RAG chromatin scanning during V (D) J recombination and chromatin loop extrusion are related processes

SG Lin, Z Ba, FW Alt, Y Zhang - Advances in immunology, 2018 - Elsevier
An effective adaptive immune system depends on the ability of developing B and T cells to
generate diverse immunoglobulin (Ig) and T cell receptor repertoires, respectively. Such …

RNA exosome drives early B cell development via noncoding RNA processing mechanisms

B Laffleur, CR Batista, W Zhang, J Lim, B Yang… - Science …, 2022 - science.org
B cell development is linked to successful V (D) J recombination, allowing B cell receptor
expression and ultimately antibody secretion for adaptive immunity. Germline noncoding …

Enhancer-instructed epigenetic landscape and chromatin compartmentalization dictate a primary antibody repertoire protective against specific bacterial pathogens

EM Barajas-Mora, L Lee, H Lu, JA Valderrama… - Nature …, 2023 - nature.com
Antigen receptor loci are organized into variable (V), diversity (D) and joining (J) gene
segments that rearrange to generate antigen receptor repertoires. Here, we identified an …

Individualized VDJ recombination predisposes the available Ig sequence space

A Slabodkin, M Chernigovskaya, I Mikocziova… - Genome …, 2021 - genome.cshlp.org
The process of recombination between variable (V), diversity (D), and joining (J)
immunoglobulin (Ig) gene segments determines an individual's naive Ig repertoire and …

LeNup: learning nucleosome positioning from DNA sequences with improved convolutional neural networks

J Zhang, W Peng, L Wang - Bioinformatics, 2018 - academic.oup.com
Motivation Nucleosome positioning plays significant roles in proper genome packing and its
accessibility to execute transcription regulation. Despite a multitude of nucleosome …

Chromatin remodeling is required for sRNA‐guided DNA elimination in Paramecium

A Singh, XX Maurer‐Alcalá, T Solberg… - The EMBO …, 2022 - embopress.org
Small RNAs mediate the silencing of transposable elements and other genomic loci,
increasing nucleosome density and preventing undesirable gene expression. The …

T cell repertoire abnormality in immunodeficiency patients with DNA repair and methylation defects

M Fang, Z Su, H Abolhassani, W Zhang, C Jiang… - Journal of Clinical …, 2022 - Springer
Both DNA damage response and methylation play a crucial role in antigen receptor
recombination by creating a diverse repertoire in developing lymphocytes, but how their …

Nucleosome repositioning during differentiation of a human myeloid leukemia cell line

VB Teif, JP Mallm, T Sharma, DB Mark Welch, K Rippe… - Nucleus, 2017 - Taylor & Francis
Cell differentiation is associated with changes in chromatin organization and gene
expression. In this study, we examine chromatin structure following differentiation of the …

Distinguishing between monozygotic twins' blood samples through immune repertoire sequencing

D Meng, P Zhou, M Li, J Xu, L Lu, Y Guo, C Yu… - Forensic Science …, 2023 - Elsevier
Monozygotic (MZ) twins with highly similar genomic DNA sequences can not be
distinguished by conventional forensic DNA testing. The immune repertoire (IR) reflects an …

Genome-wide characterization of fragile and resistant nucleosomes in response to cold stress in maize

R Huang, Q Zhu, S Tao, J Gao, Y Shi, Y Feng… - Environmental and …, 2024 - Elsevier
Distinct nucleosome (Nuc) architectures decode key regulatory information related to
various cellular processes. However, how fragile nucleosomes (FNs) and resistant …