Journal ArticleDOI
The Transition from Quiescent to Activated States in Human Hematopoietic Stem Cells Is Governed by Dynamic 3D Genome Reorganization
Naoya Takayama,Naoya Takayama,Alex Murison,Shin-ichiro Takayanagi,Christopher Arlidge,Stanley Zhou,Stanley Zhou,Laura García-Prat,Michelle Chan-Seng-Yue,Sasan Zandi,Olga I. Gan,Héléna Boutzen,Kerstin B. Kaufmann,Aaron Trotman-Grant,Erwin M. Schoof,Ken Kron,Noelia Díaz,John J.Y. Lee,Tiago Medina,Daniel D. De Carvalho,Daniel D. De Carvalho,Michael D. Taylor,Juan M. Vaquerizas,Stephanie Z. Xie,John E. Dick,John E. Dick,John E. Dick,Mathieu Lupien,Mathieu Lupien,Mathieu Lupien +29 more
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TLDR
3D chromatin interactions centrally mediated by CTCF endow a gatekeeper function that governs the earliest fate transitions HSCs make by coordinating disparate stemness pathways linked to quiescence and self-renewal.About:
This article is published in Cell Stem Cell.The article was published on 2021-03-04. It has received 40 citations till now. The article focuses on the topics: CTCF & Chromatin.read more
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Discovery and characterization of chromatin states for systematic annotation of the human genome
Jason Ernst,Manolis Kellis +1 more
TL;DR: In this article, a multivariate Hidden Markov Model was used to reveal chromatin states in human T cells, based on recurrent and spatially coherent combinations of chromatin marks.
Journal ArticleDOI
Enhancer Hijacking Drives Oncogenic BCL11B Expression in Lineage-Ambiguous Stem Cell Leukemia.
Lindsey E. Montefiori,Sonja Bendig,Zhaohui Gu,Xiao-Long Chen,Petri Pölönen,Xiaotu Ma,Alex Murison,Andy G.X. Zeng,Laura García-Prat,Kirsten Dickerson,Ilaria Iacobucci,Sherif Abdelhamed,Ryan Hiltenbrand,Paul E. Mead,Cyrus M. Mehr,Beisi Xu,Zhongshan Cheng,Ti-Cheng Chang,Tamara Westover,Jing Ma,Anna Stengel,Shunsuke Kimura,Chunxu Qu,Marcus B. Valentine,Marissa Rashkovan,Selina M. Luger,Mark R. Litzow,Jacob M. Rowe,Monique L. den Boer,Victoria Wang,Jun Yin,Steven M. Kornblau,Stephen P. Hunger,Mignon L. Loh,Ching-Hon Pui,Wenjian Yang,Kristine R. Crews,Kathryn G. Roberts,Jun J. Yang,Mary V. Relling,William E. Evans,Wendy Stock,Elisabeth Paietta,Adolfo A. Ferrando,Jinghui Zhang,Wolfgang Kern,Torsten Haferlach,Gang Wu,John E. Dick,Jeffery M. Klco,Claudia Haferlach,Charles G. Mullighan +51 more
TL;DR: In this paper, the authors describe a distinct subgroup of acute leukemia with expression of myeloid, T lymphoid, and stem cell markers driven by aberrant allele-specific deregulation of BCL11B, a master transcription factor responsible for thymic T-lineage commitment and specification.
Journal ArticleDOI
A cellular hierarchy framework for understanding heterogeneity and predicting drug response in acute myeloid leukemia
Andy G.X. Zeng,Suraj Bansal,Liqing Jin,Amanda Mitchell,Weihsu Claire Chen,Hussein A. Abbas,Michelle Chan-Seng-Yue,Veronique Voisin,Peter van Galen,Anne Tierens,Meyling Cheok,Claude Preudhomme,Hervé Dombret,Naval Daver,P. Andrew Futreal,Mark D. Minden,James A. Kennedy,Jean C.Y. Wang,John E. Dick +18 more
TL;DR: In this paper , the authors determined the leukemia cell hierarchy makeup from bulk transcriptomes of more than 1,000 patients through deconvolution using single-cell reference profiles of leukemia stem, progenitor and mature cell types.
Journal ArticleDOI
Polystyrene micro-/nanoplastics induced hematopoietic damages via the crosstalk of gut microbiota, metabolites, and cytokines.
TL;DR: In this article , the authors evaluated the hematopoietic toxicity induced by polystyrene micro-nanoplastics and potential mechanisms via combining 16S rRNA, metabolomics, and cytokine chips.
Journal ArticleDOI
A latent subset of human hematopoietic stem cells resists regenerative stress to preserve stemness.
Kerstin B. Kaufmann,Andy G.X. Zeng,Andy G.X. Zeng,Etienne Coyaud,Laura García-Prat,Efthymia Papalexi,Alex Murison,Estelle M.N. Laurent,Michelle Chan-Seng-Yue,Michelle Chan-Seng-Yue,Olga I. Gan,Kristele Pan,Jessica McLeod,Héléna Boutzen,Sasan Zandi,Sasan Zandi,Shin ichiro Takayanagi,Rahul Satija,Brian Raught,Brian Raught,Stephanie Z. Xie,John E. Dick,John E. Dick +22 more
TL;DR: Dick et al. as discussed by the authors identified distinct subsets of human long-term (LT)-HSCs that responded differently to regeneration-mediated stress: an immune checkpoint ligand CD112lo subset that exhibited a transient engraftment restraint (termed latency) before contributing to hematopoietic reconstitution and a primed CD112hi subset that responded rapidly.
References
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Journal ArticleDOI
Fast and accurate short read alignment with Burrows–Wheeler transform
Heng Li,Richard Durbin +1 more
TL;DR: Burrows-Wheeler Alignment tool (BWA) is implemented, a new read alignment package that is based on backward search with Burrows–Wheeler Transform (BWT), to efficiently align short sequencing reads against a large reference sequence such as the human genome, allowing mismatches and gaps.
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Ultrafast and memory-efficient alignment of short DNA sequences to the human genome
TL;DR: Bowtie extends previous Burrows-Wheeler techniques with a novel quality-aware backtracking algorithm that permits mismatches and can be used simultaneously to achieve even greater alignment speeds.
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An integrated encyclopedia of DNA elements in the human genome
TL;DR: The Encyclopedia of DNA Elements project provides new insights into the organization and regulation of the authors' genes and genome, and is an expansive resource of functional annotations for biomedical research.
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Model-based Analysis of ChIP-Seq (MACS)
Yong Zhang,Tao Liu,Clifford A. Meyer,Jérôme Eeckhoute,David S. Johnson,Bradley E. Bernstein,Bradley E. Bernstein,Chad Nusbaum,Richard M. Myers,Myles Brown,Wei Li,X. Shirley Liu +11 more
TL;DR: This work presents Model-based Analysis of ChIP-Seq data, MACS, which analyzes data generated by short read sequencers such as Solexa's Genome Analyzer, and uses a dynamic Poisson distribution to effectively capture local biases in the genome, allowing for more robust predictions.
Journal ArticleDOI
Learning the parts of objects by non-negative matrix factorization
TL;DR: An algorithm for non-negative matrix factorization is demonstrated that is able to learn parts of faces and semantic features of text and is in contrast to other methods that learn holistic, not parts-based, representations.