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Author Correction: ChromaFold predicts the 3D contact map from single-cell chromatin accessibility

Vianne R. Gao
Rui Yang
Christina S. Leslie
Amendments and CorrectionsOpen Access15 Jan 2025
Nature Communications

Volume: 16, P: 1
Decoding heterogeneous single-cell perturbation responses

In two independent studies, Song et al. and Jiang, Dalgarno et al. present computational frameworks, perturbation-response score and Mixscale, respectively, to determine individual cellular variation in response to perturbation.

Bicna Song
Dingyu Liu
Wei Li
ResearchOpen Access26 Feb 2025
Nature Cell Biology

Volume: 27, P: 493-504
ChromaFold predicts the 3D contact map from single-cell chromatin accessibility

Obtaining a high-resolution contact map using current 3D genomics technologies can be challenging with small input cell numbers. Here, the authors develop ChromaFold, a deep learning model that predicts cell-type-specific 3D contact maps from single-cell chromatin accessibility data alone.

Vianne R. Gao
Rui Yang
Christina S. Leslie
ResearchOpen Access01 Nov 2024
Nature Communications

Volume: 15, P: 1-15
Induction of pluripotent stem cells from primary human fibroblasts with only Oct4 and Sox2

One strategy for advancing induced pluripotent stem (iPS) cell technology toward the clinic is to replace the reprogramming genes with small molecules. Huangfu et al. show that the HDAC inhibitor valproic acid can substitute for the reprogramming gene Klf4, allowing human iPS cells to be generated with only two transgenes, Oct4 and Sox2.

Danwei Huangfu
Kenji Osafune
Douglas A Melton
Research12 Oct 2008
Nature Biotechnology

Volume: 26, P: 1269-1275
Author Correction: TET proteins safeguard bivalent promoters from de novo methylation in human embryonic stem cells

Nipun Verma
Heng Pan
Danwei Huangfu
Amendments and Corrections18 Dec 2017
Nature Genetics

Volume: 50, P: 764
Publisher Correction: TET proteins safeguard bivalent promoters from de novo methylation in human embryonic stem cells

Nipun Verma
Heng Pan
Danwei Huangfu
Amendments and Corrections18 Dec 2017
Nature Genetics

Volume: 50, P: 764
Parallel genome-scale CRISPR-Cas9 screens uncouple human pluripotent stem cell identity versus fitness

Pluripotent cells are defined by their ability to self-renew: to proliferate indefinitely while maintaining their identity. Here, authors use genome-scale CRISPR knockout screens to untangle these two aspects of self-renewal.

Bess P. Rosen
Qing V. Li
Danwei Huangfu
ResearchOpen Access17 Oct 2024
Nature Communications

Volume: 15, P: 1-19
Induction of pluripotent stem cells by defined factors is greatly improved by small-molecule compounds

Existing methods for reprogramming somatic cells to 'induced pluripotent stem cells' are inefficient, with only a small fraction of the starting cell population becoming pluripotent. Working with mouse embryonic fibroblasts, Hunagfu et al. increase reprogramming efficiency by treatment with DNA methyltransferase and histone deacetylase inhibitors.

Danwei Huangfu
René Maehr
Douglas A Melton
Research22 Jun 2008
Nature Biotechnology

Volume: 26, P: 795-797
Hedgehog signalling in the mouse requires intraflagellar transport proteins

Danwei Huangfu
Aimin Liu
Kathryn V. Anderson
Research06 Nov 2003
Nature

Volume: 426, P: 83-87
Dynamic network-guided CRISPRi screen identifies CTCF-loop-constrained nonlinear enhancer gene regulatory activity during cell state transitions

CRISPRi-based screen identifies enhancers that nonlinearly regulate lineage-specifying transcription factors during definitive endoderm differentiation. A new CTCF-loop-constrained Interaction Activity (CIA) model is better at predicting functional enhancers than previous Hi-C-based enhancer–promoter contact frequency models.

Renhe Luo
Jielin Yan
Michael A. Beer
Research24 Jul 2023
Nature Genetics

Volume: 55, P: 1336-1346
TET proteins safeguard bivalent promoters from de novo methylation in human embryonic stem cells

TET1, TET2 and TET3 triple-knockout (TKO) human embryonic stem cells (hESCs) exhibit bivalent promoter hypermethylation without a corresponding decrease in gene expression in the undifferentiated state. However, PAX6 promoter hypermethylation in TKO hESCs impairs neural differentiation.

Nipun Verma
Heng Pan
Danwei Huangfu
Research04 Dec 2017
Nature Genetics

Volume: 50, P: 83-95
MorPhiC Consortium: towards functional characterization of all human genes

This Perspective discusses strategies and challenges for the Molecular Phenotypes of Null Alleles in Cells (MorPhiC) Consortium as it aims to catalogue the molecular and cellular phenotypes associated with null alleles of all human genes.

Mazhar Adli
Laralynne Przybyla
Justina Žurauskienė
Reviews12 Feb 2025
Nature

Volume: 638, P: 351-359
MLL3 loss drives metastasis by promoting a hybrid epithelial–mesenchymal transition state

Cui et al. identify an important role for MLL3 in regulating the hybrid epithelial–mesenchymal transition state in breast cancer and show that deletion of MLL3 enhances metastatic capacity through increased IFNγ signalling.

Jihong Cui
Chi Zhang
Wenjun Guo
Research05 Jan 2023
Nature Cell Biology

Volume: 25, P: 145-158
Abnormal exocrine–endocrine cell cross-talk promotes β-cell dysfunction and loss in MODY8

Kahraman et al. show that transfer of mutant CEL protein from pancreatic acinar cells to β cells causes β-cell dysfunction, providing insight into the mechanism underlying MODY8.

Sevim Kahraman
Ercument Dirice
Rohit N. Kulkarni
Research20 Jan 2022
Nature Metabolism

Volume: 4, P: 76-89
CRISPR screening uncovers a central requirement for HHEX in pancreatic lineage commitment and plasticity restriction

Yang et al. report that HHEX acts as a gatekeeper of pancreatic lineage specification against the liver and duodenum fates via guiding FOXA1, FOXA2 and GATA4 to activate pancreatic genes, while restraining them from activating alternative lineages.

Dapeng Yang
Hyunwoo Cho
Danwei Huangfu
Research04 Jul 2022
Nature Cell Biology

Volume: 24, P: 1064-1076
Genome-scale screens identify JNK–JUN signaling as a barrier for pluripotency exit and endoderm differentiation

CRISPR screens identify JNK–JUN family genes as repressors of definitive endoderm differentiation in human pluripotent stem cells. JUN co-occupies stem cell enhancers with OCT4, NANOG, SMAD2 and SMAD3 and inhibits the exit from pluripotency.

Qing V. Li
Gary Dixon
Danwei Huangfu
Research20 May 2019
Nature Genetics

Volume: 51, P: 999-1010
Discovery of a drug candidate for GLIS3-associated diabetes

GLIS3 mutations are associated with type 1, type 2, and neonatal diabetes. Here, the authors generate mono-hormonal glucose-responding pancreatic β-like cells in vitro and through a screen identify a drug that rescues pancreatic β-like cell death in GLIS3 mutants by inhibiting the abnormally activated TGFβ pathway.

Sadaf Amin
Brandoch Cook
Shuibing Chen
ResearchOpen Access11 Jul 2018
Nature Communications

Volume: 9, P: 1-12
Functional analysis of a chromosomal deletion associated with myelodysplastic syndromes using isogenic human induced pluripotent stem cells

Cellular reprogramming is used to pinpoint the genetic abnormalities in a blood cancer caused by a large chromosomal deletion.

Andriana G Kotini
Chan-Jung Chang
Eirini P Papapetrou
Research23 Mar 2015
Nature Biotechnology

Volume: 33, P: 646-655
Glutamine independence is a selectable feature of pluripotent stem cells

Glutamine is a major fuel for proliferating cells. Here the authors show that reduced dependence on exogenous glutamine is a generalizable feature of self-renewing pluripotent stem cells that can be exploited to select for mouse and human pluripotent stem cells with high self-renewal potential.

Santosha A. Vardhana
Paige K. Arnold
Lydia W. S. Finley
Research08 Jul 2019
Nature Metabolism

Volume: 1, P: 676-687
Deciphering the impact of genomic variation on function

The Impact of Genomic Variation on Function Consortium is combining single-cell mapping, genomic perturbations and predictive modelling to investigate relationships between human genomic variation, genome function and phenotypes and will provide an open resource to the community.

Jesse M. Engreitz
Heather A. Lawson
Ella K. Samer
Reviews04 Sept 2024
Nature

Volume: 633, P: 47-57
Generation of human embryonic stem cell models to exploit the EWSR1-CREB fusion promiscuity as a common pathway of transformation in human tumors

Fabio Vanoli
Brigita Meskauskaite
Cristina R. Antonescu
Research30 Jun 2021
Oncogene

Volume: 40, P: 5095-5104

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Author Correction: ChromaFold predicts the 3D contact map from single-cell chromatin accessibility

Decoding heterogeneous single-cell perturbation responses

ChromaFold predicts the 3D contact map from single-cell chromatin accessibility

Induction of pluripotent stem cells from primary human fibroblasts with only Oct4 and Sox2

Author Correction: TET proteins safeguard bivalent promoters from de novo methylation in human embryonic stem cells

Publisher Correction: TET proteins safeguard bivalent promoters from de novo methylation in human embryonic stem cells

Parallel genome-scale CRISPR-Cas9 screens uncouple human pluripotent stem cell identity versus fitness

Induction of pluripotent stem cells by defined factors is greatly improved by small-molecule compounds

Hedgehog signalling in the mouse requires intraflagellar transport proteins

Dynamic network-guided CRISPRi screen identifies CTCF-loop-constrained nonlinear enhancer gene regulatory activity during cell state transitions

TET proteins safeguard bivalent promoters from de novo methylation in human embryonic stem cells

MorPhiC Consortium: towards functional characterization of all human genes

MLL3 loss drives metastasis by promoting a hybrid epithelial–mesenchymal transition state

Abnormal exocrine–endocrine cell cross-talk promotes β-cell dysfunction and loss in MODY8

CRISPR screening uncovers a central requirement for HHEX in pancreatic lineage commitment and plasticity restriction

Genome-scale screens identify JNK–JUN signaling as a barrier for pluripotency exit and endoderm differentiation

Discovery of a drug candidate for GLIS3-associated diabetes

Functional analysis of a chromosomal deletion associated with myelodysplastic syndromes using isogenic human induced pluripotent stem cells

Glutamine independence is a selectable feature of pluripotent stem cells

Deciphering the impact of genomic variation on function

Generation of human embryonic stem cell models to exploit the EWSR1-CREB fusion promiscuity as a common pathway of transformation in human tumors

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