Tetranucleotide Sequence Research Articles

Transposon-mediated directed mutation in bacteria and eukaryotes.

Transposon-mediated "directed" mutations occur at higher frequencies when beneficial than when detrimental and relieve the stress that causes them. The first and best-studied example involves regulation of Insertion Sequence-5 (IS5) insertion into a specific activating site upstream of the glycerol utilization operon in Escherichia coli, glpFK. This event promotes high level expression of the glpFK operon, allowing glycerol utilization in wild type cells under inhibitory conditions. The phosphoenolpyruvate-dependent, sugar transporting, phosphotransferase system (PTS) influences this process by regulating cytoplasmic glycerol-3-phosphate and cyclic AMP concentrations. Insertion frequencies are determined by IS5-specific tetranucleotide target sequences in stress-induced (DNA) duplex destabilization (SIDD) structures counteracted by two DNA binding proteins, GlpR and Crp which directly inhibit insertion, responding to cytoplasmic glycerol-3-phosphate and cyclic AMP, respectively. Expression of the E. coli master regulator of flagellar gene control, flhDC, is subject to activation by IS elements by a directed mechanism, and zinc-induced transposon-mediated zinc resistance has been demonstrated in Cupriavidus metallidurans. The use of DNA conformation and DNA binding proteins to control transposon hopping also occurs in eukaryotes.

Revisiting GNRA and UNCG folds: U-turns versus Z-turns in RNA hairpin loops.

When thinking about RNA three-dimensional structures, coming across GNRA and UNCG tetraloops is perceived as a boon since their folds have been extensively described. Nevertheless, analyzing loop conformations within RNA and RNP structures led us to uncover several instances of GNRA and UNCG loops that do not fold as expected. We noticed that when a GNRA does not assume its “natural” fold, it adopts the one we typically associate with a UNCG sequence. The same folding interconversion may occur for loops with UNCG sequences, for instance within tRNA anticodon loops. Hence, we show that some structured tetranucleotide sequences starting with G or U can adopt either of these folds. The underlying structural basis that defines these two fold types is the mutually exclusive stacking of a backbone oxygen on either the first (in GNRA) or the last nucleobase (in UNCG), generating an oxygen–π contact. We thereby propose to refrain from using sequences to distinguish between loop conformations. Instead, we suggest using descriptors such as U-turn (for “GNRA-type” folds) and a newly described Z-turn (for “UNCG-type” folds). Because tetraloops adopt for the largest part only two (inter)convertible turns, we are better able to interpret from a structural perspective loop interchangeability occurring in ribosomes and viral RNA. In this respect, we propose a general view on the inclination for a given sequence to adopt (or not) a specific fold. We also suggest how long-noncoding RNAs may adopt discrete but transient structures, which are therefore hard to predict.

Characterization of perfect microsatellite based on genome-wide and chromosome level in Rhesus monkey (Macaca mulatta)

Microsatellite studies based on chromosomes level would contribute to the biometric correlation analysis of chromosome and microsatellite applications on the specific chromosome. In this study, the total microsatellite length of 1,141,024 loci was 21.8Mb, which covered about 0.74% of the male Rhesus monkey genome. Perfect mononucleotide SSRs were the most abundant, followed by the pattern: perfect di->tetra->tri->penta->hexanucleotide SSRs. The main range of repeat times focused on 12–32 times (mono-), 7–23 times (di-), 5–10 times (tri-), 4–14 times (tetra-), 4–9 times (penta-), 4–8 times (hexa-), respectively. The largest SSRs number was found in chromosome 1 with 94,347 loci, followed by chromosome 3, 2, 7 and 5, and the smallest number was in chromosome 18. The predominant repeat types in male Rhesus monkey genome and chromosome Y were basically A, AC, AG, AAT, AAC, AAAT, AAAC, AAAG, AAACA and AAACAA. SSRs number of all chromosomes was closely positively correlated with chromosome sequence size (r=0.969, p<0.01), and significantly negatively correlated with abundance (r=−0.24, 0.01<p<0.05). The lengths of all chromosomes were significantly negatively correlated with microsatellite density (r=−0.456, 0.01<p<0.05), and relative abundance and density of SSRs in all chromosomes were significantly negatively correlated with SSR GC content (r=−0.939/−0.928, p<0.01). The SSRs GC content on chromosome X (accounting for 16.71%) was found to be the highest in female Rhesus monkey, which might contributed to the DNA methylation of CpG islands for sex chromosome X inactivation and expression regulation. These results and exported tetranucleotide repeat sequences in each chromosome for primer design would facilitate the exploration of microsatellites structural function, composition mode and molecular markers development in Rhesus monkey genome.

Characterization of three mycoviruses co-infecting the plant pathogenic fungus Sclerotinia nivalis

Two dsRNAs of approximately 6.0-kb and 3.0-kb in length were detected in strain SsSn-1 of Sclerotinia nivalis. Genomic analysis showed that the 6.0-kb dsRNA was a victorivirus, named as Sclerotinia nivalis victorivirus 1 (SnVV1). The genome of SnVV1 is 5162bp in length containing two large open reading frames (ORFs), ORF1 and ORF2. ORF1 was deduced to encode a coat protein (CP) showing homology to CPs of viruses belonging to the family Totiviridae. The stop codon of ORF1 overlaps the start codon of ORF2 in the tetranucleotide sequence AUGA. ORF2 was predicted to encode for a RNA-dependent RNA polymerase (RdRp) that was very similar to the RdRps of victoriviruses. The 3.0-kb dsRNA was consisted of two species of mitoviruses, named as Sclerotinia nivalis mitovirus 1/SsSn-1 (SnMV1/SsSn-1) and Sclerotinia sclerotiorum mitovirus 3/SsSn-1 (SsMV3/SsSn-1). The genomes of SnMV1/SsSn-1 and SsMV3/SsSn-1 were 2720nt and 2583nt in length, respectively. Both mitoviruses were AU-rich and deduced to contain a major large ORF encoding a mitoviral RdRp with the fungal mitochondrial codon usages. SnMV1/SsSn-1 was most closely related to Sclerotinia sclerotiorum mitovirus 4 (SsMV4/NZ1) and shared 76.5% and 80.1% identity with SsMV4/NZ1 for nucleotide and RdRp sequences, respectively. In addition, the nucleotide and RdRp sequences of SsMV3/SsSn-1 were 90.6% and 95.9% identical to the nucleotide and RdRp sequences of SsMV3/NZ1, respectively. Considering their nucleotide and RdRp sequence identities with other mitoviruses, SnMV1/SsSn-1 may belong to the genus Mitovirus, whereas SsMV3/SsSn-1 is possibly a strain of SsMV3. Both SnMV1/SsSn-1 and SsMV3/SsSn-1 were transmitted to a recipient virus-free colony faster than was SnVV1 through hyphal anastomosis. Co-infection by these mycoviruses had no apparent effects on growth and pathogenicity of S. nivalis.

Large-Scale Analysis of 48 DNA and 48 RNA Tetranucleotides Studied by 1 μs Explicit-Solvent Molecular Dynamics Simulations.

An understanding of how the conformational behavior of single-stranded DNAs and RNAs depend on sequence is likely to be important for attempts to rationalize the thermodynamics of nucleic acid folding. In an attempt to further our understanding of such sequence dependences, we report here the results of 192 (1 μs) explicit-solvent molecular dynamics (MD) simulations of 48 DNA and 48 RNA tetranucleotide sequences performed using recently reported modifications to the AMBER force field. Each tetranucleotide was simulated starting from two different conformations, a fully natively stacked and a completely unstacked conformation, and populations of the various possible base stacking arrangements were analyzed. The simulations indicate that, for both DNA and RNA, the populations of fully natively stacked conformations increase linearly with increasing numbers of purines in the sequence, while the conformational entropies, computed by two complementary methods, decrease. Despite the comparatively short simulation times, the computed free energies of stacking of the 16 possible combinations of bases in the middle of the sequences are found to be in good correspondence with values reported recently from simulations of dinucleoside monophosphates using the same force field. Finally, consistent with recent reports from other groups, non-native stacking interactions, i.e., between bases that are not adjacent in sequence, are shown to be a recurring feature of the simulations; in particular, stacking interactions of bases in a i:i+2 relationship are shown to occur significantly more frequently when the intervening base is a pyrimidine. Given that the high prevalence of non-native stacking interactions is thought to be unrealistic, it appears that further parametrization work will be required before accurate conformational descriptions of single-stranded nucleic acids can be obtained with current force fields.

Genomic organization of a novel victorivirus from the rice blast fungus Magnaporthe oryzae.

Two double-stranded RNA (dsRNA) mycoviruses were found in isolate QSP5 of the rice blast fungus Magnaporthe oryzae. Sequence analysis of the two dsRNA mycoviruses revealed that one is closely related to Magnaporthe oryzae virus 2 (MoV2), and the other one is related to Magnaporthe oryzae chrysovirus 1-A (MoCV1-A). Therefore, they were named Magnaporthe oryzae virus 3 (MoV3) and Magnaporthe oryzae chrysovirus 1-C (MoCV1-C), respectively. In this paper, the molecular and structural characteristics of MoV3 were analyzed in detail. The full genome sequence (5181 bp) of MoV3 was obtained by cDNA cloning. Sequence analysis indicated that MoV3 has two overlapping open reading frames (ORF1 and ORF2). The 5'-proximal ORF1 encodes a putative coat protein (CP) with a molecular weight of 80,939 Da; the 3'-proximal ORF2 encodes a putative RNA-dependent RNA polymerase (RdRp) with a molecular weight of 90,506 Da. The stop codon of ORF1 overlaps the start codon of ORF2, with the tetranucleotide sequence AUGA, which is characteristic of members of the genus Victorivirus of the family Totiviridae. Phylogenetic analysis of RdRp and CP further supported the view that MoV3, a novel mycovirus, belongs to the genus Victorivirus of the family Totiviridae.

120. Generation of Transgene-Only Gene-Modified Human Cells Via Transposition

DNA transposons such as piggyBac and Sleeping Beauty employ a cut-and-paste mechanism of transposition that has proven effective for numerous gene transfer and cellular reprogramming applications. Therapeutic transposons are carried into cells usually on plasmid DNA vectors either on the same plasmid as the transposase expression cassette in “cis” or on another plasmid in “trans.” We examined the fate of the remaining plasmid backbone after transposition. It has been assumed that the recircularized plasmid backbone remains episomal and is quickly lost from dividing cells. We delivered transposons containing a neomycin resistance gene and the transposase in either “cis” or “trans” to human embryonic kidney (HEK-293) cells, then selected the cells for 8 weeks and evaluated transposase expression by immunoblot. All of the piggyBac and 5 out of 6 of the Sleeping Beauty “cis” transfections resulted in transposase-positive clones. In contrast, none of the piggyBac “trans” transfections resulted in transposase-positive clones. We were concerned that the prolonged expression of the transposase might result in some instability of the transgenes delivered “cis” in vivo; however, we found that mice that received a piggyBac “cis” luciferase transposon vector by hydrodynamic injection had long-term luciferase values that were not statistically different from mice receiving the plasmids in “trans.” We next evaluated if piggyBac “trans” delivery could be modified to reduce the amount of backbone integration and found that clones that were transfected with lower amounts of transposase showed a decrease in the frequency of backbone integrations. We found no evidence that transposition increases the frequency of integration of co-delivered linear DNA. We sequenced backbone integration events and found that that the majority of the time, once the transposon is excised from its parent plasmid, the plasmid backbone is repaired by re-ligation and integrated into the genome at a site other than the excision site. Alternatively, a rare event may occur in which the linearized plasmid backbone can be integrated without excision repair. None of the integration events occurred at the TTAA tetranucleotide sequence, indicating that they are not directly mediated by piggyBac transposase. We next devised a strategy to measure and eliminate the backbones from human cells. We created a plasmid containing the neomycin-resistance gene in the transposon portion of the plasmid and the eGFP marker in the backbone. Transfected HEK-293 cells were selected with geneticin and sorted for eGFP. While the selected cells contained approximately ten copies of the transposon per diploid cell, unsorted cells typically had one to two copies of plasmid backbone per diploid genome. eGFP sorting effectively eliminated recovery of backbone-negative transgene-only cells. We expect further improvements to improve recovery of transgene-only cells. We will also investigate the extent of backbone integration in therapeutically relevant cell types and in vivo.

Genome-wide survey and analysis of microsatellites in giant panda (Ailuropoda melanoleuca), with a focus on the applications of a novel microsatellite marker system.

BackgroundThe giant panda (Ailuropoda melanoleuca) is a critically endangered species endemic to China. Microsatellites have been preferred as the most popular molecular markers and proven effective in estimating population size, paternity test, genetic diversity for the critically endangered species. The availability of the giant panda complete genome sequences provided the opportunity to carry out genome-wide scans for all types of microsatellites markers, which now opens the way for the analysis and development of microsatellites in giant panda.ResultsBy screening the whole genome sequence of giant panda in silico mining, we identified microsatellites in the genome of giant panda and analyzed their frequency and distribution in different genomic regions. Based on our search criteria, a repertoire of 855,058 SSRs was detected, with mono-nucleotides being the most abundant. SSRs were found in all genomic regions and were more abundant in non-coding regions than coding regions. A total of 160 primer pairs were designed to screen for polymorphic microsatellites using the selected tetranucleotide microsatellite sequences. The 51 novel polymorphic tetranucleotide microsatellite loci were discovered based on genotyping blood DNA from 22 captive giant pandas in this study. Finally, a total of 15 markers, which showed good polymorphism, stability, and repetition in faecal samples, were used to establish the novel microsatellite marker system for giant panda. Meanwhile, a genotyping database for Chengdu captive giant pandas (n = 57) were set up using this standardized system. What’s more, a universal individual identification method was established and the genetic diversity were analysed in this study as the applications of this marker system.ConclusionThe microsatellite abundance and diversity were characterized in giant panda genomes. A total of 154,677 tetranucleotide microsatellites were identified and 15 of them were discovered as the polymorphic and stable loci. The individual identification method and the genetic diversity analysis method in this study provided adequate material for the future study of giant panda.Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-015-1268-z) contains supplementary material, which is available to authorized users.

μABC: a systematic microsecond molecular dynamics study of tetranucleotide sequence effects in B-DNA.

We present the results of microsecond molecular dynamics simulations carried out by the ABC group of laboratories on a set of B-DNA oligomers containing the 136 distinct tetranucleotide base sequences. We demonstrate that the resulting trajectories have extensively sampled the conformational space accessible to B-DNA at room temperature. We confirm that base sequence effects depend strongly not only on the specific base pair step, but also on the specific base pairs that flank each step. Beyond sequence effects on average helical parameters and conformational fluctuations, we also identify tetranucleotide sequences that oscillate between several distinct conformational substates. By analyzing the conformation of the phosphodiester backbones, it is possible to understand for which sequences these substates will arise, and what impact they will have on specific helical parameters.

Characterization of 19 new microsatellite loci for the Omani barb Garra barreimiae from 454 sequences.

BackgroundGarra barreimiae is a cyprinid fish from the southeastern Arabian Peninsula, which inhabits regularly desiccating wadis and survives in isolated ponds or underground. In 1984 a cave-dwelling population was found in the Al Hoota cave system and previous genetic analyses revealed some differentiation with limited gene flow between the surface populations and the cave population. Since no suitable markers are available for evaluation of gene flow between the cave population and the adjacent surface populations, we focused on designing and establishing novel microsatellite markers from next generation sequencing data.Findings19 microsatellite markers containing di- and tetranucleotide simple sequence repeats were developed from 454 sequences. Forty-four individuals from two surface populations (Wadi Al Falahi and Misfat Al Abriyeen) of G. barreimiae (sampling permission number 13/2012, export permission number 29/2012) were used for analyses and characterization of the loci. On average, the number of alleles per locus is 7.6 (range: 2–20). Two markers displayed indication of linkage disequilibrium in both populations (DL6X, 9XNC). Significant deviation from Hardy-Weinberg equilibrium was observed at four loci in the Misfat Al Abriyeen population (2PUM, 88CM, 1EHE, 3Z7M) and at two loci in the Wadi Al Falahi population (QLIM, 3 N43). Three of the microsatellite loci were significant for null alleles in one of the two populations (Misfat Al Abriyeen: CJHG; Wadi Al Falahi: PH8A, 3ROZ). Expected and observed heterozygosities ranged from 0 to 95.0% respectively from 0 to 95.8% (Wadi Al Falahi) and from 0 to 89.1% respectively from 0 to 95.0% (Misfat Al Abriyeen). Fourteen of these markers were successfully cross-amplified in G. rufa.ConclusionThis 19 microsatellite loci provide a useful tool to understand the structure and genetic differences of populations. Moreover, these markers will help to evaluate species delimitation in G. barreimiae and potentially even in related species.

DNA-AuNPs based signal amplification for highly sensitive detection of DNA methylation, methyltransferase activity and inhibitor screening

A sensitive and selective electrochemical method was developed for the detection of DNA methylation, determination of DNA methyltransferase (MTase) activity and screening of MTase inhibitor. Methylene blue (MB) was employed as electrochemical indicator and DNA-modified gold nanoparticles (AuNPs) were used as signal amplification unit because the DNA strands in this composite have strong adsorption ability for MB. First, the thiolated single-stranded DNA S1 was self-assembled on gold electrode, hybridization between the lower portion of DNA S1 and its complementary DNA S2 formed an identical double-stranded tetranucleotide target sequence for both DNA adenine methylation (Dam) MTase and methylation-resistant endonuclease Mbo I, then the upper portion of DNA S1 was hybridized with its complementary DNA S3 modified on AuNPs to bring the DNA S3-AuNPs amplification units onto the electrode. The DNA S1/S2/S3-AuNPs bioconjugate has lots of DNA strands, and they can adsorb abundant MB. Mbo I endounuclease could not cleave the identical target sequence after it was methylated by Dam MTase. On the contrary, the sequence without methylation could be cleaved, which would decrease the amount of adsorbed MB. The presence of redox-active MB was detected electrochemically by differential pulse voltammetry (DPV). Thus, the activity of Dam MTase and methylation status were sensitively converted to the DNA S3-AuNPs amplified DPV signals. The DPV signal demonstrated a linear relationship with logarithm of Dam concentration ranging from 0.075 to 30U/mL, achieving a detection limit of 0.02U/mL (S/N=3). Also, screening of Dam MTase inhibitor 5-fluorouracil was successfully investigated using this fabricated sensor.

Recognition rules for binding of Zn-Cys2His2 transcription factors to operator DNA

The molecules of Zn-finger transcription factors consist of several similar small protein units. We analyzed the crystal structures 46 basic units of 22 complexes of Zn-Cys2His2 family with the fragments of operator DNA. We showed that the recognition of DNA occurs via five protein contacts. The canonical binding positions of the recognizing α-helix were −1, 3, 6, and 7, which make contacts with the tetra-nucleotide sequence ZXYZ of the coding DNA strand; here the canonical binding triplet is underlined. The non-coding DNA strand forms only one contact at α-helix position 2. We have discovered that there is a single highly conservative contact His7α with the phosphate group of nucleotide Z, which precedes each triplet XYZ of the coding DNA chain. This particular contact is invariant for the all Zn-Cys2His2 family with high frequency of occurrence 83%, which we considered as an invariant recognition rule. We have also selected a previously unreported Zn-Cys2His2-Arg subfamily of 21 Zn-finger units bound with DNA triplets, which make two invariant contacts with residues Arg6α and His7α with the coding DNA chain. These contacts show frequency of occurrence 100 and 90%, and are invariant recognition rule. Three other variable protein-DNA contacts are formed mainly with the bases and specify the recognition patterns of individual factor units. The revealed recognition rules are inherent for the Zn-Cys2His2 family and Zn-Cys2His2-Arg subfamily of different taxonomic groups and can distinguish members of these families from any other family of transcription factors.

Donor and Recipient STR Analysis Before Allogeneic Haematopoietic Stem Cell Transplantation: Possible Correlation With Post-Transplant Outcome

Background The chimerism analysis after allogeneic haematopoietic stem cell transplantation (HSCT) is a useful tool to monitor the engraftment of donor cells and to early predict graft failure or disease relapse. Among several available methods to perform chimerism study, multiplex fluorescent short tandem repeat (STR) analysis represent a sensitive, accurate and reproducible technique. It provide a high rate of discrimination between donor and recipient cells since that fluorescent signal is proportional to the cells number, obtaining a quantitative assessment of chimerism. Aims Evaluation of a possible correlation between basal donor/recipient allelic discrepancies and post-transplant outcome in terms of graft versus host disease (GvHD) development, neutrophil engraftment, relapse, DFS and OS. Methods We enrolled 111 patients (pts) affected by onco-haematological diseases, consecutively submitted to HSCT at our division between February 2005 and December 2012. Pts were 67 males and 44 females with a median age of 51 years (range 14-70). Underlying diseases were: 58 AML, 10 MDS, 16 ALL, 8 CLL, 6 MM, 2 HL, 9 NHL, 1 IMF, 1 MPD. Myeloablative conditioning regimen was used in 26 pts while a reduced conditioning regimen was used for the other 85 pts. Graft was obtained from sibling donor and unrelated donor in 65 and 46 pts, respectively. GvHD prophylaxis was performed with cyclosporine (CSA) and methotrexate in 61 pts, CSA and mycophenolate mofetil in 43 pts and CSA in 7 pts. Donor and recipient allelic status was performed using a multiplex PCR amplification of ten STR loci: Amelogenin alleles X/Y, D3S1358, FGA, D8S1179, D18S51, D13S317, vWA, D21S11, D5S818, D7S820. We evaluated the donor/recipient (D/R) match or mismatch for each locus and the following variables: GvHD development and onset time, time to neutrophil engraftment, relapse, DFS and OS. Statistical analysis was performed by Kaplan Meier analysis using IBM SPSS Statistics 20 Core System. Results Pts with D/R mismatch for D8S1179 locus achieved neutrophil engraftment (ANC&gt;1* 109/L) at a median time of 18 days (CI 95% 17.202-18.798) compared with 21 days (CI 95% 17.328-24.672) of pts with D/R match for the same locus (p=0.007) (Figure 1A). Pts with D/R mismatch for D3S1358 locus developed acute GvHD at a median time of 20 days (CI 95% 15.781-24.219) compared with 29 days (CI 95% 15.421-42.579) of pts with D/R match for the same locus (p=0.031) (Figure 1B). Pts with D/R mismatch for D3S1358 locus showed an OS of 16 months (CI 95% 11.016-20.984) compared with 41 months (CI 95% 25.420-56.580) of pts with D/R match for the same locus (p=0.025) (Figure 1C). Pts with D/R mismatch for D8S1179 locus showed an OS of 16 months (CI 95% 8.528-23.472) compared with 56 months (CI 95% 11.254-78.057) of pts with D/R match for the same locus (p=0.012) (Figure 1D). No relationships were found with relapse, DFS neither for the other loci. Summary Our results highlight that pts who presented a D/R mismatch for D8S1179 locus showed an earlier neutrophil engraftment but a worse OS compared with the others. Moreover, for D3S1358 locus, D/R mismatch was associated with an earlier onset of acute GvHD after HSCT and with a shorter OS than the D/R match ones. Conclusion STRs are highly polymorphic di-, tri- and tetra-nucleotide repeat non-coding sequences, which are interspersed throughout the genome. Whether or not discrepancies between donor and recipient basal allelic status could be considered useful in predicting post-transplant outcome will require validation in a large sample of pts. Disclosures: No relevant conflicts of interest to declare.

New Polymorphic EST-SSR Markers in Sugarcane

New polymorphic SSR markers in sugarcane has potential usefulness to studies genetic diversity, genetic mapping, DNA fingerprinting and determination offspring as true hybrids, selfing or contaminant in germplasm from breeding program. SSR markers can be obtained in several ways, and the search for SSR-EST sequences an alternative with significant results. The aim of this study was to develop highly polymorphic SSR markers for germplasm studies in sugarcane. Di- tri- and tetra-nucleotide sequences were mined in the TGI bank and 53 EST-SSR markers developed. These markers were analyzed in five genotypes and showed to be highly polymorphic, with the PIC ranging between 0.48 and 0.95 with a mean of 0.86. The discriminatory power ranged from 0.35 to 0.94 with a mean of 0.82 and the genetic similarity was high in the accessions evaluated.

Association of the genes for tumor necrosis factor-α and myelin basic protein with delayed encephalopathy after acute carbon monoxide poisoning

There is structural damage to myelin and secondary immune injury in the development of delayed encephalopathy after acute carbon monoxide (CO) poisoning (DEACMP). In order to assess the role of genetic factors in this mechanism, we studied the association between tumor necrosis factor-α308 (TNF-α308) and myelin basic protein (MBP) 5'-side tetranucleotide repetitive sequence (TGGA) n gene polymorphism and DEACMP. We selected 109 DEACMP patients from the Han population in the Northern Henan Province as the case group, and 115 patients without delayed encephalopathy (called the acute CO poisoning group or the control group). There were no significant differences in TNF-α308 and MBP 5'-side TGGA n genotype distribution and allele frequency between the DEACMP group and the acute CO poisoning group (all P > 0.05). When the population was stratified by gender, only the MBP 5'-side TGGA n allele frequency was significantly different, and the frequency of allele L in the DEACMP group was significantly higher than that of the acute CO poisoning group in males (χ(2) = 4.089, P = 0.043, odds ratio = 2.103, 95% confidence interval = 1.014-4.363). The results showed that there was association between MBP 5'-side TGGA n gene polymorphism and DEACMP, and that allele L could increase the risk of occurrence in male patients with DEACMP. DEACMP may be the result of interaction of environmental and genetic factors.

Two length variants of the microsatellite FH2295 as markers for body size of female Portuguese water dogs

Genetic studies in purebred Portuguese water dogs (PWD) have previously identified genetic loci controlling skeleton size. The FH2295 genetic marker was reported to control 43.6% of the size variation in this breed. In the present study, we amplified and sequenced the genomic DNA from female PWD of different sizes in the region of the FH2295 genetic marker. Polymerase chain reaction (PCR) products of 700 and 800 bp were generated and sequencing revealed the presence of a microsatellite marker including either 5 or 24 repeats of the tetranucleotide sequence "CTTT". Dogs were divided into groups based on their genotypes: homozygote for the short allele (II) or homozygote for the long allele (BB) or heterozygote (IB). The smallest dogs were homozygous with 24 repeats and the largest dogs were homozygous with five repeats. Genetic transmission of the microsatellite marker appears to follow Mendelian laws since all puppies born to a homozygous small dog genotyped "BB" included one or two "B" allele. We applied a PCR method to characterize the sequence of the previously identified dog genetic marker FH2295 and propose that the length of the microsatellite identified could be used as a predictor for the body size of female PWD.

A study on the relationship between TCTA tetranucleotide polymorphism of the HPRT gene and primary hyperuricemia

We examined polymorphism of the TCTA tetranucleotide sequence in the 3rd intron of the hypoxanthine-guanine phosphoribosyltransferase (HPRT) gene in the Han population of Ningxia Province in China. We also looked for a possible relationship between STR polymorphism in the 3rd intron of the HPRT gene and primary hyperuricemia. We used Chelex-100 to extract DNA, then PCR, PAGE and silver staining for allele genotyping and DNA sequencing to obtain the distribution of the alleles. We found, for the first time, that there is high STR polymorphism in the 3rd intron of the HPRT gene. We detected 5 STR alleles in this intron in the Han population of Ningxia Province, with 15 genotypes in females; significant differences were observed in the distribution of alleles and genotypes between control and patient groups for both males and females. Alleles of the TCTA repeat in the 3rd intron of the HPRT gene were found to be associated with primary hyperuricemia; consequently, these alleles may be considered risk factors for primary hyperuricemia.

Report From the Jerusalem Workshop on Lynch Syndrome-Hereditary Nonpolyposis Colorectal Cancer

A Workshop was held in Jerusalem, Israel, on October 26 and 27, 2009 to discuss the management of Lynch syndrome-hereditary nonpolyposis colorectal cancer (CRC), with the primary goal to develop consensus for the optimal management of this disease. A second goal was to identify areas of research with the potential to advance the clinical management of Lynch syndrome. The perspectives and recommendations from the workshop are meant to be a platform for discussion and deliberation. The Workshop was organized by Moshe Shike (Memorial Sloan Kettering Cancer Center, New York) and sponsored by The Colon Cancer Foundation. More details of each presentation are available in an on-line supplement.

TUT4 in Concert with Lin28 Suppresses MicroRNA Biogenesis through Pre-MicroRNA Uridylation

As key regulators in cellular functions, microRNAs (miRNAs) themselves need to be tightly controlled. Lin28, a pluripotency factor, was reported to downregulate let-7 miRNA by inducing uridylation of let-7 precursor (pre-let-7). But the enzyme responsible for the uridylation remained unknown. Here we identify a noncanonical poly (A) polymerase, TUTase4 (TUT4), as the uridylyl transferase for pre-let-7. Lin28 recruits TUT4 to pre-let-7 by recognizing a tetra-nucleotide sequence motif (GGAG) in the terminal loop. TUT4 in turn adds an oligouridine tail to the pre-let-7, which blocks Dicer processing. Other miRNAs with the same sequence motif (miR-107, -143, and -200c) are regulated through the same mechanism. Knockdown of TUT4 and Lin28 reduces the level of stem cell markers, suggesting that they are required for stem cell maintenance. This study uncovers the role of TUT4 and Lin28 as specific suppressors of miRNA biogenesis, which has implications for stem cell research and cancer biology.

Human Postmeiotic Segregation 2 Exhibits Biased Repair at Tetranucleotide Microsatellite Sequences

The mismatch repair (MMR) system plays a major role in removing DNA polymerization errors, and loss of this pathway results in hereditary cancers characterized by microsatellite instability. We investigated microsatellite stability during DNA replication within human postmeiotic segregation 2 (hPMS2)-deficient and proficient human lymphoblastoid cell lines. Using a shuttle vector assay, we measured mutation rates at reporter cassettes containing defined mononucleotide, dinucleotide, and tetranucleotide microsatellite sequences. A mutator phenotype was observed in the hPMS2-deficient cell line. The mutation rate of vectors containing [G/C](10) or [GT/CA](10) alleles was elevated 20-fold to 40-fold in hPMS2-deficient cells, relative to an hPMS2-expressing cell line. We observed a 6-fold and 12-fold relative increase in mutation rate of [TTTC/AAAG](9) and [TTCC/AAGG](9) sequences, respectively, in hPMS2-deficient cells. Mutational specificity analyses suggested that repair by hPMS2 is biased. In the absence of hPMS2, a greater number of microsatellite expansion versus deletion mutations was observed, and expansion rates of the tetranucleotide alleles were similar. In the presence of hPMS2, we observed a 29-fold decrease in the [TTCC/AAGG](9) expansion rate but only a 6-fold decrease for the [TTTC/AAAG](9) allele. Our data indicate that hPMS2 is more protective of tetranucleotide expansions than deletions and that hPMS2 displays a sequence bias, wherein [TTCC/AAGG] sequences are stabilized to a greater extent than [TTTC/AAAG]. Our results allow for greater accuracy during identification of MMR defects by providing a mutational signature characteristic of hPMS2 defect. This study also provides clues to possible mechanisms of repair by hPMS2 in the context of the MMR system.