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1. Full Text Tcf3 is an integral component of the core regulatory circuitry of embryonic stem cells
by Cole, Megan F and Johnstone, Sarah E and Newman, Jamie J and Kagey, Michael H and Young, Richard A
Genes and Development, ISSN 0890-9369, 03/2008, Volume 22, Issue 6, pp. 746 - 755
Embryonic stem (ES) cells have a unique regulatory circuitry, largely controlled by the transcription factors Oct4, Sox2, and Nanog, which generates a gene... 
Tcf3 | Regulatory circuitry | Embryonic stem cells | Wnt pathway | DEVELOPMENTAL REGULATORS | embryonic stem cells | ESCHERICHIA-COLI | SELF-RENEWAL | DEVELOPMENTAL BIOLOGY | BETA-CATENIN | HUMAN BLASTOCYSTS | regulatory circuitry | CELL BIOLOGY | SIGNALING PATHWAY | GENETICS & HEREDITY | GENE-EXPRESSION | MOUSE ES CELLS | DIFFERENTIATION | TRANSCRIPTIONAL REGULATION | Embryonic Stem Cells - metabolism | TCF Transcription Factors - physiology | Homeodomain Proteins - metabolism | RNA, Messenger - metabolism | Wnt Proteins - metabolism | Immunoenzyme Techniques | DNA-Binding Proteins - metabolism | Gene Expression Regulation, Developmental | HMGB Proteins - metabolism | SOXB1 Transcription Factors | Binding Sites | Fibroblasts - metabolism | Nanog Homeobox Protein | Signal Transduction | RNA, Messenger - genetics | Cells, Cultured | Transcription Factor 7-Like 1 Protein | Reverse Transcriptase Polymerase Chain Reaction | Lentivirus | Transcription Factors - metabolism | Animals | Octamer Transcription Factor-3 - metabolism | Fibroblasts - cytology | Mice | Genome | Research | T cell proliferation | Genetic transcription | Analysis | Research Paper
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2. Full Text Core transcriptional regulatory circuitry in human hepatocytes
by Young, Richard A and Fraenkel, Ernest and Jacobsen, Elizabeth S and Odom, Duncan T and Rolfe, P Alexander and Bell, Graeme I and Gifford, David K and Danford, Timothy W and Dowell, Robin D and Nekludova, Lena
Molecular Systems Biology, ISSN 1744-4292, 05/2006, Volume 2, Issue 1, pp. 2006.0017 - n/a
We mapped the transcriptional regulatory circuitry for six master regulators in human hepatocytes using chromatin immunoprecipitation and high‐resolution... 
Autoregulation | Chromatin immunoprecipitation | Regulatory hierarchy | Hepatocyte | Transcriptional regulation | regulatory hierarchy | hepatocyte | transcriptional regulation | BIOCHEMISTRY & MOLECULAR BIOLOGY | ESCHERICHIA-COLI | autoregulation | GENOME | chromatin immunoprecipitation | GENE | EMBRYONIC STEM-CELLS | NETWORK MOTIFS | DIFFERENTIATION | LIVER DEVELOPMENT | BINDING-SITES | Promoter Regions, Genetic | Hepatocytes | Humans | Gene Expression Regulation | Homeostasis | Protein Array Analysis | Transcription, Genetic | Transcription Factors | Regulators | Chromatin | Transcription factors | Immunoprecipitation | Circuits | Liver | Genomes | Gene expression | Metabolism | Hypotheses | DNA microarrays | Binomial distribution | Binding sites | Deoxyribonucleic acid--DNA
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3. Full Text An Update on the Acinetobacter baumannii Regulatory Circuitry
by Wood, Cecily R and Mack, Lydia E and Actis, Luis A
Trends in Microbiology, ISSN 0966-842X, 07/2018, Volume 26, Issue 7, pp. 560 - 562
adapts to different environmental conditions by expressing complex regulatory circuitry. Recent studies revealed that this circuitry includes regulatory... 
persistence | bacterial subpopulations | virulence | Transcriptional regulation | resistance | MICROBIOLOGY | BIOCHEMISTRY & MOLECULAR BIOLOGY | SWITCH | Genes, Bacterial | Genome, Bacterial | Virulence | Acinetobacter baumannii - pathogenicity | Drug Resistance, Bacterial | Host Specificity | Virulence Factors | Acinetobacter baumannii - physiology | Anti-Bacterial Agents - pharmacology | Acinetobacter baumannii - drug effects | Acinetobacter baumannii - genetics | Gene Expression Regulation, Bacterial | Acinetobacter Infections - microbiology
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4. Full Text Cpeb4-Mediated Translational Regulatory Circuitry Controls Terminal Erythroid Differentiation
by Hu, Wenqian and Yuan, Bingbing and Lodish, Harvey F
Developmental Cell, ISSN 1534-5807, 09/2014, Volume 30, Issue 6, pp. 660 - 672
While we have considerable understanding of the transcriptional networks controlling mammalian cell differentiation, our knowledge of posttranscriptional... 
LEUKEMIC-CELLS | MESSENGER-RNA | INITIATION | CPEB-FAMILY | ERYTHROPOIESIS | COMPLEXES | GENOME-WIDE | DEVELOPMENTAL BIOLOGY | PROTEINS | BINDING | EXPRESSION | CELL BIOLOGY | Erythropoiesis | Proto-Oncogene Proteins - metabolism | RNA-Binding Proteins - genetics | Mice, Inbred C57BL | Transcriptional Activation | Erythroblasts - metabolism | GATA1 Transcription Factor - metabolism | DNA-Binding Proteins - metabolism | Transcription Factors - metabolism | Feedback, Physiological | Animals | Basic Helix-Loop-Helix Transcription Factors - metabolism | Gene Expression Regulation, Developmental | Protein Binding | Mice | Erythroblasts - cytology | RNA-Binding Proteins - metabolism | T-Cell Acute Lymphocytic Leukemia Protein 1 | RNA | Analysis | Genetic research | Cell differentiation | Genetic translation | Cells | Protein binding
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5. Full Text CD8+ T Cells Utilize Highly Dynamic Enhancer Repertoires and Regulatory Circuitry in Response to Infections
by He, Bing and Xing, Shaojun and Chen, Changya and Gao, Peng and Teng, Li and Shan, Qiang and Gullicksrud, Jodi A and Martin, Matthew D and Yu, Shuyang and Harty, John T and Badovinac, Vladimir P and Tan, Kai and Xue, Hai-Hui
Immunity, ISSN 1074-7613, 12/2016, Volume 45, Issue 6, pp. 1341 - 1354
Differentiation of effector and memory CD8 T cells is accompanied by extensive changes in the transcriptome and histone modifications at gene promoters;... 
Super enhancers | Enhancers | Central memory | Effector CD8 T cells | Hi-C | Naïve CD8 T cells | Epigenetics | Enhancer-promoter interactome | CD8 T cells | Transcriptional regulatory network | TRANSCRIPTION FACTORS | EFFECTOR | IDENTITY | SUPER-ENHANCERS | MEMORY | SIGNATURES | DISEASE | GENE-EXPRESSION | DIFFERENTIATION | IMMUNOLOGY | INSIGHTS | Computational Biology - methods | Gene Expression Regulation - immunology | Enhancer Elements, Genetic - immunology | Gene Regulatory Networks | Promoter Regions, Genetic - genetics | Cell Differentiation - genetics | Cell Differentiation - immunology | Lymphocyte Activation - genetics | Lymphocyte Activation - immunology | Algorithms | Animals | Lymphocytic choriomeningitis virus | Chromatin Immunoprecipitation | Epigenomics - methods | Enhancer Elements, Genetic - genetics | High-Throughput Nucleotide Sequencing | Mice | Promoter Regions, Genetic - immunology | CD8-Positive T-Lymphocytes - immunology | Arenaviridae Infections - immunology | Disease Models, Animal | Antigens | Pathogens | Cytokines | Lymphocytes | Genomics | Cytotoxicity | T cell receptors | Infections | Genomes | Gene expression | Binding sites
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6. Full Text Modeling disease risk through analysis of physical interactions between genetic variants within chromatin regulatory circuitry
by Corradin, Olivia and Cohen, Andrea J and Luppino, Jennifer M and Bayles, Ian M and Schumacher, Fredrick R and Scacheri, Peter C
Nature Genetics, ISSN 1061-4036, 11/2016, Volume 48, Issue 11, pp. 1313 - 1320
SNPs associated with disease susceptibility often reside in enhancer clusters, or super-enhancers. Constituents of these enhancer clusters cooperate to... 
TRANSCRIPTION FACTORS | IMMUNE-RESPONSE | ELEMENTS | MULTIPLE-SCLEROSIS | SUPER-ENHANCERS | CELL IDENTITY GENES | GENETICS & HEREDITY | EXPRESSION | CANCER | LOCUS | GENOME-WIDE ASSOCIATION | Genetic Variation | Inheritance Patterns | Genetic Predisposition to Disease | Genome-Wide Association Study | Risk Assessment | Regulatory Elements, Transcriptional | Humans | Gene Expression Regulation | Chromatin - genetics | Linkage Disequilibrium | Genome-wide association studies | Genetic susceptibility | Genetic research | Heritability | Genetic aspects | Research | Single nucleotide polymorphisms | Identification and classification | Health aspects | Methods | Studies | Haplotypes | Lupus | Hypotheses | Multiple sclerosis | Disease | Cooperation | Influence | Genomes | Autoimmune diseases | Gene expression
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7. Full Text A systems approach reveals regulatory circuitry for Arabidopsis trichome initiation by the GL3 and GL1 selectors
by Morohashi, Kengo and Grotewold, Erich
PLoS Genetics, ISSN 1553-7390, 02/2009, Volume 5, Issue 2, p. e1000396
Position-dependent cell fate determination and pattern formation are unique aspects of the development of plant structures. The establishment of single-celled... 
ENCODES | FIDDLEHEAD | EPIDERMAL DIFFERENTIATION | GENE | MYB TRANSCRIPTION FACTORS | THALIANA | GENETICS & HEREDITY | BHLH PROTEINS | CHIP-CHIP | CELL-DIFFERENTIATION | MICROARRAY DATA | Plant Epidermis - growth & development | Arabidopsis Proteins - genetics | Basic Helix-Loop-Helix Transcription Factors - genetics | Arabidopsis - growth & development | Arabidopsis - cytology | Plant Epidermis - genetics | DNA-Binding Proteins - genetics | Gene Regulatory Networks | Plant Epidermis - metabolism | Plant Leaves - cytology | Arabidopsis - metabolism | Arabidopsis - genetics | Arabidopsis Proteins - metabolism | DNA-Binding Proteins - metabolism | Basic Helix-Loop-Helix Transcription Factors - metabolism | Plant Leaves - genetics | Plant Leaves - metabolism | Gene Expression Regulation, Developmental | Plant Leaves - growth & development | Gene Expression Regulation, Plant | Plant Epidermis - cytology | Chromatin Immunoprecipitation - methods | Physiological aspects | Genetic aspects | Trichomes | Research | Genetic regulation | Arabidopsis | Cluster analysis | Leaves | Cyclin-dependent kinases | Regulation | Genomes | Gene expression | Kinases | Experiments
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8. Full Text A genome-scale analysis of the cis-regulatory circuitry underlying sonic hedgehog-mediated patterning of the mammalian limb
by Vokes, Steven A and Ji, Hongkai and Wong, Wing H and McMahon, Andrew P
Genes and Development, ISSN 0890-9369, 10/2008, Volume 22, Issue 19, pp. 2651 - 2663
Sonic hedgehog (Shh) signals via Gli transcription factors to direct digit number and identity in the vertebrate limb. We characterized the Gli-dependent... 
Sonic hedgehog | Morphogen | Gli | Limb | Cis-regulatory network | limb | CELLS | gli | GREMLIN EXPRESSION | cis-regulatory network | DEVELOPMENTAL BIOLOGY | GLI3 | FEEDBACK LOOP | CELL BIOLOGY | BUD | morphogen | EXON ARRAYS | SHH | IN-VIVO | GENETICS & HEREDITY | sonic hedgehog | TRANSCRIPTIONAL REPRESSOR | VERTEBRATE LIMB | Genomics | Zinc Finger Protein Gli3 | Hedgehog Proteins - physiology | Gene Regulatory Networks | Genetic Complementation Test | Extremities - embryology | Intercellular Signaling Peptides and Proteins - physiology | Chromatin Immunoprecipitation | Hedgehog Proteins - genetics | Female | Basic Helix-Loop-Helix Transcription Factors - physiology | Nerve Tissue Proteins - physiology | Transcription Factors - physiology | Basic Helix-Loop-Helix Transcription Factors - genetics | Signal Transduction | Intercellular Signaling Peptides and Proteins - genetics | Kruppel-Like Transcription Factors - physiology | Mice, Transgenic | Binding Sites - genetics | Transcription Factors - genetics | Nerve Tissue Proteins - genetics | Body Patterning - physiology | Pregnancy | Animals | Enhancer Elements, Genetic | Models, Biological | Mice | Body Patterning - genetics | Kruppel-Like Transcription Factors - genetics | Positive Regulatory Domain I-Binding Factor 1 | Analysis | Genetic aspects | Genetic transcription | Gene expression | Genetic regulation | DNA-ligand interactions | Extremities (Anatomy) | Research Paper
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9. Full Text Regulatory circuitry of TWEAK-Fn14 system and PGC-1α in skeletal muscle atrophy program
by Hindi, Sajedah M and Mishra, Vivek and Bhatnagar, Shephali and Tajrishi, Marjan M and Ogura, Yuji and Yan, Zhen and Burkly, Linda C and Zheng, Timothy S and Kumar, Ashok
FASEB Journal, ISSN 0892-6638, 2014, Volume 28, Issue 3, pp. 1398 - 1411
Skeletal muscle wasting attributed to inactivity has significant adverse functional consequences. Accumulating evidence suggests that peroxisome... 
NF-κB | Mitochondria | MAFBx | Ubiquitinproteasome system | MuRF1 | SP-1 | Denervation | TRANSCRIPTIONAL COACTIVATOR PGC-1-ALPHA | KAPPA-B ACTIVATION | PROTEIN | denervation | mitochondria | DNA-DELETION MUTATIONS | BIOCHEMISTRY & MOLECULAR BIOLOGY | NF-B | TARGETED ABLATION | SARCOPENIA | CELL BIOLOGY | ubiquitin-proteasome system | PGC-1 COACTIVATORS | TRAF6 | BIOLOGY | CONTRIBUTES | EXPRESSION | Tumor Necrosis Factors - physiology | Cytokine TWEAK | Transcription Factors - physiology | Animals | Muscular Atrophy - pathology | Peroxisome Proliferator-Activated Receptor Gamma Coactivator 1-alpha | Mice, Transgenic | Electrophoretic Mobility Shift Assay | Mice | Muscle, Skeletal - pathology | TWEAK Receptor | Receptors, Tumor Necrosis Factor - physiology | Research Communications
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10. Full Text A regulatory circuitry locking pluripotent sternness to embryonic stem cell: Interaction between threonine catabolism and histone methylation
by Chen, GH and Wang, J
SEMINARS IN CANCER BIOLOGY, ISSN 1044-579X, 08/2019, Volume 57, pp. 72 - 78
Mouse embryonic stem cell (ESC) is a prototype of pluripotent stem cell that undergoes endless self-renewal in culture without losing the pluripotency, the... 
DNA METHYLATION | GROUND-STATE | CHROMATIN-STRUCTURE | Histone methylation | Embryonic stem cell | SELF-RENEWAL | MOUSE DEVELOPMENT | Set1A | ONCOLOGY | Stem cell metabolism | LYSINE-9 METHYLATION | KINETIC MECHANISM | TDH | COMPASS FAMILY | TRANSCRIPTIONAL REGULATION | H3K4 TRIMETHYLATION
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11. YY1-C/EBPα-miR34a regulatory circuitry is involved in renal cell carcinoma progression
by Weng, Wenhao and Weng, Wenhao and Wang, Minli and Xie, Suhong and Xie, Suhong and Long, Yin and Li, Feng and Sun, Fenyong and Yu, Yongchun and Yu, Yongchun and Li, Zhi and Li, Zhi
Oncology Reports, ISSN 1021-335X, 2014, Volume 31, Issue 4, pp. 1921 - 1927
Renal cell carcinoma (RCC) is a common urological malignancy. It remains unclear, however, whether Yin Yang 1 (YY1) plays a functional role in the development... 
YY1 | C/EBPα | MiR-34a | Renal cell carcinoma | miR-34a | C/EBP alpha | TRANSCRIPTIONAL REPRESSION | C-MYC | CANCER | renal cell carcinoma | YIN YANG 1 | C/EBP-ALPHA | ONCOLOGY | GENE-EXPRESSION | ADENOVIRUS E1A | TUMOR-SUPPRESSOR | CCAAT-Enhancer-Binding Protein-alpha - metabolism | Kidney Neoplasms - genetics | Carcinoma, Renal Cell - pathology | Humans | Carcinoma, Renal Cell - genetics | MicroRNAs - metabolism | Kidney Neoplasms - metabolism | YY1 Transcription Factor - genetics | YY1 Transcription Factor - metabolism | Blotting, Western | Disease Progression | Carcinoma, Renal Cell - metabolism | CCAAT-Enhancer-Binding Protein-alpha - genetics | Kidney Neoplasms - pathology | Signal Transduction - physiology | MicroRNAs - genetics | Gene Expression Regulation, Neoplastic - physiology | Real-Time Polymerase Chain Reaction
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12. Full Text Positive autoregulation of cI is a dispensable feature of the phage lambda gene regulatory circuitry
by Michalowski, CB and Little, JW
JOURNAL OF BACTERIOLOGY, ISSN 0021-9193, 09/2005, Volume 187, Issue 18, pp. 6430 - 6442
Complex gene regulatory circuits contain many features that are likely to contribute to their operation. It is unclear; however, whether all these features are... 
PRM PROMOTER | SYSTEM | MECHANISM | BACTERIOPHAGE-LAMBDA | ESCHERICHIA-COLI | MICROBIOLOGY | TRANSCRIPTIONAL ACTIVATION FUNCTION | MUTATIONS | REPRESSOR | P-RM | BINDING | Repressor Proteins - physiology | DNA-Binding Proteins - physiology | Gene Expression Regulation, Viral | Genes, Regulator | Viral Proteins - physiology | Bacteriophage lambda - physiology | Bacteriophage lambda - genetics | Viral Regulatory and Accessory Proteins
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13. Full Text Synthetic control systems for high performance gene expression in mammalian cells
by Lillacci, Gabriele and Benenson, Yaakov and Khammash, Mustafa
Nucleic Acids Research, ISSN 0305-1048, 10/2018, Volume 46, Issue 18, pp. 9855 - 9863
Abstract Tunable induction of gene expression is an essential tool in biology and biotechnology. In spite of that, current induction systems often exhibit... 
TRANSCRIPTIONAL REGULATORY CIRCUITRY | DESIGN | BIOCHEMISTRY & MOLECULAR BIOLOGY | Synthetic Biology and Bioengineering
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14. Full Text Control of the Embryonic Stem Cell State
by Young, Richard A
Cell, ISSN 0092-8674, 2011, Volume 144, Issue 6, pp. 940 - 954
Embryonic stem cells and induced pluripotent stem cells hold great promise for regenerative medicine. These cells can be propagated in culture in an... 
RNA-POLYMERASE-II | LONG NONCODING RNA | BIOCHEMISTRY & MOLECULAR BIOLOGY | TRANSCRIPTIONAL REGULATORY CIRCUITRY | SELF-RENEWAL | DE-LANGE-SYNDROME | MAMMALIAN MEDIATOR COMPLEX | LEUKEMIA INHIBITORY FACTOR | MOUSE ES CELLS | POLYCOMB TARGET GENES | PROTEIN-INTERACTION NETWORK | CELL BIOLOGY | Pluripotent Stem Cells - metabolism | Transcription Factors - metabolism | Chromatin - metabolism | Embryonic Stem Cells - metabolism | Animals | Embryonic Stem Cells - cytology | Pluripotent Stem Cells - cytology | Signal Transduction | Humans | Gene Expression Regulation | Animal genetics | Embryonic stem cells | Gene expression | Analysis
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