Oxygen Sensing Flashcards
snRNA
small nuclear RNA
Involved in RNA splicing and processing
snoRNA
small nucleolar RNA
Covalently modify RNA (tRNA, rRNA)
lncRNA
Long non-coding RNA
Mostly unclear, but a few well-described lncRNAs, including Xist, which is involved in X-chromosome inactivation in females.
Coding gene structure in DNA

Organization of EPO gene

nucleolus
where the expression of ribosomal RNA occurs and where ribosomes assemble
Euchromatin vs Heterochromatin

Nice Diagram of DNA structure

DNA Supercoiling

Histone octamer structure

“Coactivators” and “Corepressors”
Co-activators and co-repressors bind to the regulatory transcription factors and activate or repress transcription through a variety of mechanisms.
DO NOT have a DNA binding domain
One example would be writers and erasers that are recruited by regulatory transcription factors.
Extrusion of DNA and loop domains
The yellow rings here are referred to as “extrusion complexes.” They are made from cohesins.
The motifs upon which they land are CTCF motifs, which help direct which DNA should be extruded.

Topologially Associated Domains
Neighboring cohesin-derived DNA loops that interact with one-another. TADs contain actively transcribed chromatin, and tend to cluster with one another while inactive chromatin clusters with other inactive chromatin.
These acive TADs represent euchromatin, while inactive chromatin represents heterochromatin.
Among these differential clusters, chromatin originating from the same chromosome tends to cluster together.

“Reader” protein
Protein which targets specific chromatin domains by recognizing histone tail modifications.
Display a diversity of structures and mechanisms for interacting with histones. Each reader has an affinity for a specific type of modification.
Five types of modification for histone tails
Acetylation
Methylation
Ubiquitination
Phosphorylation
Proline isomerization
“Writer” proteins
Add histone modifications
“Eraser” proteins
Remove histone modifications
Components required for transcription

Reactions Performed by Writers and Erasers
Notably, degree of methylation of lysine may also change. Histone-associated lysines may be unmethylated, methylated, dimethylated, or trimethylated.

How readers affect gene expression
An important point to emphasize is that regulatory transcription factors can also recruit writers and erasers. In this case, the writers or erasers are called co-activators or co-repressors, depending on whether they tend to activate or repress transcription

Reader-Writer Epigenetic Propagation
When histone H3 lysine 9 is methylated, this recruits a reader called HP1, which can bind to itself and therefore promote a compact chromatin structure. HP1 can also bind the writer that makes the mark, a histone methyltransferase. Because the reader recruits its own writer, it helps maintain the mark, and can also lead to propagation of the mark down the chromatin. Specific sequences called boundary elements are necessary to prevent the propagation into active regions of chromatin.

Pioneer Factors
Some transcription factors can bind to more compacted chromatin, and then initiate changes in chromatin structure. These are called pioneer factors because they can initiate the process of opening chromatin.
Other transcription factors, called non-pioneer factors, can only work on chromatin that has already been opened by pioneer factors.
Pioneer factors are particularly important in the initiation of cellular differentiation.



Transcription Initiation
It is important to note that RNA polymerase cannot do this on its own—it needs a series of additional factors called general transcription factors (TFII proteins) to bind the promoter and initiate transcription.


















