scholarly journals Bmp2 Transcription in Osteoblast Progenitors Is Regulated by a Distant 3′ Enhancer Located 156.3 Kilobases from the Promoter

2007 ◽  
Vol 27 (8) ◽  
pp. 2934-2951 ◽  
Author(s):  
Ronald L. Chandler ◽  
Kelly J. Chandler ◽  
Karen A. McFarland ◽  
Douglas P. Mortlock
Keyword(s):  
Risk Factor ◽  
Osteoblast Differentiation ◽  
Expression Patterns ◽  
Artificial Chromosome ◽  
Regulatory Elements ◽  
Bone Morphogenetic Protein 2 ◽  
Regulatory Function ◽  
Regulatory Sequences ◽  
Bac Clone ◽  
Osteoblast Progenitor

ABSTRACT Bone morphogenetic protein 2 (encoded by Bmp2) has been implicated as an important signaling ligand for osteoblast differentiation and bone formation and as a genetic risk factor for osteoporosis. To initially survey a large genomic region flanking the mouse Bmp2 gene for cis-regulatory function, two bacterial artificial chromosome (BAC) clones that extend far upstream and downstream of the gene were engineered to contain a lacZ reporter cassette and tested in transgenic mice. Each BAC clone directs a distinct subset of normal Bmp2 expression patterns, suggesting a modular arrangement of distant Bmp2 regulatory elements. Strikingly, regulatory sequences required for Bmp2 expression in differentiating osteoblasts, as well as tooth buds, hair placodes, kidney, and other tissues, are located more than 53 kilobases 3′ to the promoter. By testing BACs with engineered deletions across this distant 3′ region, we parsed these regulatory elements into separate locations and more closely refined the location of the osteoblast progenitor element. Finally, a conserved osteoblast progenitor enhancer was identified within a 656-bp sequence located 156.3 kilobases 3′ from the promoter. The identification of this enhancer should permit further investigation of upstream regulatory mechanisms that control Bmp2 transcription during osteoblast differentiation and are relevant to further studies of Bmp2 as a candidate risk factor gene for osteoporosis.

P-element-mediated enhancer detection applied to the study of oogenesis in Drosophila

Development ◽  
1989 ◽  
Vol 107 (2) ◽  
pp. 189-200 ◽  
Author(s):  
U. Grossniklaus ◽  
H.J. Bellen ◽  
C. Wilson ◽  
W.J. Gehring
Keyword(s):  
Germ Line ◽  
Expression Patterns ◽  
Cell Types ◽  
Regulatory Elements ◽  
P Element ◽  
Regulatory Sequences ◽  
Transcriptional Regulatory ◽  
Morphological Criteria ◽  
Enhancer Detection ◽  
New Strategies

We have stained the ovaries of nearly 600 different Drosophila strains carrying single copies of a P-element enhancer detector. This transposon detects neighbouring genomic transcriptional regulatory sequences by means of a beta-galactosidase reporter gene. Numerous strains are stained in specific cells and at specific stages of oogenesis and provide useful ovarian markers for cell types that in some cases have not previously been recognized by morphological criteria. Since recent data have suggested that a substantial number of the regulatory elements detected by enhancer detection control neighbouring genes, we discuss the implications of our results concerning ovarian gene expression patterns in Drosophila. We have also identified a small number of insertion-linked recessive mutants that are sterile or lead to ovarian defects. We observe a strong correlation with specific germ line staining patterns in these strains, suggesting that certain patterns are more likely to be associated with female sterile genes than others. On the basis of our results, we suggest new strategies, which are not primarily based on the generation of mutants, to screen for and isolated female sterile genes.

scholarly journals Transposable elements as a potent source of diverse cis -regulatory sequences in mammalian genomes

2020 ◽  
Vol 375 (1795) ◽  
pp. 20190347 ◽  
Author(s):  
Vasavi Sundaram ◽  
Joanna Wysocka
Keyword(s):  
Gene Regulation ◽  
Transposable Elements ◽  
Regulatory Networks ◽  
Regulatory Elements ◽  
Regulatory Function ◽  
Specific Gene ◽  
Regulatory Sequences ◽  
Dependent Manner ◽  
Unique Contribution ◽  
Regulatory Potential

Eukaryotic gene regulation is mediated by cis -regulatory elements, which are embedded within the vast non-coding genomic space and recognized by the transcription factors in a sequence- and context-dependent manner. A large proportion of eukaryotic genomes, including at least half of the human genome, are composed of transposable elements (TEs), which in their ancestral form carried their own cis -regulatory sequences able to exploit the host trans environment to promote TE transcription and facilitate transposition. Although not all present-day TE copies have retained this regulatory function, the preexisting regulatory potential of TEs can provide a rich source of cis -regulatory innovation for the host. Here, we review recent evidence documenting diverse contributions of TE sequences to gene regulation by functioning as enhancers, promoters, silencers and boundary elements. We discuss how TE-derived enhancer sequences can rapidly facilitate changes in existing gene regulatory networks and mediate species- and cell-type-specific regulatory innovations, and we postulate a unique contribution of TEs to species-specific gene expression divergence in pluripotency and early embryogenesis. With advances in genome-wide technologies and analyses, systematic investigation of TEs' cis -regulatory potential is now possible and our understanding of the biological impact of genomic TEs is increasing. This article is part of a discussion meeting issue ‘Crossroads between transposons and gene regulation’.

scholarly journals Distinct gene expression patterns in skeletal and cardiac muscle are dependent on common regulatory sequences in the MLC1/3 locus.

1996 ◽  
Vol 16 (8) ◽  
pp. 4524-4534 ◽  
Author(s):  
M J McGrew ◽  
N Bogdanova ◽  
K Hasegawa ◽  
S H Hughes ◽  
R N Kitsis ◽  
...  
Keyword(s):  
Gene Expression ◽  
Skeletal Muscle ◽  
Cardiac Muscle ◽  
Consensus Sequence ◽  
Expression Patterns ◽  
Methylation Status ◽  
Regulatory Elements ◽  
Protein Isoforms ◽  
Regulatory Sequences ◽  
Enhancer Element

The myosin light-chain 1/3 locus (MLC1/3) is regulated by two promoters and a downstream enhancer element which produce two protein isoforms in fast skeletal muscle at distinct stages of mouse embryogenesis. We have analyzed the expression of transcripts from the internal MLC3 promoter and determined that it is also expressed in the atria of the heart. Expression from the MLC3 promoter in these striated muscle lineages is differentially regulated during development. In transgenic mice, the MLC3 promoter is responsible for cardiac-specific reporter gene expression while the downstream enhancer augments expression in skeletal muscle. Examination of the methylation status of endogenous and transgenic promoter and enhancer elements indicates that the internal promoter is not regulated in a manner similar to that of the MLC1 promoter or the downstream enhancer. A GATA protein consensus sequence in the proximal MLC3 promoter but not the MLC1 promoter binds with high affinity to GATA-4, a cardiac muscle- and gut-specific transcription factor. Mutation of either the MEF2 or GATA motifs in the MLC3 promoter attenuates its activity in both heart and skeletal muscles, demonstrating that MLC3 expression in these two diverse muscle types is dependent on common regulatory elements.

Repression of Pax-2 by WT1 during normal kidney development

Development ◽  
1995 ◽  
Vol 121 (3) ◽  
pp. 867-875 ◽  
Author(s):  
G. Ryan ◽  
V. Steele-Perkins ◽  
J.F. Morris ◽  
F.J. Rauscher ◽  
G.R. Dressler
Keyword(s):  
Transcriptional Repression ◽  
Kidney Development ◽  
Expression Patterns ◽  
Regulatory Gene ◽  
Regulatory Elements ◽  
Suppressor Gene ◽  
Regulatory Sequences ◽  
Dependent Manner ◽  
Proliferating Cells ◽  
Kidney Tumors

The developmental, regulatory gene Pax-2 is activated during early kidney morphogenesis and repressed in mature renal epithelium. Persistent Pax-2 expression is also observed in a variety of kidney tumors. Yet, little is known about the signals regulating this transient expression pattern in the developing kidney. We have examined the spatial and temporal expression patterns of Pax-2 and the Wilm's tumor suppresser protein WT1 with specific antibodies in developing mouse kidneys. A marked increase in WT1 protein levels coincided precisely with down-regulation of the Pax-2 gene in the individual precursor cells of the visceral glomerular epithelium, suggesting a direct effect of the WT1 repressor protein on Pax-2 regulatory elements. To examine whether WT1 could directly repress Pax-2 transcription, binding of WT1 to three high affinity sites in the 5′ untranslated Pax-2 leader sequence was demonstrated by DNAseI footprinting analysis. Furthermore, co-transfection assays using CAT reporter constructs under the control of Pax-2 regulatory sequences demonstrated WT1-dependent transcriptional repression. These three WT1 binding sites were also able to repress transcription, in a WT1-dependent manner, when inserted between a heterologous promoter and the reporter gene. The data indicate that Pax-2 is a likely target gene for WT1 and suggest a direct link, at the level of transcriptional regulation, between a developmental control gene, active in undifferentiated and proliferating cells, and a known tumor suppressor gene.

scholarly journals Evolution of the embryonic cis-regulatory landscapes between divergent Phallusia and Ciona ascidians.

2018 ◽  
Author(s):  
Alicia Madgwick ◽  
Marta Silvia Magri ◽  
Christelle Dantec ◽  
Damien Gailly ◽  
Ulla-Maj Fiuza ◽  
...  
Keyword(s):  
Transcriptional Control ◽  
Expression Patterns ◽  
Sequence Divergence ◽  
Regulatory Elements ◽  
Chromatin Accessibility ◽  
Regulatory Genes ◽  
Open Chromatin ◽  
Regulatory Sequences ◽  
Last Common Ancestor ◽  
Approximate Distance

Ascidian species of the Phallusia and Ciona genera are distantly related, their last common ancestor dating several hundred million years ago. Although their genome sequences have extensively diverged since this radiation, Phallusia and Ciona species share almost identical early morphogenesis and stereotyped cell lineages. Here, we explored the evolution of transcriptional control between P. mammillata and C. robusta. We combined genome-wide mapping of open chromatin regions in both species with a comparative analysis of the regulatory sequences of a test set of 10 pairs of orthologous early regulatory genes with conserved expression patterns. We find that ascidian chromatin accessibility landscapes obey similar rules as in other metazoa. Open-chromatin regions are short, highly conserved within each genus and cluster around regulatory genes. The dynamics of chromatin accessibility and closest-gene expression are strongly correlated during early embryogenesis. Open-chromatin regions are highly enriched in cis-regulatory elements: 73% of 49 open chromatin regions around our test genes behaved as either distal enhancers or proximal enhancer/promoters following electroporation in Phallusia eggs. Analysis of this datasets suggests a pervasive use in ascidians of shadow enhancers with partially overlapping activities. Cross-species electroporations point to a deep conservation of both the trans-regulatory logic between these distantly-related ascidians and the cis-regulatory activities of individual enhancers. Finally, we found that the relative order and approximate distance to the transcription start site of open chromatin regions can be conserved between Ciona and Phallusia species despite extensive sequence divergence, a property that can be used to identify orthologous enhancers, whose regulatory activity can partially diverge.

Human SM22α BAC encompasses regulatory sequences for expression in vascular and visceral smooth muscles at fetal and adult stages

2003 ◽  
Vol 284 (4) ◽  
pp. H1398-H1407 ◽  
Author(s):  
Rui Xu ◽  
Ye-Shih Ho ◽  
Raquel P. Ritchie ◽  
Li Li
Keyword(s):  
Bacterial Artificial Chromosome ◽  
Dna Sequences ◽  
Expression Patterns ◽  
Smooth Muscles ◽  
Artificial Chromosome ◽  
Developmental Expression ◽  
Regulatory Mechanisms ◽  
Regulatory Sequences ◽  
Cardiovascular Development ◽  
Evolutionarily Conserved

The SM22α gene has widely been used to study the regulatory mechanisms of smooth muscle cell (SMC) gene expression during cardiovascular development. To determine the regulatory mechanisms for the evolutionarily conserved human SM22α (h SM22α) gene, we demonstrated that 445 bp upstream DNA sequences of h SM22α gene exhibited a high transcriptional activity in arterial SMC, not in venous nor in visceral SMCs during embryogensis. However, this promoter was gradually turned off in adulthood. Inclusion of the first intron in this promoter suppressed the promoter activity in pulmonary trunk arterial SMCs, whereas the expression in other systemic vasculature remained similar to that of the h SM22-445 promoter during the fetal and adult stages. To determine whether additional sequences are required for SM22α expression in all subtypes of SMCs, we examined the expression of a bacterial artificial chromosome containing the h SM22α locus in transgenic mice. The h SM22α transgene showed similar developmental expression patterns as the endogenous mouse SM22α gene, suggesting that this bacterial artificial chromosome contains essential regulatory sequences for its expression in arterial, venous, and visceral tissues during development.

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 Spatially regulated expression of retrovirus-like transposons during Drosophila melanogaster embryogenesis

1994 ◽  
Vol 64 (3) ◽  
pp. 167-181 ◽  
Author(s):  
Dali Ding ◽  
Howard D. Lipshitz
Keyword(s):  
Drosophila Melanogaster ◽  
Expression Patterns ◽  
Regulatory Elements ◽  
Host Gene ◽  
Regulatory Sequences ◽  
Wild Type ◽  
Control Of Gene Expression ◽  
Spatial Expression ◽  
Regulated Expression ◽  
Type Strains

SummaryOver twenty distinct families of long terminal direct repeat (LTR)-containing retrotransposons have been identified in Drosophila melanogaster. While there have been extensive analyses of retrotransposon transcription in cultured cells, there have been few studies of the spatial expression of retrotransposons during normal development. Here we report a detailed analysis of the spatial expression patterns of fifteen families of retrotransposons during Drosophila melanogaster embryogenesis (17.6, 297, 412, 1731, 3S18, blood, copia, gypsy, HMS Beagle, Kermit/flea, mdg1, mdg3, opus, roo/B104 and springer). In each case, analyses were carried out in from two to four wild-type strains. Since the chromosomal insertion sites of any particular family of retrotransposons vary widely among wild-type strains, a spatial expression pattern that is conserved among strains is likely to have been generated through interaction of host transcription factors with cis-regulatory elements resident in the retrotransposons themselves. All fifteen families of retrotransposons showed conserved patterns of spatially and temporally regulated expression during embryogenesis. These results suggest that all families of retrotransposons carry cis-acting elements that control their spatial and temporal expression patterns. Thus, transposition of a retrotransposon into or near a particular host gene-possibly followed by an excision event leaving behind the retrotransposon's cis-regulatory sequences-might impose novel developmental control on such a host gene. Such a mechanism would serve to confer evolutionarily significant alterations in the spatio-temporal control of gene expression.

scholarly journals GimmeMotifs: an analysis framework for transcription factor motif analysis

2018 ◽  
Author(s):  
Niklas Bruse ◽  
Simon J. van Heeringen
Keyword(s):  
Dna Sequences ◽  
Motif Discovery ◽  
High Throughput Sequencing ◽  
Performance Metrics ◽  
De Novo ◽  
Expression Patterns ◽  
Regulatory Elements ◽  
Ensemble Method ◽  
Regulatory Sequences ◽  
Motif Analysis

AbstractBackgroundTranscription factors (TFs) bind to specific DNA sequences, TF motifs, in cis-regulatory sequences and control the expression of the diverse transcriptional programs encoded in the genome. The concerted action of TFs within the chromatin context enables precise temporal and spatial expression patterns. To understand how TFs control gene expression it is essential to model TF binding. TF motif information can help to interpret the exact role of individual regulatory elements, for instance to predict the functional impact of non-coding variants.FindingsHere we present GimmeMotifs, a comprehensive computational framework for TF motif analysis. Compared to the previously published version, this release adds a whole range of new functionality and analysis methods. It now includes tools for de novo motif discovery, motif scanning and sequence analysis, motif clustering, calculation of performance metrics and visualization. Included with GimmeMotifs is a non-redundant database of clustered motifs. Compared to other motif databases, this collection of motifs shows competitive performance in discriminating bound from unbound sequences. Using our de novo motif discovery pipeline we find large differences in performance between de novo motif finders on ChIP-seq data. Using an ensemble method such as implemented in GimmeMotifs will generally result in improved motif identification compared to a single motif finder. Finally, we demonstrate maelstrom, a new ensemble method that enables comparative analysis of TF motifs between multiple high-throughput sequencing experiments, such as ChIP-seq or ATAC-seq. Using a collection of ~200 H3K27ac ChIP-seq data sets we identify TFs that play a role in hematopoietic differentiation and lineage commitment.ConclusionGimmeMotifs is a fully-featured and flexible framework for TF motif analysis. It contains both command-line tools as well as a Python API and is freely available at: https://github.com/vanheeringen-lab/gimmemotifs.

scholarly journals QuASAR-MPRA: Accurate allele-specific analysis for massively parallel reporter assays

2017 ◽  
Author(s):  
Cynthia A. Kalita ◽  
Gregory A. Moyerbrailean ◽  
Christopher Brown ◽  
Xiaoquan Wen ◽  
Francesca Luca ◽  
...  
Keyword(s):  
Data Analysis ◽  
High Throughput ◽  
Regulatory Elements ◽  
Massively Parallel ◽  
Regulatory Function ◽  
Regulatory Sequences ◽  
Analysis Tools ◽  
Specific Analysis ◽  
Allele Specific ◽  
Reporter Assays

ABSTRACTMotivationThe majority of the human genome is composed of non-coding regions containing regulatory elements such as enhancers, which are crucial for controlling gene expression. Many variants associated with complex traits are in these regions, and may disrupt gene regulatory sequences. Consequently, it is important to not only identify true enhancers but also to test if a variant within an enhancer affects gene regulation. Recently, allele-specific analysis in high-throughput reporter assays, such as massively parallel reporter assays (MPRA), have been used to functionally validate non-coding variants. However, we are still missing high-quality and robust data analysis tools for these datasets.ResultsWe have further developed our method for allele-specific analysis QuASAR (quantitative allele-specific analysis of reads) to analyze allele-specific signals in barcoded read counts data from MPRA. Using this approach, we can take into account the uncertainty on the original plasmid proportions, over-dispersion, and sequencing errors. The provided allelic skew estimate and its standard error also simplifies meta-analysis of replicate experiments. Additionally, we show that a beta-binomial distribution better models the variability present in the allelic imbalance of these synthetic reporters and results in a test that is statistically well calibrated under the null. Applying this approach to the MPRA data by Tewheyet al.(2016), we found 602 SNPs with significant (FDR 10%) allele-specific regulatory function in LCLs. We also show that we can combine MPRA with QuASAR estimates to validate existing experimental and computational annotations of regulatory variants. Our study shows that with appropriate data analysis tools, we can improve the power to detect allelic effects in high throughput reporter assays.Availabilityhttp://github.com/piquelab/QuASAR/tree/master/[email protected];[email protected]

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