4.8 Article

An updated definition of V(D)J recombination signal sequences revealed by high-throughput recombination assays

Related references

Note: Only part of the references are listed.
Review Immunology

Dynamic 3D Locus Organization and Its Drivers Underpin Immunoglobulin Recombination

Carolyn H. Rogers et al.

Summary: This article reviews the complex mechanisms of antigen receptor gene recombination in the immune system, focusing on recent advances in the study of the mouse immunoglobulin heavy chain locus. Key regulatory elements, local chromatin state at V genes, and imaging studies providing insights into the dynamic looping and contraction of the Igh locus during recombination are discussed. Additionally, higher resolution pictures of Igh locus structure using chromosome conformation capture-based technologies and the roles of transcription and architectural factors in regulating these processes are explored. Exciting recent mechanistic findings, such as Rag recombinase scanning and a new phase separation model for Igh locus compartmentalization, are also highlighted.

FRONTIERS IN IMMUNOLOGY (2021)

Review Biophysics

A molecular view of DNA flexibility

Alberto Marin-Gonzalez et al.

Summary: Understanding the complex mechanical behavior of DNA at different scales requires taking a molecular perspective, which recent single-molecule experiments and molecular dynamics simulations have provided insights into. These studies have identified sequence-dependent properties, effects of cytosine methylation and DNA mismatches, as well as differences in mechanical properties between DNA and double-stranded RNA. Thorough examination of single-molecule literature has led to the establishment of general 'rules' explaining the mechanics of nucleic acids at the base pair level, which can be valuable for designing DNA and RNA nanostructures in the future.

QUARTERLY REVIEWS OF BIOPHYSICS (2021)

Article Biochemistry & Molecular Biology

Cutting antiparallel DNA strands in a single active site

Xuemin Chen et al.

NATURE STRUCTURAL & MOLECULAR BIOLOGY (2020)

Article Multidisciplinary Sciences

Alterations in chromatin at antigen receptor loci define lineage progression during B lymphopoiesis

Mattia Lion et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2020)

Article Biochemistry & Molecular Biology

Sequence-dependent dynamics of synthetic and endogenous RSSs in V(D)J recombination

Soichi Hirokawa et al.

NUCLEIC ACIDS RESEARCH (2020)

Article Immunology

Poor quality V beta recombination signal sequences stochastically enforce TCR beta allelic exclusion

Glendon S. Wu et al.

JOURNAL OF EXPERIMENTAL MEDICINE (2020)

Article Multidisciplinary Sciences

CTCF orchestrates long-range cohesin-driven V(D)J recombinational scanning

Zhaoqing Ba et al.

NATURE (2020)

Article Multidisciplinary Sciences

Inefficient V(D)J recombination underlies monogenic T cell receptor β expression

Glendon S. Wu et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2020)

Article Biochemistry & Molecular Biology

Sequence-dependent response of DNA to torsional stress: a potential biological regulation mechanism

Anna Reymer et al.

NUCLEIC ACIDS RESEARCH (2018)

Article Biochemistry & Molecular Biology

Cracking the DNA Code for V(D)J Recombination

Min-Sung Kim et al.

MOLECULAR CELL (2018)

Article Biochemistry & Molecular Biology

DNA melting initiates the RAG catalytic pathway

Heng Ru et al.

NATURE STRUCTURAL & MOLECULAR BIOLOGY (2018)

Review Biochemistry & Molecular Biology

Riches in RAGs: Revealing the V(D)J Recombinase through High-Resolution Structures

Karla K. Rodgers

TRENDS IN BIOCHEMICAL SCIENCES (2017)

Article Biochemical Research Methods

Parmbsc1: a refined force field for DNA simulations

Ivan Ivani et al.

NATURE METHODS (2016)

Article Biochemistry & Molecular Biology

Discovery of an Active RAG Transposon Illuminates the Origins of V(D)J Recombination

Shengfeng Huang et al.

Article Biochemistry & Molecular Biology

DNA Breaks and End Resection Measured Genome-wide by End Sequencing

Andres Canela et al.

MOLECULAR CELL (2016)

Article Cell Biology

Two Mutually Exclusive Local Chromatin States Drive Efficient V(D)J Recombination

Daniel J. Bolland et al.

CELL REPORTS (2016)

Article Biochemistry & Molecular Biology

RAG Represents a Widespread Threat to the Lymphocyte Genome

Grace Teng et al.

Article Biochemistry & Molecular Biology

IMGT®, the international ImMunoGeneTics information system® 25 years on

Marie-Paule Lefranc et al.

NUCLEIC ACIDS RESEARCH (2015)

Article Biochemistry & Molecular Biology

Synapsis Alters RAG-Mediated Nicking at Tcrb Recombination Signal Sequences: Implications for the Beyond 12/23 Rule

Joydeep K. Banerjee et al.

MOLECULAR AND CELLULAR BIOLOGY (2014)

Article Biochemistry & Molecular Biology

μABC: a systematic microsecond molecular dynamics study of tetranucleotide sequence effects in B-DNA

Marco Pasi et al.

NUCLEIC ACIDS RESEARCH (2014)

Review Immunology

The Response to and Repair of RAG-Mediated DNA Double-Strand Breaks

Beth A. Helmink et al.

ANNUAL REVIEW OF IMMUNOLOGY, VOL 30 (2012)

Article Biochemistry & Molecular Biology

The mechanics behind DNA sequence-dependent properties of the nucleosome

Eugene Y. D. Chua et al.

NUCLEIC ACIDS RESEARCH (2012)

Review Genetics & Heredity

V(D)J Recombination: Mechanisms of Initiation

David G. Schatz et al.

ANNUAL REVIEW OF GENETICS, VOL 45 (2011)

Article Biochemical Research Methods

Quality control and preprocessing of metagenomic datasets

Robert Schmieder et al.

BIOINFORMATICS (2011)

Review Immunology

Recombination centres and the orchestration of V(D)J recombination

David G. Schatz et al.

NATURE REVIEWS IMMUNOLOGY (2011)

Article Biochemistry & Molecular Biology

A Non-Sequence-Specific DNA Binding Mode of RAG1 Is Inhibited by RAG2

Shuying Zhao et al.

JOURNAL OF MOLECULAR BIOLOGY (2009)

Article Biochemistry & Molecular Biology

Structure of the RAG1 nonamer binding domain with DNA reveals a dimer that mediates DNA synapsis

Fang Fang Yin et al.

NATURE STRUCTURAL & MOLECULAR BIOLOGY (2009)

Article Biochemistry & Molecular Biology

Bind-n-Seq: high-throughput analysis of in vitro protein-DNA interactions using massively parallel sequencing

Artem Zykovich et al.

NUCLEIC ACIDS RESEARCH (2009)

Article Biochemistry & Molecular Biology

V(D)J recombinase binding and cleavage of cryptic recombination signal sequences identified from lymphoid malignancies

Ming Zhang et al.

JOURNAL OF BIOLOGICAL CHEMISTRY (2008)

Article Multidisciplinary Sciences

RAG2 PHD finger couples histone H3 lysine 4 trimethylation with V(D)J recombination

Adam G. W. Matthews et al.

NATURE (2007)

Article Biochemistry & Molecular Biology

A novel roll-and-slide mechanism of DNA folding in chromatin: Implications for nucleosome positioning

Michael Y. Tolstorukov et al.

JOURNAL OF MOLECULAR BIOLOGY (2007)

Article Multidisciplinary Sciences

ATM stabilizes DNA double-strand-break complexes during V(D)J recombination

Andrea L. Bredemeyer et al.

NATURE (2006)

Article Biochemistry & Molecular Biology

DNA cleavage of a cryptic recombination signal sequence by RAG1 and RAG2 -: Implications for partial VH gene replacement

NS Rahman et al.

JOURNAL OF BIOLOGICAL CHEMISTRY (2006)

Review Chemistry, Multidisciplinary

GROMACS: Fast, flexible, and free

D Van der Spoel et al.

JOURNAL OF COMPUTATIONAL CHEMISTRY (2005)

Article Immunology

Beyond the 12/23 rule of VDJ recombination independent of the rag proteins

A Olaru et al.

JOURNAL OF IMMUNOLOGY (2005)

Review Immunology

The role of the non-homologous end-joining pathway in lymphocyte development

S Rooney et al.

IMMUNOLOGICAL REVIEWS (2004)

Article Biochemistry & Molecular Biology

A functional analysis of the spacer of V(D)J recombination signal sequences

AI Lee et al.

PLOS BIOLOGY (2003)

Article Biochemistry & Molecular Biology

The central domain of core RAG1 preferentially recognizes single-stranded recombination signal sequence heptamer

MM Peak et al.

JOURNAL OF BIOLOGICAL CHEMISTRY (2003)

Article Biochemistry & Molecular Biology

A RAG-1/RAG-2 tetramer supports 12/23-regulated synapsis, cleavage, and transposition of V(D)J recombination signals

PC Swanson

MOLECULAR AND CELLULAR BIOLOGY (2002)