scholarly journals The BMP signaling gradient is interpreted through concentration thresholds in dorsal–ventral axial patterning

PLoS Biology ◽  
2021 ◽  
Vol 19 (1) ◽  
pp. e3001059
Author(s):  
Hannah Greenfeld ◽  
Jerome Lin ◽  
Mary C. Mullins
Keyword(s):  
Gene Expression ◽  
Single Cell ◽  
Target Gene ◽  
Target Genes ◽  
Gene Activation ◽  
Spatial Relationship ◽  
Bmp Signaling ◽  
Target Gene Expression ◽  
Gradient Slope ◽  
Distinct Cell

Bone Morphogenetic Protein (BMP) patterns the dorsal–ventral (DV) embryonic axis in all vertebrates, but it is unknown how cells along the DV axis interpret and translate the gradient of BMP signaling into differential gene activation that will give rise to distinct cell fates. To determine the mechanism of BMP morphogen interpretation in the zebrafish gastrula, we identified 57 genes that are directly activated by BMP signaling. By using Seurat analysis of single-cell RNA sequencing (scRNA-seq) data, we found that these genes are expressed in at least 3 distinct DV domains of the embryo. We distinguished between 3 models of BMP signal interpretation in which cells activate distinct gene expression through interpretation of thresholds of (1) the BMP signaling gradient slope; (2) the BMP signal duration; or (3) the level of BMP signal activation. We tested these 3 models using quantitative measurements of phosphorylated Smad5 (pSmad5) and by examining the spatial relationship between BMP signaling and activation of different target genes at single-cell resolution across the embryo. We found that BMP signaling gradient slope or BMP exposure duration did not account for the differential target gene expression domains. Instead, we show that cells respond to 3 distinct levels of BMP signaling activity to activate and position target gene expression. Together, we demonstrate that distinct pSmad5 threshold levels activate spatially distinct target genes to pattern the DV axis.

FLT3ITD Target Enhancers Are Primed but Inaccessible in Fetal Hematopoietic Progenitors

Blood ◽  
2019 ◽  
Vol 134 (Supplement_1) ◽  
pp. 1228-1228
Author(s):  
Yanan Li ◽  
Riddhi M Patel ◽  
Emily Casey ◽  
Jeffrey A. Magee
Keyword(s):  
Gene Expression ◽  
Transcription Factors ◽  
Target Gene ◽  
Target Genes ◽  
Conflicts Of Interest ◽  
Gene Activation ◽  
Chromatin Accessibility ◽  
Luciferase Reporter ◽  
Enhancer Activity ◽  
Target Gene Expression

The FLT3 Internal Tandem Duplication (FLT3ITD) is common somatic mutation in acute myeloid leukemia (AML). We have previously shown that FLT3ITD fails to induce changes in HSC self-renewal, myelopoiesis and leukemogenesis during fetal stages of life. FLT3ITD signal transduction pathways are hyperactivated in fetal progenitors, but FLT3ITD target genes are not. This suggests that postnatal-specific transcription factors may be required to help induce FLT3ITD target gene expression. Alternatively, repressive histone modifications may impose a barrier to FLT3ITD target gene activation in fetal HPCs that is relaxed during postnatal development. To resolve these possibilities, we used ATAC-seq, as well as H3K4me1, H3K27ac and H3K27me3 ChIP-seq, to identify cis-elements that putatively control FLT3ITD target gene expression in fetal and adult hematopoietic progenitor cells (HPCs). We identified many enhancer elements (ATAC-seq peaks with H3K4me1 and H3K27ac) that exhibited increased chromatin accessibility and activity in FLT3ITD adult HPCs relative to wild type adult HPCs. These elements were enriched near FLT3ITD target genes. HOMER analysis showed enrichment for STAT5, ETS, RUNX1 and IRF binding motifs within the FLT3ITD target enhancers, but motifs for temporally dynamic transcription factors were not identified. We cloned a subset of the enhancers and confirmed that they could synergize with their promoter to activate a luciferase reporter. For representative enhancers, STAT5 binding sites were required to activate the enhancer - as anticipated - and RUNX1 repressed enhancer activity. We tested whether accessibility or priming changed between fetal and adult stages of HPC development. FLT3ITD-dependent changes in chromatin accessibility were not observed in fetal HPCs, though the enhancers were primed early in development as evidenced by the presence of H3K4me1. Repressive H3K27me3 were not present at FLT3ITD target enhancers in either or adult HPCs. The data show that FLT3ITD target enhancers are demarcated early in hematopoietic development, long before they become responsive to FLT3ITD signaling. Repressive marks do not appear to create an epigenetic barrier to enhancer activation in the fetal stage. Instead, age-specific transcription factors are likely required to pioneer enhancer elements so that they can respond to STAT5 and other FLT3ITD effectors. Disclosures No relevant conflicts of interest to declare.

scholarly journals On the way toward regulatable expression systems in acetic acid bacteria: target gene expression and use cases

2021 ◽  
Author(s):  
Philipp Moritz Fricke ◽  
Angelika Klemm ◽  
Michael Bott ◽  
Tino Polen
Keyword(s):  
Gene Expression ◽  
Acetic Acid ◽  
Literature Search ◽  
Target Gene ◽  
Target Genes ◽  
Recombinant Dna ◽  
Acetic Acid Bacteria ◽  
Homoserine Lactone ◽  
Expression Systems ◽  
Target Gene Expression

Abstract Acetic acid bacteria (AAB) are valuable biocatalysts for which there is growing interest in understanding their basics including physiology and biochemistry. This is accompanied by growing demands for metabolic engineering of AAB to take advantage of their properties and to improve their biomanufacturing efficiencies. Controlled expression of target genes is key to fundamental and applied microbiological research. In order to get an overview of expression systems and their applications in AAB, we carried out a comprehensive literature search using the Web of Science Core Collection database. The Acetobacteraceae family currently comprises 49 genera. We found overall 6097 publications related to one or more AAB genera since 1973, when the first successful recombinant DNA experiments in Escherichia coli have been published. The use of plasmids in AAB began in 1985 and till today was reported for only nine out of the 49 AAB genera currently described. We found at least five major expression plasmid lineages and a multitude of further expression plasmids, almost all enabling only constitutive target gene expression. Only recently, two regulatable expression systems became available for AAB, an N-acyl homoserine lactone (AHL)-inducible system for Komagataeibacter rhaeticus and an l-arabinose-inducible system for Gluconobacter oxydans. Thus, after 35 years of constitutive target gene expression in AAB, we now have the first regulatable expression systems for AAB in hand and further regulatable expression systems for AAB can be expected. Key points • Literature search revealed developments and usage of expression systems in AAB. • Only recently 2 regulatable plasmid systems became available for only 2 AAB genera. • Further regulatable expression systems for AAB are in sight.

The Interaction Between DOT1L and AF10 Is Required for H3K79 Dimethylation and MLL-AF9 Leukemia

Blood ◽  
2012 ◽  
Vol 120 (21) ◽  
pp. 401-401
Author(s):  
Aniruddha J Deshpande ◽  
Liying Chen ◽  
Kathrin M Bernt ◽  
Stuart Dias ◽  
Deepti Banka ◽  
...  
Keyword(s):  
Gene Expression ◽  
Mass Spectrometry ◽  
Target Gene ◽  
Leucine Zipper ◽  
Target Genes ◽  
Fusion Gene ◽  
Transformed Cells ◽  
Target Gene Expression ◽  
Transforming Activity ◽  
H3k79 Methylation

Abstract Abstract 401 MLL-fusion proteins induce changes in histone modifications that result in the abnormal and sustained expression of downstream oncogenic target genes. A number of recent studies have identified aberrant histone 3 lysine 79 (H3K79) methylation by the chromatin modifying enzyme DOT1L as an important epigenetic modification that sustains MLL-target gene expression. Aberrant H3K79 methylation has been shown to be necessary for oncogenic transformation mediated by a number of MLL-fusions. These recent findings have generated tremendous interest in H3K79 methylation as a therapeutic target in the MLL rearranged leukemias. The plant-homeodomain (PHD) and leucine zipper-containing protein AF10 biochemically interacts with DOT1L and is believed to influence H3K79 methylation. We generated conditional knockout mice in which the Dot1l-interacting octapeptide-motif leucine zipper (OM-LZ) domain of Af10 was flanked by LoxP sites. Deletion of the Af10OM-LZ domain with the Cre recombinase is predicted to abrogate the Af10-Dot1l interaction. Deletion of the Af10OM-LZ domain greatly reduced global H3K79 dimethylation as assessed by immunoblotting as well as mass spectrometry in Af10OM-LZ deleted HoxA9/Meis1a transformed cells. Given the importance of H3K79 methylation in MLL-rearranged leukemias, we sought to assess whether the transforming activity of the MLL-AF9 fusion gene was dependent on the Af10-Dot1l interaction. Using an MLL-AF9-IRES-GFP encoding retrovirus, we established immortalized blast-colony forming cultures from mouse lineage negative Sca-1 positive/Kit positive (LSK) bone marrow cells bearing floxed Af10OM-LZ alleles. Deletion of the Af10OM-LZ domain with Cre-recombinase dramatically reduced H3K79me2 on the MLL-target genes Hoxa5-10 and Meis1, leading to downregulation of these transcripts. We performed colony-forming cell (CFC) assays from MLL-AF9 transformed cells in the presence or absence of the Af10OM-LZ allele. In the first week, Af10OM-LZ deletion profoundly impaired the blast-colony forming potential of MLL-AF9 transformed LSKs and the only clones that could serially replate in subsequent passages had escaped Af10OM-LZ excision. Af10OM-LZ deleted colonies were very small and spread-out and showed morphological features of terminal myeloid differentiation. In contrast, HoxA9/Meis1 transformed LSK cells expanded normally in the absence of the Af10OM-LZ domain. These results demonstrate that the Af10OM-LZ, much like Dot1l, is critical for the in vitro transforming activity of the MLL-AF9 fusion gene, but does not non-specifically inhibit cellular proliferation. We then sought to investigate the potential role of the Af10OM-LZ domain in the in vivo leukemogenic activity of MLL-AF9. We generated primary MLL-AF9 leukemias from LSKs harboring floxed Af10OM-LZ alleles. Deletion of the Af10OM-LZ domain in cells explanted from the MLL-AF9 primary leukemias led to a significant increase in the disease latency in secondary recipient mice. Moreover, limiting dilution analysis of MLL-AF9 leukemias with or without the Af10OM-LZ domain demonstrated a >100 fold decrease in the frequency of leukemia initiating cells in the absence of the Af10OM-LZ domain. Microarray analysis showed that a vast majority of MLL-AF9 target genes were significantly downregulated in Af10OM-LZ deleted as compared to Af10OM-LZ wildtype MLL-AF9 leukemias. However, the Af10OM-LZ deleted cells could still eventually cause leukemia. This is intriguing given that Af10OM-LZ deletion, similar to Dot1l deletion, leads to a significant reduction in H3K79 dimethylation as well as MLL-target gene expression. A more detailed analysis of H3K79 methylation using mass spectrometry revealed that in contrast to H3K79 dimethylation, global levels of H3K79 mono-methylation were largely unchanged in Af10OM-LZ deleted cells. This suggests the residual MLL-AF9 target gene expression seen in Af10OM-LZ deleted cells is maintained by H3K79 monomethylation. Our results demonstrate a surprising role for Af10 in the conversion of H3K79 monomethylation to dimethylation and reveal the AF10-DOT1L interaction as an attractive therapeutic target in MLL-rearranged leukemias. Disclosures: Armstrong: Epizyme: Consultancy.

scholarly journals E2f1, E2f2, and E2f3 Control E2F Target Expression and Cellular Proliferation via a p53-Dependent Negative Feedback Loop

2007 ◽  
Vol 27 (1) ◽  
pp. 65-78 ◽  
Author(s):  
Cynthia Timmers ◽  
Nidhi Sharma ◽  
Rene Opavsky ◽  
Baidehi Maiti ◽  
Lizhao Wu ◽  
...  
Keyword(s):  
Gene Expression ◽  
Target Gene ◽  
Target Genes ◽  
Cellular Proliferation ◽  
Kinase Activity ◽  
Cyclin Dependent Kinase ◽  
Control Of Gene Expression ◽  
Target Gene Expression ◽  
Rb Phosphorylation ◽  
P53 Target Genes

ABSTRACT E2F-mediated control of gene expression is believed to have an essential role in the control of cellular proliferation. Using a conditional gene-targeting approach, we show that the targeted disruption of the entire E2F activator subclass composed of E2f1, E2f2, and E2f3 in mouse embryonic fibroblasts leads to the activation of p53 and the induction of p53 target genes, including p21 CIP1 . Consequently, cyclin-dependent kinase activity and retinoblastoma (Rb) phosphorylation are dramatically inhibited, leading to Rb/E2F-mediated repression of E2F target gene expression and a severe block in cellular proliferation. Inactivation of p53 in E2f1-, E2f2-, and E2f3-deficient cells, either by spontaneous mutation or by conditional gene ablation, prevented the induction of p21 CIP1 and many other p53 target genes. As a result, cyclin-dependent kinase activity, Rb phosphorylation, and E2F target gene expression were restored to nearly normal levels, rendering cells responsive to normal growth signals. These findings suggest that a critical function of the E2F1, E2F2, and E2F3 activators is in the control of a p53-dependent axis that indirectly regulates E2F-mediated transcriptional repression and cellular proliferation.

scholarly journals SAT-726 Estrogen Receptor Alpha as a Potential Target for Bisphenol A-Mediated Epigenetic Reprogramming: An in Vitro Analysis

2020 ◽  
Vol 4 (Supplement_1) ◽  
Author(s):  
Morgan Gallo ◽  
Lindsey S Treviño ◽  
Tiffany A Katz
Keyword(s):  
Gene Expression ◽  
Target Gene ◽  
Target Genes ◽  
Hepatic Cell ◽  
Time Points ◽  
Target Gene Expression ◽  
Er Alpha ◽  
Hepatic Cell Lines ◽  
Gene Expression Levels

Abstract Perinatal exposure to bisphenol A (BPA) has been shown to reprogram the hepatic epigenome of rodents and may promote the development of various metabolic diseases later in life, such as nonalcoholic fatty liver disease (NAFLD). This developmental reprogramming is characterized by the creation of “super promoters” at target genes implicated in metabolic pathways. While it is unclear how these “super promoters” are created, their creation is potentially mediated through BPA and estrogen receptor (ER) interaction. In order to test this potential mechanism, in vitro methods were used to examine ER target gene expression via RT-qPCR in 2 human hepatic cell lines transiently transfected with the ER isoform, ER alpha, prior to BPA exposure for various lengths of time. Within individual time points, there were no significant differences in target gene expression levels between cells that had been transfected with ER alpha and the vector control. Gene expression levels in the target genes were visibly increased at the 24-hour exposure mark in both transfection groups in comparison to the 0- and 6-hour time points, however only a fraction of these increases were found to be statistically significant. These gene expression patterns are not only consistent with previous studies examining target gene expression in BPA-treated hepatic cell lines, but more importantly, suggest BPA does not act via ER alpha to orchestrate the epigenetic changes seen in vitro. BPA may interact with a different ER isoform or an unknown target to create the observed “super promoters” at target genes, reinforcing the promiscuity of BPA and other xenoestrogens in facilitating epigenetic modifications, and ultimately, disease phenotypes.

scholarly journals DUX4 expressing immortalized FSHD lymphoblastoid cells express genes elevated in FSHD muscle biopsies, correlating with the early stages of inflammation

2020 ◽  
Vol 29 (14) ◽  
pp. 2285-2299 ◽  
Author(s):  
Christopher R S Banerji ◽  
Maryna Panamarova ◽  
Peter S Zammit
Keyword(s):  
Gene Expression ◽  
Cell Lines ◽  
Target Gene ◽  
Target Genes ◽  
Ectopic Expression ◽  
Lymphoblastoid Cell Lines ◽  
Immune Gene ◽  
Target Gene Expression ◽  
Early Stages ◽  
Muscle Biopsies

Abstract Facioscapulohumeral muscular dystrophy (FSHD) is an incurable disorder linked to ectopic expression of DUX4. However, DUX4 is notoriously difficult to detect in FSHD muscle cells, while DUX4 target gene expression is an inconsistent biomarker for FSHD skeletal muscle biopsies, displaying efficacy only on pathologically inflamed samples. Immune gene misregulation occurs in FSHD muscle, with DUX4 target genes enriched for those associated with inflammatory processes. However, there lacks an assessment of the FSHD immune cell transcriptome, and its contribution to gene expression in FSHD muscle biopsies. Here, we show that EBV-immortalized FSHD lymphoblastoid cell lines express DUX4 and both early and late DUX4 target genes. Moreover, a biomarker of 237 up-regulated genes derived from FSHD lymphoblastoid cell lines is elevated in FSHD muscle biopsies compared to controls. The FSHD Lymphoblast score is unaltered between FSHD myoblasts/myotubes and their controls however, implying a non-myogenic cell source in muscle biopsies. Indeed, the FSHD Lymphoblast score correlates with the early stages of muscle inflammation identified by histological analysis on muscle biopsies, while our two late DUX4 target gene expression biomarkers associate with macroscopic inflammation detectable via MRI. Thus, FSHD lymphoblastoid cell lines express DUX4 and early and late DUX4 target genes, therefore, muscle-infiltrated immune cells may contribute the molecular landscape of FSHD muscle biopsies.

scholarly journals RelA Ser276 Phosphorylation Is Required for Activation of a Subset of NF-κB-Dependent Genes by Recruiting Cyclin-Dependent Kinase 9/Cyclin T1 Complexes

2008 ◽  
Vol 28 (11) ◽  
pp. 3623-3638 ◽  
Author(s):  
David E. Nowak ◽  
Bing Tian ◽  
Mohammad Jamaluddin ◽  
Istvan Boldogh ◽  
Leoncio A. Vergara ◽  
...  
Keyword(s):  
Gene Expression ◽  
Target Gene ◽  
Gene Activation ◽  
Elongation Factor ◽  
Genetic Network ◽  
Transcriptional Elongation ◽  
Cyclin Dependent Kinase ◽  
Pol Ii ◽  
Target Gene Expression ◽  
Cyclin T1

ABSTRACT NF-κB plays a central role in cytokine-inducible inflammatory gene expression. Previously we empirically determined the identity of 92 members of the genetic network under direct NF-κB/RelA control that show marked heterogeneity in magnitude of transcriptional induction and kinetics of peak activation. To investigate this network further, we have applied a recently developed two-step chromatin immunoprecipitation assay that accurately reflects association and disassociation of RelA binding to its chromatin targets. Although inducible RelA binding occurs with similar kinetics on all NF-κB-dependent genes, serine 276 (Ser276)-phosphorylated RelA binding is seen primarily on a subset of genes that are rapidly induced by tumor necrosis factor (TNF), including Gro-β, interleukin-8 (IL-8), and IκBα. Previous work has shown that TNF-inducible RelA Ser276 phosphorylation is controlled by a reactive oxygen species (ROS)-protein kinase A signaling pathway. To further understand the role of phospho-Ser276 RelA in target gene expression, we inhibited its formation by ROS scavengers and antioxidants, treatments that disrupt phospho-Ser276 formation but not the translocation and DNA binding of nonphosphorylated RelA. Here we find that phospho-Ser276 RelA is required only for activation of IL-8 and Gro-β, with IκBα being unaffected. These data were confirmed in experiments using RelA−/− murine embryonic fibroblasts reconstituted with a RelA Ser276Ala mutation. In addition, we observe that phospho-Ser276 RelA binds the positive transcription elongation factor b (P-TEFb), a complex containing the cyclin-dependent kinase 9 (CDK-9) and cyclin T1 subunits. Inhibition of P-TEFb activity by short interfering RNA (siRNA)-mediated knockdown shows that the phospho-Ser276 RelA-P-TEFb complex is required for IL-8 and Gro-β gene activation but not for IκBα gene activation. These studies indicate that TNF induces target gene expression by heterogeneous mechanisms. One is mediated by phospho-Ser276 RelA formation and chromatin targeting of P-TEFb controlling polymerase II (Pol II) recruitment and carboxy-terminal domain phosphorylation on the IL-8 and Gro-β genes. The second involves a phospho-Ser276 RelA-independent activation of genes preloaded with Pol II, exemplified by the IκBα gene. Together, these data suggest that the binding kinetics, selection of genomic targets, and mechanisms of promoter induction by RelA are controlled by a phosphorylation code influencing its interactions with coactivators and transcriptional elongation factors.

scholarly journals Identification and Evaluation of Reference Genes for Normalization of Gene Expression in Developmental Stages, Sexes, and Tissues of Diaphania caesalis (Lepidoptera, Pyralidae)

2020 ◽  
Vol 20 (1) ◽  
Author(s):  
Zheng Wang ◽  
Qianqian Meng ◽  
Xi Zhu ◽  
Shiwei Sun ◽  
Aiqin Liu ◽  
...  
Keyword(s):  
Gene Expression ◽  
Reference Genes ◽  
Target Gene ◽  
Target Genes ◽  
Developmental Stages ◽  
Expression Profiles ◽  
Transcriptional Level ◽  
Internal Reference ◽  
Target Gene Expression ◽  
Qrt Pcr

Abstract Diaphania caesalis (Walker) is an important boring insect mainly distributed in subtropical and tropical areas and attacked tropical woody grain crops, such as starchy plants of Artocarpus. Quantitative real-time polymerase chain reaction (qRT-PCR) is a powerful approach for investigating target genes expression profiles at the transcriptional level. However, the identification and selection of internal reference genes, which is often overlooked, is the most vital step before the analysis of target gene expression by qRT-PCR. So far, the reliable internal reference genes under a certain condition of D. caesalis have not been investigated. Therefore, this study evaluated the expression stability of eight candidate reference genes including ACT, β-TUB, GAPDH, G6PDH, RPS3a, RPL13a, EF1α, and EIF4A in different developmental stages, tissues and sexes using geNorm, NormFinder and BestKeeper algorithms. To verify the stability of the recommended internal reference genes, the expression levels of DcaeOBP5 were analyzed under different treatment conditions. The results indicated that ACT, RPL13a, β-TUB, RPS3a, and EF1α were identified as the most stable reference genes for further studies on target gene expression involving different developmental stages of D. caesalis. And ACT and EIF4A were recommended as stable reference genes for different tissues. Furthermore, ACT, EF1α, and RPS3a were ranked as the best reference genes in different sexes based on three algorithms. Our research represents the critical first step to normalize qRT-PCR data and ensure the accuracy of expression of target genes involved in phylogenetic and physiological mechanism at the transcriptional level in D. caesalia.

scholarly journals Differential Target Gene Activation by the Staphylococcus aureus Two-Component System saeRS

2009 ◽  
Vol 192 (3) ◽  
pp. 613-623 ◽  
Author(s):  
Markus Mainiero ◽  
Christiane Goerke ◽  
Tobias Geiger ◽  
Christoph Gonser ◽  
Silvia Herbert ◽  
...  
Keyword(s):  
Gene Expression ◽  
Staphylococcus Aureus ◽  
Target Gene ◽  
Target Genes ◽  
Gene Activation ◽  
Gene Expression Pattern ◽  
Class Ii ◽  
Class I ◽  
Single Amino Acid ◽  
Single Amino Acid Change

ABSTRACT The saePQRS system of Staphylococcus aureus controls the expression of major virulence factors and encodes a histidine kinase (SaeS), a response regulator (SaeR), a membrane protein (SaeQ), and a lipoprotein (SaeP). The widely used strain Newman is characterized by a single amino acid change in the sensory domain of SaeS (Pro18 in strain Newman [SaeSP], compared with Leu18 in other strains [SaeSL]). SaeSP determines activation of the class I sae target genes (coa, fnbA, eap, sib, efb, fib, sae), which are highly expressed in strain Newman. In contrast, class II target genes (hla, hlb, cap) are not sensitive to the SaeS polymorphism. The SaeSL allele (saeSL ) is dominant over the SaeSP allele, as shown by single-copy integration of saePQRSL in strain Newman, which results in severe repression of class I target genes. The differential effect on target gene expression is explained by different requirements for SaeR phosphorylation. From an analysis of saeS deletion strains and strains with mutated SaeR phosphorylation sites, we concluded that a high level of SaeR phosphorylation is required for activation of class I target genes. However, a low level of SaeR phosphorylation, which can occur independent of SaeS, is sufficient to activate class II target genes. Using inducible saeRS constructs, we showed that the expression of both types of target genes is independent of the saeRS dosage and that the typical growth phase-dependent gene expression pattern is not driven by SaeRS.

scholarly journals Mapping the evolving landscape of super-enhancers during cell differentiation

2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Yan Kai ◽  
Bin E. Li ◽  
Ming Zhu ◽  
Grace Y. Li ◽  
Fei Chen ◽  
...  
Keyword(s):  
Gene Expression ◽  
Cell Differentiation ◽  
Target Gene ◽  
Target Genes ◽  
De Novo ◽  
Cell Types ◽  
Functional Enrichment ◽  
Target Gene Expression ◽  
Differentiated Cells ◽  
Super Enhancer

Abstract Background Super-enhancers are clusters of enhancer elements that play critical roles in the maintenance of cell identity. Current investigations on super-enhancers are centered on the established ones in static cell types. How super-enhancers are established during cell differentiation remains obscure. Results Here, by developing an unbiased approach to systematically analyze the evolving landscape of super-enhancers during cell differentiation in multiple lineages, we discover a general trend where super-enhancers emerge through three distinct temporal patterns: conserved, temporally hierarchical, and de novo. The three types of super-enhancers differ further in association patterns in target gene expression, functional enrichment, and 3D chromatin organization, suggesting they may represent distinct structural and functional subtypes. Furthermore, we dissect the enhancer repertoire within temporally hierarchical super-enhancers, and find enhancers that emerge at early and late stages are enriched with distinct transcription factors, suggesting that the temporal order of establishment of elements within super-enhancers may be directed by underlying DNA sequence. CRISPR-mediated deletion of individual enhancers in differentiated cells shows that both the early- and late-emerged enhancers are indispensable for target gene expression, while in undifferentiated cells early enhancers are involved in the regulation of target genes. Conclusions In summary, our analysis highlights the heterogeneity of the super-enhancer population and provides new insights to enhancer functions within super-enhancers.

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