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Interplay between CTCF-binding and CTCF-lacking regulatory elements in generating an architectural stripe at the Igh locus

Three-dimensional genome organization is crucial for the recombination and transcription of immunoglobulin heavy chain (Igh) genes. Here, the authors elucidate how regulatory elements in the 3′Igh domain influence chromatin structure and stripe formation.

Fei Ma
Noah Ollikainen
Xiang Qiu
ResearchOpen Access03 Mar 2025
Nature Communications

Volume: 16, P: 1-15
Three-dimensional chromatin reorganization regulates B cell development during ageing

Ma, Cao et al. uncover dynamic changes of chromatin reorganization in progenitor B cells during ageing, associated with altered H3K27ac levels and expression of genes that are critical for B cell development.

Fei Ma
Yaqiang Cao
Ranjan Sen
ResearchOpen Access12 Jun 2024
Nature Cell Biology

Volume: 26, P: 991-1002
Long non-coding RNAs: spatial amplifiers that control nuclear structure and gene expression

Mechanistic insights are emerging into how long non-coding RNAs (lncRNAs) regulate gene expression by coordinating regulatory proteins, localizing to genomic loci and shaping nuclear organization. Interestingly, lncRNAs can perform functions that cannot be carried out by DNA elements or proteins alone, such as amplifying regulatory signals in the nucleus.

Jesse M. Engreitz
Noah Ollikainen
Mitchell Guttman
Reviews26 Oct 2016
Nature Reviews Molecular Cell Biology

Volume: 17, P: 756-770
Systems-level effects of allosteric perturbations to a model molecular switch

Interface mutations in the GTPase switch protein Gsp1 (the yeast homologue of human RAN) allosterically affect the kinetics of the switch cycle, revealing a systems-level mechanism of multi-specificity.

Tina Perica
Christopher J. P. Mathy
Tanja Kortemme
Research13 Oct 2021
Nature

Volume: 599, P: 152-157
Integrated spatial genomics reveals global architecture of single nuclei

Multiplexed imaging of 3,660 chromosomal loci in individual mouse embryonic stem cells by DNA seqFISH+ with immunofluorescence of 17 chromatin marks and subnuclear structures reveals invariant organization of loci within individual cells, and heterogeneous and long-lived distinct combinatorial chromatin states in cellular subpopulations.

Yodai Takei
Jina Yun
Long Cai
Research27 Jan 2021
Nature

Volume: 590, P: 344-350
Single-cell measurement of higher-order 3D genome organization with scSPRITE

Long-range genome interactions are measured in thousands of single cells.

Mary V. Arrastia
Joanna W. Jachowicz
Mitchell Guttman
Research23 Aug 2021
Nature Biotechnology

Volume: 40, P: 64-73
Macromolecular modeling and design in Rosetta: recent methods and frameworks

This Perspective reviews tools developed over the past five years in the macromolecular modeling, docking and design software Rosetta.

Julia Koehler Leman
Brian D. Weitzner
Richard Bonneau
Reviews01 Jun 2020
Nature Methods

Volume: 17, P: 665-680
SPRITE: a genome-wide method for mapping higher-order 3D interactions in the nucleus using combinatorial split-and-pool barcoding

This protocol describes an experimental and computational approach for mapping higher-order DNA interactions that relies on tagging cross-linked fragmented chromatin through an iterative split-and-pool barcoding process.

Sofia A. Quinodoz
Prashant Bhat
Mitchell Guttman
Protocols10 Jan 2022
Nature Protocols

Volume: 17, P: 36-75
A combined risk score enhances prediction of type 1 diabetes among susceptible children

In a study of children with high genetic risk aged 2 years or older, a risk score integrating pancreatic islet autoantibodies, genetic factors and family history is highly predictive of type 1 diabetes in the subsequent 8 years.

Lauric A. Ferrat
Kendra Vehik
Roy Tamura
Research07 Aug 2020
Nature Medicine

Volume: 26, P: 1247-1255
Author Correction: A combined risk score enhances prediction of type 1 diabetes among susceptible children

Lauric A. Ferrat
Kendra Vehik
Roy Tamura
Amendments and Corrections14 Feb 2022
Nature Medicine

Volume: 28, P: 599
Risk of celiac disease autoimmunity is modified by interactions between CD247 and environmental exposures

Anna Eurén
Kristian Lynch
Eric Triplett
ResearchOpen Access26 Oct 2024
Scientific Reports

Volume: 14, P: 1-14
Telomere length is not a main factor for the development of islet autoimmunity and type 1 diabetes in the TEDDY study

Carina Törn
Xiang Liu
Eric W. Triplett
ResearchOpen Access16 Mar 2022
Scientific Reports

Volume: 12, P: 1-11
Dynamic changes in immune gene co-expression networks predict development of type 1 diabetes

Ingrid Brænne
Suna Onengut-Gumuscu
Eric Triplett
ResearchOpen Access22 Nov 2021
Scientific Reports

Volume: 11, P: 1-13
Children’s erythrocyte fatty acids are associated with the risk of islet autoimmunity

Sari Niinistö
Iris Erlund
Eric Triplett
ResearchOpen Access11 Feb 2021
Scientific Reports

Volume: 11, P: 1-12
Metabolite-related dietary patterns and the development of islet autoimmunity

Randi K. Johnson
Lauren Vanderlinden
Eric Triplett
ResearchOpen Access15 Oct 2019
Scientific Reports

Volume: 9, P: 1-11

Search

Interplay between CTCF-binding and CTCF-lacking regulatory elements in generating an architectural stripe at the Igh locus

Three-dimensional chromatin reorganization regulates B cell development during ageing

Long non-coding RNAs: spatial amplifiers that control nuclear structure and gene expression

Systems-level effects of allosteric perturbations to a model molecular switch

Integrated spatial genomics reveals global architecture of single nuclei

Single-cell measurement of higher-order 3D genome organization with scSPRITE

Macromolecular modeling and design in Rosetta: recent methods and frameworks

SPRITE: a genome-wide method for mapping higher-order 3D interactions in the nucleus using combinatorial split-and-pool barcoding

A combined risk score enhances prediction of type 1 diabetes among susceptible children

Author Correction: A combined risk score enhances prediction of type 1 diabetes among susceptible children

Risk of celiac disease autoimmunity is modified by interactions between CD247 and environmental exposures

Telomere length is not a main factor for the development of islet autoimmunity and type 1 diabetes in the TEDDY study

Dynamic changes in immune gene co-expression networks predict development of type 1 diabetes

Children’s erythrocyte fatty acids are associated with the risk of islet autoimmunity

Metabolite-related dietary patterns and the development of islet autoimmunity

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