on a crosstalk map of  s, anti- s, and promoters

(2013) V. A. Rhodius et al.   Molecular Systems Biology

Precise and reliable gene expression via standard transcription and translation initiation elements

(2013) Vivek K Mutalik et al.   NATURE METHODS

Gene regulation by antisense transcription

(2013) Vicent Pelechano et al.   NATURE REVIEWS GENETICS

The SEED and the Rapid Annotation of microbial genomes using Subsystems Technology (RAST)

(2013) Ross Overbeek et al.   NUCLEIC ACIDS RESEARCH

Direct Detection of Alternative Open Reading Frames Translation Products in Human Significantly Expands the Proteome

(2013) Benoît Vanderperre et al.   PLoS One

High-resolution view of bacteriophage lambda gene expression by ribosome profiling

(2013) X. Liu et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Genomically Recoded Organisms Expand Biological Functions

(2013) M. J. Lajoie et al.   SCIENCE

Origin and Length Distribution of Unidirectional Prokaryotic Overlapping Genes

(2013) Miguel M. Fonseca et al.   G3-Genes Genomes Genetics

Genetic Architecture Promotes the Evolution and Maintenance of Cooperation

(2013) Antoine Frénoy et al.   PLoS Computational Biology

Viral Proteins Originated De Novo by Overprinting Can Be Identified by Codon Usage: Application to the “Gene Nursery” of Deltaretroviruses

(2013) Angelo Pavesi et al.   PLoS Computational Biology

Reprogramming the Genetic Code: From Triplet to Quadruplet Codes

(2012) Kaihang Wang et al.   ANGEWANDTE CHEMIE-INTERNATIONAL EDITION

Bidirectional regulation between WDR83 and its natural antisense transcript DHPS in gastric cancer

(2012) Wen-Yu Su et al.   CELL RESEARCH

New and Xisting regulatory mechanisms of X chromosome inactivation

(2012) Yesu Jeon et al.   CURRENT OPINION IN GENETICS & DEVELOPMENT

A unified framework of overlapping genes: Towards the origination and endogenic regulation

(2012) Meng-Ru Ho et al.   GENOMICS

Peptidomic discovery of short open reading frame–encoded peptides in human cells

(2012) Sarah A Slavoff et al.   Nature Chemical Biology

The excludon: a new concept in bacterial antisense RNA-mediated gene regulation

(2012) Nina Sesto et al.   NATURE REVIEWS MICROBIOLOGY

BG7: A New Approach for Bacterial Genome Annotation Designed for Next Generation Sequencing Data

(2012) Pablo Pareja-Tobes et al.   PLoS One

Efficient and sequence-independent replication of DNA containing a third base pair establishes a functional six-letter genetic alphabet

(2012) Denis A. Malyshev et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Refactoring the nitrogen fixation gene cluster from Klebsiella oxytoca

(2012) K. Temme et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

A fully decompressed synthetic bacteriophage øX174 genome assembled and archived in yeast

(2012) Paul R. Jaschke et al.   VIROLOGY

Evolutionary Stability of a Refactored Phage Genome

(2012) Rachael Springman et al.   ACS Synthetic Biology

Refactored M13 Bacteriophage as a Platform for Tumor Cell Imaging and Drug Delivery

(2012) Debadyuti Ghosh et al.   ACS Synthetic Biology

Dual-function RNA regulators in bacteria

(2011) Carin K. Vanderpool et al.   BIOCHIMIE

Structure and expression of two nuclear receptor genes in marsupials: insights into the evolution of the antisense overlap between the α-thyroid hormone receptor and Rev-erbα

(2011) Brandon C Rindfleisch et al.   BMC MOLECULAR BIOLOGY

Extensive relationship between antisense transcription and alternative splicing in the human genome

(2011) A. Sorana Morrissy et al.   GENOME RESEARCH

RNA Sequence Determinants of a Coupled Termination-Reinitiation Strategy for Downstream Open Reading Frame Translation in Helminthosporium victoriae Virus 190S and Other Victoriviruses (Family Totiviridae)

(2011) H. Li et al.   JOURNAL OF VIROLOGY

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

(2011) Ci Chu et al.   MOLECULAR CELL

lncRNAs transactivate STAU1-mediated mRNA decay by duplexing with 3′ UTRs via Alu elements

(2011) Chenguang Gong et al.   NATURE

Bacterial transcriptomics: what is beyond the RNA horiz-ome?

(2011) Marc Güell et al.   NATURE REVIEWS MICROBIOLOGY

A survey of computational methods and error rate estimation procedures for peptide and protein identification in shotgun proteomics

(2010) Alexey I. Nesvizhskii   Journal of Proteomics

An antisense RNA that governs the expression kinetics of a multifunctional virulence gene

(2010) Eun-Jin Lee et al.   MOLECULAR MICROBIOLOGY

The primary transcriptome of the major human pathogen Helicobacter pylori

(2010) Cynthia M. Sharma et al.   NATURE

Operons

(2009) Anne E. Osbourn et al.   CELLULAR AND MOLECULAR LIFE SCIENCES

An Overview of Nested Genes in Eukaryotic Genomes

(2009) Anuj Kumar   EUKARYOTIC CELL

Synthesis of Methyl Halides from Biomass Using Engineered Microbes

(2009) Travis S. Bayer et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Evolution of Relative Reading Frame Bias in Unidirectional Prokaryotic Gene Overlaps

(2009) P. J. A. Cock et al.   MOLECULAR BIOLOGY AND EVOLUTION

Effect of Genome Size on AAV Vector Packaging

(2009) Zhijian Wu et al.   MOLECULAR THERAPY

The impact of retrotransposons on human genome evolution

(2009) Richard Cordaux et al.   NATURE REVIEWS GENETICS

Regulatory roles of natural antisense transcripts

(2009) Mohammad Ali Faghihi et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Posttranslational interference of Ty1 retrotransposition by antisense RNAs

(2009) E. Matsuda et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Genome-Wide Analysis in Vivo of Translation with Nucleotide Resolution Using Ribosome Profiling

(2009) N. T. Ingolia et al.   SCIENCE

Non-random retention of protein-coding overlapping genes in Metazoa

(2008) Giulia Soldà et al.   BMC GENOMICS

Overlapping genes in the human and mouse genomes

(2008) Chaitanya R Sanna et al.   BMC GENOMICS

Large gene overlaps in prokaryotic genomes: result of functional constraints or mispredictions?

(2008) Albert Pallejà et al.   BMC GENOMICS

Translational Coupling Controls Expression and Function of the DrrAB Drug Efflux Pump

(2008) Prajakta Pradhan et al.   JOURNAL OF MOLECULAR BIOLOGY

Epigenetic silencing of tumour suppressor gene p15 by its antisense RNA

(2008) Wenqiang Yu et al.   NATURE

RNA-based gene duplication: mechanistic and evolutionary insights

(2008) Henrik Kaessmann et al.   NATURE REVIEWS GENETICS

Nested genes and increasing organizational complexity of metazoan genomes

(2008) Raquel Assis et al.   TRENDS IN GENETICS