Biology subjects

Yun Chen

Publications and source records attributed to Yun Chen.

3 recordsLinked to original sources

bioRxiv2016

Principles for RNA metabolism and alternative transcription initiation within closely spaced promoters

Mammalian transcriptomes are complex and formed by extensive promoter activity. In addition, gene promoters are largely divergent and initiate transcription of reverse-oriented promoter upstream transcripts (PROMPTs). Although PROMPTs are commonly terminated early, influenced by polyadenylation sites, promoters often cluster so that the divergent activity of one might impact another. Here, we find that the distance between promoters strongly correlates with the expression, stability and length of their associated PROMPTs. Adjacent promoters driving divergent mRNA transcription support PROMPT formation, but due to polyadenylation site constraints, these transcripts tend to spread into the neighboring mRNA on the same strand. This mechanism to derive new alternative mRNA transcription start sites (TSSs) is also evident at closely spaced promoters supporting convergent mRNA transcription. We suggest that basic building blocks of divergently transcribed core promoter pairs, in combination with the wealth of TSSs in mammalian genomes, provides a framework with which evolution shapes transcriptomes.

Genomics↗

bioRxiv2016

Mapping and Inheritance analysis of a novel dominant rice male sterility mutant, OsDMS-1

We found a rice dominant genetic male sterile mutant OsDMS-1 from the tissue culture regenerated offspring of Zhonghua 11 (japonica rice). Compared to wild Zhonghua 11, OsDMS-1 mutant anthers were thinner and whiter, and could not release any pollen although the glume opened normally; most of the mutant pollen was small and malformed, and could not be stained by iodine treatment; a paraffin section assay showed the degradation of OsDMS-1 mutant tapetum was delayed, with no accumulation of starch in the mutant pollen, ultimately leading to pollen abortion. Classical genetic analysis indicated that only one dominant gene was controlling the sterility in the OsDMS-1 mutant. However, molecular mapping suggested three loci simultaneously control male sterility in this mutant: OsDMS-1A, flanked by InDel markers C1D4 and C1D5 with a genetic distance of 0.15 and 0.30 cM, respectively; OsDMS-1B, flanked by InDel markers C2D3 and C2D10 with a genetic distance of 0.44 and 0.88 cM, respectively; OsDMS-1C, flanked by InDel markers 0315 and C3D3 with a genetic distance of 0.44 and 0.88 cM, respectively. Molecular mapping disagreed with classical genetic analysis about the number of controlling genes in the OsDMS-1 mutant, indicating a novel mechanism underlying sterility in OsDMS-1. We present two hypotheses to explain this novel inheritance behavior: one is described as Parent-Originated Loci Tying Inheritance (POLTI); or the hypothesis is described as Loci Recombination Lethal (LRL).\n\nKey messageThree loci, which were localized on the chromosomes 1, 2 and 3 respectively, simultaneously control a dominant rice male sterility in this mutant: OsDMS-1.

Genetics↗

bioRxiv2015

The KIAA0319 Gene Polymorphisms are Associated with Developmental Dyslexia in Chinese Uyghur Children

To investigate the association of KIAA0319 gene polymorphisms and developmental dyslexia in individuals of Uyghurian descent. Eighteen single nucleotide polymorphisms (SNP) of gene KIAA0319 were screened in a group of 196 patients with dyslexia and 196 controls of Uyghur descent by determined the genotypes using a custom-by-design 48-Plex SNPscan Kit. SAS 9.1.3 software were used for data analysis. Seven SNPs(Pmm=0.001) of KIAA0319 have significant differences between the cases and controls under specific genotype models. Especially for rs6935076(Padjusted=0.020 under dominant model; Padjusted=0.028 under additive model) and rs3756821(Padjusted=0.021 under additive model), which still associated with dyslexia after Bonferroni correction. The linkage disequilibrium analysis showed four block within gene KIAA0319 and only the ten-maker haplotype(P=0.013) in block 4 was significantly more common in dyslexia children than in controls. The results indicated that genetic polymorphisms of KIAA0319 are associated with increased risk of developmental dyslexia in Uyghur population.

Genetics↗