A purine-rich intronic element enhances alternative splicing of thyroid hormone receptor mRNA

Hastings, Michelle L.; Wilson, Catherine; Munroe, Stephen H.

doi:10.1017/s1355838201002084

Cited by 66 publications

(74 citation statements)

References 53 publications

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“…In our in vitro model only one alternative splice site is present, which is the distal splice site leading to TR 2 that is chosen over polyadenylation of TR 1. The discovery of the intronic enhancer element, SE 2, within the final intron of TR 2 mRNA supports the idea that these splicing factors are involved and that the model proposed for calcitonin would be valid in this case as well (Hastings et al 2001). However, involvement of other, possibly tissue-specific splicing factors that play a role in the splicing process of the TR pre-mRNA cannot be ruled out.…”

Section: Discussionmentioning

confidence: 57%

“…The ratio of SR proteins and hnRNP A1-like proteins is therefore an important determinant for alternative 5 -splice-site selection in transfected cells (Caceres et al 1994). The identification of a splicing enhancer element (SE 2) within the final intron of TR 2 mRNA that stimulates TR 2 mRNA splicing and interacts with ASF:SF2 (SF2) supports the idea that these splicing factors are involved (Hastings et al 2001).…”

Section: Introductionmentioning

confidence: 85%

“…In the intron of TR 2 a splicing enhancer element (SE 2) was characterized which stimulates TR 2 mRNA splicing in vitro. SE 2 binds SF2 which indicates that the splicing process might be influenced by binding of specific splicing proteins to this element (Lazar et al 1989, Laudet et al 1991, Hastings et al 2001. T 3 added at a concentration of 10 9 M increased the hnRNP A1:SF2 ratio in HepG2 cells, which coincided with an increase in TR 2 expression.…”

Section: Discussionmentioning

confidence: 99%

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Triiodothyronine affects the alternative splicing of thyroid hormone receptor alpha mRNA

Timmer

Bakker²,

Wiersinga

2003

Journal of Endocrinology

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The c-erbA gene encodes two thyroid hormone receptors, TR 1 and TR 2, that arise from alternative splicing of the TR pre-mRNA. TR 2 is not able to bind triiodothyronine (T 3 ) and acts as a weak antagonist of TRs. It has been suggested that the balance of TR 1 to TR 2 is important in maintaining homeostasis. Here, we study the effect of thyroid hormone on the splicing of TR under various conditions in HepG2 cells. First, T 3 was added to HepG2 cells that endogenously express TR . This resulted in a decrease in the TR 1:TR 2 mRNA ratio after the addition of 10 8 M or 10 7 M T 3 . Then, HepG2 cells were incubated with sera from hypothyroid or hyperthyroid patients. Sera from hyperthyroid patients (n=6) decreased the TR 1:TR 2 ratio compared with HepG2 cells incubated with sera from euthyroid patients (n=8). Sera from hypothyroid patients (n=6) had no effect on the TR 1:TR 2 ratio but supplementation with T 3 caused a decrease in the ratio. Finally, we tested sera from patients with nonthyroidal illness (NTI; n=17) which showed no effect on TR splicing when compared with controls. Free thyroxine levels in sera from hypo-, eu-, and hyperthyroid patients, but not that of NTI patients, were negatively correlated (P,0·01) to the TR 1:TR 2 ratio. We next studied the expression of the splicing factors hnRNP A1 and ASF/SF2 (SF2) in relation to the splicing of the TR gene. In HepG2 cells incubated with NTI sera a negative relationship was found between the ratio of hnRNP A1:SF2 and the TR 1:TR 2 ratio. A high hnRNP A1:SF2 ratio is associated with the use of the distal 5 -splice site. The splicing direction should then change towards TR 2, which is indeed the case. Rev-ErbA, which is partly complementary to TR 2 and could therefore interfere in the splicing process, did not relate to the TR 1:TR 2 ratio.In conclusion, high T 3 levels induce a low TR 1:TR 2 ratio which could protect the cell from excessive T 3 -induced gene expression. In vivo, this might be a mechanism to keep tissues relatively euthyroid during high serum T 3 levels.

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Section: Discussionmentioning

confidence: 57%

Section: Introductionmentioning

confidence: 85%

Section: Discussionmentioning

confidence: 99%

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Triiodothyronine affects the alternative splicing of thyroid hormone receptor alpha mRNA

Timmer

Bakker²,

Wiersinga

2003

Journal of Endocrinology

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“…Computational analyses indicate that sequence motifs for ESEs are more frequent in exons than in introns (28). However, there are a number of examples in which SR protein binding sites are located within the intron and can function to promote splicing of upstream 5Ј splice sites (8,(29)(30)(31)(32). At the same time, negative intronic regulatory elements with which SR proteins interact have also been found (20,29,33,34).…”

Section: Discussionmentioning

confidence: 99%

Serine/arginine-rich protein-dependent suppression of exon skipping by exonic splicing enhancers

Ibrahim

Schaal

Hertel

et al. 2005

Proc. Natl. Acad. Sci. U.S.A.

111

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The 5 and 3 splice sites within an intron can, in principle, be joined to those within any other intron during pre-mRNA splicing. However, exons are joined in a strict 5 to 3 linear order in constitutively spliced pre-mRNAs. Thus, specific mechanisms must exist to prevent the random joining of exons. Here we report that insertion of exon sequences into an intron can inhibit splicing to the downstream 3 splice site and that this inhibition is independent of intron size. The exon sequences required for splicing inhibition were found to be exonic enhancer elements, and their inhibitory activity requires the binding of serine͞arginine-rich splicing factors. We conclude that exonic enhancers can act as barriers to prevent exon skipping and thereby may play a key role in ensuring the correct 5 to 3 linear order of exons in spliced mRNA.intronic splicing silencers ͉ pre-mRNA splicing ͉ accurate splice-site recognition and pairing M ost genes in higher eukaryotes contain multiple introns and exons that are transcribed to generate pre-mRNA. The production of mature mRNA requires the precise removal of introns and joining of exons by splicing. In constitutively spliced pre-mRNAs all of the introns are excised, and the exons are joined in the correct 5Ј to 3Ј order. This is a consequence of the fact that 5Ј splice sites are ligated to a 3Ј splice site exclusively within the same intron, thus avoiding the exclusion of exons (''exon skipping''). Two key problems in understanding the mechanisms of accurate pre-mRNA splicing are how the splicing machinery recognizes exons and how exons are joined in the correct 5Ј to 3Ј order (i.e., how exon skipping is avoided).Significant advances have been made in understanding the mechanisms involved in accurate exon recognition (1-3). This process requires weakly conserved sequence elements located at the 5Ј and 3Ј splice sites and at the branchpoint sequence (BPS) within introns. In addition, exons contain sequence elements known as exonic splicing enhancers (ESEs), which function as binding sites for members of the serine͞arginine-rich (SR) family of splicing factors. The bound SR proteins promote the use of flanking 5Ј and 3Ј splice sites through both protein-protein and protein-RNA interactions (4-6). Although splicing enhancer͞SR protein complexes provide a mechanism for exon recognition, the mechanisms by which exon skipping is avoided are not understood.An important insight into this problem was provided by the observation that many human genetic diseases are the consequence of single base mutations in ESEs and that these mutations cause exon skipping (7). Further insights were provided by studies of regulated alternative splicing, where it was shown that the inclusion of an alternate exon requires an ESE and the presence of specific SR proteins (8). Thus, exonic enhancer͞SR protein complexes are required to avoid exon skipping in both constitutive and alternative splicing. Although these observations indicate that exon recognition is a necessary step in avoiding exon skipping, it ...

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“…Given the size and complexity of spliceosomes and their multistep assembly, it is perhaps not surprising that the activities of factors that interact with core spliceosome components would vary depending on their locations relative to these components. For example, the G-run-binding factor hnRNP H can participate in a splicing enhancer complex when G runs are located downstream of the 59ss (Chou et al 1999;Caputi and Zahler 2001;Hastings et al 2001;Schaub et al 2007) but can inhibit splicing when similar sequences are located in an exon (Chen et al 1999;Caputi and Zahler 2001).…”

Section: Context Dependence Of Sresmentioning

confidence: 99%

Splicing regulation: From a parts list of regulatory elements to an integrated splicing code

Wang¹,

Burge²

2008

RNA

881

761

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Alternative splicing of pre-mRNAs is a major contributor to both proteomic diversity and control of gene expression levels. Splicing is tightly regulated in different tissues and developmental stages, and its disruption can lead to a wide range of human diseases. An important long-term goal in the splicing field is to determine a set of rules or ''code'' for splicing that will enable prediction of the splicing pattern of any primary transcript from its sequence. Outside of the core splice site motifs, the bulk of the information required for splicing is thought to be contained in exonic and intronic cis-regulatory elements that function by recruitment of sequence-specific RNA-binding protein factors that either activate or repress the use of adjacent splice sites. Here, we summarize the current state of knowledge of splicing cis-regulatory elements and their context-dependent effects on splicing, emphasizing recent global/genome-wide studies and open questions.Keywords: context dependence; pre-mRNA splicing; splicing code; splicing factor; splicing regulation PRE-MRNA SPLICING Because human genes typically contain multiple introns, the process of pre-mRNA splicing is an essential step in the expression of most genes. A majority of human genes undergo alternative splicing (AS), generating multiple splicing isoforms containing different combinations of exons (Johnson et al. 2003). The effects of AS on protein products can be dramatic, e.g., producing soluble versus membranebound forms of the Fas receptor that have opposing effects on apoptosis (Cascino et al. 1995), or producing isoforms of the Drosophila fruitless protein that act to specify sexual orientation (Demir and Dickson 2005). The major forms of AS are summarized in Figure 1A. Splicing regulation has been comprehensively described in several recent reviews (Black 2003;Konarska and Query 2005;Matlin et al. 2005;Blencowe 2006;House and Lynch 2008). Here, we briefly summarize some aspects of splicing specificity and regulation before turning to our main topic of splicing regulatory elements and the rules governing their activity.The sequential phosphodiester transfer reactions involved in splicing are catalyzed by large ribonucleoprotein complexes known as spliceosomes. Containing more than 100 core proteins and five small nuclear RNAs (snRNAs U1, U2, U4, U5, and U6), spliceosomes may be the most complex machines in the cell (Zhou et al. 2002;Jurica and Moore 2003;Nilsen 2003). In addition to these core factors, additional regulatory proteins participate in the splicing of particular pre-mRNAs. Splicing of most introns is thought to occur cotranscriptionally with fairly extensive interactions between splicing factors and the core transcription machinery ( CORE SPLICING SIGNALSThree sites, the 59 splice site (59ss), the 39 splice site (39ss), and the branch point sequence (BPS), participate in the splicing reaction and are present in every intron, and thus are known as the core splicing signals. These signals are recognized multiple times during spl...

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A purine-rich intronic element enhances alternative splicing of thyroid hormone receptor mRNA

Cited by 66 publications

References 53 publications

Triiodothyronine affects the alternative splicing of thyroid hormone receptor alpha mRNA

Triiodothyronine affects the alternative splicing of thyroid hormone receptor alpha mRNA

Serine/arginine-rich protein-dependent suppression of exon skipping by exonic splicing enhancers

Splicing regulation: From a parts list of regulatory elements to an integrated splicing code

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