Control of the expression of the bithorax complex genes abdominal-A and abdominal-B by cis-regulatory regions in Drosophila embryos

Development ◽  
1991 ◽  
Vol 111 (2) ◽  
pp. 437-449 ◽  
Author(s):  
E. Sanchez-Herrero
Keyword(s):  
Regulatory Sequences ◽  
Bithorax Complex ◽  
Regulatory Regions ◽  
Drosophila Embryos

The abdominal-A (abd-A) and Abdominal-B (Abd-B) genes of the bithorax complex (BX-C) specify the identity of most of the Drosophila abdomen. Six different classes of infraabdominal (iab) mutations within the BX-C transform a subset of the parasegments affected by the lack of these two genes. It is thought that these mutations define parasegmental cis-regulatory regions that control the expression of abd-A and Abd-B. By staining embryos mutant for different iab mutations with anti-abd-A and anti-Abd-B antibodies I show here that the expression of Abd-B (and probably also abd-A) exhibit a parasegmental regulation. I have also studied the significance of the chromosomal order of parasegmental iab regulatory sequences, and the possible presence of chromosomal ‘boundaries’ between them, by looking at the expression of abd-A and Abd-B in embryos carrying the Uab and Mcp mutations. These data are discussed in the light of models of parasegmental-specific regulatory regions within the BX-C.

scholarly journals Interactions of Drosophila Ultrabithorax Regulatory Regions With Native and Foreign Promoters

Genetics ◽  
1997 ◽  
Vol 145 (1) ◽  
pp. 123-137 ◽  
Author(s):  
Fernando Casares ◽  
Welcome Bender ◽  
John Merriam ◽  
Ernesto Sánchez-Herrero
Keyword(s):  
P Element ◽  
Lacz Gene ◽  
Bithorax Complex ◽  
Lacz Reporter ◽  
Normal Pattern ◽  
Lacz Reporter Gene ◽  
Regulatory Regions ◽  
Long Range Interactions ◽  
In Trans ◽  
Dependent Interaction

The Ultrabithorax (Ubx) gene of the Drosophila bithorax complex is required to specify parasegments 5 and 6. Two P-element “enhancer traps” have been recovered within the locus that contain the bacterial lacZ gene under the control of the P-element promoter. The P insertion that is closer to the Ubx promoter expresses lucZ in a pattern similar to that of the normal Ubx gene, but also in parasegment 4 during embryonic development. Two deletions have been recovered that remove the normal Ubx promoter plus several kilobases on either side, but retain the lacZ reporter gene. The lacZ patterns from the deletion derivatives closely match the normal pattern of Ubx expression in late embryos and imaginal discs. The lacZ genes in the deletion derivatives are also negatively regulated by Ubx and activated in trans by Contrabithorax mutations, again like the normal Ubx gene. Thus, the deleted regions, including several kilobases around the Ubx promoter, are not required for long range interactions with Ubx regulatory regions. The deletion derivatives also stimulate transvection, a pairing-dependent interaction with the Ubx promoter on the homologous chromosome.

Positioning adjacent pair-rule stripes in the posterior Drosophila embryo

Development ◽  
1994 ◽  
Vol 120 (10) ◽  
pp. 2945-2955 ◽  
Author(s):  
J.A. Langeland ◽  
S.F. Attai ◽  
K. Vorwerk ◽  
S.B. Carroll
Keyword(s):  
Binding Sites ◽  
Drosophila Embryo ◽  
Regulatory Sequences ◽  
Posterior Border ◽  
Adjacent Pair ◽  
Gap Gene ◽  
Competitive Mechanism ◽  
Pair Rule ◽  
Drosophila Embryos ◽  
Do So

We present a genetic and molecular analysis of two hairy (h) pair-rule stripes in order to determine how gradients of gap proteins position adjacent stripes of gene expression in the posterior of Drosophila embryos. We have delimited regulatory sequences critical for the expression of h stripes 5 and 6 to 302 bp and 526 bp fragments, respectively, and assayed the expression of stripe-specific reporter constructs in several gap mutant backgrounds. We demonstrate that posterior stripe boundaries are established by gap protein repressors unique to each stripe: h stripe 5 is repressed by the giant (gt) protein on its posterior border and h stripe 6 is repressed by the hunchback (hb) protein on its posterior border. Interestingly, Kruppel (Kr) limits the anterior expression limits of both stripes and is the only gap gene to do so, indicating that stripes 5 and 6 may be coordinately positioned by the Kr repressor. In contrast to these very similar cases of spatial repression, stripes 5 and 6 appear to be activated by different mechanisms. Stripe 6 is critically dependent upon knirps (kni) for activation, while stripe 5 likely requires a combination of activating proteins (gap and non-gap). To begin a mechanistic understanding of stripe formation, we locate binding sites for the Kr protein in both stripe enhancers. The stripe 6 enhancer contains higher affinity Kr-binding sites than the stripe 5 enhancer, which may allow for the two stripes to be repressed at different Kr protein concentration thresholds. We also demonstrate that the kni activator binds to the stripe 6 enhancer and present evidence for a competitive mechanism of Kr repression of stripe 6.

Discrete Polycomb-binding sites in each parasegmental domain of the bithorax complex

Development ◽  
1995 ◽  
Vol 121 (6) ◽  
pp. 1681-1689 ◽  
Author(s):  
A. Chiang ◽  
M.B. O'Connor ◽  
R. Paro ◽  
J. Simon ◽  
W. Bender
Keyword(s):  
Binding Sites ◽  
Polytene Chromosomes ◽  
Homeotic Genes ◽  
Bithorax Complex ◽  
Lacz Reporter Gene ◽  
Regulatory Regions ◽  
Cooperative Action ◽  
Polycomb Protein ◽  
Regulatory Dna ◽  
Segmental Expression

The Polycomb protein of Drosophila melanogaster maintains the segmental expression limits of the homeotic genes in the bithorax complex. Polycomb-binding sites within the bithorax complex were mapped by immunostaining of salivary gland polytene chromosomes. Polycomb bound to four DNA fragments, one in each of four successive parasegmental regulatory regions. These fragments correspond exactly to the ones that can maintain segmentally limited expression of a lacZ reporter gene. Thus, Polycomb acts directly on discrete multiple sites in bithorax regulatory DNA. Constructs combining fragments from different regulatory regions demonstrate that Polycomb-dependent maintenance elements can act on multiple pattern initiation elements, and that maintenance elements can work together. The cooperative action of maintenance elements may motivate the linear order of the bithorax complex.

scholarly journals Genetic structure of the abd-A gene of Drosophila

Development ◽  
1989 ◽  
Vol 107 (3) ◽  
pp. 575-583 ◽  
Author(s):  
A. Busturia ◽  
J. Casanova ◽  
E. Sanchez-Herrero ◽  
R. Gonzalez ◽  
G. Morata
Keyword(s):  
Genetic Structure ◽  
Regulatory Region ◽  
Regulatory Elements ◽  
Transcription Unit ◽  
Bithorax Complex ◽  
Coding Region ◽  
Regulatory Regions ◽  
Protein Coding ◽  
Spatial Regulation ◽  
Correct Level

We report the embryonic and adult phenotypes of a number of mutations of the abd-A gene of the bithorax complex. Some of them result in loss of abd-A function in the whole abd-A domain and are usually lethal. These probably eliminate or inactivate abd-A protein products. Other mutations affect only part of the abd-A domain. These are viable, appear to map outside the abd-A transcription unit, and presumably alter the normal spatial regulation of abd-A products. We propose a model of abd-A structure based on a protein-coding region and two cis-regulatory regions. Regulatory region 1, 3′ to the transcription unit, contains positive and negative regulatory elements. Regulatory region 2, 5′ to the transcription unit, establishes the correct level of abd-A activity in the abdominal metameres.

scholarly journals Modeling of Epigenetic Modification-Induced Changes in CRX-dependent Genes cis-Regulatory Elements

2017 ◽  
Author(s):  
Reafa A. Hossain ◽  
Nicholas R. Dunham ◽  
Megan E. Harris ◽  
Taylor L. Hutchinson ◽  
Justin M. Kidd ◽  
...  
Keyword(s):  
Dna Methylation ◽  
Epigenetic Regulation ◽  
Binding Sites ◽  
Epigenetic Modification ◽  
Inverse Correlation ◽  
Regulatory Elements ◽  
Specific Gene ◽  
Regulatory Sequences ◽  
Ocular Tissues ◽  
Regulatory Regions

AbstractPurposeDNA methylation is a well characterized epigenetic repressor of mRNA transcription in many plant and vertebrate systems. However, the mechanism of this repression is not fully understood. The process of synthesizing a strand of RNA from DNA, or transcription, is controlled by proteins that regulate RNA polymerase activity by binding to specific gene regulatory sequences. Cone-rod homeobox (CRX) is a well-characterized mammalian transcription factor that controls photoreceptor cell specific gene expression. While much is known about the functions and DNA binding specificity of CRX, less is known about how DNA methylation modulates CRX binding affinity to genomic cis-regulatory elements.MethodsWe used bisulfite pyrosequencing of human ocular tissues to measure DNA methylation levels of the regulatory regions of RHO, PDE6B, PAX6, and LINE. To describe the molecular mechanism of repression, we used molecular modeling to illustrate the effect of DNA methylation on human RHO regulatory sequences.ResultsIn this study, we demonstrate an inverse correlation between DNA methylation in regulatory regions adjacent to the human RHO and PDE6B genes and their subsequent transcription in human ocular tissues. Docking of CRX to our DNA models shows that CRX interacts with the grooves of these sequences, suggesting changes in groove structure could regulate binding. Molecular dynamics simulations of the RHO promoter and enhancer regions show changes in the flexibility and groove width upon epigenetic modification. Models also demonstrate that changes to the local dynamics of CRX binding sites within RHO regulatory sequences which may account for the repression of CRX dependent transcription.ConclusionCollectively, these data demonstrate epigenetic regulation of CRX binding sites in human retinal tissue and provide insight into the mechanism of this mode of epigenetic regulation to be tested in future experiments.

Transcription activates repressed domains in theDrosophilabithorax complex

Development ◽  
2002 ◽  
Vol 129 (21) ◽  
pp. 4923-4930 ◽  
Author(s):  
Welcome Bender ◽  
Daniel P. Fitzgerald
Keyword(s):  
Abdominal Segment ◽  
Mutant Phenotype ◽  
P Element ◽  
Bithorax Complex ◽  
Regulatory Regions ◽  
P Elements

A series of mutations have been recovered in the bithorax complex of D. melanogaster that transform the first segment of the abdomen into a copy of the second or third abdominal segment. These dominantUltraabdominal alleles are all associated with P element insertions which are transcribed in the first abdominal segment. The transcripts proceed past the end of the P element for up to 50 kb, extending through the regulatory regions for the second and third abdominal segments. Blocking transcription from the P element promoter reverts the mutant phenotype. Previously identified Ultraabdominal alleles, not associated with P elements, also show abnormal transcription of the same region.

Regulation of human embryonic globin genes zeta 2 and epsilon in stably transformed mouse erythroleukemia cells

Blood ◽  
1992 ◽  
Vol 80 (7) ◽  
pp. 1832-1837 ◽  
Author(s):  
P Vyas ◽  
JA Sharpe ◽  
P Watt ◽  
DR Higgs ◽  
WG Wood
Keyword(s):  
Regulatory Elements ◽  
Erythroid Cell ◽  
Regulatory Sequences ◽  
Globin Genes ◽  
Promoter Regions ◽  
Regulatory Regions ◽  
Chromosomal Organization ◽  
Erythroleukemia Cells ◽  
Cast Doubt ◽  
Mouse Erythroleukemia

Previous work has suggested that the promoter regions of the human embryonic zeta 2 and epsilon globin genes contain negative regulatory regions that could play a role in the repression of these genes in postembryonic erythroblasts. We have examined this possibility by studying the expression of these genes in mouse erythroleukemia cells, an adult erythroid cell line that might be expected to contain repressor molecules that would bind to the putative negative regulatory regions. When attached to appropriate upstream regulatory elements (alpha HS-40 and beta HS1,2) both the zeta and epsilon genes were expressed in these cells at a low level, but no increase in expression was observed when similar constructs lacking the proposed negative regulatory sequences were introduced into these cells. These results cast doubt on the possibility that these sequences play a major role in the developmental repression of the embryonic globin genes, unless they function only in a normal chromosomal organization.

scholarly journals Regulation of human embryonic globin genes zeta 2 and epsilon in stably transformed mouse erythroleukemia cells

Blood ◽  
1992 ◽  
Vol 80 (7) ◽  
pp. 1832-1837 ◽  
Author(s):  
P Vyas ◽  
JA Sharpe ◽  
P Watt ◽  
DR Higgs ◽  
WG Wood
Keyword(s):  
Regulatory Elements ◽  
Erythroid Cell ◽  
Regulatory Sequences ◽  
Globin Genes ◽  
Promoter Regions ◽  
Regulatory Regions ◽  
Chromosomal Organization ◽  
Erythroleukemia Cells ◽  
Cast Doubt ◽  
Mouse Erythroleukemia

Abstract Previous work has suggested that the promoter regions of the human embryonic zeta 2 and epsilon globin genes contain negative regulatory regions that could play a role in the repression of these genes in postembryonic erythroblasts. We have examined this possibility by studying the expression of these genes in mouse erythroleukemia cells, an adult erythroid cell line that might be expected to contain repressor molecules that would bind to the putative negative regulatory regions. When attached to appropriate upstream regulatory elements (alpha HS-40 and beta HS1,2) both the zeta and epsilon genes were expressed in these cells at a low level, but no increase in expression was observed when similar constructs lacking the proposed negative regulatory sequences were introduced into these cells. These results cast doubt on the possibility that these sequences play a major role in the developmental repression of the embryonic globin genes, unless they function only in a normal chromosomal organization.

scholarly journals UNDERSTANDING DISTAL TRANSCRIPTIONAL REGULATION FROM SEQUENCE, EXPRESSION AND INTERACTOME PERSPECTIVES

2010 ◽  
Vol 08 (02) ◽  
pp. 219-246 ◽  
Author(s):  
ARVIND RAO ◽  
DAVID J. STATES ◽  
ALFRED O. HERO ◽  
JAMES DOUGLAS ENGEL
Keyword(s):  
Computational Biology ◽  
De Novo ◽  
Sequence Data ◽  
Regulatory Elements ◽  
Proximal Promoter ◽  
Regulatory Sequences ◽  
Sequence Motifs ◽  
Specific Sequence ◽  
Specific Expression ◽  
Regulatory Regions

Gene regulation in eukaryotes involves a complex interplay between the proximal promoter and distal genomic elements (such as enhancers) which work in concert to drive precise spatio-temporal gene expression. The experimental localization and characterization of gene regulatory elements is a very complex and resource-intensive process. The computational identification of regulatory regions that confer spatiotemporally specific tissue-restricted expression of a gene is thus an important challenge for computational biology. One of the most popular strategies for enhancer localization from DNA sequence is the use of conservation-based prefiltering and more recently, the use of canonical (transcription factor motifs) or de novo tissue-specific sequence motifs. However, there is an ongoing effort in the computational biology community to further improve the fidelity of enhancer predictions from sequence data by integrating other, complementary genomic modalities. In this work, we propose a framework that complements existing methodologies for prospective enhancer identification. The methods in this work are derived from two key insights: (i) that chromatin modification signatures can discriminate proximal and distally located regulatory regions and (ii) the notion of promoter-enhancer cross-talk (as assayed in 3C/5C experiments) might have implications in the search for regulatory sequences that co-operate with the promoter to yield tissue-restricted, gene-specific expression.

scholarly journals Discovering single nucleotide variants and indels from bulk and single-cell ATAC-seq

2021 ◽  
Author(s):  
Arya R. Massarat ◽  
Arko Sen ◽  
Jeff Jaureguy ◽  
Sélène T. Tyndale ◽  
Yi Fu ◽  
...  
Keyword(s):  
Whole Genome Sequencing ◽  
Single Cell ◽  
Genome Sequencing ◽  
Superior Performance ◽  
Whole Genome Sequencing Data ◽  
Regulatory Sequences ◽  
Whole Genome ◽  
Single Nucleotide Variants ◽  
Single Nucleotide ◽  
Regulatory Regions

ABSTRACTGenetic variants and de novo mutations in regulatory regions of the genome are typically discovered by whole-genome sequencing (WGS), however WGS is expensive and most WGS reads come from non-regulatory regions. The Assay for Transposase-Accessible Chromatin (ATAC-seq) generates reads from regulatory sequences and could potentially be used as a low-cost ‘capture’ method for regulatory variant discovery, but its use for this purpose has not been systematically evaluated. Here we apply seven variant callers to bulk and single-cell ATAC-seq data and evaluate their ability to identify single nucleotide variants (SNVs) and insertions/deletions (indels). In addition, we develop an ensemble classifier, VarCA, which combines features from individual variant callers to predict variants. The Genome Analysis Toolkit (GATK) is the best-performing individual caller with precision/recall on a bulk ATAC test dataset of 0.92/0.97 for SNVs and 0.87/0.82 for indels. On bulk ATAC-seq reads, VarCA achieves superior performance with precision/recall of 0.99/0.95 for SNVs and 0.93/0.80 for indels. On single-cell ATAC-seq reads, VarCA attains precision/recall of 0.98/0.94 for SNVs and 0.82/0.82 for indels. In summary, ATAC-seq reads can be used to accurately discover non-coding regulatory variants in the absence of whole-genome sequencing data and our ensemble method, VarCA, has the best overall performance.

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