Faculty Opinions recommendation of Identification of a nitrate-responsive cis-element in the Arabidopsis NIR1 promoter defines the presence of multiple cis-regulatory elements for nitrogen response.

Author(s):  
Caren Chang ◽  
Heng-Cheng "Alvis" Hu
Blood ◽  
2009 ◽  
Vol 113 (7) ◽  
pp. 1543-1546 ◽  
Author(s):  
Maria Diamandis ◽  
Andrew D. Paterson ◽  
Johanna M. Rommens ◽  
D. Kika Veljkovic ◽  
Jessica Blavignac ◽  
...  

Abstract Quebec platelet disorder (QPD) is an autosomal dominant disorder with high penetrance that is associated with increased risks for bleeding. The hallmark of QPD is a gain-of-function defect in fibrinolysis due to increased platelet content of urokinase plasminogen activator (uPA) without systemic fibrinolysis. We hypothesized that increased expression of uPA by differentiating QPD megakaryocytes is linked to PLAU. Genetic marker analyses indicated that QPD was significantly linked to a 2-Mb region on chromosome 10q containing PLAU with a maximum multipoint logarithm of the odds (LOD) score of +11 between markers D10S1432 and D10S1136. Analysis of PLAU by sequencing and Southern blotting excluded mutations within PLAU and its known regulatory elements as the cause of QPD. Analyses of uPA mRNA indicated that QPD distinctly increased transcript levels of the linked PLAU allele with megakaryocyte differentiation. These findings implicate a mutation in an uncharacterized cis element near PLAU as the cause of QPD.


Blood ◽  
2011 ◽  
Vol 117 (10) ◽  
pp. 2827-2838 ◽  
Author(s):  
Mathias Leddin ◽  
Chiara Perrod ◽  
Maarten Hoogenkamp ◽  
Saeed Ghani ◽  
Salam Assi ◽  
...  

Abstract The transcription factor PU.1 occupies a central role in controlling myeloid and early B-cell development, and its correct lineage-specific expression is critical for the differentiation choice of hematopoietic progenitors. However, little is known of how this tissue-specific pattern is established. We previously identified an upstream regulatory cis element whose targeted deletion in mice decreases PU.1 expression and causes leukemia. We show here that the upstream regulatory cis element alone is insufficient to confer physiologic PU.1 expression in mice but requires the cooperation with other, previously unidentified elements. Using a combination of transgenic studies, global chromatin assays, and detailed molecular analyses we present evidence that PU.1 is regulated by a novel mechanism involving cross talk between different cis elements together with lineage-restricted autoregulation. In this model, PU.1 regulates its expression in B cells and macrophages by differentially associating with cell type–specific transcription factors at one of its cis-regulatory elements to establish differential activity patterns at other elements.


Genetics ◽  
2002 ◽  
Vol 161 (2) ◽  
pp. 793-801
Author(s):  
Wilailak Pooma ◽  
Christos Gersos ◽  
Erich Grotewold

Abstract The understanding of control of gene regulation in higher eukaryotes relies heavily on results derived from non-in vivo studies, but rarely can the significance of these approximations be established in vivo. Here, we investigated the effect of Mutator and Spm insertions on the expression of the flavonoid biosynthetic gene a1, independently regulated by the transcription factors C1 and P. The a1-mum2 and a1-m2 alleles carry Mu1 and Spm insertions, respectively, in a cis-element (ARE) of unknown function located between the P- and C1-binding sites. We show that the insertions of Mu1 and Spm similarly influence the expression of a1 controlled by C1 or P. The P-controlled a1 expression in a1-m2 is Spm dependent, and the mutant phenotype of a1-mum2 is suppressed in the pericarp in the absence of the autonomous MuDR element. Footprints within the ARE affect the regulation of a1 by C1 and P differently, providing evidence that these factors control a1 expression using distinct cis-acting regulatory elements. Together, our findings contribute significantly to one of the best-described plant regulatory systems, while stressing the need to complement with in vivo experiments current approaches used for the study of control of gene expression.


Development ◽  
1999 ◽  
Vol 126 (11) ◽  
pp. 2527-2538 ◽  
Author(s):  
M. Fujioka ◽  
Y. Emi-Sarker ◽  
G.L. Yusibova ◽  
T. Goto ◽  
J.B. Jaynes

The entire functional even-skipped locus of Drosophila melanogaster is contained within a 16 kilobase region. As a transgene, this region is capable of rescuing even-skipped mutant flies to fertile adulthood. Detailed analysis of the 7.7 kb of regulatory DNA 3′ of the transcription unit revealed ten novel, independently regulated patterns. Most of these patterns are driven by non-overlapping regulatory elements, including ones for syncytial blastoderm stage stripes 1 and 5, while a single element specifies both stripes 4 and 6. Expression analysis in gap gene mutants showed that stripe 5 is restricted anteriorly by Kruppel and posteriorly by giant, the same repressors that regulate stripe 2. Consistent with the coregulation of stripes 4 and 6 by a single cis-element, both the anterior border of stripe 4 and the posterior border of stripe 6 are set by zygotic hunchback, and the region between the two stripes is ‘carved out’ by knirps. Thus the boundaries of stripes 4 and 6 are set through negative regulation by the same gap gene domains that regulate stripes 3 and 7 (Small, S., Blair, A. and Levine, M. (1996) Dev. Biol. 175, 314–24), but at different concentrations. The 3′ region also contains a single element for neurogenic expression in ganglion mother cells 4–2a and 1–1a, and neurons derived from them (RP2, a/pCC), suggesting common regulators in these lineages. In contrast, separable elements were found for expression in EL neurons, U/CQ neurons and the mesoderm. The even-skipped 3′ untranslated region is required to maintain late stage protein expression in RP2 and a/pCC neurons, and appears to affect protein levels rather than mRNA levels. Additionally, a strong pairing-sensitive repression element was localized to the 3′ end of the locus, but was not found to contribute to efficient functional rescue.


2019 ◽  
Vol 81 (4) ◽  
Author(s):  
Aimi Farehah Omar ◽  
Ismanizan Ismail

Sesquiterpene synthase is an enzyme involved in sesquiterpene biosynthesis which catalyzed sesquiterpene formation from farnesyl diphosphate (FDP). In this research, the sesquiterpene synthase promoter (PmSS) was isolated from Persicaria minor (P.minor) to identify the functional region of the promoter and possible cis - regulatory element involved in the regulation of sesquiterpene synthase gene. Various putative cis - regulatory element involved in environmental stress and hormones were identified on PmSS promoter. The PmSS promoter and three series of deletion promoter were fused to β-glucuronidase (gus) gene and transformed into Arabidopsis thaliana. This study showed PmSS promoter was regulated in a developmental -specific manner and response to wounding, drought, heat, abscisic acid (ABA) and methyl jasmonate (MeJa) treatment. The results revealed the existence of cis regulatory elements that control the regulation of promoter activity in a developmental specific manner at -1758 to -1078 promoter sequences. The presence of cis-element acting as a repressor is expected to be present at the promoter between -1540 to -1078 bp. The region from -1078 to -855 was critical for maximal PmSS promoter activity. Deletion of promoter region from -1758 to -855 induced regulation of promoter in an organ-specific manner. Drought stress treatment did not induced GUS activity in deleted ABRE motif construct, suggested that ABRE motif is essential cis element during drought stress.  


2019 ◽  
Author(s):  
Haoyue Zhang ◽  
Daniel J. Emerson ◽  
Thomas G. Gilgenast ◽  
Katelyn R. Titus ◽  
Yemin Lan ◽  
...  

AbstractHigher-order chromatin organization such as A/B compartments, TADs and chromatin loops are temporarily disrupted during mitosis. These structures are thought to organize aspects of gene regulation, and thus it is important to understand how they are re-established after mitosis. We examined the dynamics of chromosome reorganization by Hi-C at defined time points following exit from mitosis in highly purified, synchronous cell populations. We observed that A/B compartments are rapidly established and progressively gain in strength following mitotic exit. Contact domain formation occurs from the “bottom-up” with smaller sub-TADs forming initially, followed by convergence into multi-domain TAD structures. CTCF is strongly retained at a significant fraction of sites on mitotic chromosomes and immediately resumes full binding at ana/telophase, the earliest tested time point. In contrast, cohesin is completely evicted from mitotic chromosomes and resumes focal binding with delayed kinetics. The formation of CTCF/cohesin co-anchored structural loops follows the kinetics of cohesin positioning. Stripe-shaped contacts anchored by CTCF grow in length, consistent with a loop extrusion process after mitosis. Interactions between cis-regulatory elements can form rapidly, preceding CTCF/cohesin anchored structural loops. Strikingly, we identified a group of rapidly emerging transient contacts between cis-regulatory elements in ana/telophase, that are dissolved upon G1 entry, co-incident with the establishment of inner boundaries or nearby interfering loops. Our findings indicate that distinct but mutually influential forces drive post-mitotic chromatin re-configuration to shape compartments, contact domains, cis-element contacts, and CTCF/cohesin dependent loops.


Author(s):  
C. Van der Geest

I am a 30-year-old sharemilker on my parent's 600 cow developing farm near Blackball on the western side of the Grey Valley. Earlier this year I competed in the National Young Farmer of the Year competition and finished a close third. So what is information? There are two types of information that I use. There is data gathered from my farm to help fine tune the running of the day to day operations on the farm And directional information This is the information that arrives in papers and directs the long-term direction and plans of the farm and farming businesses. Due to the variability in weather on the Coast there is a greater need to monitor and adjust the farming system compared to an area like Canterbury. This was shown last year (2001/02) when the farm was undergoing a rapid period of development and I was under time restraints from increasing the herd size, building a new shed as well as developing the farm. The results of the time pressure was that day to day information gathering was lower resulting in per cow production falling by 11% or around $182 per cow. So what information was lacking that caused this large drop in profit. • Pasture growth rates • Cow condition • Nitrogen requirements • Paddock performance • Milk production • Pre-mating heat detection As scientists and advisers I hear you say that it is the farmer's responsibility to gather and analyse this information. You have the bigger topics to research and discover, gene marking, improving pasture species, sexing of sperm and ideas that I have not even contemplated yet. This is indeed very valuable research. Where would farming be without the invention of electric fences, artificial breeding and nitrogen research? But my problem is to take a farm with below average production to the top 10% in production with the existing technology and farming principles. I have all the technical information I need at the end of a phone. I can and do ring my consultant, fertiliser rep, vet, neighbour and due to the size and openness of New Zealand science, at present if they do not know I can ring an expert in agronomy, nutrition, soils and receive the answer that I require. I hope that this openness remains as in a time of privatisation and cost cutting it is a true advantage. I feel that for myself the next leap in information is not in the growing of grass or production of milk but in the tools to collect, store and utilise that information. This being tied to a financial benefit to the farming business is the real reason that I farm. Think of the benefits of being able to read pasture cover on a motorbike instantly downloaded, overlaying cow intake with milk production, changes in cow weight, daily soil temperature and predicted nitrogen response. Telling me low producing cows and poor producing paddocks, any potential feed deficits or surpluses. This would be a powerful information tool to use. The majority of this information is already available but until the restraints of time and cost are removed from data gathering and storage, this will not happen.


2015 ◽  
Vol 37 (s1) ◽  
pp. 87-105
Author(s):  
Benedek Nobilis ◽  
András Svraka

Governments throughout the EU and OECD countries rely on revenues raised on capital income. Albeit several arguments can be made for keeping these taxes, in their widespread form they hinder capital accumulation and significantly lower potential growth due to their savings and investment distorting nature. At the same time, the actual economic impact of tax types is largely influenced by their structure. An elegant method, which is also simple in its concept, for eliminating the economic distortions of profit taxes is cash-flow taxation which moves income taxes closer to the more growth-friendly value-added taxes. The small business tax, which was introduced in Hungary in 2013, was designed along these principles. In this paper we review the theoretical literature on cash-flow taxation and discuss the main regulatory elements of the small business tax, as well as the solutions elaborated for working out the challenges related to its implementation.


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