Ten Years of Enhancer Detection: Lessons from the Fly

1999 ◽  
Vol 11 (12) ◽  
pp. 2271
Author(s):  
Hugo J. Bellen
Keyword(s):  
Enhancer Detection

scholarly journals A Novel Position-Specific Encoding Algorithm (SeqPose) of Nucleotide Sequences and Its Application for Detecting Enhancers

2021 ◽  
Vol 22 (6) ◽  
pp. 3079
Author(s):  
Xuechen Mu ◽  
Yueying Wang ◽  
Meiyu Duan ◽  
Shuai Liu ◽  
Fei Li ◽  
...  
Keyword(s):  
Transcriptional Regulation ◽  
Dna Sequence ◽  
Prediction Models ◽  
Nucleotide Sequences ◽  
Attention Mechanism ◽  
Training Dataset ◽  
Regulation Mechanism ◽  
Independent Test ◽  
Regulation Strength ◽  
Enhancer Detection

Enhancers are short genomic regions exerting tissue-specific regulatory roles, usually for remote coding regions. Enhancers are observed in both prokaryotic and eukaryotic genomes, and their detections facilitate a better understanding of the transcriptional regulation mechanism. The accurate detection and transcriptional regulation strength evaluation of the enhancers remain a major bioinformatics challenge. Most of the current studies utilized the statistical features of short fixed-length nucleotide sequences. This study introduces the location information of each k-mer (SeqPose) into the encoding strategy of a DNA sequence and employs the attention mechanism in the two-layer bi-directional long-short term memory (BD-LSTM) model (spEnhancer) for the enhancer detection problem. The first layer of the delivered classifier discriminates between enhancers and non-enhancers, and the second layer evaluates the transcriptional regulation strength of the detected enhancer. The SeqPose-encoded features are selected by the Chi-squared test, and 45 positions are removed from further analysis. The existing studies may focus on selecting the statistical DNA sequence descriptors with large contributions to the prediction models. This study does not utilize these statistical DNA sequence descriptors. Then the word vector of the SeqPose-encoded features is obtained by using the word embedding layer. This study hypothesizes that different word vector features may contribute differently to the enhancer detection model, and assigns different weights to these word vectors through the attention mechanism in the BD-LSTM model. The previous study generously provided the training and independent test datasets, and the proposed spEnhancer is compared with the three existing state-of-the-art studies using the same experimental procedure. The leave-one-out validation data on the training dataset shows that the proposed spEnhancer achieves similar detection performances as the three existing studies. While spEnhancer achieves the best overall performance metric MCC for both of the two binary classification problems on the independent test dataset. The experimental data shows that the strategy of removing redundant positions (SeqPose) may help improve the DNA sequence-based prediction models. spEnhancer may serve well as a complementary model to the existing studies, especially for the novel query enhancers that are not included in the training dataset.

Dissecting the complexity of the nervous system by enhancer detection

BioEssays ◽  
1990 ◽  
Vol 12 (5) ◽  
pp. 199-204 ◽  
Author(s):  
Hugo J. Bellen ◽  
Clive Wilson ◽  
Walter J. Gehring
Keyword(s):  
Nervous System ◽  
Enhancer Detection

scholarly journals The Drosophila couch potato gene: an essential gene required for normal adult behavior.

Genetics ◽  
1992 ◽  
Vol 131 (2) ◽  
pp. 365-375 ◽  
Author(s):  
H J Bellen ◽  
H Vaessin ◽  
E Bier ◽  
A Kolodkin ◽  
D D'Evelyn ◽  
...  
Keyword(s):  
Nervous System ◽  
Essential Gene ◽  
Flight Behavior ◽  
Regulatory Sequences ◽  
Adult Behavior ◽  
The Central Nervous System ◽  
Enhancer Detection ◽  
Dna Fragment ◽  
Mother Cells

Abstract Through enhancer detection screens we have isolated 14 insertions in an essential gene that is expressed in embryonic sensory mother cells (SMC), in most cells of the mature embryonic peripheral nervous system (PNS), and in glial cells of the PNS and the central nervous system (CNS). Embryos homozygote for amorphic alleles die, but show no obvious defects in their cuticle, PNS or CNS. The gene has been named couch potato (cpo) because several insertional alleles alter adult behavior. Homozygous hypomorphic cpo flies recover slowly from ether anaesthesia, show aberrant flight behavior, fail to move toward light and do not exhibit normal negative behavior. However, the flies are able to groom and walk, and some are able to fly when prodded, indicating that not all processes required for behavior are severely affected. A molecular analysis shows that the 14 insertions are confined to a few hundred nucleotides which probably contain key regulatory sequences of the gene. The orientation of these insertions and their position within this DNA fragment play an important role in the couch potato phenotype. In situ hybridization to whole mount embryos suggest that some insertions affect the levels of transcription of cpo in most cells in which it is expressed.

P-element-mediated enhancer detection applied to the study of oogenesis in Drosophila

Development ◽  
1989 ◽  
Vol 107 (2) ◽  
pp. 189-200 ◽  
Author(s):  
U. Grossniklaus ◽  
H.J. Bellen ◽  
C. Wilson ◽  
W.J. Gehring
Keyword(s):  
Germ Line ◽  
Expression Patterns ◽  
Cell Types ◽  
Regulatory Elements ◽  
P Element ◽  
Regulatory Sequences ◽  
Transcriptional Regulatory ◽  
Morphological Criteria ◽  
Enhancer Detection ◽  
New Strategies

We have stained the ovaries of nearly 600 different Drosophila strains carrying single copies of a P-element enhancer detector. This transposon detects neighbouring genomic transcriptional regulatory sequences by means of a beta-galactosidase reporter gene. Numerous strains are stained in specific cells and at specific stages of oogenesis and provide useful ovarian markers for cell types that in some cases have not previously been recognized by morphological criteria. Since recent data have suggested that a substantial number of the regulatory elements detected by enhancer detection control neighbouring genes, we discuss the implications of our results concerning ovarian gene expression patterns in Drosophila. We have also identified a small number of insertion-linked recessive mutants that are sterile or lead to ovarian defects. We observe a strong correlation with specific germ line staining patterns in these strains, suggesting that certain patterns are more likely to be associated with female sterile genes than others. On the basis of our results, we suggest new strategies, which are not primarily based on the generation of mutants, to screen for and isolated female sterile genes.

scholarly journals Material barriers to diffusive and stochastic transport

2018 ◽  
Vol 115 (37) ◽  
pp. 9074-9079 ◽  
Author(s):  
George Haller ◽  
Daniel Karrasch ◽  
Florian Kogelbauer
Keyword(s):  
Coherent Structures ◽  
Fluid Transport ◽  
Order Term ◽  
Velocity Fields ◽  
Leading Order ◽  
Transport Barrier ◽  
Material Surfaces ◽  
Stochastic Transport ◽  
Transport Barriers ◽  
Enhancer Detection

We seek transport barriers and transport enhancers as material surfaces across which the transport of diffusive tracers is minimal or maximal in a general, unsteady flow. We find that such surfaces are extremizers of a universal, nondimensional transport functional whose leading-order term in the diffusivity can be computed directly from the flow velocity. The most observable (uniform) transport extremizers are explicitly computable as null surfaces of an objective transport tensor. Even in the limit of vanishing diffusivity, these surfaces differ from all previously identified coherent structures for purely advective fluid transport. Our results extend directly to stochastic velocity fields and hence enable transport barrier and enhancer detection under uncertainties.

scholarly journals P-element-mediated enhancer detection: an efficient method for isolating and characterizing developmentally regulated genes in Drosophila.

1989 ◽  
Vol 3 (9) ◽  
pp. 1301-1313 ◽  
Author(s):  
C Wilson ◽  
R K Pearson ◽  
H J Bellen ◽  
C J O'Kane ◽  
U Grossniklaus ◽  
...  
Keyword(s):  
Efficient Method ◽  
P Element ◽  
Developmentally Regulated ◽  
Enhancer Detection

scholarly journals Enhancer detection in the ascidianCiona intestinalis with transposase-expressing lines ofMinos

2007 ◽  
Vol 237 (1) ◽  
pp. spc1-spc1
Author(s):  
Yasunori Sasakura ◽  
Aru Konno ◽  
Katsutoshi Mizuno ◽  
Nori Satoh ◽  
Kazuo Inaba
Keyword(s):  
Enhancer Detection

Cracking the genome’s second code: Enhancer detection by combined phylogenetic footprinting and transgenic fish and frog embryos

Methods ◽  
2006 ◽  
Vol 39 (3) ◽  
pp. 212-219 ◽  
Author(s):  
Miguel L. Allende ◽  
Miguel Manzanares ◽  
Juan J. Tena ◽  
Carmen G. Feijóo ◽  
José Luis Gómez-Skarmeta
Keyword(s):  
Transgenic Fish ◽  
Phylogenetic Footprinting ◽  
Enhancer Detection
Sign in / Sign up

Export Citation Format

Share Document