scholarly journals A molecular toolkit for the green seaweed Ulva mutabilis

2021 ◽  
Author(s):  
Jonas Blomme ◽  
Xiaojie Liu ◽  
Thomas B Jacobs ◽  
Olivier De Clerck
Keyword(s):  
Transgene Expression ◽  
Large Scale ◽  
Expression Vectors ◽  
Regulatory Sequences ◽  
Gene Characterization ◽  
Transit Peptides ◽  
Intracellular Compartments ◽  
Green Seaweed ◽  
Primary Producer ◽  
Golden Gate Cloning

Abstract The green seaweed Ulva is an ecologically-important marine primary producer as well as a promising cash crop cultivated for multiple uses. Despite its importance, several molecular tools are still needed to better understand seaweed biology. Here, we report the development of a flexible and modular molecular cloning toolkit for the green seaweed Ulva mutabilis based on a Golden Gate cloning system. The toolkit presently contains 125 entry vectors, 26 destination vectors and 107 functionally validated expression vectors. We demonstrate the importance of endogenous regulatory sequences for transgene expression and characterize three endogenous promoters suitable to drive transgene expression. We describe two vector architectures to express transgenes via two expression cassettes or a bicistronic approach. The majority of selected transformants (50-80%) consistently give clear visual transgene expression. Furthermore, we made different marker lines for intracellular compartments after evaluating 13 transit peptides and 11 tagged endogenous Ulva genes. Our molecular toolkit enables the study of Ulva gain-of-function lines and paves the way for gene characterization and large-scale functional genomics studies in a green seaweed.

scholarly journals A molecular toolkit for the green seaweed Ulva mutabilis

2020 ◽  
Author(s):  
Jonas Blomme ◽  
Xiaojie Liu ◽  
Thomas B Jacobs ◽  
Olivier De Clerck
Keyword(s):  
Transgene Expression ◽  
Large Scale ◽  
Expression Vectors ◽  
Regulatory Sequences ◽  
Gene Characterization ◽  
Transit Peptides ◽  
Intracellular Compartments ◽  
Green Seaweed ◽  
Primary Producer ◽  
Golden Gate Cloning

The green seaweed Ulva is an ecologically-important marine primary producer as well as a promising cash crop cultivated for multiple uses. Despite its importance, several molecular tools are still needed to better understand seaweed biology. Here, we report the development of a flexible and modular molecular cloning toolkit for the green seaweed Ulva mutabilis based on a Golden Gate cloning system. The toolkit presently contains 125 entry vectors, 26 destination vectors and 107 functionally validated expression vectors. We demonstrate the importance of endogenous regulatory sequences for transgene expression and characterize three endogenous promoters suitable to drive transgene expression. We describe two vector architectures to express transgenes via two expression cassettes or a bicistronic approach. The majority of selected transformants (50-80%) consistently give clear visual transgene expression. Furthermore, we made different marker lines for intracellular compartments after evaluating 13 transit peptides and 11 tagged endogenous Ulva genes. Our molecular toolkit enables the study of Ulva gain-of-function lines and paves the way for gene characterization and large-scale functional genomics studies in a green seaweed.

Modular long-range regulation of Myf5 reveals unexpected heterogeneity between skeletal muscles in the mouse embryo

Development ◽  
2000 ◽  
Vol 127 (20) ◽  
pp. 4455-4467 ◽  
Author(s):  
J. Hadchouel ◽  
S. Tajbakhsh ◽  
M. Primig ◽  
T.H. Chang ◽  
P. Daubas ◽  
...  
Keyword(s):  
Mouse Embryo ◽  
Transgene Expression ◽  
Distal Region ◽  
Trunk Muscles ◽  
Regulatory Sequences ◽  
Spatiotemporal Expression ◽  
Branchial Arches ◽  
Early Expression ◽  
Myogenic Factor ◽  
The Brain

The myogenic factor Myf5 plays a key role in muscle cell determination, in response to signalling cascades that lead to the specification of muscle progenitor cells. We have adopted a YAC transgenic approach to identify regulatory sequences that direct the complex spatiotemporal expression of this gene during myogenesis in the mouse embryo. Important regulatory regions with distinct properties are distributed over 96 kb upstream of the Myf5 gene. The proximal 23 kb region directs early expression in the branchial arches, epaxial dermomyotome and in a central part of the myotome, the epaxial intercalated domain. Robust expression at most sites in the embryo where skeletal muscle forms depends on an enhancer-like sequence located between −58 and −48 kb from the Myf5 gene. This element is active in the epaxial and hypaxial myotome, in limb muscles, in the hypoglossal chord and also at the sites of Myf5 transcription in prosomeres p1 and p4 of the brain. However later expression of Myf5 depends on a more distal region between −96 and −63 kb, which does not behave as an enhancer. This element is necessary for expression in head muscles but strikingly only plays a role in a subset of trunk muscles, notably the hypaxially derived ventral body muscles and also those of the diaphragm and tongue. Transgene expression in limb muscle masses is not affected by removal of the −96/-63 region. Epaxially derived muscles and some hypaxial muscles, such as the intercostals and those of the limb girdles, are also unaffected. This region therefore reveals unexpected heterogeneity between muscle masses, which may be related to different facets of myogenesis at these sites. Such regulatory heterogeneity may underlie the observed restriction of myopathies to particular muscle subgroups.

beta-MHC transgene expression in suspended and mechanically overloaded/suspended soleus muscle of transgenic mice

1997 ◽  
Vol 272 (5) ◽  
pp. R1552-R1561 ◽  
Author(s):  
J. J. McCarthy ◽  
A. M. Fox ◽  
G. L. Tsika ◽  
L. Gao ◽  
R. W. Tsika
Keyword(s):  
Transgenic Mice ◽  
Soleus Muscle ◽  
Transgene Expression ◽  
Specific Activity ◽  
Fiber Type ◽  
Weight Bearing ◽  
Troponin C ◽  
Hindlimb Suspension ◽  
Regulatory Sequences ◽  
Type I

Non-weight-bearing (NWB) activity [space flight and hindlimb suspension (HS)] results in the loss of soleus muscle mass, a slow-to-fast fiber-type conversion, and decreased beta-myosin heavy chain (beta-MHC) protein and mRNA expression. To identify beta-MHC promoter sequences required for decreased beta-MHC expression in response to HS, we have modified an existing noninvasive hindlimb unweighting model to accommodate the use of (transgenic) mice. After 2 wk of HS, body and muscle (soleus > gastrocnemius > plantaris) weights were decreased as was the proportion of histochemically classified type I fibers in HS soleus muscle. Northern blot analysis revealed decreases in endogenous mRNA representing beta-MHC, slow myosin light chain 1 and 2, and cardiac/slow troponin C, whereas those representing skeletal troponin C, muscle creatine kinase, and glyceraldehyde-3-phosphate dehydrogenase increased. Protein extracts prepared from HS soleus (SS) muscle of mice harboring transgenes comprised of 5.6 or 0.6 kilobase of wild type (wt) mouse beta-MHC promoter (beta 5.6 wt, beta 0.6wt) and those carrying the simultaneous mutation (mut) of the MCAT, C-rich, and beta e3 subregions (beta 5.6mut3, beta 0.6mut3) revealed decreases in chloramphenicol acetyltransferase (CAT) specific activity relative to respective controls. Decreased CAT mRNA was observed for transgene beta 5.6mut3, line 85. Two weeks of the simultaneous imposition of mechanical overload (synergist ablation) and HS (MOV/HS) countermanded the loss in absolute and normalized SS weight but did not decrease beta 0.6wt transgene expression. These transgenic results demonstrate that regulatory sequences within a 600-base pair beta-MHC promoter are sufficient to direct decreased transcription of beta-MHC transgenes after 2 wk of HS.

scholarly journals Canopy cover and anurans: nutrients are the most important predictor of growth and development

2016 ◽  
Vol 94 (3) ◽  
pp. 225-232 ◽  
Author(s):  
Freya E. Rowland ◽  
Sara K. Tuttle ◽  
María J. González ◽  
Michael J. Vanni
Keyword(s):  
Growth And Development ◽  
Large Scale ◽  
Food Resource ◽  
Canopy Cover ◽  
Resource Quality ◽  
Bottom Up ◽  
Growth And Survival ◽  
Primary Producer ◽  
Full Factorial ◽  
Potential Food

Bottom-up effects such as the availability of light and nutrients can have large impacts on primary producer quantity and quality, which is then translated into the growth and development of consumers. The use of “canopy cover” as a bottom-up predictive factor is a broad categorization, as canopy cover controls both the amount of light allowed into a pond and the nutrient load through leaf litter. To test how light and nutrients influence pond ecosystems, we manipulated inorganic nutrients and light in a 2 × 3 full-factorial, large-scale mesocosm experiment. Larval American Bullfrogs (Lithobates catesbeianus (Shaw, 1802)) were reared for 6 weeks at low densities and then assessed for development, growth, and survival at the end of the experiment. We also collected weekly samples of potential food resources (phytoplankton and periphyton) for the estimation of algal production and stoichiometric quality (carbon:nitrogen:phosphorus). Light had strong effects on food resource quality; however, resource quality did not significantly predict tadpole growth or development. Instead, nutrients seemed to be the most important factor as a stimulator of total algal primary production and some unknown pathway, which in turn affected tadpole development. Ours is the first study to investigate canopy cover using a comprehensive causal model, and our results suggest in regards to tadpole growth and development, canopy cover is important mainly as a source of nutrients to ponds.

scholarly journals Coronaviruses as Vectors: Position Dependence of Foreign Gene Expression

2003 ◽  
Vol 77 (21) ◽  
pp. 11312-11323 ◽  
Author(s):  
Cornelis A. M. de Haan ◽  
Linda van Genne ◽  
Jeroen N. Stoop ◽  
Haukeline Volders ◽  
Peter J. M. Rottier
Keyword(s):  
Gene Expression ◽  
Expression Vectors ◽  
Luciferase Expression ◽  
Foreign Gene ◽  
Regulatory Sequences ◽  
Expression Levels ◽  
Genomic Position ◽  
Position Dependence ◽  
Foreign Genes

ABSTRACT Coronaviruses are the enveloped, positive-stranded RNA viruses with the largest RNA genomes known. Several features make these viruses attractive as vaccine and therapeutic vectors: (i) deletion of their nonessential genes is strongly attenuating; (ii) the genetic space thus created allows insertion of foreign information; and (iii) their tropism can be modified by manipulation of the viral spike. We studied here their ability to serve as expression vectors by inserting two different foreign genes and evaluating systematically the genomic position dependence of their expression, using a murine coronavirus as a model. Renilla and firefly luciferase expression cassettes, each provided with viral transcription regulatory sequences (TRSs), were inserted at several genomic positions, both independently in different viruses and combined within one viral genome. Recombinant viruses were generated by using a convenient method based on targeted recombination and host cell switching. In all cases high expression levels of the foreign genes were observed without severe effects on viral replication in vitro. The expression of the inserted gene appeared to be dependent on its genomic position, as well as on the identity of the gene. Expression levels increased when the luciferase gene was inserted closer to the 3′ end of the genome. The foreign gene insertions generally reduced the expression of upstream viral genes. The results are consistent with coronavirus transcription models in which the transcription from upstream TRSs is attenuated by downstream TRSs. Altogether, our observations clearly demonstrate the potential of coronaviruses as (multivalent) expression vectors.

scholarly journals E-box sites and a proximal regulatory region of the muscle creatine kinase gene differentially regulate expression in diverse skeletal muscles and cardiac muscle of transgenic mice.

1996 ◽  
Vol 16 (9) ◽  
pp. 5058-5068 ◽  
Author(s):  
M A Shield ◽  
H S Haugen ◽  
C H Clegg ◽  
S D Hauschka
Keyword(s):  
Creatine Kinase ◽  
Skeletal Muscles ◽  
Transgene Expression ◽  
Regulatory Region ◽  
Regulatory Sequences ◽  
Striated Muscles ◽  
Muscle Creatine Kinase ◽  
E Box ◽  
Muscle Creatine ◽  
E Boxes

Previous analysis of the muscle creatine kinase (MCK) gene indicated that control elements required for transcription in adult mouse muscle differed from those required in cell culture, suggesting that distinct modes of muscle gene regulation occur in vivo. To examine this further, we measured the activity of MCK transgenes containing E-box and promoter deletions in a variety of striated muscles. Simultaneous mutation of three E boxes in the 1,256-bp MCK 5' region, which abolished transcription in muscle cultures, had strikingly different effects in mice. The mutations abolished transgene expression in cardiac and tongue muscle and caused a reduction in expression in the soleus muscle (a muscle with many slow fibers) but did not affect expression in predominantly fast muscles: quadriceps, abdominals, and extensor digitorum longus. Other regulatory sequences with muscle-type-specific activities were found within the 358-bp 5'-flanking region. This proximal region conferred relatively strong expression in limb and abdominal skeletal muscles but was inactive in cardiac and tongue muscles. However, when the 206-bp 5' enhancer was ligated to the 358-bp region, high levels of tissue-specific expression were restored in all muscle types. These results indicate that E boxes and a proximal regulatory region are differentially required for maximal MCK transgene expression in different striated muscles. The overall results also imply that within skeletal muscles, the steady-state expression of the MCK gene and possibly other muscle genes depends on transcriptional mechanisms that differ between fast and slow fibers as well as between the anatomical and physiological attributes of each specific muscle.

scholarly journals Disease Gene Characterization through Large-Scale Co-Expression Analysis

PLoS ONE ◽  
2009 ◽  
Vol 4 (12) ◽  
pp. e8491 ◽  
Author(s):  
Allen Day ◽  
Jun Dong ◽  
Vincent A. Funari ◽  
Bret Harry ◽  
Samuel P. Strom ◽  
...  
Keyword(s):  
Expression Analysis ◽  
Large Scale ◽  
Disease Gene ◽  
Gene Characterization

scholarly journals Paired CRISPR/Cas9 guide-RNAs enable high-throughput deletion scanning (ScanDel) of a Mendelian disease locus for functionally critical non-coding elements

2016 ◽  
Author(s):  
Molly Gasperini ◽  
Gregory M. Findlay ◽  
Aaron McKenna ◽  
Jennifer H. Milbank ◽  
Choli Lee ◽  
...  
Keyword(s):  
Large Scale ◽  
Transcriptional Start Site ◽  
Regulatory Elements ◽  
Mendelian Disease ◽  
Regulatory Sequences ◽  
Coding Region ◽  
Endogenous Gene ◽  
Distal Regulatory Elements

AbstractThe extent to which distal non-coding mutations contribute to Mendelian disease remains a major unknown in human genetics. Given that a gene’s in vivo function can be appropriately modeled in vitro, CRISPR/Cas9 genome editing enables the large-scale perturbation of distal non-coding regions to identify functional elements in their native context. However, early attempts at such screens have relied on one individual guide RNA (gRNA) per cell, resulting in sparse mutagenesis with minimal redundancy across regions of interest. To address this, we developed a system that uses pairs of gRNAs to program thousands of kilobase-scale deletions that scan across a targeted region in a tiling fashion (“ScanDel”). As a proof-of-concept, we applied ScanDel to program 4,342 overlapping 1- and 2- kilobase (Kb) deletions that tile a 206 Kb region centered on HPRT1, the gene underlying Lesch-Nyhan syndrome, with median 27-fold redundancy per base. Programmed deletions were functionally assayed by selecting for loss of HPRT1 function with 6-thioguanine. HPRT1 exons served as positive controls, and all were successfully identified as functionally critical by the screen. Remarkably, HPRT1 function appeared robust to deletion of any intergenic or deeply intronic non-coding region across the 206 Kb locus, indicating that proximal regulatory sequences are sufficient for its expression. A sparser mutagenesis screen of the same 206 Kb with individual gRNAs also failed to identify critical distal regulatory elements. Although our screen did find programmed deletions and individual gRNAs with putative functional consequences that targeted exon-proximal non-coding sequences (e.g. the promoter), long-read sequencing revealed that this signal was driven almost entirely by rare, unexpected deletions that extended into exonic sequence. These targeted validation experiments defined a small region surrounding the transcriptional start site as the only non-coding sequence essential to HPRT1 function. Overall, our results suggest that distal regulatory elements are not critical for HPRT1 expression, and underscore the necessity of comprehensive edited-locus genotyping for validating the results of CRISPR screens. The application of ScanDel to additional loci will enable more insight into the extent to which the disruption of distal non-coding elements contributes to Mendelian diseases. In addition, dense, redundant, large-scale deletion scanning with gRNA pairs will facilitate a deeper understanding of endogenous gene regulation in the human genome.

scholarly journals Population-scale study of eRNA transcription reveals bipartite functional enhancer architecture

2018 ◽  
Author(s):  
Katla Kristjánsdóttir ◽  
Yeonui Kwak ◽  
Nathaniel D. Tippens ◽  
John T. Lis ◽  
Hyun Min Kang ◽  
...  
Keyword(s):  
Transcription Initiation ◽  
Large Scale ◽  
High Sensitivity ◽  
Regulatory Sequences ◽  
Lymphoblastoid Cell Lines ◽  
Human Lymphoblastoid Cell ◽  
Regulatory Variants ◽  
Transcription Sites ◽  
Non Coding Rnas ◽  
Human Lymphoblastoid Cell Lines

AbstractEnhancer RNAs (eRNA) are non-coding RNAs transcribed bidirectionally from active regulatory sequences. Their expression levels correlate with the activating potentials of the enhancers, but due to their instability, eRNAs have proven difficult to quantify in large scale. To overcome this, we use capped-nascent-RNA sequencing to efficiently capture the bidirectional initiation of eRNAs. We apply this in large scale to the human lymphoblastoid cell lines from the Yoruban population, and detected nearly 75,000 eRNA transcription sites with high sensitivity and specificity. We identify genetic variants significantly associated with overall eRNA initiation levels, as well as the transcription directionality between the two divergent eRNA pairs, namely the transcription initiation and directional initiation quantitative trait loci (tiQTLs and diQTLs) respectively. High-resolution analyses of these two types of eRNA QTLs reveal distinct positions of enrichment not only at the central transcription factor (TF) binding regions but also at the flanking eRNA initiation regions, both of which are equivalently associated with mRNA expression QTLs. These two regions - the central TF binding footprint and the eRNA initiation cores - define the bipartite architecture and the function of enhancers, and may provide further insights into interpreting the significance of non-coding regulatory variants.

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