RNA methyltransferase BCDIN3D is crucial for female fertility and miRNA and mRNA profiles in Drosophila ovaries

RNA methyltransferases post-transcriptionally add methyl groups to RNAs, which can regulate their fates and functions. Human BCDIN3D (Bicoid interacting 3 domain containing RNA methyltransferase) has been reported to specifically methylate the 5′-monophosphates of pre-miR-145 and cytoplasmic tRNAHis. Methylation of the 5′-monophosphate of pre-miR-145 blocks its cleavage by the miRNA generating enzyme Dicer, preventing generation of miR-145. Elevated expression of BCDIN3D has been associated with poor prognosis in breast cancer. However, the biological functions of BCDIN3D and its orthologs remain unknown. Here we studied the biological and molecular functions of CG1239, a Drosophila ortholog of BCDIN3D. We found that ovary-specific knockdown of Drosophila BCDIN3D causes female sterility. High-throughput sequencing revealed that miRNA and mRNA profiles are dysregulated in BCDIN3D knockdown ovaries. Pathway analysis showed that many of the dysregulated genes are involved in metabolic processes, ribonucleoprotein complex regulation, and translational control. Our results reveal BCDIN3D’s biological role in female fertility and its molecular role in defining miRNA and mRNA profiles in ovaries.


Introduction
The epitranscriptome describes over 200 types of post-transcriptional RNA modifications, which can regulate the fates and functions of RNAs [1][2][3]. Post-transcriptional modification can occur on bases, riboses, and termini of RNAs. Dysregulation of RNA modification is associated with neurological disorders, cancers, and other diseases in human [4].
Among the many types of RNA modifications, methylation modification is the most prevalent. A wide variety of RNAs such as mRNAs, tRNAs, rRNAs, and small silencing RNAs, receive methylation modification on their bases, riboses, and termini, typically catalyzed by RNA methyltransferase enzymes that use S-Adenosyl methionine (SAM) as a methyl donor. For example, methylation of bases and caps of mRNAs can regulate their translation efficiency and stability [3,5]. Methylation of bases and riboses in tRNAs can regulate their stability and codon-anticodon interaction [6]. Methylation of bases and riboses in rRNAs is important for PLOS ONE | https://doi.org/10.1371/journal.pone.0217603 May 30, 2019 1 / 19 a1111111111 a1111111111 a1111111111 a1111111111 a1111111111 efficient and accurate translation by ribosome [7]. Methylation of the 3 0 -terminal ribose of small silencing RNAs can stabilize them [8]. However, we are still far from the complete understanding of RNA methylation. Which RNAs on which positions are methylated by which RNA methyltransferase enzymes? What are the molecular and biological roles of each of these RNA methylation? Human RNA methyltransferase BCDIN3D (Bicoid interacting 3 domain containing RNA methyltransferase) contains a methyltransferase domain and a Bicoid-interacting protein 3 domain (Fig 1A). It was previously reported that BCDIN3D specifically di-methylates 5 0monophosphate of pre-miR-145 using SAM as a methyl donor [9]. Dimethylation of 5 0 -monophosphate of pre-miR-145 blocks its cleavage by the miRNA generating enzyme Dicer, preventing production of miR-145. It was also reported that BCDIN3D specifically monomethylates the 5 0 -monophosphate of cytoplasmic tRNA His [10]. Functional consequence of the monomethylation of tRNA His remains unknown. In addition, BCDIN3D mRNA is overexpressed in human breast cancer cells [11] and elevated expression of BCDIN3D mRNA has been associated with poor prognosis in breast cancer [12]. BCDIN3D depletion in breast cancer cells abolishes their tumorigenic phenotypes [9]. Although BCDIN3D is conserved from worm to human, the biological functions of human BCDIN3D and its orthologs remain unknown. Moreover, molecular functions of BCDIN3D orthologs also remain elusive.
CG1239 is a Drosophila ortholog of BCDIN3D, and thus we name it Drosophila BCDIN3D ( Fig 1A). Drosophila BCDIN3D and human BCDIN3D share 26% identity and 38% similarity in their amino acid sequences. Here, we studied Drosophila BCDIN3D to gain insights into its biological and molecular functions. Ovary-specific depletion of BCDIN3D caused complete female sterility. High-throughput sequencing showed dysregulation of miRNA and mRNA profiles in BCDIN3D knockdown ovaries. Pathway analysis suggested dysregulated pathways such as those involved in metabolic processes, ribonucleoprotein complex regulation, and translational control. Our results reveal that Drosophila BCDIN3D plays crucial roles in female fertility and contributes to normal miRNA and mRNA profiles in ovaries.
BCDIN3D knockdown ovaries did not have dramatically different morphologies compared with control knockdown ovaries ( Fig 1C). However, none of the BCDIN3D knockdown flies could lay eggs while control knockdown flies laid~60-70 eggs per day per female (Fig 1D). These results revealed that BCDIN3D is required for female fertility.

Ovary-specific knockdown of BCDIN3D causes dysregulation of miRNA profile
To gain insight into the molecular mechanism by which ovary-specific knockdown of BCDIN3D causes female sterility, we performed high-throughput sequencing of ovary small RNAs (sRNA-seq) using three biological replicates for each genotype (S1 Table). We found that BCDIN3D knockdown causes dysregulation of miRNA profile in ovaries. Some miRNAs are significantly upregulated and others are downregulated in BCDIN3D knockdown ovaries compared with control knockdown ovaries (Fig 2). Endo-siRNAs (esi-1.1, esi-1.2, and esi-2.1) were generally upregulated in BCDIN3D knockdown ovaries. The trends of the miRNA and siRNA dysregulation were similar among the four different BCDIN3D shRNA knockdown flies, showing reproducibility.
To confirm dysregulation of miRNA profiles in BCDIN3D knockdown ovaries, we performed Northern blots to examine levels of individual miRNAs. Consistent with the sRNA-seq results (Fig 2), miR-311-3p and miR-312-3p were downregulated in BCDIN3D knockdown ovaries compared with control ovaries (Figs 3 and 4). In contrast, miR-318-3p, miR-994-5p, and miR-276a-3p were upregulated in BCDIN3D knockdown ovaries compared with control ovaries (Figs 3 and 4). We did not observe bands corresponding to precursors of these miR-NAs (pre-miRNAs), which are~60-80 nt long (Fig 3). These results show that the abundance of these miRNAs is changed by BCDIN3D knockdown without a clear change in that of corresponding pre-miRNAs.
As human BCDIN3D was reported to mono-methylates the 5 0 -monophosphate of tRNA His [10], we also examined abundance of a few tRNAs (tRNA His , tRNA Phe , and tRNA Asn ) by Northern blots. We observed no significant change in levels of tRNA His , tRNA Phe , and tRNA Asn in BCDIN3D knockdown ovaries compared with control ovaries (Figs 3 and 4).

Ovary-specific knockdown of BCDIN3D causes dysregulation of mRNA profile
Next, we performed high-throughput sequencing of poly-A+ mRNAs (mRNA-seq) using three biological replicates for each genotype (S2 Table). Principal component analysis and sample-to-sample distance analysis showed that mRNA profiles in BCDIN3D knockdown (four different fly strains [shRNA-BCDIN3D-no1, shRNA-BCDIN3D-no2, shRNA-BC-DIN3D-no3, shRNA-BCDIN3D-no4], three biological replicates each [rep1, rep2, rep3]) clustered together, away from those in control knockdown (two different strains [shRNA-mCherry, shRNA-white], three biological replicates each) (Fig 5A and 5B). We examined differential expression of~17,000 individual genes ( Fig 5C). Only 517 genes were significantly (FDR<0.05) upregulated and 781 genes were downregulated in shRNA-white compared with shRNA-mCherry. In contrast,~3000 genes were upregulated and~3000 genes were downregulated in each of the four BCDIN3D knockdown strains compared with shRNA-mCherry. Venn diagram analysis showed that among them, as many as 1694 genes were significantly upregulated and 1416 genes were downregulated in all of the four BCDIN3D knockdown Relative abundance of BCDIN3D mRNA normalized with rp49 mRNA in the ovaries of ovary-specific BCDIN3D knockdown and control knockdown flies. Mean ± SD for three biological replicates. P-value <0.05 is indicated by � (Student's t-test). (C) Stereomicroscope images of ovaries dissected from control and BCDIN3D knockdown flies. Scale bar shows 0.5 mm. (D) The numbers of eggs laid by control and BCDIN3D knockdown females crossed with OregonR wild-type males. Mean ± SD for three biological replicates. Each biological replicate datum represents the average number of eggs laid per single female in the cage containing 5 females and 3 males. P-value <0.05 is indicated by � (Student's t-test).

GO term pathway enrichment analysis of differentially expressed genes
1694 genes were significantly upregulated and 1416 genes were downregulated consistently in BCDIN3D knockdown ovaries compared with control knockdown ovaries. Using these sets of differentially expressed genes, we performed GO term pathway enrichment analysis to predict the pathways dysregulated in BCDIN3D knockdown ovaries.
GO term analysis of the 1694 upregulated genes revealed high enrichment for GO term biological processes related with ribonucleoprotein complex (i.e. ribonucleoprotein complex assembly and ribonucleoprotein), translation (i.e. formation of translation initiation ternary complex, translational termination, translational elongation, translation, cytoplasmic translation) and RNAs (i.e. ncRNA metabolic process, rRNA metabolic process, rRNA processing, RNA metabolic process) ( Table 1). GO term molecular functions related with ribosomes and RNA binding (i.e. structural constituent of ribosome, RNA binding, rRNA binding) were enriched. GO term cellular components related with ribosome (i.e. cytosolic large ribosomal subunit, ribosomal subunit, large ribosomal subunit, cytosolic small ribosomal subunit, preribosome, ribonucleoprotein complex, mitochondrial large ribosomal subunit) were highly enriched.
GO term analysis of the 1416 downregulated genes revealed high enrichment for GO term biological processes related with metabolism (i.e. cellular macromolecule metabolic process, DNA metabolic process, macromolecule metabolic process, metabolic process, organic substance metabolic process, and regulation of metabolic process) and cell cycles (i.e. nuclear division, regulation of cell cycle, cell cycle process, mitotic nuclear division, cell cycle, meiotic nuclear division, cell cycle phase transition, spindle organization, chromosome segregation) ( Table 2). GO term molecular functions related with binding and catalytic activity were enriched. Various GO term cellular components were enriched. Dysregulation of these pathways may cause the female sterility by ovary-specific BCDIN3D knockdown.

Discussion
In this study, we show that ovary-specific knockdown of Drosophila BCDIN3D causes female sterility without clear morphological defect in ovaries (Fig 1). High-throughput sequencing studies demonstrated that BCDIN3D plays important roles in defining miRNA and mRNA profiles in ovaries (Figs 2-6). Ovary-specific knockdown of BCDIN3D causes dysregulation of miRNA profile in ovaries. Heatmap of normalized miRNA and endo-siRNA (esi-1.1, esi-1.2, and esi-2.1) abundance in control and BCDIN3D knockdown ovaries determined by high-throughput sequencing. Mean log2 fold-change of three biological replicates relative to shRNA-mCherry control is shown. miRNAs are sorted in descending order of log2 fold-change in shRNA-BCDIN3D-no4. To eliminate miRNAs with very low expression levels, only miRNAs (n = 50) whose normalized mean abundance was more than 100 reads per million total reads in either of the strains are shown. https://doi.org/10.1371/journal.pone.0217603.g002 Some miRNAs were upregulated and other miRNAs were downregulated in BCDIN3D knockdown ovaries (Figs 2-4). Previous studies showed that human BCDIN3D reduces miR-145 level by di-methylating the 5 0 -monophosphate of pre-miR-145, which prevents its  processing by Dicer [9]. If Drosophila BCDIN3D similarly di-methylates certain pre-miRNAs and thereby blocks the production of the corresponding miRNAs, BCDIN3D knockdown is expected to cause upregulation of such miRNAs. We found that BCDIN3D knockdown causes upregulation of miR-318-3p, miR-994-5p, and miR-276a-3p (Figs 3 and 4). In contrast, we did not observe accumulation of pre-miR-318, pre-miR-994, and pre-miR-276a in control knockdown ovaries compared with BCDIN3D knockdown ovaries in our Northern blots (Fig 3). Thus, if these pre-miRNAs (pre-miR-318, pre-miR-994, and pre-miR-276a) are BCDIN3D substrates and are di-methylated blocking Dicer cleavage, such di-methylated pre-miRNAs might be degraded by other RNases rather than stably accumulated.
Other previous study showed that human BCDIN3D mono-methylates the 5 0 -monophosphate of tRNA His [10]. The presence or absence of monomethylation did not affect the steady state level of tRNA His in culture cells and therefore the molecular and biological functions of this tRNA His monomethylation remain unknown. We found that the levels of tRNA His , tRNA Phe , and tRNA Asn are not changed in BCDIN3D knockdown ovaries. This implies that, if BCDIN3D mono-methylates tRNA His , the modification does not affect steady-state stability of x-axis shows mean of normalized counts among the 6 biological samples tested (3 biological replicates each for two genotypess compared in each graph). y-axis shows log2 fold-change in the normalized counts relative to tRNA His in Drosophila ovaries either. Further study should examine whether Drosophila BCDIN3D methylates candidate pre-miRNAs and tRNA His .
We identified tens of miRNAs and thousands of mRNAs whose expression level is dysregulated upon BCDIN3D knockdown. Unbiased, transcriptome-wide approach to determine RNAs that are directly bound and methylated by Drosophila BCDIN3D and characterizing RNA methylation profiles between control and BCDIN3D knockdown ovaries will provide useful insight on the mechanisms by which BCDIN3D regulates these RNA levels.
In this study, we showed for the first time the biological function of evolutionary conserved RNA methyltransferase BCDIN3D in Drosophila female fertility. We also showed that Drosophila BCDIN3D is important for normal miRNA and mRNA profiles in ovaries. Our results indicate that RNA methylation by BCDIN3D plays crucial biological and molecular functions.

Fertility assay
For the female fertility assay, five test virgin females were mated with three wild-type (Ore-gonR) males in a cage with a 6-cm grape juice agar plate with wet yeast paste (Genesee) [16][17][18]. The grape juice agar plate was exchanged with a fresh one every day. The number of eggs laid on the third grape juice agar plate (set up on day 3 and recovered on day 4) was counted.

RNA preparation
Ovaries were hand-dissected from 2-5 days old flies fed with wet yeast paste [19]. Total RNA from ovaries was purified using miRVana (ThermoFisher). Tens of ovaries were used for each biological replicate preparation of the ovary RNA, resulting in tens to hundreds of microgram of purified total ovary RNAs.

Northern blot
Northern blot was performed as described previously [16,23]: 12 μg total ovary RNA was denatured in formamide loading buffer (98% v/v formamide, 0.1% w/v bromophenol blue and xylene cyanol, 10mM EDTA) at 95 C for 5 min and was resolved on a 0.4 mm thick, 12% denaturing polyacrylamide 7 M urea sequencing gel in 0.5×TBE (Tris-Borate-EDTA) buffer. After electrophoresis, RNA was transferred at 20 V for 1 hr to a Hybond-N+ membrane (GE health- care) in 0.5×TBE buffer using a semi-dry transfer system (Transblot SD, Bio-Rad). The RNA was UV cross-linked (HL2000, UVP) to the membrane and pre-hybridized in Church buffer for at least 60 min at 37 C. DNA oligonucleotide probes were 5 0 32 P-radiolabeled with T4 polynucleotide kinase (NEB) and γ-32 P-ATP. After labelling, non-incorporated nucleotides were removed using a Sephadex G-25 spin column (GE healthcare) and the probes were added to the Church buffer and hybridized for at least 6 hrs at 37 C. Membranes were washed three times for 10 min in 2×SSC containing 0.05% (w/v) SDS at 37 C, subsequently exposed to Storage Phosphor Screens (GE healthcare) and analyzed using FLA-9500 (GE healthcare). Probes were stripped from the membranes in boiling 0.1% SDS solution. The membranes were reprobed with the next probe. The DNA oligo probes used were as follows.

Deposited sequenced libraries
The SRA accession number for the small RNA-seq and mRNA-seq libraries reported in this manuscript is PRJNA518149.

Statistical test
Unpaired two-tailed Student's t-test was performed to determine statistical significance. The Benjamini-Hochberg method was used to adjust P-values for multiple comparisons.