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Return to the RNAi world: rethinking gene expression and
... remarkably stable differentiation events can be maintained for the entire life of an organism without any underlying changes in the DNA sequence. The germline cells, which in C. elegans inherit PIE-1 protein, are the only cells that retain the potential to launch the developmental program again in t ...
... remarkably stable differentiation events can be maintained for the entire life of an organism without any underlying changes in the DNA sequence. The germline cells, which in C. elegans inherit PIE-1 protein, are the only cells that retain the potential to launch the developmental program again in t ...
Age-Related Loss of the Transforming Growth Factor β Receptor
... differentiation and cell death, whereas pSmad1/5/8 induces these processes. In cartilage, two TGFβ receptors that induce Smad phosphorylation are ALK for Smad1/5/8 and ALK5 for Smad2/3. Previously, we have shown an age-related shift in receptor balance towards dominant Alk1 expression compared to Al ...
... differentiation and cell death, whereas pSmad1/5/8 induces these processes. In cartilage, two TGFβ receptors that induce Smad phosphorylation are ALK for Smad1/5/8 and ALK5 for Smad2/3. Previously, we have shown an age-related shift in receptor balance towards dominant Alk1 expression compared to Al ...
Transcription in Prokaryotes
... 8 A:T base pairs. The resulting RNA forms a stem-loop structure, which disrupts the elongation complex. A stretch of A:U base pairs in the DNA/RNA hybrid are weaker than other base pairs and are more easily disrupted as a consequence of stem loop formation. Rho dependent termination: terminators are ...
... 8 A:T base pairs. The resulting RNA forms a stem-loop structure, which disrupts the elongation complex. A stretch of A:U base pairs in the DNA/RNA hybrid are weaker than other base pairs and are more easily disrupted as a consequence of stem loop formation. Rho dependent termination: terminators are ...
Naming `junk`: Human non-protein coding RNA (ncRNA) gene
... subunit. The 18S, 5.8S and 28S rRNA genes are arranged in tandem repeats, with the genes separated by transcribed spacers known as externally and internally transcribed sequences (abbreviated to ETS and ITS). Each repeat found in the arrangement 50 ETS-18S-ITS1-5.8S-ITS2-28S-30 ETS produces one prec ...
... subunit. The 18S, 5.8S and 28S rRNA genes are arranged in tandem repeats, with the genes separated by transcribed spacers known as externally and internally transcribed sequences (abbreviated to ETS and ITS). Each repeat found in the arrangement 50 ETS-18S-ITS1-5.8S-ITS2-28S-30 ETS produces one prec ...
RNA
... The Structure of RNA There are four main differences between RNA and DNA: • The sugar in RNA is ribose instead of deoxyribose. • RNA is single-stranded. DNA is double-stranded. • RNA contains uracil in place of thymine. • DNA stays in the nucleus, but RNA can leave the nucleus and go into the cytopl ...
... The Structure of RNA There are four main differences between RNA and DNA: • The sugar in RNA is ribose instead of deoxyribose. • RNA is single-stranded. DNA is double-stranded. • RNA contains uracil in place of thymine. • DNA stays in the nucleus, but RNA can leave the nucleus and go into the cytopl ...
RNA structure and synthesis:
... strands as a template strand by the action of the enzyme RNA polymerase that reads the template strand in the 3’ 5’ direction and synthesizes RNA in the 5’ 3’. It utilizes the ribonucleoside triphosphate as a building units. The other DNA strand is called coding strand. A given strand may serve a ...
... strands as a template strand by the action of the enzyme RNA polymerase that reads the template strand in the 3’ 5’ direction and synthesizes RNA in the 5’ 3’. It utilizes the ribonucleoside triphosphate as a building units. The other DNA strand is called coding strand. A given strand may serve a ...
Transcription
... within nucleus • snRNA: a class of small RNA molecules within the nucleus snRNA ...
... within nucleus • snRNA: a class of small RNA molecules within the nucleus snRNA ...
Document
... being synthesized is bound by a cap-synthesizing complex associated with RNA polymerase. This enzymatic complex catalyzes the chemical reactions that are required for mRNA capping. ...
... being synthesized is bound by a cap-synthesizing complex associated with RNA polymerase. This enzymatic complex catalyzes the chemical reactions that are required for mRNA capping. ...
Lecture ten
... – 1. RNA polymerases differ – only one in prokaryotes; 3 in eukaryotes – 2. transcription factors used by eukaryotes – 3. transcription is terminated differently in prokaryotes vs. eukaryotes • eukaryotes – polyA signal is transcribed prior to termination ...
... – 1. RNA polymerases differ – only one in prokaryotes; 3 in eukaryotes – 2. transcription factors used by eukaryotes – 3. transcription is terminated differently in prokaryotes vs. eukaryotes • eukaryotes – polyA signal is transcribed prior to termination ...
Gene7-05
... 5. A typical mRNA contains both a nontranslated 5 leader and 3 trailer as well as coding region(s). 6. A growing E. coli bacterium has ~20,000 ribosomes and ~200,000 tRNAs, mostly in the form of aminoacyltRNA. 7. Many ribosomes may translate a single mRNA simultaneously, generating a polyribosome (o ...
... 5. A typical mRNA contains both a nontranslated 5 leader and 3 trailer as well as coding region(s). 6. A growing E. coli bacterium has ~20,000 ribosomes and ~200,000 tRNAs, mostly in the form of aminoacyltRNA. 7. Many ribosomes may translate a single mRNA simultaneously, generating a polyribosome (o ...
Slide 1
... Use RNAi to characterize regulatory function in protein secretion areA is a positively acting regulatory gene which has been shown to be essential for activating genes encoding enzymes, permeases, needed to acquire nitrogen for the environment areA has recently been shown in Aspergillus to play a p ...
... Use RNAi to characterize regulatory function in protein secretion areA is a positively acting regulatory gene which has been shown to be essential for activating genes encoding enzymes, permeases, needed to acquire nitrogen for the environment areA has recently been shown in Aspergillus to play a p ...
Document
... Orchestra • genetic and biochemical work in bacteria identified two things – 1. protein-binding regulatory sequences associated with genes – 2. proteins that can bind these regulatory sequences – either activating or repressing gene expression ...
... Orchestra • genetic and biochemical work in bacteria identified two things – 1. protein-binding regulatory sequences associated with genes – 2. proteins that can bind these regulatory sequences – either activating or repressing gene expression ...
file
... • Search in the space of possible Ns to look for a one that maximizes the above probability • Impossible to enumerate all possible networks • Use cross validation: partition the data into 5 gene sets, learn the rules based on all but one and test based on the left-out, each time. ...
... • Search in the space of possible Ns to look for a one that maximizes the above probability • Impossible to enumerate all possible networks • Use cross validation: partition the data into 5 gene sets, learn the rules based on all but one and test based on the left-out, each time. ...
RNA is synthesized by a DNA-dependent RNA polymerase (uses
... the thousands of transcription units in the genome of an organism. Figure below illustrates the arrangement and direction of transcription for several genes on a DNA molecule. ...
... the thousands of transcription units in the genome of an organism. Figure below illustrates the arrangement and direction of transcription for several genes on a DNA molecule. ...
Document
... and a very small fraction of the non-protein-coding DNA consists of genes for RNA such as rRNA and tRNA • A significant amount of the genome may be transcribed into noncoding RNAs (ncRNAs) • Noncoding RNAs regulate gene expression at two points: mRNA translation and chromatin configuration ...
... and a very small fraction of the non-protein-coding DNA consists of genes for RNA such as rRNA and tRNA • A significant amount of the genome may be transcribed into noncoding RNAs (ncRNAs) • Noncoding RNAs regulate gene expression at two points: mRNA translation and chromatin configuration ...
emboj200858-sup
... Activation of EGFR was monitored by induction of pointedP1 expression. Normally, pntP1 is expressed in two cell rows on each side of the midline. Upon expression of Rhomboid proteins by prd-Gal4, the pattern of ectopic pntP1 expression was monitored within the stripes, and adjacent to them. (A) Rho- ...
... Activation of EGFR was monitored by induction of pointedP1 expression. Normally, pntP1 is expressed in two cell rows on each side of the midline. Upon expression of Rhomboid proteins by prd-Gal4, the pattern of ectopic pntP1 expression was monitored within the stripes, and adjacent to them. (A) Rho- ...
Gene Regulation and Expression
... This alternative splicing can be haphazard, but more often it is controlled and acts as a mechanism of gene regulation, with the frequency of dierent splicing alternatives controlled by the cell as a way to control the production of dierent protein products in dierent cells or at dierent stages ...
... This alternative splicing can be haphazard, but more often it is controlled and acts as a mechanism of gene regulation, with the frequency of dierent splicing alternatives controlled by the cell as a way to control the production of dierent protein products in dierent cells or at dierent stages ...
High performance solution-based target selection using individually
... spiked into array-derived RNA baits to enhance coverage of high-GC regions. For these captures, either 1,000 oligo baits (~133kb target territory) or 3 oligo baits (1 exon) were mixed with the array/RNA baits; otherwise the conditions were equivalent to Foundation Medicine’s ...
... spiked into array-derived RNA baits to enhance coverage of high-GC regions. For these captures, either 1,000 oligo baits (~133kb target territory) or 3 oligo baits (1 exon) were mixed with the array/RNA baits; otherwise the conditions were equivalent to Foundation Medicine’s ...
Genetic Manipulation of Kinetoplastida
... off essential functions. However, these methods are not equally applicable in all parasites. Here, Christine Clayton highlights the differences and similarities between the most commonly used model organisms, and assesses the relative advantages of different approaches and parasites for different ty ...
... off essential functions. However, these methods are not equally applicable in all parasites. Here, Christine Clayton highlights the differences and similarities between the most commonly used model organisms, and assesses the relative advantages of different approaches and parasites for different ty ...
Hao Nguyen
... once in the cytoplasm. 3. What is so unique about the function of small nuclear RNA’s (snRNA)? (5 points) Small nuclear RNA is a very important component of a complex called small nuclear ribonuclear protein (or snRNP). It [snRNA] possesses enzymatic activities that are essential during mRNA splicin ...
... once in the cytoplasm. 3. What is so unique about the function of small nuclear RNA’s (snRNA)? (5 points) Small nuclear RNA is a very important component of a complex called small nuclear ribonuclear protein (or snRNP). It [snRNA] possesses enzymatic activities that are essential during mRNA splicin ...
Reading the Blueprint of Life Chromosome DNA Gene Transcription
... Reading the Blueprint of Life: Translation 1. mRNA must be decoded by the ribosome Message from DNA the Gene! Instructions to ribosome on how to assemble a protein mRNA Code words are called Codons Codons are 3 base pairs long Every message has a start codon Every message has a stop cod ...
... Reading the Blueprint of Life: Translation 1. mRNA must be decoded by the ribosome Message from DNA the Gene! Instructions to ribosome on how to assemble a protein mRNA Code words are called Codons Codons are 3 base pairs long Every message has a start codon Every message has a stop cod ...
Applications of RNA minimum free energy computations
... A related and equally important algorithmic task is the detection of regulatory and retranslation signals in the untranslated region (UTR), both upstream 5 and downstream 3 of the coding sequence (cds) of messenger RNA. For instance, (Lescure et al., 1999) used Vienna RNA Package RNAfold in a simp ...
... A related and equally important algorithmic task is the detection of regulatory and retranslation signals in the untranslated region (UTR), both upstream 5 and downstream 3 of the coding sequence (cds) of messenger RNA. For instance, (Lescure et al., 1999) used Vienna RNA Package RNAfold in a simp ...
MicroRNA
A micro RNA (abbreviated miRNA) is a small non-coding RNA molecule (containing about 22 nucleotides) found in plants, animals, and some viruses, which functions in RNA silencing and post-transcriptional regulation of gene expression.Encoded by eukaryotic nuclear DNA in plants and animals and by viral DNA in certain viruses whose genome is based on DNA, miRNAs function via base-pairing with complementary sequences within mRNA molecules. As a result, these mRNA molecules are silenced by one or more of the following processes: 1) cleavage of the mRNA strand into two pieces, 2) destabilization of the mRNA through shortening of its poly(A) tail, and 3) less efficient translation of the mRNA into proteins by ribosomes. miRNAs resemble the small interfering RNAs (siRNAs) of the RNA interference (RNAi) pathway, except miRNAs derive from regions of RNA transcripts that fold back on themselves to form short hairpins, whereas siRNAs derive from longer regions of double-stranded RNA. The human genome may encode over 1000 miRNAs, which are abundant in many mammalian cell types and appear to target about 60% of the genes of humans and other mammals.miRNAs are well conserved in both plants and animals, and are thought to be a vital and evolutionarily ancient component of genetic regulation. While core components of the microRNA pathway are conserved between plants and animals, miRNA repertoires in the two kingdoms appear to have emerged independently with different primary modes of action. Plant miRNAs usually have near-perfect pairing with their mRNA targets, which induces gene repression through cleavage of the target transcripts. In contrast, animal miRNAs are able to recognize their target mRNAs by using as little as 6–8 nucleotides (the seed region) at the 5' end of the miRNA, which is not enough pairing to induce cleavage of the target mRNAs. Combinatorial regulation is a feature of miRNA regulation in animals. A given miRNA may have hundreds of different mRNA targets, and a given target might be regulated by multiple miRNAs.The first miRNA was discovered in the early 1990s. However, miRNAs were not recognized as a distinct class of biological regulators until the early 2000s. Since then, miRNA research has revealed different sets of miRNAs expressed in different cell types and tissuesand has revealed multiple roles for miRNAs in plant and animal development and in many other biological processes. Aberrant expression of miRNAs has been implicated in numerous disease states, and miRNA-based therapies are under investigation.Estimates of the average number of unique messenger RNAs that are targets for repression by a typical microRNA vary, depending on the method used to make the estimate, but several approaches show that mammalian miRNAs can have many unique targets. For example, an analysis of the miRNAs highly conserved in vertebrate animals shows that each of these miRNAs has, on average, roughly 400 conserved targets. Likewise, experiments show that a single miRNA can reduce the stability of hundreds of unique messenger RNAs, and other experiments show that a single miRNA may repress the production of hundreds of proteins, but that this repression often is relatively mild (less than 2-fold).