Where are G-quadruplexes located in the human transcriptome?

Abstract: It has been demonstrated that RNA G-quadruplexes (G4) are structural motifs present in transcriptomes and play important regulatory roles in several posttranscriptional mechanisms. However, the full picture of RNA G4 locations and the extent of their implication remain elusive. Solely computational prediction analysis of the whole transcriptome may reveal all potential G4, since experimental identifications are always limited to specific conditions or specific cell lines. The present study reports the first in-depth computational prediction of potential G4 region across the complete human transcriptome. Although using a relatively stringent approach based on three prediction scores that accounts for the composition of G4 sequences, the composition of their neighboring sequences, and the various forms of G4, over 1.1 million of potential G4 (pG4) were predicted. The abundance of G4 was computationally confirmed in both 5 and 3 UTR as well as splicing junction of mRNA, appreciate for the first time in the long ncRNA, while almost absent of most of the small ncRNA families. The present results constitute an important step toward a full understanding of the roles of G4 in posttranscriptional mechanisms

Violating the splicing rules: TG dinucleotides function as alternative 3' splice sites in U2-dependent introns

TG dinucleotides functioning as alternative 3' splice sites were identified and experimentally verified in 36 human genes

Biogenesis of mammalian microRNAs by a non-canonical processing pathway

Canonical microRNA biogenesis requires the Microprocessor components, Drosha and DGCR8, to generate precursor-miRNA, and Dicer to form mature miRNA. The Microprocessor is not required for processing of some miRNAs, including mirtrons, in which spliceosome-excised introns are direct Dicer substrates. In this study, we examine the processing of putative human mirtrons and demonstrate that although some are splicing-dependent, as expected, the predicted mirtrons, miR-1225 and miR-1228, are produced in the absence of splicing. Remarkably, knockout cell lines and knockdown experiments demonstrated that biogenesis of these splicing-independent mirtron-like miRNAs, termed ‘simtrons’, does not require the canonical miRNA biogenesis components, DGCR8, Dicer, Exportin-5 or Argonaute 2. However, simtron biogenesis was reduced by expression of a dominant negative form of Drosha. Simtrons are bound by Drosha and processed in vitro in a Drosha-dependent manner. Both simtrons and mirtrons function in silencing of target transcripts and are found in the RISC complex as demonstrated by their interaction with Argonaute proteins. These findings reveal a non-canonical miRNA biogenesis pathway that can produce functional regulatory RNAs

Algorithms and tools for splicing junction donor recognition in genomic DNA sequences

The consensus sequences at splicing junctions in genomic DNA are required for pre-mRNA breaking and rejoining which must be carried out precisely. Programs currently available for identification or prediction of transcribed sequences from within genomic DNA are far from being powerful enough to elucidate genomic structure completely[4]. In this research, we develop a degenerate pattern match algorithm for 5\u27 splicing site (Donor Site) recognition.. Using the Motif models we developed, we can mine out the degenerate pattern information from the consensus splicing junction sequences. Our experimental results show that, this algorithm can correctly recognize 93% of the total donor sites at the right positions in the test DNA group. And more than 91% of the donor sites the algorithm predicted are correct. These precision rates are higher than the best existing donor classification algorithm[25]. This research made a very important progress toward our full gene structure detection algorithm development

The zebrafish progranulin gene family and antisense transcripts

BACKGROUND: Progranulin is an epithelial tissue growth factor (also known as proepithelin, acrogranin and PC-cell-derived growth factor) that has been implicated in development, wound healing and in the progression of many cancers. The single mammalian progranulin gene encodes a glycoprotein precursor consisting of seven and one half tandemly repeated non-identical copies of the cystine-rich granulin motif. A genome-wide duplication event hypothesized to have occurred at the base of the teleost radiation predicts that mammalian progranulin may be represented by two co-orthologues in zebrafish. RESULTS: The cDNAs encoding two zebrafish granulin precursors, progranulins-A and -B, were characterized and found to contain 10 and 9 copies of the granulin motif respectively. The cDNAs and genes encoding the two forms of granulin, progranulins-1 and -2, were also cloned and sequenced. Both latter peptides were found to be encoded by precursors with a simplified architecture consisting of one and one half copies of the granulin motif. A cDNA encoding a chimeric progranulin which likely arises through the mechanism of trans-splicing between grn1 and grn2 was also characterized. A non-coding RNA gene with antisense complementarity to both grn1 and grn2 was identified which may have functional implications with respect to gene dosage, as well as in restricting the formation of the chimeric form of progranulin. Chromosomal localization of the four progranulin (grn) genes reveals syntenic conservation for grna only, suggesting that it is the true orthologue of mammalian grn. RT-PCR and whole-mount in situ hybridization analysis of zebrafish grns during development reveals that combined expression of grna and grnb, but not grn1 and grn2, recapitulate many of the expression patterns observed for the murine counterpart. This includes maternal deposition, widespread central nervous system distribution and specific localization within the epithelial compartments of various organs. CONCLUSION: In support of the duplication-degeneration-complementation model of duplicate gene retention, partitioning of expression between grna and grnb was observed in the intermediate cell mass and yolk syncytial layer, respectively. Taken together these expression patterns suggest that the function of an ancestral grn gene has been devolved upon four paralogues in zebrafish

Molecular basis of the human ApoAII exon 3 splicing

Among human genes, CFTR intron Vlll/exon 9 and apolipoprotein All intron Il/exon 3 boundaries share the characteristic feature given by the presence of a peculiar tract of alternating pyrimidines and purines close to the 3’ splice site. In the case of CFTR gene, the pyrimidine rich tract is composed by a stretch of Ts in a row and a stretch of alternating pyrimidines and purines (microsatellite TG dinucleotide repeats) and both tracts are polymorphic for their length. On the other hand, in the case of ApoAII gene the pyrimidine rich tract is made exclusively of alternating pyrimidines and purines (microsatellite TG dinucleotide repeats) and it is also polymorphic for its length in both genes. This apparent sequence similarity, concerning the TG tract, is contrasted by the different splicing pattern exhibited by the two genes. In fact, CFTR exon 9 undergoes alternative splicing to a variable extent, depending on the variations in length of the pyrimidine rich tract, whereas ApoAII exon 3 is constitutively included in mRNA. Previous studies of our group have shown in the CFTR intron Vlll/exon 9 context, the stretch of pyrimidines alternated with purines (within the UG tract) alone is not equivalent to a functional continuous polypyrimidine tract, contrarily to what has been observed for the apolipoprotein All gene. Moreover, the comparison of splice sites strength of human ApoAII exon 3 and human CFTR exon 9 has outlined an apparent contradiction between the splicing behavior of the two exons and the strength of the splice sites. In fact, both the 3’ and the 5’ splice sites of CFTR exon 9 display a good match with the consensus whereas the match of the ApoAII exon 3 splice sites is not good. Altogether these observations prompted us to investigate the mechanisms underlying the constitutive splicing of ApoAII exon 3 and, in particular, to characterize the cis-acting elements and the trans-acting factors involved in ApoAII exon 3 definition to assure its constitutive splicing. In order to study in vivo the splicing mechanism of ApoAII exon 3, we set up an eukaryotic expression system by cloning the whole ApoAII gene, from its promoter to the poly-A signal. Then, the effects of point mutations, deletions or substitutions on splicing of exon 3 were analyzed by RT-PCR after transient transfection in Hep3B cell line. Deletion or replacement of the UG repeats at the 3’ splice site of intron 2 resulted in a significant increase in exon 3 skipping, indicating the importance of this alternated arrangement of U and G as a functional polypyrmidine tract or at least as an important sequence able to lead the exon 3 definition. Furthermore, UV-crosslinking assays showed that the (UG)I6 repeats of ApoAII intron 2 are recognized by TDP-43, a protein that binds specifically the UG tract within the context of the 3' end of CFTR intron VIII and that affects negatively CFTR exon 9 splicing. Next, we characterized the exonic cis-acting elements able to affect the splicing efficiency of ApoAII exon 3. Transient transfections of different constructs of the ApoAII gene system carrying deletions or point mutations showed that the region spanning from nucleotide 87 to 113 of human ApoAII exon 3 is important for its close to the 5’ splice site. In order to identify trans-acting factor/s able to bind the 9nt-ESE within ApoAII exon 3, both Electro Mobility Shift Assay (EMSA) and UV-crosslinking coupled to immunoprécipitation assays were carried out. EMSA showed a broad band of shifted material with the ESEwt RNA, whereas no significant shift was seen with mutated ESE RNA. This suggested that one or more proteins interact specifically with the wild type ApoAII exon 3 across the 9nt-sequence. Then, UV-crosslinking followed by immunoprécipitation with monoclonal antibodies anti-SR proteins ASF/SF2 and anti-SC-35 showed that ESEwt but not mutated ESE RNA was able to immunoprecipitate a band whose molecular weight corresponds to that of ASF/SF2 and, even if to a lower extent, also a band whose molecular weight corresponds to that of SC35. Thus, these results provided an evidence that at least two SR proteins are able to interact with the sequence across the ESE sequence. Subsequently, the relevance of ESE position within an internal intron (and therefore with other flanking cis-acting elements) was also tested. Both in vitro and in vivo experiments showed that the ApoAII exon 3 ESE works only if it is localized within an internal exon and not if it is placed within the first or the last exon. These results also suggested the presence of other splicing regulatory elements within the flanking intronic regions of ApoAII exon 3. Thus, to explore intron 2 and 3 for the presence of cis-acting elements able to affect the splicing of exon 3, a series of deletions within both introns were carried out. Thus, we found at least one regulatory element placed within intron 3 that regulates positively exon 3 inclusion. In conclusion, the constitutive splicing of ApoAII exon 3 seems to be the result of the balance between positive and negative action of the regulatory elements found in the exon 3 and its flanking introns. Future studies will be aimed at identifying the factors interacting with the intronic regulatory elements and at defining a possible model to explain the mechanism of ApoAII exon 3 constitutive splicing by integrating the network of interactions among the identified cis-acting elements and trans-acting factors

Beiträge zu Verbreitung und Analytik des subtilen alternativen Spleißens

Das alternative Spleißen (AS) ist ein Hauptakteur der Diversifizierung von Transkriptom und Proteom eines eukaryotischen Organismus. Die Studien dieser Dissertationsschrift thematisieren das erst kürzlich entdeckte subtile AS, das die Einführung kleiner Variationen im Transkript und in vielen Fällen auch im kodierten Protein bewirkt. Im Arabidopsis thaliana-Genom konnte eine häufige Präsenz von NAGNAG Tandem-Motiven nachgewiesen werden, die in den Spleißfaktor-kodierenden SR-Protein-Genen überrepräsentiert sind. Ausgewählte experimentell analysierte Fälle zeigten ähnliche organ- und bedingungsspezifische Änderungen der Splei߬varianten-Verhältnisse. Im Mensch wurde ein völlig neuer, seltener Typus des subtilen AS entdeckt. Eine Population von 36 Introns verwendet TG Dinukleotide als alternative 3’ Splei߬stellen und widerspricht damit den etablierten Spleißregeln. TG-3‘-Splei߬stellen wurden ausschließlich im Kontext einer AG Splei߬stelle mit einer maximalen Distanz von 28 nt gefunden. In deren orthologen 3’ Splei߬stellen sind TG-Dinukleotid und flankierende Intronsequenz zwischen Säuge¬tieren auffällig stark konserviert. Deren Verwendungshäufigkeit steigt mit der Konservierung von Splei߬stelle und flankierender Intronsequenz und wird höchstwahrscheinlich durch cis- und/oder trans-Elemente vermittelt. Zur quantitativen Ermittlung der Splei߬variantenverhältnisse wurden die Pyrosequenzierung und die Fluoreszenz-basierte Kapillarelektro¬phorese verwendet. Beide Methoden wurden hinsichtlich Reproduzierbarkeit und Genauigkeit, Experimentaufbau und Datenanalyse im Vergleich zur häufig verwendeten Polyacrylamid-Gelelektrophorese mit Ethidiumbromid-vermittelter Densitometrie analysiert. CE-LIF erzielte dabei die höchste Genauigkeit und Reproduzierbarkeit und stellte gleichzeitig die arbeits- und zeiteffizienteste Methode dar

UCHL1 protein synthesis upon rapamycin treatment involves its antisense RNA trough embedded SINEB2 repeat

The initial description of genomes organization has consisted in the separation between regulatory and protein-coding DNA stretches. This simple and elegant model has supported the \u201cone region-one function\u201d theory: a genome is a linear arrangement of functional elements interspersed with nonfunctional regions. Recently the advances in transcriptomics technologies have shown that a genomic region can be used for different purposes and that functional elements can co-locate in the same region of the genome

Putting the Pieces Together: Exons and piRNAs: A Dissertation

Analysis of gene expression has undergone a technological revolution. What was impossible 6 years ago is now routine. High-throughput DNA sequencing machines capable of generating hundreds of millions of reads allow, indeed force, a major revision toward the study of the genome’s functional output—the transcriptome. This thesis examines the history of DNA sequencing, measurement of gene expression by sequencing, isoform complexity driven by alternative splicing and mammalian piRNA precursor biogenesis. Examination of these topics is framed around development of a novel RNA-templated DNA-DNA ligation assay (SeqZip) that allows for efficient analysis of abundant, complex, and functional long RNAs. The discussion focuses on the future of transcriptome analysis, development and applications of SeqZip, and challenges presented to biomedical researchers by extremely large and rich datasets