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Transcriptional Heterogeneity and Lineage Commitment in Myeloid Progenitors

Franziska Paul, Ya'ara Arkin, Amir Giladi, Diego Adhemar Jaitin, Ephraim Kenigsberg, Hadas Keren-Shaul, Deborah Winter, David Lara-Astiaso, Meital Gury, Assaf Weiner, Eyal David, Nadav Cohen (+10 others)
2015 Cell  
Research in I.A. and A.  ...  Colors are as indicated inFigure 2A.(C) Color-coded expression of key genes that mark the enriched subpopulation.  ...  AUTHOR CONTRIBUTIONS Figure 2 . 2 Transcriptional Networks Define Myeloid Progenitor Populations (A) Schematic showing mean expression of a single gene across clusters C1-C18 colored by the index sorting  ... 
doi:10.1016/j.cell.2015.11.013 pmid:26627738 fatcat:x5wvmeckybcdzfpzzky4c7mb6q

Lineage specification of human dendritic cells is marked by IRF8 expression in hematopoietic stem cells and multipotent progenitors

Jaeyop Lee, Yu Jerry Zhou, Wenji Ma, Wanwei Zhang, Arafat Aljoufi, Thomas Luh, Kimberly Lucero, Deguang Liang, Matthew Thomsen, Govind Bhagat, Yufeng Shen, Kang Liu
2017 Nature Immunology  
lineage bias defined by specific transcriptional programs correlated with the relative IRF8/PU.1 ratios, which is transmitted to most progeny and reinforced by FLT3Ldriven IRF8 upregulation over division  ...  monocytes, lymphocytes and three subsets of DCs from single human CD34 + progenitor cells, we show DC lineage specification occurs in parallel with myeloid and lymphoid lineages in HSCs, starting as a  ...  Boxes correspond to the gates for relative IRF8 and PU.1 expression level in each of the six mature cell lineages. t-SNE maps in b (bottom) show distribution of clones derived from progenitors, with colors  ... 
doi:10.1038/ni.3789 pmid:28650480 pmcid:PMC5743223 fatcat:4fqxxquabjc7jof6ycgd43ctzm

Chromatin state dynamics during blood formation

D. Lara-Astiaso, A. Weiner, E. Lorenzo-Vivas, I. Zaretsky, D. A. Jaitin, E. David, H. Keren-Shaul, A. Mildner, D. Winter, S. Jung, N. Friedman, I. Amit
2014 Science  
An important model system for differentiation is hematopoiesis where a single hematopoietic stem cell gives rise to a large number of cell types (comprising the blood) through a series of characterized  ...  According to this model, differentiation is a gradual transition from an open chromatin state in multipotent stem cells to a compacted chromatin state in differentiated cells.  ...  A patent application for iChIP has been filed by Yeda, Weizmann Institute of Science, Israel.  ... 
doi:10.1126/science.1256271 pmid:25103404 pmcid:PMC4412442 fatcat:ap43vx3pkne6livl5ruya7ydpa

Active enhancers are delineated de novo during hematopoiesis, with limited lineage fidelity among specified primary blood cells

Annouck Luyten, Chongzhi Zang, X. Shirley Liu, Ramesh A. Shivdasani
2014 Genes & Development  
Chromatin dynamics in hematopoiesis provide a useful foundation to consider classical observations such as cellular reprogramming and multilineage locus priming.  ...  This work was supported by National Institutes of Health grants R01HL63143 (R.A.S.) and R01GM099409 (X.S.L.) and a fellowship from the Leukemia and Lymphoma Society (C.Z.).  ...  j on gene i, and j refers to a dynamic process between two consecutive differentiation steps; i.e., HSC to CMP, CMP to GMP or MEP, GMP to GRAN IMM , GRAN IMM to GRAN MAT , etc.  ... 
doi:10.1101/gad.240101.114 pmid:25128499 pmcid:PMC4197967 fatcat:suvgfg3fyndjne4rbdhwyayafi

Sequestration of a two-component response regulator by a riboswitch-regulated noncoding RNA

J. R. Mellin, M. Koutero, D. Dar, M.-A. Nahori, R. Sorek, P. Cossart
2014 Science  
In contrast, enhancer loss is a more gradual process that initiates in the CMP or MEP stage (for myeloid and erythrocyte development, respectively) with a large proportion (40 to 50%) of enhancers lost  ...  An important model system for differentiation is hematopoiesis, in which a single hematopoietic stem cell gives rise to a large number of cell types (comprising the blood) through a series of characterized  ... 
doi:10.1126/science.1255083 pmid:25146292 fatcat:pn26wgzhwna7ldope23pqffcie

Single-cell epigenomics maps the continuous regulatory landscape of human hematopoietic differentiation [article]

Jason Daniel Buenrostro, Ryan Corces, Beijing Wu, Alicia N Schep, Caleb Lareau, Ravindra Majeti, Howard Chang, William Greenleaf
2017 bioRxiv   pre-print
While epigenomic landscapes of this process have been explored in immunophenotypically-defined populations, the single-cell regulatory variation that defines hematopoietic differentiation has been hidden  ...  , and observe relatively simple TF motif dynamics give rise to a broad diversity of accessibility dynamics at cis-regulatory elements.  ...  In concordance with these findings we find four CMP clusters, with significant variability across GATA1, BCL11A and SPI1 (PU.1), TFs implicated in myeloid/erythroid specification (Fig. 4a) .  ... 
doi:10.1101/109843 fatcat:qgxj7zqhnrdtrnxklwtf53abh4

Mapping Cellular Hierarchy by Single-Cell Analysis of the Cell Surface Repertoire

Guoji Guo, Sidinh Luc, Eugenio Marco, Ta-Wei Lin, Cong Peng, Marc A. Kerenyi, Semir Beyaz, Woojin Kim, Jian Xu, Partha Pratim Das, Tobias Neff, Keyong Zou (+2 others)
2013 Cell Stem Cell  
The strategy has broad applicability in other cellular systems.  ...  The comprehensive single cell data set permits mapping of the mouse hematopoietic stem cell differentiation hierarchy by computational lineage progression analysis.  ...  Examples of single-cell GEDI map from different cell types are presented. Color scale is as described in Figure 1B .  ... 
doi:10.1016/j.stem.2013.07.017 pmid:24035353 pmcid:PMC3845089 fatcat:d57jpv6grzg3dahjwyctku66re

Technical Advance: Transcription factor, promoter, and enhancer utilization in human myeloid cells

Anagha Joshi, Christopher Pooley, Tom C. Freeman, Andreas Lennartsson, Magda Babina, Christian Schmidl, Teunis Geijtenbeek, Tom Michoel, Jessica Severin, Masayoshi Itoh, Timo Lassmann, Hideya Kawaji (+5 others)
2015 Journal of Leukocyte Biology  
The PU.1-expressing CMPs were found to have myeloid potential, whereas PU.1-deficient CMPs had erythroid potential, suggesting that PU.1 expression determines the developmental fate of a CMP [35] .  ...  A description of sample preparation, quality control, and data processing is provided in Supplemental Methods.  ... 
doi:10.1189/jlb.6ta1014-477rr pmid:25717144 pmcid:PMC4398258 fatcat:bxlskkzlavhxvohahx4223nfcy

Intelligent Trace and Evaluation for Parallel Programming Based on Architectural Details

Jiaxin Li, Feng Shi, Ning Deng, Qi Zuo, Zuo Wang, Mengxiao Liu
2009 Journal of Computers  
As CMP became the main stream of processer design, parallel programming is a new challenge for programmer.  ...  How could programmers figure out if their programs, which based on specific multi-processing architectures and mapping strategies, are efficient and even portable?  ...  It maps computing task into 9 Of objects, and the shared memory is mapped to hierarchy memory system of TriBA.  ... 
doi:10.4304/jcp.4.11.1125-1132 fatcat:2psiet5uijheppq53xplzkyplq

A microRNA expression signature of osteoclastogenesis

T. Sugatani, J. Vacher, K. A. Hruska
2011 Blood  
Diminished PDCD4 removes a repression from c-Fos, a critical transcription factor for osteoclastogenesis and osteoclast-specific downstream target genes.  ...  Thus, our studies provide a new molecular mechanism, including a positive feedback loop of c-Fos/miR-21/PDCD4, regulating osteoclastogenesis. (Blood. 2011;117(13): 3648-3657)  ...  because PU.1-deficient mice have a decreased number of macrophages and no osteoclasts. 2, 3 CMPs are classified into Ն 2 subpopulations which are PU.1-expressing CMPs and PU.1 nonexpressing CMPs. 35  ... 
doi:10.1182/blood-2010-10-311415 pmid:21273303 pmcid:PMC3072882 fatcat:phhhlrhlnjfpnobbggoa4uamxa


Junwen Pu, Jian-Hang Lin, Qiang Zhao, Shu-Ke Zhou, Sheng Yao, Mian Xing
2010 BioResources  
Before single-stage hydrogen peroxide bleaching, CMP was sonicated at 1.5% pulp consistency and 50oC for 20min with 90% amplitude and 20s pulse; these conditions showed the most favorable effect of a 3.5%  ...  ISO increase of brightness, reaching a final value of 80.2% ISO.  ...  bleaching process.  ... 
doaj:da3802b05bfc4a4b9d1cdf2ea884e46d fatcat:vdkfmx4j4rfufmlfudbrdvxwri


Luis Angel D. Bathen, Yongjin Ahn, Sudeep Pasricha, Nikil D. Dutt
2013 ACM Transactions on Embedded Computing Systems  
The increasing demand for low-power and high-performance multimedia embedded systems has motivated the need for effective solutions to satisfy application bandwidth and latency requirements under a tight  ...  Our approach decomposes the application's tasks into smaller units of computations called kernels, which are distributed and pipelined across the different processing resources.  ...  For example, if |β| 2 is bigger than the random variable, the Q-bit can be mapped to C PU 1 processor and if not it is mapped to C PU 0 .  ... 
doi:10.1145/2435227.2435255 fatcat:cgyrtmttoff6hfdxgo2bwsakqq

Integrated Single-Cell Analysis Maps the Continuous Regulatory Landscape of Human Hematopoietic Differentiation

Jason D. Buenrostro, M. Ryan Corces, Caleb A. Lareau, Beijing Wu, Alicia N. Schep, Martin J. Aryee, Ravindra Majeti, Howard Y. Chang, William J. Greenleaf
2018 Cell  
We observe that the 4 CMP clusters within our data show significant variability across motifs associated with GATA1, BCL11A and SPI1 (PU.1), TFs implicated in myeloid/erythroid specification ( Figure  ...  Given these differences, we assigned CMP clusters as CMP-K3 (early erythroid), CMP-K5 (late erythroid), CMP-K4 (unknown) and CMP-K2 (myeloid primed).  ...  Highlights • Single-cell chromatin accessibility reveals a heterogeneous hematopoietic landscape  ... 
doi:10.1016/j.cell.2018.03.074 pmid:29706549 pmcid:PMC5989727 fatcat:2jcbbnm4gbdolonx5r7hux4lda

A Highly Sensitive and Robust Method for Genome-wide 5hmC Profiling of Rare Cell Populations

Dali Han, Xingyu Lu, Alan H. Shih, Ji Nie, Qiancheng You, Meng Michelle Xu, Ari M. Melnick, Ross L. Levine, Chuan He
2016 Molecular Cell  
We present a highly sensitive and selective chemical labeling and capture approach for genomewide profiling of 5-hydroxylmethylcytosine (5hmC) using DNA isolated from ~1,000 cells (nano-hmC-Seal).  ...  .), a Starr Cancer Consortium grant (R.L.L. and A.M.M) and a Leukemia Lymphoma Society (LLS) SCOR grant 7006-13 (A.M.M.). A.H.S is a Special Fellow of the LLS and RLL is a Scholar of the LLS.  ...  Genes in the same terms were linked to each other.The genes within the same clusters are surrounded by a common background color.  ... 
doi:10.1016/j.molcel.2016.06.028 pmid:27477909 pmcid:PMC4992443 fatcat:2ldgunirbvdshe3j5kj3srpgh4

Overexpression of a hematopoietic transcriptional regulator EDAG induces myelopoiesis and suppresses lymphopoiesis in transgenic mice

C-Y Li, Y-Q Zhan, W Li, C-W Xu, W-X Xu, D-H Yu, R-Y Peng, Y-F Cui, X Yang, N Hou, Y-H Li, B Dong (+2 others)
2007 Leukemia  
Moreover, we showed that EDAG was a transcriptional regulator which had transactivation activity and regulated the expression of several key transcription factors such as PU.1 and Pax5 in transgenic hematopoietic  ...  Erythroid differentiation-associated gene (EDAG) is a hematopoietic tissue-specific gene that is highly expressed in the earliest CD34 þ lin À bone marrow (BM) cells and involved in the proliferation and  ...  For the analysis of CMP, BM CMPs were seeded at a density of 5 Â 10 2 cells/ml. For the analysis of CLP, BM CLPs were seeded at a density of 5 Â 10 3 cells/ml.  ... 
doi:10.1038/sj.leu.2404901 pmid:17690693 fatcat:twd4ymrj7vcjzehlbalppbsagu
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