Bioinformatic identification of candidate <i>cis</i>-regulatory elements involved in human mRNA polyadenylation

Hu, Jun; Lutz, Carol S.; Wilusz, Jeffrey; Tian, Bin

doi:10.1261/rna.2107305

Cited by 224 publications

(327 citation statements)

References 44 publications

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“…S4B). This result is consistent with our earlier observation that multiple UGUA elements are often observed within poly(A) site upstream sequences (37). Thus the structure of the CFI m 25 homodimer suggests a mechanism for the coordinate recognition of eight nucleotides: a set of two UGUA elements separated by a variable number of bases.…”

Section: Resultssupporting

confidence: 92%

“…We speculate that the array of recognition mechanisms that we observe provides strong selective pressure to maintain not only the integrity of the protein fold and the identity of key amino acids but also the specific RNA sequence required for binding. Indeed, the UGUA sequence has been found to be a component of the poly(A) signals of a wide range of organisms, from Chlamydomonas to humans (37,38).…”

Section: Resultsmentioning

confidence: 99%

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Structural basis of UGUA recognition by the Nudix protein CFI _m 25 and implications for a regulatory role in mRNA 3′ processing

Yang

Gilmartin

Doublié

2010

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

130

144

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Human Cleavage Factor Im (CFI m ) is an essential component of the pre-mRNA 3′ processing complex that functions in the regulation of poly(A) site selection through the recognition of UGUA sequences upstream of the poly(A) site. Although the highly conserved 25 kDa subunit (CFI m 25) of the CFI m complex possesses a characteristic α/β/α Nudix fold, CFI m 25 has no detectable hydrolase activity. Here we report the crystal structures of the human CFI m 25 homodimer in complex with UGUAAA and UUGUAU RNA sequences. CFI m 25 is the first Nudix protein to be reported to bind RNA in a sequencespecific manner. The UGUA sequence contributes to binding specificity through an intramolecular G:A Watson-Crick/sugar-edge base interaction, an unusual pairing previously found to be involved in the binding specificity of the SAM-III riboswitch. The structures, together with mutational data, suggest a novel mechanism for the simultaneous sequence-specific recognition of two UGUA elements within the pre-mRNA. Furthermore, the mutually exclusive binding of RNA and the signaling molecule Ap 4 A (diadenosine tetraphosphate) by CFI m 25 suggests a potential role for small molecules in the regulation of mRNA 3′ processing.T he transcriptome complexity of higher eukaryotes requires the coordinate recognition of an array of alternative pre-mRNA processing signals in a developmental and tissue-specific manner (1, 2). The sequences that direct pre-mRNA splicing and 3′ processing are initially recognized within the nascent transcript in a process that is intimately coupled to transcription (3, 4). While the recognition of exons within the pre-mRNA is mediated by both RNA:RNA and protein:RNA interactions (5), the 3′ processing of polyadenylated mRNAs appears to rely solely on the interaction of protein factors (6) with unstructured RNA sequences (7) within the nascent transcript.Vertebrate pre-mRNA 3′ processing signals are recognized by a tripartite mechanism through which a set of short RNA sequences direct the cooperative binding of three multimeric 3′ processing factors, cleavage factor I m (CFI m ), cleavage and polyadenylation specificity factor (CPSF), and cleavage stimulation factor (CstF) (8). CPSF and CstF bind the AAUAAA hexamer and downstream GU-rich elements that flank the poly(A) site, respectively, whereas CFI m interacts with upstream sequences that may function in the regulation of alternative polyadenylation (9-11). SELEX and biochemical analyses have identified the sequence UGUAN (N ¼ A > U > G, C) as the preferred binding site of CFI m (11). In this report we have taken a structural approach to determine the mechanism of sequence-specific RNA binding by CFI m .CFI m is composed of a large subunit of 59, 68, or 72 kDa and a small subunit of 25 kDa (CFI m 25, also referred to as CPSF5 or NUDT21) (12, 13), both of which contribute to RNA binding (14). The large subunit, encoded by either of two paralogs (CPSF6 and CPSF7), contains an N-terminal RNA Recognition Motif (RRM), an internal polyproline-rich region, and a C-termina...

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Section: Resultssupporting

confidence: 92%

Section: Resultsmentioning

confidence: 99%

Structural basis of UGUA recognition by the Nudix protein CFI _m 25 and implications for a regulatory role in mRNA 3′ processing

Yang

Gilmartin

Doublié

2010

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

130

144

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“…According to Retelska et al (2006), 46.73% polyadenylation events are dependent on the AAUAAA canonical polyadenylation signal (PAS) but 37.08% of them also occur in the presence of infrequently used PAS including GAUAAA (1.64%). As we found a conserved 'GATAAA' motif in mammals (Figure 1f and Supplementary Figure S1) as well as TGTA, TATA, G-rich and C-rich polyadenylation regulatory elements in intron2 (Gilmartin 2005;Hu et al, 2005;Lee et al, 2008) we performed 3 0 RACE PCR on polyA-mRNA from DLD1 cells, which confirmed the existence of SOX9 mRNA ended by a polyA tract located 409-bp downstream of the exon2 border (Figure 1f and Supplementary Figure S1). …”

Section: Sox9 Mrna Variants Are Expressed In Colon Cancer Cellssupporting

confidence: 55%

MiniSOX9, a dominant-negative variant in colon cancer cells

et al. 2011

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Inherited and acquired changes in pre-mRNA processing have significant roles in human diseases, especially cancer. Characterization of aberrantly spliced mRNAs may thus contribute to understand malignant transformation. We recently reported an anti-oncogenic potential for the SOX9 transcription factor in the colon. For instance, the Sox9 gene knock out in the mouse intestine results in an excess of proliferation with appearance of hyperplasia. SOX9 is expressed in colon cancer cells but its endogenous activity is weak. We looked for SOX9 variants that may impair SOX9 activity in colon cancer cells and we discovered MiniSOX9, a truncated version of SOX9 devoid of transactivation domain as a result of retention of the second intron. A significant overexpression of MiniSOX9 mRNA in human tumor samples compared with their matched normal tissues was observed by realtime reverse transcriptase-PCR. Immunohistochemistry revealed that MiniSOX9 is expressed at high levels in human colon cancer samples whereas it is undetectable in the surrounding healthy tissues. Finally, we discovered that MiniSOX9 behaves as a SOX9 inhibitor, inhibits protein kinase Ca promoter activity and stimulates the canonical Wnt pathway. This potential oncogenic activity of the SOX9 locus gives new insights on its role in colon cancer.

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“…1A), does not have a consensus sequence, but often consists of a U-rich element (UUUU) [2] or similar sequences (UGUA, UAUA) [54]. The efficiency of cleavage and polyadenylation is enhanced by the presence of this auxiliary element, as it promotes the binding of other polyadenylation factors to the cleavage site [55][56][57][58].…”

Section: The Downstream Element (Dse)-mentioning

confidence: 99%

Protein factors in pre-mRNA 3′-end processing

Mandel

Bai

Tong

2007

Cell. Mol. Life Sci.

364

482

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Most eukaryotic mRNA precursors (pre-mRNAs) must undergo extensive processing, including cleavage and polyadenylation at the 3′-end. Processing at the 3′-end is controlled by sequence elements in the pre-mRNA (cis elements) as well as protein factors. Despite the seeming biochemical simplicity of the processing reactions, more than 14 proteins have been identified for the mammalian complex, and more than 20 proteins have been identified for the yeast complex. The 3′-end processing machinery also has important roles in transcription and splicing. The mammalian machinery contains several sub-complexes, including cleavage and polyadenylation specificity factor (CPSF), cleavage stimulation factor (CstF), cleavage factor I (CF I m ), and cleavage factor II (CF II m ). Additional protein factors include poly(A) polymerase (PAP), poly(A) binding protein (PABP), symplekin, and the C-terminal domain (CTD) of RNA polymerase II largest subunit. The yeast machinery includes cleavage factor IA (CF IA), cleavage factor IB (CF IB), and cleavage and polyadenylation factor (CPF).

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Bioinformatic identification of candidate cis-regulatory elements involved in human mRNA polyadenylation

Cited by 224 publications

References 44 publications

Structural basis of UGUA recognition by the Nudix protein CFI _m 25 and implications for a regulatory role in mRNA 3′ processing

Structural basis of UGUA recognition by the Nudix protein CFI _m 25 and implications for a regulatory role in mRNA 3′ processing

MiniSOX9, a dominant-negative variant in colon cancer cells

Protein factors in pre-mRNA 3′-end processing

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Bioinformatic identification of candidate cis-regulatory elements involved in human mRNA polyadenylation

Cited by 224 publications

References 44 publications

Structural basis of UGUA recognition by the Nudix protein CFI m 25 and implications for a regulatory role in mRNA 3′ processing

Structural basis of UGUA recognition by the Nudix protein CFI m 25 and implications for a regulatory role in mRNA 3′ processing

MiniSOX9, a dominant-negative variant in colon cancer cells

Protein factors in pre-mRNA 3′-end processing

Contact Info

Product

Resources

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Structural basis of UGUA recognition by the Nudix protein CFI _m 25 and implications for a regulatory role in mRNA 3′ processing

Structural basis of UGUA recognition by the Nudix protein CFI _m 25 and implications for a regulatory role in mRNA 3′ processing