Explanipedia

A single-cell time-lapse of mouse prenatal development from gastrula to birth Open

Chengxiang Qiu, Beth Martin, Ian Welsh, Riza M. Daza, Truc-Mai Le , et al. · 2024

The house mouse ( Mus musculus ) is an exceptional model system, combining genetic tractability with close evolutionary affinity to humans 1,2 . Mouse gestation lasts only 3 weeks, during which the genome orchestrates the astonishing trans…

Single-cell, whole-embryo phenotyping of mammalian developmental disorders Open

Xingfan Huang, Jana Henck, Chengxiang Qiu, Varun K. A. Sreenivasan, Saranya Balachandran , et al. · 2023

Mouse models are a critical tool for studying human diseases, particularly developmental disorders 1 . However, conventional approaches for phenotyping may fail to detect subtle defects throughout the developing mouse 2 . Here we set out t…

A single-cell multi-omic atlas spanning the adult rhesus macaque brain Open

Kenneth L. Chiou, Xingfan Huang, Martin O. Bohlen, Sébastien Tremblay, Alex R. DeCasien , et al. · 2023

Cataloging the diverse cellular architecture of the primate brain is crucial for understanding cognition, behavior, and disease in humans. Here, we generated a brain-wide single-cell multimodal molecular atlas of the rhesus macaque brain. …

A single-cell transcriptional timelapse of mouse embryonic development, from gastrula to pup Open

Chengxiang Qiu, Beth Martin, Ian Welsh, Riza M. Daza, Truc-Mai Le , et al. · 2023

The house mouse, Mus musculus , is an exceptional model system, combining genetic tractability with close homology to human biology. Gestation in mouse development lasts just under three weeks, a period during which its genome orchestrates…

A single-cell multi-omic atlas spanning the adult rhesus macaque brain Open

Kenneth L. Chiou, Xingfan Huang, Martin O. Bohlen, Sébastien Tremblay, Diana R. O’Day , et al. · 2022

Cataloging the diverse cellular architecture of the primate brain is crucial for understanding cognition, behavior and disease in humans. Here, we generated a brain-wide single-cell multimodal molecular atlas of the rhesus macaque brain. A…

The continuum of Drosophila embryonic development at single-cell resolution Open

Diego Calderon, Ronnie Blecher‐Gonen, Xingfan Huang, Stefano Secchia, James A. Kentro , et al. · 2022

Drosophila melanogaster is a powerful, long-standing model for metazoan development and gene regulation. We profiled chromatin accessibility in almost 1 million and gene expression in half a million nuclei from overlapping windows spanning…

Single cell, whole embryo phenotyping of pleiotropic disorders of mammalian development Open

Xingfan Huang, Jana Henck, Chengxiang Qiu, Varun K. A. Sreenivasan, Saranya Balachandran , et al. · 2022

Mouse models are a critical tool for studying human diseases, particularly developmental disorders, as well as for advancing our general understanding of mammalian biology. However, it has long been suspected that conventional approaches f…

Systematic reconstruction of cellular trajectories across mouse embryogenesis Open

Chengxiang Qiu, Junyue Cao, Beth Martin, Tony Li, Ian Welsh , et al. · 2022

Systematic reconstruction of the cellular trajectories of mammalian embryogenesis Open

Chengxiang Qiu, Junyue Cao, Tony Li, Sanjay Srivatsan, Xingfan Huang , et al. · 2021

Mammalian embryogenesis is characterized by rapid cellular proliferation and diversification. Within a few weeks, a single cell zygote gives rise to millions of cells expressing a panoply of molecular programs, including much of the divers…

Large DNA Methylation Nadirs Anchor Chromatin Loops Maintaining Hematopoietic Stem Cell Identity Open

Xiaotian Zhang, Mira Jeong, Xingfan Huang, Xue Qing David Wang, Xinyu Wang , et al. · 2020

ESCO1 and CTCF enable formation of long chromatin loops by protecting cohesinSTAG1 from WAPL Open

Gordana Wutz, René Ladurner, Brian Glenn St Hilaire, Roman R. Stocsits, Kota Nagasaka , et al. · 2020

Eukaryotic genomes are folded into loops. It is thought that these are formed by cohesin complexes via extrusion, either until loop expansion is arrested by CTCF or until cohesin is removed from DNA by WAPL. Although WAPL limits cohesin’s …

Author response: ESCO1 and CTCF enable formation of long chromatin loops by protecting cohesinSTAG1 from WAPL Open

Gordana Wutz, René Ladurner, Brian Glenn St Hilaire, Roman R. Stocsits, Kota Nagasaka , et al. · 2019

ESCO1 and CTCF enable formation of long chromatin loops by protecting cohesinSTAG1 from WAPL Open

Gordana Wutz, René Ladurner, Brian St. Hilaire, Roman R. Stocsits, Kota Nagasaka , et al. · 2019

Eukaryotic genomes are folded into loops. It is thought that these are formed by cohesin complexes via extrusion, either until loop expansion is arrested by CTCF or until cohesin is removed from DNA by WAPL. Although WAPL limits cohesin’s …

Robust CTCF-Based Chromatin Architecture Underpins Epigenetic Changes in the Heart Failure Stress–Gene Response Open

Dominic Paul Lee, Wilson Lek Wen Tan, Chukwuemeka George Anene-Nzelu, Chang Jie Mick Lee, Peter Yiqing Li , et al. · 2019

Background: The human genome folds in 3 dimensions to form thousands of chromatin loops inside the nucleus, encasing genes and cis -regulatory elements for accurate gene expression control. Physical tethers of loops are anchored by the DNA…

Accurate classification of BRCA1 variants with saturation genome editing Open

Gregory M. Findlay, Riza M. Daza, Beth Martin, Melissa D. Zhang, Anh Leith , et al. · 2018

A Single-Cell Atlas of In Vivo Mammalian Chromatin Accessibility Open

Darren A. Cusanovich, Andrew J. Hill, Delasa Aghamirzaie, Riza M. Daza, Hannah A. Pliner , et al. · 2018

Accurate functional classification of thousands of BRCA1 variants with saturation genome editing Open

Gregory M. Findlay, Riza M. Daza, Beth Martin, Melissa D. Zhang, Anh Leith , et al. · 2018

Variants of uncertain significance (VUS) fundamentally limit the utility of genetic information in a clinical setting. The challenge of VUS is epitomized by BRCA1 , a tumor suppressor gene integral to DNA repair and genomic stability. Germ…

A Cell type-specific Class of Chromatin Loops Anchored at Large DNA Methylation Nadirs Open

Mira Jeong, Xingfan Huang, Xiaotian Zhang, Jianzhong Su, Muhammad S. Shamim , et al. · 2017

Higher order chromatin structure and DNA methylation are implicated in multiple developmental processes, but their relationship to cell state is unknown. Here, we found that large (~10kb) DNA methylation nadirs can form long loops connecti…

Cohesin Loss Eliminates All Loop Domains Open

Suhas S.P. Rao, Su-Chen Huang, Brian Glenn St Hilaire, J Engreitz, Elizabeth M. Perez , et al. · 2017

Cohesin Loss Eliminates All Loop Domains Open

Suhas S.P. Rao, Su‐Chen Huang, Brian Glenn St Hilaire, J Engreitz, Elizabeth M. Perez , et al. · 2017

The human genome folds to create thousands of intervals, called “contact domains,” that exhibit enhanced contact frequency within themselves. “Loop domains” form because of tethering between two loci—almost always bound by CTCF and cohesin…

Cohesin loss eliminates all loop domains, leading to links among superenhancers and downregulation of nearby genes Open

Suhas S.P. Rao, Su‐Chen Huang, Brian Glenn St Hilair, J Engreitz, Elizabeth M. Perez , et al. · 2017

SUMMARY The human genome folds to create thousands of intervals, called “contact domains,” that exhibit enhanced contact frequency within themselves. “Loop domains” form because of tethering between two loci - almost always bound by CTCF a…

The systematic analysis of coding and long non-coding RNAs in the sub-chronic and chronic stages of spinal cord injury Open

Raquel Cuevas‐Díaz Durán, Han Yan, Yiyan Zheng, Xingfan Huang, Raymond J. Grill , et al. · 2017

Xingfan Huang YOU? Author Swipe