Updating the rna polymerase ctd code
The packaging of eukaryotic DNA into nucleosomal arrays permits cells to tightly regulate and fine-tune gene expression.
The ordered disassembly and reassembly of these nucleosomes allows RNA polymerase II (RNAPII) conditional access to the underlying DNA sequences.
Expression of nc RNAs is observed only in particular growth conditions, and usually to a lower extent when compared to the m RNA levels of protein-coding genes [ Non-coding RNAs and chromatin organization.
(A) Protein-coding genes are transcribed in the sense direction in order to produce m RNA.
Technological advances in the field of genomics (Ch IP-chip and Ch IP-Seq) merged with well-established biochemical tools (MNase digestion) have generated precise nucleosome maps in several organisms .
Despite variations in the nucleosomal spacing among different cells and organisms, the organization of nucleosomes over genes showed robust similarities.
Association of the polyadenylation complex factor Ssu72 with both the 5’ and 3’ ends of genes mediates gene looping and results in the reengagement of RNAPII, thereby ensuring directional expression of m RNAs. Loss of Isw2 leads to reduced nucleosome occupancy over NDRs and the production of nc RNA, often initiated from 3’ NDRs and is mostly transcribed in the antisense direction of known coding sequences , which maintains an open NDR structure.
The maintenance of chromatin organization throughout the genome is therefore key to preventing aberrant transcription initiation.
The non-coding transcriptome includes numerous RNA species involved in the regulation of translation (t RNAs and r RNAs), but more recent studies have indicated the presence of several types of RNA molecules that have the potential to regulate gene expression [A).
Disruption of nucleosome reassembly following RNAPII passage results in spurious transcription initiation events, leading to the production of non-coding RNA (nc RNA).
We review the molecular mechanisms involved in the suppression of these cryptic initiation events and discuss the role played by nc RNAs in regulating gene expression.
For the purposes of this review, we refer to data obtained from the genome-wide nucleosomal mapping in ].
NDRs are also enriched for regulatory DNA sequences including transcription factor binding sites.