Search results for: Interval DEA

Authors: Nadezhda M. Usmanova, Nikolai V. Tomilin

Abstract:

Mammalian genomes contain large number of retroelements (SINEs, LINEs and LTRs) which could affect expression of protein coding genes through associated transcription factor binding sites (TFBS). Activity of the retroelement-associated TFBS in many genes is confirmed experimentally but their global functional impact remains unclear. Human SINEs (Alu repeats) and mouse SINEs (B1 and B2 repeats) are known to be clustered in GCrich gene rich genome segments consistent with the view that they can contribute to regulation of gene expression. We have shown earlier that Alu are involved in formation of cis-regulatory modules (clusters of TFBS) in human promoters, and other authors reported that Alu located near promoter CpG islands have an increased frequency of CpG dinucleotides suggesting that these Alu are undermethylated. Human Alu and mouse B1/B2 elements have an internal bipartite promoter for RNA polymerase III containing conserved sequence motif called B-box which can bind basal transcription complex TFIIIC. It has been recently shown that TFIIIC binding to B-box leads to formation of a boundary which limits spread of repressive chromatin modifications in S. pombe. SINEassociated B-boxes may have similar function but conservation of TFIIIC binding sites in SINEs located near mammalian promoters has not been studied earlier. Here we analysed abundance and distribution of retroelements (SINEs, LINEs and LTRs) in annotated sequences of the Database of mammalian transcription start sites (DBTSS). Fractions of SINEs in human and mouse promoters are slightly lower than in all genome but >40% of human and mouse promoters contain Alu or B1/B2 elements within -1000 to +200 bp interval relative to transcription start site (TSS). Most of these SINEs is associated with distal segments of promoters (-1000 to -200 bp relative to TSS) indicating that their insertion at distances >200 bp upstream of TSS is tolerated during evolution. Distribution of SINEs in promoters correlates negatively with the distribution of CpG sequences. Using analysis of abundance of 12-mer motifs from the B1 and Alu consensus sequences in genome and DBTSS it has been confirmed that some subsegments of Alu and B1 elements are poorly conserved which depends in part on the presence of CpG dinucleotides. One of these CpG-containing subsegments in B1 elements overlaps with SINE-associated B-box and it shows better conservation in DBTSS compared to genomic sequences. It has been also studied conservation in DBTSS and genome of the B-box containing segments of old (AluJ, AluS) and young (AluY) Alu repeats and found that CpG sequence of the B-box of old Alu is better conserved in DBTSS than in genome. This indicates that Bbox- associated CpGs in promoters are better protected from methylation and mutation than B-box-associated CpGs in genomic SINEs. These results are consistent with the view that potential TFIIIC binding motifs in SINEs associated with human and mouse promoters may be functionally important. These motifs may protect promoters from repressive histone modifications which spread from adjacent sequences. This can potentially explain well known clustering of SINEs in GC-rich gene rich genome compartments and existence of unmethylated CpG islands.

Keywords: Retroelement, promoter, CpG island, DNAmethylation.

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Authors: M. Keshavarzi

Abstract:

Grasslands of Iran are encountered with a vast desertification and destruction. Some legumes are plants of forage importance with high palatability. Studied legumes in this project are Onobrychis, Medicago sativa (alfalfa) and Trifolium repens. Seeds were cultivated in research field of Kaboutarabad (33 km East of Isfahan, Iran) with an average 80 mm. annual rainfall. Plants were cultivated in a split plot design with 3 replicate and two water treatments (weekly irrigation, and under stress with same amount per 15 days interval). Water entrance to each plots were measured by Partial flow. This project lasted 20 weeks. Destructive samplings (1m2 each time) were done weekly. At each sampling plants were gathered and weighed separately for each vegetative parts. An Area Meter (Vista) was used to measure root surface and leaf area. Total shoot and root fresh and dry weight, leaf area index and soil coverage were evaluated too. Dry weight was achieved in 750c oven after 24 hours. Statgraphic and Harvard Graphic software were used to formulate and demonstrate the parameters curves due to time. Our results show that Trifolium repens has affected 60 % and Medicago sativa 18% by water stress. Onobrychis total fresh weight was reduced 45%. Dry weight or Biomass in alfalfa is not so affected by water shortage. This means that in alfalfa fields we can decrease the irrigation amount and have some how same amount of Biomass. Onobrychis show a drastic decrease in Biomass. The increases in total dry matter due to time in studied plants are formulated. For Trifolium repens if removal or cattle entrance to meadows do not occurred at perfect time, it will decrease the palatability and water content of the shoots. Water stress in a short period could develop the root system in Trifolium repens, but if it last more than this other ecological and soil factors will affect the growth of this plant. Low level of soil water is not so important for studied legume forges. But water shortage affect palatability and water content of aerial parts. Leaf area due to time in studied legumes is formulated. In fact leaf area is decreased by shortage in available water. Higher leaf area means higher forage and biomass production. Medicago and Onobrychis reach to the maximum leaf area sooner than Trifolium and are able to produce an optimum soil cover and inhibit the transpiration of soil water of meadows. Correlation of root surface to Total biomass in studied plants is formulated. Medicago under water stress show a 40% decrease in crown cover while at optimum condition this amount reach to 100%. In order to produce forage in areas without soil erosion Medicago is the best choice even with a shortage in water resources. It is tried to represent the growth simulation of three famous Forage Legumes. By growth simulation farmers and range managers could better decide to choose best plant adapted to water availability without designing different time and labor consuming field experiments.

Keywords: Ecological parameters, Medicago, Onobrychis, Trifolium.

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