Out or decay: fate determination of nuclear RNAs

Abstract In eukaryotes, RNAs newly synthesized by RNA polymerase II (RNAPII) undergo several processing steps prior to transport to the cytoplasm. It has long been known that RNAs with defects in processing or export are removed in the nucleus. Recent studies revealed that RNAs without apparent defects are also subjected to nuclear degradation, indicating that nuclear RNA fate is determined in a more complex and dynamic way than previously thought. Nuclear RNA sorting directly determines the quality and quantity of RNA pools for future translation and thus is of significant importance. In this essay, we will summarize recent studies on this topic, mainly focusing on findings in mammalian system, and discuss about important remaining questions and possible biological relevance for nuclear RNA fate determination.

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Structural Determination of A Transcribing RNA Polymerase II Complex

10.21236/ada367567 ◽

1999 ◽

Author(s):

Averall Gnatt

Keyword(s):

Rna Polymerase ◽

Rna Polymerase Ii ◽

Structural Determination

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Structural Biology of RNA Polymerase II Transcription: 20 Years On

Annual Review of Cell and Developmental Biology ◽

10.1146/annurev-cellbio-042020-021954 ◽

2020 ◽

Vol 36 (1) ◽

pp. 1-34 ◽

Cited By ~ 1

Author(s):

Sara Osman ◽

Patrick Cramer

Keyword(s):

Rna Polymerase ◽

Rna Polymerase Ii ◽

Transcription Initiation ◽

Focal Point ◽

Dna Lesions ◽

Cellular Regulation ◽

Pol Ii ◽

Associated Proteins ◽

Rna Polymerase Ii Transcription

Gene transcription by RNA polymerase II (Pol II) is the first step in the expression of the eukaryotic genome and a focal point for cellular regulation during development, differentiation, and responses to the environment. Two decades after the determination of the structure of Pol II, the mechanisms of transcription have been elucidated with studies of Pol II complexes with nucleic acids and associated proteins. Here we provide an overview of the nearly 200 available Pol II complex structures and summarize how these structures have elucidated promoter-dependent transcription initiation, promoter-proximal pausing and release of Pol II into active elongation, and the mechanisms that Pol II uses to navigate obstacles such as nucleosomes and DNA lesions. We predict that future studies will focus on how Pol II transcription is interconnected with chromatin transitions, RNA processing, and DNA repair.

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Selective inhibition of rat liver nuclear RNA polymerase II by actinomycin D in vivo

Carcinogenesis ◽

10.1093/carcin/1.7.577 ◽

1980 ◽

Vol 1 (7) ◽

pp. 577-581 ◽

Cited By ~ 11

Author(s):

Fu-Li Yu

Keyword(s):

Rna Polymerase ◽

Rna Polymerase Ii ◽

Rat Liver ◽

Actinomycin D ◽

Selective Inhibition ◽

Nuclear Rna ◽

Nuclear Rna Polymerase ◽

Nuclear Rna Polymerase Ii

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Proximal sequence element-binding transcription factor (PTF) is a multisubunit complex required for transcription of both RNA polymerase II- and RNA polymerase III-dependent small nuclear RNA genes.

Molecular and Cellular Biology ◽

10.1128/mcb.15.4.2019 ◽

1995 ◽

Vol 15 (4) ◽

pp. 2019-2027 ◽

Cited By ~ 73

Author(s):

J B Yoon ◽

S Murphy ◽

L Bai ◽

Z Wang ◽

R G Roeder

Keyword(s):

Rna Polymerase ◽

Rna Polymerase Ii ◽

Small Nuclear Rna ◽

Class Iii ◽

Sequence Element ◽

Pol Ii ◽

Proximal Sequence Element ◽

Nuclear Rna ◽

Class Iii Genes ◽

Pol Iii

The proximal sequence element (PSE), found in both RNA polymerase II (Pol II)- and RNA Pol III-transcribed small nuclear RNA (snRNA) genes, is specifically bound by the PSE-binding transcription factor (PTF). We have purified PTF to near homogeneity from HeLa cell extracts by using a combination of conventional and affinity chromatographic methods. Purified PTF is composed of four polypeptides with apparent molecular masses of 180, 55, 45, and 44 kDa. A combination of preparative electrophoretic mobility shift and sodium dodecyl sulfate-polyacrylamide gel electrophoresis analyses has conclusively identified these four polypeptides as subunits of human PTF, while UV cross-linking experiments demonstrate that the largest subunit of PTF is in close contact with the PSE. The purified PTF activates transcription from promoters of both Pol II- and Pol III-transcribed snRNA genes in a PSE-dependent manner. In addition, we have investigated factor requirements in transcription of Pol III-dependent snRNA genes. We show that in extracts that have been depleted of TATA-binding protein (TBP) and associated factors, recombinant TBP restores transcription from U6 and 7SK promoters but not from the VAI promoter, whereas the highly purified TBP-TBP-associated factor complex TFIIIB restores transcription from the VAI but not the U6 or 7SK promoter. Furthermore, by complementation of heat-treated extracts lacking TFIIIC activity, we show that TFIIIC1 is required for transcription of both the 7SK and VAI genes, whereas TFIIIC2 is required only for transcription of the VAI gene. From these observations, we conclude (i) that PTF and TFIIIC2 function as gene-specific as gene-specific factors for PSE-and B-box-containing Pol III genes, respectively, (ii) that the form of TBP used by class III genes with upstream promoter elements differs from the from used by class III genes with internal promoters, and (iii) that TFIIIC1 is required for both internal and external Pol III promoters.

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Integrator, a Multiprotein Mediator of Small Nuclear RNA Processing, Associates with the C-Terminal Repeat of RNA Polymerase II

Cell ◽

10.1016/j.cell.2005.08.019 ◽

2005 ◽

Vol 123 (2) ◽

pp. 265-276 ◽

Cited By ~ 254

Author(s):

David Baillat ◽

Mohamed-Ali Hakimi ◽

Anders M. Näär ◽

Ali Shilatifard ◽

Neil Cooch ◽

...

Keyword(s):

Rna Polymerase ◽

Rna Polymerase Ii ◽

Rna Processing ◽

Terminal Repeat ◽

Small Nuclear Rna ◽

Nuclear Rna ◽

Nuclear Rna Processing

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The General Transcription Factors IIA, IIB, IIF, and IIE Are Required for RNA Polymerase II Transcription from the Human U1 Small Nuclear RNA Promoter

Molecular and Cellular Biology ◽

10.1128/mcb.19.3.2130 ◽

1999 ◽

Vol 19 (3) ◽

pp. 2130-2141 ◽

Cited By ~ 39

Author(s):

T. C. Kuhlman ◽

H. Cho ◽

D. Reinberg ◽

N. Hernandez

Keyword(s):

Transcription Factors ◽

Rna Polymerase ◽

Rna Polymerase Ii ◽

Transcription Initiation ◽

Small Nuclear Rna ◽

Initiation Complex ◽

General Transcription Factors ◽

Nuclear Rna ◽

Transcription Initiation Complex ◽

Rna Polymerase Ii Transcription

ABSTRACT RNA polymerase II transcribes the mRNA-encoding genes and the majority of the small nuclear RNA (snRNA) genes. The formation of a minimal functional transcription initiation complex on a TATA-box-containing mRNA promoter has been well characterized and involves the ordered assembly of a number of general transcription factors (GTFs), all of which have been either cloned or purified to near homogeneity. In the human RNA polymerase II snRNA promoters, a single element, the proximal sequence element (PSE), is sufficient to direct basal levels of transcription in vitro. The PSE is recognized by the basal transcription complex SNAPc. SNAPc, which is not required for transcription from mRNA-type RNA polymerase II promoters such as the adenovirus type 2 major late (Ad2ML) promoter, is thought to recruit TATA binding protein (TBP) and nucleate the assembly of the snRNA transcription initiation complex, but little is known about which GTFs other than TBP are required. Here we show that the GTFs IIA, IIB, IIF, and IIE are required for efficient RNA polymerase II transcription from snRNA promoters. Thus, although the factors that recognize the core elements of RNA polymerase II mRNA and snRNA-type promoters differ, they mediate the recruitment of many common GTFs.

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Transcription boundaries of U1 small nuclear RNA

Molecular and Cellular Biology ◽

10.1128/mcb.5.9.2332-2340.1985 ◽

1985 ◽

Vol 5 (9) ◽

pp. 2332-2340

Author(s):

G R Kunkel ◽

T Pederson

Keyword(s):

Rna Polymerase ◽

Rna Polymerase Ii ◽

Small Nuclear Rna ◽

Cell Nuclei ◽

Sm Proteins ◽

Isolated Nuclei ◽

Nuclear Rna ◽

Rna Biosynthesis ◽

Labeled Rna ◽

Alpha Amanitin

Transcription-proximal stages of U1 small nuclear RNA biosynthesis were studied by 32P labeling of nascent chains in isolated HeLa cell nuclei. Labeled RNA was hybridized to nitrocellulose-immobilized, single-stranded M13 DNA clones corresponding to regions within or flanking a human U1 RNA gene. Transcription of U1 RNA was inhibited by greater than 95% by alpha-amanitin at 1 microgram/ml, consistent with previous evidence that it is synthesized by RNA polymerase II. No hybridization to DNA immediately adjacent to the 5' end of mature U1 RNA (-6 to -105 nucleotides) was detected, indicating that, like all studied polymerase II initiation, transcription of U1 RNA starts at or very near the cap site. However, in contrast to previously described transcription units for mRNA, in which equimolar transcription occurs for hundreds or thousands of nucleotides beyond the mature 3' end of the mRNA, labeled U1 RNA hybridization dropped off sharply within a very short region (approximately 60 nucleotides) immediately downstream from the 3' end of mature U1 RNA. Also in contrast to pre-mRNA, which is assembled into ribonucleoprotein (RNP) particles while still nascent RNA chains, the U1 RNA transcribed in isolated nuclei did not form RNP complexes by the criterion of reaction with a monoclonal antibody for the small nuclear RNP Sm proteins. This suggests that, unlike pre-mRNA-RNP particle formation, U1 small nuclear RNP assembly does not occur until after the completion of transcription. These results show that, despite their common synthesis by RNA polymerase II, mRNA and U1 small nuclear RNA differ markedly both in their extents of 3' processing and their temporal patterns of RNP assembly.

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