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

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 A CRISPR/Cas9 vector system for neutrophil-specific gene disruption in zebrafish

2020 ◽  
Author(s):  
Yueyang Wang ◽  
Alan Y. Hsu ◽  
Eric M. Walton ◽  
Ramizah Syahirah ◽  
Tianqi Wang ◽  
...  
Keyword(s):  
Cell Motility ◽  
Neutrophil Migration ◽  
Transgenic Fish ◽  
Subcellular Location ◽  
Vector System ◽  
Specific Gene ◽  
Tissue Specific ◽  
Biological Studies

AbstractTissue-specific knockout techniques are widely applied in biological studies to probe the tissue-specific roles of specific genes in physiology, development, and disease. CRISPR/Cas9 is a widely used technology to perform fast and efficient genome editing in vitro and in vivo. Here, we report a robust CRISPR-based gateway system for tissue-specific gene inactivation in zebrafish. A transgenic fish line expressing Cas9 under the control of a neutrophil-restricted promoter was constructed. As proof of principle, we transiently disrupted rac2 or cdk2 in neutrophils using plasmids driving the expression of sgRNAs from U6 promoters. Loss of the rac2 or cdk2 gene in neutrophils resulted in significantly decreased cell motility, which could be restored by re-expressing Rac2 or Cdk2 in neutrophils in the corresponding knockout background. The subcellular location of Rac activation and actin structure and stress in the context of neutrophil migration was determined in both the wild-type and rac2 knockout neutrophils in vivo. In addition, we evaluated an alternative approach where the Cas9 protein is ubiquitously expressed while the sgRNA is processed by ribozymes and expressed in a neutrophil-restricted manner. Cell motility was also reduced upon rac2 sgRNA expression. Together, our work provides a potent tool that can be used to advance the utility of zebrafish in identification and characterization of gene functions in neutrophils.

scholarly journals OPTIMAL ELECTROPORATION CONDITION FOR SPERM MEDIATED GENE TRANSFER IN STRIPPED CATFISH (Pangasionodon hypophthalmus)

2010 ◽  
Vol 5 (1) ◽  
pp. 1
Author(s):  
Raden Roro Sri Pudji Sinarni Dewi ◽  
Alimuddin Alimuddin ◽  
Agus Oman Sudrajat ◽  
Komar Sumantadinata ◽  
Sularto Sularto
Keyword(s):  
Sperm Motility ◽  
Fluorescent Protein ◽  
Pulse Length ◽  
Transgenic Fish ◽  
Pulse Number ◽  
Pulse Interval ◽  
Hatching Rate ◽  
Exogenous Dna ◽  
Motility Of Sperm ◽  
Green Fluorescent

The success of transgenic fish production has been achieved through eggs fertilization using electroporated sperms carrying exogenous DNA. This study was conducted in order to obtain the optimal electroporation condition for stripped catfish sperm. A plasmid containing green fluorescent protein (GFP) gene driven by carp β-actin promoter was transferred into sperm using electrophoresis method towards transgenic stripped catfish (Pangasionodon hypophthalmus) production. Electroporation was carried out using square wave shock with pulse length of 30 ms and pulse interval of 0.1 sec. Treatments are combination between voltage (50 V, 75 V, and 100 V) and pulse number (1 and 3). Exogenous DNA concentration used was 10 μg/mL of Tris-EDTA. Results showed that increasing the voltage from 50 to 100 decreased sperm motility, while pulse number did not affect sperm motility. Voltage of 50 gave the best motility of sperm, although sperm viability relatively similar between treatments and control except at 100 V with 3 pulses number. Further, electroporation-treated sperms were able to fertilize eggs. Higher hatching rate of eggs was obtained in electroporation treatment at 50 V with pulse number of 1 and 3. The persistence of transferred GFP was detected in electroporated and incubated sperms (control). However, GFP was only detected in larvae from eggs that were fertilized by electroporated sperm. Thus, electroporation could be applied to produce transgenic stripped catfish. 

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.

scholarly journals Unrealistic phylogenetic trees may improve phylogenetic footprinting

2017 ◽  
pp. btx033 ◽  
Author(s):  
Martin Nettling ◽  
Hendrik Treutler ◽  
Jesus Cerquides ◽  
Ivo Grosse
Keyword(s):  
Phylogenetic Trees ◽  
Phylogenetic Footprinting
Sign in / Sign up

Export Citation Format

Share Document