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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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0 answers
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Number of regulators required for specify the total state of genes

My course notes make the following claim: If the regulation of each gene could include all transcription regulators available, then in principle the total state of all genes could be specified with ...
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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 ...
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What is the best way to learn about gene regulation?

For those of you who already have a decent knowledge of how gene regulation works, how should someone new to the topic acquire a detailed overview? Is there a particularly good and up-to-date resource?...
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Are there limitations in using DNase I hypersensitive sites (DHSs) to identify candidate enhancers?

Candidate enhancer regions are often defined in studies by DHSs and/or certain chromatin marks. I was wondering if DHSs are exhaustive for identifying possible enhancer regions, and if there is any ...
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Is there a resource/paper containing information about which co-activators are often associated with a given transcription factor?

Given a list of human transcription factors, I would be interested in which co-activators they are often associated with. I imagine that one could combine co-expression, pull-down, and other kinds of ...
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What's the term for "Amino acid regulating the expression of components used to synthesize it"?

In the tryptophan operon wikipedia page, it says under the Attenuation title: A similar attenuation mechanism regulates the synthesis of histidine, phenylalanine and threonine. If my reading is ...
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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 ...
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1 answer
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How to biologically interpret path weight summation in weighted and directed gene regulation network?

I've considered asking this question on Bioinformatics SE, Mathematics SE, and Stats SE, however I've judged that my question belongs on Biology SE because I am interested in a biological (domain-...
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what are the nodes and edges in gene regulatory networks

I am trying to find out how one can using gene expression data can infer gene regulatory network applying graph theory concepts. But I could not find a proper reference that 1)explain how one can get ...
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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 ...
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1 answer
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If the AraC protein was a gene repressor when it binds arabinose, would there be high or low transcription levels when arabinose is present? [closed]

If the AraC protein were to function as a gene repressor when it binds arabinose, would there be high or low transcription levels when arabinose is present?
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Do transcription factors need to undergo extensive post-translational modification?

Some proteins need additional processing to become fully functional, for example NiFe-hydrogenases need to be cleaved by endopeptidases for some of their subunits to be active. Is it known whether ...
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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 ...
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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 ...
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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 ...
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1 answer
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Gene regulation and epigenetics in specialized cells

Gene regulation is aided by epigenetics. Epigenetics determines which genes are turned off and which are switched on, and it varies throughout our lifetimes. Is it feasible that epigenetic ...
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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/...
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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 ...
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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 ...
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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 ...
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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 ...
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Difference between viral and native RNA

I am a data scientist with really next to no training in microbiology. I hope you'll all forgive my ignorance to entertain these questions. The attention COVID-19 has gotten recently got me thinking:...
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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 ...
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Is there a difference between "genetic cross regulation" and "crosstalk"?

What is the difference between genetic cross regulation and crosstalk? I'm a physics major and learning about bioinformatics now. So it might seem trivial to many but from the article "Wanner BL. ...
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1 answer
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Can a miRNA be upregulated and downregulated in the same disease

I am computational guy and hence apologies if the question is silly. Can the same miRNA show upregulation and downregulation in the same disease? (Not in the same experiment, though). For e.g. can ...
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1 answer
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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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2 answers
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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 ...
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2 answers
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Finding targets of transcription factors

I'm trying to find an easy way to get a list of putative targets of a particular transcription factor (for example, STAT1). I'm interested in targets determined using both experimental and ...
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what happens when you put enhancer and caat box in prokaryotes

what happens when you put enhancer and caat box in prokaryotes
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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 ...
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response elements in transcription regulation

I'm studying eukaryotic gene regulation and I want to know whether there are some instances where transcription factors don't need to bind to response elements to initiate transcription. RNA ...
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What are some online databases that I can search to find the pathways for sythesis of Lignin, Cellulose, GAX?

I am trying to obtain the pathway information for synthesis of Lignin,GAX and Cellulose in Sorghum. I am quite new to biology and genetics (EE background). I would appreciate it if y'all can provide ...
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1 answer
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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 ...
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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 ...
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How is the breakdown of lactose regulated at the gene level?

How is the breakdown of lactose regulated at the gene level? This is my answer: Without lactose in the cell, the repressor protein binds to the operator and prevents the read through of RNA ...
2 votes
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Consensus sequence for selection of initiation codon in eukaryotes

In bacteria the AUG (or other) codon at which translation of mRNA is initiated is preceded at a precise distance by a sequence known as the Shine and Dalgarno sequence, to which the 30S subunit ...
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Length of upstream and downstream of tss important for gene regulation o

I want to find SNPs in the upstream and downstream regions of transcription start sites of some 42 genes implicated in a disease (on which I am working). Are there any suggestions on what length ...
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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 ...
2 votes
1 answer
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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 ...
4 votes
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 ...
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1 answer
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How do messenger RNAs regulate each other's expression levels?

I know that researchers learn gene regulatory networks from microarray experiments that measure the mRNA expression levels. However, I do not understand how mRNAs regulate each other's levels. Do they ...
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1 answer
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On enhancers, strands, and zygosity

I came across a passage on enhancers that sounds out-of-whack to me: ...an enhancer sits on just one of DNA's two strands (usually the same strand as the protein-coding DNA gene itself). This is ...
2 votes
1 answer
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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 ...
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How are constitutive enzymes regulated?

I found that inducible enzymes can be regulated by many ways, but I cannot find how constitutive enzymes are regulated...
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Are the subordinate genes of a repressed operon really "turned off"?

Operons are often described using all or nothing language. A repressor binding to the operator is usually presented as "turning off" the regulated genes. Case in point, Scitable at Nature.com says: ...
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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 ...
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2 answers
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Does a gene that regulates itself necessarily be a transcription factor?

I am not a biologist, so please pardon the overly noob question. Some genes are transcription factors (TF) and regulate other genes. My question is: if a gene is NOT a TF gene, can it regulate itself? ...
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Transcription of Genes: Are Specific Transcription Factors + Enhancers Necessary?

I learned about transcription in my AP Biology class and we discussed how transcription occurs, but I was wondering whether transcription always requires the enhancers, activators (specific ...
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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-...
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Ways to identify that proteins are regulating different genes experimentally

As part of my study I have been given this hypothesis: HIF 1a and HIF 2a regulate different genes in multiple myeloma What ways do we have to identify that these proteins are regulating different ...