Rapid In Vivo Mapping of Hematopoietic Cis-Regulatory Elements.

Blood ◽  
2004 ◽  
Vol 104 (11) ◽  
pp. 4209-4209
Author(s):  
John A. Stamatoyannopouylos ◽  
Michael Hawrylycz ◽  
Richard Humbert ◽  
James C. Wallace ◽  
Man Yu ◽  
...  
Keyword(s):  
Chromatin Structure ◽  
Regulatory Elements ◽  
Regulatory Sequences ◽  
Beta Globin ◽  
Cis Acting ◽  
Human Genomic ◽  
Chromatin Profiling ◽  
Hematopoietic Cell Lines ◽  
Entire Gene

Abstract Cis-acting sequences play defining roles in the control of genes involved in hematopoiesis. However, for the vast majority of such genes, regulatory sequences remain to be defined. We describe a powerful, generic approach to identification of cis-regulatory sequences that may be applied to any gene locus in the context of any cell type. We used densely tiled primers and a novel real-time PCR-based assay to create continuous, high-resolution quantitative profiles of in vivo chromatin structure across entire gene domains. Such profiles can be analyzed using robust statistical algorithms to pinpoint disruptions in chromatin structure that are characteristic of cis-regulatory elements. We analyzed >1Mb of human genomic terrain from diverse gene loci in the context of several hematopoietic cell lines and cleanly delineated a spectrum of classical cis-regulatory activities including enhancers, promoters, insulators, and locus control regions. The approach displayed outstanding sensitivity (100%) and specificity (>99.6%) for known elements and was successful in defining novel elements even in heavily-explored terrain such as the alpha- and beta-globin loci. Since only small quantities of cells are required, the approach can be used readily in the context of hematopoietic progenitors. Systematic application of quantitative chromatin profiling to relevant genes promises to expand dramatically our understanding of the regulation of hematopoiesis.

Transcription of the chicken histone H5 gene is mediated by distinct tissue-specific elements within the promoter and the 3' enhancer

1989 ◽  
Vol 9 (5) ◽  
pp. 2228-2232
Author(s):  
C D Trainor ◽  
J D Engel
Keyword(s):  
Regulatory Element ◽  
Molecular Genetic ◽  
Regulatory Elements ◽  
Molecular Genetic Analysis ◽  
Erythroid Cell ◽  
Regulatory Sequences ◽  
Beta Globin ◽  
Tissue Specific ◽  
Cis Acting ◽  
Histone H5

Molecular genetic analysis of a number of vertebrate erythroid cell-specific genes has identified at least two types of cis-acting regulatory sequences which control the complex developmental pattern of gene expression during erythroid cell maturation. Tissue-specific cellular enhancers have been identified 3' to three erythroid cell-specific genes, and additional regulatory elements have been identified in the promoters of many erythroid genes. We show that the histone H5 enhancer, like the adult beta-globin enhancer, is involved in mediating the developmental induction of histone H5 mRNA as erythroid cells mature. We also describe the preliminary characterization of a tissue-specific regulatory element within the 5' region of the H5 locus and describe investigations of the interaction between this element and the histone H5 enhancer in mediating histone H5 regulation.

scholarly journals Boundary sequences flanking the mouse tyrosinase locus ensure faithful pattern of gene expression

2020 ◽  
Vol 10 (1) ◽  
Author(s):  
Davide Seruggia ◽  
Almudena Fernández ◽  
Marta Cantero ◽  
Ana Fernández-Miñán ◽  
José Luis Gomez-Skarmeta ◽  
...  
Keyword(s):  
Gene Expression ◽  
Chromatin Structure ◽  
Expression Patterns ◽  
Regulatory Elements ◽  
Regulatory Sequences ◽  
Cell Type ◽  
Chromosome Conformation ◽  
Control Of Gene Expression ◽  
Cell Type Specific

Abstract Control of gene expression is dictated by cell-type specific regulatory sequences that physically organize the structure of chromatin, including promoters, enhancers and insulators. While promoters and enhancers convey cell-type specific activating signals, insulators prevent the cross-talk of regulatory elements within adjacent loci and safeguard the specificity of action of promoters and enhancers towards their targets in a tissue specific manner. Using the mouse tyrosinase (Tyr) locus as an experimental model, a gene whose mutations are associated with albinism, we described the chromatin structure in cells at two distinct transcriptional states. Guided by chromatin structure, through the use of Chromosome Conformation Capture (3C), we identified sequences at the 5′ and 3′ boundaries of this mammalian gene that function as enhancers and insulators. By CRISPR/Cas9-mediated chromosomal deletion, we dissected the functions of these two regulatory elements in vivo in the mouse, at the endogenous chromosomal context, and proved their mechanistic role as genomic insulators, shielding the Tyr locus from the expression patterns of adjacent genes.

scholarly journals Transcription of the chicken histone H5 gene is mediated by distinct tissue-specific elements within the promoter and the 3' enhancer.

1989 ◽  
Vol 9 (5) ◽  
pp. 2228-2232 ◽  
Author(s):  
C D Trainor ◽  
J D Engel
Keyword(s):  
Regulatory Element ◽  
Molecular Genetic ◽  
Regulatory Elements ◽  
Molecular Genetic Analysis ◽  
Erythroid Cell ◽  
Regulatory Sequences ◽  
Beta Globin ◽  
Tissue Specific ◽  
Cis Acting ◽  
Histone H5

Molecular genetic analysis of a number of vertebrate erythroid cell-specific genes has identified at least two types of cis-acting regulatory sequences which control the complex developmental pattern of gene expression during erythroid cell maturation. Tissue-specific cellular enhancers have been identified 3' to three erythroid cell-specific genes, and additional regulatory elements have been identified in the promoters of many erythroid genes. We show that the histone H5 enhancer, like the adult beta-globin enhancer, is involved in mediating the developmental induction of histone H5 mRNA as erythroid cells mature. We also describe the preliminary characterization of a tissue-specific regulatory element within the 5' region of the H5 locus and describe investigations of the interaction between this element and the histone H5 enhancer in mediating histone H5 regulation.

Genome-Scale Analysis of Hematopoietic Regulatory Sequences by Digital Analysis of Chromatin Structure.

Blood ◽  
2004 ◽  
Vol 104 (11) ◽  
pp. 4163-4163
Author(s):  
John A. Stamatoyannopoulos ◽  
Richard Humbert ◽  
Michael Hawrylycz ◽  
James Wallace ◽  
Michael O. Dorschner ◽  
...  
Keyword(s):  
Chromatin Structure ◽  
Regulatory Elements ◽  
Regulatory Sequences ◽  
Hematopoietic Stem ◽  
Genome Wide ◽  
Hypersensitive Sites ◽  
Chromatin Structural ◽  
Tag Clustering ◽  
Genome Scale

Abstract In vivo, cis-regulatory elements coincide with focal disruptions in chromatin structure that manifest as DNaseI hypersensitive sites (HSs). We developed a novel stochastic methodology for comprehensive, genome-wide mapping of DNaseI HSs in vivo. We show that 19–20bp genomic DNA tags can be used to effect genome-wide localization of individual DNaseI cutting events in nuclear chromatin, and that such tags can be generated and sequenced in large numbers from limited numbers of starting cells. We analyzed 257,000 tags from a hematopoietic cell line (K562) and applied a quantitative algorithm to discriminate statistically significant tag clustering events. Such tag clusters identified both known and novel functional elements of hematopoietic genes across the genome. A unique feature of this approach is that it permits unbiased evaluation of the chromatin context of regulatory sequences from disperse genomic loci. We observed surprisingly large differences in the chromatin structural configuration of a variety of active erythroid and hematopoietic regulatory sequences, suggesting a discrete hierarchy of nuclear organization that is not apparent with conventional assays. This approach can be applied readily to generate a comprehensive catalogue of cis-regulatory sequences active in hematopoietic stem cells.

scholarly journals Boundary sequences flanking the mouse tyrosinase locus ensure faithful pattern of gene expression

2020 ◽  
Author(s):  
Davide Seruggia ◽  
Almudena Fernández ◽  
Marta Cantero ◽  
Ana Fernández-Miñán ◽  
José Luis Gomez-Skarmeta ◽  
...  
Keyword(s):  
Gene Expression ◽  
Chromatin Structure ◽  
Expression Patterns ◽  
Regulatory Elements ◽  
Regulatory Sequences ◽  
Cell Type ◽  
Chromosome Conformation ◽  
Control Of Gene Expression ◽  
Cell Type Specific

ABSTRACTControl of gene expression is dictated by cell-type specific regulatory sequences that physically organize the structure of chromatin, including promoters, enhancers and insulators. While promoters and enhancers convey cell-type specific activating signals, insulators prevent the cross-talk of regulatory elements within adjacent loci and safeguard the specificity of action of promoters and enhancers towards their targets in a tissue specific manner. Using the mouse tyrosinase (Tyr) locus as an experimental model, a gene whose mutations are associated with albinism, we described the chromatin structure in cells at two distinct transcriptional states. Guided by chromatin structure, through the use of Chromosome Conformation Capture (3C), we identified sequences at the 5’ and 3’ boundaries of this mammalian gene that function as enhancers and insulators. By CRISPR/Cas9-mediated chromosomal deletion, we dissected the functions of these two regulatory elements in vivo in the mouse, at the endogenous chromosomal context, and proved their role as genomic insulators, shielding the Tyr locus from the expression patterns of adjacent genes.

scholarly journals An opportunistic promoter sharing regulatory sequences with either a muscle-specific or a ubiquitous promoter in the human aldolase A gene.

1993 ◽  
Vol 13 (1) ◽  
pp. 9-17 ◽  
Author(s):  
J P Concordet ◽  
M Salminen ◽  
J Demignon ◽  
C Moch ◽  
P Maire ◽  
...  
Keyword(s):  
Skeletal Muscle ◽  
Integration Site ◽  
Regulatory Elements ◽  
Regulatory Sequences ◽  
Beta Globin ◽  
Fast Skeletal Muscle ◽  
High Level Expression ◽  
Adult Skeletal Muscle ◽  
High Level ◽  
Aldolase A

The human aldolase A gene is transcribed from three different promoters, pN, pM, and pH, all of which are clustered within a small 1.6-kbp DNA domain. pM, which is highly specific to adult skeletal muscle, lies in between pN and pH, which are ubiquitous but particularly active in heart and skeletal muscle. A ubiquitous enhancer, located just upstream of pH start sites, is necessary for the activity of both pH and pN in transient transfection assays. Using transgenic mice, we studied the sequence controlling the muscle-specific promoter pM and the relations between the three promoters and the ubiquitous enhancer. A 4.3-kbp fragment containing the three promoters and the ubiquitous enhancer showed an expression pattern consistent with that known in humans. In addition, while pH was active in both fast and slow skeletal muscles, pM was active only in fast muscle. pM activity was unaltered by the deletion of a 1.8-kbp region containing the ubiquitous enhancer and the pH promoter, whereas pN remained active only in fast skeletal muscle. These findings suggest that in fast skeletal muscle, a tissue-specific enhancer was acting on both pN and pM, whereas in other tissues, the ubiquitous enhancer was necessary for pN activity. Finally, a 2.6-kbp region containing the ubiquitous enhancer and only the pH promoter was sufficient to bring about high-level expression of pH in cardiac and skeletal muscle. Thus, while pH and pM function independently of each other, pN, remarkably, shares regulatory elements with each of them, depending on the tissue. Importantly, expression of the transgenes was independent of the integration site, as originally described for transgenes containing the beta-globin locus control region.

Delimiting regulatory sequences of the Drosophila melanogaster Ddc gene

1986 ◽  
Vol 6 (12) ◽  
pp. 4548-4557
Author(s):  
J Hirsh ◽  
B A Morgan ◽  
S B Scholnick
Keyword(s):  
Drosophila Melanogaster ◽  
Germ Line ◽  
Regulatory Elements ◽  
P Element ◽  
Developmental Expression ◽  
Upstream Region ◽  
Regulatory Sequences ◽  
Flanking Sequences

We delimited sequences necessary for in vivo expression of the Drosophila melanogaster dopa decarboxylase gene Ddc. The expression of in vitro-altered genes was assayed following germ line integration via P-element vectors. Sequences between -209 and -24 were necessary for normally regulated expression, although genes lacking these sequences could be expressed at 10 to 50% of wild-type levels at specific developmental times. These genes showed components of normal developmental expression, which suggests that they retain some regulatory elements. All Ddc genes lacking the normal immediate 5'-flanking sequences were grossly deficient in larval central nervous system expression. Thus, this upstream region must contain at least one element necessary for this expression. A mutated Ddc gene without a normal TATA boxlike sequence used the normal RNA start points, indicating that this sequences is not required for start point specificity.

scholarly journals The chromatin, topological and regulatory properties of pluripotency-associated poised enhancers are conserved in vivo

2021 ◽  
Author(s):  
Giuliano Crispatzu ◽  
Rizwan Rehimi ◽  
Tomas Pachano ◽  
Tore Bleckwehl ◽  
Sara de la Cruz Molina ◽  
...  
Keyword(s):  
Embryonic Stem ◽  
Regulatory Elements ◽  
Small Subset ◽  
Regulatory Sequences ◽  
Pluripotent Cells ◽  
Developmental Genes ◽  
Topological Features ◽  
Regulatory Properties

AbstractPoised enhancers (PEs) represent a limited and genetically distinct set of distal regulatory elements that control the induction of developmental genes in a hierarchical and non-redundant manner. Before becoming activated in differentiating cells, PEs are already bookmarked in pluripotent cells with unique chromatin and topological features that could contribute to their privileged regulatory properties. However, since PEs were originally identified and subsequently characterized using embryonic stem cells (ESC) as an in vitro differentiation system, it is currently unknown whether PEs are functionally conserved in vivo. Here, we generate and mine various types of genomic data to show that the chromatin and 3D structural features of PEs are conserved among mouse pluripotent cells both in vitro and in vivo. We also uncovered that, in mouse pluripotent cells, the interactions between PEs and their bivalent target genes are globally controlled by the combined action of Polycomb, Trithorax and architectural proteins. Moreover, distal regulatory sequences located close to developmental genes and displaying the typical genetic (i.e. proximity to CpG islands) and chromatin (i.e. high accessibility and H3K27me3 levels) features of PEs are commonly found across vertebrates. These putative PEs show high sequence conservation, preferentially within specific vertebrate clades, with only a small subset being evolutionary conserved across all vertebrates. Lastly, by genetically disrupting evolutionary conserved PEs in mouse and chicken embryos, we demonstrate that these regulatory elements play essential and non-redundant roles during the induction of major developmental genes in vivo.

Genomic Organization, Chromatin Structure, and Transcriptional Regulation of the Murine Alpha Hemoglobin Stabilizing Protein (AHSP) Gene.

Blood ◽  
2005 ◽  
Vol 106 (11) ◽  
pp. 3633-3633
Author(s):  
Louis C. Dore ◽  
Christopher R. Vakoc ◽  
Gerd A. Blobel ◽  
Ross C. Hardison ◽  
David M. Bodine ◽  
...  
Keyword(s):  
Chromatin Structure ◽  
Gene Activation ◽  
Inverse Correlation ◽  
Regulatory Elements ◽  
Genomic Region ◽  
Beta Thalassemia ◽  
Syntenic Block ◽  
Coding Region ◽  
Specific Expression

Abstract Alpha Hemoglobin Stabilizing Protein (AHSP, Eraf) is an abundant erythroid protein that binds and stabilizes alpha globin and alpha hemoglobin (Hb). In mice, loss of AHSP causes hemolytic anemia, with elevated levels of reactive oxygen species and Hb precipitation in erythrocytes. Loss of AHSP exacerbates beta thalassemia phenotypes in mice, presumably by enhancing the toxicity of excessive free alpha Hb. Based on these findings, AHSP is a candidate modifier gene for beta thalassemia in humans. No mutations in the AHSP coding region have been identified in patients to date. However, several groups reported an inverse correlation between beta thalassemia severity and erythroid AHSP expression levels, raising the possibility that AHSP is a quantitative trait modifier of beta thalassemia. To address this possibility, it is important to define the mechanisms that control expression of the AHSP gene. Transcripts of murine Ahsp are inducible by GATA-1. The goals of the current studies are to investigate the mechanisms of this induction and to define the DNA domain that regulates the locus. Using phylogenetic comparisons, we identified a hotspot for mammalian chromosomal rearrangement just downstream of the Ahsp gene. This hotspot is located at the end of a syntenic block of approximately 350 kb that is conserved in mammals and likely marks the 3′ end of the gene regulatory domain. We focused our initial functional studies on a 7 kb genomic region bounded at the 5′ (centromeric) end of Ahsp by the nearest adjacent gene, an EST expressed in multiple tissues, and at the 3′ (telomeric) end by the rearrangement hotspot. In transient transfection assays, the Ahsp promoter region conferred erythroid-specific expression to a linked reporter gene. In heterologous cells, GATA-1 transactivated the Ahsp promoter in a dose-dependent fashion. To examine GATA-1 binding and its subsequent effects on the Ahsp gene in vivo, we used G1E-ER4 cells, a GATA-1 null erythroblast line that undergoes terminal erythroid maturation after activation of an estradiol-inducible form of GATA-1. We made several findings with regards to the role of GATA-1 in Ahsp gene regulation. First, GATA-1 and its cofactor, Friend of GATA-1 (FOG-1), bind directly to the Ahsp locus at regions that contain conserved GATA consensus motifs and are predicted to be important erythroid regulatory elements by our bioinformatic studies. Second, GATA-1 induces epigenetic changes in chromatin structure that are associated with gene activation, including formation of a DNase I hypersensitive site, hyperacetylation of histones H3 and H4, and methylation of histone H3 lysine-4. Together, these findings begin to establish the DNA region and mechanisms that control Ahsp transcription, allowing for further studies to map the cis elements responsible for population variations in gene expression.

scholarly journals Developmentally Regulated Recruitment of Transcription Factors and Chromatin Modification Activities to Chicken Lysozyme cis-Regulatory Elements In Vivo

2003 ◽  
Vol 23 (12) ◽  
pp. 4386-4400 ◽  
Author(s):  
Pascal Lefevre ◽  
Svitlana Melnik ◽  
Nicola Wilson ◽  
Arthur D. Riggs ◽  
Constanze Bonifer
Keyword(s):  
Transcription Factors ◽  
Chromatin Structure ◽  
Chromatin Modification ◽  
Regulatory Elements ◽  
Chromatin Domain ◽  
Creb Binding Protein ◽  
Developmentally Regulated ◽  
Myeloid Differentiation Factor ◽  
Chicken Lysozyme

ABSTRACT Expression of the chicken lysozyme gene is upregulated during macrophage differentiation and reaches its highest level in bacterial lipopolysaccharide (LPS)-stimulated macrophages. This is accompanied by complex alterations in chromatin structure. We have previously shown that chromatin fine-structure alterations precede the onset of gene expression in macrophage precursor cells and mark the lysozyme chromatin domain for expression later in development. To further examine this phenomenon and to investigate the basis for the differentiation-dependent alterations of lysozyme chromatin, we studied the recruitment of transcription factors to the lysozyme locus in vivo at different stages of myeloid differentiation. Factor recruitment occurred in several steps. First, early-acting transcription factors such as NF1 and Fli-1 bound to a subset of enhancer elements and recruited CREB-binding protein. LPS stimulation led to an additional recruitment of C/EBPβ and a significant change in enhancer and promoter structure. Transcription factor recruitment was accompanied by specific changes in histone modification within the lysozyme chromatin domain. Interestingly, we present evidence for a transient interaction of transcription factors with lysozyme chromatin in lysozyme-nonexpressing macrophage precursors, which was accompanied by a partial demethylation of CpG sites. This indicates that a partially accessible chromatin structure of lineage-specific genes is a hallmark of hematopoietic progenitor cells.

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