Transcription elongation is a dynamic process that alters depending upon the sequence heterogeneity of the DNA being transcribed. Hence, it is not surprising that the elongation complex's composition also varies along the way while transcribing a gene.
The transcription elongation is regulated via pausing of RNA polymerase on several occasions during transcription. In bacteria, these halts are necessary because the transcription of DNA into mRNA is coupled to the translation of that mRNA into a protein. However, in eukaryotes, the transcription is coupled with mRNA processing. Hence, pausing of RNA polymerase around exon-intron junctions is necessary for increasing the efficiency of mRNA splicing.
These halts in RNA Polymerase activity may be reversible or irreversible. In case of a reversible pause, proteins such as TFIIF, elongins, ELL, ensure that the RNA Polymerase resumes elongation after a brief pause. However, if the halt in RNA Polymerase activity is irreversible, it becomes a transcriptional arrest. If transcription is arrested, then the enzyme cannot resume elongation on its own. In such a situation, elongation factors such as TFIIS and pTEFb enable RNA Polymerase II to read through the DNA template at transcriptional arrest sites.
In addition, ATP-dependent chromatin remodeling factors and histone chaperones are also involved in the regulation of transcription elongation. Together they can alter the positions of nucleosomes along the DNA, making it accessible or inaccessible to the transcription machinery.
Hence, RNA polymerase needs the help of several factors to cruise through chromatin and specific sequences that interfere with transcription.
