scholarly journals Functional repurposing of regulatory element activity during mammalian evolution

2018 ◽  
Author(s):  
Francesco N. Carelli ◽  
Angélica Liechti ◽  
Jean Halbert ◽  
Maria Warnefors ◽  
Henrik Kaessmann
Keyword(s):  
Regulatory Element ◽  
Chromatin Modification ◽  
Regulatory Elements ◽  
Mammalian Evolution ◽  
Control Of Gene Expression ◽  
New Genes ◽  
Functional Features ◽  
Element Activity ◽  
Organismal Development ◽  
Species Specific

ABSTRACTThe spatiotemporal control of gene expression exerted by promoters and enhancers is central for organismal development, physiology and behaviour. These two types of regulatory elements have long been distinguished from each other based on their function, but recent work highlighted common architectural and functional features. It also suggested that inheritable alterations in the epigenetic and sequence context of regulatory elements might underlie evolutionary changes of their principal activity, which could result in changes in the transcriptional profile of genes under their control or even facilitate the birth of new genes. Here, based on integrated cross-mammalian analyses of DNase hypersensitivity, chromatin modification and transcriptional data, we provide support for this hypothesis by detecting 449 regulatory elements with signatures of activity turnover in sister species from the primate and rodent lineages (termed “P/E” elements). Through the comparison with outgroup species, we defined the directionality of turnover events, which revealed that most instances represent transformations of ancestral enhancers into promoters, leading to the emergence of species-specific transcribed loci or 5’ exons. Notably, P/E elements have distinct GC sequence compositions and stabilizing 5’ splicing (U1) regulatory motif patterns, which may predispose them to functional repurposing during evolution. Moreover, we trace changes in the U1 and polyadenylation signal densities and distributions that accompanied and likely drove the evolutionary activity switches. Overall, our work suggests rather widespread evolutionary remodelling of regulatory element functions. Functional repurposing thus represents a notable mechanism that likely facilitated regulatory innovation and the origination of new genes and exons during mammalian evolution.

scholarly journals Locally acting transcription factors are required for p53-dependent cis-regulatory element activity

2019 ◽  
Author(s):  
Allison N. Catizone ◽  
Gizem Karsli Uzunbas ◽  
Petra Celadova ◽  
Sylvia Kuang ◽  
Daniel Bose ◽  
...  
Keyword(s):  
Transcription Factors ◽  
Regulatory Element ◽  
Regulatory Elements ◽  
Mrna Levels ◽  
Sequence Context ◽  
Endogenous Expression ◽  
Damage Repair ◽  
Local Sequence ◽  
Element Activity ◽  
Massively Parallel Reporter Assay

AbstractThe master tumor suppressor p53 controls transcription of a wide-ranging gene network involved in apoptosis, cell cycle arrest, DNA damage repair, and senescence. Recent studies revealed pervasive binding of p53 to cis-regulatory elements (CRE), which are non-coding segments of DNA that spatially and temporally control transcription through the combinatorial binding of local transcription factors (TFs). Although the role of p53 as a strong trans-activator of gene expression is well known, the co-regulatory factors and local sequences acting at p53-bound CREs are comparatively understudied. We designed and executed a massively parallel reporter assay (MPRA) to investigate the effect of transcription factor binding motifs and local sequence context on p53-bound CRE activity. Our data indicate that p53-bound CREs are both positively and negatively affected by alterations in local sequence context and changes to co-regulatory TF motifs. We identified a SP1/KLF family motif located in an intronic p53 CRE that is required for the endogenous expression of the p53-dependent gene CCNG1. We also identified ATF3 as a factor that co-regulates the expression of the p53-dependent gene GDF15 through binding with p53 in an upstream CRE. Loss of either p53 or ATF3 severely reduces CRE activity and alters endogenous GDF15 mRNA levels in the cell. Our data suggests that p53 has the flexibility to cooperate with a variety of transcription factors in order to regulate CRE activity. By utilizing different sets of co-factors across CREs, we hypothesize that p53 activity is guarded against loss of any one regulatory partner allowing for dynamic and redundant control of p53-mediated transcription.

scholarly journals Locally acting transcription factors regulate p53-dependent cis-regulatory element activity

2020 ◽  
Vol 48 (8) ◽  
pp. 4195-4213 ◽  
Author(s):  
Allison N Catizone ◽  
Gizem Karsli Uzunbas ◽  
Petra Celadova ◽  
Sylvia Kuang ◽  
Daniel Bose ◽  
...  
Keyword(s):  
Transcription Factors ◽  
Regulatory Element ◽  
Regulatory Elements ◽  
Sequence Context ◽  
Binding Motifs ◽  
Cycle Arrest ◽  
Damage Repair ◽  
Local Sequence ◽  
Element Activity ◽  
Massively Parallel Reporter Assay

Abstract The master tumor suppressor p53 controls transcription of a wide-ranging gene network involved in apoptosis, cell cycle arrest, DNA damage repair, and senescence. Recent studies revealed pervasive binding of p53 to cis-regulatory elements (CREs), which are non-coding segments of DNA that spatially and temporally control transcription through the combinatorial binding of local transcription factors. Although the role of p53 as a strong trans-activator of gene expression is well known, the co-regulatory factors and local sequences acting at p53-bound CREs are comparatively understudied. We designed and executed a massively parallel reporter assay (MPRA) to investigate the effect of transcription factor binding motifs and local sequence context on p53-bound CRE activity. Our data indicate that p53-bound CREs are both positively and negatively affected by alterations in local sequence context and changes to co-regulatory TF motifs. Our data suggest p53 has the flexibility to cooperate with a variety of transcription factors in order to regulate CRE activity. By utilizing different sets of co-factors across CREs, we hypothesize that global p53 activity is guarded against loss of any one regulatory partner, allowing for dynamic and redundant control of p53-mediated transcription.

scholarly journals RNA polymerase mapping in plants identifies intergenic regulatory elements enriched in causal variants

2021 ◽  
Author(s):  
Roberto Lozano ◽  
Gregory T Booth ◽  
Bilan Yonis Omar ◽  
Bo Li ◽  
Edward S Buckler ◽  
...  
Keyword(s):  
Rna Polymerase ◽  
Cell Function ◽  
Regulatory Element ◽  
Crop Improvement ◽  
Regulatory Elements ◽  
Open Chromatin ◽  
Control Of Gene Expression ◽  
Causal Variants ◽  
Divergent Transcription ◽  
Genomic Regions

Abstract Control of gene expression is fundamental at every level of cell function. Promoter-proximal pausing and divergent transcription at promoters and enhancers, which are prominent features in animals, have only been studied in a handful of research experiments in plants. PRO-Seq analysis in cassava (Manihot esculenta) identified peaks of transcriptionally engaged RNA polymerase at both the 5′ and 3′ end of genes, consistent with paused or slowly moving Polymerase. In addition, we identified divergent transcription at intergenic sites. A full genome search for bi-directional transcription using an algorithm for enhancer detection developed in mammals (dREG) identified many intergenic regulatory element (IRE) candidates. These sites showed distinct patterns of methylation and nucleotide conservation based on genomic evolutionary rate profiling (GERP). SNPs within these IRE candidates explained significantly more variation in fitness and root composition than SNPs in chromosomal segments randomly ascertained from the same intergenic distribution, strongly suggesting a functional importance of these sites. Maize GRO-Seq data showed RNA polymerase occupancy at IREs consistent with patterns in cassava. Furthermore, these IREs in maize significantly overlapped with sites previously identified on the basis of open chromatin, histone marks, and methylation, and were enriched for reported eQTL. Our results suggest that bidirectional transcription can identify intergenic genomic regions in plants that play an important role in transcription regulation and whose identification has the potential to aid crop improvement.

scholarly journals Quantitative spatial and temporal assessment of regulatory element activity in zebrafish

eLife ◽  
2021 ◽  
Vol 10 ◽  
Author(s):  
Shipra Bhatia ◽  
Dirk Jan Kleinjan ◽  
Kirsty Uttley ◽  
Anita Mann ◽  
Nefeli Dellepiane ◽  
...  
Keyword(s):  
Disease Risk ◽  
Regulatory Element ◽  
Regulatory Elements ◽  
Wild Type ◽  
Enhancer Activity ◽  
Fluorescent Reporter ◽  
Dual Reporter ◽  
Transgenic Lines ◽  
Element Activity ◽  
The Impact

Mutations or genetic variation in noncoding regions of the genome harbouring cis-regulatory elements (CREs), or enhancers, have been widely implicated in human disease and disease risk. However, our ability to assay the impact of these DNA sequence changes on enhancer activity is currently very limited because of the need to assay these elements in an appropriate biological context. Here, we describe a method for simultaneous quantitative assessment of the spatial and temporal activity of wild-type and disease-associated mutant human CRE alleles using live imaging in zebrafish embryonic development. We generated transgenic lines harbouring a dual-CRE dual-reporter cassette in a pre-defined neutral docking site in the zebrafish genome. The activity of each CRE allele is reported via expression of a specific fluorescent reporter, allowing simultaneous visualisation of where and when in development the wild-type allele is active and how this activity is altered by mutation.

scholarly journals Systematic identification of human SNPs affecting regulatory element activity

2018 ◽  
Author(s):  
Joris van Arensbergen ◽  
Ludo Pagie ◽  
Vincent FitzPatrick ◽  
Marcel de Haas ◽  
Marijke Baltissen ◽  
...  
Keyword(s):  
Association Studies ◽  
Regulatory Element ◽  
Regulatory Elements ◽  
Genome Wide Association ◽  
Genome Wide Association Studies ◽  
Nucleotide Polymorphisms ◽  
Genome Wide ◽  
A Cell ◽  
Element Activity ◽  
Systematic Identification

AbstractMost of the millions of single-nucleotide polymorphisms (SNPs) in the human genome are non-coding, and many overlap with putative regulatory elements. Genome-wide association studies have linked many of these SNPs to human traits or to gene expression levels, but rarely with sufficient resolution to identify the causal SNPs. Functional screens based on reporter assays have previously been of insufficient throughput to test the vast space of SNPs for possible effects on enhancer and promoter activity. Here, we have leveraged the throughput of the SuRE reporter technology to survey a total of 5.9 million SNPs, including 57% of the known common SNPs. We identified more than 30 thousand SNPs that alter the activity of putative regulatory elements, often in a cell-type specific manner. These data indicate that a large proportion of human non-coding SNPs may affect gene regulation. Integration of these SuRE data with genome-wide association studies may help pinpoint SNPs that underlie human traits.

scholarly journals Q-STARZ: Quantitative Spatial and Temporal Assessment of Regulatory element activity in Zebrafish

2020 ◽  
Author(s):  
Shipra Bhatia ◽  
Wendy Bickmore ◽  
Dirk Jan Kleinjan ◽  
Kirsty Uttley ◽  
Anita Mann ◽  
...  
Keyword(s):  
Embryonic Development ◽  
Regulatory Element ◽  
Regulatory Elements ◽  
Nucleotide Polymorphisms ◽  
Wild Type ◽  
Fluorescent Reporter ◽  
Temporal Gene Expression ◽  
Dual Reporter ◽  
Transgenic Lines ◽  
Element Activity

Noncoding regions of the genome harbouring cis-regulatory elements (CREs) or enhancers drive spatial and temporal gene expression. Mutations or single nucleotide polymorphisms (SNPs) in enhancers have been widely implicated in human diseases and disease-predispositions. However, our ability to assay the regulatory potential of genetic variants in enhancers is currently very limited, in part because of the need to assay these elements in an appropriate biological context. Here, we describe a method for simultaneous quantitative assessment of the spatial and temporal activity of wild-type (Wt) and disease-associated, mutant (Mut) human CRE alleles using live imaging in zebrafish embryonic development. We generated transgenic lines harbouring a dual-CRE dual-reporter cassette in a pre-defined neutral docking site in the zebrafish genome. Using this single transgenic cassette, the functional activity of each CRE allele is reported via expression of a specific fluorescent reporter, allowing the simultaneous visualisation of the activity of both alleles. This can reveal where and when in embryonic development the wild-type allele is active and how this activity is altered by the disease-associated mutation.

Novel Toxin-antitoxin System Xn-mazEF from Xenorhabdus nematophi-la: Identification, Characterization and Functional Exploration

2020 ◽  
Vol 16 ◽  
Author(s):  
Jogendra Singh Nim ◽  
Mohit Yadav ◽  
Lalit Kumar Gautam ◽  
Chaitali Ghosh ◽  
Shakti Sahi ◽  
...  
Keyword(s):  
Interaction Analysis ◽  
Functional Characterization ◽  
Host Cells ◽  
System Control ◽  
Xenorhabdus Nematophila ◽  
Functional Features ◽  
Dynamics Simulations ◽  
Species Specific ◽  
Rna Interaction

Background: Xenorhabdus nematophila maintains species-specific mutual interaction with nematodes of Steinernema genus. Type II Toxin Antitoxin (TA) systems, the mazEF TA system controls stress and programmed cell death in bacteria. Objective: This study elucidates the functional characterization of Xn-mazEF, a mazEF homolog in X. nematophila by computational and in vitro approaches. Methods: 3 D- structural models for Xn-MazE toxin and Xn-MazF antitoxin were generated, validated and characterized for protein - RNA interaction analysis. Further biological and cellular functions of Xn-MazF toxin were also predicted. Molecular dynamics simulations of 50ns for Xn-MazF toxin complexed with nucleic acid units (DU, RU, RC, and RU) were performed. The MazF toxin and complete MazEF operon were endogenously expressed and monitored for the killing of Escherichia coli host cells under arabinose induced tightly regulated system. Results: Upon induction, E. coli expressing toxin showed rapid killing within four hours and attained up to 65% growth inhibition, while the expression of the entire operon did not show significant killing. The observation suggests that the Xn-mazEF TA system control transcriptional regulation in X. nematophila and helps to manage stress or cause toxicity leading to programmed death of cells. Conclusion: The study provides insights into structural and functional features of novel toxin, XnMazF and provides an initial inference on control of X. nematophila growth regulated by TA systems.

scholarly journals High-throughput identification of human SNPs affecting regulatory element activity

2019 ◽  
Vol 51 (7) ◽  
pp. 1160-1169 ◽  
Author(s):  
Joris van Arensbergen ◽  
Ludo Pagie ◽  
Vincent D. FitzPatrick ◽  
Marcel de Haas ◽  
Marijke P. Baltissen ◽  
...  
Keyword(s):  
High Throughput ◽  
Regulatory Element ◽  
Element Activity

scholarly journals A microRNA expression and regulatory element activity atlas of the mouse immune system

2021 ◽  
Author(s):  
Samuel A. Rose ◽  
Aleksandra Wroblewska ◽  
Maxime Dhainaut ◽  
Hideyuki Yoshida ◽  
Jonathan M. Shaffer ◽  
...  
Keyword(s):  
Immune System ◽  
Regulatory Element ◽  
Microrna Expression ◽  
Element Activity

Transvection and Silencing of the Scr Homeotic Gene of Drosophila melanogaster

Genetics ◽  
2002 ◽  
Vol 161 (2) ◽  
pp. 733-746
Author(s):  
Jeffrey W Southworth ◽  
James A Kennison
Keyword(s):  
Drosophila Melanogaster ◽  
Chromosomal Aberrations ◽  
Regulatory Element ◽  
Regulatory Elements ◽  
Anomalous Behavior ◽  
Polycomb Group ◽  
Homeotic Gene ◽  
Polycomb Group Proteins ◽  
Sex Combs Reduced ◽  
In Cis

Abstract The Sex combs reduced (Scr) gene specifies the identities of the labial and first thoracic segments in Drosophila melanogaster. In imaginal cells, some Scr mutations allow cis-regulatory elements on one chromosome to stimulate expression of the promoter on the homolog, a phenomenon that was named transvection by Ed Lewis in 1954. Transvection at the Scr gene is blocked by rearrangements that disrupt pairing, but is zeste independent. Silencing of the Scr gene in the second and third thoracic segments, which requires the Polycomb group proteins, is disrupted by most chromosomal aberrations within the Scr gene. Some chromosomal aberrations completely derepress Scr even in the presence of normal levels of all Polycomb group proteins. On the basis of the pattern of chromosomal aberrations that disrupt Scr gene silencing, we propose a model in which two cis-regulatory elements interact to stabilize silencing of any promoter or cis-regulatory element physically between them. This model also explains the anomalous behavior of the Scx allele of the flanking homeotic gene, Antennapedia. This allele, which is associated with an insertion near the Antennapedia P1 promoter, inactivates the Antennapedia P1 and P2 promoters in cis and derepresses the Scr promoters both in cis and on the homologous chromosome.

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