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Identification of Target Genes and transcription factors Implicated in Translation-Dependent Retrograde Sig- naling in Arabidopsis

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Molecular Plant 2014年第7期7卷 1228-1247页

作者： Dario Leister Isidora Romani Lukas Mittermayr Francesca Paieri Elena Fenino Tatjana Kleine Plant Molecular Biology (Botany) Department Biology I Ludwig-Maximilians-University Munich Gro0haderner Str. 2 D-82152Martinsried Germany

Changes in organellar gene expression （OGE） trigger retrograde signaling. The molecular dissection of OGE-dependent retrograde signaling based on analyses of mutants with altered OGE is complicated by compensatory responses that mask the primary signaling defect and by secondary effects that influence other retrograde signaling pathways. Therefore, to identify the earliest effects of altered OGE on nuclear transcript accumulation, we have induced OGE defects in adult plants by ethanol-dependent repression of PRORS1, which encodes a prolyl-tRNA synthetase located in chloroplasts and mitochondria. After 32 h of PRORS1 repression, the translational capacity of chloroplasts was reduced, and this effect subsequently intensified, while basic photosynthetic parameters were still unchanged at 51 h. Analysis of changes in whole-genome transcriptomes during exposure to ethanol revealed that induced PRORS1 silencing affects the expression of 1020 genes in all. Some of these encode photosynthesis-related proteins, including several down-regulated light-harvesting chlorophyll a/b binding （LHC） proteins. Interestingly, genes for presumptive endoplasmic reticulum pro- teins are transiently up-regulated. Furthermore, several NAC-domain-containing proteins are among the transcription factors regulated. Candidate cis-acting elements which may coordinate the transcriptional co-regulation of genes sets include both G-box variants and sequence motifs with no similarity to known plant c/s-elements.

关键词： Arabidopsis chloroplast mitochondrion retrograde signaling target genes transcription factors cis-elements.

SQUAMOSA Promoter-Binding Protein-Like transcription factors:Star Players for Plant Growth and Development

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Journal of Integrative Plant Biology 2010年第11期52卷 946-951页

作者： Xiaobo Chen Zenglin Zhang Danmei Liu Kai Zhang Aili Li Long Mao National Key Facility for Crop Gene Resources and Genetic Improvement (NFCRI) MOA Key Laboratory of Crop Germplasm & BiotechnologyInstitute of Crop ScienceChinese Academy of Agricultural Sciences (CAAS)Beijing 100081China

SQUAMOSA Promoter-Binding Protein-Like （SPL） genes encode plantspecific transcription factors that play important roles in plant phase transition,flower and fruit development,plant architecture,gibberellins signaling,sporogenesis,and response to copper and fungal toxins.In Arabidopsis,many SPL genes are post-transcriptionally regulated by the microRNA （miRNA） miR156,among which AtSPL9 in turn positively regulates the expression of the second miRNA miR172.This miR156AtSPL9-miR172 regulatory pathway plays critical roles during juvenile to adult leaf development and the miR156-SPLs feedback interaction persists all through the plant development,which may be conserved in other plants.In the present paper,we provide a concise review on the most recent progress in the regulatory mechanisms associated with plant SPL transcription factors,especially in relation to miRNAs.The potential application of these discoveries in agriculture is briefly discussed.

关键词： transcription factors transcription Plants Planting Genes Regulations

A High-Throughput Screening System for Arabidopsis transcription factors and Its Application to Med25-Dependent transcriptional Regulation

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Molecular Plant 2011年第3期4卷 546-555页

作者： Bin Oua Kang-Quan Yin Sai-Nan Liu Yan Yang Tren Gu Jennifer Man Wing Hui Li Zhang Jin Miao Youichi Kondou Minami Matsui Hong-Ya Gu Li-Jia Qu National Laboratory for Protein Engineering and Plant Genetic Engineering College of Life Sciences Peking University Beijing 100871 People's Republic ofChina Plant Science Center RIKEN Yokohama Institute 1-7-22 Suehiro-cho Tsurumi-ku Yokohama City Kanagawa 230-0045 Japan The National Plant Gene Research Center (Beijing) Beijing 100101 People's Republic of China

The activities of transcription factors （TFs） require interactions with specific DNA sequences and other reg- ulatory proteins. To detect such interactions in Arabidopsis, we developed a high-throughput screening system with a Gateway-compatible Gal4-AD-TF library of 1589 Arabidopsis TFs, which can be easily screened by mating-based yeast-one-hybrid （YIH） and yeast-two-hybrid （Y2H） methods. The efficiency of the system was validated by examining two well-characterized TF-DNA and TF-protein interactions： the CHE-CCA1 promoter interaction by YIH and NPR1-TGAs interactions by Y2H. We used this system to identify eight TFs that interact with a Mediator subunit, Med25, a key reg- ulator in JA signaling. We identified five TFs that interacted with the GCC-box cis-element in the promoter of PDF1.2, a downstream gene of Med25. We found that three of these TFs, all from the AP2-EREBP family, interact directly both with Med25 and the GCC-box of PDF1.2, suggesting that Med25 regulates PDF1.2 expression through these three TFs. These results demonstrate that this high-throughput Y1H/Y2H screening system is an efficient tool for studying transcrip- tional regulation networks in Arabidopsis. This system will be available for other Arabidopsis researchers, and thus it provides a vital resource for the Arabidopsis community.

关键词： transcription factors Arabidopsis yeast-one-hybrid yeast-two-hybrid Med25.

Molecular mechanisms of the suppression of axon regeneration by KLF transcription factors

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Neural Regeneration Research 2014年第15期9卷 1418-1421页

作者： Akintomide Apara Jeffrey L.Goldberg University of Miami Miller School of Medicine MiamiFL USA Shiley Eye CenterUniversity of California San Diego La JollaCA USA

Molecular mechanisms of the Kruppel-like family of transcription factors （KLFs） have been studied more in proliferating cells than in post-mitotic cells such as neurons. We recently found that KLFs regulate intrinsic axon growth ability in central nervous system （CNS） neurons in- cluding retinal ganglion cells, and hippocampal and cortical neurons. With at least 15 of 17 KLF family members expressed in neurons and at least 5 structurally unique subfamilies, it is import- ant to determine how this complex family functions in neurons to regulate the intricate genetic programs of axon growth and regeneration. By characterizing the molecular mechanisms of the KLF family in the nervous system, including binding partners and gene targets, and comparing them to defined mechanisms defined outside the nervous system, we may better understand how KLFs regulate neurite growth and axon regeneration.

关键词： optic nerve regeneration axon growth retina retinal ganglion cells spinal cord transcription factors

Culture conditions for equine bone marrow mesenchymal stem cells and expression of key transcription factors during their differentiation into osteoblasts

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Journal of Animal Science and Biotechnology 2014年第2期5卷 163-172页

作者： Elizabeth R A Glynn Alfredo Sanchez Londono Steven A Zinn Thomas A Hoagl Kristen E Govoni Department of Animal Science University of Connecticut3636 Horsebarn Road Ext.Unit 4040StorrsCT 06269-4040USA Department of Environmental and Population Health Tufts University North GraftonMA 01536USA

Background： The use of equine bone marrow mesenchymal stem cells （BMSC） is a novel method to improve fracture healing in horses. However, additional research is needed to identify optimal culture conditions and to determine the mechanisms involved in regulating BMSC differentiation into osteoblasts. The objectives of the experiments were to determine： 1） if autologous or commercial serum is better for proliferation and differentiation of equine BMSC into osteoblasts, and 2） the expression of key transcription factors during the differentiation of equine BMSC into osteoblasts. Equine BMSC were isolated from the sterna of 3 horses, treated with purchased fetal bovine serum （FBS） or autologous horse serum （HS）, and cell proliferation determined. To induce osteoblast differentiation, cells were incubated with L-ascorbic acid-2-phosphate and glycerol-2-phosphate in the presence or absence of human bone morphogenetic protein2 （BMP2）, dexamethasone （DEX）, or combination of the two. Alkaline phosphatase （ALP） activity, a marker of osteoblast differentiation, was determined by ELISA. Total RNA was isolated from differentiating BMSC between d 0 to 18 to determine expression of runt-reloted tronscrJption foctor2 （Runx2）, osterix （Osx）, and T-box3 （Tbx3）. Data were analyzed by ANOVA. Results： Relative to control, FBS and HS increased cell number （133 ± 5 and 116 ± 5%, respectively; P 〈 0.001） and 5-bromo- 2＇-deoxyuridine （BrdU） incorporation （167 ± 6 and 120 ± 6%, respectively; P 〈 0.001）. Treatment with DEX increased ALP activity compared with control （1,638 ± 38%; P 〈 0.001）. In the absence and presence of Dex, BMP-2 did not alter ALP activity （P 〉 0.8）. Runt-reloted transcription foctor2 expression increased 3-fold （P 〈 0.001） by d 6 of culture. Osterix expression increased 94old （P 〈 0.05） by d 18 of culture. Expression of Tbx3 increased 1.8-fold at d 3 （P 〈 0.01）; however expression was reduced 4-fold at d 18 （P 〈 0.01）. Conclusions： Dexamethasone, but not BMP-2, is required for differentiation of equine BMSC into osteo

关键词： Bone marrow mesenchymal stem cells Cell culture Equine Osteoblasts transcription factors

Oocyte-associated transcription factors in reprogramming after somatic cell nuclear transfer:a review

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Frontiers of Agricultural Science and Engineering 2014年第2期1卷 104-113页

作者： Fengxia YIN Hui LIU Shorgan BOU Guangpeng LI The Key Laboratory of National Education Ministry for Mammalian Reproductive Biology and Biotechnology the College of Life SciencesInner Mongolia UniversityHohhot 010070China

Oocytes are unique cells with the inherent capability to reprogram nuclei.The reprogramming of the somatic nucleus from its original cellular state to a totipotent state is essential for term development after somatic cell nuclear transfer.The nuclear-associated factors contained within oocytes are critical for normal fertilization by sperm or for somatic cell nuclear reprogramming.The chromatin of somatic nuclei can be reprogrammed by factors in the egg cytoplasm whose natural function is to reprogram sperm chromatin.The oocyte first obtains its reprogramming capability in the early fetal follicle,and then its capacity is enriched in the late growth phase and reaches its highest capability for reprogramming as fully-grown germinal vesicle oocytes.The cytoplasmic milieu most likely contains all of the specific transcription and/or reprogramming factors necessary for cellular reprogramming.Certain transcription factors in the cytoplast may be critical as has been demonstrated for induced pluripotent stem cells.The maternal pronucleus exerts a predominant,transcriptiondependent effect on embryo cytofragmentation,with a lesser effect imposed by the ooplasm and the paternal pronucleus.With deep analysis of transcriptomics in oocytes and early developmental stage embryos more maternal transcription factors inducing cellular reprogramming will be identified.

关键词： nuclear reprogramming somatic cell transcription factors transcriptomics

transcription regulators differentiate mesenchymal stem cells into chondroprogenitors,and their in vivo implantation regenerated the intervertebral disc degeneration

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World Journal of Stem Cells 2022年第2期14卷 163-182页

作者： Shumaila Khalid Sobia Ekram Asmat Salim G.Rasul Chaudhry Irfan Khan Dr.Panjwani Center for Molecular Medicine and Drug Research International Center for Chemical and Biological SciencesUniversity of KarachiKarachi 75270SindhPakistan Department of Biological Sciences Oakland UniversityRochesterMI 48309United States

BACKGROUND Intervertebral disc degeneration(IVDD)is the leading cause of lower back pain.Disc degeneration is characterized by reduced cellularity and decreased production of extracellular matrix(ECM).Mesenchymal stem cells(MSCs)have been envisioned as a promising treatment for degenerative illnesses.Cell-based therapy using ECM-producing chondrogenic derivatives of MSCs has the potential to restore the functionality of the intervertebral disc(IVD).AIM To investigate the potential of chondrogenic transcription factors to promote differentiation of human umbilical cord MSCs into chondrocytes,and to assess their therapeutic potential in IVD regeneration.METHODS MSCs were isolated and characterized morphologically and immunologically by the expression of specific markers.MSCs were then transfected with Sox-9 and Six-1 transcription factors to direct differentiation and were assessed for chondrogenic lineage based on the expression of specific markers.These differentiated MSCs were implanted in the rat model of IVDD.The regenerative potential of transplanted cells was investigated using histochemical and molecular analyses of IVDs.RESULTS Isolated cells showed fibroblast-like morphology and expressed CD105,CD90,CD73,CD29,and Vimentin but not CD45 antigens.Overexpression of Sox-9 and Six-1 greatly enhanced the gene expression of transforming growth factor beta-1 gene,BMP,Sox-9,Six-1,and Aggrecan,and protein expression of Sox-9 and Six-1.The implanted cells integrated,survived,and homed in the degenerated intervertebral disc.Histological grading showed that the transfected MSCs regenerated the IVD and restored normal architecture.CONCLUSION Genetically modified MSCs accelerate cartilage regeneration,providing a unique opportunity and impetus for stem cell-based therapeutic approach for degenerative disc diseases.

关键词： Intervertebral disc degeneration Human umbilical cord transcription factors Mesenchymal stem cells Gene expression Regeneration

Effects of the Ratio of Lysine to Digestible Energy Level in the Diet on the Expression and Activity of transcription factors Involved in Lipogenesis in Rongchang Pigs

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Journal of Animal Science and Biotechnology 2010年第3期1卷 165-174页

作者： Yuan Lu Xiaolei Yang Defa Li Jingdong Yin Ministry of Agriculture Feed Industry Centre State Key Laboratory of Animal Nutrition China Agricultural University Beijing 100193 China College of Animal Science and Medicine Inner Mongolia Agricultural University Huhehot Inner Mongolia010018 China

This study was conducted to determine the effects of varying the ratio of lysine to digestible energy level On the activity and gene expression of the transcription factors peroxisome proliferator-activated receptor-γ （PPAR-γ） and CCAAT/enhancer-binding protein-or and -β （C/EBP-α and C/EBP-β） to better understand the regulatory mechanisms controlling adipogenesis in fat and muscle tissue of the Rongchang pig. A total of 144 castrated Rongchang pigs weighing approximately 20 kg were used in a 2 ×2 factorial design experiment. Diets were formulated to contain a high （14.22 MJ/kg） or low （13.11 MJ/kg） digesti- ble energy （DE） level. Within each energy level, pigs were fed diets containing a high lysine： DE ratio （0.67,0. 53, or 0. 42） or a low lysine ： DE ratio （0.49,0.38 ,or 0.30） during the periods from 20 to 50 kg, 50 to 80 kg, and 80 kg to slaughter, respectively. Each diet was fed to six replicate pens, each containing nine pigs. When the pigs reached average live weights of 20,35,60, and 90 kg ,one pig from each of the replicates was chosen at random and slaughtered.Samples of back fat and longissimus dorsi muscle were collected for the assessment of transcriptional factor. The results showed that feeding a high DE level significantly increased （ P 〈 0.05 ） the expression of PPAR-T at 60 and 90 kg in muscle and at 35,60, and 90 kg in back fat. Energy level also significantly increased the expression of C/EBP-fl at 35 and 60 kg in both muscle and back fat （ P 〈 0.05 ）. Higher dieta- ry lysine increased the expression of C/EBP-fl in muscle at 35 and 90 kg （ P 〈 0.05）, but decreased the expression in back fat at 35 （P = 0.03 ） and 90 kg （P = 0.09）. The lysine level increased the expression of PPAR-3~ in muscle at 60 kg only. Energy level and lysine content had no significant effects on promote the activity of PPAR-γ, C/EBP-α, or C/EBP-β either in muscle or in back fat at any level of the body weights tested. Collectively, these data indicated that dietary energy density and lysine level were equally important for

关键词： activity adipogenesis digestible energy gene expression lysine pigs transcription factors

Dysregulated miRNA Associated with transcription factors of Insulin Gene Expression in Chronic Pancreatitis

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Open Journal of Endocrine and Metabolic Diseases 2016年第10期6卷 205-227页

作者： K. Murali Manohar M. Sasikala P. Pavan Kumar G. V. Rao D. Nageshwar Reddy Institute of Basic Science and Translational Research Asian Healthcare Foundation Hyderabad India Asian Institute of Gastroenterology Somajiguda Hyderabad India

Background/Aim: MicroRNAs with regulatory functions in gene expression are implicated in different diseases. The present study investigated differentially expressed miRNAs that possibly influence transcription factors involved in insulin gene expression in Chronic Pancreatitis (CP) employing bioinformatics approaches. Methods: Pancreatic tissues were collected from CP patients undergoing partial pancreatectomy (n = 16) and controls (n = 15) undergoing resections for non-pancreatic malignancies. MiRNA profiles obtained using microarrays were validated by qRT-PCR. Target search involving miRWalk and TarBase as well as functional annotation employing KEGG (Kyoto encyclopedia of genes and genomes) and DAVID (Database for Annotation) databases were performed. Ingenuity pathway analysis (IPA) was used to construct networks relating miRNAs to their target genes. mRNA and proteins related to insulin gene transcription factors and hormones were evaluated by qRT-PCR and western blotting followed by confirmation upon immunofluorescent staining. Results: Microarray data revealed 10 up-regulated and 15 down-regulated miRNAs in CP as compared to controls (Log2 FC > 2). Bioinformatic analysis showed 8399 target genes and KEGG pathway analysis suggested a role for the dysregulated miRNAs in modulating cytokine signaling, fibrosis, JAK-STAT signaling and insulin synthesis. IPA analysis suggested a simplified network attributing dysregulated miRNAs to NFκB-dependent cytokine signaling. Further, associations could be noted between miRNA 200b with Maf A, 138-1 with Neuro D and 27b with FoxO1. Decreases in mRNA levels of Pdx1, Neuro D and increases of Maf A and FoxO1 transcription factors could be noted (P Conclusion: Our results identified dysregulation of miRNAs 138-1, 27b and 200b which were found to be associated with insulin gene transcription factors Neuro D, FoxO1 and Maf A respectively.

关键词： MicroRNAs transcription factors Networks β-Cell Dysfunction