High conservation of cis -regulatory elements between quail and human for the Pax-6 gene

1999 ◽  
Vol 209 (3) ◽  
pp. 165-173 ◽  
Author(s):  
S. Plaza ◽  
Simon Saule ◽  
C. Dozier
Keyword(s):  
Regulatory Elements ◽  
High Conservation

scholarly journals Characterization and expression QTL analysis of TaABI4, a pre-harvest sprouting related gene in wheat

2020 ◽  
Author(s):  
Chunsheng Xiao ◽  
Yujiao Liu ◽  
Wenshuai Chen ◽  
Jian Yang ◽  
Mengping Cheng ◽  
...  
Keyword(s):  
Wheat Cultivar ◽  
Recombinant Inbred Lines ◽  
Regulatory Elements ◽  
Specific Gene ◽  
Transcript Accumulation ◽  
Trait Variation ◽  
Severe Reduction ◽  
Potential Pest ◽  
High Conservation ◽  
Ap2 Domain

AbstractPre-harvest sprouting (PHS) induced by the decline of seed dormancy causes a severe reduction in crop yield and flour quality. In this study, we isolated and characterized TaABI4, an ABA-responsive transcription factor that participates in regulating seed germination in wheat. Sequence analysis revealed that TaABI4 has three homologues, located on chromosomes 1A/1B/1D. TaABI4 contains a conserved AP2 domain, and AP2-associated, LRP, and potential PEST motifs. Putative cis-acting regulatory elements (CE1-like box, W-box, ABRE elements, and RY-elements) were identified in the TaABI4 promoter region that showed high conservation in 17 wheat cultivars and wheat-related species. Expression profiling of TaABI4 indicated that it is a seed-specific gene accumulating during the middle stages of seed development. Transcript accumulation of TaABI4 in wheat cultivar Chuanmai 32 (CM32, PHS susceptible) was 5.07-fold and 1.39-fold higher than that in synthetic hexaploidy wheat SHW-L1 (PHS resistant) at 15DPA and 20DPA, respectively. Six expression quantitative trait loci (eQTL) of TaABI4 on chromosome 2A, 2D, 3B, and 4A were characterized based on the accumulated transcripts of TaABI4 in SHW-L1 and CM32 derived recombinant inbred lines. These QTLs explained from 10.7% to 46.1% of the trait variation with 4.53~10.59 of LOD scores, which contain genes that may affect the expression of TaABI4.

scholarly journals Characterization and expression quantitative trait loci analysis of TaABI4, a pre-harvest sprouting related gene in wheat

2021 ◽  
pp. 1-11
Author(s):  
Chunsheng Xiao ◽  
Yujiao Liu ◽  
Wenshuai Chen ◽  
Jian Yang ◽  
Mengping Cheng ◽  
...  
Keyword(s):  
Quantitative Trait Loci ◽  
Quantitative Trait ◽  
Recombinant Inbred Lines ◽  
Regulatory Elements ◽  
Specific Gene ◽  
Expression Quantitative Trait Loci ◽  
Transcript Accumulation ◽  
Trait Loci ◽  
Potential Pest ◽  
High Conservation

Abstract Pre-harvest sprouting (PHS) induced by the absence of seed dormancy causes a severe reduction in crop yield and flour quality. In this study, we isolated and characterized TaABI4, an ABA-responsive transcription factor that participates in regulating seed germination in wheat. Sequence analysis revealed that TaABI4 has three homologues, located on chromosomes 1A/1B/1D. TaABI4 contains a conserved AP2 domain, and AP2-associated, LRP and potential PEST motifs. Putative cis-acting regulatory elements (CE1-like box, W-box, ABRE elements and RY elements) were identified in the TaABI4 promoter region that showed high conservation in 17 wheat cultivars and wheat-related species. Expression profiling of TaABI4 indicated that it is a seed-specific gene accumulating during the middle stages of seed development. Transcript accumulation of TaABI4 in wheat cultivar Chuanmai 32 (CM32, PHS susceptible) was 5.07-fold and 1.39-fold higher than that in synthetic hexaploidy wheat SHW-L1 (PHS resistant) at 15 and 20 DPA, respectively. Six expression quantitative trait loci (eQTL) of TaABI4 on chromosomes 2A, 2D, 3B and 4A were characterized based on the accumulated transcripts of TaABI4 in SHW-L1 and CM32-derived recombinant inbred lines. These QTLs explained 10.7 to 46.1% of the trait variation with 4.53–10.59 of LOD scores, which contain genes that may affect the expression of TaABI4.

scholarly journals Genome-Wide Characterization of B-Box Gene Family and Its Roles in Responses to Light Quality and Cold Stress in Tomato

2021 ◽  
Vol 12 ◽  
Author(s):  
Xin Bu ◽  
Xiujie Wang ◽  
Jiarong Yan ◽  
Ying Zhang ◽  
Shunyuan Zhou ◽  
...  
Keyword(s):  
Cold Stress ◽  
Cold Tolerance ◽  
Genome Mapping ◽  
Electron Flow ◽  
Regulatory Elements ◽  
Photochemical Quenching ◽  
Protein Motif ◽  
Tomato Plants ◽  
High Conservation ◽  
Non Photochemical Quenching

Perceiving incoming environmental information is critical for optimizing plant growth and development. Multiple B-box proteins (BBXs) play essential roles in light-dependent developmental processes in plants. However, whether BBXs function as a signal integrator between light and temperature in tomato plants remains elusive. In this study, 31 SlBBX genes were identified from the newly released tomato (Solanum lycopersicum) genome sequences and were clustered into five subgroups. Gene structure and protein motif analyses showed relatively high conservation of closely clustered SlBBX genes within each subgroup; however, genome mapping analysis indicated the uneven distribution of the SlBBX genes on tomato chromosomes. Promoter cis-regulatory elements prediction and gene expression indicated that SlBBX genes were highly responsive to light, hormones, and stress conditions. Reverse genetic approaches revealed that disruption of SlBBX7, SlBBX9, and SlBBX20 largely suppressed the cold tolerance of tomato plants. Furthermore, the impairment of SlBBX7, SlBBX9, and SlBBX20 suppressed the photosynthetic response immediately after cold stress. Due to the impairment of non-photochemical quenching (NPQ), the excess photon energy and electron flow excited by low temperature were not consumed in SlBBX7-, SlBBX9-, and SlBBX20- silenced plants, leading to the over reduction of electron carriers and damage of the photosystem. Our study emphasized the positive roles of light signaling transcription factors SlBBXs in cold tolerance in tomato plants, which may improve the current understanding of how plants integrate light and temperature signals to adapt to adverse environments.

scholarly journals EpiSAFARI: Sensitive detection of valleys in epigenetic signals for enhancing annotations of functional elements

2019 ◽  
Author(s):  
Arif Harmanci ◽  
Akdes Serin Harmanci ◽  
Jyothishmathi Swaminathan ◽  
Vidya Gopalakrishnan
Keyword(s):  
Bisulfite Sequencing ◽  
Regulatory Elements ◽  
Computational Method ◽  
Sensitive Detection ◽  
Sparse Signals ◽  
High Conservation ◽  
Technical Factors ◽  
Nucleotide Resolution ◽  
Large Clusters ◽  
Systematic Identification

AbstractThe genomewide signal profiles from functional genomics experiments are dense information sources for annotating the regulatory elements. These profiles measure epigenetic activity at the nucleotide resolution and they exhibit distinct patterns along the genome. Most notable of these patterns are the valley patterns that are prevalently observed in many epigenetic assays such as ChIP-Seq and bisulfite sequencing. Valleys mark locations of cis-regulatory elements such as enhancers. Systematic identification of the valleys provides novel information for delineating the annotation of regulatory elements using epigenetic data. Nevertheless, the valleys are generally not reported by analysis pipelines. Here, we describe EpiSAFARI, a computational method for sensitive detection of valleys from diverse types of epigenetic profiles. EpiSAFARI employs a novel smoothing method for decreasing noise in signal profiles and accounts for technical factors such as sparse signals, mappability, and nucleotide content. In performance comparisons, EpiSAFARI performs favorably in terms of accuracy. The histone modification and DNA methylation valleys detected by EpiSAFARI exhibit high conservation, transcription factor binding, and they are enriched in nascent transcription. In addition, the large clusters of histone valleys are found to be enriched at the promoters of the developmentally associated genes.

scholarly journals Genome-Wide Characterization of B-BOX Gene Family and Their Responses to Light Quality and Cold Stress in Tomato

2020 ◽  
Author(s):  
Xin Bu ◽  
Xiujie Wang ◽  
Jiarong Yan ◽  
Ying Zhang ◽  
Shunyuan Zhou ◽  
...  
Keyword(s):  
Gene Family ◽  
Low Temperatures ◽  
Light Quality ◽  
Genome Mapping ◽  
Regulatory Elements ◽  
Protein Motif ◽  
Genome Wide ◽  
A Genome ◽  
Duplication Events ◽  
High Conservation

Abstract Background: Perceiving incoming environmental information is critical for optimizing plant growth and development. Multiple B-box proteins (BBXs) play essential roles in light-dependent developmental processes in plants. However, whether BBXs function as a signal integrator between light and temperature in tomato plants remains elusive.Results: In this study, 31 SlBBX genes were identified from the newly released tomato (Solanum lycopersicum) genome sequences, and were clustered into five subgroups with phylogenetic analysis. Gene structure and protein motif analyses showed relatively high conservation of closely clustered SlBBX genes within each subgroup; however, genome mapping analysis indicated the uneven distribution of the SlBBX genes on tomato chromosomes. Synteny analysis indicated that segmental duplication events happened in the expansion of the SlBBX genes in tomato. Promoter cis-regulatory elements prediction indicated that SlBBX genes were highly responsive to light, hormones, and stress conditions. Furthermore, the transcript analysis revealed that various SlBBX genes differed significantly in expression after exposure to different light quality and low temperatures, while 61.3% of SlBBX genes were responsive to both light and low temperatures. Conclusions: Our study presented a genome-wide survey of SlBBX gene family in tomato, and emphasized their functions in perceiving light quality and low temperature, which may improve the current understanding of SlBBX gene functions in integrating light and temperature signals for plant adaptation to adverse environments.

Hungarian small business tax and possibilities to minimize distortions from capital income taxation

2015 ◽  
Vol 37 (s1) ◽  
pp. 87-105
Author(s):  
Benedek Nobilis ◽  
András Svraka
Keyword(s):  
Small Business ◽  
Cash Flow ◽  
Capital Accumulation ◽  
Value Added ◽  
Regulatory Elements ◽  
Capital Income ◽  
Potential Growth ◽  
Elegant Method ◽  
Business Tax ◽  
Working Out

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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