Pseudouridines in spliceosomal snRNAs

Spliceosomal RNAs are a family of small nuclear RNAs(snRNAs)that are essential for pre-mRNA splicing.All vertebrate spliceosomal snRNAs are extensively pseudouridylated after transcription.Pseudouridines in spliceosomal snRNAs are generally clustered in regions that are functionally important during splicing.Many of these modified nucleotides are conserved across species lines.Recent studies have demonstrated that spliceosomal snRNA pseudouridylation is catalyzed by two different mechanisms:an RNA-dependent mechanism and an RNA-independent mechanism.The functions of the pseudouridines in spliceosomal snRNAs(U2 snRNA in particular)have also been extensively studied.Experimental data indicate that virtually all pseudouridines in U2 snRNA are functionally important.Besides the currently known pseudouridines(constitutive modifications),recent work has also indicated that pseudouridylation can be induced at novel positions under stress conditions,thus strongly suggesting that pseudouridylation is also a regulatory modification.

Epitranscriptomics of cancer

The functional impact of modifications of cellular RNAs,including m RNAs,mi RNAs and lnc RNAs,is a field of intense study.The role of such modifications in cancer has started to be elucidated.Diverse and sometimes opposite effects of RNA modifications have been reported.Some RNA modifications promote,while ot-hers decrease the growth and invasiveness of cancer.The present manuscript reviews the current knowledge on the potential impacts of N6-Methyladenosine,Pse-udouridine,Inosine,2’O-methylation or methylcytidine in cancer’s RNA.It also highlights the remaining qu-estions and provides hints on research avenues and potential therapeutic applications,whereby modulating dynamic RNA modifications may be a new method to treat cancer.

Insight into the mechanisms and functions of spliceosomal snRNA pseudouridylation

Pseudouridines(Ψs) are the most abundant and highly conserved modified nucleotides found in various stable RNAs of all organisms. Most Ψs are clustered in regions that are functionally important for pre-m RNA splicing. Ψ has an extra hydrogen bond donor that endows RNA molecules with distinct properties that contribute significantly to RNA-mediated cellular processes. Experimental data indicate that spliceosomal sn RNA pseudouridylation can be catalyzed by both RNA-dependent and RNA-independent mechanisms. Recent work has also demonstrated that pseudouridylation can be induced at novel positions under stress conditions, suggesting a regulatory role for Ψ.

Sequencing methods and functional decoding of mRNA modifications

More than 160 types of post-transcriptional RNA modifications have been reported;there is substantial variation in modification type,abundance,site,and function across species,tissues,and RNA type.The recent development of high-throughput detection technology has enabled identification of diverse dynamic and reversible RNA modifications,including N6,2′-O-dimethyladenosine(m6Am),N1-methyladenosine(m1A),5-methylcytosine(m5C),N6-methyladenosine(m6A),pseudouridine(Ψ),and inosine(I).In this review,we focus on eukaryotic mRNA modifications.We summarize their biogenesis,regulatory mechanisms,and biological functions,as well as highthroughput methods for detection of mRNA modifications.We also discuss challenges that must be addressed in mRNA modification research.

Deciphering the epitranscriptome： A green perspective

The advent of high-throughput sequencing technol- ogies coupled with new detection methods of RNA modifica- tions has enabled investigation of a new layer of gene regulation - the epitranscriptome. With over loo known RNA modifications, understanding the repertoire of RNA modifications is a huge undertaking. This review summarizes what is known about RNA modifications with an emphasis on discoveries in plants. RNA ribose modifications, base methyl- ations and pseudouridylation are required for normal develop- ment in Arabidopsis, as mutations in the enzymes modifying them have diverse effects on plant development and stress responses. These modifications can regulate RNA structure, turnover and translation. Transfer RNA and ribosomal RNA modifications have been mapped extensively and their functions investigated in many organisms, including plants. Recent work exploring the locations, functions and targeting of N6-methyladenosine （m^6A）, 5-methylcytosine （m^5C）, pseudour- idine （up）, and additional modifications in mRNAs and ncRNAs are highlighted, as well as those previously known on tRNAs and rRNAs. Many questions remain as to the exact mechanisms of targeting and functions of specific modified sites and whether these modifications have distinct functions in the different classes of RNAs.

CLINICAL VALUE OF URINARY AND SERUM PSEUDOURIDINE IN DIAGNOSIS AND MONITORING OF PRIMARY LIVER CANCER

Urinary and serum pseudouridine concentrations were determined by high-performance liquid chromatography in 80 patients with primary liver cancer, 32 with benign space occupying lesions of the liver, 42 with liver cirrhosis and 40 healthy subjects. Their mean urinary and serum pseudouridine levels were 39.2=11.5 nmol / /μmol creatinine and 3.4 ± 1.3 μmol / L, 24.5 = 5.4 nmol / μmol creatinine and 2.5 = 0.5 μmol / L, 22.8 ± 7.8 nmol / μmol creatinine and 2.3 = 0.4 μmol / L, 26.4 ± 4.6 nmol / μmol creatinine and 2.3 = 0.4 μmol / L, respectively. Exceeding the mean plus 2SD of pseudouridine of healthy control was considered as positive value for the diagnosis of primary liver cancer. Thus the positivity of urinary and serum pseudouridine in hepatoma was 71.3% and 70.0%, respectively. The positive rate of combined pseudouridine and alpha-fetoprotein assay was 91.3% in patients with hepatoma. Besides, pseudouridine levels could elevate before positive localization and reduce to normal levels after tumor resection. The results showed that the determination of pseudouridine is of clinical significance in the diagnosis and monitoring of primary liver cancer.