chapters 7,8 (control of gene expression, work with cells) Flashcards
what are transcriptional regulators and where are they located?
- proteins that bind to specific DNA sequences (cis-regulatory element) to regulate gene expression
- distributed unevenly within the cytoplasm providing positional information to distinguish between different parts of the embryo
- ex: glugocorticoid hormone bindind to its receptor can promote expression of multiple genes depending on starvation/stress
Syncytium
multiple nuclei contained in a common cytoplasm
What is combinatorial gene control?
- can make many cell types with few starting things through lots of combinations
- have to be together to elicit effect
- ex: 3 neuron-specific transcription regulators in cultured liver cells converted them into neuronal cells by activation of neuron-specific genes and repression of liver-specific genes
master transcription regulators
- Oct4, Sox2, Klf4
- enough to trigger a change in cell identity
even-skipped (Eve)
- a gene critical for embryonic development in Drosophilia Combinatorial regulation of Eve promoter region by transcription regulators will devetermine the stripe expression and position
- witout this gene, embryo will die early on
induced pulipotent stem cells (iPS cells)
- expression of the 3 transcription regulators Oct4, Sox2, Klf4 in fully differentiated cells will produce cells that adopt characteristics of pluripotent cells derived from embryo
- if you over-express the 3 genes in differentiated cells, you can turn them into iPS cells
- erases identity completetly for something new to be added
what is cell memory?
- a pattern of gene expression within a given cell that is responsible for maintaining that cell’s identity and is passed on to a daughter cell upon division
- follows positive feedback loop (ensures continous gene transcription in the absence of initital signal)
Mechanisms involved in maintaining cell memory
- DNA methylation/ dense DNA methylation
- CG islands
- x chromosome inactivation
- x chromosome dosage compensation
What are transcriptional circuits? What is an example of it?
- gene regulatory switches that produce different outcomes on cell function and development
- network motif: a type of gene expression switching arrangement (small, repeating pattern of connections within a complex network)
- positive, negative feedback loop, feed-forward loop, flip-flop device
what is DNA methylation?
- addition of methyl group to cytosine when in sequence with guanine (CG)
- for genomic imprinting (only 1 copy from 1 parent expressed, and the other one is silenced- methylated)
- can repress gene transcription
histone modification
trimethylation on lysine promotes nucleosome compaction and heterochromatin formation
dense DNA methylation process
- methylated Cs can interfere with binding of transcription regulators/factors for transcription initiation
- DNA methyl binding proteins + histone modifying enzyme+ DNA methylase enzymes = induce heterochromatin formation
if packed in heterocromatin region –> not transcribed –> not expressed
When does DNA demethylation occur? And what enzyme removes them?
occurs shortly after fertilization, where most methyl groups are removed by DNA demethylase
maintenance methyl transferase
- enzyme adds methyl group to C when in sequence CG that are base paried with methylated CG sequences
- allows methylation pattern to be inherited after DNA replication
- old strand methylated
- ensures methylation pattern is inherited
What is genomic imprinting?
either maternal or paternal inherited genes are expressed, while the other is silenced (methylated)
what is x inactivation?
- where one of the X chromosomes is silenced in mammalian females
- random producing females with a mosaic of clonal groups of cells with either maternal or paternal X silenced
CG island
- CG-rich regions unevenly distributed in the genome
- area of many gene promoters
- deamination of C turns into T
- throughout evolution, majority of methylated CG sequences were lost due to deamination of C to T
- remain unmethylated by binding specizalized proteins that methylate histone H3and repel de novo methylases
what is dosage compensation?
- a process to ensure similar levels of gene expression in males and females
- differes across multiple species
- mammals: random inactivation
- fly: increase expression on X to match levels in female
- marsupials: inactivation of paternal
- nematode: decreased of all
In mammals occurs when more than one X is present in somatic cell
what is x chromosome inactivation triggered by?
- synthesis of long noncoding RNA Xist
- synthesized by one of the 2 X chromosomes
- contains binding sites for multiple proteins like DNa methylases and histone-modifying enzymes, promoting fomraiton of compact DNA structure and silencing gene transcription
monoallelic gene expression
in a diploid organism, only one copy of the gene is expressed
epigenetic inheritence
heritable change in the cell’s phenotype that does not result in a change in teh nucleotidde sequence of DNA
Posttranscriptional controls
- transcription attenuation aborting gene expression
- riboswitches- abort transcription in response to a signal
- alternative splicing
- RNA cleavage and poly-A addition
- RNA nucleotides can be covalently modified
- regulation of nuclear transport
What are P bodies?
- membraneless aggregates of RNA proteins
- storage facilities for mRNA, which can be stored for later used or degraded
What are stress granules?
- membraneless organelle that forms in response to starvation or stress when translation is suddenly blocked
- mRNA accumulates in stress granules and are released to the cyctosol to be translated when stress is alleviated