5,191 results match your criteria atac-seq identified

Live-Cell Imaging Probes to Track Chromatin Modification Dynamics.

Microscopy (Oxf) 2021 Jul 30. Epub 2021 Jul 30.

Cell Biology Center, Institute of Innovative Research, 4259 Nagatsuta-cho, Midori-ku, Yokohama, 226-8503, Japan.

The spatiotemporal organization of chromatin is regulated at different levels in the nucleus. Epigenetic modifications such as DNA methylation and histone modifications are involved in chromatin regulation and play fundamental roles in genome function. While the one-dimensional epigenomic landscape in many cell types has been revealed by chromatin immunoprecipitation and sequencing, the dynamic changes of chromatin modifications and their relevance to chromatin organization and genome function remain elusive. Read More

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Identification of a rice metallochaperone for cadmium tolerance by an epigenetic mechanism and potential use for clean up in wetland.

Environ Pollut 2021 Jul 22;288:117837. Epub 2021 Jul 22.

Department of Biochemistry and Molecular Biology, College of Life Science, Nanjing Agricultural University, Nanjing, 210095, China. Electronic address:

Cadmium (Cd) is a toxic heavy metal that initiates diverse chronic diseases through food chains. Developing a biotechnology for manipulating Cd uptake in plants is beneficial to reduce environmental and health risks. Here, we identified a novel epigenetic mechanism underlying Cd accumulation regulated by an uncharacterized metallochaperone namely Heavy Metal Responsive Protein (HMP) in rice plants. Read More

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RECOGNICER: A coarse-graining approach for identifying broad domains from ChIP-seq data.

Quant Biol 2020 Dec 19;8(4):359-368. Epub 2020 Nov 19.

Department of Physics, The George Washington University, Washington, DC 20052, USA.

Background: Histone modifications are major factors that define chromatin states and have functions in regulating gene expression in eukaryotic cells. Chromatin immunoprecipitation coupled with high-throughput sequencing (ChIP-seq) technique has been widely used for profiling the genome-wide distribution of chromatin-associating protein factors. Some histone modifications, such as H3K27me3 and H3K9me3, usually mark broad domains in the genome ranging from kilobases (kb) to megabases (Mb) long, resulting in diffuse patterns in the ChIP-seq data that are challenging for signal separation. Read More

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December 2020

EGR2-mediated regulation of mA reader IGF2BP proteins drive RCC tumorigenesis and metastasis via enhancing S1PR3 mRNA stabilization.

Cell Death Dis 2021 Jul 29;12(8):750. Epub 2021 Jul 29.

Department of Urology, First Affiliated Hospital, School of Medicine, Zhejiang University, 310000, Hangzhou, Zhejiang, China.

Emerging discoveries of dynamic and reversible N6-methyladenosine (mA) modification on RNA in mammals have revealed the key roles of the modification in human tumorigenesis. As known mA readers, insulin-like growth factor 2 mRNA-binding proteins (IGF2BPs) are upregulated in most cancers and mediates the enhancement of mA-modified mRNAs stability. However, the mechanisms of IGF2BPs in renal cell cancer (RCC) still remain unclear. Read More

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The ubiquitin-interacting motif-type ubiquitin receptor HDR3 interacts with and stabilizes the histone acetyltransferase GW6a to control grain size in rice.

Plant Cell 2021 Jul 29. Epub 2021 Jul 29.

Key Laboratory of Plant Molecular Physiology, Institute of Botany, the Chinese Academy of Sciences, No.20 Nanxincun, Xiangshan, Beijing 100093, China.

For grain crops such as rice (Oryza sativa), grain size substantially affects yield. The histone acetyltransferase GRAIN WEIGHT 6a (GW6a) determines grain size and yield in rice. However, the gene regulatory network underlying GW6a-mediated regulation of grain size has remained elusive. Read More

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The Novel Non-coding Transcriptional Regulator Gm18840 Drives Cardiomyocyte Apoptosis in Myocardial Infarction Post Ischemia/Reperfusion.

Front Cell Dev Biol 2021 12;9:615950. Epub 2021 Jul 12.

Department of Cardiology, Fuwai Hospital, Chinese Academy of Medical Sciences, Shenzhen, (Shenzhen Sun Yat-sen Cardiovascular Hospital), Shenzhen, China.

Background: Ischemia/reperfusion-mediated myocardial infarction (MIRI) is a major pathological factor implicated in the progression of ischemic heart disease, but the key factors dysregulated during MIRI have not been fully elucidated, especially those essential non-coding factors required for cardiovascular development.

Methods: A murine MIRI model and RNA sequencing (RNA-seq) were used to identify key lncRNAs after myocardial infarction. qRT-PCR was used to validate expression in cardiac muscle tissues and myocardial cells. Read More

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Epigenetic modifications underlie the differential adipogenic potential of preadipocytes derived from human subcutaneous fat tissue.

Am J Physiol Cell Physiol 2021 07 28. Epub 2021 Jul 28.

Department of Plastic Surgery, Chiba University, Chiba-city, Chiba, Japan.

Aim: Ceiling culture-derived preadipocytes (ccdPAs) and adipose-derived stem cells (ASCs) can be harvested from human subcutaneous fat tissue using the specific gravity method. Both cell types possess a similar spindle shape without lipid droplets. We previously reported that ccdPAs have a higher adipogenic potential than ASCs, even after a 7-week culture. Read More

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Aspirin enhances the therapeutic efficacy of cisplatin in oesophageal squamous cell carcinoma by inhibition of putative cancer stem cells.

Br J Cancer 2021 Jul 27. Epub 2021 Jul 27.

Department of Etiology and Carcinogenesis, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China.

Background: Cancer stem cells (CSCs) are related to the patient's prognosis, recurrence and therapy resistance in oesophageal squamous cell carcinoma (ESCC). Although increasing evidence suggests that aspirin (acetylsalicylic acid, ASA) could lower the incidence and improve the prognosis of ESCC, the mechanism(s) remains to be fully understood.

Methods: We investigated the role of ASA in chemotherapy/chemoprevention in human ESCC cell lines and an N-nitrosomethylbenzylamine-induced rat ESCC carcinogenesis model. Read More

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MSI4/FVE is required for accumulation of 24-nt siRNAs and DNA methylation at a subset of target regions of RNA-directed DNA methylation.

Plant J 2021 Jul 27. Epub 2021 Jul 27.

Shanghai Center for Plant Stress Biology, National Key Laboratory of Plant Molecular Genetics, Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, 201602, China.

DNA methylation is an important epigenetic mark. In plants, de novo DNA methylation occurs mainly through the RNA-directed DNA methylation (RdDM) pathway. Researchers have previously inferred that a flowering regulator, MULTICOPY SUPPRESSOR OF IRA1 4 (MSI4) /FVE, is involved in non-CG methylation at several RdDM targets, suggesting a role of FVE in RdDM. Read More

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Discovering single nucleotide variants and indels from bulk and single-cell ATAC-seq.

Nucleic Acids Res 2021 Jul 27. Epub 2021 Jul 27.

Integrative Biology Laboratory, Salk Institute for Biological Studies, 10010 N. Torrey Pines Road, La Jolla, CA 92037, USA.

Genetic variants and de novo mutations in regulatory regions of the genome are typically discovered by whole-genome sequencing (WGS), however WGS is expensive and most WGS reads come from non-regulatory regions. The Assay for Transposase-Accessible Chromatin (ATAC-seq) generates reads from regulatory sequences and could potentially be used as a low-cost 'capture' method for regulatory variant discovery, but its use for this purpose has not been systematically evaluated. Here we apply seven variant callers to bulk and single-cell ATAC-seq data and evaluate their ability to identify single nucleotide variants (SNVs) and insertions/deletions (indels). Read More

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A CREB1-miR-181a-5p loop regulates the pathophysiologic features of bone marrow stromal cells in fibrous dysplasia of bone.

Mol Med 2021 Jul 22;27(1):81. Epub 2021 Jul 22.

Jiangsu Province Key Laboratory of Oral Diseases, Nanjing Medical University, No.136, Hanzhong Road, Nanjing, 210029, Jiangsu Province, China.

Background: Fibrous dysplasia (FD) is a bone marrow stromal cell (BMSC) disease caused by activating mutations of guanine nucleotide-binding protein alpha-stimulating activity polypeptide (GNAS) and is characterized by increased proliferative activity and disrupted osteogenesis of BMSCs. However, the molecular mechanisms regulating the pathophysiologic features of BMSCs in FD remain unknown. This study aimed to identify and verify the roles of the CREB1-miR-181a-5p regulatory loop in FD pathophysiology. Read More

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FACS-based isolation of fixed mouse neuronal nuclei for ATAC-seq and Hi-C.

STAR Protoc 2021 Sep 9;2(3):100643. Epub 2021 Jul 9.

Department of Life Sciences, Ben-Gurion University of the Negev, Beer Sheva 84105, Israel.

The organization of chromatin structure plays a crucial role in gene expression, DNA replication, and repair. Chromatin alterations influence gene expression, and modifications could be associated with genomic instability in the cells during aging or diseases. Here, we provide a modified protocol to isolate fixed neuronal nuclei from a single mouse cortex to investigate the spatial organization of chromatin structure on a genome-wide scale by ATAC-seq (the assay for transposase-accessible chromatin with high-throughput sequencing) and chromatin conformation by Hi-C (high-throughput chromosome conformation capture). Read More

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September 2021

Uniaxial Cyclic Stretching Promotes Chromatin Accessibility of Gene Loci Associated With Mesenchymal Stem Cells Morphogenesis and Osteogenesis.

Front Cell Dev Biol 2021 7;9:664545. Epub 2021 Jul 7.

CAS Key Laboratory of Mechanical Behavior and Design of Materials, Department of Modern Mechanics, University of Science and Technology of China, Hefei, China.

It has been previously demonstrated that uniaxial cyclic stretching (UCS) induces differentiation of mesenchymal stem cells (MSCs) into osteoblasts . It is also known that interactions between cells and external forces occur at various aspects including cell-matrix, cytoskeleton, nucleus membrane, and chromatin. However, changes in chromatin landscape during this process are still not clear. Read More

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Bioremediation of heavy metals from industrial effluents by endophytes and their metabolic activity: Recent advances.

Bioresour Technol 2021 Jul 14;339:125589. Epub 2021 Jul 14.

CSIR-National Environmental and Engineering Research Institute (CSIR-NEERI), Nagpur 440 020, India. Electronic address:

Worldwide, heavy metals pollution is mostly caused by rapid population growth and industrial development which is accumulated in food webs causing a serious public health risk. Endophytic microorganisms have a variety of mechanisms for metal sequestration having metal biosorption capacities.Endophytic organisms like bacteria and fungi provide beneficial qualities that help plants to improve their health, reduce stress, and detoxify metals. Read More

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Individual functions of the histone acetyl transferases CBP and p300 in regulating the inflammatory response of synovial fibroblasts.

J Autoimmun 2021 Jul 23;123:102709. Epub 2021 Jul 23.

Center of Experimental Rheumatology, Department of Rheumatology, University Hospital Zurich, University of Zurich, Switzerland; Department of BioMedical Research, University of Bern, Bern, Switzerland; Department of Rheumatology and Immunology, University Hospital Bern, Bern, Switzerland. Electronic address:

Chromatin remodeling, and a persistent histone 3 lysine 27 acetylation (H3K27ac) in particular, are associated with a sustained inflammatory response of synovial fibroblasts (SF) in rheumatoid arthritis (RA). Here we investigated individual functions of the writers of H3K27ac marks, the homologues histone acetyl transferases (HAT) CBP and p300, in controlling the constitutive and inflammatory gene expression in RA SF. We applied a silencing strategy, followed by RNA-sequencing and pathway analysis, complemented with the treatment of SF with inhibitors targeting the HAT (C646) or bromo domains (I-CBP) of CBP and p300. Read More

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Chromatin Dynamics and Gene Expression Response to Heat Exposure in Field-Conditioned versus Laboratory-Cultured .

Int J Mol Sci 2021 Jul 12;22(14). Epub 2021 Jul 12.

Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gan 52900, Israel.

Organisms' survival is associated with the ability to respond to natural or anthropogenic environmental stressors. Frequently, these responses involve changes in gene regulation and expression, consequently altering physiology, development, or behavior. Here, we present modifications in response to heat exposure that mimics extreme summertime field conditions of lab-cultured and field-conditioned . Read More

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Single cell functional genomics reveals plasticity of subcutaneous white adipose tissue (WAT) during early postnatal development.

Mol Metab 2021 Jul 20:101307. Epub 2021 Jul 20.

Center for Molecular Medicine and Genetics, Wayne State University, Detroit, MI, USA; Center for Integrative Metabolic and Endocrine Research, Wayne State University, Detroit, MI, USA. Electronic address:

Objective: The current study addressed the cellular complexity and plasticity of subcutaneous (inguinal) white adipose tissue (iWAT) in mice during the critical periods of perinatal growth and establishment.

Methods: We performed a large-scale single cell transcriptomic (scRNA-seq) and epigenomic (snATAC-seq) characterization of cellular subtypes (adipose stromal cells (ASC) and adipocyte nuclei) during inguinal WAT (subcutaneous; iWAT) development in mice, capturing the early postnatal period (postnatal days (PND) 06 and 18) through adulthood (PND56).

Results: Perinatal and adult iWAT contains 3 major ASC subtypes that can be independently identified by RNA expression profiles and DNA transposase accessibility. Read More

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Impaired SNF2L Chromatin Remodeling Prolongs Accessibility at Promoters Enriched for Fos/Jun Binding Sites and Delays Granule Neuron Differentiation.

Front Mol Neurosci 2021 6;14:680280. Epub 2021 Jul 6.

Regenerative Medicine Program, Ottawa Hospital Research Institute, Ottawa, ON, Canada.

Chromatin remodeling proteins utilize the energy from ATP hydrolysis to mobilize nucleosomes often creating accessibility for transcription factors within gene regulatory elements. Aberrant chromatin remodeling has diverse effects on neuroprogenitor homeostasis altering progenitor competence, proliferation, survival, or cell fate. Previous work has shown that inactivation of the genes, (encoding Snf2h) and (encoding Snf2l) have dramatic effects on brain development. Read More

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[CRL4B complex promotes the development of pancreatic cancer by inhibiting secreted frizzled related protein 1].

Y Chen S Leng Y Wang

Zhonghua Zhong Liu Za Zhi 2021 Jun;43(6):646-656

Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Tianjin Medical University, Collaborative Innovation Center of Tianjin for Medical Epigenetics, Tianjin Key Laboratory of Medical Epigenetics, Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), Tianjin 300070, China.

To investigate the role of CUL4B-RING E3 ubiquitin ligase (CRL4B) complex in pancreatic tumorigenesis and the molecular mechanism. Pancreatic cells were divided into control group (transfected with negative control lentivirus), shCUL4B group (transfected with CUL4B lentivirus), shDDB1 group [transfected with DNA damage binding protein 1 (DDB1) lentivirus], and shCUL4B+ siSFRP1 group (transfected with CUL4B lentivirus and SFRP1-siRNA). RNA-seq was performed in pancreatic cancer cell lines with CUL4B and DDB1 knocked down respectively, to identify the target genes regulated by CRL4B complex. Read More

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ChIP-seq Experiment and Data Analysis in the Cyanobacterium sp. PCC 6803.

Bio Protoc 2018 Jun 20;8(12):e2895. Epub 2018 Jun 20.

Systems Biology and Bioinformatics Laboratory, Centre for Biomedical Research (CBMR), University of Algarve, Faro, Portugal.

Nitrogen is an essential nutrient for all living organisms. In cyanobacteria, a group of oxygenic photosynthetic bacteria, nitrogen homeostasis is maintained by an intricate regulatory network around the transcription factor NtcA. Although mechanisms controlling NtcA activity appear to be well understood, the sets of genes under its control (, its regulon) remain poorly defined. Read More

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Gene Regulatory Network of Human GM-CSF-Secreting T Helper Cells.

J Immunol Res 2021 3;2021:8880585. Epub 2021 Jul 3.

Unit of Computational Medicine, Center for Molecular Medicine, Department of Medicine Solna, Karolinska Institutet, ki.se Karolinska University Hospital & Science for Life Laboratory, 17176 Solna, Stockholm, Sweden.

GM-CSF produced by autoreactive CD4-positive T helper cells is involved in the pathogenesis of autoimmune diseases, such as multiple sclerosis. However, the molecular regulators that establish and maintain the features of GM-CSF-positive CD4 T cells are unknown. In order to identify these regulators, we isolated human GM-CSF-producing CD4 T cells from human peripheral blood by using a cytokine capture assay. Read More

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A universal framework for detecting -regulatory diversity in DNA regulatory regions.

Genome Res 2021 Jul 19. Epub 2021 Jul 19.

CSIR-National Chemical Laboratory, Academy of Scientific and Innovative Research

High-throughput sequencing-based assays measure different biochemical activities pertaining to gene regulation, genome-wide. These activities include transcription factor (TF)-DNA binding, enhancer activity, open chromatin, and more. A major goal is to understand underlying sequence components, or motifs, that can explain the measured activity. Read More

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CoBRA: Containerized Bioinformatics Workflow for Reproducible ChIP/ATAC-seq Analysis.

Genomics Proteomics Bioinformatics 2021 Jul 17. Epub 2021 Jul 17.

Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02215, USA. Electronic address:

Chromatin immunoprecipitation sequencing (ChIP-seq) and the Assay for Transposase-Accessible Chromatin with high-throughput sequencing (ATAC-seq) have become essential technologies to effectively measure protein-DNA interactions and chromatin accessibility. However, there is a need for a scalable and reproducible pipeline that incorporates proper normalization between samples, correction of copy number variations, and integration of new downstream analysis tools. Here we present Containerized Bioinformatics workflow for Reproducible ChIP/ATAC-seq Analysis (CoBRA), a modularized computational workflow which quantifies ChIP-seq and ATAC-seq peak regions and performs unsupervised and supervised analyses. Read More

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Life Cycle Stage-Specific Accessibility of Leishmania donovani Chromatin at Transcription Start Regions.

mSystems 2021 Jul 20:e0062821. Epub 2021 Jul 20.

Leishmaniasis Group, Bernhard Nocht Institute for Tropical Medicinegrid.424065.1, Hamburg, Germany.

Leishmania donovani is a parasitic protist that causes the lethal Kala-azar fever in India and East Africa. Gene expression in is regulated by gene copy number variation and inducible translation while RNA synthesis initiates at a small number of sites per chromosome and proceeds through polycistronic transcription units, precluding a gene-specific regulation (C. Clayton and M. Read More

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A plate-based single-cell ATAC-seq workflow for fast and robust profiling of chromatin accessibility.

Nat Protoc 2021 Jul 19. Epub 2021 Jul 19.

Shenzhen Key Laboratory of Gene Regulation and Systems Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, China.

Profiling chromatin accessibility at the single-cell level provides critical information about cell type composition and cell-to-cell variation within a complex tissue. Emerging techniques for the interrogation of chromatin accessibility in individual cells allow investigation of the fundamental mechanisms that lead to the variability of different cells. This protocol describes a fast and robust method for single-cell chromatin accessibility profiling based on the assay for transposase-accessible chromatin using sequencing (ATAC-seq). Read More

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Novel germline variant in the histone demethylase and transcription regulator KDM4C induces a multi-cancer phenotype.

J Med Genet 2021 Jul 19. Epub 2021 Jul 19.

Applied Tumor Genomics Research Program and Department of Medical and Clinical Genetics, University of Helsinki Faculty of Medicine, Helsinki, Finland

Background: Genes involved in epigenetic regulation are central for chromatin structure and gene expression. Specific mutations in these might promote carcinogenesis in several tissue types.

Methods: We used exome, whole-genome and Sanger sequencing to detect rare variants shared by seven affected individuals in a striking early-onset multi-cancer family. Read More

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H3K27Ac modification and gene expression in psoriasis.

J Dermatol Sci 2021 Jul 6. Epub 2021 Jul 6.

Laboratory of Molecular Cell Biology, Center for Cancer Research and Department of Medicine C, Sheba Medical Center, Tel Hashomer, Israel; Faculty of Medicine, Sackler School of Medicine, Tel Aviv University, Tel Aviv, Israel. Electronic address:

Background: Numerous alterations in gene expression have been described in psoriatic lesions compared to uninvolved or healthy skin. However, the mechanisms which induce this altered expression remain unclear. Epigenetic modifications play a key role in regulating genes' expression. Read More

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-regulatory switches establish scale colour identity and pattern diversity in .

Elife 2021 Jul 19;10. Epub 2021 Jul 19.

Department of Zoology, University of Cambridge, Downing St., Cambridge, United Kingdom.

In butterflies, wing colour pattern diversity and scale types are controlled by a few genes of large effect that regulate colour pattern switches between morphs and species across a large mimetic radiation. One of these genes, , has been repeatedly associated with colour pattern evolution in butterflies. Here we carried out CRISPR knockouts in multiple species and show that is a major determinant of scale cell identity. Read More

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Characterization of Chromatin Accessibility and Gene Expression Upon Cold Stress Reveals the Transcription Factor RAV1 Functions in Cold Response in Vitis amurensis.

Plant Cell Physiol 2021 Jul 19. Epub 2021 Jul 19.

Beijing Key Laboratory of Grape Sciences and Enology, Key Laboratory of Plant Resource, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, PR China.

Cold tolerance is regulated by a variety of transcription factors (TFs) and their target genes. Except for the well-characterized C-repeat binding factors (CBFs)-dependent transcriptional cascade, the mechanisms of cold tolerance mediated by other transcriptional regulatory networks are still largely unknown. Here we used the assay for transposase-accessible chromatin with sequencing (ATAC-seq) and RNA-seq to identify cold responsive TFs in Vitis amurensis, a grape species with high cold hardiness. Read More

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Transcription-Based Multidimensional Regulation of Fatty Acid Metabolism by HIF1α in Renal Tubules.

Front Cell Dev Biol 2021 2;9:690079. Epub 2021 Jul 2.

National Clinical Research Center of Kidney Diseases, Jinling Hospital, Medical School of Nanjing University, Nanjing, China.

Lipid metabolism plays a basic role in renal physiology, especially in tubules. Hypoxia and hypoxia-induced factor (HIF) activation are common in renal diseases; however, the relationship between HIF and tubular lipid metabolism is poorly understood. Using prolyl hydroxylase inhibitor roxadustat (FG-4592), we verified and further explored the relationship between sustained HIF1α activation and lipid accumulation in cultured tubular cells. Read More

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