CDK regulation of transcription by RNAP II: Not over ‘til it's over?

Abstract In all domains of life, the regulation of transcription by DNA-dependent RNA polymerases (RNAPs) is achieved at the level of initiation to a large extent. Whereas bacterial promoters are recognized by a σ-factor bound to the RNAP, a complex set of transcription factors that recognize specific promoter elements is employed by archaeal and eukaryotic RNAPs. These initiation factors are of particular interest since the regulation of transcription critically relies on initiation rates and thus formation of pre-initiation complexes. The most conserved initiation factor is the TATA-binding protein (TBP), which is of crucial importance for all archaeal-eukaryotic transcription initiation complexes and the only factor required to achieve full rates of initiation in all three eukaryotic and the archaeal transcription systems. Recent structural, biochemical and genome-wide mapping data that focused on the archaeal and specialized RNAP I and III transcription system showed that the involvement and functional importance of TBP is divergent from the canonical role TBP plays in RNAP II transcription. Here, we review the role of TBP in the different transcription systems including a TBP-centric discussion of archaeal and eukaryotic initiation complexes. We furthermore highlight questions concerning the function of TBP that arise from these findings.

Download Full-text

Regulation of transcription termination by glucosylated hydroxymethyluracil, base J, in Leishmania major and Trypanosoma brucei

Nucleic Acids Research ◽

10.1093/nar/gku714 ◽

2014 ◽

Vol 42 (15) ◽

pp. 9717-9729 ◽

Cited By ~ 39

Author(s):

David Reynolds ◽

Laura Cliffe ◽

Konrad U. Förstner ◽

Chung-Chau Hon ◽

T. Nicolai Siegel ◽

...

Keyword(s):

Cell Death ◽

Trypanosoma Brucei ◽

Leishmania Major ◽

Nuclear Dna ◽

Epigenetic Modification ◽

Transcription Termination ◽

Gene Clusters ◽

Regulation Of Transcription ◽

Genome Wide ◽

Rnap Ii

Abstract Base J, β-d-glucosyl-hydroxymethyluracil, is an epigenetic modification of thymine in the nuclear DNA of flagellated protozoa of the order Kinetoplastida. J is enriched at sites involved in RNA polymerase (RNAP) II initiation and termination. Reduction of J in Leishmania tarentolae via growth in BrdU resulted in cell death and indicated a role of J in the regulation of RNAP II termination. To further explore J function in RNAP II termination among kinetoplastids and avoid indirect effects associated with BrdU toxicity and genetic deletions, we inhibited J synthesis in Leishmania major and Trypanosoma brucei using DMOG. Reduction of J in L. major resulted in genome-wide defects in transcription termination at the end of polycistronic gene clusters and the generation of antisense RNAs, without cell death. In contrast, loss of J in T. brucei did not lead to genome-wide termination defects; however, the loss of J at specific sites within polycistronic gene clusters led to altered transcription termination and increased expression of downstream genes. Thus, J regulation of RNAP II transcription termination genome-wide is restricted to Leishmania spp., while in T. brucei it regulates termination and gene expression at specific sites within polycistronic gene clusters.

Download Full-text

Identification of cell-specific targets of sumoylation during mouse spermatogenesis

Reproduction ◽

10.1530/rep-15-0239 ◽

2016 ◽

Vol 151 (2) ◽

pp. 149-166 ◽

Cited By ~ 11

Author(s):

Yuxuan Xiao ◽

Daniel Pollack ◽

Miriam Andrusier ◽

Avi Levy ◽

Myrasol Callaway ◽

...

Keyword(s):

Cell Cycle Control ◽

Testicular Tissue ◽

Amino Acid Sequences ◽

Multiple Roles ◽

Regulation Of Transcription ◽

Meiotic Progression ◽

Cytoplasmic Transport ◽

Rnap Ii ◽

Enzymatic Pathways

Recent findings suggest diverse and potentially multiple roles of small ubiquitin-like modifier (SUMO) in testicular function and spermatogenesis. However, SUMO targets remain uncharacterized in the testis due to the complex multicellular nature of testicular tissue, the inability to maintain and manipulate spermatogenesis in vitro, and the technical challenges involved in identifying low-abundance endogenous SUMO targets. In this study, we performed cell-specific identification of sumoylated proteins using concentrated cell lysates prepared with de-sumoylation inhibitors from freshly purified spermatocytes and spermatids. One-hundred and twenty proteins were uniquely identified in the spermatocyte and/or spermatid fractions. The identified proteins are involved in the regulation of transcription, stress response, microRNA biogenesis, regulation of major enzymatic pathways, nuclear–cytoplasmic transport, cell-cycle control, acrosome biogenesis, and other processes. Several proteins with important roles during spermatogenesis were chosen for further characterization by co-immunoprecipitation, co-localization, and in vitro sumoylation studies. GPS-SUMO Software was used to identify consensus and non-consensus sumoylation sites within the amino acid sequences of the proteins. The analyses confirmed the cell-specific sumoylation and/or SUMO interaction of several novel, previously uncharacterized SUMO targets such as CDK1, RNAP II, CDC5, MILI, DDX4, TDP-43, and STK31. Furthermore, several proteins that were previously identified as SUMO targets in somatic cells (KAP1 and MDC1) were identified as SUMO targets in germ cells. Many of these proteins have a unique role in spermatogenesis and during meiotic progression. This research opens a novel avenue for further studies of SUMO at the level of individual targets.

Download Full-text

High resolution mapping of nucleic acid containing complexes in vitro and in situ

Proceedings, annual meeting, Electron Microscopy Society of America ◽

10.1017/s0424820100162703 ◽

1996 ◽

Vol 54 ◽

pp. 48-49

Author(s):

D. P. Bazett-Jones ◽

M. J. Hendzel

Keyword(s):

Nucleic Acid ◽

High Resolution ◽

Transcription Initiation ◽

Molecular Mechanisms ◽

Heavy Atom ◽

Regulation Of Transcription ◽

High Exposure ◽

Resolution Mapping ◽

Tata Sequence

Structural analysis of combinations of nucleosomes and transcription factors on promoter and enhancer elements is necessary in order to understand the molecular mechanisms responsible for the regulation of transcription initiation. Such complexes are often not amenable to study by high resolution crystallographic techniques. We have been applying electron spectroscopic imaging (ESI) to specific problems in molecular biology related to transcription regulation. There are several advantages that this technique offers in studies of nucleoprotein complexes. First, an intermediate level of spatial resolution can be achieved because heavy atom contrast agents are not necessary. Second, mass and stoichiometric relationships of protein and nucleic acid can be estimated by phosphorus detection, an element in much higher proportions in nucleic acid than protein. Third, wrapping or bending of the DNA by the protein constituents can be observed by phosphorus mapping of the complexes. Even when ESI is used with high exposure of electrons to the specimen, important macromolecular information may be provided. For example, an image of the TATA binding protein (TBP) bound to DNA is shown in the Figure (top panel). It can be seen that the protein distorts the DNA away from itself and much of its mass sits off the DNA helix axis. Moreover, phosphorus and mass estimates demonstrate whether one or two TBP molecules interact with this particular promoter TATA sequence.

Download Full-text

Linking transcription, RNA polymerase II elongation and alternative splicing

Biochemical Journal ◽

10.1042/bcj20200475 ◽

2020 ◽

Vol 477 (16) ◽

pp. 3091-3104 ◽

Cited By ~ 1

Author(s):

Luciana E. Giono ◽

Alberto R. Kornblihtt

Keyword(s):

Gene Expression ◽

Alternative Splicing ◽

Rna Polymerase Ii ◽

Environmental Changes ◽

Transcription Elongation ◽

Single Gene ◽

Regulation Of Gene Expression ◽

Regulation Of Transcription ◽

Stepping Stones ◽

Eukaryotic Transcription

Gene expression is an intricately regulated process that is at the basis of cell differentiation, the maintenance of cell identity and the cellular responses to environmental changes. Alternative splicing, the process by which multiple functionally distinct transcripts are generated from a single gene, is one of the main mechanisms that contribute to expand the coding capacity of genomes and help explain the level of complexity achieved by higher organisms. Eukaryotic transcription is subject to multiple layers of regulation both intrinsic — such as promoter structure — and dynamic, allowing the cell to respond to internal and external signals. Similarly, alternative splicing choices are affected by all of these aspects, mainly through the regulation of transcription elongation, making it a regulatory knob on a par with the regulation of gene expression levels. This review aims to recapitulate some of the history and stepping-stones that led to the paradigms held today about transcription and splicing regulation, with major focus on transcription elongation and its effect on alternative splicing.

Download Full-text

Protein expression changes in cells inoculated with Equine Influenza Virus: antibody microarray analysis

Polish Journal of Veterinary Sciences ◽

10.2478/pjvs-2013-0094 ◽

2013 ◽

Vol 16 (4) ◽

pp. 663-669

Author(s):

W. Rozek ◽

M. Kwasnik ◽

J.F. Zmudzinski

Keyword(s):

Influenza Virus ◽

Protein Quality ◽

Biological Properties ◽

Regulation Of Transcription ◽

Equine Influenza Virus ◽

Virus Antibody ◽

Antibody Microarray ◽

Equine Influenza ◽

Microarray Technique ◽

In Cells

AbstractChanges in the level of cellular proteins in cells inoculated with equine influenza virus H7N7 and H3N8 were studied with microarray technique. H3N8 induced pro-apoptotic proteins while H7N7 induced both pro- as well as anti-apoptotic factors. The higher level of some cytoskeleton components and proteins involved in the protein quality control was recorded. Relatively high number of proteins involved in the regulation of transcription was down-regulated. The pattern of changes observed for H7N7 and H3N8 may reflect differences in the biological properties of both serotypes.

Download Full-text