CHD4 Conceals Aberrant CTCF-Binding Sites at TAD Interiors by Regulating Chromatin Accessibility in Mouse Embryonic Stem Cells.

CCCTC-binding factor (CTCF) critically contributes to 3D chromatin organization by determining topologically associated domain (TAD) borders. Although CTCF primarily binds at TAD borders, there also exist putative CTCF-binding sites within TADs, which are spread throughout the genome by retrotransposition. However, the detailed mechanism responsible for masking the putative CTCF-binding sites remains largely elusive. Here, we show that the ATP-dependent chromatin remodeler, chromodomain helicase DNA-binding 4 (CHD4), regulates chromatin accessibility to conceal aberrant CTCF-binding sites embedded in H3K9me3-enriched heterochromatic B2 short interspersed nuclear elements (SINEs) in mouse embryonic stem cells (mESCs). Upon CHD4 depletion, these aberrant CTCF-binding sites become accessible and aberrant CTCF recruitment occurs within TADs, resulting in disorganization of local TADs. RNA-binding intrinsically disordered domains (IDRs) of CHD4 are required to prevent this aberrant CTCF binding, and CHD4 is critical for the repression of B2 SINE transcripts. These results collectively reveal that a CHD4-mediated mechanism ensures appropriate CTCF binding and associated TAD organization in mESCs.

Novel culture system via wirelessly controllable optical stimulation of the FGF signaling pathway for human and pig pluripotency.

Stem cell fate is largely determined by cellular signaling networks and is heavily dependent on the supplementation of exogenous recombinant proteins into culture media; however, uneven distribution and inconsistent stability of recombinant proteins are closely associated with the spontaneous differentiation of pluripotent stem cells (PSCs) and result in significant costs in large-scale manufacturing. Here, we report a novel PSC culture system via wirelessly controllable optical activation of the fibroblast growth factor (FGF) signaling pathway without the need for supplementation of recombinant FGF2 protein, a key molecule for maintaining pluripotency of PSCs. Using a fusion protein between the cytoplasmic region of the FGF receptor-1 and a light-oxygen-voltage domain, we achieved tunable, blue light-dependent activation of FGF signaling in human and porcine PSCs. Our data demonstrate that a highly controllable optical stimulation of the FGF signaling pathway is sufficient for long-term maintenance of PSCs, without the loss of differentiation potential into three germ layers. This culture system will be a cost-effective platform for a large-scale stem cell culture.

Biogenesis and regulation of the let-7 miRNAs and their functional implications.

The let-7 miRNA was one of the first miRNAs discovered in the nematode, Caenorhabditis elegans, and its biological functions show a high level of evolutionary conservation from the nematode to the human. Unlike in C. elegans, higher animals have multiple isoforms of let-7 miRNAs; these isoforms share a consensus sequence called the 'seed sequence' and these isoforms are categorized into let-7 miRNA family. The expression of let-7 family is required for developmental timing and tumor suppressor function, but must be suppressed for the self-renewal of stem cells. Therefore, let-7 miRNA biogenesis must be carefully controlled. To generate a let-7 miRNA, a primary transcript is produced by RNA polymerase II and then subsequently processed by Drosha/DGCR8, TUTase, and Dicer. Because dysregulation of let-7 processing is deleterious, biogenesis of let-7 is tightly regulated by cellular factors, such as the RNA binding proteins, LIN28A/B and DIS3L2. In this review, we discuss the biological functions and biogenesis of let-7 miRNAs, focusing on the molecular mechanisms of regulation of let-7 biogenesis in vertebrates, such as the mouse and the human.

SET7/9 methylation of the pluripotency factor LIN28A is a nucleolar localization mechanism that blocks let-7 biogenesis in human ESCs.

LIN28-mediated processing of the microRNA (miRNA) let-7 has emerged as a multilevel program that controls self-renewal in embryonic stem cells. LIN28A is believed to act primarily in the cytoplasm together with TUT4/7 to prevent final maturation of let-7 by Dicer, whereas LIN28B has been suggested to preferentially act on nuclear processing of let-7. Here, we find that SET7/9 monomethylation in a putative nucleolar localization region of LIN28A increases its nuclear retention and protein stability. In the nucleoli of human embryonic stem cells, methylated LIN28A sequesters pri-let-7 and blocks its processing independently of TUT4/7. The nuclear form of LIN28A regulates transcriptional changes in MYC-pathway targets, thereby maintaining stemness programs and inhibiting expression of early lineage-specific markers. These findings provide insight into the molecular mechanism underlying the posttranslational methylation of nuclear LIN28A and its ability to modulate pluripotency by repressing let-7 miRNA expression in human embryonic stem cells.

Fine-tuned grayscale optofluidic maskless lithography for three-dimensional freeform shape microstructure fabrication.

This article presents free-floating three-dimensional (3D) microstructure fabrication in a microfluidic channel using direct fine-tuned grayscale image lithography. The image is designed as a freeform shape and is composed of gray shades as light-absorbing features. Gray shade levels are modulated through multiple reflections of light in a digital micromirror device (DMD) to produce different height formations. Whereas conventional photolithography has several limitations in producing grayscale colors on photomask features, our method focuses on a maskless, single-shot process for fabrication of freeform 3D micro-scale shapes. The fine-tuned gray image is designed using an 8-bit grayscale color; thus, each pixel is capable of displaying 256 gray shades. The pattern of the UV light reflecting on the DMD is transferred to a photocurable resin flowing through a microfluidic channel. Here, we demonstrate diverse free-floating 3D microstructure fabrication using fine-tuned grayscale image lithography. Additionally, we produce polymeric microstructures with locally embedded gray encoding patterns, such as grayscale-encoded microtags. This functional microstructure can be applied to a biophysical detection system combined with 3D microstructures. This method would be suitable for fabricating 3D microstructures that have a specific morphology to be used for particular biological or medical applications.

Astrocytes contribute to gamma oscillations and recognition memory.

Glial cells are an integral part of functional communication in the brain. Here we show that astrocytes contribute to the fast dynamics of neural circuits that underlie normal cognitive behaviors. In particular, we found that the selective expression of tetanus neurotoxin (TeNT) in astrocytes significantly reduced the duration of carbachol-induced gamma oscillations in hippocampal slices. These data prompted us to develop a novel transgenic mouse model, specifically with inducible tetanus toxin expression in astrocytes. In this in vivo model, we found evidence of a marked decrease in electroencephalographic (EEG) power in the gamma frequency range in awake-behaving mice, whereas neuronal synaptic activity remained intact. The reduction in cortical gamma oscillations was accompanied by impaired behavioral performance in the novel object recognition test, whereas other forms of memory, including working memory and fear conditioning, remained unchanged. These results support a key role for gamma oscillations in recognition memory. Both EEG alterations and behavioral deficits in novel object recognition were reversed by suppression of tetanus toxin expression. These data reveal an unexpected role for astrocytes as essential contributors to information processing and cognitive behavior.

Human histone H3K79 methyltransferase DOT1L protein [corrected] binds actively transcribing RNA polymerase II to regulate gene expression.

Histone-modifying enzymes play a pivotal role in gene expression and repression. In human, DOT1L (Dot1-like) is the only known histone H3 lysine 79 methyltransferase. hDOT1L is associated with transcriptional activation, but the general mechanism connecting hDOT1L to active transcription remains largely unknown. Here, we report that hDOT1L interacts with the phosphorylated C-terminal domain of actively transcribing RNA polymerase II (RNAPII) through a region conserved uniquely in multicellular DOT1 proteins. Genome-wide profiling analyses indicate that the occupancy of hDOT1L largely overlaps with that of RNAPII at actively transcribed genes, especially surrounding transcriptional start sites, in embryonic carcinoma NCCIT cells. We also find that C-terminal domain binding or H3K79 methylations by hDOT1L is important for the expression of target genes such as NANOG and OCT4 and a marker for pluripotency in NCCIT cells. Our results indicate that a functional interaction between hDOT1L and RNAPII targets hDOT1L and subsequent H3K79 methylations to actively transcribed genes.

Self-assembled monolayers made of 6-(5-((6-((5-hexylthiophen-2-yl)ethynyl)-9,10-bis(phenylethynyl)anthracen-2-yl)ethynyl)thiophen-2-yl)hexyl 3-(triethoxysilyl)propylcarbamate for ultrathin film transistors.

A new functionalized triethoxysilane bearing an X-shaped, anthracene-based semiconducting molecule on one arm was designed and synthesized as a precursor for the preparation of a self-assembled monolayer (SAM) on a SiO(2) substrate. 3-Isocyanatopropyl triethoxysilane was reacted with a monohydroxyl-terminated X-shaped, anthracene-based semiconducting molecule in the presence of tin catalyst. The 6-(5-((6-((5-hexylthiophen-2-yl)ethynyl)-9,10-bis(phenylethynyl)anthracen-2-yl)ethynyl)thiophen-2-yl)hexyl 3-(triethoxysilyl)propylcarbamate (BATHT-TEOS) was found to be stable and sufficiently reactive to form organic monolayers on hydroxylated SiO(2) surfaces. The structures and properties of these SAMs were investigated using X-ray photoelectron spectroscopy, UV-vis absorption spectroscopy, photoluminescence (PL) spectroscopy, laser scanning confocal microscopy-PL spectrometry, and spectroscopic ellipsometry. In this work, BATHT-SAM was employed as an interfacial layer on SiO(2) to fabricate ultrathin film transistors (UTFTs, active layer thickness ∼ 16.09 nm). The device UTFT-I, made of 0.06 wt % 5,5'-(9,10-bis(phenylethynyl)anthracene-2,6-diyl)bis(ethyne-2,1-diyl)bis(2-hexylthiophene) (BATHT) solution on an n-octyltrichlorosilane-SAM/SiO(2) layer, showed no gate effect for the carrier transport behavior; however, the device UTFT-II, fabricated on BATHT-SAM/SiO(2), exhibited field effect mobilities of 0.04 cm(2) V(-1) s(-1) (I(on/off) ∼ 6.3 × 10(3) to 1.0 × 10(4)). This can be attributed to the effect of BATHT-SAM inducing uniform coverage and ordering of BATHT molecules as an upper layer.

Review Article: Recent advancements in optofluidic flow cytometer.

There is an increasing need to develop optofluidic flow cytometers. Optofluidics, where optics and microfluidics work together to create novel functionalities on a small chip, holds great promise for lab-on-a-chip flow cytometry. The development of a low-cost, compact, handheld flow cytometer and microfluorescence-activated cell sorter system could have a significant impact on the field of point-of-care diagnostics, improving health care in, for example, underserved areas of Africa and Asia, that struggle with epidemics such as HIV∕AIDS. In this paper, we review recent advancements in microfluidics, on-chip optics, novel detection architectures, and integrated sorting mechanisms.

Sorting directionally oriented microstructures using railed microfluidics.

We demonstrate the microfluidic sorting of directionally oriented (anisotropic) microstructures by their orientational state in solution using the concept of railed microfluidics. After being injected into a microfluidic channel, the microstructures rotate and flip in various directions. In order to sort microstructures in an organized way, we designed the microstructures and the microchannel to allow for orientation-based control of microstructure movement. In order to sort microstructures based on their rotation, we used a wedge shaped fin on the microstructures and a Y-shaped railed microfluidic channel. For sorting flipped particles, we use a double-railed microfluidic channel that has grooves on both its top and bottom surfaces. By integrating the two sorting methods we demonstrated high throughput, autonomous sorting into four different orientational states: unrotated-unflipped, rotated-unflipped, unrotated-flipped, and rotated-flipped. Here we not only demonstrate orientational assembly of directionally dependent microstructures, but also present design considerations for future work.