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Questions tagged [gene-regulation]

The processes by which gene products (largely RNA and proteins) are increased or decreased.

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120-year-old gene regulation problem independently solved by a computer. How?

My Background: I'm a mathematics graduate student with a physics background. I have a very little biology knowledge and a little knowledge of machine learning and statistics. Topic: I recently ...
Christian Bueno's user avatar
14 votes
3 answers
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Databases for gene regulatory network graphs?

What databases are available for gene regulatory network graphs starting from a given gene? For example, starting from p53 gene, where can I find a gene regulatory network image that can be exported ...
yahoo301503's user avatar
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Percentage of genome devoted to regulating gene expression

Recently I've been studying the p53 tumor suppressor gene as a model for regulation of gene expression. It's amazing how many different post-translational modifications are known to regulate p53 ...
Daniel Standage's user avatar
12 votes
2 answers
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Modularity of transcription factors

I attended a seminar about neurogenesis that presented results for PAX6 as an important TF that contains 3 domains with very distinct patterns of downstream expression. The speaker ended up saying ...
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Books on machine learning applications in Biology

I have recently engaged with a collaboration, which requires me to construct, then train an unsupervised artificial neural network (ANN). However, I have only a very coarse understanding of what ...
hello_there_andy's user avatar
9 votes
1 answer
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Hill's function for translational regulation

Transcriptional regulation is generally modeled as a Hill's function (similar to Michaelis-Menten Kinetics): $$\frac{dm_X}{dt}=\alpha _{m_X}.\frac{R}{K+R} -\beta _{m_X}.m_X$$ Where $m_X$ is the mRNA ...
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What is it about the housekeeping genes that makes them almost immune to gene regulation?

When it comes to eukaryotes, including ourselves, we have all different kinds of specialized cells and tissues that are so different, yet originally all came from the same single cell. And apparently ...
Raed Tabani's user avatar
8 votes
1 answer
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Number of transcription factor genes in the human genome

What is the number of the transcription factor genes present in the human genome? Does this value differ compared to Mus musculus, Drosophila melanogaster, Arabidopsis thaliana, C. elegans and S. ...
Katz's user avatar
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How to validate the regulatory interactions inferred from gene expression data?

My algorithm learns regulatory interaction between genes using Bayesian Network approach from gene expression data. After the algorithm has converged to a network of interacting genes, how to validate ...
Aparajita's user avatar
8 votes
1 answer
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DNA methylation and genome size

Is there any relationship between DNA methylation as a level of stability to epigenetic states and genome size? For example, it is claimed that DNA methylation is not required for epigenetic stability ...
yahoo301503's user avatar
7 votes
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How can CI repressor both activate and repress $P_{RM}$ promoter found in $\lambda$ phage?

I'm reading a paper where the authors constructed a toggle switch that uses bidirectional $P_R/P_{RM}$ promoter found in the $\lambda$ phage. There are 3 binding sites - $O_{R1}$, $O_{R2}$, $O_{R3}$ - ...
w128's user avatar
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Do nucleosomes ever completely unwrap during transcription?

In eukaryotic transcription will the nucleosomes ever completely unwind the DNA and the histone complex disassemble? If an operon is more 160 base pairs it seems it must.
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Do DNA repressors exist?

I know about enhancers and the mechanism that lead them to increase the gene expression of their targets but I was wondering if similarly DNA repressors exist. I know about protein repressors but I am ...
cagliari2005's user avatar
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How do nuclear receptors locate each other to form a DNA loop?

Nuclear receptors can influence transcription far up- or downstream from their own binding sites by looping DNA (Rubina et al.; J Mol Bio 2004). I am not sure how exactly the receptors first attach ...
Armatus's user avatar
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How significant is RNA degradation with removal of cap/polyA's in eukaryotes, or UTR's in prokaryotes?

Question is rather self-explanatory, but segmented into two parts. I'm attempting to make use of a repression system that employs cleaving RNA at specific areas with ribozymes with the intent of ...
LanceLafontaine's user avatar
7 votes
1 answer
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What is the mechanism by which lamins regulate gene expression?

The heterochromatin is generally localized at the nuclear periphery (also near nuclear lamina), whereas active genes are preferentially found in the nuclear interior. Children with Hutchinson-...
user114141's user avatar
6 votes
1 answer
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Which genetic oscillator should I use to generate oscillations in range of 2-20 mins?

I'm looking to phase-separate the expression of two enzymes and hence am looking for a multi-component genetic oscillator. However, repressilators and metabolators have a large period of around 45 ...
Siddharth Fitwe's user avatar
6 votes
1 answer
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"Enhancers" of enhancers?

I am looking for examples (if any) of genomic regions which regulates the activity of enhancers, either augmenting or reducing it. Essentially some kind of enhancers (or repressors) of enhancers to ...
cagliari2005's user avatar
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5 votes
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High frequency human genetic oscillators?

The most well studied genetic oscillators in human genomes are involved in regulating the circadian clock (which operates on an approximately 24-hour cycle) and cell cycle activity (with single cycles ...
boloyao's user avatar
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2 answers
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What are some atypical examples of positive transcriptional cooperativity?

Cooperativity in gene expression is an important feature of many regulatory networks. Described using the Hill function, the most common example is a transcription factor (TF) that when bound to its ...
boloyao's user avatar
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2 answers
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tools to reconstruct the transcriptional regulatory circuits?

What are commonly used tools to reconstruct the transcriptional regulatory circuits that govern diverse cellular responses and what input data sets do they accept?
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How do enhancers induce transcription?

DNA response elements are DNA sequences that are could be found upstream, downstream of genes that regulate gene expression at the transcriptional level. One type -Enhancers- bind specific ...
Positron12's user avatar
5 votes
1 answer
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What regulates these two methods of splicing?

Alternative splicing can shuffle the exon order and select from the exon sequence of a single gene site to provide a combinatorial selection of possible transcription products from the one gene. Can ...
Cris's user avatar
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1 answer
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How much time do the different mechanisms of gene regulation need to take effect?

I am thinking of the major regulatory mechanisms, like general transcription factors, activators, repressors, and RNA interference. If non-active regulator genes using each of the different ...
CircleSquared's user avatar
4 votes
1 answer
866 views

Why are most transcription factors enhancing the expression rather than repressing?

One can classify the effects of Transcription Factors (TF) on gene expression into two types: it either enhance or repress the gene expression. I have always been told that most of transcription ...
Remi.b's user avatar
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Can the same target gene be regulated differently by the same transcription factor under different conditions?

I'm very new in biology and doing more computational analysis. I'm confused with the type of interactions between Transcription Factors (TF) and target genes. Is it possible that the same ...
sbmm's user avatar
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1 answer
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Can genes be expressed sequentially?

As I understand it, any gene on an exposed/unpacked region of a chromosome is continuously being expressed. Regulatory genes may increase or decrease the amount of protein synthesised due to its ...
Inquiz's user avatar
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3 votes
2 answers
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enhancers in cell-type-specific signatures

I was reading an article in nature : Epigenomics: Roadmap for regulation and was confused by the definition or/and interpretation of enhancers. Enhancers are activated through interactions with ...
Alina's user avatar
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2 answers
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Heterochromatin production limitations

Currently playing with some ideas for a project and needed some guidance. I am wondering, both in Drosophila melanogaster and in general, is the amount of heterochromatin a cell/nucleus can produce ...
rg255's user avatar
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3 votes
1 answer
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How can I re-format my DNA motifs' position weight matrices?

I am working with a set of DNA motifs that are predicted as potential regulatory motifs (e.g. transcription factor binding sites). The motifs belong to several species, and I wanted to cluster these ...
hello_there_andy's user avatar
3 votes
1 answer
381 views

How to determine the direction of regulation of a gene by comparing gene expressions?

I am just learning about the gene expressions and regulation. Several researches focus on finding the genes of altered gene expressions on a microarray to claim that they have a correlation to a ...
Cassie's user avatar
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1 answer
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What are the relative roles of coding DNA versus regulatory DNA thought to be in evolution?

Intuitively, once you have the idea that some DNA is responsible for turning on and off the DNA that codes for proteins, it's possible to imagine that the regulatory DNA is actually the most important ...
Mark Foskey's user avatar
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2 answers
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Why are tumor suppressor genes recessive?

In my Intro. to Biochemistry course, we have been studying cancer. The professor has pointed out that tumor suppressor genes are "recessive" while proto-oncogenes are "dominant". Since only one ...
Bee's user avatar
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3 votes
1 answer
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Is RNA polymerase affected by proteins bound to the coding sequence of a gene?

I am designing a synthetic gene construct to express genes in E. coli driven by either Ptet or PLacO. The construct would look like: -Ptet-(Gene1)-PLacO-(Gene2)- I want to express each gene using ...
Gilbert Baldwin's user avatar
3 votes
1 answer
572 views

Regulation of V. cholerae virulence factors

So I know that several different environmental signals, such as pH, bile, and temperature, regulate virulence gene expression in V. cholerae. Specifically, they control expression of the genes ...
Soph's user avatar
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1 answer
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mutant down but not out

I am interested in a gene which is null lethal but I need to temporary induce diminished capacity. If a cell is homozygous is it possible to induce heterozygous phenotypes or a partial knockout from ...
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3 votes
0 answers
47 views

What is the "anatomy" of transcriptional regulation in Archaea?

I want to know what are the DNA elements that are recognized by transcription factors in Archaea and so what is the "anatomy" of transcriptional regulation in this case. I found in this ...
Manuela's user avatar
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0 answers
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Conservation Law in Gene Regulatory Network modelling

I was going through the GRN modelling from Chemical and enzyme kinetics by D. Gonze & M. Kaufman (PDF). The gene has 2 sites for activator/repressor. It say the DNA $D_0$ combines with activator/...
A Q's user avatar
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0 answers
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Review paper on gene expression regulatory mechanisms

I'm a junior grad student in bioinformatics with CS background. I am involved in a project around discovering gene regulatory networks in some data, which got me curious about the gene expression ...
Matthew Cerioli's user avatar
3 votes
0 answers
4k views

What is the difference between "dysregulation" and "deregulation" of miRNA?

I've started to study the role of miRNA in cancer. Wikipedia says: Just as miRNA is involved in the normal functioning of eukaryotic cells, so has dysregulation of miRNA been associated with ...
user avatar
2 votes
2 answers
2k views

Promoter in the lac operon

Here is the question: Suppose an experimenter becomes proficient with a technique that allows her to move DNA sequences within a prokaryotic genome. If she moves the promoter for the lac operon to ...
louie mcconnell's user avatar
2 votes
1 answer
224 views

Are all genes capable of being switched on or off?

Are all genes capable of being switched on or off or only some genes? Are there some genes that permanently do not have the functionality that enables them to be switched on or off? Everything I have ...
NetCentric's user avatar
2 votes
1 answer
672 views

Can the brain influence gene expression?

A neuroscientist told me (according to my hazy memory) that the brain/nervous system can have an epigenetic function, ie directly regulate gene expression. I'm not a biologist, but she talked me ...
George's user avatar
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2 votes
1 answer
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qPCR - different results total RNA vs mRNA

I have performed qPCR on a tissue, where I have extracted total RNA and also purified mRNA. I ran the qPCR samples together, and have therefore been exposed to the same conditions except the ...
F.Sal's user avatar
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2 votes
1 answer
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Question about alternative polyadenylation

I know that alternative polyadenylation creates different transcript isoforms. My question is whether alternative polyadenylation ever results in differences in the terminal/last exon? The only case I ...
Vinay Swamy's user avatar
2 votes
2 answers
92 views

Can gene-gene interactions result in gene expression?

I am building a project on Inferring Gene Regulatory Networks using ARACNE and PCA-CMI algorithms, and the input to these algorithms is taken from the DREAM3 challenge. The format of the input data ...
Steve Doson's user avatar
2 votes
1 answer
101 views

Finding Regulatory Elements: How Have People Been Doing This?

First up, I am NOT asking about how to search for and match regulatory elements using a database. I'm asking about how people found what to search for and match in a genome, how they built those ...
Cedar's user avatar
  • 183
2 votes
1 answer
58 views

Do the phage repressors CI and Mnt exhibit crosstalk?

I am interested in using the CI and Mnt proteins as well as their respective promoters (pR and Pmnt) within the same synthetic system, but am concerned as to their similarity and potential crosstalk. ...
LanceLafontaine's user avatar
2 votes
0 answers
49 views

How does the phosphorylation state of 4E-BPs affect translation of nuclear-encoded mitochondrial transcripts?

A 2020 review paper about mTOR (ref. 1) says: because biomass accumulation demands vast reserves of energetic currency, mTORC1 enhances translation of nuclear-encoded mitochondrial transcripts ...
Oren Milman's user avatar
2 votes
2 answers
3k views

What is the difference between a response element and a enhancer?

I have been confused as to the difference between a response element and an enhancer. Wikipedia has the definition of response element as the following: Response elements are short sequences of ...
Hawkeye's user avatar
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