Parental squabbles and genome expression: lessons from the polyploids

The merger of evolutionarily diverged genomes to form a new polyploid genetic system can involve extensive remodeling of gene regulation. A recent paper in BMC Biology provides important insights into regulatory events that have affected the evolution of allopolyploid cotton

A conserved and species-specific functional interaction between the Werner syndrome-like exonuclease atWEX and the Ku heterodimer in Arabidopsis

Werner syndrome is associated with mutations in the DNA helicase RecQ3 [a.k.a. Homo sapiens (hs)WRN]. The function of hsWRN is unknown although biochemical studies suggest a role in DNA ends stability and repair. Unlike other RecQ family members, hsWRN possesses an N-terminal domain with exonuclease activity, which is stimulated by interaction with the Ku heterodimer. While this interaction is intriguing, we do not know whether it is important for hsWRN function. Although flies, worms, fungi and plants do not have RecQ-like (RQL) helicases with an intrinsic exonuclease activity, they possess proteins having domains homologous to the hsWRN exonuclease. The genome of Arabidopsis thaliana (at) encodes multiple RQL and a single protein with homology to the WRN exonuclease domain, atWEX (Werner-like Exonuclease). Here we show that atWEX has properties that are similar to hsWRN. atWEX binds to and is stimulated by atKu. Interestingly, stimulation by Ku is species-specific, as hsKu does not stimulate atWEX exonuclease activity. Likewise, atKu fails to enhance the exonuclease activity of hsWRN. Thus, in spite of the differences in structural organization, the functional interaction between WRN-like exonucleases and Ku has been preserved through evolutionary radiation of species, emphasizing the importance of this interaction in cell function

Rice Overexpressing OsNUC1-S Reveals Differential Gene Expression Leading to Yield Loss Reduction after Salt Stress at the Booting Stage.

Rice nucleolin (OsNUC1), consisting of two isoforms, OsNUC1-L and OsNUC1-S, is a multifunctional protein involved in salt-stress tolerance. Here, OsNUC1-S's function was investigated using transgenic rice lines overexpressing OsNUC1-S. Under non-stress conditions, the transgenic lines showed a lower yield, but higher net photosynthesis rates, stomatal conductance, and transpiration rates than wild type only in the second leaves, while in the flag leaves, these parameters were similar among the lines. However, under salt-stress conditions at the booting stage, the higher yields in transgenic lines were detected. Moreover, the gas exchange parameters of the transgenic lines were higher in both flag and second leaves, suggesting a role for OsNUC1-S overexpression in photosynthesis adaptation under salt-stress conditions. Moreover, the overexpression lines could maintain light-saturation points under salt-stress conditions, while a decrease in the light-saturation point owing to salt stress was found in wild type. Based on a transcriptome comparison between wild type and a transgenic line, after 3 and 9 days of salt stress, the significantly differentially expressed genes were enriched in the metabolic process of nucleic acid and macromolecule, photosynthesis, water transport, and cellular homeostasis processes, leading to the better performance of photosynthetic processes under salt-stress conditions at the booting stage

Large-scale polymorphism of heterochromatic repeats in the DNA of Arabidopsis thaliana

Background: The composition of the individual eukaryote's genome and its variation within a species remain poorly defined. Even for a sequenced genome such as that of the model plant Arabidopsis thaliana accession Col-0, the large arrays of heterochromatic repeats are incompletely sequenced, with gaps of uncertain size persisting in them. Results: Using geographically separate populations of A. thaliana, we assayed variation in the heterochromatic repeat arrays using two independent methods and identified significant polymorphism among them, with variation by as much as a factor of two in the centromeric 180 bp repeat, in the 45S rDNA arrays and in the Athila retroelements. In the accession with highest genome size as measured by flow cytometry, Loh-0, we found more than a two-fold increase in 5S RNA gene copies relative to Col-0; results from fluorescence in situ hybridization with 5S probes were consistent with the existence of size polymorphism between Loh-0 and Col-0 at the 5S loci. Comparative genomic hybridization results of Loh-0 and Col-0 did not support contiguous variation in copy number of protein-coding genes on the scale needed to explain their observed genome size difference. We developed a computational data model to test whether the variation we measured in the repeat fractions could account for the different genome sizes determined with flow cytometry, and found that this proposed relationship could account for about 50% of the variance in genome size among the accessions. Conclusion: Our analyses are consistent with substantial repeat number polymorphism for 5S and 45S ribosomal genes among accession of A. thaliana. Differences are also suggested for centromeric and pericentromeric repeats. Our analysis also points to the difficulties in measuring the repeated fraction of the genome and suggests that independent validation of genome size should be sought in addition to flow cytometric measurements

Statistical Mutation Calling from Sequenced Overlapping DNA Pools in TILLING Experiments

<p>Abstract</p> <p>Background</p> <p>TILLING (Targeting induced local lesions IN genomes) is an efficient reverse genetics approach for detecting induced mutations in pools of individuals. Combined with the high-throughput of next-generation sequencing technologies, and the resolving power of overlapping pool design, TILLING provides an efficient and economical platform for functional genomics across thousands of organisms.</p> <p>Results</p> <p>We propose a probabilistic method for calling TILLING-induced mutations, and their carriers, from high throughput sequencing data of overlapping population pools, where each individual occurs in two pools. We assign a probability score to each sequence position by applying Bayes' Theorem to a simplified binomial model of sequencing error and expected mutations, taking into account the coverage level. We test the performance of our method on variable quality, high-throughput sequences from wheat and rice mutagenized populations.</p> <p>Conclusions</p> <p>We show that our method effectively discovers mutations in large populations with sensitivity of 92.5% and specificity of 99.8%. It also outperforms existing SNP detection methods in detecting real mutations, especially at higher levels of coverage variability across sequenced pools, and in lower quality short reads sequence data. The implementation of our method is available from: <url>http://www.cs.ucdavis.edu/filkov/CAMBa/</url>.</p