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Zhen Lin

Publications and source records attributed to Zhen Lin.

At least 19 recordsLinked to original sources
PubMed2025

SETD1B-mediated broad H3K4me3 controls proper temporal patterns of gene expression critical for spermatid development.

Epigenetic programming governs cell fate determination during development through intricately controlling sequential gene activation and repression. Although H3K4me3 is widely recognized as a hallmark of gene activation, its role in modulating transcription output and timing within a continuously developing system remains poorly understood. In this study, we provide a detailed characterization of the epigenomic landscapes in developing male germ cells. We identified thousands of spermatid-specific broad H3K4me3 domains regulated by the SETD1B-RFX2 axis, representing a previously underappreciated form of H3K4me3. These domains, overlapping with H3K27ac-marked enhancers and promoters, play critical roles in orchestrating robust transcription and accurate temporal control of gene expression. Mechanistically, these broad H3K4me3 compete effectively with regular H3K4me3 for transcriptional machinery, thereby ensuring robust levels and precise timing of master gene expression in mouse spermiogenesis. Disruption of this mechanism compromises the accuracy of transcription dosage and timing, ultimately impairing spermiogenesis. Additionally, we unveil remarkable changes in the distribution of heterochromatin marks, including H3K27me3 and H3K9me2, during the mitosis-to-meiosis transition and completion of meiotic recombination, which closely correlates with gene silencing. This work underscores the highly orchestrated epigenetic regulation in spermatogenesis, highlighting the previously unrecognized role of Setd1b in the formation of broad H3K4me3 domains and transcriptional control, and provides an invaluable resource for future studies toward the elucidation of spermatogenesis.

Male↗
PubMed2025

GT1 regulates maize sex determination by affecting the jasmonate pathway.

Maize (Zea mays L.) is a monoecious plant with male and female flowers physically separated on different inflorescences-the tassel and the ear. Maize sex determination is controlled by a series of complicated developmental signals. Here, we characterized an EMS-induced maize feminized tassel mutant,tasselsilk1 (tsk1), and identified GRASSY TILLERS1 (GT1) as the causative gene. Phenotypic analysis of tsk1 mutants revealed that pistils fail to abort in both the tassel and ear, resulting in long sterile silks in the tassel and the development of an extra small kernel from the lower floret in the ear. RNA-seq and CUT&Tag analysis indicated that GT1 functioned as a repressor for flower organ development by regulating the JA biosynthesis and signaling pathways, specifically by directly promoting the expression of TASSELSEED1 (TS1), ZmMYC2A, ZmMYC2B. Together, we identified a new allele of GT1 and proposed that GT1 functions through JA biosynthesis and signaling pathways to regulate sex determination in maize.

Zea mays↗
PubMed2006

Sequence-specific recognition of RNA hairpins by the SAM domain of Vts1p.

The SAM domain of the Saccharomyces cerevisiae post-transcriptional regulator Vts1p epitomizes a subfamily of SAM domains conserved from yeast to humans that function as sequence-specific RNA-binding domains. Here we report the 2.0-A X-ray structure of the Vts1p SAM domain bound to a high-affinity RNA ligand. Specificity of RNA binding arises from the association of a guanosine loop base with a shallow pocket on the SAM domain and from multiple SAM domain contacts to the unique backbone structure of the loop, defined in part by a nonplanar base pair within the loop. We have validated NNF1 as an endogenous target of Vts1p among 79 transcripts that copurify with Vts1p. Bioinformatic analysis of these mRNAs demonstrates that the RNA-binding specificity of Vts1p in vivo is probably more stringent than that of the isolated SAM domain in vitro.

Base Pairing↗
PubMed2006

The chondrocyte: biology and clinical application.

Chondrocyte is a unique cell type in articular cartilage tissue and is essential for cartilage formation and functionality. It arises from mesenchymal stem cells (MSCs) and is regulated by a series of cytokine and transcription factor interactions, including the transforming growth factor-beta super family, fibroblast growth factors, and insulin-like growth factor-1. To understand the biomechanisms of the chondrocyte differentiation process, various cellular model systems have been employed, such as primary chondrocyte culture, clonal normal cell lines (HCS-2/8, Ch-1, ATDC5, CFK-2, and RCJ3.1C5.18), and transformed clonal cell lines (T/C-28a2, T/C-28a4, C-28/I2, tsT/AC62, and HPV-16 E6/E7). Additionally, cell culture methods, including conventional monolayer culture, three-dimensional scaffold culture, bioreactor culture, pellet culture, and organ culture, have been established to create stable environments for the expansion, phenotypic maintenance, and subsequent biological study of chondrocytes for clinical application. Knowledge gained through these study systems has allowed for the use of chondrocytes in orthopedics for the treatment of cartilage injury and epiphyseal growth plate defects using tissue-engineering approaches. Furthermore, the potential of chondrocyte implantation for facial reconstruction, the treatment of long segmental tracheal defects, and urinary incontinence and vesicoureteral reflux are being investigated. This review summarizes the present study of chondrocyte biology and the potential uses of this cell in orthopedics and other disciplines.

Animals↗
PubMed2006

Choosing SNPs using feature selection.

A major challenge for genomewide disease association studies is the high cost of genotyping large number of single nucleotide polymorphisms (SNPs). The correlations between SNPs, however, make it possible to select a parsimonious set of informative SNPs, known as "tagging" SNPs, able to capture most variation in a population. Considerable research interest has recently focused on the development of methods for finding such SNPs. In this paper, we present an efficient method for finding tagging SNPs. The method does not involve computation-intensive search for SNP subsets but discards redundant SNPs using a feature selection algorithm. In contrast to most existing methods, the method presented here does not limit itself to using only correlations between SNPs in local groups. By using correlations that occur across different chromosomal regions, the method can reduce the number of globally redundant SNPs. Experimental results show that the number of tagging SNPs selected by our method is smaller than by using block-based methods. Supplementary website: http://htsnp.stanford.edu/FSFS/.

Algorithms↗
PubMed2005

Choosing SNPs using feature selection.

A major challenge for genomewide disease association studies is the high cost of genotyping large number of single nucleotide polymorphisms (SNP). The correlations between SNPs, however, make it possible to select a parsimonious set of informative SNPs, known as "tagging" SNPs, able to capture most variation in a population. Considerable research interest has recently focused on the development of methods for finding such SNPs. In this paper, we present an efficient method for finding tagging SNPs. The method does not involve computation-intensive search for SNP subsets but discards redundant SNPs using a feature selection algorithm. In contrast to most existing methods, the method presented here does not limit itself to using only correlations between SNPs in local groups. By using correlations that occur across different chromosomal regions, the method can reduce the number of globally redundant SNPs. Experimental results show that the number of tagging SNPs selected by our method is smaller than by using block-based methods.

Artificial Intelligence↗
PubMed2005

Inhibition of urokinase receptor gene expression and cell invasion by anti-uPAR DNAzymes in osteosarcoma cells.

The urokinase-type plasminogen activator (uPA) receptor (uPAR) has been implicated in signal transduction and biological processes including cancer metastasis, angiogenesis, cell migration, and wound healing. It is a specific cell surface receptor for its ligand uPA, which catalyzes the formation of plasmin from plasminogen, thereby activating the proteolytic cascade that contributes to the breakdown of extracellular matrix, a key step in cancer metastasis. We have synthesized three different DNA enzymes (Dz372, Dz483 and Dz720) targeting uPAR mRNA at three separate purine (A or G)-pyrimidine (U or C) junctions. Two of these DNAzymes, Dz483 and Dz720, cleaved uPAR transcript in vitro with high efficacy and specificity at a molar ratio (uPAR to Dz) as low as 1 : 0.2. When analyzed over 2 h with a 200-fold molar excess of DNAzymes to uPAR transcript, Dz720 and Dz483 were able to decrease uPAR transcript in vitro by approximately 93% and approximately 84%, respectively. They also showed an ability to cleave uPAR mRNA in the human osteosarcoma cell line Saos-2 after transfection. The DNAzyme Dz720 decreased uPAR mRNA within 4 h of transfection, and inhibited uPAR protein concentrations by 55% in Saos-2 cells. The decrease in uPAR mRNA and protein concentrations caused by Dz720 significantly suppressed Saos-2 cell invasion as assessed by an in vitro Matrigel assay. The use of DNAzyme methodology adds a new potential clinical agent for decreasing uPAR mRNA expression and inhibiting cancer invasion and metastasis.

Cell Line, Tumor↗
PubMed2004

Finding haplotype tagging SNPs by use of principal components analysis.

The immense volume and rapid growth of human genomic data, especially single nucleotide polymorphisms (SNPs), present special challenges for both biomedical researchers and automatic algorithms. One such challenge is to select an optimal subset of SNPs, commonly referred as "haplotype tagging SNPs" (htSNPs), to capture most of the haplotype diversity of each haplotype block or gene-specific region. This information-reduction process facilitates cost-effective genotyping and, subsequently, genotype-phenotype association studies. It also has implications for assessing the risk of identifying research subjects on the basis of SNP information deposited in public domain databases. We have investigated methods for selecting htSNPs by use of principal components analysis (PCA). These methods first identify eigenSNPs and then map them to actual SNPs. We evaluated two mapping strategies, greedy discard and varimax rotation, by assessing the ability of the selected htSNPs to reconstruct genotypes of non-htSNPs. We also compared these methods with two other htSNP finders, one of which is PCA based. We applied these methods to three experimental data sets and found that the PCA-based methods tend to select the smallest set of htSNPs to achieve a 90% reconstruction precision.

Chromosome Mapping↗
PubMed2004

High rates of sustained smoking cessation in women hospitalized with cardiovascular disease: the Women's Initiative for Nonsmoking (WINS).

BACKGROUND: Although men hospitalized with cardiovascular disease (CVD) show high smoking-cessation rates, similar data for women are lacking. We tested the efficacy of smoking-cessation intervention in women hospitalized for CVD. METHODS AND RESULTS: In this randomized controlled trial conducted from 1996 to 2001, 277 women diagnosed with CVD (mean age 61+/-10 years) were randomly assigned within 1 of 12 San Francisco Bay Area hospitals to a usual-care group (UG; n=135) or intervention group (IG; n=142). Baseline histories were obtained, and interviews to ascertain self-reported smoking status occurred at 6, 12, 24, and 30 months after hospitalization. The UG received strong physician's advice, a self-help pamphlet, and a list of community resources. The IG received strong physician's advice and a nurse-managed cognitive behavioral relapse-prevention intervention at bedside, with telephone contact at intervals after discharge. The groups were similar demographically and had smoked cigarettes for a median of 38 (IG) or 40 (UG) years. Time to resumption of continuous smoking was assessed by Kaplan-Meier analysis, and risk differences between groups were determined. Time smoke-free was significantly greater for the IG than the UG (P=0.038). Point prevalence for nonsmoking at the interviews was somewhat greater for the IG than the UG (P>0.15 at all times). CONCLUSIONS: Cognitive behavioral intervention resulted in longer average times to resumption of smoking, but in these 2 groups of older women with limited social and financial resources, long-term success rates were similar. Systematic identification of smokers and even the brief intervention afforded the UG yielded a high smoking-cessation rate over time.

Adult↗
PubMed2004

An efficient and novel method for the synthesis of cardiolipin and its analogs.

A novel synthetic method has been developed for cardiolipin and its analog via a chlorophosphoramidite coupling reaction followed by oxidation. The reagent, N,N-diisopropylmethylphosphoramidic chloride, couples effectively with 1,2-O-dimyristoyl-sn-glycerol in the presence of an amidite activator to form a phosphoamidite intermediate, which then reacts with 2-O-benzylglycerol in the presence of a basic catalyst followed by in situ oxidation to give the corresponding protected cardiolipin. Deprotection of the protecting groups provides tetramyristoyl cardiolipin in good overall yield of 60%. The synthetic method is applicable to large-scale synthesis of cardiolipin and various analogs with or without unsaturation for liposomal drug delivery.

Cardiolipins↗
PubMed2004

Identification of a negative regulatory element in the Epstein-Barr virus Zta transactivation domain that is regulated by the cell cycle control factors c-Myc and E2F1.

Reactivation in Epstein-Barr virus (EBV) is closely associated with a G(0)/G(1) cell cycle arrest which can be induced either by lytic cycle-inducing agents or by the immediate-early gene product Zta. Accumulating evidence shows that in epithelial cells, downregulation of the proto-oncogene, c-myc, plays an important role in lytic cycle-associated cell growth arrest. Here, we provide evidence that c-Myc provides a gatekeeper function to ensure that certain cell cycle inhibitory events have been capitulated prior to full progression into the lytic cycle. Specifically, we show that reconstitution of c-Myc expression during the lytic cycle to levels observed in cycling uninduced cells inhibits the transactivation function of Zta. Nuclear localization studies show that c-Myc does not grossly alter the nuclear localization of Zta or its association with the insoluble nuclear fraction. Enforced expression of another transcription factor that promotes cell cycle progression, E2F1, also inhibits Zta transactivation. Analysis of c-Myc- and E2F1-mediated inhibition of a panel of Zta mutants shows parallel genetics and inhibition maps to a small bipartite sequence located between amino acids 29 and 53 of Zta, containing homology to the proline-rich domain of the tumor suppressor protein p53. Mutation of a conserved tryptophan residue located at amino acid 49 of Zta largely prevents inhibition by both c-Myc and E2F1. These studies identify a negative regulatory element within the Zta activation domain that is regulated by the cell cycle-promoting factors c-Myc and E2F1.

Amino Acid Sequence↗
PubMed2004

[Serum PSA and transition zone index as predictors of acute urinary retention in benign prostate hyperplasia].

OBJECTIVE: To evaluate prostate specific antigen (PSA) and transition zone index (TZI) as predictors of acute urinary retention (AUR) in men with benign prostate hyperplasia(BPH). METHODS: The complete data of 602 cases of BPH were reviewed and analyzed. RESULTS: Mean serum PSA and TZI were (6.60 +/- 3.4) microgram/L and (0.71 +/- 0.14) in AUR group, (3.51 +/- 2.3) microgram/L and (0.46 +/- 0.21) in non-AUR group, respectively. There were significant differences in serum PSA and TZI between the two groups(P < 0.05). The difference in incidence of AUR between serum PSA < 4.0 micrograms/L, 4.0-10.0 micrograms/L and PSA > 10.0 micrograms/L was significant (P < 0.05). There was significant positive correlation between serum PSA and TZI(r = 0.213, P < 0.01). CONCLUSION: Serum PSA and TZI were powerful predictors of the risk of AUR in men with BPH.

Acute Disease↗
PubMed2004

[Investigation of sexual function rehabilitation of 11 male heart transplant recipients].

OBJECTIVE: To investigate the rehabilitation of the sexual function of male patients after heart transplantation. METHODS: Eleven discharged adult male cardiac transplant recipients (ranging 32-54 years) with a normally functioning allograft for at least 9 months were questioned on their pre- and post-operative sexual function. RESULTS: All the recipients complained of a significant pretransplantive decrease and 10 stated a significant posttransplantive increase in sexual function. CONCLUSION: The sexual function of the male recipients was significantly improved after cardiac transplantation. Psychosocial factors affecting the rehabilitation of sexual function should not be neglected.

Adult↗
PubMed2004

[Changes of P-selectin and E-selectin in children with Kawasaki disease].

OBJECTIVE: Kawasaki disease (KD) is a kind of febrile disorder without definite etiology. The pathologic change of KD is characterized by nonspecific vasculitis, which mainly involves the coronary artery. Some patients may have coronary angioma formation, and some of them will result in the coronary narrowing or embolism. Notwithstanding that KD has been one of the most common causes for acquired heart diseases in childhood in addition to the rheumatic fever, the pathogenesis of the vascular damage remains unknown. This study was conducted to explore the pathophysiological role of cell adhesion molecules (P-selectin and E-selectin) on the endothelial lesions in KD, and to look for the evidence of direct relationship between the plasma levels of soluble cell adhesion molecules (P- and E-selectin) and the incidence of the coronary artery lesion (CAL). METHODS: Soluble P-selectin (PS), E-selectin (ES), thromboxane-B(2)(TXB(2)), 6-keto-PGF(1)alpha (6-KPGF(1)alpha) were measured in 36 patients with KD, 20 patients with febrile disease and 30 healthy children by using double antibody sandwich enzyme linked immunosorbent assay (ELISA) and radioimmunoassay. Patients with KD were separated into acute phase group, subacute phase group, recovery phase group, coronary artery lesion group (CAL), non-coronary artery lesion group (NCAL), intravenous immunoglobulin (IVIG) effective group (body temperature back to normal after 48 hours of using IVIG), and IVIG ineffective group. RESULTS: Plasma PS and ES levels in the acute phase group [(211 +/- 28 and 186 +/- 14) ng/ml], subacute phase group [(238 +/- 27 and 151 +/- 13) ng/ml] and recovery phase group [(198 +/- 21 and 1008 +/- 9) ng/ml] were significantly higher than those in the healthy group [(102 +/- 36 and 72 +/- 10) ng/ml, P < 0.01]. The plasma PS levels remained higher after the treatment, but in IVIG effective group, the PS and ES levels declined significantly (P < 0.01) compared with those in acute phase group. Plasma PS and ES levels of CAL group [(281 +/- 78 and 210 +/- 52) ng/ml] were significantly higher than those of NCAL group [(217 +/- 15 and 108 +/- 10) ng/ml, P < 0.01]. In contrast to 1 week after the treatment, the PS and ES in IVIG effective group at the time point of 2 weeks after the treatment decreased more significantly (P < 0.01). While the PS and ES in IVIG ineffective group remained higher at the time point of 2 weeks after the treatment, which showed no significant difference compared with those 1 week after the treatment (P > 0.05). One week after the treatment, the PS levels of IVIG effective and ineffective groups did not descend, and there was no significant difference in PS between these two groups at this time point. Two weeks after the treatment, the PS and ES in IVIG ineffective group remained higher than those in IVIG effective group, and there was a significant difference between them. The peak level of PS appeared in the subacute phase. TXB(2) levels of KD in acute phase group increased markedly, which were significantly higher than those of healthy group [(345 +/- 127 and 190 +/- 69) ng/L, P < 0.01]. There was no significant difference between subacute phase group and healthy group. No significant difference was found between CAL group and NCAL group (P > 0.05). The levels of TXB(2) declined quickly after the treatment. The 6-KPGF(1)alpha level in KD of acute phase group, subacute phase group and recovery phase group [(7.1 +/- 2.8, 10.8 +/- 3.7 and 11.3 +/- 4.0) ng/L, respectively] was significantly lower than that of healthy group [(17.7 +/- 5.8) ng/L, P < 0.01], and the levels did not recover to normal even 2 weeks after the treatment. There was no significant difference 6-KPGF(1)alpha levels between CAL group and NCAL group (P > 0.05). In the febrile group, PS and ES levels showed no significant differences compared with healthy children (P > 0.05). ES level of KD patients was significantly correlated with CRP levels (r = 0.79 P < 0.01). In febrile group, there was no significant correlation between ES and CRP. There was a significant correlation between PS and PLT levels in KD patients (r = 0.75 P < 0.01), and no significant correlation between PS and PLT levels in febrile patients. CONCLUSION: The increase of plasma PS and ES levels in KD acute phase and subacute phase might play an important role in the pathophysiology of the endothelial damage. E- and P-selectin may potentially be a predictor of CAL in patients with KD.

Child↗