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Articles by Y Cheng
Total Records ( 10 ) for Y Cheng
  Z Liu , M Liu , G Niu , Y Cheng and J. Fei

Transcriptional repression is as important as transcriptional activation in establishing cell-type specific patterns of gene expression. RE1-silencing transcription factor (REST), also known as neuronal restrictive silencing factor (NRSF), is a transcriptional regulator that represses a battery of neuronal differentiation genes in non-neuronal cells or in neural progenitor cells by binding to a specific DNA sequence (repressor element-1/neuron-restrictive silencer element, RE1/NRSE). REST/NRSF functions in the neuronal development are widely studied, however, little is known about target genes in various non-neuronal lineages that may result in cell differentiation. Here, we use RNA interference (RNAi) technology combined with the microarray strategy to identify potential REST/NRSF targets and RE1/NRSEs in human non-neuronal cell line HEK 293. Expression of 54 genes was up-regulated by inhibition of REST/NRSF in the HEK 293 cells according to the microarray experiment and 13 of those were further confirmed by quantitative RT-PCR. Our results confirmed the good confidence and reliability of current research data based on in silico, chromatin immunoprecipitation in combination with microarrays (ChIP-chip), and high-throughput sequencing (ChIP-seq). However, in view of the fact that thousands of genes have been testified or predicted to be recognized by REST/NRSF, our data show that only a few genes among those are directly up-regulated by the interaction of REST/NRSF with RE1/NRSEs sites in gene sequences.

  M. D Levine , K. A Perkins , M. A Kalarchian , Y Cheng , P. R Houck , J. D Slane and M. D. Marcus

Background  We previously documented that cognitive behavioral therapy for smoking-related weight concerns (CONCERNS) improves cessation rates. However, the efficacy of combining CONCERNS with cessation medication is unknown. We sought to determine if the combination of CONCERNS and bupropion therapy would enhance abstinence for weight-concerned women smokers.

Methods  In a randomized, double-blind, placebo-controlled trial, weight-concerned women (n = 349; 86% white) received smoking cessation counseling and were randomized to 1 of 2 adjunctive counseling components: CONCERNS or STANDARD (standard cessation treatment with added discussion of smoking topics but no specific weight focus), and 1 of 2 medication conditions: bupropion hydrochloride sustained release (B) or placebo (P) for 6 months. Rates and duration of biochemically verified prolonged abstinence were the primary outcomes. Point-prevalent abstinence, postcessation weight gain, and changes in nicotine withdrawal, depressive symptoms, and weight concerns were evaluated.

Results  Women in the CONCERNS + B group had higher rates of abstinence (34.0%) and longer time to relapse than did those in the STANDARD + B (21%; P = .05) or CONCERNS + P (11.5%; P = .005) groups at 6 months, although rates of prolonged abstinence in the CONCERNS + B and STANDARD + B groups did not differ significantly at 12 months. Abstinence rates and duration did not differ in the STANDARD + B group (21% and 19%) compared with the STANDARD + P group (10% and 7%) at 6 and 12 months, respectively. There were no differences among abstinent women in postcessation weight gain or weight concerns, although STANDARD + B produced greater decreases in nicotine withdrawal and depressive symptoms than did STANDARD + P.

Conclusions  Weight-concerned women smokers receiving the combination of CONCERNS + B were most likely to sustain abstinence. This effect was not related to differences in postcessation weight gain or changes in weight concerns.

Trial Registration Identifier: NCT00006170

  Y Cheng , Z. q Li , J. z Huang , F Xue , M. j Jiang , K. m Wu and Q. p. Wang

Objectives  To apply the technique of injection of a combination of autologous fascia lata and fat into the vocal fold via the cricothyroid gap for unilateral vocal fold paralysis and to evaluate the therapeutic effect in 12 patients who underwent the procedure.

Design  Retrospective analysis of 12 patients.

Setting  Academic research.

Patients  A mixture of autologous fascia lata and fat was injected into the thyroarytenoid muscle of the paralyzed vocal fold in 12 patients.

Main Outcome Measures  Videolaryngostroboscopy was performed to observe the changes to the vocal fold. The patients' phonatory function before and after surgery was assessed by computerized acoustic analysis and by blinded perceptual evaluation.

Results  Videolaryngostroboscopy demonstrated that the paralyzed vocal folds in these patients were pushed medially after the procedure. Statistically significant improvements were found in the perturbation measurements (jitter and shimmer), harmonics to noise ratio, and maximum phonation time. Ratings by a panel of voice experts also showed each voice to be statistically significantly improved after the procedure. No complications were noted.

Conclusion  A combination of autologous fascia lata and fat injected into the vocal fold for unilateral vocal fold paralysis is a safe and effective therapy.

  Y Cheng , X Liu , J Yang , Y Lin , D. Z Xu , Q Lu , E. A Deitch , Y Huo , E. S Delphin and C. Zhang

Phenotypic modulation of vascular smooth muscle cells (VSMCs) plays a critical role in the pathogenesis of a variety of proliferative vascular diseases. Recently, we have found that microRNA (miRNA) miR-145 is the most abundant miRNA in normal vascular walls and in freshly isolated VSMCs; however, the role of miR-145 in VSMC phenotypic modulation and vascular diseases is currently unknown. Here we find that miR-145 is selectively expressed in VSMCs of the vascular wall and its expression is significantly downregulated in the vascular walls with neointimal lesion formation and in cultured dedifferentiated VSMCs. More importantly, both in cultured rat VSMCs in vitro and in balloon-injured rat carotid arteries in vivo, we demonstrate that the noncoding RNA miR-145 is a novel phenotypic marker and a novel phenotypic modulator of VSMCs. VSMC differentiation marker genes such as SM -actin, calponin, and SM-MHC are upregulated by premiR-145 or adenovirus expressing miR-145 (Ad-miR-145) but are downregulated by the miR-145 inhibitor 2'OMe-miR-145. We have further identified that miR-145-mediated phenotypic modulation of VSMCs is through its target gene KLF5 and its downstream signaling molecule, myocardin. Finally, restoration of miR-145 in balloon-injured arteries via Ad-miR-145 inhibits neointimal growth. We conclude that miR-145 is a novel VSMC phenotypic marker and modulator that is able of controlling vascular neointimal lesion formation. These novel findings may have extensive implications for the diagnosis and therapy of a variety of proliferative vascular diseases.

  D Summerer , H Wu , B Haase , Y Cheng , N Schracke , C. F Stahler , M. S Chee , P. F Stahler and M. Beier

The lack of efficient high-throughput methods for enrichment of specific sequences from genomic DNA represents a key bottleneck in exploiting the enormous potential of next-generation sequencers. Such methods would allow for a systematic and targeted analysis of relevant genomic regions. Recent studies reported sequence enrichment using a hybridization step to specific DNA capture probes as a possible solution to the problem. However, so far no method has provided sufficient depths of coverage for reliable base calling over the entire target regions. We report a strategy to multiply the enrichment performance and consequently improve depth and breadth of coverage for desired target sequences by applying two iterative cycles of hybridization with microfluidic Geniom biochips. Using this strategy, we enriched and then sequenced the cancer-related genes BRCA1 and TP53 and a set of 1000 individual dbSNP regions of 500 bp using Illumina technology. We achieved overall enrichment factors of up to 1062-fold and average coverage depths of 470-fold. Combined with high coverage uniformity, this resulted in nearly complete consensus coverages with >86% of target region covered at 20-fold or higher. Analysis of SNP calling accuracies after enrichment revealed excellent concordance, with the reference sequence closely mirroring the previously reported performance of Illumina sequencing conducted without sequence enrichment.

  Y Cheng , W Wu , S Ashok Kumar , D Yu , W Deng , T Tripic , D. C King , K. B Chen , Y Zhang , D Drautz , B Giardine , S. C Schuster , W Miller , F Chiaromonte , G. A Blobel , M. J Weiss and R. C. Hardison

The transcription factor GATA1 regulates an extensive program of gene activation and repression during erythroid development. However, the associated mechanisms, including the contributions of distal versus proximal cis-regulatory modules, co-occupancy with other transcription factors, and the effects of histone modifications, are poorly understood. We studied these problems genome-wide in a Gata1 knockout erythroblast cell line that undergoes GATA1-dependent terminal maturation, identifying 2616 GATA1-responsive genes and 15,360 GATA1-occupied DNA segments after restoration of GATA1. Virtually all occupied DNA segments have high levels of H3K4 monomethylation and low levels of H3K27me3 around the canonical GATA binding motif, regardless of whether the nearby gene is induced or repressed. Induced genes tend to be bound by GATA1 close to the transcription start site (most frequently in the first intron), have multiple GATA1-occupied segments that are also bound by TAL1, and show evolutionary constraint on the GATA1-binding site motif. In contrast, repressed genes are further away from GATA1-occupied segments, and a subset shows reduced TAL1 occupancy and increased H3K27me3 at the transcription start site. Our data expand the repertoire of GATA1 action in erythropoiesis by defining a new cohort of target genes and determining the spatial distribution of cis-regulatory modules throughout the genome. In addition, we begin to establish functional criteria and mechanisms that distinguish GATA1 activation from repression at specific target genes. More broadly, these studies illustrate how a "master regulator" transcription factor coordinates tissue differentiation through a panoply of DNA and protein interactions.

  Z Li , R. K Hite , Y Cheng and T. Walz

We evaluated imaging plates (IPs) and the DITABIS Micron scanner for their use in recording images of negatively stained single-particle specimens and electron diffraction patterns of two-dimensional crystals. We first established the optimal imaging and read-out conditions for images of negatively stained single-particle specimens using the signal-to-noise ratio of the images as the evaluation criterion. We found that images were best recorded on IPs at a magnification of 67 000x, read out with a gain setting of 20 000 and a laser power setting of 30% with subsequent binning over 2 x 2 pixels. Our results show that for images of negatively stained specimens, for which the resolution is limited to ~20 Å, IPs are a good alternative to EM film. We also compared IPs with a 2K x 2K Gatan charge-coupled device (CCD) camera for their use in recording electron diffraction patterns of sugar-embedded two-dimensional crystals. Diffraction patterns of aquaporin-0 recorded on IPs and with the CCD camera showed reflections beyond 3 Å and had similar RFriedel as well as Rmerge values. IPs can thus be used to collect diffraction patterns, but CCD cameras are more convenient and remain the best option for recording electron diffraction patterns.

  Y Ling , Y Ma , W Guan , Y Cheng , Y Wang , J Han , D Jin , L Mang and H. Mahmut

Y chromosome acts as a single nonrecombining unit that is male specific and in effect haploid, thus ensuring the preservation of mutational events as a single haplotype via male lines. In this study, 6 Y chromosome–specific microsatellites (SSR) were tested for the patrilineal genetic variations of 573 male samples from Chinese domestic horse (30 breeds), Przewalski's horse, and donkey. All the 6 loci appeared as a haplotype block in Przewalski's horse and the domestic donkey. There were notable differences, however, at Y chromosome markers between horse and donkey. There were 2 haplotypes of Eca.YA16 in the domestic horse breeds, Haplotype A (Allele A: 156 bp) and Haplotype B (Allele B: 152 bp). Allele A was the common allele among 30 horse breeds, and Allele B was found in 11 horse breeds. This is the first description of a Y chromosome variant for horses. The 2 haplotypes of Y chromosome discovered in the domestic horse breeds in China could be helpful in unveiling their intricate genetic genealogy.

  X Liu , Y Cheng , J Yang , T. J Krall , Y Huo and C. Zhang

It is well established that vascular smooth muscle cell (VSMC) apoptosis and proliferation are critical cellular events in a variety of human vascular diseases. However, the molecular mechanisms involved in controlling VSMC apoptosis and proliferation are still unclear. In the current study, we have found that programmed cell death 4 (PDCD4) is significantly downregulated in balloon-injured rat carotid arteries in vivo and in platelet-derived growth factor-stimulated VSMCs in vitro. Overexpression of PDCD4 via adenovirus (Ad-PDCD4) increases VSMC apoptosis in an apoptotic model induced by serum deprivation. In contrast, VSMC apoptosis is significantly decreased by knockdown of PDCD4 via its small interfering RNA. In the rat carotid arteries in vivo, VSMC apoptosis is increased by Ad-PDCD4. We have further identified that activator protein 1 is a downstream signaling molecule of PDCD4 that is associated with PDCD4-mediated effects on VSMC apoptosis. In addition, VSMC proliferation was inhibited by overexpression of PDCD4. The current study has identified, for the first time, that PDCD4 is an essential regulator of VSMC apoptosis and proliferation. The downregulation of PDCD4 expression in diseased vascular walls may be responsible for the imbalance of VSMC proliferation and apoptosis. The results indicate that PDCD4 may be a new therapeutic target in proliferative vascular diseases.

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