Faculty Opinions recommendation of Size-Dependent Increase in RNA Polymerase II Initiation Rates Mediates Gene Expression Scaling with Cell Size.

The recognition of changes in environmental conditions, and the ability to adapt to these changes, is essential for the viability of cells. There are numerous well characterized systems by which the presence or absence of an individual metabolite may be recognized by a cell. However, the recognition of a metabolite is just one step in a process that often results in changes in the expression of whole sets of genes required to respond to that metabolite. In higher eukaryotes, the signalling pathway between metabolite recognition and transcriptional control can be complex. Recent evidence from the relatively simple eukaryote yeast suggests that complex signalling pathways may be circumvented through the direct interaction between individual metabolites and regulators of RNA polymerase II-mediated transcription. Biochemical and structural analyses are beginning to unravel these elegant genetic control elements.

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Insertion of the promoter for a variant surface glycoprotein gene expression site in an RNA polymerase II transcription unit of procyclic Trypanosoma brucei

Molecular and Biochemical Parasitology ◽

10.1016/0166-6851(93)90205-c ◽

1993 ◽

Vol 57 (2) ◽

pp. 295-304 ◽

Cited By ~ 8

Author(s):

Joost C.B.M. Zomerdijk ◽

Rudo Kieft ◽

Piet Borst

Keyword(s):

Gene Expression ◽

Rna Polymerase ◽

Rna Polymerase Ii ◽

Trypanosoma Brucei ◽

Transcription Unit ◽

Surface Glycoprotein ◽

Variant Surface Glycoprotein ◽

Glycoprotein Gene ◽

Expression Site ◽

Rna Polymerase Ii Transcription

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Acute perturbation strategies in interrogating RNA polymerase II elongation factor function in gene expression

Genes & Development ◽

10.1101/gad.346106.120 ◽

2021 ◽

Vol 35 (3-4) ◽

pp. 273-285

Author(s):

Bin Zheng ◽

Yuki Aoi ◽

Avani P. Shah ◽

Marta Iwanaszko ◽

Siddhartha Das ◽

...

Keyword(s):

Gene Expression ◽

Rna Polymerase ◽

Rna Polymerase Ii ◽

Elongation Factor ◽

Factor Function

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The Role of RNA Polymerase II Contiguity and Long-Range Interactions in the Regulation of Gene Expression in Human Pluripotent Stem Cells

Stem Cells International ◽

10.1155/2019/1375807 ◽

2019 ◽

Vol 2019 ◽

pp. 1-12

Author(s):

Livia Eiselleova ◽

Viktor Lukjanov ◽

Simon Farkas ◽

David Svoboda ◽

Karel Stepka ◽

...

Keyword(s):

Gene Expression ◽

Stem Cells ◽

Rna Polymerase ◽

Rna Polymerase Ii ◽

Long Range ◽

Pluripotent Stem Cells ◽

Human Pluripotent Stem Cells ◽

Transcription Factories ◽

Long Range Interactions ◽

Rnap Ii

The eukaryotic nucleus is a highly complex structure that carries out multiple functions primarily needed for gene expression, and among them, transcription seems to be the most fundamental. Diverse approaches have demonstrated that transcription takes place at discrete sites known as transcription factories, wherein RNA polymerase II (RNAP II) is attached to the factory and immobilized while transcribing DNA. It has been proposed that transcription factories promote chromatin loop formation, creating long-range interactions in which relatively distant genes can be transcribed simultaneously. In this study, we examined long-range interactions between the POU5F1 gene and genes previously identified as being POU5F1 enhancer-interacting, namely, CDYL, TLE2, RARG, and MSX1 (all involved in transcriptional regulation), in human pluripotent stem cells (hPSCs) and their early differentiated counterparts. As a control gene, RUNX1 was used, which is expressed during hematopoietic differentiation and not associated with pluripotency. To reveal how these long-range interactions between POU5F1 and the selected genes change with the onset of differentiation and upon RNAP II inhibition, we performed three-dimensional fluorescence in situ hybridization (3D-FISH) followed by computational simulation analysis. Our analysis showed that the numbers of long-range interactions between specific genes decrease during differentiation, suggesting that the transcription of monitored genes is associated with pluripotency. In addition, we showed that upon inhibition of RNAP II, long-range associations do not disintegrate and remain constant. We also analyzed the distance distributions of these genes in the context of their positions in the nucleus and revealed that they tend to have similar patterns resembling normal distribution. Furthermore, we compared data created in vitro and in silico to assess the biological relevance of our results.

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Nhp6p and Med3p Regulate Gene Expression by Controlling the Local Subunit Composition of RNA Polymerase II

Journal of Molecular Biology ◽

10.1016/j.jmb.2008.03.069 ◽

2008 ◽

Vol 379 (2) ◽

pp. 212-230 ◽

Cited By ~ 8

Author(s):

Xiaowei Xue ◽

Norbert Lehming

Keyword(s):

Gene Expression ◽

Rna Polymerase ◽

Rna Polymerase Ii ◽

Subunit Composition ◽

Regulate Gene Expression ◽

Regulate Gene

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Modifications of RNA polymerase II are pivotal in regulating gene expression states

EMBO Reports ◽

10.1038/embor.2009.221 ◽

2009 ◽

Vol 10 (11) ◽

pp. 1213-1219 ◽

Cited By ~ 103

Author(s):

Emily Brookes ◽

Ana Pombo

Keyword(s):

Gene Expression ◽

Rna Polymerase ◽

Rna Polymerase Ii

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The largest subunit of RNA polymerase II in Dictyostelium: conservation of the unique tail domain and gene expression

Biochemistry and Cell Biology ◽

10.1139/o92-120 ◽

1992 ◽

Vol 70 (9) ◽

pp. 792-799 ◽

Cited By ~ 4

Author(s):

Tak Yee Lam ◽

Lawrence Chan ◽

Patrick Yip ◽

Chi-Hung Siu

Keyword(s):

Gene Expression ◽

Rna Polymerase ◽

Rna Polymerase Ii ◽

Developmental Process ◽

Developmental Regulation ◽

Consensus Sequence ◽

Protein Band ◽

Tail Domain ◽

Mrna Accumulation ◽

Carboxyl Terminal

cDNAs encoding the largest subunit of RNA polymerase II were isolated from a Dictyostelium cDNA library. A total of 2.9 kilobases (kb) of cDNA was sequenced and the amino acid sequence of the carboxyl-terminal half of the protein was deduced. Similar to other eukaryotic RNA polymerases II, the largest subunit of Dictyostelium RNA polymerase II contains a unique repetitive tail domain at its carboxyl-terminal region. It consists of 24 highly conserved heptapeptide repeats, with a consensus sequence of Tyr-Ser-Pro-Thr-Ser-Pro-Ser. In addition to the tail domain, five segments of the deduced primary structure show > 50% sequence identity with either yeast or mouse protein. RNA blots show that cDNA probes hybridized with a single mRNA species of ~ 6 kb and immunoblots using a monoclonal antibody raised against the tail domain lighted up a single protein band of 200 kilodaltons. Interestingly, expression of the largest subunit of RNA polymerase II appears to be under developmental regulation. The accumulation of its mRNA showed a 60% increase during the first 3 h of development, followed by a steady decrease during the next 6 h. Cells began to accumulate a higher level of the RNA polymerase II mRNA after 9 h of development. When cells were treated with low concentrations of cAMP pulses to stimulate the developmental process, the pattern of mRNA accumulation moved 3 h ahead, but otherwise remained similar to that of control cells.Key words: RNA polymerase, cDNA, sequence homology, gene expression, Dictyostelium.

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