Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

TCF7 is a key regulator of the switch of self-renewal and differentiation in a multipotential hematopoietic cell line

ABSTRACT: A critical problem in biology is understanding how cells choose between self-renewal and differentiation. To generate a comprehensive view of the mechanisms controlling early hematopoietic precursor self-renewal and differentiation, we used systems-based approaches and murine EML multipotential hematopoietic precursor cells as a primary model. EML cells give rise to a mixture of self-renewing Lin-SCA+CD34+ cells and partially differentiated non-renewing Lin-SCA-CD34- cells in a cell autonomous fashion. We identified and validated the HMG box protein TCF7 as a key regulator in this self-renewal/differentiation switch, and it operates in the absence of canonical Wnt signaling. We found that TCF7 is the most downregulated transcription factor when CD34+ cells switch into CD34- cells using RNA-Seq. We subsequently identified the target genes bound by TCF7 using ChIP-Seq. We show that TCF7 binds to Runx1 (Aml1) promoter region, and RUNX1 and TCF7 co-regulate. Gene Set Enrichment Analysis suggests that TCF7 primarily acts as a positive regulator of genes preferentially expressed in CD34+ cells. Consistent with this possibility, knocking-down TCF7 represses many up-regulated genes in Lin-CD34+ cells. Finally a network of up-regulated transcription factors of CD34+ cells which defines the self-renewing state was constructed. These studies in EML cells demonstrate fundamental cell-intrinsic properties of the switch between self-renewal and differentiation, and yield valuable insights for manipulating HSCs and other differentiating systems. Examining the transcription factor binding targets of TCF7 and RUNX1.

ORGANISM(S): Mus musculus

SUBMITTER: Jiaqian Wu

PROVIDER: E-GEOD-31221 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Publications

Tcf7 is an important regulator of the switch of self-renewal and differentiation in a multipotential hematopoietic cell line.

Wu Jia Qian JQ Seay Montrell M Schulz Vincent P VP Hariharan Manoj M Tuck David D Lian Jin J Du Jiang J Shi Minyi M Ye Zhijia Z Gerstein Mark M Snyder Michael P MP Weissman Sherman S

PLoS genetics 20120308 3

A critical problem in biology is understanding how cells choose between self-renewal and differentiation. To generate a comprehensive view of the mechanisms controlling early hematopoietic precursor self-renewal and differentiation, we used systems-based approaches and murine EML multipotential hematopoietic precursor cells as a primary model. EML cells give rise to a mixture of self-renewing Lin-SCA+CD34+ cells and partially differentiated non-renewing Lin-SCA-CD34- cells in a cell autonomous f ...[more]

PMID: 22412390

Similar Datasets

Project description:The mammalian blood system is a hierarchically structured tissue. Hematopoietic stem cells (HSC) reside at the top of this hierarchy and the HSC-derived progenitor cells (HPC) have capacities for both differentiation and self-renewal. Systematic study of the regulatory mechanisms of HSC self-renewal and differentiation is fundamentally important for understanding hematopoiesis and for manipulating HSCs for therapeutic purposes. Herein, the mechanisms regulating HSC biology were studied on a genome-wide scale by integrating epigenomic, transcriptomic, proteomic, and protein-protein interaction data. Previously, we have characterized gene expression and identified important transcription factors (TFs) regulating the switch between self-renewal and differentiation in a multipotent hematopoietic progenitor cell line, EML (Erythroid, Myeloid, and Lymphoid). In the present study, we report binding maps for three additional TFs (SOX4, STAT3, and GABP) that were developed by chromatin immunoprecipitation (ChIP)-Sequencing. Assay for Transposase Accessible Chromatin (ATAC)-Sequencing was applied to globally identify the open chromatin regions associated with TF binding in the self-renewing subpopulation lin-CD34+.Mass spectrometry (MS) was also used to identify proteins and assess differences in their relative abundances. We found that MAPK (Mitogen-activated protein kinase) pathway and JAK-STAT (Janus kinase-signal transducer and activator of transcription) pathway components were highly enriched among the binding targets of these TFs in CD34+ cells, and that the TGF-β/SMAD signaling pathway comprised a sub-network of molecules that were differentially expressed between the lin-CD34+ and partially differentiated lin-CD34- cellular states. The present study integrates regulatory information at multiple levels to paint for the first time a more comprehensive picture of the mechanisms underlying the decision between HPC self-renewal and differentiation. We anticipate that this work will provide valuable clues for understanding the molecular switch that controls cell fate decisions between self-renewal or differentiation and blood formation.

Project description:Human embryonic stem cells (hESCs) offer an important model for investigating the human hematopoietic celldevelopment. Here, we used long serial analysis of gene expression and quantitative real-time PCR to characterize two subsets of primitive hematopoietic cells derived in vitro from hESCs. This revealed differences in their expression of genes associated with lymphoid and myeloid development, cellular biosynthetic processes, and cell cycle regulation. Further comparisons with analogous data for primitive hematopoietic cells isolated from first trimester human fetal liver and newborn cord blood showed a strong similarity between the transcriptomes of the most primitive hESC- and in vivo-derived populations, with the main differences involving genes that regulate HSC development, self-renewal and homing, chromatin remodeling, AP1 transcription complex genes, and non-coding RNAs. These data suggest that primitive hematopoietic cells are generated from hESCs in vitro by processes similar to those operative during human embryogenesis in vivo, although some differences were also detected. Human embryonic stem cells (hESCs) are capable of indefinite self-renewal but can also be induced to undergo a stepwise process of differentiation into a spectrum of recognizable mature blood cell types. However, a clear understanding of the molecular mechanism by which the first hematopoietic stem cells (HSCs) acquire their unique defining properties of self-renewal and repopulating potential is lacking. As a first step towards obtaining the information needed to close this gap, we have undertaken a comparative gene expression analysis of different highly purified primitive human hematopoietic subpopulations (erythroid-megakaryocytic progenitor enriched CD43+CD235a+CD41a+/- cells, mutiplepotent progenitor enriched lin-CD34+CD43+CD45-, and lin-CD34+CD43+CD45+ cells) generated either in vitro from hESCs or in vivo from fetal (human fetal liver lin-CD34+CD38- cells) or neonatal hematopoietic primitive cells (human cord blood lin-CD34+CD38- and lin-CD34+CD38+ cells). This involved preparing a long serial analysis of gene expression (LongSAGE) library from an extracts of each prospectively isolated subpopulation and then sequencing each library to a depth of 200,000 tags.

Dataset Information

TCF7 is a key regulator of the switch of self-renewal and differentiation in a multipotential hematopoietic cell line

Publications

Tcf7 is an important regulator of the switch of self-renewal and differentiation in a multipotential hematopoietic cell line.

Similar Datasets

OmicsDI is part of the ELIXIR infrastructure

Tweets