Keywords: Trophoblast invasion; Cis-regulation; Gene-enhancer network;
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Review articleOrigin and evolution of the metazoan non-coding regulatory genome
Keywords: Evolution; Gene regulation; Metazoans; Complexity; Cis-regulation; Non-coding RNAs; Enhancers; Multicellularity; Holozoans;
Favorable genomic environments for cis-regulatory evolution: A novel theoretical framework
Keywords: Cis-regulation; Transcription factor binding site (TFBS); Enhancer evolution; Chromatin environment; Transposable element; Enhancer overprinting
Mutagenesis of GATA motifs controlling the endoderm regulator elt-2 reveals distinct dominant and secondary cis-regulatory elements
Keywords: Endoderm; Cis-regulation; Promoter; smFISH; Transcription; GATA; C. elegans;
Understanding how cis-regulatory function is encoded in DNA sequence using massively parallel reporter assays and designed sequences
Keywords: cis-regulation; Massively parallel reporter assays; Genomics; Enhancers;
Recent advances in genomics and transcriptomics of cnidarians
Keywords: Cnidaria; Genome evolution; cis-Regulation; Transcriptome; Nematostella; Hydra;
Transcription factors: specific DNA binding and specific gene regulation
Keywords: response element; transcription factor; cis-regulation; gene expression; transcription; ChIP-seq;
The expansion of body coloration involves coordinated evolution in cis and trans within the pigmentation regulatory network of Drosophila prostipennis
Keywords: Morphological evolution; Gene regulatory network; Co-expression; Drosophila; Pigmentation; cis-regulation;
Transcriptional control of early vein expression of CYCA2; 1 and CYCA2;4 in Arabidopsis leaves
Keywords: Brassicaceae; Arabidopsis thaliana; Leaf development; Vascular patterning; Procambium; Cis-regulation;
In silico identification and in vivo validation of a set of evolutionary conserved plant root-specific cis-regulatory elements
Keywords: Root; Cis-regulation; Gene regulation; Development; Arabidopsis;
Cis-regulatory logic driving glial cells missing: Self-sustaining circuitry in later embryogenesis
Keywords: Echinoid; Pigment cell; Mesoderm; cis-regulation; Autoregulatory; Intergenic feedback loop
Differential allelic expression of c.1568C > A at UGT2B15 is due to variation in a novel cis-regulatory element in the 3′UTR
Keywords: UGT, UDP-glucuronosyltransferase; DAE, differential allelic expression; AI, allelic imbalance; miRNA, microRNA; 3′UTR, 3′ untranslated region; LD, linkage disequilibrium; CNV, copy number variationUGT2B15; Differential allelic expression; cis-regulation;
Promoting the promoter
Keywords: cis-Regulation; Evolutionary and developmental biology; Integrative evolution; Plant development; Population genetics; Transcription
Expression of the Distalless-B gene in Ciona is regulated by a pan-ectodermal enhancer module
Keywords: Ascidians; Dlx genes; Cis-regulation; Ci-Dll-B; Ci-fog;
Molecular dissection of cis-regulatory modules at the Drosophila bithorax complex reveals critical transcription factor signature motifs
Keywords: Drosophila; Bithorax complex; cis-regulation; Evolution; Enhancer; Transcription factor; Homeotic gene;
Precise cis-regulatory control of spatial and temporal expression of the alx-1 gene in the skeletogenic lineage of s. purpuratus
Keywords: Alx1 gene; Cis-regulation; Skeletogenic micromere lineage; Gene-regulatory network; Tagged reporter assay
When needles look like hay: How to find tissue-specific enhancers in model organism genomes
Keywords: Cis-regulatory element; Fish; Zebrafish; Medaka; Transgenesis; Cis-regulation; Transcriptional regulation; Non-coding elements; Genome analysis; Enhancers;
A cis-Phase Interaction Study of Genetic Variants Within the MAOA Gene in Major Depressive Disorder
Keywords: cis-regulation; expression; gene internal interaction; major depressive disorder; MAOA gene
Cis-regulatory analysis of the sea urchin pigment cell gene polyketide synthase
Keywords: Cis-regulation; Pigment cell; Sea urchin; Polyketide synthase; Glial cells missing; Notch; Differentiation; Mesoderm; Transcriptional regulation; Gene regulatory network;
Comparing anterior and posterior Hox complex formation reveals guidelines for predicting cis-regulatory elements
Keywords: Hox; Extradenticle; Homothorax; Transcription factor; cis-regulation;
Cis-regulatory characterization of sequence conservation surrounding the Hox4 genes
Keywords: Hox; Cis-regulation; CNE; Zebrafish; GFP; Transgenesis; Amphioxus; Sequence conservation; Cluster;
Control of BMP gene expression by long-range regulatory elements
Keywords: BMP; Enhancer; cis-Regulation; Skeletal development
Development and evolution of insect pigmentation: Genetic mechanisms and the potential consequences of pleiotropy
Keywords: Drosophila; Lepidoptera; Melanization; cis-regulation; Variation
Similar regulatory logic in Ciona intestinalis for two Wnt pathway modulators, ROR and SFRP-1/5
Keywords: Tunicate; Wnt pathway; Cis-regulation; FoxA target; Anterior ectoderm
A novel conserved evx1 enhancer links spinal interneuron morphology and cis-regulation from fish to mammals
Keywords: Spinal cord; V0 interneuron; evx1; Enhancer; Cis-regulation; Pufferfish; Zebrafish; Chick; Mouse; Rat
Identification of an ancient Bmp4 mesoderm enhancer located 46 kb from the promoter
Keywords: Bmp4; Mesoderm; Enhancer; Bacterial artificial chromosome; Cis-regulation
The evolutionarily conserved leprecan gene: Its regulation by Brachyury and its role in the developing Ciona notochord
Keywords: AP; anterior-posterior; bp; base pair(s); CNS; central nervous system; ER; endoplasmic reticulum; EST; expressed sequence tag; GFP; green fluorescent protein; GST; glutathione S-transferase; kb; kilobase(s), or 1000 base pairs; PCR; polymerase chain rea
Identification of cis-regulatory elements from the C. elegans T-box gene mab-9 reveals a novel role for mab-9 in hypodermal function
Keywords: C. elegans; T-box; mab-9; Hypodermis; cis-regulation;
The surprising complexity of the transcriptional regulation of the spdri gene reveals the existence of new linkages inside sea urchin's PMC and Oral Ectoderm Gene Regulatory Networks
Keywords: Spdeadringer; spdri; Sea urchin embryo; cis-regulation; Endomesoderm; PMCs; Oral Ectoderm; Gene Regulatory Networks;
Regulation of spblimp1/krox1a, an alternatively transcribed isoform expressed in midgut and hindgut of the sea urchin gastrula
Keywords: Strongylocentrotus purpuratus; Lytechinus variegatus; Blimp1/krox; Spblimp1/krox1a; Cis-regulation; Gut specific regulatory module
Cis-regulation of the amphioxus engrailed gene: Insights into evolution of a muscle-specific enhancer
Keywords: Enhancer; Cis-regulation; Branchiostoma; Muscle evolution; Conserved non-coding DNA; Ciona; Lancelet; Amphioxus; Engrailed
The function and regulation of Ultrabithorax in the legs of Drosophila melanogaster
Keywords: Cis-regulation; Evolution; Drosophila; Leg; Trichome; Ultrabithorax
Condition-specific coregulation with cis-regulatory motifs and modules in the mouse genome
Keywords: Coregulation; Cis-regulation; Motif; Module; Cluster; Microarray; Transcription factor; Stress response; Gene expression; Mouse
Unraveling cis-regulatory mechanisms at the abdominal-A and Abdominal-B genes in the Drosophila bithorax complex
Keywords: Drosophila; Bithorax complex; Insulator; Promoter; Enhancer; cis-regulation; Nongenic; Transcription;
Evidence for motoneuron lineage-specific regulation of Olig2 in the vertebrate neural tube
Keywords: Motor neuron; Lineage mapping; Oligodendrocyte; Olig2; Transcription factor; Bacterial Artificial Chromosome (BAC); cis-regulation; Enhancer; Neural tube;
Complementation rescue of Pdx1 null phenotype demonstrates distinct roles of proximal and distal cis-regulatory sequences in pancreatic and duodenal expression
Keywords: Pancreas; β Cell; Foregut development; Enteroendocrine; Pdx1; Ipf1; Transcription factor; cis-Regulation
cis-regulatory processing of Notch signaling input to the sea urchin glial cells missing gene during mesoderm specification
Keywords: cis-regulation; Glial cells missing; Specification; Mesoderm; Pigment; Suppressor of Hairless; Notch; Transcriptional switch; Strongylocentrotus purpuratus
Conserved co-regulation and promoter sharing of hoxb3a and hoxb4a in zebrafish
Keywords: Hox; Transcription; cis-regulation; Exon sharing; Conserved non-coding sequences; Genome; Transient transgenics; Enhancer detection; Hindbrain; Micro-RNA; miR-10b
cis-Regulatory inputs of the wnt8 gene in the sea urchin endomesoderm network
Keywords: wnt8; cis-regulation; Gene network; Sea urchin embryo;