Circular RNAs and host genes act synergistically in regulating cellular processes and functions in skeletal myogenesis.

Circular RNAs (circRNAs) are post-transcriptional regulators generated from backsplicing of pre-mRNAs of host genes. A major circRNA regulatory mechanism involves microRNA (miRNA) sequestering, relieving miRNA-blocked mRNAs for translation and functions. To investigate possible circRNA-host gene relationship, skeletal myogenesis is chosen as a study model for its developmental importance and for readily available muscle tissues from farm animals for studies at different myogenic stages.

The rhythmic mind: brain functions of percussionists in improvisation.

Introduction: Percussionists stand out for their expertise in rhythm, with the network for musical rhythm (NMR) serving a vital neurological function in their improvisation, which is deeply rooted in comprehensive musical knowledge. Our research examines the central representations of various improvisation tactics used by percussionists and investigates the interactions between the NMR and other relevant neural networks.

Methods: Twenty-five percussionists participated in functional magnetic resonance imaging (fMRI) sessions, which included two cognitive strategies of improvisation.

Inner sense of rhythm: percussionist brain activity during rhythmic encoding and synchronization.

Introduction: The main objective of this research is to explore the core cognitive mechanisms utilized by exceptionally skilled percussionists as they navigate complex rhythms. Our specific focus is on understanding the dynamic interactions among brain regions, respectively, related to externally directed cognition (EDC), internally directed cognition (IDC), and rhythm processing, defined as the neural correlates of rhythm processing (NCRP).

Methods: The research involved 26 participants each in the percussionist group (PG) and control group (CG), who underwent task-functional magnetic resonance imaging (fMRI) sessions focusing on rhythm encoding and synchronization.

Delay Analysis in Closed-Loop EEG Phase-Triggered Transcranial Magnetic Stimulation.

The recent development of closed-loop EEG phase-triggered transcranial magnetic stimulation (TMS) has advanced potential applications of adaptive neuromodulation based on the current brain state. Closed-loop TMS involves instantaneous acquisition of the EEG rhythm, timing prediction of the target phase, and triggering of TMS. However, the accuracy of EEG phase prediction algorithms is largely influenced by the system's transport delay, and their relationship is rarely considered in related work.

Circular RNA ZNF800 (hsa_circ_0082096) regulates cancer stem cell properties and tumor growth in colorectal cancer.

Background: Cancer stem cells form a rare cell population in tumors that contributes to metastasis, recurrence and chemoresistance in cancer patients. Circular RNAs (circRNAs) are post-transcriptional regulators of gene expression that sponge targeted microRNA (miRNAs) to affect a multitude of downstream cellular processes. We previously showed in an expression profiling study that circZNF800 (hsa_circ_0082096) was up-regulated in cancer stem cell-enriched spheroids derived from colorectal cancer (CRC) cell lines.

Circular RNA- and microRNA-Mediated Post-Transcriptional Regulation of Preadipocyte Differentiation in Adipogenesis: From Expression Profiling to Signaling Pathway.

Adipogenesis is an indispensable cellular process that involves preadipocyte differentiation into mature adipocyte. Dysregulated adipogenesis contributes to obesity, diabetes, vascular conditions and cancer-associated cachexia. This review aims to elucidate the mechanistic details on how circular RNA (circRNA) and microRNA (miRNA) modulate post-transcriptional expression of targeted mRNA and the impacted downstream signaling and biochemical pathways in adipogenesis.

PADAr: physician-oriented artificial intelligence-facilitating diagnosis aid for retinal diseases.

Retinopathy screening via digital imaging is promising for early detection and timely treatment, and tracking retinopathic abnormality over time can help to reveal the risk of disease progression. We developed an innovative physician-oriented artificial intelligence-facilitating diagnosis aid system for retinal diseases for screening multiple retinopathies and monitoring the regions of potential abnormality over time. Our dataset contains 4908 fundus images from 304 eyes with image-level annotations, including diabetic retinopathy, age-related macular degeneration, cellophane maculopathy, pathological myopia, and healthy control (HC).

The MicroRNA-signaling-peroxisome proliferator-activated receptor gamma connection in the modulation of adipogenesis: bioinformatics projection on chicken.

Meat quality and nutritional value hinge on many factors, including fat content in the adipose tissue. In the adipogenesis process, stem cells are first committed to become preadipocytes, followed by preadipocyte differentiation. In the later event, peroxisome proliferator activated receptor gamma (PPARγ) is the gateway through which adipogenic genes are activated.

MicroRNA-362 negatively and positively regulates SMAD4 expression in TGF-β/SMAD signaling to suppress cell migration and invasion.

Cell migration and invasion are modulated by epithelial-to-mesenchymal transition (EMT) and the reverse MET process. Despite the detection of microRNA-362 (miR-362, both the miR-362-5p and -3p species) in cancers, none of the identified miR-362 targets is a mesenchymal or epithelial factor to link miR-362 with EMT/MET and metastasis. Focusing on the TGF-β/SMAD signaling pathway in this work, luciferase assays and western blot data showed that miR-362 targeted and negatively regulated expression of SMAD4 and E-cadherin, but not SNAI1, which is regulated by SMAD4.

Mapping a Circular RNA-microRNA-mRNA-Signaling Regulatory Axis That Modulates Stemness Properties of Cancer Stem Cell Populations in Colorectal Cancer Spheroid Cells.

Spheroidal cancer cell cultures have been used to enrich cancer stem cells (CSC), which are thought to contribute to important clinical features of tumors. This study aimed to map the regulatory networks driven by circular RNAs (circRNAs) in CSC-enriched colorectal cancer (CRC) spheroid cells. The spheroid cells established from two CRC cell lines acquired stemness properties in pluripotency gene expression and multi-lineage differentiation capacity.

Oxidative Stress Down-Regulates MiR-20b-5p, MiR-106a-5p and E2F1 Expression to Suppress the G1/S Transition of the Cell Cycle in Multipotent Stromal Cells.

Oxidative stress has been linked to senescence and tumorigenesis via modulation of the cell cycle. Using a hydrogen peroxide (HO)-induced oxidative stress-induced premature senescence (OSIPS) model previously reported by our group, this study aimed to investigate the effects of oxidative stress on microRNA (miRNA) expression in relation to the G1-to-S-phase (G1/S) transition of the cell cycle and cell proliferation. On global miRNA analysis of the OSIPS cells, twelve significantly up- or down-regulated miRNAs were identified, the target genes of which are frequently associated with cancers.

Incomplete cellular reprogramming of colorectal cancer cells elicits an epithelial/mesenchymal hybrid phenotype.

Background: Induced pluripotency in cancer cells by ectopic expression of pluripotency-regulating factors may be used for disease modeling of cancers. MicroRNAs (miRNAs) are negative regulators of gene expression that play important role in reprogramming somatic cells. However, studies on the miRNA expression profile and the expression patterns of the mesenchymal-epithelial transition (MET)/epithelial-mesenchymal transition (EMT) genes in induced pluripotent cancer (iPC) cells are lacking.

miR-524-5p of the primate-specific C19MC miRNA cluster targets TP53IPN1- and EMT-associated genes to regulate cellular reprogramming.

Background: Introduction of the transcription factors Oct4, Sox2, Klf4, and c-Myc (OSKM) is able to 'reprogram' somatic cells to become induced pluripotent stem cells (iPSCs). Several microRNAs (miRNAs) are known to enhance reprogramming efficiency when co-expressed with the OSKM factors. The primate-specific chromosome 19 miRNA cluster (C19MC) is essential in primate reproduction, development, and differentiation.

Selective activation of miRNAs of the primate-specific chromosome 19 miRNA cluster (C19MC) in cancer and stem cells and possible contribution to regulation of apoptosis.

Background: The human chromosome 19 miRNA cluster (C19MC) of 43 genes is a primate-specific miRNA cluster that may have biological significance in the genetic complexity of the primate. Despite previous reports on individual C19MC miRNA expression in cancer and stem cells, systematic studies on C19MC miRNA expression and biological functions are lacking.

Results: Cluster-wide C19MC miRNA expression profiling by microarray analysis showed wholesome C19MC activation in embryonic stem cells (ESCs) and induced pluripotent stem cells (iPSCs).

Expression profile and down-regulation of argininosuccinate synthetase in hepatocellular carcinoma in a transgenic mouse model.

Background: Argininosuccinate synthetase (ASS) participates in urea and nitric oxide production and is a rate-limiting enzyme in arginine biosynthesis. Regulation of ASS expression appears complex and dynamic. In addition to transcriptional regulation, a novel post-transcriptional regulation affecting nuclear precursor RNA stability has been reported.

MicroRNA-5p and -3p co-expression and cross-targeting in colon cancer cells.

Background: Two mature miRNA species may be generated from the 5' and 3' arms of a pre-miRNA precursor. In most cases, only one species remains while the complementary species is degraded. However, co-existence of miRNA-5p and -3p species is increasingly being reported.

Oxidative stress-induced premature senescence in Wharton's jelly-derived mesenchymal stem cells.

Background: On in vitro expansion for therapeutic purposes, the regenerative potentials of mesenchymal stem cells (MSCs) decline and rapidly enter pre-mature senescence probably involving oxidative stress. To develop strategies to prevent or slow down the decline of regenerative potentials in MSC culture, it is important to first address damages caused by oxidative stress-induced premature senescence (OSIPS). However, most existing OSIPS study models involve either long-term culture to achieve growth arrest or immediate growth arrest post oxidative agent treatment and are unsuitable for post-induction studies.

Frequent co-expression of miRNA-5p and -3p species and cross-targeting in induced pluripotent stem cells.

Background: A miRNA precursor generally gives rise to one major miRNA species derived from the 5' arm, and are called miRNA-5p. However, more recent studies have shown co-expression of miRNA-5p and -3p, albeit in different concentrations, in cancer cells targeting different sets of transcripts. Co-expression and regulation of the -5p and -3p miRNA species in stem cells, particularly in the reprogramming process, have not been studied.

Differential expression of speckled POZ protein, SPOP: putative regulation by miR-145.

The speckle POZ protein, SPOP, is an adaptor of the Cul3-based ubiquitination process, and has been implicated in the carcinogenesis process. Despite recent elucidation of biological functions, regulation of SPOP gene expression has not been reported. In this study, the mRNA levels of the mouse SPOP (mSPOP) gene were first shown to vary noticeably in different tissues.

Association of the testis-specific TRIM/RBCC protein RNF33/TRIM60 with the cytoplasmic motor proteins KIF3A and KIF3B.

The Rnf33/Trim60 gene is temporally transcribed in the preimplantation embryo before being silenced at the blastocyst stage but Rnf33 expression is detected in adult testis of the mouse. The putative RNF33 protein is a tripartite motif (TRIM)/RBCC protein composed of a typical RING zinc finger, a B-box 2, two α-helical coiled-coil segments, and a B30.2 domain.

Nuclear factor kappa B and tumor necrosis factor-alpha modulation of transcription of the mouse testis- and pre-implantation development-specific Rnf33/Trim60 gene.

We have previously reported a mouse Rnf33/Trim60 gene that is temporally expressed in the pre-implantation embryo. The Rnf33 structural gene is composed of a short noncoding exon 1 and an intronless coding exon 2. In the present work, Rnf33 was shown to be expressed in the mouse testis and in the testicular cell lines TM3 and TM4.

Evolutionary expansion of SPOP and associated TD/POZ gene family: impact of evolutionary route on gene expression pattern.

Evolutionary expansion of a gene family may occur at both the DNA and RNA levels. The rat testis-specific Rtdpoz-T2 and -T1 (rT2 and rT1) retrogenes are members of the TD/POZ gene family which also includes the well-characterized SPOP gene. In this study, rT2/rT1 transcriptional activation in cancer cells is demonstrated; the cancer rT2/rT1 transcripts are structurally similar to the embryonic transcripts reported previously in frequent exonization of transposed elements.

Transcription of the rat testis-specific Rtdpoz-T1 and -T2 retrogenes during embryo development: co-transcription and frequent exonisation of transposable element sequences.

Background: Retrotransposition is an important evolutionary force for the creation of new and potentially functional intronless genes which are collectively called retrogenes. Many retrogenes are expressed in the testis and the gene products have been shown to actively participate in spermatogenesis and other unique functions of the male germline. We have previously reported a cluster of retrogenes in the rat genome that encode putative TRAF- and POZ-domain proteins.

Retrogenes in preimplantation embryo development: a unique mode of transcriptional regulation.

Our studies show that retrogenes are preferentially expressed in preimplantation embryos. These genes carry a short noncoding exon 1 that contributes directly to expression of the gene, and a second exon that contains the coding sequence without intron interruption. We show that preimplantation gene expression is first regulated by developmentally regulated transcription factors that target exon 1 and the solitary intron, followed by promoter hypermethylation on implantation and in adult tissues.

Suppression of hepatitis B viral gene expression by phosphoinositide 5-phosphatase SKIP.

Human hepatitis B virus (HBV) causes acute and chronic hepatitis, cirrhosis and hepatocellular carcinoma. Here we report that HBV core protein interacts with a cellular SKIP (skeletal muscle and kidney enriched inositol phosphatase) protein, an endoplasmic reticulum-located phosphoinositide 5-phosphatase, both in vivo and in vitro. The minimal sequence required for interaction is the amino acid region from 116 to 149 for the core protein and the SKIP carboxyl homology (SKICH) domain for SKIP.