scholarly journals Characterization and Activity Analyses of the FLOWERING LOCUS T Promoter in Gossypium Hirsutum

2019 ◽  
Vol 20 (19) ◽  
pp. 4769 ◽  
Author(s):  
Na Sang ◽  
Darun Cai ◽  
Chao Li ◽  
Yuqiang Sun ◽  
Xianzhong Huang
Keyword(s):  
Gossypium Hirsutum ◽  
Regulatory Elements ◽  
Proximal Promoter ◽  
Activity Levels ◽  
Loss Of Function ◽  
Flowering Locus T ◽  
Promoter Regions ◽  
Core Motif ◽  
Late Flowering ◽  
Flowering Locus

Flowering transition is a crucial development process in cotton (Gossypium hirsutum L.), and the flowering time is closely correlated with the timing of FLOWERING LOCUS T (FT) expression. However, the mechanism underlying the coordination of various cis-regulatory elements in the FT promoter of cotton has not been determined. In this study, a 5.9-kb promoter of FT was identified from cotton. A bioinformatics analysis showed that multiple insertion–deletion sites existed in the 5.9-kb promoter. Different expression levels of a reporter gene, and the induction by sequential deletions in GhFT promoter, demonstrated that 1.8-kb of the GhFT promoter was stronger than 4.2-, 4.8-, and 5.9-kb promoter fragments. The binding sites of the CONSTANS (CO) and NUCLEAR FACTOR Y transcription factors were located within the 1.0-kb sequence upstream of the FT transcription start site. A large number of repeat segments were identified in proximal promoter regions (−1.1 to −1.4 kb). A complementation analysis of deletion constructs between 1.0 and 1.8 kb of G. hirsutum, Gossypium arboretum, and Gossypium raimondii FT promoters revealed that the 1.0-kb fragment significantly rescued the late-flowering phenotype of the Arabidopsis FT loss-of-function mutant ft-10, whereas the 1.8-kb promoter only slightly rescued the late-flowering phenotype. Furthermore, the conserved CORE motif in the cotton FT promoter is an atypical TGTG(N2-3)ATG, but the number of arbitrary bases between TGTG and ATG is uncertain. Thus, the proximal FT promoter region might play an important role affecting the activity levels of FT promoters in cotton flowering.

scholarly journals Molecular cloning and functional analysis of the FLOWERING LOCUS T (FT ) homolog GhFT1 from Gossypium hirsutum

2015 ◽  
Vol 57 (6) ◽  
pp. 522-533 ◽  
Author(s):  
Danli Guo ◽  
Chao Li ◽  
Rui Dong ◽  
Xiaobo Li ◽  
Xiangwen Xiao ◽  
...  
Keyword(s):  
Functional Analysis ◽  
Gossypium Hirsutum ◽  
Molecular Cloning ◽  
Flowering Locus T ◽  
Flowering Locus

scholarly journals Dynamics of Cardiomyocyte Transcriptome and Chromatin Landscape Demarcates Key Events of Heart Development

2018 ◽  
Author(s):  
Michal Pawlak ◽  
Katarzyna Z. Kedzierska ◽  
Maciej Migdal ◽  
Karim Abu Nahia ◽  
Jordan A. Ramilowski ◽  
...  
Keyword(s):  
Heart Development ◽  
Regulatory Networks ◽  
Regulatory Elements ◽  
Chromatin Accessibility ◽  
Proximal Promoter ◽  
Global Changes ◽  
Open Chromatin ◽  
Sequence Motifs ◽  
Loss Of Function ◽  
Heart Looping

ABSTRACTThe development of an organ involves dynamic regulation of gene transcription and complex multipathway interactions. To better understand transcriptional regulatory mechanism driving heart development and the consequences of its disruption, we isolated cardiomyocytes (CMs) from wild-type zebrafish embryos at 24, 48 and 72 hours post fertilization corresponding to heart looping, chamber formation and heart maturation, and from mutant lines carrying loss-of-function mutations in gata5, tbx5a and hand2, transcription factors (TFs) required for proper heart development. The integration of CM transcriptomics (RNA-seq) and genome-wide chromatin accessibility maps (ATAC-seq) unravelled dynamic regulatory networks driving crucial events of heart development. These networks contained key cardiac TFs including Gata5/6, Nkx2.5, Tbx5/20, and Hand2, and are associated with open chromatin regions enriched for DNA sequence motifs belonging to the family of the corresponding TFs. These networks were disrupted in cardiac TF mutants, indicating their importance in proper heart development. The most prominent gene expression changes, which correlated with chromatin accessibility modifications within their proximal promoter regions, occurred between heart looping and chamber formation, and were associated with metabolic and hematopoietic/cardiac switch during CM maturation. Furthermore, loss of function of cardiac TFs Gata5, Tbx5a, and Hand2 affected the cardiac regulatory networks and caused global changes in chromatin accessibility profile. Among regions with differential chromatin accessibility in mutants were highly conserved non-coding elements which represent putative cis regulatory elements with potential role in heart development and disease. Altogether, our results revealed the dynamic regulatory landscape at key stages of heart development and identified molecular drivers of heart morphogenesis.

scholarly journals Deciphering Transcriptional Regulation of Human Core Promoters

2017 ◽  
Author(s):  
Shira Weingarten-Gabbay ◽  
Ronit Nir ◽  
Shai Lubliner ◽  
Eilon Sharon ◽  
Yael Kalma ◽  
...  
Keyword(s):  
Binding Site ◽  
Human Genome ◽  
Core Promoter ◽  
Regulatory Elements ◽  
Proximal Promoter ◽  
Promoter Regions ◽  
Core Promoters ◽  
Optimal Distance ◽  
Negative Effect ◽  
Positive Effect

ABSTRACTDespite its pivotal role in regulating transcription, our understanding of core promoter function, architecture, and cis-regulatory elements is lacking. Here, we devised a highthroughput assay to quantify the activity of ∼15,000 fully designed core promoters that we integrated and expressed from a fixed location within the human genome. We find that core promoters drive transcription unidirectionally, and that sequences originating from promoters exhibit stronger activity than sequences originating from enhancers. Testing multiple combinations and distances of core promoter elements, we observe a positive effect of TATA and Initiator, a negative effect of BREu and BREd, and a 10bp periodicity in the optimal distance between the TATA and the Initiator. By comprehensively screening TF binding-sites, we show that site orientation has little effect, that the effect of binding site number on expression is factor-specific, and that there is a striking agreement between the effect of binding site multiplicity in our assay and the tendency of the TF to appear in homotypic clusters throughout the genome. Overall, our results systematically assay the elements that drive expression in core- and proximal-promoter regions and shed light on organization principles of regulatory regions in the human genome.

scholarly journals Evolution of ventricular myocyte electrophysiology

2008 ◽  
Vol 35 (3) ◽  
pp. 262-272 ◽  
Author(s):  
Barbara Rosati ◽  
Min Dong ◽  
Lan Cheng ◽  
Shian-Ren Liou ◽  
Qinghong Yan ◽  
...  
Keyword(s):  
Action Potential ◽  
Functional Properties ◽  
Small Mammals ◽  
Action Potential Duration ◽  
Structural Evolution ◽  
Regulatory Elements ◽  
Proximal Promoter ◽  
Regulatory Evolution ◽  
Promoter Regions ◽  
Primary Determinant

The relative importance of regulatory versus structural evolution for the evolution of different biological systems is a subject of controversy. The primacy of regulatory evolution in the diversification of morphological traits has been promoted by many evolutionary developmental biologists. For physiological traits, however, the role of regulatory evolution has received less attention or has been considered to be relatively unimportant. To address this issue for electrophysiological systems, we examined the importance of regulatory and structural evolution in the evolution of the electrophysiological function of cardiac myocytes in mammals. In particular, two related phenomena were studied: the change in action potential morphology in small mammals and the scaling of action potential duration across mammalian phylogeny. In general, the functional properties of the ion channels involved in ventricular action potential repolarization were found to be relatively invariant. In contrast, there were large changes in the expression levels of multiple ion channel and transporter genes. For the Kv2.1 and Kv4.2 potassium channel genes, which are primary determinants of the action potential morphology in small mammals, the functional properties of the proximal promoter regions were found to vary in concordance with species-dependent differences in mRNA expression, suggesting that evolution of cis-regulatory elements is the primary determinant of this trait. Scaling of action potential duration was found to be a complex phenomenon, involving changes in the expression of a large number of channels and transporters. In this case, it is concluded that regulatory evolution is the predominant mechanism by which the scaling is achieved.

scholarly journals Decoding a Signature-Based Model of Transcription Cofactor Recruitment Dictated by Cardinal Cis-Regulatory Elements in Proximal Promoter Regions

PLoS Genetics ◽  
2013 ◽  
Vol 9 (11) ◽  
pp. e1003906 ◽  
Author(s):  
Christopher Benner ◽  
Sergiy Konovalov ◽  
Carlos Mackintosh ◽  
Kasey R. Hutt ◽  
Rieka Stunnenberg ◽  
...  
Keyword(s):  
Regulatory Elements ◽  
Proximal Promoter ◽  
Promoter Regions ◽  
Transcription Cofactor ◽  
Cofactor Recruitment

scholarly journals cis-Regulatory Elements and Chromatin State Coordinately Control Temporal and Spatial Expression of FLOWERING LOCUS T in Arabidopsis

2010 ◽  
Vol 22 (5) ◽  
pp. 1425-1440 ◽  
Author(s):  
Jessika Adrian ◽  
Sara Farrona ◽  
Julia J. Reimer ◽  
Maria C. Albani ◽  
George Coupland ◽  
...  
Keyword(s):  
Regulatory Elements ◽  
Chromatin State ◽  
Flowering Locus T ◽  
Spatial Expression ◽  
Temporal And Spatial ◽  
Flowering Locus

scholarly journals Identification of regulatory elements in the Cyp19 proximal promoter in rat luteal cells

2007 ◽  
Vol 39 (4) ◽  
pp. 211-221 ◽  
Author(s):  
Carlos Stocco ◽  
Jakub Kwintkiewicz ◽  
Zailong Cai
Keyword(s):  
Binding Site ◽  
Promoter Activity ◽  
Regulatory Elements ◽  
Binding Activity ◽  
Proximal Promoter ◽  
Promoter Regions ◽  
Pregnant Rats ◽  
Response Element ◽  
Luteal Cells ◽  
Immature Rats

AbstractThe cytochrome P450 aromatase (Cyp19) gene encodes an enzyme of crucial importance in the synthesis of estradiol. Estradiol is luteotropic in the rat. In this species, luteal Cyp19 expression increases progressively during pregnancy and falls before parturition. The mechanisms that control these changes are unknown. Using gel shift assays, we sought to identify the promoter regions that control Cyp19 expression in the rat corpus luteum (CL). The Cyp19 promoter contains a cAMP response element-like sequence (CLS), two nuclear receptor elements half sites (NREs), a GATA binding site, a Yin Yang-1 (YY1) response element, and an activation protein 3 (AP3) binding site. Nuclear extracts were obtained from CL of rats on days 4, 15, and 23 of pregnancy and from the ovaries of immature rats treated with vehicle or a hormone that induces Cyp19 expression in the follicles. CLS was active in immature ovaries but inactive in the CL of pregnant rats, whereas binding to NREs and GATA was observed in both tissues. YY1 was inactive in all samples tested. In the CL, AP3 binding was higher on day 15 of pregnancy when compared with day 4 and day 23 but it was absent in ovaries of immature rats, whereas luteinization increased AP3 binding activity. Mutation of the AP3 site blunted the stimulation of Cyp19 promoter activity in granulosa cells. Our results indicate that CLS is active only in follicles; whereas in the CL, binding to the GATA, NRE, and AP3 sites associates with changes in Cyp19 expression, suggesting that they control Cyp19 promoter activity in luteal cells.

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