Antibiotic-Induced Gut Microbiota Dysbiosis Modulates Host Transcriptome and m6A Epitranscriptome via Bile Acid Metabolism

Gut microbiota can influence host gene expression and physiology through metabolites. Besides, the presence or absence of gut microbiome can reprogram host transcriptome and epitranscriptome as represented by N6-methyladenosine (m6A), the most abundant mammalian mRNA modification. However, which and how gut microbiota-derived metabolites reprogram host transcriptome and m6A epitranscriptome remain poorly understood. Here, investigation is conducted into how gut microbiota-derived metabolites impact host transcriptome and m6A epitranscriptome using multiple mouse models and multi-omics approaches. Various antibiotics-induced dysbiotic mice are established, followed by fecal microbiota transplantation (FMT) into germ-free mice, and the results show that bile acid metabolism is significantly altered along with the abundance change in bile acid-producing microbiota. Unbalanced gut microbiota and bile acids drastically change the host transcriptome and the m6A epitranscriptome in multiple tissues. Mechanistically, the expression of m6A writer proteins is regulated in animals treated with antibiotics and in cultured cells treated with bile acids, indicating a direct link between bile acid metabolism and m6A biology. Collectively, these results demonstrate that antibiotic-induced gut dysbiosis regulates the landscape of host transcriptome and m6A epitranscriptome via bile acid metabolism pathway. This work provides novel insights into the interplay between microbial metabolites and host gene expression.

A KDPG sensor RccR governs Pseudomonas aeruginosa carbon metabolism and aminoglycoside antibiotic tolerance

Pseudomonas aeruginosa harbors sophisticated transcription factor (TF) networks to coordinately regulate cellular metabolic states for rapidly adapting to changing environments. The extraordinary capacity in fine-tuning the metabolic states enables its success in tolerance to antibiotics and evading host immune defenses. However, the linkage among transcriptional regulation, metabolic states and antibiotic tolerance in P. aeruginosa remains largely unclear. By screening the P. aeruginosa TF mutant library constructed by CRISPR/Cas12k-guided transposase, we identify that rccR (PA5438) is a major genetic determinant in aminoglycoside antibiotic tolerance, the deletion of which substantially enhances bacterial tolerance. We further reveal the inhibitory roles of RccR in pyruvate metabolism (aceE/F) and glyoxylate shunt pathway (aceA and glcB), and overexpression of aceA or glcB enhances bacterial tolerance. Moreover, we identify that 2-keto-3-deoxy-6-phosphogluconate (KDPG) is a signal molecule that directly binds to RccR. Structural analysis of the RccR/KDPG complex reveals the detailed interactions. Substitution of the key residue R152, K270 or R277 with alanine abolishes KDPG sensing by RccR and impairs bacterial growth with glycerol or glucose as the sole carbon source. Collectively, our study unveils the connection between aminoglycoside antibiotic tolerance and RccR-mediated central carbon metabolism regulation in P. aeruginosa, and elucidates the KDPG-sensing mechanism by RccR.

Co-effects of m6A and chromatin accessibility dynamics in the regulation of cardiomyocyte differentiation

BACKGROUND

Cardiomyocyte growth and differentiation rely on precise gene expression regulation, with epigenetic modifications emerging as key players in this intricate process. Among these modifications, N6-methyladenosine (m6A) stands out as one of the most prevalent modifications on mRNA, exerting influence over mRNA metabolism and gene expression. However, the specific function of m6A in cardiomyocyte differentiation remains poorly understood.

RESULTS

We investigated the relationship between m6A modification and cardiomyocyte differentiation by conducting a comprehensive profiling of m6A dynamics during the transition from pluripotent stem cells to cardiomyocytes. Our findings reveal that while the overall m6A modification level remains relatively stable, the m6A levels of individual genes undergo significant changes throughout cardiomyocyte differentiation. We discovered the correlation between alterations in chromatin accessibility and the binding capabilities of m6A writers, erasers, and readers. The changes in chromatin accessibility influence the recruitment and activity of m6A regulatory proteins, thereby impacting the levels of m6A modification on specific mRNA transcripts.

CONCLUSION

Our data demonstrate that the coordinated dynamics of m6A modification and chromatin accessibility are prominent during the cardiomyocyte differentiation.

Systematic comparison of tools used for m6A mapping from nanopore direct RNA sequencing

N6-methyladenosine (m6A) has been increasingly recognized as a new and important regulator of gene expression. To date, transcriptome-wide m6A detection primarily relies on well-established methods using next-generation sequencing (NGS) platform. However, direct RNA sequencing (DRS) using the Oxford Nanopore Technologies (ONT) platform has recently emerged as a promising alternative method to study m6A. While multiple computational tools are being developed to facilitate the direct detection of nucleotide modifications, little is known about the capabilities and limitations of these tools. Here, we systematically compare ten tools used for mapping m6A from ONT DRS data. We find that most tools present a trade-off between precision and recall, and integrating results from multiple tools greatly improve performance. Using a negative control could improve precision by subtracting certain intrinsic bias. We also observed variation in detection capabilities and quantitative information among motifs, and identified sequencing depth and m6A stoichiometry as potential factors affecting performance. Our study provides insight into the computational tools currently used for mapping m6A based on ONT DRS data and highlights the potential for further improving these tools, which may serve as the basis for future research.

High-precision mapping reveals rare N6-deoxyadenosine methylation in the mammalian genome

N⁶-deoxyadenosine methylation (6mA) is the most widespread type of DNA modification in prokaryotes and is also abundantly distributed in some unicellular eukaryotes. However, 6mA levels are remarkably low in mammals. The lack of a precise and comprehensive mapping method has hindered more advanced investigations of 6mA. Here, we report a new method MM-seq (modification-induced mismatch sequencing) for genome-wide 6mA mapping based on a novel detection principle. We found that modified DNA bases are prone to form a local open region that allows capture by antibody, for example, via a DNA breathing or base-flipping mechanism. Specified endonuclease or exonuclease can recognize the antibody-stabilized mismatch-like structure and mark the exact modified sites for sequencing readout. Using this method, we examined the genomic positions of 6mA in bacteria (E. coli), green algae (C. reinhardtii), and mammalian cells (HEK239T, Huh7, and HeLa cells). In contrast to bacteria and green algae, human cells possess a very limited number of 6mA sites which are sporadically distributed across the genome of different cell types. After knocking out the RNA m⁶A methyltransferase METTL3 in mouse ES cells, 6mA becomes mostly diminished. Our results imply that rare 6mA in the mammalian genome is introduced by RNA m⁶A machinery via a non-targeted mechanism.

[A two-stitch continuous suture method for single-lumen ileostomy]

Objective: To explore the value of a two-stitch continuous suture in single- lumen ileostomy. Methods: This was a retrospective cohort study. Data for 98 patients who underwent single-lumen enterostomy were retrospectively collected between 1 January 2021 and 1 May 2022 at Zhujiang Hospital of Southern Medical University. All patients met the indications for prophylactic single-lumen ileostomy. Those older than 80 years of age, with complex underlying diseases, extremely poor systemic conditions who could not tolerate surgery, poor blood supply at the end of the bowel, and severe edema or severe infection at the end of the bowel were excluded. Among the included patients, patients who underwent surgery before 1 October 2021 underwent ileostomy with interrupted suture (control group, n=60), and patients operated on and after 1 October 2021 routinely underwent two-stitch continuous suture ileostomy (two-stitch stoma group, n=38). Two-stitch continuous suture ileostomy is performed as follows: the first continuous suture is used to suture the intestinal seromuscular layer, peritoneum, posterior sheath, and anterior sheath from deep to superficial layers. The bowel wall is then opened. The second continuous suture is used to suture the full thickness of the bowel and the skin. The differences in postoperative ostomy-related complications and operation time were compared between the groups. Results: There were no significant differences in baseline data between the groups (all, P>0.05). The operative time in the two-stitch stoma group was shorter than that of the control group (16.6±2.2 minutes vs. 25.1±2.4 minutes, respectively; t=-17.874;P<0.001). The incidences of mucocutaneous separation, dermatitis, and stoma rebound in the two-stitch stoma group were lower than those of the control group [5.3% (2/38) vs. 31.7% (19/60), χ²=9.633, P=0.002;5.3% (2/38) vs. 28.3% (17/60), χ²=7.923, P=0.005; and 2.6% (1/38) vs. 18.3% (11/60), P=0.026, respectively], while the incidences of parastomal hernia and stoma prolapse, and the postoperative visual analog scale scores in the two groups were similar (all P>0.05). Conclusion: Compared with traditional single-lumen ileostomy, two-stitch continuous suture ileostomy has the advantages of short operation time, simplicity, esthetic appearance of the stoma, and a significant reduction in the postoperative complications associated with ileostomy.

Targeted genetic screening in bacteria with a Cas12k-guided transposase

Microbes employ sophisticated cellular networks encoded by complex genomes to rapidly adapt to changing environments. High-throughput genome engineering methods are valuable tools for functionally profiling genotype-phenotype relationships and understanding the complexity of cellular networks. However, current methods either rely on special homologous recombination systems and are thus applicable in only limited bacterial species or can generate only nonspecific mutations and thus require extensive subsequent screening. Here, we report a site-specific transposon-assisted genome engineering (STAGE) method that allows high-throughput Cas12k-guided mutagenesis in various microorganisms, such as Pseudomonas aeruginosa and Klebsiella pneumoniae. Exploiting the powerful STAGE technique, we construct a site-specific transposon mutant library that focuses on all possible transcription factors (TFs) in P. aeruginosa, enabling the comprehensive identification of essential genes and antibiotic-resistance-related factors. Given its broad host range activity and easy programmability, this method can be widely adapted to diverse microbial species for rapid genome engineering and strain evolution.

[A comparative study on the construction methods of animal models of aortic arch dissection]

Objective: To compare the effectiveness and safety of different methods to construct animal models of aortic arch dissection (AAD), and explore safe and effective methods for constructing AAD animal models. Methods: Twenty-four healthy mongrel dogs were divided into 4 groups by random number table (n=6). Group A: Venous incision needle high pressure water flow impact method; Group B: Venous incision needle non-high pressure water flow impact method; Group C: Transarterial sheath non-high pressure water flow impact method; Group D: Two-way balloon expansion combined with elastase perfusion method. Imaging examinations were performed immediately and 7 days after operation, aortic tissue biopsy and pathological staining were performed 15 days after operation to observe the formation of AAD. The operation time, aortic blood flow block time, model construction success rate, dissection tear length, postoperative survival rate and survival time of four groups of experimental dogs were collected to compare the effectiveness and safety of different construction methods. Results: There were no significant difference of the gender, age and weight between four groups of experimental dogs (all P>0.05). The operation time of four groups of experimental dogs were (111.6±8.0), (168.0±17.4), (164.4±13.9), (202.8±21.5)min, and the difference was statistically significant (F=39.973, P<0.001). The operation time of group A was significantly lower than group B, C and D (all P<0.001). The aortic blood flow block time of four groups of experimental dogs were (5.2±1.8), (19.6±3.8), (20.6±3.9), and (18.6±3.0) min, and the difference was statistically significant (all P<0.001). The aortic blood flow block time of group A was significantly lower than group B, C and D (F=27.598, P<0.001). The four groups of experimental dogs had 5, 5, 4, and 1 model were successfully constructed, respectively, and the difference was statistically significant (P=0.008). The successful rate of model construction in group A was significantly higher than that in group D (P=0.040). The dissection tear length of four groups were (14.4±3.0), (11.3±4.2), (7.0±2.3), (4.7±0.6) cm,and the difference was statistically significant (F=8.103, P=0.003). The dissection tear length of group A was significantly longer than group C, D (all P<0.05). The postoperative survival time were 15.0(10.0, 15.0), 5.0(3.0, 10.0), 3.5(1.5, 4.8), 10.0(2.8, 15.0) days, and the difference was statistically significant (χ²=7.825,P=0.036). The postoperative survival time of group A was significantly higher than group B, C (all P<0.05). There was no significant difference in the survival rate of the four groups (P=1.000). The pathological staining results showed that the elastic fiber at the tearing point of AAD was destroyed, and the elastic fiber on the outer wall of the false cavity was over-stretched, which was consistent with the pathological changes of aortic dissection. Conclusion: Transvenous incision needle high-pressure water flow impact modeling method is easy to operate. The aortic blood flow block time is short, the dissection tear length is wide, and the postoperative survival time is long, can be used as the preferred method of animal AAD model construction.

RNA m6A Modification Functions in Larval Development and Caste Differentiation in Honeybee (Apis mellifera)

Genetically identical female honeybee larvae with different diets develop into sterile workers or fertile queens. It remains unknown whether the reversible RNA N⁶-methyladenosine (m⁶A) mark functionally impact this "caste differentiation." Here, we profile the transcriptome-wide m⁶A methylome of honeybee queen and worker larvae at three instar stages and discover that m⁶A methylation dynamics are altered by differential feeding. Multiple methylome comparisons show an obvious increase in m⁶A marks during larval development and reveal a negative correlation between gene expression and m⁶A methylation. Notably, we find that worker larvae contain more hypermethylated m⁶A peaks than do queen larvae, and many caste-differentiation-related transcripts are differentially methylated. Chemical suppression of m⁶A methylation in worker larvae by 3-deazaadenosine (DAA) reduces overall m⁶A methylation levels and triggers worker larvae to develop queen caste features. Thus, our study demonstrates that m⁶A functionally impacts caste differentiation and larval development, yet it does not exclude potential contributions from other factors.

Mapping and editing of nucleic acid modifications

Modification on nucleic acid plays a pivotal role in controlling gene expression. Various kinds of modifications greatly increase the information-encoding capacity of DNA and RNA by introducing extra chemical group to existing bases instead of altering the genetic sequences. As a marker on DNA or RNA, nucleic acid modification can be recognized by specific proteins, leading to versatile regulation of gene expression. However, modified and regular bases are often indistinguishable by most conventional molecular methods, impeding detailed functional studies that require the information of genomic location. Recently, new technologies are emerging to resolve the positions of varied modifications on both DNA and RNA. Intriguingly, by integrating regional targeting tools and effector proteins, researchers begin to actively control the modification status of desired gene in vivo. In this review, we summarize the characteristics of DNA and RNA modifications, the available mapping and editing tools, and the potential application as well as deficiency of these technologies in basic and translational researches.

Single-base mapping of m6A by an antibody-independent method

N ⁶-methyladenosine (m⁶A) is one of the most abundant messenger RNA modifications in eukaryotes involved in various pivotal processes of RNA metabolism. The most popular high-throughput m⁶A identification method depends on the anti-m⁶A antibody but suffers from poor reproducibility and limited resolution. Exact location information is of great value for understanding the dynamics, machinery, and functions of m⁶A. Here, we developed a precise and high-throughput antibody-independent m⁶A identification method based on the m⁶A-sensitive RNA endoribonuclease recognizing ACA motif (m⁶A-sensitive RNA-Endoribonuclease-Facilitated sequencing or m⁶A-REF-seq). Whole-transcriptomic, single-base m⁶A maps generated by m⁶A-REF-seq quantitatively displayed an explicit distribution pattern with enrichment near stop codons. We used independent methods to validate methylation status and abundance of individual m⁶A sites, confirming the high reliability and accuracy of m⁶A-REF-seq. We applied this method on five tissues from human, mouse, and rat, showing that m⁶A sites are conserved with single-nucleotide specificity and tend to cluster among species.

Improving the performance of optical antenna for optical phased arrays through high-contrast grating structure on SOI substrate

A novel optical antenna for optical phased arrays is proposed and simulated. A high-contrast grating structure is used to achieve extremely efficient emission. The emission efficiency is as high as 93.94% at 1.55 μm, which exceeds 50% in a range of wavelength from 1.48 μm to 1.62 μm. The antenna can achieve a perfect grating lobe suppression with background suppression of 28.4 dB when the phase difference between adjacent waveguides is 0. A 16-wire optical phased array can easily achieve a scan range of ± 22.8° × 20.2° with a beam width of 2.4° × 2.5°, by employing the optical antenna proposed.

N6-methyldeoxyadenosine directs nucleosome positioning in Tetrahymena DNA

BACKGROUND

N6-methyldeoxyadenosine (6mA or m6dA) was shown more than 40 years ago in simple eukaryotes. Recent studies revealed the presence of 6mA in more prevalent eukaryotes, even in vertebrates. However, functional characterizations have been limited.

RESULTS

We use Tetrahymena thermophila as a model organism to examine the effects of 6mA on nucleosome positioning. Independent methods reveal the enrichment of 6mA near and after transcription start sites with a periodic pattern and anti-correlation relationship with the positions of nucleosomes. The distribution pattern can be recapitulated by in vitro nucleosome assembly on native Tetrahymena genomic DNA but not on DNA without 6mA. Model DNA containing artificially installed 6mA resists nucleosome assembling compared to unmodified DNA in vitro. Computational simulation indicates that 6mA increases dsDNA rigidity, which disfavors nucleosome wrapping. Knockout of a potential 6mA methyltransferase leads to a transcriptome-wide change of gene expression.

CONCLUSIONS

These findings uncover a mechanism by which DNA 6mA assists to shape the nucleosome positioning and potentially affects gene expression.

YTHDC1 mediates nuclear export of N6-methyladenosine methylated mRNAs

N⁶-methyladenosine (m⁶A) is the most abundant internal modification of eukaryotic messenger RNA (mRNA) and plays critical roles in RNA biology. The function of this modification is mediated by m⁶A-selective ‘reader’ proteins of the YTH family, which incorporate m⁶A-modified mRNAs into pathways of RNA metabolism. Here, we show that the m⁶A-binding protein YTHDC1 mediates export of methylated mRNA from the nucleus to the cytoplasm in HeLa cells. Knockdown of YTHDC1 results in an extended residence time for nuclear m⁶A-containing mRNA, with an accumulation of transcripts in the nucleus and accompanying depletion within the cytoplasm. YTHDC1 interacts with the splicing factor and nuclear export adaptor protein SRSF3, and facilitates RNA binding to both SRSF3 and NXF1. This role for YTHDC1 expands the potential utility of chemical modification of mRNA, and supports an emerging paradigm of m⁶A as a distinct biochemical entity for selective processing and metabolism of mammalian mRNAs.

Ubiquitously expressed genes participate in cell-specific functions via alternative promoter usage

How do different cell types acquire their specific identities and functions is a fundamental question of biology. Previously significant efforts have been devoted to search for cell-type-specifically expressed genes, especially transcription factors, yet how do ubiquitously expressed genes participate in the formation or maintenance of cell-type-specific features remains largely unknown. Here, we have identified 110 mouse embryonic stem cell (mESC) specifically expressed transcripts with cell-stage-specific alternative transcription start sites (SATS isoforms) from 104 ubiquitously expressed genes, majority of which have active epigenetic modification- or stem cell-related functions. These SATS isoforms are specifically expressed in mESCs, and tend to be transcriptionally regulated by key pluripotency factors through direct promoter binding. Knocking down the SATS isoforms of Nmnat2 or Usp7 leads to differentiation-related phenotype in mESCs. These results demonstrate that cell-type-specific transcription factors are capable to produce cell-type-specific transcripts with alternative transcription start sites from ubiquitously expressed genes, which confer ubiquitously expressed genes novel functions involved in the establishment or maintenance of cell-type-specific features.

Widespread occurrence of N6-methyladenosine in bacterial mRNA

N⁶-methyladenosine (m⁶A) is the most abundant internal modification in eukaryotic messenger RNA (mRNA). Recent discoveries of demethylases and specific binding proteins of m⁶A as well as m⁶A methylomes obtained in mammals, yeast and plants have revealed regulatory functions of this RNA modification. Although m⁶A is present in the ribosomal RNA of bacteria, its occurrence in mRNA still remains elusive. Here, we have employed ultra-high pressure liquid chromatography coupled with triple-quadrupole tandem mass spectrometry (UHPLC-QQQ-MS/MS) to calculate the m⁶A/A ratio in mRNA from a wide range of bacterial species, which demonstrates that m⁶A is an abundant mRNA modification in tested bacteria. Subsequent transcriptome-wide m⁶A profiling in Escherichia coli and Pseudomonas aeruginosa revealed a conserved m⁶A pattern that is distinct from those in eukaryotes. Most m⁶A peaks are located inside open reading frames and carry a unique consensus motif of GCCAU. Functional enrichment analysis of bacterial m⁶A peaks indicates that the majority of m⁶A-modified genes are associated with respiration, amino acids metabolism, stress response and small RNAs, suggesting potential functional roles of m⁶A in these pathways.

N6-methyldeoxyadenosine marks active transcription start sites in Chlamydomonas

N(6)-methyldeoxyadenosine (6mA or m(6)A) is a DNA modification preserved in prokaryotes to eukaryotes. It is widespread in bacteria and functions in DNA mismatch repair, chromosome segregation, and virulence regulation. In contrast, the distribution and function of 6mA in eukaryotes have been unclear. Here, we present a comprehensive analysis of the 6mA landscape in the genome of Chlamydomonas using new sequencing approaches. We identified the 6mA modification in 84% of genes in Chlamydomonas. We found that 6mA mainly locates at ApT dinucleotides around transcription start sites (TSS) with a bimodal distribution and appears to mark active genes. A periodic pattern of 6mA deposition was also observed at base resolution, which is associated with nucleosome distribution near the TSS, suggesting a possible role in nucleosome positioning. The new genome-wide mapping of 6mA and its unique distribution in the Chlamydomonas genome suggest potential regulatory roles of 6mA in gene expression in eukaryotic organisms.

High-resolution N(6) -methyladenosine (m(6) A) map using photo-crosslinking-assisted m(6) A sequencing

N(6) -methyladenosine (m(6) A) is an abundant internal modification in eukaryotic mRNA and plays regulatory roles in mRNA metabolism. However, methods to precisely locate the m(6) A modification remain limited. We present here a photo-crosslinking-assisted m(6) A sequencing strategy (PA-m(6) A-seq) to more accurately define sites with m(6) A modification. Using this strategy, we obtained a high-resolution map of m(6) A in a human transcriptome. The map resembles the general distribution pattern observed previously, and reveals new m(6) A sites at base resolution. Our results provide insight into the relationship between the methylation regions and the binding sites of RNA-binding proteins.

Genetic modification and screening in rat using haploid embryonic stem cells

The rat is an important animal model in biomedical research, but practical limitations to genetic manipulation have restricted the application of genetic analysis. Here we report the derivation of rat androgenetic haploid embryonic stem cells (RahESCs) as a tool to facilitate such studies. Our approach is based on removal of the maternal pronucleus from zygotes to generate androgenetic embryos followed by derivation of ESCs. The resulting RahESCs have 21 chromosomes, express pluripotency markers, differentiate into three germ layer cells, and contribute to the germline. Homozygous mutations can be introduced by both large-scale gene trapping and precise gene targeting via homologous recombination or the CRISPR-Cas system. RahESCs can also produce fertile rats after intracytoplasmic injection into oocytes and are therefore able to transmit genetic modifications to offspring. Overall, RahESCs represent a practical tool for functional genetic studies and production of transgenic lines in rat.

ISRNA: an integrative online toolkit for short reads from high-throughput sequencing data

Integrative Short Reads NAvigator (ISRNA) is an online toolkit for analyzing high-throughput small RNA sequencing data. Besides the high-speed genome mapping function, ISRNA provides statistics for genomic location, length distribution and nucleotide composition bias analysis of sequence reads. Number of reads mapped to known microRNAs and other classes of short non-coding RNAs, coverage of short reads on genes, expression abundance of sequence reads as well as some other analysis functions are also supported. The versatile search functions enable users to select sequence reads according to their sub-sequences, expression abundance, genomic location, relationship to genes, etc. A specialized genome browser is integrated to visualize the genomic distribution of short reads. ISRNA also supports management and comparison among multiple datasets.

AVAILABILITY

ISRNA is implemented in Java/C++/Perl/MySQL and can be freely accessed at http://omicslab.genetics.ac.cn/ISRNA/.

MicroRNA-323-3p regulates the activity of polycomb repressive complex 2 (PRC2) via targeting the mRNA of embryonic ectoderm development (Eed) gene in mouse embryonic stem cells

PRC2 (Polycomb repressive complex 2) mediates epigenetic gene silencing by catalyzing the triple methylation of histone H3 Lys-27 (H3K27me3) to establish a repressive epigenetic state. PRC2 is involved in the regulation of many fundamental biological processes and is especially essential for embryonic stem cells. However, how the formation and function of PRC2 are regulated is largely unknown. Here, we show that a microRNA encoded by the imprinted Dlk1-Dio3 region of mouse chromosome 12, miR-323-3p, targets Eed (embryonic ectoderm development) mRNA, which encodes one of the core components of PRC2, the EED protein. Binding of miR-323-3p to Eed mRNA resulted in reduced EED protein abundance and cellular H3K27me3 levels, indicating decreased PRC2 activity. Such regulation seems to be conserved among mammals, at least between mice and humans. We demonstrate that induced pluripotent stem cells with varied developmental abilities had different miR-323-3p as well as EED and H3K27me3 levels, indicating that miR-323-3p may be involved in the regulation of stem cell pluripotency through affecting PRC2 activity. Mouse embryonic fibroblast cells had much higher miR-323-3p expression and nearly undetectable H3K27me3 levels. These findings identify miR-323-3p as a new regulator for PRC2 and provide a new approach for regulating PRC2 activity via microRNAs.

In vivo suppression of microRNA-24 prevents the transition toward decompensated hypertrophy in aortic-constricted mice

RATIONALE

During the transition from compensated hypertrophy to heart failure, the signaling between L-type Ca(2+) channels in the cell membrane/T-tubules and ryanodine receptors in the sarcoplasmic reticulum becomes defective, partially because of the decreased expression of a T-tubule-sarcoplasmic reticulum anchoring protein, junctophilin-2. MicroRNA (miR)-24, a junctophilin-2 suppressing miR, is upregulated in hypertrophied and failing cardiomyocytes.

OBJECTIVE

To test whether miR-24 suppression can protect the structural and functional integrity of L-type Ca(2+) channel-ryanodine receptor signaling in hypertrophied cardiomyocytes.

METHODS AND RESULTS

In vivo silencing of miR-24 by a specific antagomir in an aorta-constricted mouse model effectively prevented the degradation of heart contraction, but not ventricular hypertrophy. Electrophysiology and confocal imaging studies showed that antagomir treatment prevented the decreases in L-type Ca(2+) channel-ryanodine receptor signaling fidelity/efficiency and whole-cell Ca(2+) transients. Further studies showed that antagomir treatment stabilized junctophilin-2 expression and protected the ultrastructure of T-tubule-sarcoplasmic reticulum junctions from disruption.

CONCLUSIONS

MiR-24 suppression prevented the transition from compensated hypertrophy to decompensated hypertrophy, providing a potential strategy for early treatment against heart failure.

Genome-wide annotation and analysis of zebra finch microRNA repertoire reveal sex-biased expression

BACKGROUND

MicroRNAs (miRNAs) are small noncoding RNAs that regulate gene expression post-transcriptionally in a wide range of biological processes. The zebra finch (Taeniopygia guttata), an oscine songbird with characteristic learned vocal behavior, provides biologists a unique model system for studying vocal behavior, sexually dimorphic brain development and functions, and comparative genomics.

RESULTS

We deep sequenced small RNA libraries made from the brain, heart, liver, and muscle tissues of adult male and female zebra finches. By mapping the sequence reads to the zebra finch genome and to known miRNAs in miRBase, we annotated a total of 193 miRNAs. Among them, 29 (15%) are avian specific, including three novel zebra finch specific miRNAs. Many of the miRNAs exhibit sequence heterogeneity including length variations, untemplated terminal nucleotide additions, and internal substitution events occurring at the uridine nucleotide within a GGU motif. We also identified seven Z chromosome-encoded miRNAs. Among them, miR-2954, an avian specific miRNA, is expressed at significantly higher levels in males than in females in all tissues examined. Target prediction analysis reveals that miR-2954, but not other Z-linked miRNAs, preferentially targets Z chromosome-encoded genes, including several genes known to be expressed in a sexually dimorphic manner in the zebra finch brain.

CONCLUSIONS

Our genome-wide systematic analysis of mature sequences, genomic locations, evolutionary sequence conservation, and tissue expression profiles of the zebra finch miRNA repertoire provides a valuable resource to the research community. Our analysis also reveals a miRNA-mediated mechanism that potentially regulates sex-biased gene expression in avian species.

Mir-24 regulates junctophilin-2 expression in cardiomyocytes

RATIONALE

Failing cardiomyocytes exhibit decreased efficiency of excitation-contraction (E-C) coupling. The downregulation of junctophilin-2 (JP2), a protein anchoring the sarcoplasmic reticulum to T-tubules, has been identified as a major mechanism underlying the defective E-C coupling. However, the regulatory mechanism of JP2 remains unknown.

OBJECTIVE

To determine whether microRNAs regulate JP2 expression.

METHODS AND RESULTS

Bioinformatic analysis predicted 2 potential binding sites of miR-24 in the 3'-untranslated regions of JP2 mRNA. Luciferase assays confirmed that miR-24 suppressed JP2 expression by binding to either of these sites. In the aortic stenosis model, miR-24 was upregulated in failing cardiomyocytes. Adenovirus-directed overexpression of miR-24 in cardiomyocytes decreased JP2 expression and reduced Ca(2+) transient amplitude and E-C coupling gain.

CONCLUSIONS

MiR-24-mediated suppression of JP2 expression provides a novel molecular mechanism for E-C coupling regulation in heart cells and suggests a new target against heart failure.

Activation of the imprinted Dlk1-Dio3 region correlates with pluripotency levels of mouse stem cells

Low reprogramming efficiency and reduced pluripotency have been the two major obstacles in induced pluripotent stem (iPS) cell research. An effective and quick method to assess the pluripotency levels of iPS cells at early stages would significantly increase the success rate of iPS cell generation and promote its applications. We have identified a conserved imprinted region of the mouse genome, the Dlk1-Dio3 region, which was activated in fully pluripotent mouse stem cells but repressed in partially pluripotent cells. The degree of activation of this region was positively correlated with the pluripotency levels of stem cells. A mammalian conserved cluster of microRNAs encoded by this region exhibited significant expression differences between full and partial pluripotent stem cells. Several microRNAs from this cluster potentially target components of the polycomb repressive complex 2 (PRC2) and may form a feedback regulatory loop resulting in the expression of all genes and non-coding RNAs encoded by this region in full pluripotent stem cells. No other genomic regions were found to exhibit such clear expression changes between cell lines with different pluripotency levels; therefore, the Dlk1-Dio3 region may serve as a marker to identify fully pluripotent iPS or embryonic stem cells from partial pluripotent cells. These findings also provide a step forward toward understanding the operating mechanisms during reprogramming to produce iPS cells and can potentially promote the application of iPS cells in regenerative medicine and cancer therapy.