Biomedical subjects

Yin Shen

Publications and source records attributed to Yin Shen.

12 recordsLinked to original sources

PubMed2026

3D epigenome of glial cell types in developing human cortex.

The human cortex is complex and heterogeneous, undergoing extensive expansion during development1,2. Our prior study of neurogenesis, including radial glia (RG), intermediate progenitor cells, excitatory neurons and interneurons demonstrated that chromatin looping underlies transcriptional regulation for lineage-specific genes, shedding light on how non-coding genetic variants contribute to neuropsychiatric disorders by means of cell-type-specific gene regulation3. RG have a crucial role in generating cellular diversity through both neurogenesis and gliogenesis and can be further classified into ventricular RG (vRG) and outer RG (oRG)4,5. Given their significance in cortical development, we conducted a comprehensive three-dimensional (3D) epigenomic analysis of four main glial populations, including vRG, oRG, oligodendrocyte precursor cells and microglia, from the mid-gestational human neocortex. By integrating gene expression, chromatin accessibility, DNA methylation and 3D chromatin interactions, we identified cell-type-specific candidate cis-regulatory elements (cCREs) and validated their regulatory function using transgenic mouse embryos. Using machine learning, we prioritized 112 schizophrenia risk variants within glia cCREs and further confirmed the predicted vRG enhancer disruption by the rs4449074 risk allele in vivo. Finally, oRG cCREs are enriched for human accelerated regions compared with other cCREs and a subset of human accelerated regions show activity differences from their chimpanzee orthologues that interact with genes involved in neuronal development. Our findings advance the understanding of human-specific gene regulation during corticogenesis.

Journal Article↗

PubMed2026

De novo structural variants in autism spectrum disorder disrupt distal regulatory interactions of neuronal genes.

Three-dimensional genome organization plays a critical role in gene regulation, and disruptions can lead to developmental disorders by altering the contact between genes and their distal regulatory elements. Structural variants (SVs) can disturb local genome organization, such as the merging of topologically associating domains upon boundary deletion. Testing large numbers of SVs experimentally for their effects on chromatin structure and gene expression is time and cost prohibitive. To address this, we propose a computational approach to predict SV impacts on genome folding, which can help prioritize causal hypotheses for functional testing. We develop a weighted scoring method that measures chromatin contact changes specifically affecting regions of interest, such as regulatory elements or promoters, and implement it in the SuPreMo-Akita software. With this tool, we rank hundreds of de novo SVs (dnSVs) from autism spectrum disorder (ASD) individuals and their unaffected siblings based on predicted disruptions to nearby neuronal regulatory interactions. This reveals that putative cis-regulatory element interactions (CREints) are more disrupted by dnSVs from ASD probands versus unaffected siblings. We prioritize candidate variants that disrupt ASD CREints and validate our top-ranked locus using isogenic excitatory neurons with and without the dnSV, confirming accurate predictions of disrupted chromatin contacts. This study suggests that disrupted genome folding is a potential genetic mechanism in a subset of ASD cases and provides a general strategy for prioritizing variants predicted to disrupt regulatory interactions across tissues.

Humans↗

PubMed2024

De novo structural variants in autism spectrum disorder disrupt distal regulatory interactions of neuronal genes.

Three-dimensional genome organization plays a critical role in gene regulation, and disruptions can lead to developmental disorders by altering the contact between genes and their distal regulatory elements. Structural variants (SVs) can disturb local genome organization, such as the merging of topologically associating domains upon boundary deletion. Testing large numbers of SVs experimentally for their effects on chromatin structure and gene expression is time and cost prohibitive. To address this, we propose a computational approach to predict SV impacts on genome folding, which can help prioritize causal hypotheses for functional testing. We developed a weighted scoring method that measures chromatin contact changes specifically affecting regions of interest, such as regulatory elements or promoters, and implemented it in the SuPreMo-Akita software (Gjoni and Pollard 2024). With this tool, we ranked hundreds of de novo SVs (dnSVs) from autism spectrum disorder (ASD) individuals and their unaffected siblings based on predicted disruptions to nearby neuronal regulatory interactions. This revealed that putative cis-regulatory element interactions (CREints) are more disrupted by dnSVs from ASD probands versus unaffected siblings. We prioritized candidate variants that disrupt ASD CREints and validated our top-ranked locus using isogenic excitatory neurons with and without the dnSV, confirming accurate predictions of disrupted chromatin contacts. This study establishes disrupted genome folding as a potential genetic mechanism in ASD and provides a general strategy for prioritizing variants predicted to disrupt regulatory interactions across tissues.

Journal Article↗

PubMed2024

A conserved molecular logic for neurogenesis to gliogenesis switch in the cerebral cortex.

During development, neural stem cells in the cerebral cortex, also known as radial glial cells (RGCs), generate excitatory neurons, followed by production of cortical macroglia and inhibitory neurons that migrate to the olfactory bulb (OB). Understanding the mechanisms for this lineage switch is fundamental for unraveling how proper numbers of diverse neuronal and glial cell types are controlled. We and others recently showed that Sonic Hedgehog (Shh) signaling promotes the cortical RGC lineage switch to generate cortical oligodendrocytes and OB interneurons. During this process, cortical RGCs generate intermediate progenitor cells that express critical gliogenesis genes Ascl1, Egfr, and Olig2. The increased Ascl1 expression and appearance of Egfr+ and Olig2+ cortical progenitors are concurrent with the switch from excitatory neurogenesis to gliogenesis and OB interneuron neurogenesis in the cortex. While Shh signaling promotes Olig2 expression in the developing spinal cord, the exact mechanism for this transcriptional regulation is not known. Furthermore, the transcriptional regulation of Olig2 and Egfr has not been explored. Here, we show that in cortical progenitor cells, multiple regulatory programs, including Pax6 and Gli3, prevent precocious expression of Olig2, a gene essential for production of cortical oligodendrocytes and astrocytes. We identify multiple enhancers that control Olig2 expression in cortical progenitors and show that the mechanisms for regulating Olig2 expression are conserved between the mouse and human. Our study reveals evolutionarily conserved regulatory logic controlling the lineage switch of cortical neural stem cells.

Animals↗

PubMed2006

Functional N-methyl-D-aspartate receptors are expressed in cone-driven horizontal cells in carp retina.

Glutamate works as a major excitatory neurotransmitter in the vertebrate retina. Whole-cell recordings made from isolated carp cone horizontal cells (H1 cells) showed that N-methyl-D-aspartate (NMDA), co-applied with glycine, induced inward currents that were blocked by the NMDA receptor competitive antagonist D-2-amino-5-phosphonopentanoate (D-AP5) and 5,7-dichlorokynurenic acid (DCKA), a selective NMDA receptor antagonist acting at the glycine site on the NMDA receptor complex. Moreover, calcium imaging showed that NMDA caused a significant elevation of intracellular calcium levels ([Ca(2+)](i)) of H1 cells, which was also blocked by D-AP5. In contrast, neither inward currents nor changes in [Ca(2+)](i) could be induced by NMDA in rod horizontal cells (H4 cells). Intracellular recordings made from H1 cells in the isolated retina, superfused with Ringer's containing 1 mM Mg(2+), in the dark demonstrated that NMDA reduced the light-off overshoot of H1 cells. We therefore conclude that the functional NMDA receptor is expressed in carp H1 cells, from which this receptor has been thought to be absent, and this receptor may play a role in modulating cone-driven signal of horizontal cells in the dark.

Animals↗

PubMed2006

Abnormal CpG island methylation occurs during in vitro differentiation of human embryonic stem cells.

Directed differentiation of human embryonic stem cells (hESCs) into specific somatic cells holds great promise for cell replacement therapies. However, it is unclear if in vitro hESC differentiation causes any epigenetic abnormality such as hypermethylation of CpG islands. Using a differential methylation hybridization method, we identified 65 CpG islands (out of 4608 CpG islands or 1.4%) that exhibited increased DNA methylation during the conversion of hESCs into neural progenitor/stem cells (NPCs). These methylated CpG islands belong to genes in cell metabolism, signal transduction and cell differentiation, which are distinctively different from oncogenic CpG island hypermethylation observed in cancer-related genes during tumorigenesis. We further determined that methylation in these CpG islands, which is probably triggered by de novo DNA methyltransferase Dnmt3a, is abnormally higher in hESC-NPCs than in primary NPCs and astrocytes. Correlating with hypermethylation in promoter CpG islands of metabolic enzyme gene CPT1A and axoneme apparatus gene SPAG6, levels of CPT1A and SPAG6 mRNAs are significantly reduced in hESC-NPCs when compared with hESCs or primary neural cells. Because CPT1A is involved in lipid metabolism and CPT1A deficiency in human is associated with the hypoketotic hypoglycemia disorder, the reduced CPT1A expression in hESC-NPCs raises a potential concern for the suitability of these cells in cell transplantation. Collectively, our data show that abnormal CpG island methylation takes place in a subset of genes during the differentiation/expansion of hESC derivatives under current culture conditions, which may need to be monitored and corrected in future cell transplantation studies.

Astrocytes↗

PubMed2005

Glycine modulates the center response of ON type rod-dominant bipolar cells in carp retina.

Effects of glycine on ON type rod-dominant bipolar cells (RBCs) were studied in isolated, superfused carp retina by intracellular recording technique and in carp retinal slice preparation by whole cell recording. Glycine of 4mM hyperpolarized RBCs and potentiated their light responses to large light spots, which was reversed by co-application of 10 microM strychnine. It was further found that illumination of the receptive field surround did not affect the depolarizing center response of RBCs. The above result therefore suggests that glycine modulates the center response of RBCs. Focal application of glycine to either dendrites or axon terminals of RBCs failed to induce any currents in both isolated cell and retinal slice preparations. On the other hand, glycine of 4mM increased the amplitude of the scotopic electroretinographic PIII component, which reflects the activity of rod photoreceptors. It seems likely that modulation by glycine of the RBC center response may be in part ascribed to a consequence of the potentiation of rod responses by glycine.

Animals↗

PubMed2005

Changes in soil microbial community composition induced by cometabolism of toluene and trichloroethylene.

The effects of trichloroethylene (TCE) on microbial community composition were analyzed by reverse sample genome probing. Soil enrichments were incubated in dessicators containing an organic phase of either 1 or 10% (w/w) toluene in vacuum pump oil, delivering constant equilibrium aqueous concentrations of 16 and 143 mg/l, respectively. Increasing the equilibrium aqueous concentration of TCE from 0 to 10 mg/l led to shifts in community composition at 16, but not at 143 mg/l of toluene. In closed system co-degradation studies, TCE at an aqueous concentration of 1 mg/l was effectively degraded by toluene-degrading soil enrichments once the aqueous toluene concentration dropped below 25 mg/l. Little TCE degradation was observed at higher toluene concentrations (50-250 mg/l). The results indicate that TCE changes microbial community composition under conditions where it is being actively metabolized.

Biodegradation, Environmental↗

PubMed2005

DNA methylation controls the timing of astrogliogenesis through regulation of JAK-STAT signaling.

DNA methylation is a major epigenetic factor that has been postulated to regulate cell lineage differentiation. We report here that conditional gene deletion of the maintenance DNA methyltransferase I (Dnmt1) in neural progenitor cells (NPCs) results in DNA hypomethylation and precocious astroglial differentiation. The developmentally regulated demethylation of astrocyte marker genes as well as genes encoding the crucial components of the gliogenic JAK-STAT pathway is accelerated in Dnmt1-/- NPCs. Through a chromatin remodeling process, demethylation of genes in the JAK-STAT pathway leads to an enhanced activation of STATs, which in turn triggers astrocyte differentiation. Our study suggests that during the neurogenic period, DNA methylation inhibits not only astroglial marker genes but also genes that are essential for JAK-STAT signaling. Thus, demethylation of these two groups of genes and subsequent elevation of STAT activity are key mechanisms that control the timing and magnitude of astroglial differentiation.

Animals↗

PubMed2004

AMPA receptor is involved in transmission of cone signal to ON bipolar cells in carp retina.

The present work focuses on characterization of glutamate receptor subtypes mediating cone signal transmission to ON bipolar cells (BCs) in the carp retina, using intracellular recording techniques. Glutamate (5 mM) hyperpolarized cone-dominant ON BCs, which was associated with a suppression of light responses, whereas Co(2+) (1 mM) depolarized these cells and suppressed their light responses. On the other hand, alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid (AMPA) of 20 microM caused a membrane depolarization and blocked depolarizing light responses, L-2-amino-4-phosphonobutryic acid (l-AP4) was without effect. The effects of AMPA were reversed by coapplication of GYKI 52466, an AMPA receptor selective non-competitive antagonist, but persisted in the presence of picrotoxin and strychnine. For rod-dominant ON BCs, both l-AP4 and AMPA reversibly blocked depolarizing light responses, but with membrane potential changes of opposite polarities (hyperpolarization for l-AP4 and depolarization for AMPA). In the inner retina, AMPA depolarized transient ON-OFF amacrine cells and blocked both ON and OFF cone-driven depolarizing responses, but l-AP4 did not. These results suggest that AMPA receptors, but not l-AP4 receptors, are involved in synaptic transmission of cone signal to ON bipolar cells in carp retina.

Animals↗

PubMed2003

Uncoupling of horizontal cells alters the receptive fields of retinal bipolar cells.

Effects of uncoupling of horizontal cells by 1-octanol, a non-specific gap junction uncoupling agent, on the receptive field organization of cone-dominant bipolar cells were investigated in isolated, superfused carp retina, using intracellular recording techniques. At 1 mM, 1-octanol increased responses of cone driven horizontal cells to light spots, but decreased those to light annuli, indicating a reduction of the receptive field size of these cells by uncoupling. Furthermore, 1-octanol eliminated the surround response of OFF type bipolar cells and increased their center response. Similar effects of 1-octanol on the center and surround responses were observed in ON type bipolar cells. These results suggest that uncoupling of horizontal cells can significantly alter the receptive field organization of retinal bipolar cells.

1-Octanol↗

PubMed2003

The development of reduced size STR amplicons as tools for analysis of degraded DNA.

New multiplex PCR sets of commonly used short tandem repeat (STR) markers have been developed to produce PCR products that are reduced in size when compared to standard commercial STR kits. The reduction in size of these amplicons can facilitate the examination and analysis of degraded DNA evidence by improving amplification efficiency. This "miniSTR" approach will permit current forensic practitioners to use STR markers and instrumentation already present in their laboratories and to generate genotyping data that is directly comparable to reference samples and searchable through the FBI's Combined DNA Index System (CODIS) databases. This paper discusses the development of these new primer sets and presents some initial results in the analysis of degraded and aged DNA samples. A method for removal of problematic fluorescent dye artifacts is also described. Comparison studies in over 100 samples have verified that these miniSTR primers can provide fully concordant results to commercial STR kits and can provide improved signal from degraded DNA specimens. These miniplex sets should prove valuable in the analysis of samples where allele dropout and reduced sensitivity of larger STR alleles occurs.

Blotting, Southern↗