Regulation of RNA Polymerase II Transcription Initiation and Elongation by Transcription Factor TFII-I.
TL;DR: In this article, the authors reviewed the known functions of TFII-I related to the regulation of RNA polymerase II transcription at the stages of initiation and elongation, and showed that TFII is essential for the development of mice and represents a barrier for the induction of pluripotency.
Abstract: Transcription by RNA polymerase II (Pol II) is regulated by different processes, including alterations in chromatin structure, interactions between distal regulatory elements and promoters, formation of transcription domains enriched for Pol II and co-regulators, and mechanisms involved in the initiation, elongation, and termination steps of transcription. Transcription factor TFII-I, originally identified as an initiator (INR)-binding protein, contains multiple protein-protein interaction domains and plays diverse roles in the regulation of transcription. Genome-wide analysis revealed that TFII-I associates with expressed as well as repressed genes. Consistently, TFII-I interacts with co-regulators that either positively or negatively regulate the transcription. Furthermore, TFII-I has been shown to regulate transcription pausing by interacting with proteins that promote or inhibit the elongation step of transcription. Changes in TFII-I expression in humans are associated with neurological and immunological diseases as well as cancer. Furthermore, TFII-I is essential for the development of mice and represents a barrier for the induction of pluripotency. Here, we review the known functions of TFII-I related to the regulation of Pol II transcription at the stages of initiation and elongation.
Citations
More filters
2 citations
TL;DR: In this article , muscle transcriptome sequencing of two groups of individuals belonging to the tenth generation of rohu carp was performed using the Illumina HiSeq 2000 platform, and a total of 178 million paired-end raw reads were generated to give rise to 173 million reads after quality control and trimming.
Abstract: In most of the aquaculture selection programs, harvest body weight has been a preferred performance trait for improvement. Molecular interplay of genes linked to higher body weight is not elucidated in major carp species. The genetically improved rohu carp with 18% average genetic gain per generation with respect to harvest body weight is a promising candidate for studying genes’ underlying performance traits. In the present study, muscle transcriptome sequencing of two groups of individuals, with significant difference in breeding value, belonging to the tenth generation of rohu carp was performed using the Illumina HiSeq 2000 platform. A total of 178 million paired-end raw reads were generated to give rise to 173 million reads after quality control and trimming. The genome-guided transcriptome assembly and differential gene expression produced 11,86,119 transcripts and 451 upregulated and 181 downregulated differentially expressed genes (DEGs) between high-breeding value and low-breeding value (HB & LB) groups, respectively. Similarly, 39,158 high-quality coding SNPs were identified with the Ts/Tv ratio of 1.23. Out of a total of 17 qPCR-validated transcripts, eight were associated with cellular growth and proliferation and harbored 13 SNPs. The gene expression pattern was observed to be positively correlated with RNA-seq data for genes such as myogenic factor 6, titin isoform X11, IGF-1 like, acetyl-CoA, and thyroid receptor hormone beta. A total of 26 miRNA target interactions were also identified to be associated with significant DETs (p-value < 0.05). Genes such as Myo6, IGF-1-like, and acetyl-CoA linked to higher harvest body weight may serve as candidate genes in marker-assisted breeding and SNP array construction for genome-wide association studies and genomic selection.
References
More filters
TL;DR: The Inr constitutes the simplest functional promoter that has been identified and provides one explanation for how promoters that lack TATA elements direct transcription initiation.
1,462 citations
TL;DR: A model is developed to show that the measured saturation concentrations of phase separation are inversely proportional to the product of the numbers of arginine and tyrosine residues, which suggests it is possible to predict phase-separation properties based on amino acid sequences.
1,219 citations
TL;DR: This work provides the first evidence that a DNA-binding protein, CCCTC-binding factor (CTCF), can promote inclusion of weak upstream exons by mediating local RNA polymerase II pausing both in a mammalian model system for alternative splicing, CD45, and genome-wide.
Abstract: Alternative splicing of pre-messenger RNA is a key feature of transcriptome expansion in eukaryotic cells, yet its regulation is poorly understood. Spliceosome assembly occurs co-transcriptionally, raising the possibility that DNA structure may directly influence alternative splicing. Supporting such an association, recent reports have identified distinct histone methylation patterns, elevated nucleosome occupancy and enriched DNA methylation at exons relative to introns. Moreover, the rate of transcription elongation has been linked to alternative splicing. Here we provide the first evidence that a DNA-binding protein, CCCTC-binding factor (CTCF), can promote inclusion of weak upstream exons by mediating local RNA polymerase II pausing both in a mammalian model system for alternative splicing, CD45, and genome-wide. We further show that CTCF binding to CD45 exon 5 is inhibited by DNA methylation, leading to reciprocal effects on exon 5 inclusion. These findings provide a mechanistic basis for developmental regulation of splicing outcome through heritable epigenetic marks.
916 citations
TL;DR: Three distinct RNA polymerase activities have been isolated from developing sea urchin embryos, and in rat liver nuclei there are two RNA polymerases activities.
Abstract: Three distinct RNA polymerase activities have been isolated from developing sea urchin embryos. In rat liver nuclei there are two RNA polymerase activities. One polymerase (I) is probably localized in the nucleolus and one (II) in the nucleoplasm.
895 citations
TL;DR: This review covers current understanding of the biology of Williams–Beuren syndrome, a disorder of microdeletion or contiguous gene deletion, and its causes.
Abstract: Williams–Beuren syndrome, a multisystem disorder caused by the deletion of a chromosome region of 1.5 million to 1.8 million base pairs containing 26 to 28 genes, is a disorder of microdeletion or contiguous gene deletion. This review covers current understanding of the biology of this disorder.
621 citations