Identification of a Binding Site for ASF/SF2 on an RNA Fragment Derived from the Hepatitis delta Virus Genome

Sikora, Dorota; Zhang, Dajiang; Bojic, Teodora; Beeharry, Yasnee; Tanara, Ali; Pelchat, Martin

doi:10.1371/journal.pone.0054832

Cited by 7 publications

(10 citation statements)

References 69 publications

(92 reference statements)

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“…Several cellular proteins associating with HDV RNA have been previously identified 23 , 24 , 50 , 51 . However, only a few interactions have been confirmed in a cellular system replicating the HDV RNA genome, and a role for most of those proteins in HDV biology is still unknown.…”

Section: Discussionmentioning

confidence: 99%

The Hepatitis Delta Virus accumulation requires paraspeckle components and affects NEAT1 level and PSP1 localization

Beeharry

Goodrum

Imperiale

et al. 2018

Sci Rep

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The Hepatitis Delta Virus (HDV) relies mainly on host proteins for its replication. We previously identified that PSF and p54nrb associate with the HDV RNA genome during viral replication. Together with PSP1, these proteins are part of paraspeckles, which are subnuclear bodies nucleated by the long non-coding RNA NEAT1. In this work, we established the requirement for PSF, p54nrb and PSP1 in HDV replication using RNAi-mediated knockdown in HEK-293 cells replicating the HDV RNA genome. We determined that HDV replication induces the delocalization of PSP1 to cytoplasmic foci containing PABP and increases NEAT1 level causing an enlargement of NEAT1 foci. Overall, our data support a role for the main paraspeckles proteins in HDV life cycle and indicate that HDV replication causes a cellular stress and induces both a delocalization of the PSP1 to the cytoplasm and a disruption of paraspeckles.

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Section: Discussionmentioning

confidence: 99%

The Hepatitis Delta Virus accumulation requires paraspeckle components and affects NEAT1 level and PSP1 localization

Beeharry

Goodrum

Imperiale

et al. 2018

Sci Rep

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“…(N) SRSF1 sites (complement to SRSASGA (-)) [47]. (O) SRSF1 sites (complement to RGAAGARR(-)) [50]. (P) SRSF1 sites (complement to RGAAGAAC (-)) [51].…”

Section: Scheme Of 15q11-12 Locusmentioning

confidence: 99%

“…For SRSF 1 proteins, following the data obtained by the functional UV cross-linking and immunoprecipitation (CLIP) method [49,67] and SELEX [50,51,68], we mapped potential sites for RNA binding on the locus sequence [Fig. 2M-R].…”

Section: Mapping Of Protein Binding Sitesmentioning

confidence: 99%

“…The binding sites derived by the functional method (Fig. 2N) had a consensus sequence SRSASGA (7-mer, S:G or C, R-purine) [49], which was more complicated by its nucleotide diversity than those derived on the basis of hepatitis delta virus genome sequence, which had a purine-rich consensus RGAAGARR (8-mer, R-purine) (Fig 2O) [50] or by the SELEX method (Fig. 2P), which was represented by RGAAGAAC (8-mer, R-purine) [51].…”

Section: Mapping Of Protein Binding Sitesmentioning

confidence: 99%

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Secondary structure of pre-mRNA introns for genes in the 15q11-12 locus. Mapping of functionally significant motives for RNA-binding proteins and nucleosome positioning signals

Fedoseyeva

Zharinova

Alexandrov

2018

Preprint

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31In this study, we identified reproducible substructures in the folded structures of long intron 32 RNAs for recursive spliced variants and annotated pre-mRNA for GABRB3 and GABRA5. We 33 mapped the RNA motives recognized by RNA-binding proteins for the specified locus and 34 characterized the area of preferred localization. A comparison of pre-mRNA variants revealed the 35 dominant type of protein potential effects. We determined the structural specifics of RNA in the 36 dense Alu cluster and clarified the analogy of apical substructure to the A-Xist fragment of 37 transcriptional variant. Mapping of the nucleosome potential reveals alternation of strong and weak 38 signals at the 3'-end portion of GABRB3 and clusters of nucleosome positioning signal in the 39 vicinity of the Alu cluster. Distribution of simple oligonucleotides among reproducible 40 substructures revealed an enrichment in Py-tracts; for some of them, this may be considered as a 41 complementary supplement to the Pu-tract enrichment of ncRNA Malat1 as a component of nuclear 42 speckles. The secondary structure elements of bidirectional transcripts are predisposed for somatic 43 homolog pairing in this locus, as was previously shown experimentally. 44 A model of potential intron RNA influence on splicing has been suggested based on its interaction 45 with Py-tract-binding RNP, serine-arginine SRSF proteins, ncRNA Malat1, as well as the action of 46 Alu cluster.47 49 The splicing model for exons surrounded by long introns is based on the assumption of a 50 pre-assembly of future spliceosome elements [1]. Splicing processes are assisted by components of 51 other processes, such as transcription (RNA-Pol II CTD) and chromosomal activation [2-6], 52including the SAGA and SWI/SNF complexes [7][8][9][10][11][12]. A large fraction of introns spanning 53 thousands of nucleotides participates in co-transcriptional splicing (coTS) without hindering 54 splicing [13]; however, among them, there is a fraction (up to 20%) that may be subject to splicing 55 at the post-transcriptional level (postTS) [14,15]. For example, the first long intron(s) is removed 3 56 from pre-mRNA more slowly than the others [14] and thus is the first candidate for postTS. The 57 role of the large introns themselves, at least of their main portion, remains poorly understood in the 58 splicing process. Still, a separate facet of the interaction has long been known, namely, that the 59 association between the nascent RNA and splicing factors in the nucleus is intron-dependent [16]. 60The significance of long introns is emphasized by the phenomenon of protecting long pre-mRNAs 61 from premature cleavage and polyadenylation [17][18]. The role of long introns can be clarified 62 by identifying the interaction of pre-mRNA (annotated as coding and/or in silico predicted RNA) 63 with RNA-binding proteins and other RNAs, for example, non-coding RNA, pertaining to 64 spliceosome pre-assembly. Non-coding RNA Malat1 is associated with recruitment of SR family 65 pre-mRNA-splicing factors from n...

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“…Мы ограничились серией из 15, для каждого из которых было выполнено картирование. Для белка SRSF1 (альтернативные обозначения ASR/SF2, SRp30a, SFRS1) последовательности сайтов связывания с РНК были использованы из данных [7][8][9]. Для белка SRSF1 повышенная плотность потенциальных мест связывания имеет тенденцию локализоваться в разных частях длинных интронов и с обязательным связыванием на 3´ конце генов, включающем более дробную экзон-интронную структуру.…”

Section: особенности локализации мест связывания белка Srsf1unclassified

The distribution of RNA recognizing protein sites for long genes on chromosome 15 of Homo sapiens

Fedoseyeva¹,

Zharinova²,

Alexandrov³

2018

Proceedings of the International Conference "Mathematical Biology and Bioinformatics"

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Identification of a Binding Site for ASF/SF2 on an RNA Fragment Derived from the Hepatitis delta Virus Genome

Cited by 7 publications

References 69 publications

The Hepatitis Delta Virus accumulation requires paraspeckle components and affects NEAT1 level and PSP1 localization

The Hepatitis Delta Virus accumulation requires paraspeckle components and affects NEAT1 level and PSP1 localization

Secondary structure of pre-mRNA introns for genes in the 15q11-12 locus. Mapping of functionally significant motives for RNA-binding proteins and nucleosome positioning signals

The distribution of RNA recognizing protein sites for long genes on chromosome 15 of Homo sapiens

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