scholarly journals A Human Accelerated Region participates in early human forebrain patterning and expansion

2019 ◽  
Author(s):  
Sandra Acosta ◽  
Jaydeep Sidhaye ◽  
Luciano Fiore ◽  
Isabel Rollan ◽  
Giovanni Iacono ◽  
...  
Keyword(s):  
Transgenic Mice ◽  
Developmental Stages ◽  
Regulatory Elements ◽  
Mammalian Brain ◽  
Enhancer Activity ◽  
Evolutionary Changes ◽  
Active Enhancer ◽  
Phylotypic Stage ◽  
Early Developmental ◽  
Human Specific

AbstractThe expansion of the mammalian brain is associated with specific developmental processes; however, not much is known about how evolutionary changes participated in the acquisition of human brain traits during early developmental stages. Here we investigated whether enhancers active during the phylotypic stage show human-specific genomic divergence which could contribute to the evolutionary expansion of the forebrain. Notably, we identified an active enhancer containing a human accelerated region (HAR) located in the Chromosome 14q12, a region enriched with neurodevelopmental genes, such as Foxg1, Nkx2.1 and Nova1. Reporter analysis revealed that the human variant is active in the forebrain in transgenic mice and that it has stronger enhancer activity than the mouse or chimpanzee versions. Humanization of the mouse enhancer variant in transgenic mice and in mouse organoids resulted in an expansion of Foxg1 expressing domains in the forebrain early neural progenitors with a bias towards dorsal identities. Overall, our results suggest that human-specific mutations in critical regulatory elements controlling early brain development impact the expansion and patterning of the forebrain.

scholarly journals Monocyte Subsets with High Osteoclastogenic Potential and Their Epigenetic Regulation Orchestrated by IRF8

2020 ◽  
Author(s):  
Amitabh Das ◽  
Xiaobei Wang ◽  
Jessica Kang ◽  
Alyssa Coulter ◽  
Amol C. Shetty ◽  
...  
Keyword(s):  
Developmental Stages ◽  
Nuclear Translocation ◽  
De Novo ◽  
Primary Source ◽  
Regulatory Elements ◽  
Monocyte Subsets ◽  
Enhancer Activity ◽  
Signaling Receptors ◽  
Early Developmental ◽  
Deficient Mice

SUMMARYOsteoclasts (OCs) are bone resorbing cells formed by the serial fusion of monocytes. In mice and humans, three distinct subsets of monocytes exist; however, it is unclear if all of them exhibit osteoclastogenic potential. Here we show that in wild-type mice, Ly6Chi and Ly6Cint monocytes are the primary source of OC formation when compared to Ly6C− monocytes. Their osteoclastogenic potential is dictated by increased expression of signaling receptors and activation of pre-established transcripts, as well as de novo gain in enhancer activity and promoter changes. In the absence of IRF8, a transcription factor important for myelopoiesis and osteoclastogenesis, all three monocyte subsets are programmed to display higher osteoclastogenic potential. Enhanced NFATc1 nuclear translocation and amplified transcriptomic and epigenetic changes initiated at early developmental stages direct the increased osteoclastogenesis in Irf8 deficient mice. Collectively, our study provides novel insights into the transcription factors and active cis-regulatory elements that regulate OC differentiation.

scholarly journals MacroH2A histone variants modulate enhancer activity to repress oncogenic programs and cellular reprogramming

2021 ◽  
Author(s):  
Alexandre Gaspar-Maia ◽  
Wazim Mohammed Ismail ◽  
Amelia Mazzone ◽  
Jagneet Kaur ◽  
Stephanie Safgren ◽  
...  
Keyword(s):  
Regulatory Elements ◽  
Histone Variants ◽  
Cellular Reprogramming ◽  
Negative Regulator ◽  
Cellular Heterogeneity ◽  
Enhancer Activity ◽  
Active Enhancer ◽  
A Cell ◽  
Cell Type Specific

Abstract Considerable efforts have been made to characterize active enhancer elements, which can be annotated by accessible chromatin and H3 lysine 27 acetylation (H3K27ac). However, apart from poised enhancers that are observed in early stages of development and putative silencers, the functional significance of cis-regulatory elements lacking H3K27ac is poorly understood. Here we show that macroH2A histone variants mark a subset of enhancers in normal and cancer cells, which we coined ‘macroH2A-Bound Enhancers’, that negatively modulate enhancer activity. We find macroH2A variants enriched at enhancer elements that are devoid of H3K27ac in a cell type-specific manner, indicating a role for macroH2A at inactive enhancers to maintain cell identity. In following, reactivation of macro-bound enhancers is associated with oncogenic programs in breast cancer and its repressive role is correlated with the activity of macroH2A2 as a negative regulator of BRD4 chromatin occupancy. Finally, through single cell epigenomic profiling, we show that the loss of macroH2A2 leads to increased cellular heterogeneity that may help to explain the role of macroH2A variants in defining oncogenic transcriptional dependencies.

scholarly journals Differential regulation of the N-myc gene in transfected cells and transgenic mice.

1990 ◽  
Vol 10 (5) ◽  
pp. 2096-2103 ◽  
Author(s):  
K Zimmerman ◽  
E Legouy ◽  
V Stewart ◽  
R Depinho ◽  
F W Alt
Keyword(s):  
Transgenic Mice ◽  
Developmental Stages ◽  
Specific Expression ◽  
Endogenous Gene ◽  
Numerous Cell ◽  
Transgenic Lines ◽  
Myc Gene ◽  
Early Developmental

The N-myc gene is expressed specifically in the early developmental stages of numerous cell lineages. To assay for sequences that could potentially regulate N-myc expression, we transfected constructs that contained murine N-myc genomic sequences linked to a reporter gene and genomic clones that contained the complete human or murine N-myc genes into cell lines that either express or do not express the endogenous N-myc gene. Following either transient or stable transfection, the introduced N-myc sequences were expressed regardless of the expression status of the endogenous gene. In contrast, when the clones containing the complete human N-myc gene were introduced into the germline of transgenic mice, expression in some transgenic lines paralleled the tissue- and stage-specific expression of the endogenous murine gene. These findings demonstrate differences in the regulation of N-myc genes in recipient cells following in vitro versus in vivo introduction, suggesting that early developmental events may play a role in the regulation of N-myc expression.

Transcriptional Enhancers in the FOXP2 Locus Underwent Accelerated Evolution in the Human Lineage

2019 ◽  
Vol 36 (11) ◽  
pp. 2432-2450 ◽  
Author(s):  
Alfredo Leandro Caporale ◽  
Catalina M Gonda ◽  
Lucía Florencia Franchini
Keyword(s):  
Developmental Stages ◽  
Evolutionary Process ◽  
Regulatory Sequences ◽  
Human Lineage ◽  
Coding Region ◽  
Transcriptional Enhancers ◽  
Accelerated Evolution ◽  
Evolutionary Changes ◽  
Human Specific

Abstract Unique human features, such as complex language, are the result of molecular evolutionary changes that modified developmental programs of our brain. The human-specific evolution of the forkhead box P2 (FOXP2) gene-coding region has been linked to the emergence of speech and language in the human kind. However, little is known about how the expression of FOXP2 is regulated and whether its regulatory machinery evolved in a lineage-specific manner in humans. In order to identify FOXP2 regulatory regions containing human-specific changes, we used databases of human-accelerated noncoding sequences or HARs. We found that the topologically associating domain determined using developing human cerebral cortex containing the FOXP2 locus includes two clusters of 12 HARs, placing the locus occupied by FOXP2 among the top regions showing fast acceleration rates in noncoding regions in the human genome. Using in vivo enhancer assays in zebrafish, we found that at least five FOXP2-HARs behave as transcriptional enhancers throughout different developmental stages. In addition, we found that at least two FOXP2-HARs direct the expression of the reporter gene EGFP to foxP2-expressing regions and cells. Moreover, we uncovered two FOXP2-HARs showing reporter expression gain of function in the nervous system when compared with the chimpanzee ortholog sequences. Our results indicate that regulatory sequences in the FOXP2 locus underwent a human-specific evolutionary process suggesting that the transcriptional machinery controlling this gene could have also evolved differentially in the human lineage.

scholarly journals Massively parallel discovery of human-specific substitutions that alter enhancer activity

2020 ◽  
Vol 118 (2) ◽  
pp. e2007049118
Author(s):  
Severin Uebbing ◽  
Jake Gockley ◽  
Steven K. Reilly ◽  
Acadia A. Kocher ◽  
Evan Geller ◽  
...  
Keyword(s):  
Human Evolution ◽  
Regulatory Elements ◽  
Massively Parallel ◽  
Enhancer Activity ◽  
Genetic Changes ◽  
Gene Regulatory Elements ◽  
Enhancer Function ◽  
Human Accelerated Regions ◽  
The Impact ◽  
Human Specific

Genetic changes that altered the function of gene regulatory elements have been implicated in the evolution of human traits such as the expansion of the cerebral cortex. However, identifying the particular changes that modified regulatory activity during human evolution remain challenging. Here we used massively parallel enhancer assays in neural stem cells to quantify the functional impact of >32,000 human-specific substitutions in >4,300 human accelerated regions (HARs) and human gain enhancers (HGEs), which include enhancers with novel activities in humans. We found that >30% of active HARs and HGEs exhibited differential activity between human and chimpanzee. We isolated the effects of human-specific substitutions from background genetic variation to identify the effects of genetic changes most relevant to human evolution. We found that substitutions interacted in both additive and nonadditive ways to modify enhancer function. Substitutions within HARs, which are highly constrained compared to HGEs, showed smaller effects on enhancer activity, suggesting that the impact of human-specific substitutions is buffered in enhancers with constrained ancestral functions. Our findings yield insight into how human-specific genetic changes altered enhancer function and provide a rich set of candidates for studies of regulatory evolution in humans.

scholarly journals Evolutionary Analysis of Candidate Non-Coding Elements Regulating Neurodevelopmental Genes in Vertebrates

2017 ◽  
Author(s):  
Francisco J. Novo
Keyword(s):  
Gene Networks ◽  
Evolutionary Biology ◽  
Developmental Stages ◽  
General Pattern ◽  
Regulatory Elements ◽  
Chromatin Accessibility ◽  
Evolutionary Analysis ◽  
Enhancer Activity ◽  
Expression Of Genes ◽  
Peer Community

ABSTRACTMany non-coding regulatory elements conserved in vertebrates regulate the expression of genes involved in development and play an important role in the evolution of morphology through the rewiring of developmental gene networks. Available biological datasets allow the identification of non-coding regulatory elements with high confidence; furthermore, chromatin conformation data can be used to confirm enhancer-promoter interactions in specific tissue types and developmental stages. We have devised an analysis pipeline that integrates datasets about gene expression, enhancer activity, chromatin accessibility, epigenetic marks, and Hi-C contact frequencies in various brain tissues and developmental stages, leading to the identification of eight non-coding elements that might regulate the expression of three genes with important roles in brain development in vertebrates. We have then performed comparative sequence and microsynteny analyses in order to reconstruct the evolutionary history of the regulatory landscape around these genes; we observe a general pattern of ancient regulatory elements conserved across most vertebrate lineages, together with younger elements that appear to be mammal and primate innovations. This preprint has been reviewed and recommended by Peer Community In Evolutionary Biology (http://dx.doi.org/10.24072/pci.evolbiol.100035)

scholarly journals A reference map of murine cardiac transcription factor chromatin occupancy identifies dynamic and conserved enhancers

2019 ◽  
Vol 10 (1) ◽  
Author(s):  
Brynn N. Akerberg ◽  
Fei Gu ◽  
Nathan J. VanDusen ◽  
Xiaoran Zhang ◽  
Rui Dong ◽  
...  
Keyword(s):  
Heart Development ◽  
Molecular Mechanisms ◽  
Developmental Stages ◽  
Transcriptional Regulatory Network ◽  
Regulatory Elements ◽  
Chromatin Accessibility ◽  
Specific Gene ◽  
Mouse Heart ◽  
Transcriptional Enhancer ◽  
Enhancer Activity

Abstract Mapping the chromatin occupancy of transcription factors (TFs) is a key step in deciphering developmental transcriptional programs. Here we use biotinylated knockin alleles of seven key cardiac TFs (GATA4, NKX2-5, MEF2A, MEF2C, SRF, TBX5, TEAD1) to sensitively and reproducibly map their genome-wide occupancy in the fetal and adult mouse heart. These maps show that TF occupancy is dynamic between developmental stages and that multiple TFs often collaboratively occupy the same chromatin region through indirect cooperativity. Multi-TF regions exhibit features of functional regulatory elements, including evolutionary conservation, chromatin accessibility, and activity in transcriptional enhancer assays. H3K27ac, a feature of many enhancers, incompletely overlaps multi-TF regions, and multi-TF regions lacking H3K27ac retain conservation and enhancer activity. TEAD1 is a core component of the cardiac transcriptional network, co-occupying cardiac regulatory regions and controlling cardiomyocyte-specific gene functions. Our study provides a resource for deciphering the cardiac transcriptional regulatory network and gaining insights into the molecular mechanisms governing heart development.

scholarly journals Massively parallel discovery of human-specific substitutions that alter neurodevelopmental enhancer activity

2019 ◽  
Author(s):  
Severin Uebbing ◽  
Jake Gockley ◽  
Steven K. Reilly ◽  
Acadia A. Kocher ◽  
Evan Geller ◽  
...  
Keyword(s):  
Binding Sites ◽  
Experimental Studies ◽  
Regulatory Elements ◽  
Massively Parallel ◽  
Enhancer Activity ◽  
Genetic Changes ◽  
Human Neural Stem Cells ◽  
Human Accelerated Regions ◽  
The Impact ◽  
Human Specific

AbstractGenetic changes that altered the function of gene regulatory elements have been implicated in the evolution of the human brain. However, identifying the particular changes that modified regulatory activity during neurodevelopment remains challenging. Here we used massively parallel enhancer assays in human neural stem cells to measure the impact of 32,776 human-specific substitutions on enhancer activity in 1,363 Human Accelerated Regions (HARs) and 3,027 Human Gain Enhancers (HGEs), which include enhancers with novel activities in humans. We found that 31.9% of active HARs and 36.4% of active HGEs exhibited differential activity between human and chimpanzee. This enabled us to isolate the effects of 401 human-specific substitutions from other types of genetic variation in HARs and HGEs. Substitutions acted in both an additive and non-additive manner to alter enhancer activity. Human-specific substitutions altered predicted binding sites for a specific set of human transcription factors (TFs) that were a subset of TF binding sites associated with enhancer activity in our assay. Substitutions within HARs, which are overall highly constrained compared to HGEs, showed smaller effects on enhancer activity, suggesting that the impact of human-specific substitutions may be buffered in enhancers with constrained ancestral functions. Our findings yield insight into the mechanisms by which human-specific genetic changes impact enhancer function and provide a rich set of candidates for experimental studies of regulatory evolution in humans.

scholarly journals The role of chromatin accessibility in cis-regulatory evolution

2018 ◽  
Author(s):  
Pei-Chen Peng ◽  
Pierre Khoueiry ◽  
Charles Girardot ◽  
James P. Reddington ◽  
David A. Garfield ◽  
...  
Keyword(s):  
Developmental Stages ◽  
Chromatin Accessibility ◽  
Binding Motif ◽  
Evolutionary Divergence ◽  
Core Network ◽  
Enhancer Activity ◽  
Mesoderm Specification ◽  
Evolutionary Changes ◽  
In Cis

ABSTRACTTranscription factor (TF) binding is determined by sequence as well as chromatin accessibility. While the role of accessibility in shaping TF-binding landscapes is well recorded, its role in evolutionary divergence of TF binding, which in turn can alter cis-regulatory activities, is not well understood. In this work, we studied the evolution of genome-wide binding landscapes of five major transcription factors (TFs) in the core network of mesoderm specification, between D. melanogaster and D. virilis, and examined its relationship to accessibility and sequence-level changes. We generated chromatin accessibility data from three important stages of embryogenesis in both D. melanogaster and D. virilis, and recorded conservation and divergence patterns. We then used multi-variable models to correlate accessibility and sequence changes to TF binding divergence. We found that accessibility changes can in some cases, e.g., for the master regulator Twist and for earlier developmental stages, more accurately predict binding change than is possible using TF binding motif changes between orthologous enhancers. Accessibility changes also explain a significant portion of the co-divergence of TF pairs. We noted that accessibility and motif changes offer complementary views of the evolution of TF binding, and developed a combined model that captures the evolutionary data much more accurately than either view alone. Finally, we trained machine learning models to predict enhancer activity from TF binding, and used these functional models to argue that motif and accessibility-based predictors of TF binding change can substitute for experimentally measured binding change, for the purpose of predicting evolutionary changes in enhancer activity.

scholarly journals Transcription imparts architecture, function, and logic to enhancer units

2019 ◽  
Author(s):  
Nathaniel D Tippens ◽  
Jin Liang ◽  
King Y Leung ◽  
Abdullah Ozer ◽  
James G Booth ◽  
...  
Keyword(s):  
Core Promoter ◽  
Regulatory Elements ◽  
Maximum Activity ◽  
Enhancer Activity ◽  
Transcription Start Sites ◽  
Promoter Sequences ◽  
Cumulative Activity ◽  
Active Enhancer ◽  
Reporter Assays ◽  
Winner Takes All

AbstractDistal enhancers remain one of the least understood regulatory elements with pivotal roles in development and disease. We used massively parallel reporter assays to perform functional comparisons of two leading enhancer models and find that gene-distal transcription start sites (TSSs) are robust predictors of enhancer activity with higher resolution and specificity than histone modifications. We show that active enhancer units are precisely delineated by active TSSs, validate that these boundaries are sufficient to capture enhancer function, and confirm that core promoter sequences are required for this activity. Finally, we assay pairs of adjacent units and find that their cumulative activity is best predicted by the strongest unit within the pair. Synthetic fusions of enhancer units demonstrate that adjacency imposes winner-takes-all logic, revealing a simple design for a maximum-activity filter of enhancer unit outputs. Together, our results define fundamental enhancer units and a principle of non-cooperativity between adjacent units.

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