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Flashcards in Oxygen Sensing Deck (49)
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small nuclear RNA


Involved in RNA splicing and processing



small nucleolar RNA


Covalently modify RNA (tRNA, rRNA)



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



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





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.


Transcription Elongation and Termination

The mechanism of termination differs for the various RNA polymerases. For RNA polymerase II, termination occurs when a specific sequence is reached that causes cleavage the mRNA and the addition of a polyA tail.


Animal RNA Pol II

RNA polymerase II is composed of multiple subunits (12 in humans and yeast). Rbp1 is the largest subunit and contributes to the catalytic activity of the enzyme. Rbp1 also contains an extended C-terminal domain (CTD) that is composed of a repeating heptad (7 amino acids). These sequences become phosphorylated differentially during initiation and elongation. The bottom of the diagram shows an illustration of the relative size of the polymerase compared to the extended CTD. The CTD serves as a platform that allows other proteins to bind during the process of transcription and RNA processing (splicing). You can think of the CTD in a manner similar to a histone tail in that it gets modified by enzymes at various points during transcription (kinases act as ”writers”) and various proteins can then bind the phosphorylated CTD (“readers”). These readers can help promote processing of the newly synthesized mRNA as it emerges from the polymerase.


general transcription factors

The general transcription factors help RNA polymerase where to bind the DNA, and therefore, where to start transcription. These proteins can be found at most/all genes that are transcribed. For this reason, they are called “general” transcription factors. There is a limited number of different general transcription factors. Some of these proteins bind directly to DNA whereas others do not.


regulatory transcription factors

The regulatory transcription factors help decide how much of a transcript should be made. There are hundreds of different regulatory transcription factors, each of which has specificity for different DNA sequences. As we will discuss, these proteins do not work by themselves, but have to work in partnership with other proteins called co-regulators (co-activators or co-repressors, depending on how they affect transcription).



There are a series of general transcription factors that recognize specific DNA sequences around the promoter. Some of these are located upstream of the promoter, like the TATA box, and others are located at the start site or downstream of the start site. (Note: in molecular biology, regions of evolutionarily conserved sequences are often called “boxes”. The TATA box is the best characterized sequence element, and is named because it is enriched in thymidine (T) and adenine (A) bases. It is recognized by a protein called TATA box-binding protein or TBP, which is part of a complex of proteins called TFIID (any time you see “TFII” this is a general transcription factor). Around the TATA box are additional sequence elements (BRE) that are recognized by a different general transcription factor called TFIIB. Furthermore, there are sequence elements at the transcription start site (Inr) and also downstream (DCE, MTE, DPE) that are also recognized by proteins in the TFIID complex.


RNA Pol II and TATA-box interaction