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      Splicing and transcription touch base: co-transcriptional spliceosome assembly and function

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          Abstract

          Several macromolecular machines collaborate to produce eukaryotic messenger RNA. RNA polymerase II (Pol II) translocates along genes that are up to millions of base pairs in length and generates a flexible RNA copy of the DNA template. This nascent RNA harbours introns that are removed by the spliceosome, which is a megadalton ribonucleoprotein complex that positions the distant ends of the intron into its catalytic centre. Emerging evidence that the catalytic spliceosome is physically close to Pol II in vivo implies that transcription and splicing occur on similar timescales and that the transcription and splicing machineries may be spatially constrained. In this Review, we discuss aspects of spliceosome assembly, transcription elongation and other co-transcriptional events that allow the temporal coordination of co-transcriptional splicing.

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          Histone exchange, chromatin structure and the regulation of transcription.

          The packaging of DNA into strings of nucleosomes is one of the features that allows eukaryotic cells to tightly regulate gene expression. The ordered disassembly of nucleosomes permits RNA polymerase II (Pol II) to access the DNA, whereas nucleosomal reassembly impedes access, thus preventing transcription and mRNA synthesis. Chromatin modifications, chromatin remodellers, histone chaperones and histone variants regulate nucleosomal dynamics during transcription. Disregulation of nucleosome dynamics results in aberrant transcription initiation, producing non-coding RNAs. Ongoing research is elucidating the molecular mechanisms that regulate chromatin structure during transcription by preventing histone exchange, thereby limiting non-coding RNA expression.
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            The pairwise energy content estimated from amino acid composition discriminates between folded and intrinsically unstructured proteins.

            The structural stability of a protein requires a large number of interresidue interactions. The energetic contribution of these can be approximated by low-resolution force fields extracted from known structures, based on observed amino acid pairing frequencies. The summation of such energies, however, cannot be carried out for proteins whose structure is not known or for intrinsically unstructured proteins. To overcome these limitations, we present a novel method for estimating the total pairwise interaction energy, based on a quadratic form in the amino acid composition of the protein. This approach is validated by the good correlation of the estimated and actual energies of proteins of known structure and by a clear separation of folded and disordered proteins in the energy space it defines. As the novel algorithm has not been trained on unstructured proteins, it substantiates the concept of protein disorder, i.e. that the inability to form a well-defined 3D structure is an intrinsic property of many proteins and protein domains. This property is encoded in their sequence, because their biased amino acid composition does not allow sufficient stabilizing interactions to form. By limiting the calculation to a predefined sequential neighborhood, the algorithm was turned into a position-specific scoring scheme that characterizes the tendency of a given amino acid to fall into an ordered or disordered region. This application we term IUPred and compare its performance with three generally accepted predictors, PONDR VL3H, DISOPRED2 and GlobPlot on a database of disordered proteins.
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              Getting up to speed with transcription elongation by RNA polymerase II.

              Recent advances in sequencing techniques that measure nascent transcripts and that reveal the positioning of RNA polymerase II (Pol II) have shown that the pausing of Pol II in promoter-proximal regions and its release to initiate a phase of productive elongation are key steps in transcription regulation. Moreover, after the release of Pol II from the promoter-proximal region, elongation rates are highly dynamic throughout the transcription of a gene, and vary on a gene-by-gene basis. Interestingly, Pol II elongation rates affect co-transcriptional processes such as splicing, termination and genome stability. Increasing numbers of factors and regulatory mechanisms have been associated with the steps of transcription elongation by Pol II, revealing that elongation is a highly complex process. Elongation is thus now recognized as a key phase in the regulation of transcription by Pol II.
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                Author and article information

                Journal
                100962782
                22271
                Nat Rev Mol Cell Biol
                Nat. Rev. Mol. Cell Biol.
                Nature reviews. Molecular cell biology
                1471-0072
                1471-0080
                18 April 2018
                09 August 2017
                October 2017
                01 May 2018
                : 18
                : 10
                : 637-650
                Affiliations
                [1 ]Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut 06520, USA
                Author notes
                Correspondence to K.M.N. karla.neugebauer@ 123456yale.edu
                [2]

                Present address: Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA

                [*]

                These authors contributed equally to this work.

                Article
                PMC5928008 PMC5928008 5928008 nihpa916505
                10.1038/nrm.2017.63
                5928008
                28792005
                4ecd2230-3208-4867-ae1d-6a9076d0e1dd
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