Picoruptor ® ソニケーター

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ChIP-seq Analysis
Easy to use
All-in-one solution
Processing of 6-16 samples
Sample size 5 µl – 2 ml
No soundproof box
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Picoruptor は剪断の最新の技術革新であり、最大5mlから最大2mlまでの剪断マイクロボリュームのために最適化されたオールインワン剪断システムとしての新たなブレークスルーを表しています。 冷却システム(ウォータークーラーとシングルサイクルバルブ)により、高精度の温度制御が可能になり、より高品質のサンプルが得られます。

  • オールインワンシャーリングソリューション
  • 6-12個のサンプルの同時超音波処理
  • 小型で、軽く、使いやすい
  • 温度制御された


  • 次世代シークエンシングのためのDNAシェアリング(5〜100μl)
  • クロマチン剪断(10μl〜2ml)
  • RNAシアリング
  • 組織や細胞からのタンパク質抽出
  • FFPE DNA抽出


My group is mostly focused on epigenetic reprogramming and I have been using Diagenode products for the last 5 years. My experience with both antibodies, ChIP-Kits and the Bioruptor is nothing but positive. Diagenode products are unique for reproducibility, and this has always been a great plus for the success of my experiments.

Dr. Raffaele Teperino - Environmental Epigenetic Group - Institute of Experimental Genetics, Helmholtz Zentrum Muenchen GmbH, Germany

High throughput sequencing has dramatically reduced sequencing costs and the development of duel indexing strategies makes it possible to combine 384 samples in a single sequencing run. By developing library preparation methods to enrich for retroviral integration sites and retroviral transcripts we have been able to produce large numbers of low cost libraries to track the evolution of infection and to characterise patterns of expression from our virus of interest. The Bioruptor® Pico has been essential part of our protocols and provides straightforward and consistent shearing of our samples.

Dr Keith Durkin, Unit of Animal Genomics, GIGA-R, Université de Liège , 4000 Liège, Belgium
  • User manual
  • Recommended settings for DNA shearing with Bioruptor® Pico

    Follow our guidelines and find the good parameters for your expected DNA size: DNA shearing with the Bioruptor® Pico

  • Testimonials

    The Bioruptor® NGS* is a robust user-friendly sonication system that is key for both reproducible chromatin shearing and DNA shearing. The Bioruptor® NGS consistently delivered optimal DNA shearing that was critical in generating homogeneous sequencing libraries for our experiments. We also observed excellent chromatin shearing result that were crucial for our epigenetic mapping projects.

    Dr. Sascha Tierling, Department of Genetics and Epigenetics, Prof . Dr. Jörn Walter's lab, Universität des Saarlandes, Germany.

    The new Bioruptor® Pico machine has reduced the amount of time spent sonicating Chromatin by a massive amount. Some protocols require quite harsh fixing conditions which meant fragmenting DNA on the old machine was taking many rounds and several times. With the new Bioruptor® Pico machine these sonications were taking just one round of 10 cycles thereby reducing the fragmentation time substantially. Following sonication, I have used the new IDeal ChIP-seq kit. This is a nice straight forward kit that if followed with an appropriate chip validated antibody gave amazing chip-seq results that worked time and again with several different transcription factors. I would recommend both kits for good, consistant chromatin work.

    Dr. Karen Dawson, RNA Biology Group, Cancer Research UK Manchester Institute at the University of Manchester

    Diagenode has provided a Bioruptor® Pico demo instrument to us for 2 weeks in September. We were getting very reproducible results between different tubes in the same sonication as well as between replicate experiments. We have obtained considerably improved results especially  for cross-linked chromatin from mammalian cells that has always been a problem for us with the old Bioruptor. A bonus also was a reduced sonication time, although the preparation time is slightly delayed due to the glutinous nature of the beads.

    Dr. Tatyana Nesterova, Department of Biochemistry, University of Oxford

    We are particularly satisfied with the Bioruptor® Pico that we have recently purchased. Since we have started using this novel machine, all experiments for our epignetics research have been much more easy to perform. This machine is really a great thing for us. The whole department has now started using this novel device.

    Dr. Marco Pontoglio, Head of the Team "Expression Génique, Développement et Maladies" (EGDM) and Director of the “Development, Cancer and Reproduction”, Department Institut Cochin, Université Paris-Descartes

    I have extensively used the antibodies against the histone modifications H3K4me3, H3k27me3, H3K9ac, H4k8ac and H3K18ac provided by Diagenode. The high level of specificity and selectivity of these antibodies in mouse brain samples, confirmed by using several negative and positive controls run in parallel with mouse brain tissue samples, ensured successful and reproducible results. I have been a Diagenode costumer for over one year now and I am extremely satisfied with the efficiency of the Bioruptor Pico for chromatin shearing as well as all of the ChIP materials (i.e., antibodies, blocking peptides, primer pairs for qPCR) provided by this company. Many thanks.

    Dr. Ermelinda Lomazzo, Institute of Physiological Chemistry, AG Prof. Beat Lutz. University Medical Center of the Johannes Gutenberg University Mainz, Germany

    I work with Diagenode’s Plant ChIP-seq kit and shear the DNA on the Bioruptor Pico for the last year and I have to say that these two products saved my PhD project! Some time ago, our well-established ChIP protocol suddenly stopped to work and after long time of figuring out the reason, we invested into Bioruptor Pico. I am very satisfied from the way it works, plus it’s super quiet! Combining the sonicator with the Plant ChIP-seq kit we finally got things working. I have also decided to try the Microplex Library Prep kit, which is amazing. I have been working with other kits and I find this one efficient and very easy to use. Recently, I have tested one of the epigenetics antibody (H3K4me3) and it works very well on the plant tissue, together with the ChIP-seq kit and Bioruptor.

    Thanks Diagenode for saving my PhD!

    Kamila Kwasniewska, Plant Developmental Genetics, Smurfit Institute, Trinity College, Dublin

    Neonatal screening cards provide a valuable bio-bank for retrospective studies. We have used the Bioruptor Pico and IP-Star Compact instrument along with the Auto MeDIP and IPure v2 kit to generate genome-wide DNA methylation profiles using only minute DNA inputs. Using the Diagenode instruments and products has generated reproducible results and saved us hands-on time. We are satisfied with the level of service and technical support and would recommend Diagenode to all others working in the field of epigenetics.

    Read the full abstract for Genome-wide DNA methylation profiling with MeDIP-seq using archived dried blood spots

    Dr. Nicklas Heine Staunstrup, Faculty of Health, Institute of Biomedicine, Aarhus University, Denmark
  • Protocols
    Chromatin shearing - Guide for successful chromatin preparation using the Bioruptor® Pico
    Chromatin immunoprecipitation (ChIP) is a common tool used to study protein-DNA interactions in c...
    Chromatin shearing from tissue protocol using Diagenode’s Chromatin shearing optimization kit - Low SDS and Bioruptor® Standard, Plus or Pico
    This protocol describes the chromatin preparation from fresh or frozen tissues. The isolated chro...
    Chromatin shearing with the Bioruptor Pico 10 µl - 300 µl
    HeLa cells are fixed with 1% molecular grade formaldehyde (for 8 min at room temperature). Nucleu...
    Chromatin shearing with the Bioruptor® Pico 500 µl - 2 ml
    Chromatin shearing from HeLa cells is performed according to Diagenode’s Chromatin Shearing...
    Chromatin shearing with the Bioruptor® Pico, 0.2 ml Bioruptor® Microtubes and the corresponding holder
    The first critical step of a successful ChIP experiment is the preparation of sheared chromatin w...
    Deparaffinization - Procedure for FFPE nucleic acid extraction with the Bioruptor®
    Deparafinization of FFPE samples is typically performed using a non-polar solvent, such as xylene...
    DNA Shearing for Bioruptor® Pico - Standard 100 μl Volume
    Standard protocols for programmable DNA size distributions, excellent reproducibility, and high d...
    DNA Shearing for Bioruptor® Pico - 50 μl Volume
    For DNA shearing in 50 μl we highly recommend to use the 0.1 ml tube holder & tube adaptor...
    DNA shearing for Next-Generation Sequencing with the Bioruptor® pico, 0.2 ml Bioruptor® microtubes and the corresponding holder
    Optimal data generation using NGS platforms relies on a few sample-preparation prerequisites, amo...
    DNA Shearing with Bioruptor® Pico - Small Volume (10 µl)
    For DNA shearing we highly recommend to use the 0.1 ml tube holder & tube adaptors (Cat. No. ...
    FFPE DNA extraction protocol using the Bioruptor®
    The number of archival formalin-fixed paraffin embedded (FFPE) samples is in the millions, provid...
    iST Sample Preparation with the Bioruptor®
    The PreOmics iST sample preparation of proteins combined with the Diagenode Bioruptor® Pico e...
    PCR amplicons shearing using the Bioruptor Pico
    With the Bioruptor® Pico and the former model Bioruptor® NGS it is possible to shear PCR ...
    Protein extraction from Tissues and Cultured Cells using Bioruptor® Pico
    Protein extraction from tissues and cultured cells is the first step for many biochemical and ana...
    Re-shearing of decrosslinked immunoprecipitated DNA using the Bioruptor® Pico
    ChIP-seq is a common tool used to study protein-DNA interactions in cells and tissues on a genome...
    RNA Shearing for Bioruptor® NGS and Pico
    The Diagenode ACT (Adaptative Cavitation Transfer technology) process is highly reproducible, how...
    Ultrasensitive proteomics for microdissected fresh frozen tissue samples using the Bioruptor® Pico for sample preparation
    Histology-defined proteomics investigations are a fundamental tool in modern molecular pathology....
  • Applications
    近年の次世代シーケンシング(NGS)の進歩はゲノミクスや生物学に革命をもたらしました。 この成長により、最適なサンプル調製、ゲノムライブラリー構築には欠かせない高度技術の要求、必要性がさらに高まっています。 最適なライブラリー調製に最も重要な要因の一つは、シーケンシングされるDNAの品質です。 まずは、DNAを効果的かつ一貫してシーケンシングプラットフォームに応じた適切な断片サイズに切断し、具体的で信頼できるNGS結果を実現する必要があります。 Picoruptor and Megar... Read more
    ChIPの成功に最も重要なステップは細胞の固定と溶解、そしてクロマチンの断片化の両方です。 研究者の中には、これらのステップの両方の重要な性質を見過すことがあります。断片化工程の不一致を解消するDiagenodeのPicoruptor®は、最先端の超音波ACT(Adaptive Cavitation Technology)を駆使し、効率的にクロマチンを断片します。ACTは、穏やかかつ非常に有効な断片力を用いて、ChIP実験に必須の高いIP効率および感度を持つ最高のクロマチン品質... Read more
    ホルマリン固定 DNA抽出
    Diagenode's high yields FFPE DNA extraction using Bioruptor® is a superior method for extracting DNA for Next-Gen Sequencing. Our FFPE DNA Extraction kit contains optimized reagents that are added directly to the FFPE samples to remove paraf... Read more
    DNAせん断、ライブラリー作成、自動化:NGSのワンストップショップ 1. せん断装置を選択してください:150 bp〜75 kbの範囲でDNAをせん断します。 5μlまでせん断:150 bp〜2 kbNGS DNAライブラリー調製およびFFPE核酸抽出に最適で、 2 kb〜75 kbの範囲をせんできます。メイトペアライブラリー調製および長いフラグメントDNAシーケンシングに最適で、この軽量デスクトップデバイス... Read more
    検出方法(ChIP-seq)としてハイスループットシーケンシングと結合したクロマチン免疫沈降(ChIP)は、今やエピゲノム研究、すなわちゲノム規模でのタンパク質-DNA相互作用の研究において主要な方法の1つされています。また、この技術は現在、細胞分化、腫瘍抑制遺伝子のサイレンシング、および遺伝子発現に対するヒストン修飾の効果を含む様々なライフサイエンス分野で使用されています。 ChIP-seqワークフロー クロマチン調製 : DNAへのヒストンまたは転... Read more
    Various biochemical and analytical techniques require the extraction of protein from tissues or mammalian, yeast and bacterial cells. Obtaining high quality and yields of proteins is important for further downstream protein characterization such... Read more
    The MBD approach is based on the very high affinity of a H6-GST-MBD fusion protein for methylated DNA. This protein consists of the methyl binding domain (MBD) of human MeCP2, as a C-terminal fusion with Glutathione-S-transferase (GST) containin... Read more
    エピジェネティクス研究は、異なる転写パターン、遺伝子発現およびサイレンシングを引き起こすクロマチンの変化に対処します。クロマチンの主成分はDNAおよびヒストン蛋白質です。 各ヒストンコア蛋白質(H2A、H2B、H3およびH4)の2つのコピーを8量体に組み込み、DNAで包んでヌクレオソームコアを形成させます。 ヌクレオソームは、転写機械のDNAへの接近可能性およびクロマチン再構成因子を制御します。 クロマチン免疫沈降(ChIP)は、関心対象の特定の蛋白質に対... Read more
  • Documents
    Bioruptor® Sonicator Brochure BROCHURE
    Diagenode’s Bioruptor® uses state-of-the-art shearing device to disrupt, disp...
    Bioruptor® DNA shearing for Agilent SureSelect library preparation: a perfect combination APPLICATION NOTE
    The Cologne Center for Genomics (CCG), headed by Prof. Dr. Peter Nürnberg, shows that t...
    Which tubes for which Bioruptor®? QUICK GUIDE
    Diagenode tubes were developed specifically for use with the Bioruptor®. They ensure a maximu...
    Bioruptor® NGS: Unbiased DNA shearing for Next-Generation Sequencing CASE STUDY
    Wouter Coppieters, PhD, and his colleagues operate the genomics core facility at the GIGA center,...
    True MicroChIP and MicroPlex kits APPLICATION NOTE
    From minuscule amounts to magnificent results: reliable ChIP-seq data from 10,000 cells with the ...
    ChIP-seq from human tumor tissue APPLICATION NOTE
    Application of the Bioruptor® Pico for shearing chromatin fragments for ChIP-seq from human t...
    ChIP kit results with True MicroChIP kit POSTER
    Chromatin immunoprecipitation coupled with high-throughput sequencing (ChIP-seq) has become the g...
    Bioruptor® NGS System – Designed Exclusively for Fast & Accurate DNA Shearing POSTER
    The Bioruptor®NGS is the DNA shearing device of choice for sequencing applications, providing...
    Application of the Bioruptor® Pico for best shearing of yeast genomic DNA for NGS APPLICATION NOTE
    DNA shearing is important step for next-generation sequencing library preparation. Important is r...
    DNA shearing for Next-Generation Sequencing with the Bioruptor® pico, 0.2 ml Bioruptor® microtubes and the corresponding holder PROTOCOL
    Optimal data generation using NGS platforms relies on a few sample-preparation prerequisites, amo...
    Chromatin shearing with the Bioruptor® Pico, 0.2 ml Bioruptor® Microtubes and the corresponding holder PROTOCOL
    The first critical step of a successful ChIP experiment is the preparation of sheared chromatin w...
    Workflow for FFPE-derived DNA shearing prior to Next Generation Sequencing APPLICATION NOTE
    Formalin fixation and paraffin embedding (FFPE) is a standard method for long-term preservation o...
    Efficient and streamlined solution for high-quality NGS library preparation using the Bioruptor® Pico and JetSeqTM Flex DNA Library Preparation Kit APPLICATION NOTE
    Next Generation Sequencing workflows include a number of critical steps which can have a signific...
    Comparison of the S. cerevisae chromatin shearing with Covaris™ S2 and Bioruptor® Pico APPLICATION NOTE
    The chromatin shearing is very important step for all kind of ChIP analysis followed by next-gene...
    Ultrasensitive proteomics for microdissected fresh frozen tissue samples APPLICATION NOTE
    This protocol, specifically designed for ultrasensitive proteomics, enables high throughput quant...
    Bioruptor® Pico Sonication System Manual MANUAL
    The Bioruptor® Pico is the latest innovation in shearing and represents a new breakthrough as...
  • Publications

    How to properly cite this product in your work

    Diagenode strongly recommends using this: Picoruptor ® ソニケーター (Diagenode Cat# B01060010). Click here to copy to clipboard.

    Using our products in your publication? Let us know!

    Analysis of Meiotic Double-Strand Break Initiation in Mammals
    Kevin Brick, Florencia Pratto, Chi-Yu Sun, Rafael D.Camerini-Otero, Galina Petukhova
    The repair of programmed DNA double-strand breaks (DSBs) physically tethers homologous chromosomes in meiosis to allow for accurate segregation through meiotic cell divisions. This process, known as recombination, also results in the exchange of alleles between pare...

    Differential α-synuclein expression contributes to selective vulnerability of hippocampal neuron subpopulations to fibril-induced toxicity
    Esteban LunaSamantha C. DeckerDawn M. RiddleAnna CaputoBin ZhangTracy ColeCarrie CaswellSharon X. XieVirginia M. Y. LeeKelvin C. Luk
    The accumulation of misfolded α-synuclein (aSyn) and neuron loss define several neurodegenerative disorders including Parkinson’s disease (PD) and dementia with Lewy bodies (DLB). However, the precise relationship between pathology and neurotoxicity and why these processes disproportionately affect certa...

    Lyar-mediated recruitment of Brd2 to the chromatin attenuates Nanog downregulation following induction of differentiation
    Noelia Luna-Peláez, Mario García-Domínguez
    During development, cellular differentiation programs need of tight regulation for proper display of the activity of multiple factors in time and space. Chromatin adaptors of the BET family (Brd2, Brd3, Brd4 and Brdt in vertebrates) are transcription co-regulators tightly associated with the progression of the cell ...

    The transcription factors Runx3 and ThPOK cross-regulate acquisition of cytotoxic function by human Th1 lymphocytes
    Yasmina Serroukh et al
    Cytotoxic CD4 (CD4CTX) T cells are emerging as an important component of antiviral and antitumor immunity, but the molecular basis of their development remains poorly understood. In the context of human cytomegalovirus infection, a significant proportion of CD4 T cells displays cytotoxic functions. We observed that ...

    β1-integrin impacts Rad51 stability and DNA double-strand break repair by homologous recombination
    Kazi Mokim Ahmed, Raj K. Pandita, Dharmendra Kumar Singh, Clayton R. Hunt and Tej K. Pandita
    The molecular mechanisms underlying resistance to radiotherapy in breast cancer cells remain elusive. Previously, we reported that elevated β1-integrin is associated with enhanced breast cancer cell survival post-irradiation, but how β1-integrin conferred radioresistance was unclear. Ionizing radiation (...

    TGFβ signaling hyperactivation-induced tumorigenicity during the derivation of neural progenitors from mouse ESCs
    Xianfa Yang et al
    Clinical therapies of pluripotent stem cells (PSCs)-based transplantation have been hindered by frequent development of teratomas or tumors in animal models and clinical patients. Therefore, clarifying the mechanism of carcinogenesis in stem cell therapy is of great importance for reducing the risk of tumorigenicity...

    MAX to MYCN intracellular ratio drives the aggressive phenotype and clinical outcome of high risk neuroblastoma
    Francesca Ferruccia et. al.
    Childhood neuroblastoma, a disease of the sympathetic nervous system, is the most common solid tumour of infancy, remarkably refractory to therapeutic treatments. One of the most powerful independent prognostic indicators for this disease is the amplification of the MYCN oncogene, which occurs at high levels in appr...

    SIRT6-dependent cysteine monoubiquitination in the PRE-SET domain of Suv39h1 regulates the NF-κB pathway
    Irene Santos-Barriopedro et. al.
    Sirtuins are NAD+-dependent deacetylases that facilitate cellular stress response. They include SirT6, which protects genome stability and regulates metabolic homeostasis through gene silencing, and whose loss induces an accelerated aging phenotype directly linked to hyperactivation of the NF-κB pathway. Here ...

    A novel long noncoding RNA LINC00844 regulates prostate cancer cell migration and invasion through androgen receptor signaling
    Shreyas Lingadahalli, Sudhir Jadhao, Ying Ying Sung, Mi Chen, Lingling Hu, Xin Chen and Edwin Cheung
    The majority of the human genome is transcribed, yielding a rich repository of non-coding transcripts that are involved in a myriad of biological processes including cancer. However, how non-coding transcripts such as long non-coding RNAs (lncRNAs) function in prostate cancer is still unclear. In this study, we have...

    APRDX1 mutant allele causes a MMACHC secondary epimutation in cblC patients
    Jean-Louis Guéant et. al.
    To date, epimutations reported in man have been somatic and erased in germlines. Here, we identify a cause of the autosomal recessive cblC class of inborn errors of vitamin B12 metabolism that we name “epi-cblC”. The subjects are compound heterozygotes for a genetic mutation and for a promoter epimu...

    TBR2 antagonizes retinoic acid dependent neuronal differentiation by repressing Zfp423 during corticogenesis
    Luca Massimino, Lisbeth Flores-Garcia, Bruno Di Stefano, Gaia Colasante, Cecilia Icoresi-Mazzeo, Mattia Zaghi, Bruce A. Hamilton, Alessandro Sessa
    During cerebral cortex development, neural progenitors are required to elaborate a variety of cell differentiation signals to which they are continuously exposed. RA acid is a potent inducer of neuronal differentiation as it was found to influence cortical development. We report herein that TBR2, a transcription fac...

    The CUE1 domain of the SNF2-like chromatin remodeler SMARCAD1 mediates its association with KRAB-associated protein 1 (KAP1) and KAP1 target genes
    Dong Ding et. al.
    Chromatin in embryonic stem cells (ESCs) differs markedly from that in somatic cells, with ESCs exhibiting a more open chromatin configuration. Accordingly, ATP-dependent chromatin remodeling complexes are important regulators of ESC homeostasis. Depletion of the remodeler SMARCAD1, an ATPase of the SNF2 family, has...

    Super enhancer associated RAI14 is a new potential biomarker in lung adenocarcinoma
    Chongze Yuan, Hong Hu,Muyu Kuang, Zongwei Chen,Xiaoting Tao,Shengjian Fang,Yihua Sun,Yawei Zhang, and Haiquan Chen
    Tyrosine kinase inhibitors (TKIs) are widely used to treat lung adenocarcinoma patients with EGFR mutations or ALK-fusions. However, patients with wild-type genes or TKIs-resistant mutations lack effective therapeutic targets. Extensive studies reveal that super enhancer (SE), a large cis-regulatory element, is asso...

    Transcription Factor YY1 Modulates Lung Cancer Progression by Activating lncRNA-PVT1
    Huang Tonghai, Wang Guangsuo, Yang Lin, Peng Bin, Wen Yuxin, Ding Guanggui, and Wang Zheng
    Lung cancer is the leading cause of cancer-related death worldwide. Despite the advancement in surgery and chemotherapy, the prognosis of patients with advanced lung cancer is still poor. Yin Yang-1 (YY1) is a multifunctional transcription factor that exhibits positive and negative control on a large number of cellu...

    Epigenetic control of epilepsy target genes contributes to a cellular memory of epileptogenesis in cultured rat hippocampal neurons
    K. Kiese, J. Jablonski, J. Hackenbracht, J. K. Wrosch, T. W. Groemer, J. Kornhuber, I. Blümcke and K. Kobow
    Hypersynchronous neuronal excitation manifests clinically as seizure (ictogenesis), and may recur spontaneously and repetitively after a variable latency period (epileptogenesis). Despite tremendous research efforts to describe molecular pathways and signatures of epileptogenesis, molecular pathomechanisms leading t...

    The cardiac calsequestrin gene transcription is modulated at the promoter by NFAT and MEF-2 transcription factors
    Rafael Estrada-Avilés, Gabriela Rodríguez, Angel Zarain-Herzberg
    Calsequestrin-2 (CASQ2) is the main Ca2+-binding protein inside the sarcoplasmic reticulum of cardiomyocytes. Previously, we demonstrated that MEF-2 and SRF binding sites within the human CASQ2 gene (hCASQ2) promoter region are functional in neonatal cardiomyocytes. In this work, we investigated if the calcineurin/N...

    The CCAAT box in the proximal SERCA2 gene promoter regulates basal and stress-induced transcription in cardiomyocytes
    Jorge Fragoso-Medina et. al.
    The cardiac sarco/endoplasmic reticulum Ca2+-ATPase-2a (SERCA2a) is vital for the correct handling of calcium concentration in cardiomyocytes. Recent studies showed that the induction of endoplasmic reticulum (ER) stress (ERS) with the SERCA2 inhibitor Thapsigargin (Tg) increases the mRNA and protein levels of SERCA...

    Coordinated Transcriptional Control of Adipocyte Triglyceride Lipase (Atgl) by transcription factors Sp1 and PPARγ during Adipocyte Differentiation
    Debasish Roy, Kenneth T. Farabaugh, Jing Wu, Alyssa Charrier, Cynthia Smas, Maria Hatzoglou*, Kavitha Thirumurugan and David A. Buchner
    The breakdown of stored fat deposits into its components is a highly regulated process that maintains plasma levels of free fatty acids to supply energy to cells. Insulin-mediated transcription of Atgl, the enzyme that mediates the rate-limiting step in lipolysis, is a key point of this regulation. In conditions suc...

    Novel Molecular Mechanism of Regulation of CD40 Ligand by the Transcription Factor GLI2
    Weiguo Han, David A. Jackson, Stephan J. Matissek, Jason A. Misurelli, Matthew S. Neil, Brandon Sklavanitis, Nansalmaa Amarsaikhan and Sherine F. Elsawa
    The interaction between tumor cells and their surrounding microenvironment is essential for the growth and persistence of cancer cells. This interaction is mediated, in part, by cytokines. Although the role of cytokines in normal and malignant cell biology is well established, many of the molecular mechanisms regula...

    Egr2 and 3 Inhibit T-bet–Mediated IFN-γ Production in T Cells
    Randeep Singh, Tizong Miao, Alistair L. J. Symonds, Becky Omodho, Suling Li and Ping Wang
    T-bet is important for differentiation of cytotoxic CD8 and Th1 CD4 T cells. We have discovered that Egr2 and 3 are potent inhibitors of T-bet function in CD4 and CD8 effector T cells. Egr2 and 3 were essential to suppress Th1 differentiation in Th2 and Th17 conditions in vitro and also to control IFN-γ–...

    Foxa2, a novel protein partner of tumour suppressor menin, is deregulated in mouse and human MEN1 glucagonomas
    Rémy Bonnavion, Romain Teinturier, Samuele Gherardi, Emmanuelle Leteurtre, Run Yu, Martine Cordier-Bussat, Rui Du, François Pattou, Marie-Christine Vantyghem, Philippe Bertolino, Jieli Lu, Chang Xian Zhang
    Foxa2, known as one of the pioneer factors, plays a crucial role in islet development and endocrine functions. Its expression and biological functions are regulated by various factors, including in particular insulin and glucagon. However, its expression and biological role in the adult pancreatic α-cells rema...

    m6A-dependent maternal mRNA clearance facilitates zebrafish maternal-to-zygotic transition
    Boxuan Simen Zhao, Xiao Wang, Alana V. Beadell, Zhike Lu, Hailing Shi, Adam Kuuspalu, Robert K. Ho & Chuan He
    The maternal-to-zygotic transition (MZT) is one of the most profound and tightly orchestrated processes during the early life of embryos, yet factors that shape the temporal pattern of vertebrate MZT are largely unknown. Here we show that over one-third of zebrafish maternal messenger RNAs (mRNAs) can be N6-methylad...

    A set of novel automated quantitative microproteomics protocols for small sample amounts and its application to kidney tissue substructures
    de Graaf, E. L., Pelligrini, D., & McDonnell, L. A.
    Here we assessed the ability of an automated sample preparation device equipped with disposable microcolumns to prepare mass-limited samples for high-sensitivity quantitative proteomics, using both label-free and isobaric labeling approaches. First, we compared peptide label-free quantification reproducibility for 1...

    Analysis of Cohesin Function in Gene Regulation and Chromatin Organization in Interphase
    Preksha Gupta , Thais Lavagnolli, Hegias Mira-Bontenbal, Matthias Merkenschlager
    Cohesin is essential for the maintenance of chromosomes through the cell cycle. In addition, cohesin contributes to the regulation of gene expression and the organization of chromatin in interphase cells. To study cohesin’s role in gene expression and chromatin organization, it is necessary to avoid secondary ...

    DNA fragmentation and quality control analysis
    Wassim Lakhal, Irina Panteleeva, Sharon Squazzo, Rini Saxena, Jerome Kroonen, Steve Siembieda, Markus Tilmes & Jonathan Hagopian
    Optimal data generation using NGS platforms relies on a few sample-preparation prerequisites, namely, precise DNA fragmentation, size-range analysis, and smear quantification. The Diagenode One, Bioruptor®, Megaruptor®, and Fragment Analyzer™ by Advanced Analytical ensure that these first cri...

    Genome-wide DNA methylation profiling with MeDIP-seq using archived dried blood spots
    Nicklas H. Staunstrup et al.
    Background In utero and early-life experienced environmental exposures are suggested to play an important role in many multifactorial diseases potentially mediated through lasting effects on the epigenome. As the epigenome in addition remains modifiable throughout life, identifying specific disease-relevant biomarke...

    UMI-4C for quantitative and targeted chromosomal contact profiling
    Omer Schwartzman, Zohar Mukamel, Noa Oded-Elkayam, Pedro Olivares-Chauvet, Yaniv Lubling, Gilad Landan, Shai Izraeli and Amos Tanay
    We developed a targeted chromosome conformation capture (4C) approach that uses unique molecular identifiers (umis) to derive high-complexity quantitative chromosome contact profiles with controlled signal-to-noise ratios. UMI-4C detects chromosomal interactions with improved sensitivity and specificity, and it can ...

    Characterization of novel Bovine Leukemia Virus (BLV) antisense transcripts by deep sequencing reveals constitutive expression in tumors and transcriptional interaction with viral microRNAs
    Durkin K., Rosewick N., Artesi M., Hahaut V., Griebel P., Arsic N., Burny A., Georges M., Van den Broeke A.
    Background Bovine Leukemia Virus (BLV) is a deltaretrovirus closely related to the Human T cell leukemia virus-1 (HTLV-1). Cattle are the natural host of BLV where it integrates into B-cells, producing a lifelong infection. Most infected animals remain asymptomatic but following a protracted latency period about 5 ...

    Parental epigenetic asymmetry of PRC2-mediated histone modifications in the Arabidopsis endosperm
    Moreno-Romero J et al.
    Parental genomes in the endosperm are marked by differential DNA methylation and are therefore epigenetically distinct. This epigenetic asymmetry is established in the gametes and maintained after fertilization by unknown mechanisms. In this manuscript, we have addressed the key question whether parentally inherited...

    Histamine 1 receptor-Gβγ-cAMP/PKA-CFTR pathway mediates the histamine-induced resetting of the suprachiasmatic circadian clock
    Yoon Sik Kim, Young-Beom Kim, Woong Bin Kim, Seung Won Lee, Seog Bae Oh, Hee-Chul Han, C. Justin LeeEmail author, Christopher S. Colwell and Yang In Kim
    Background Recent evidence indicates that histamine, acting on histamine 1 receptor (H1R), resets the circadian clock in the mouse suprachiasmatic nucleus (SCN) by increasing intracellular Ca2+ concentration ([Ca2+]i) through the activation of CaV1.3 L-type Ca2+ channels and Ca2+-induced Ca2+ release from ryan...

    Methylated DNA Immunoprecipitation Analysis of Mammalian Endogenous Retroviruses.
    Rebollo R, Mager DL
    Endogenous retroviruses are repetitive sequences found abundantly in mammalian genomes which are capable of modulating host gene expression. Nevertheless, most endogenous retrovirus copies are under tight epigenetic control via histone-repressive modifications and DNA methylation. Here we describe a common method us...

    TLK1B mediated phosphorylation of Rad9 regulates its nuclear/cytoplasmic localization and cell cycle checkpoint
    Sanket Awate and Arrigo De Benedetti
    The Tousled like kinase 1B (TLK1B) is critical for DNA repair and survival of cells. Upon DNA damage, Chk1 phosphorylates TLK1B at S457 leading to its transient inhibition. Once TLK1B regains its kinase activity it phosphorylates Rad9 at S328. In this work we investigated the significance of this mechanism by overex...

    The transcription factor SOX6 contributes to the developmental origins of obesity by promoting adipogenesis
    Shi Chi Leow, Jeremie Poschmann, Peh Gek Too, Juan Yin, Roy Joseph, Craig McFarlane, Shaillay Dogra, Asim Shabbir, Philip W. Ingham, Shyam Prabhakar, Melvin K. S. Leow, Yung Seng Lee, Kai Lyn Ng, Yap Seng Chong, Peter D. Gluckman, Walter Stünkel
    The association between impaired fetal growth and postnatal development of obesity has been demonstrated before. By comparing adipocytes differentiated from Mesenchymal Stem Cells (MSCs) taken from the umbilical cord and derived from normal and growth restricted neonates, we identified the transcription factor SOX6 ...

    Desensitization and incomplete recovery of hepatic target genes after chronic thyroid hormone treatment and withdrawal in male adult mice
    Kenji Ohba, Melvin Khee-Shing Leow, Brijesh Kumar Singh, Rohit Anthony Sinha, Ronny Lesmana,Xiao-Hui Liao, Paul Michael Yen
    Here, we examined changes in hepatic gene expression and serum TH/thyrotropin (TSH) levels in adult male mice treated either with a single T3 (20 g/100 g body weight) injection (acute T3) or daily injections for 14 days (chronic T3) followed by 10 days withdrawal. Chromatin immunoprecipitation analysis of repre...

    Transducin-like enhancer of split-1 is expressed and functional in human macrophages
    Federica De Paoli, Corinne Copin, Jonathan Vanhoutte, Bruno Derudas, Manjula Vinod, Christophe Zawadzki, Sophie Susen, Giulia Chinetti-Gbaguid
    Macrophages display heterogeneous phenotypes, including the classical M1 proinflammatory and the alternative M2 anti-inflammatory polarization states. The transducin-like enhancer of split-1 (TLE1) is a transcriptional corepressor whose functions in macrophages have not been studied yet. We report that TLE1 is highl...

    Standardizing chromatin research: a simple and universal method for ChIP-seq
    Laura Arrigoni, Andreas S. Richter, Emily Betancourt, Kerstin Bruder, Sarah Diehl, Thomas Manke and Ulrike Bönisch
    Here we demonstrate that harmonization of ChIP-seq workflows across cell types and conditions is possible when obtaining chromatin from properly isolated nuclei. We established an ultrasound-based nuclei extraction method (Nuclei Extraction by Sonication) that is highly effective across various organisms, cell ...

    The Deacetylase Sirtuin 1 Regulates Human Papillomavirus Replication by Modulating Histone Acetylation and Recruitment of DNA Damage Factors NBS1 and Rad51 to Viral Genomes
    Erika S. Langsfeld, Jason M. Bodily, Laimonis A. Laimins
    Human papillomaviruses (HPV) regulate their differentiation-dependent life cycles by activating a number of cellular pathways, such as the DNA damage response, through control of post-translational protein modification. Sirtuin 1 (SIRT1) is a protein deacetylase that modulates the acetylation of a number of cellular...

    The MEF2-HDAC axis controls proliferation of mammary epithelial cells and acini formation in vitro
    Andrea Clocchiatti, Eros Di Giorgio, Giulia Viviani, Charles Streuli, Andrea Sgorbissa, Raffaella Picco, Valentina Cutano, Claudio Brancolini
    The MEF2-HDAC axis is a master regulator of different developmental programs and adaptive responses in adults. In this manuscript we have investigated the contribution of the axis to the regulation of epithelial morphogenesis, using 3D organotypic cultures of MCF10A cells as a model. We have demonstrated that MEF2 t...

    LXR-Mediated ABCA1 Expression and Function Are Modulated by High Glucose and PRMT2
    Maryem A. Hussein, Elina Shrestha, Mireille Ouimet, Tessa J. Barrett, Sarah Leone, Kathryn J. Moore, Yann Hérault, Edward A. Fisher, Michael J. Garabedian
    High cholesterol and diabetes are major risk factors for atherosclerosis. Regression of atherosclerosis is mediated in part by the Liver X Receptor (LXR) through the induction of genes involved in cholesterol transport and efflux. In the context of diabetes, regression of atherosclerosis is impaired. We proposed tha...

    Runx1 Transcription Factor Is Required for Myoblasts Proliferation during Muscle Regeneration
    Kfir Baruch Umansky, Yael Gruenbaum-Cohen, Michael Tsoory, Ester Feldmesser, Dalia Goldenberg, Ori Brenner, Yoram Groner
    Following myonecrosis, muscle satellite cells proliferate, differentiate and fuse, creating new myofibers. The Runx1 transcription factor is not expressed in naïve developing muscle or in adult muscle tissue. However, it is highly expressed in muscles exposed to myopathic damage yet, the role of Runx1 in muscle...

    Concurrent whole-genome haplotyping and copy-number profiling of single cells.
    Zamani Esteki M, Dimitriadou E, Mateiu L, Melotte C, Van der Aa N, Kumar P, Das R, Theunis K, Cheng J, Legius E, Moreau Y, Debrock S, D'Hooghe T, Verdyck P, De Rycke M, Sermon K, Vermeesch JR, Voet T
    Methods for haplotyping and DNA copy-number typing of single cells are paramount for studying genomic heterogeneity and enabling genetic diagnosis. Before analyzing the DNA of a single cell by microarray or next-generation sequencing, a whole-genome amplification (WGA) process is required, but it substantially disto...

    High-throughput and quantitative assessment of enhancer activity in mammals by CapStarr-seq.
    Vanhille L, Griffon A, Maqbool MA, Zacarias-Cabeza J, Dao LT, Fernandez N, Ballester B, Andrau JC, Spicuglia S
    Cell-type specific regulation of gene expression requires the activation of promoters by distal genomic elements defined as enhancers. The identification and the characterization of enhancers are challenging in mammals due to their genome complexity. Here we develop CapStarr-Seq, a novel high-throughput strategy to ...

    Mitogenomic phylogeny of the common long-tailed macaque (Macaca fascicularis fascicularis).
    Liedigk R, Kolleck J, Böker KO, Meijaard E, Md-Zain BM, Abdul-Latiff MA, Ampeng A, Lakim M, Abdul-Patah P, Tosi AJ, Brameier M, Zinner D, Roos C
    BACKGROUND: Long-tailed macaques (Macaca fascicularis) are an important model species in biomedical research and reliable knowledge about their evolutionary history is essential for biomedical inferences. Ten subspecies have been recognized, of which most are restricted to small islands of Southeast Asia. In contras...

    Phylogenomics of Phrynosomatid Lizards: Conflicting Signals from Sequence Capture versus Restriction Site Associated DNA Sequencing
    Leaché AD, Chavez AS, Jones LN, Grummer JA, Gottscho AD, Linkem CW
    Sequence capture and restriction site associated DNA sequencing (RADseq) are popular methods for obtaining large numbers of loci for phylogenetic analysis. These methods are typically used to collect data at different evolutionary timescales; sequence capture is primarily used for obtaining conserved loci, whereas R...

    Modulation of p53 and met expression by Krüppel-like factor 8 regulates zebrafish cerebellar development.
    Tsai MY, Lu YF, Liu YH, Lien HW, Huang CJ, Wu JL, Hwang SL
    Krüppel-like factor 8 (Klf8) is a zinc-finger transcription factor implicated in cell proliferation, and cancer cell survival and invasion; however, little is known about its role in normal embryonic development. Here, we show that Klf8 is required for normal cerebellar development in zebrafish embryos. Morphol...

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