Predicting polymerase II core promoters by cooperating transcription factor binding sites in eukaryotic genes.

Abstract:

:Several discriminate functions for predicting core promoters that based on the potential cooperation between transcription factor binding sites (TFBSs) are discussed. It is demonstrated that the promoter predicting accuracy is improved when the cooperation among TFBSs is taken into consideration. The core promoter region of a newly discovered gene CKLFSF1 is predicted to locate more than 1.5 kb far away from the 5' end of the transcript and in the last intron of its upstream gene, which is experimentally confirmed later. The core promoters of 3402 human RefSeq sequences, obtained by extending the mRNAs in human genome sequences, are predicted by our algorithm, and there are about 60% of the predicted core promoters locating within the +/- 500 bp region relative to the annotated transcription start site.

authors

Ma XT,Qian MP,Tang HX

doi

10.1093/abbs/36.4.250

subject

Has Abstract

pub_date

2004-04-01 00:00:00

pages

250-8

issue

4

eissn

1672-9145

issn

1745-7270

journal_volume

36

pub_type

杂志文章
  • Effect of lentiviral vector-mediated KSR1 gene silencing on the proliferation of renal tubular epithelial cells and expression of inflammatory factors in a rat model of ischemia/reperfusion injury.

    abstract::Renal ischemia/reperfusion (I/R) is a common cause of acute renal failure in many clinical settings. Our study aimed to elucidate the role of lentiviral vector-mediated KSR1 gene silencing in inflammatory factor expression and proliferation of renal tubular epithelial cells (RTECs) in a rat model of I/R injury. Male S...

    journal_title:Acta biochimica et biophysica Sinica

    pub_type: 杂志文章

    doi:10.1093/abbs/gmy071

    authors: Bai Y,Han G,Guo K,Yu L,Du X,Xu Y

    更新日期:2018-08-01 00:00:00

  • A new recombinant pituitary adenylate cyclase-activating peptide-derived peptide efficiently promotes glucose uptake and glucose-dependent insulin secretion.

    abstract::The recombinant peptide, DBAYL, a promising therapeutic peptide for type 2 diabetes, is a new, potent, and highly selective agonist for VPAC2 generated through site-directed mutagenesis based on sequence alignments of pituitary adenylate cyclase-activating peptide (PACAP), vasoactive intestinal peptide (VIP), and rela...

    journal_title:Acta biochimica et biophysica Sinica

    pub_type: 杂志文章

    doi:10.1093/abbs/gms078

    authors: Ma Y,Luo T,Xu W,Ye Z,Hong A

    更新日期:2012-11-01 00:00:00

  • Production of the polyclonal anti-human metallothionein 2A antibody with recombinant protein technology.

    abstract::Metallothionein 2A (MT2A) is a small stress response protein that can be induced by exposure to toxic metals. It is highly expressed in breast cancer cells. In this study, the cDNA encoding the human MT2A protein was expressed as glutathione S-transferase (GST) fusion protein in Escherichia coli. Recombinant MT2A prot...

    journal_title:Acta biochimica et biophysica Sinica

    pub_type: 杂志文章

    doi:10.1111/j.1745-7270.2006.00167.x

    authors: Marikar FM,Sun QM,Hua ZC

    更新日期:2006-05-01 00:00:00

  • Cordycepin protects renal ischemia/reperfusion injury through regulating inflammation, apoptosis, and oxidative stress.

    abstract::Cordycepin (3'-deoxyadenosine) is a naturally occurring adenosine analog and one of the bioactive constituents isolated from Cordyceps sinensis, species of the fungal genus Cordyceps. It has traditionally been a prized Chinese folk medicine for the human well-being. However, the actions of cordycepin against renal isc...

    journal_title:Acta biochimica et biophysica Sinica

    pub_type: 杂志文章

    doi:10.1093/abbs/gmz145

    authors: Han F,Dou M,Wang Y,Xu C,Li Y,Ding X,Xue W,Zheng J,Tian P,Ding C

    更新日期:2020-02-03 00:00:00

  • New hope in the horizon: cancer stem cells.

    abstract::The major goal of researchers and oncologists is to develop promising ground for novel therapeutic strategies to prevent recurrence or relapse of cancer. Recent evidences suggest that a subset of cells called cancer stem cells (CSCs) are present within the tumor mass which possess tumorigenic capacity and may be respo...

    journal_title:Acta biochimica et biophysica Sinica

    pub_type: 杂志文章,评审

    doi:10.1093/abbs/gmq013

    authors: Bhattacharyya S,Khanduja KL

    更新日期:2010-04-01 00:00:00

  • Doxycycline synergizes with doxorubicin to inhibit the proliferation of castration-resistant prostate cancer cells.

    abstract::Castration-resistant prostate cancer (CRPC) is fatal and there is currently no effective clinical treatment. The antibiotic doxycycline has shown anti-cancer effect in several kinds of solid tumors including prostate cancer. In this study, a combination of doxycycline and doxorubicin was used to investigate the synerg...

    journal_title:Acta biochimica et biophysica Sinica

    pub_type: 杂志文章

    doi:10.1093/abbs/gmx097

    authors: Zhu C,Yan X,Yu A,Wang Y

    更新日期:2017-11-01 00:00:00

  • Curculigoside isolated from Curculigo orchioides prevents hydrogen peroxide-induced dysfunction and oxidative damage in calvarial osteoblasts.

    abstract::Reactive oxygen species (ROS), including H(2)O(2), play a critical role in the pathophysiology of osteoporosis. Therefore, agents or antioxidants that can inhibit ROS production have a high clinical value in the treatment of osteoporosis. Curculigoside (CUR), one of the main bioactive phenolic compounds isolated from ...

    journal_title:Acta biochimica et biophysica Sinica

    pub_type: 杂志文章

    doi:10.1093/abbs/gms014

    authors: Wang Y,Zhao L,Wang Y,Xu J,Nie Y,Guo Y,Tong Y,Qin L,Zhang Q

    更新日期:2012-05-01 00:00:00

  • Beneficial effects of C-peptide on renal morphology in diabetic rats.

    abstract::The study was undertaken to examine the effects of C-peptide on glomerular volume (V(GLOM)), mesangial matrix synthesis, and degradation in streptozotocin (STZ)-diabetic rats with poor or moderate glycemic control. Series 1 (poor glycemic control) included groups of healthy rats, hyperglycemic rats, diabetic insulin-t...

    journal_title:Acta biochimica et biophysica Sinica

    pub_type: 杂志文章

    doi:10.1093/abbs/gmq100

    authors: Sun W,Gao X,Zhao X,Cui D,Xia Q

    更新日期:2010-12-01 00:00:00

  • Effect of exogenous ghrelin on cell differentiation antigen 40 expression in endothelial cells.

    abstract::Ghrelin is a brain-gut peptide that serves as a natural ligand for growth hormone secretagogue receptor (GHSR). It also exists abundantly in the cardiovascular system. In order to evaluate the possible role of ghrelin in the development of atherosclerosis, the effect of ghrelin on the expression of cell differentiatio...

    journal_title:Acta biochimica et biophysica Sinica

    pub_type: 杂志文章

    doi:10.1111/j.1745-7270.2007.00365.x

    authors: Zhang M,Yuan F,Chen H,Qiu X,Fang W

    更新日期:2007-12-01 00:00:00

  • MicroRNA expression profiling in diabetic GK rat model.

    abstract::MicroRNAs (miRNAs), which are a newly identified class of small single-stranded non-coding RNAs, regulate their target genes via post-transcriptional pathway. It has been proved that miRNAs play important roles in many biological processes. To better understand miRNA function on type 2 diabetes, we used an oligonucleo...

    journal_title:Acta biochimica et biophysica Sinica

    pub_type: 杂志文章

    doi:10.1093/abbs/gmp035

    authors: Huang B,Qin W,Zhao B,Shi Y,Yao C,Li J,Xiao H,Jin Y

    更新日期:2009-06-01 00:00:00

  • Targeting AMPK signaling in combating ovarian cancers: opportunities and challenges.

    abstract::The development and strategic application of effective anticancer therapies have turned out to be one of the most critical approaches of managing human cancers. Nevertheless, drug resistance is the major obstacle for clinical management of these diseases especially ovarian cancer. In the past years, substantial studie...

    journal_title:Acta biochimica et biophysica Sinica

    pub_type: 杂志文章,评审

    doi:10.1093/abbs/gmv128

    authors: Yung MM,Ngan HY,Chan DW

    更新日期:2016-04-01 00:00:00

  • Emerging roles of miR-210 and other non-coding RNAs in the hypoxic response.

    abstract::Hypoxia is a key component of the tumor microenvironment and represents a well-documented source of therapeutic failure in clinical oncology. Recent work has provided support for the idea that non-coding RNAs, and in particular, microRNAs, may play important roles in the adaptive response to low oxygen in tumors. Spec...

    journal_title:Acta biochimica et biophysica Sinica

    pub_type: 杂志文章,评审

    doi:10.1093/abbs/gmt141

    authors: Huang X,Zuo J

    更新日期:2014-03-01 00:00:00

  • Photothermal treatment with EGFRmAb-AuNPs induces apoptosis in hypopharyngeal carcinoma cells via PI3K/AKT/mTOR and DNA damage response pathways.

    abstract::Hypopharyngeal carcinoma (HC) is one of the most malignant tumors in the upper aerodigestive tract. Currently, there are no effective treatments for HC. Gold nanoparticles (AuNPs) are a promising tool that can be used for plasmonic photothermal therapy (PPTT), which refers to the use of electromagnetic radiation, most...

    journal_title:Acta biochimica et biophysica Sinica

    pub_type: 杂志文章

    doi:10.1093/abbs/gmy046

    authors: Zhang Y,Cong L,He J,Wang Y,Zou Y,Yang Z,Hu Y,Zhang S,He X

    更新日期:2018-06-01 00:00:00

  • Proteomic profiling of hepatitis B virus-related hepatocellular carcinoma with magnetic bead-based matrix-assisted laser desorption/ionization time-of-flight mass spectrometry.

    abstract::Proteomic techniques are promising strategies in the surveillance of hepatocellular carcinoma (HCC). This study aimed to investigate the serum profiling with magnetic bead (MB) and matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF) mass spectrometry (MS) and to further identify the biomarkers for H...

    journal_title:Acta biochimica et biophysica Sinica

    pub_type: 杂志文章

    doi:10.1093/abbs/gmr044

    authors: Liu T,Xue R,Huang X,Zhang D,Dong L,Wu H,Shen X

    更新日期:2011-07-01 00:00:00

  • Betulinic acid induces apoptosis of gallbladder cancer cells via repressing SCD1.

    abstract::Gallbladder cancer (GBC) is the most common and aggressive malignancy of the biliary tract. Betulinic acid (BetA) has been reported to have anti-inflammatory and antitumor effects; however, the effect of BetA on GBC is still unknown. In this study, we investigated the effect of BetA on five GBC cell lines and found th...

    journal_title:Acta biochimica et biophysica Sinica

    pub_type: 杂志文章

    doi:10.1093/abbs/gmz148

    authors: Wang H,Dong F,Wang Y,Wang X,Hong D,Liu Y,Zhou J

    更新日期:2020-02-03 00:00:00

  • Proteomic profiling of cotton fiber developmental transition from cell elongation to secondary wall deposition.

    abstract::Cotton fiber developmental transition from elongation to secondary cell wall biosynthesis is a critical growth shifting phase that affects fiber final length, strength, and other properties. Morphological dynamic analysis indicated an asynchronous fiber developmental pattern between two most important commercial cotto...

    journal_title:Acta biochimica et biophysica Sinica

    pub_type: 杂志文章

    doi:10.1093/abbs/gmz111

    authors: Zhou X,Hu W,Li B,Yang Y,Zhang Y,Thow K,Fan L,Qu Y

    更新日期:2019-11-18 00:00:00

  • Identification of neuropeptide Y-like conopeptides from the venom of Conus betulinus.

    abstract::Neuropeptide Y (NPY) is a ubiquitous endocrine neuropeptide found in vertebrate and invertebrate. In our present work, two NPY-like exocrine conopeptides (designated as cono-NPYs) were first identified in the venom of cone snails. Both cono-NPYs showed sequence characteristics of invertebrate NPYs, suggesting that som...

    journal_title:Acta biochimica et biophysica Sinica

    pub_type: 杂志文章

    doi:10.1093/abbs/gmq042

    authors: Wu X,Shao X,Guo ZY,Chi CW

    更新日期:2010-07-01 00:00:00

  • HEATR1 promotes proliferation in gastric cancer in vitro and in vivo.

    abstract::HEAT repeat-containing protein 1 (HEATR1) is related to the progression of several cancers. However, the role of HEATR1 in gastric cancer (GC) remains unknown. In the present study, we aimed to detect the expression of HEATR1 in GC and identify its role. The expressions of HEATR1 in GC tissues were analyzed using The ...

    journal_title:Acta biochimica et biophysica Sinica

    pub_type: 杂志文章

    doi:10.1093/abbs/gmaa077

    authors: Zhao J,Zhu Y,Fu Q,Zhu Y,Zhao G

    更新日期:2020-09-08 00:00:00

  • Checkpoint-dependent phosphorylation of Med1/TRAP220 in response to DNA damage.

    abstract::Mediator complex subunit 1 (Med1)/Thyroid hormone receptor-associated protein 220 (TRAP220), an essential component of thyroid hormone receptor-associated proteins (TRAP)/mediator, plays important roles in hormone responses and tumorigenesis. However, the role of Med1 in the DNA damage response has not been studied. I...

    journal_title:Acta biochimica et biophysica Sinica

    pub_type: 杂志文章

    doi:10.1093/abbs/gmx036

    authors: Kim HJ,Yun J

    更新日期:2017-06-01 00:00:00

  • Fusion protein of interleukin 4 and diphtherial toxin with high cytotoxicity to cancer cells.

    abstract::Receptor of human interleukin 4 (hIL4R) has been found to be present on many types of cancer, so it may be a good target for cancer therapy. Here, fusion toxin gene DT4H has been constructed by fusing DNA sequence encoding the first 389 amino acids of diphtherial toxin (DT), which can not bind its own receptor, to hum...

    journal_title:Acta biochimica et biophysica Sinica

    pub_type: 杂志文章

    doi:10.1093/abbs/36.6.437

    authors: Zhang YJ,Hu XB,Li SX,Tian LP,Yang SL,Gong Y

    更新日期:2004-06-01 00:00:00

  • ZnPcS2P2-based photodynamic therapy induces mitochondria-dependent apoptosis in K562 cells.

    abstract::Mitochondria play a key role in the regulation of apoptosis induced by numerous antitumor chemotherapeutic and other toxic agents. Photodynamic therapy (PDT) exerts significant cellular killing efficacy through either an apoptotic or necrotic cell death pathway. This study investigated the mechanism underlying the kil...

    journal_title:Acta biochimica et biophysica Sinica

    pub_type: 杂志文章

    doi:10.1111/j.1745-7270.2005.00067.x

    authors: Huang HF,Chen YZ,Wu Y

    更新日期:2005-07-01 00:00:00

  • Regulation of membrane band 3 Tyr-phosphorylation by proteolysis of p72(Syk) and possible involvement in senescence process.

    abstract::Erythrocyte senescence is characterized by exposure of cell surface epitopes on cell membrane proteins leading to immune mediated removal of red blood cells. One mechanism for antigen formation is tyrosine phosphorylation (Tyr-P) of the transmembrane protein band 3 by Syk kinase. Our aim was to test the hypothesis tha...

    journal_title:Acta biochimica et biophysica Sinica

    pub_type: 杂志文章

    doi:10.1093/abbs/gmp071

    authors: Bordin L,Fiore C,Bragadin M,Brunati AM,Clari G

    更新日期:2009-10-01 00:00:00

  • Argininosuccinate synthase 1 suppresses cancer cell invasion by inhibiting STAT3 pathway in hepatocellular carcinoma.

    abstract::Metastasis is the main reason for high recurrence and poor survival of hepatocellular carcinoma (HCC). The molecular mechanism underlying HCC metastasis remains unclear. In this study, we found that argininosuccinate synthase 1 (ASS1) expression was significantly decreased and down-regulation of ASS1 was closely corre...

    journal_title:Acta biochimica et biophysica Sinica

    pub_type: 杂志文章

    doi:10.1093/abbs/gmz005

    authors: Tao X,Zuo Q,Ruan H,Wang H,Jin H,Cheng Z,Lv Y,Qin W,Wang C

    更新日期:2019-03-01 00:00:00

  • The water network in galectin-3 ligand binding site guides inhibitor design.

    abstract::Galectin-3 (Gal-3) which shows affinity of β-galactosides is a cancer-related protein. Thus, it is important to understand its ligand binding mechanism and then design its specific inhibitor. It was suggested that the positions of water molecules in Gal-3 ligand-binding site could be replaced by appropriate chemical g...

    journal_title:Acta biochimica et biophysica Sinica

    pub_type: 杂志文章

    doi:10.1093/abbs/gmu132

    authors: Su J,Zhang T,Wang P,Liu F,Tai G,Zhou Y

    更新日期:2015-03-01 00:00:00

  • Differential expression of neutrophilic granule proteins between Th1 and Th2 cells.

    abstract::T helper cell type 1 (Th1) and 2 (Th2) play central roles in immune regulation. To identify the novel genes differentially expressed between Th1 and Th2 cells, CD4+ T cells were isolated from DO11.10 transgenic mice and induced under Th1 or Th2 conditions. Microarray showed differential expression of neutrophilic gran...

    journal_title:Acta biochimica et biophysica Sinica

    pub_type: 杂志文章

    doi:10.1111/j.1745-7270.2007.00242.x

    authors: Xie D,Liu Z,Li Z,Ji Y,Chen J,Sun B

    更新日期:2007-01-01 00:00:00

  • Quality control system of the endoplasmic reticulum and related diseases.

    abstract::The quality control (QC) system of the endoplasmic reticulum (ER) is an important monitoring mechanism in the protein maturation process, which ensures export of properly folded proteins from the ER. Incorrectly or incompletely folded proteins are retained in the ER for refolding or degradation by the ER-residing prot...

    journal_title:Acta biochimica et biophysica Sinica

    pub_type: 杂志文章,评审

    doi:10.1111/j.1745-7270.2006.00156.x

    authors: Wu JC,Liang ZQ,Qin ZH

    更新日期:2006-04-01 00:00:00

  • Heat shock protein 90 mediates the apoptosis and autophage in nicotinic-mycoepoxydiene-treated HeLa cells.

    abstract::Heat shock protein 90 (Hsp90) is a fascinating target for cancer therapy due to its significant role in the crossroad of multiple signaling pathways associated with cell proliferation and regulation. Hsp90 inhibitors have the potential to be developed into anti-cancer drugs. Here, we identified nicotinic-mycoepoxydien...

    journal_title:Acta biochimica et biophysica Sinica

    pub_type: 杂志文章

    doi:10.1093/abbs/gmv034

    authors: Sun Y,Xiao S,Chen J,Wang M,Zheng Z,Song S,Zhang L

    更新日期:2015-06-01 00:00:00

  • Endothelial cells modified by adenovirus vector containing nine copies hypoxia response elements and human vascular endothelial growth factor as the novel seed cells for bone tissue engineering.

    abstract::Vascularization is one of the hotspots during the development of new therapeutic strategies for bone tissue engineering, which can alleviate hypoxic circumstance and prevent transplant failure. Vascular endothelial growth factor (VEGF) gene transfection using recombinant adenovirus (Ad) vector can effectively promote ...

    journal_title:Acta biochimica et biophysica Sinica

    pub_type: 杂志文章

    doi:10.1093/abbs/gmx101

    authors: Song X,Shi L,Chen L,Liu X,Qu X,Wang K,Wei F

    更新日期:2017-11-01 00:00:00

  • High glucose inhibits vascular endothelial Keap1/Nrf2/ARE signal pathway via downregulation of monomethyltransferase SET8 expression.

    abstract::Hyperglycemia-mediated reactive oxygen species (ROS) accumulation plays an important role in hyperglycemia-induced endothelial injury. Kelch-like ECH-associated protein 1 (Keap1)/nuclear factor erythroid 2-related factor 2 (Nrf2)/antioxidant response element (ARE) pathway inhibition participates in hyperglycemia-induc...

    journal_title:Acta biochimica et biophysica Sinica

    pub_type: 杂志文章

    doi:10.1093/abbs/gmaa023

    authors: Chen X,Qi J,Wu Q,Jiang H,Wang J,Chen W,Mao A,Zhu M

    更新日期:2020-05-26 00:00:00

  • Poly(ADP-ribose) polymerase 1 inhibition prevents interleukin-1β-induced inflammation in human osteoarthritic chondrocytes.

    abstract::Osteoarthritis (OA) is an age-related joint disease that is characterized by the degeneration of articular chondrocytes. Nuclear enzyme poly(ADP-ribose) polymerase 1 (PARP-1) is associated with inflammation response. We investigated the role of PARP-1 in interleukin-1β (IL-1β)-stimulated human articular chondrocytes a...

    journal_title:Acta biochimica et biophysica Sinica

    pub_type: 杂志文章

    doi:10.1093/abbs/gmv033

    authors: Sun Y,Zhou L,Lv D,Liu H,He T,Wang X

    更新日期:2015-06-01 00:00:00