המחברים מבקשים להודות לד&quot;ר לאן יי, מכון הסרטן של ניו ג&#39;רזי, לקבלת סיוע טכני בהכנת סלי רקמות. עבודה זו מומנה על ידי המכונים הלאומיים לבריאות מענקים DK083425 ו DK070219.

<ol>
	<li>Cunha, G. R. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=The+possible+influence+of+temporal+factors+in+androgenic+responsiveness+of+urogenital+tissue+recombinants+from+wild-type+and+androgen-insensitive+(Tfm)+mice.">The possible influence of temporal factors in androgenic responsiveness of urogenital tissue recombinants from wild-type and androgen-insensitive (Tfm) mice.</a> Journal of Experimental Zoology. 205, 181-181 (1978).</li><li>Cunha, G. R. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Hormonal,+cellular,+and+molecular+regulation+of+normal+and+neoplastic+prostatic+development.">Hormonal, cellular, and molecular regulation of normal and neoplastic prostatic development.</a> Journal of Steroid Biochemistry and Molecular Biology. 92, 221-221 (2004).</li><li>Price, D. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Comparative+aspects+of+development+and+structure+in+the+prostate.">Comparative aspects of development and structure in the prostate.</a> National Cancer Institute Monographs. 12, 1-1 (1963).</li><li>Cunha, G. R. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Stromal-epithelial+interactions--I.+Induction+of+prostatic+phenotype+in+urothelium+of+testicular+feminized+(Tfm/y)+mice.">Stromal-epithelial interactions--I. Induction of prostatic phenotype in urothelium of testicular feminized (Tfm/y) mice.</a> Journal of Steroid Biochemistry. 14, 1317-1317 (1981).</li><li>Rozen, S. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Primer3+on+the+WWW+for+general+users+and+for+biologist+programmers.">Primer3 on the WWW for general users and for biologist programmers.</a> Methods in Molecular Biology. 132, 365-365 (2000).</li><li>Zhang, Z. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=A+greedy+algorithm+for+aligning+DNA+sequences.">A greedy algorithm for aligning DNA sequences.</a> Journal of Computational Biology. 7, 203-203 (2000).</li><li>Vezina, C. M. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Dioxin+causes+ventral+prostate+agenesis+by+disrupting+dorsoventral+patterning+in+developing+mouse+prostate.">Dioxin causes ventral prostate agenesis by disrupting dorsoventral patterning in developing mouse prostate.</a> Toxicological Sciences. 106, 488-488 (2008).</li><li>Wilkinson, D. G. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Detection+of+messenger+RNA+by+in+situ+hybridization+to+tissue+sections+and+whole+mounts.">Detection of messenger RNA by in situ hybridization to tissue sections and whole mounts.</a> Methods in Enzymology. 225, 361-361 (1993).</li></ol>

אין ניגודי אינטרסים הכריז.

באמצעות השיטה המתוארת כאן, אפשר לזהות mRNAs בכל סוגי התאים העיקריים תאים ורקמות של LUTs עוברי עכבר זכר ונקבה כולל רפידות mesenchymal, urothelium, שרירים חלקים, בלוטות הערמונית, צינור השופכה, והנרתיק. הסעיפים 50μm להשתמש בפרוטוקול זה יש את היתרון של להיות עבה מספיק כדי לפתור ארכיטקטור?...

<table border="1" style=";text-align:right;direction:rtl"><tbody><tr><th> שם מגיב </th><th> חברה </th><th> מספר קטלוגי </th></tr><tr><td> Anti-Digoxigenin נוגדן, שברי Fab </td><td> רוש ומדע יישומי </td><td> 11214667001 </td></tr><tr><td> חסימת מגיב </td><td> רוש ומדע יישומי </td><td> 11096176001 </td></tr><tr><td> BM המצע סגול AP, מזרז </td><td> רוש ומדע יישומי </td><td> 11442074001 </td></tr><tr><td> שור סרום אלבומין </td><td> פישר סיינטיפיק </td><td> BP1600-100 </td></tr><tr><td> תרבות צלחת Cell, 24 גם </td><td> קורנינג </td><td> 3524 </td></tr><tr><td> Digoxigenin 11-UTP </td><td> רוש ומדע יישומי </td><td> 1277073910 </td></tr><tr><td> dNTPs </td><td> רוש ומדע יישומי </td><td> 11969064001 </td></tr><tr><td> פיפיות גילוח להב </td><td> ווילקינסון חרב </td><td> דגם קלאסי </td></tr><tr><td> Eliminase מסיר RNase </td><td> Decon מעבדות </td><td> 1102 </td></tr><tr><td> לפוראמיד </td><td> סיגמא </td><td> F5786-1L </td></tr><tr><td> ג&#39;ל ערכת חילוץ </td><td> Qiagen </td><td> 28704 </td></tr><tr><td> , Glutaraldehyde פתרון של 25% H 2 O </td><td> סיגמא </td><td> G6257-100 מ&quot;ל </td></tr><tr><td> הפרין, מלח נתרן </td><td> סיגמא </td><td> H3393 </td></tr><tr><td> מי חמצן, פתרון של 30% H 2 O </td><td> פישר סיינטיפיק </td><td> BP2633-500 </td></tr><tr><td> Levamisole </td><td> סיגמא </td><td> L9756 </td></tr><tr><td> Loctite 404 לקבוע מיידית דבק מהיר </td><td> הנקל קורפ </td><td> 46551 </td></tr><tr><td> מגנזיום כלוריד </td><td> פישר סיינטיפיק </td><td> M33-500 </td></tr><tr><td> Maleic חומצה </td><td> סיגמא </td><td> M0375-500 גרם </td></tr><tr><td> Microcentrifuge צינורות, 1.5mL </td><td> Biologix חברת המחקר </td><td> BP337-100 </td></tr><tr><td> צלחת Millicell תרבות להכניס </td><td> Millipore </td><td> PICM01250 </td></tr><tr><td> שרף שחיקה מולקולרית </td><td> G-Biosciences </td><td> 786-138PR </td></tr><tr><td> , Paraformaldehyde פתרון 4% פוספט שנאגרו מלוחים </td><td> Affymetrix </td><td> 19943 </td></tr><tr><td> פוספט שנאגרו מלוחים, ללא Ca &amp; Mg </td><td> MP Biomedicals </td><td> ICN1760420 </td></tr><tr><td> רשת פוליאסטר, 33 מיקרון, 12 &quot;x 24&quot; </td><td> חלקים קטנים Inc </td><td> CMY-0033-D </td></tr><tr><td> Proteinase K פתרון, 20mg/ml </td><td> Amresco </td><td> E195-5 מ&quot;ל </td></tr><tr><td> QIAshredder עמודות </td><td> Qiagen </td><td> 79654 </td></tr><tr><td> ש פתרון </td><td> Qiagen </td><td> מסופק עם ה-DNA פולימראז תקי </td></tr><tr><td> RNase </td><td> סיגמא </td><td> R6513 </td></tr><tr><td> RNase המעכב </td><td> רוש ומדע יישומי </td><td> 03335399001 </td></tr><tr><td> RNeasy מיני ערכת </td><td> Qiagen </td><td> 74104 </td></tr><tr><td> RNEASY מיני ערכת </td><td> Qiagen </td><td> 74104 </td></tr><tr><td> RQ1 RNase ללא DNase </td><td> Promega </td><td> M6101 </td></tr><tr><td> SeaPlaque נמוכה להמיס agarose </td><td> Lonza </td><td> 50101 </td></tr><tr><td> כבשים בסרום </td><td> סיגמא </td><td> S2263-500ml </td></tr><tr><td> Stericup יחידת הסינון, 0.22μm, polyethersulfone, 500ml </td><td> Millipore </td><td> SCGPU05RE </td></tr><tr><td> אזיד הנתרן, פרטנית </td><td> פישר סיינטיפיק </td><td> S227I-100 </td></tr><tr><td> נתרן כלורי </td><td> פישר סיינטיפיק </td><td> BP358-212 </td></tr><tr><td> Dodecyl נתרן גופרתי </td><td> פישר סיינטיפיק </td><td> S529-500 </td></tr><tr><td> SSC, 20X פתרון </td><td> מחקר מוצרים הבינלאומי </td><td> S24022-4000.0 </td></tr><tr><td> עילי III הראשונה גדיל סינתזה מערכת </td><td> Invitrogen </td><td> 18080-051 </td></tr><tr><td> T7 RNA פולימראז </td><td> רוש ומדע יישומי </td><td> 10881767001 </td></tr><tr><td> תקי פולימראז ה-DNA </td><td> Qiagen </td><td> 201203 </td></tr><tr><td> טריס-HCl </td><td> פישר סיינטיפיק </td><td> BP153-1 </td></tr><tr><td> Tween 20 </td><td> פישר סיינטיפיק </td><td> BP337-100 </td></tr><tr><td> רטט microtome עם אמבטיה הדגימה דלוקס </td><td> Leica Microsystems </td><td> VT1000A </td></tr><tr><td> שמרים tRNA </td><td> רוש ומדע יישומי </td><td> 109495 </td></tr></tbody></table>

a high throughput in situ hybridization method to characterize mrna expression patterns in the fetal mouse lower urogenital tract

פיתוח בדרכי השתן ואברי המין התחתון (LUT) הוא תהליך מורכב. מורכבות זו לידי ביטוי במהלך היווצרות של הערמונית של השופכה בעובר זכר, אשר מסתמכת על אותות androgenic ו אפיתל-mesenchymal 1,2 אינטראקציות. הבנת המנגנונים המולקולריים האחראים להתפתחות סרטן הערמונית עשוי לחשוף את מנגנוני צמיחה, כי הם לא הולם המתעורר בשלב מאוחר יותר בחיים לעורר מחלות הערמונית כגון היפרפלזיה שפירה של הערמונית וסרטן הערמונית. LUT פיתוח מורכב מבחינה אנטומית. על ידי הערמונית זמן ניצני מתחיל על התפיסה ימים 16.5 פוסט (DPC), סוגי תאים רבים נוכחים. בכלי הדם, העצבים שריר חלק מתגוררים בתוך stroma mesenchymal 3. Stroma זה המקיף אפיתל רב שכבתי ואת מוליד הערמונית העובר דרך קולטן האנדרוגן תלויים אותות אוטוקריני 4. זהותם של קולטן האנדרוגן סטרומה תגובה הגנים הדרושים לפיתוח הערמונית את המנגנון שבאמצעותו הערמונית צורות ductal אפיתל בתגובה הגנים האלה לא מובנת לחלוטין. היכולת לזהות במדויק סוגי תאים בתרגום הביטוי של גורמים ספציפיים בתוך אותם הוא הכרחי כדי להבין את התפתחות נוספת הערמונית. הכלאה In situ (שאני עורך) מאפשר איתור של mRNAs בתוך הרקמה. לכן, בשיטה זו ניתן להשתמש כדי לזהות דפוס והעיתוי של ביטוי של מולקולות איתות הקולטנים שלהם, ובכך הבהרת הרגולטורים הערמונית הפוטנציאל ההתפתחותי. כאן אנו מתארים תפוקה גבוהה שאני עורך טכניקה לזהות דפוסי ביטוי mRNA ב LUT העכבר העובר באמצעות רטט microtome לחתוך חלקים. שיטה זו מציעה מספר יתרונות על פני פרוטוקולים אחרים שאני עורך. ביצוע שאני עורך על סעיפים דק דבק שקופית קשה מבחינה טכנית, cryosections לעתים קרובות יש איכות מבנית העניים בעוד הן cryosections וחתכים פרפין לעיתים לגרום ברזולוציה אות חלש. ביצוע שאני עורך על כל רקמות הר יכול לגרום השמנה בדיקה. לעומת זאת, הטכניקה תפוקה גבוהה שלנו מנצל עבה לחתוך קטעים החושפים ארכיטקטורת רקמה מפורט. צינורות microfuge השתנה לאפשר טיפול קל סעיפים במהלך ההליך איש. מקסימום של 4 תעתיקי mRNA יכול להיות מוקרן מן LUT 17.5dpc יחיד עם עד 24 תעתיקי mRNA זוהה בטווח יחיד, ובכך להפחית את עלות ויעילות למקסם. שיטה זו מאפשרת לקבוצות טיפול מרובים כדי להיות מעובד ובשפה כיחידה אחת, ובכך להסיר כל הטיה של הנתונים לפרש. רוב לענייננו לחוקרים הערמונית, שיטה זו מספקת מיקום במרחב ובזמן של תעתיקי mRNA נמוך וגבוה בשפע השופכה עוברי עכבר אשר מעורר ברשת הערמונית ductal.

Watch this Scientific Journal Video about A High Throughput in situ Hybridization Method to Characterize mRNA Expression Patterns in the Fetal Mouse Lower Urogenital Tract at JoVE.com

A High Throughput in situ Hybridization Method to Characterize mRNA Expression Patterns in the Fetal Mouse Lower Urogenital Tract

כאן אנו מתארים תפוקה גבוהה ויעילה<em&gt; באתרו</em&gt; (שאני עורך) הכלאה שיטת הדמיה דפוסי ביטוי mRNA בפיתוח העובר הערמונית עכבר סעיפים רקמות. השיטה ניתן להתאים בקלות לדמיין ביטוי בדפוסי mRNA ברקמות העכבר אחרים או ברקמות ממינים אחרים.

תפוקה גבוהה באתרו הכלאה שיטה לאפיון דפוסי ביטוי mRNA של העכבר עוברית בדרכי השתן ואברי המין התחתון

Development of the lower urogenital tract (LUT) is an intricate process. This complexity is evidenced during formation of the prostate from the fetal male ...

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Biology

A High Throughput in situ Hybridization Method to Characterize mRNA Expression Patterns in the Fetal Mouse Lower Urogenital Tract

13.0K Views.  University of Wisconsin-Madison. כאן אנו מתארים תפוקה גבוהה ויעילה באתרו (שאני עורך) הכלאה שיטת הדמיה דפוסי ביטוי mRNA בפיתוח העובר הערמונית עכבר סעיפים רקמות. השיטה ניתן להתאים בקלות לדמיין ביטוי בדפוסי mRNA ברקמות העכבר אחרים או ברקמות ממינים אחרים.

Video: A High Throughput in situ Hybridization Method to Characterize mRNA Expression Patterns in the Fetal Mouse Lower Urogenital Tract

A high-throughput method to globally study the organelle morphology in S. cerevisiae

High-throughput methods to examine protein localization or organelle morphology is an effective tool for studying protein interactions and can help achieve an comprehensive understanding of molecular pathways. In Saccharomyces cerevisiae, with the development of the non-essential gene deletion array, we can globally study the morphology of different organelles like the endoplasmic reticulum (ER) and the mitochondria using GFP (or variant)-markers in different gene backgrounds. However, incorporating GFP markers in each single mutant individually is a labor-intensive process. Here, we describe a procedure that is routinely used in our laboratory. By using a robotic system to handle high-density yeast arrays and drug selection techniques, we can significantly shorten the time required and improve reproducibility. In brief, we cross a GFP-tagged mitochondrial marker (Apc1-GFP) to a high-density array of 4,672 nonessential gene deletion mutants by robotic replica pinning.  Through diploid selection, sporulation, germination and dual marker selection, we recover both alleles. As a result, each haploid single mutant contains Apc1-GFP incorporated at its genomic locus. Now, we can study the morphology of mitochondria in all non-essential mutant background. Using this high-throughput approach, we can conveniently study and delineate the pathways and genes involved in the inheritance and the formation of organelles in a genome-wide setting.

GFP-fusion proteins are widely used to visualize organelles by confocal microscopy. However, screening for mutations that affect the morphology of organelles generally requires individual mutagenesis and is time consuming. Here, we demonstrate a method to simultaneously incorporate organelle-GFP markers in almost 5,000 non-essential genes in yeast.

שיטת תפוקה גבוהה ברחבי העולם כדי ללמוד את המורפולוגיה של אברון cerevisiae ס

High-throughput methods to examine protein localization or organelle morphology is an effective tool for studying protein interactions and can help ...

Zebrafish Whole Mount High-Resolution Double Fluorescent In Situ Hybridization

Whole mount in situ hybridization is one of the most widely used techniques in developmental biology. Here, we present a high-resolution double fluorescent in situ hybridization protocol for analyzing the precise expression pattern of a single gene and for determining the overlap of the expression domains of two genes. The protocol is a modified version of the standard in situ hybridization using alkaline phosphatase and substrates such as NBT/BCIP and Fast Red 1,2. This protocol utilizes standard digoxygenin and fluorescein labeled probes along with tyramide signal amplification (TSA) 3. The commercially available TSA kits allow flexible experimental design as fluorescence emission from green to far-red can be used in combination with various nuclear stains, such as propidium iodide, or fluorescence immunohistochemistry for proteins. TSA produces a reactive fluorescent substrate that quickly covalently binds to moieties, typically tyrosine residues, in the immediate vicinity of the labeled antisense riboprobe. The resulting staining patterns are high resolution in that subcellular localization of the mRNA can be observed using laser scanning confocal microscopy 3,4. One can observe nascent transcripts at the chromosomal loci, distinguish nuclear and cytoplasmic staining and visualize other patterns such as cortical localization of mRNA. Studies in Drosophila indicate that roughly 70% of mRNAs exhibit specific patterns of subcellular localization that frequently correlate with the function of the encoded protein 5. When combined with computer-aided reconstruction of 3D confocal datasets, our protocol allows the detailed analysis of mRNA distribution with sub-cellular resolution in whole vertebrate embryos.

Zebrafish Whole Mount High-Resolution Double Fluorescent In Situ Hybridization

Whole mount in situ hybridization is one of the most widely used techniques in developmental biology. Here, we present a high-resolution double fluorescent in situ hybridization protocol for analyzing the precise expression pattern of a single gene and for determining the overlap of the expression domains of two genes. We include a propidium iodide nuclear counter-stain to highlight tissue organization.

דג הזברה שלמים הר ברזולוציה גבוהה פעמיים פלורסנט באתרו הכלאה

Whole mount in situ hybridization is one of the most widely used techniques in developmental biology.  Here, we present a high-resolution double ...

A Rapid High-throughput Method for Mapping Ribonucleoproteins (RNPs) on Human pre-mRNA

Sequencing RNAs that co-immunoprecipitate (co-IP) with RNA binding proteins has increased our understanding of splicing by demonstrating that binding location often influences function of a splicing factor.  However, as with any sampling strategy the chance of identifying an RNA bound to a splicing factor is proportional to its cellular abundance.  We have developed a novel in vitro approach for surveying binding specificity on otherwise transient pre-mRNA. This approach utilizes a specifically designed oligonucleotide pool that tiles across introns, exons, splice junctions, or other pre-mRNA.  The pool is subjected to some kind of molecular selection. Here, we demonstrate the method by separating the oligonucleotide into a bound and unbound fraction and utilize a two color array strategy to record the enrichment of each oligonucleotide in the bound fraction. The array data generates high-resolution maps with the ability to identify sequence-specific and structural determinates of ribonucleoprotein (RNP) binding on pre-mRNA.  A unique advantage to this method is its ability to avoid the sampling bias towards mRNA associated with current IP and SELEX techniques, as the pool is specifically designed and synthesized from pre-mRNA sequence. The flexibility of the oligonucleotide pool is another advantage since the experimenter chooses which regions to study and tile across, tailoring the pool to their individual needs.  Using this technique, one can assay the effects of polymorphisms or mutations on binding on a large scale or clone the library into a functional splicing reporter and identify oligonucleotides that are enriched in the included fraction.  This novel in vitro high-resolution mapping scheme provides a unique way to study RNP interactions with transient pre-mRNA species, whose low abundance makes them difficult to study with current in vivo techniques.  



A Rapid High-throughput Method for Mapping Ribonucleoproteins RNPs on Human pre-mRNA

Due to the transient nature of pre-mRNA, it can be difficult to isolate and study in vivo. Here, we present a novel in vitro approach to investigate RNA-protein interactions using a synthetic oligo pool that tiles across selected regions of pre-mRNA.

שיטה מהירה תפוקה גבוהה עבור Ribonucleoproteins מיפוי (RNPs) על mRNA מראש אדם

Sequencing RNAs that co-immunoprecipitate (co-IP) with RNA binding proteins has increased our understanding of splicing by demonstrating that binding ...

Using the Gene Pulser MXcell Electroporation System to Transfect Primary Cells with High Efficiency

It is becoming increasingly apparent that electroporation is the most effective way to introduce plasmid DNA or siRNA into primary cells. The Gene Pulser MXcell electroporation system and Gene Pulser electroporation buffer (Bio-Rad) were specifically developed to easily transfect nucleic acids into mammalian cells and difficult-to-transfect cells, such as primary and stem cells. We will demonstrate how to perform a simple experiment to quickly identify the best electroporation conditions. We will demonstrate how to run several samples through a range of electroporation conditions so that an experiment can be conducted at the same time as optimization is performed. We will also show how optimal conditions identified using 96-well electroporation plates can be used with standard electroporation cuvettes, facilitating the switch from electroporation plates to electroporation cuvettes while maintaining the same electroporation efficiency. In the video, we will also discuss some of the key factors that can lead to the success or failure of electroporation experiments.

This procedure shows how to use the Gene Pulser MXcell electroporation system to rapidly and easily identify the best electroporation conditions for mouse embryonic fibroblasts (MEFs) or other primary cells. Considerations for troubleshooting are also discussed in the associated video.

שימוש ג&#39;ין Pulser מערכת MXcell electroporation כדי Transfect תאים ראשוניים עם יעילות גבוהה

It is becoming increasingly apparent that electroporation is the most effective way to introduce plasmid DNA or siRNA into primary cells. The Gene Pulser ...

Hi-C: A Method to Study the Three-dimensional Architecture of Genomes.

The three-dimensional folding of chromosomes compartmentalizes the genome and and can bring distant functional elements, such as promoters and enhancers, into close spatial proximity 2-6. Deciphering the relationship between chromosome organization and genome activity will aid in understanding genomic processes, like transcription and replication. However, little is known about how chromosomes fold. Microscopy is unable to distinguish large numbers of loci simultaneously or at high resolution. To date, the detection of chromosomal interactions using chromosome conformation capture (3C) and its subsequent adaptations required the choice of a set of target loci, making genome-wide studies impossible 7-10.
We developed Hi-C, an extension of 3C that is capable of identifying long range interactions in an unbiased, genome-wide fashion. In Hi-C, cells are fixed with formaldehyde, causing interacting loci to be bound to one another by means of covalent DNA-protein cross-links. When the DNA is subsequently fragmented with a restriction enzyme, these loci remain linked. A biotinylated residue is incorporated as the 5' overhangs are filled in. Next, blunt-end ligation is performed under dilute conditions that favor ligation events between cross-linked DNA fragments. This results in a genome-wide library of ligation products, corresponding to pairs of fragments that were originally in close proximity to each other in the nucleus. Each ligation product is marked with biotin at the site of the junction. The library is sheared, and the junctions are pulled-down with streptavidin beads. The purified junctions can subsequently be analyzed using a high-throughput sequencer, resulting in a catalog of interacting fragments.
Direct analysis of the resulting contact matrix reveals numerous features of genomic organization, such as the presence of chromosome territories and the preferential association of small gene-rich chromosomes. Correlation analysis can be applied to the contact matrix, demonstrating that the human genome is segregated into two compartments: a less densely packed compartment containing open, accessible, and active chromatin and a more dense compartment containing closed, inaccessible, and inactive chromatin regions. Finally, ensemble analysis of the contact matrix, coupled with theoretical derivations and computational simulations, revealed that at the megabase scale Hi-C reveals features consistent with a fractal globule conformation.

The Hi-C method allows unbiased, genome-wide identification of chromatin interactions (1). Hi-C couples proximity ligation and massively parallel sequencing. The resulting data can be used to study genomic architecture at multiple scales: initial results identified features such as chromosome territories, segregation of open and closed chromatin, and chromatin structure at the megabase scale.

Hi-C: שיטה לחקר ארכיטקטורה תלת ממדי של הגנום.

The three-dimensional folding of chromosomes compartmentalizes the genome and and can bring distant functional elements, such as promoters and enhancers, ...

Whole Mount in Situ Hybridization of E8.5 to E11.5 Mouse Embryos

Whole mount in situ hybridization is a very informative approach for defining gene expression patterns in embryos. The in situ hybridization procedures are lengthy and technically demanding with multiple important steps that collectively contribute to the quality of the final result. This protocol describes in detail several key quality control steps for optimizing probe labeling and performance. Overall, our protocol provides a detailed description of the critical steps necessary to reproducibly obtain high quality results. First, we describe the generation of digoxygenin (DIG) labeled RNA probes via in vitro transcription of DNA templates generated by PCR. We describe three critical quality control assays to determine the amount, integrity and specific activity of the DIG-labeled probes. These steps are important for generating a probe of sufficient sensitivity to detect endogenous mRNAs in a whole mouse embryo. In addition, we describe methods for the fixation and storage of E8.5-E11.5 day old mouse embryos for in situ hybridization. Then, we describe detailed methods for limited proteinase K digestion of the rehydrated embryos followed by the details of the hybridization conditions, post-hybridization washes and RNase treatment to remove non-specific probe hybridization. An AP-conjugated antibody is used to visualize the labeled probe and reveal the expression pattern of the endogenous transcript. Representative results are shown from successful experiments and typical suboptimal experiments.

Whole Mount in Situ Hybridization of E8.5 to E11.5 Mouse Embryos

This whole mount in situ hybridization protocol discusses critical steps that ensure reproducible high quality results for gene expression studies in E8.5-E11.5 day old mouse embryos.

הר שלם<em&gt; באתר</em&gt; הכלאה של E8.5 לעוברי E11.5 עכבר

Whole mount in situ hybridization is a very informative approach for defining gene expression patterns in embryos. The in situ hybridization procedures ...

Radioactive in situ Hybridization for Detecting Diverse Gene Expression Patterns in Tissue

Knowing the timing, level, cellular localization, and cell type that a gene is expressed in contributes to our understanding of the function of the gene. Each of these features can be accomplished with in situ hybridization to mRNAs within cells. Here we present a radioactive in situ hybridization method modified from Clayton et al. (1988)1 that has been working successfully in our lab for many years, especially for adult vertebrate brains2-5. The long complementary RNA (cRNA) probes to the target sequence allows for detection of low abundance transcripts6,7. Incorporation of radioactive nucleotides into the cRNA probes allows for further detection sensitivity of low abundance transcripts and quantitative analyses, either by light sensitive x-ray film or emulsion coated over the tissue. These detection methods provide a long-term record of target gene expression. Compared with non-radioactive probe methods, such as DIG-labeling, the radioactive probe hybridization method does not require multiple amplification steps using HRP-antibodies and/or TSA kit to detect low abundance transcripts. Therefore, this method provides a linear relation between signal intensity and targeted mRNA amounts for quantitative analysis. It allows processing 100-200 slides simultaneously. It works well for different developmental stages of embryos. Most developmental studies of gene expression use whole embryos and non-radioactive approaches8,9, in part because embryonic tissue is more fragile than adult tissue, with less cohesion between cells, making it difficult to see boundaries between cell populations with tissue sections. In contrast, our radioactive approach, due to the larger range of sensitivity, is able to obtain higher contrast in resolution of gene expression between tissue regions, making it easier to see boundaries between populations. Using this method, researchers could reveal the possible significance of a newly identified gene, and further predict the function of the gene of interest.

Radioactive in situ Hybridization for Detecting Diverse Gene Expression Patterns in Tissue

This protocol is successfully used to quantitatively detect levels and spatial patterns of mRNA expression in multiple tissue types across vertebrate species. The method can detect low abundance transcripts and allows processing of hundreds of slides simultaneously. We present this protocol using expression profiling of avian embryonic brain formation as an example.

רדיואקטיבי באתרו הכלאה לזיהוי תבניות ביטוי מגוונות גנים רקמות

Knowing the timing, level, cellular localization, and cell type that a gene is expressed in contributes to our understanding of the function of the gene. ...

High-throughput Physical Mapping of Chromosomes using Automated in situ Hybridization

Projects to obtain whole-genome sequences for 10,000 vertebrate species1 and for 5,000 insect and related arthropod species2 are expected to take place over the next 5 years. For example, the sequencing of the genomes for 15 malaria mosquitospecies is currently being done using an Illumina platform3,4. This Anopheles species cluster includes both vectors and non-vectors of malaria. When the genome assemblies become available, researchers will have the unique opportunity to perform comparative analysis for inferring evolutionary changes relevant to vector ability. However, it has proven difficult to use next-generation sequencing reads to generate high-quality de novo genome assemblies5. Moreover, the existing genome assemblies for Anopheles gambiae, although obtained using the Sanger method, are gapped or fragmented4,6.
Success of comparative genomic analyses will be limited if researchers deal with numerous sequencing contigs, rather than with chromosome-based genome assemblies. Fragmented, unmapped sequences create problems for genomic analyses because: (i) unidentified gaps cause incorrect or incomplete annotation of genomic sequences; (ii) unmapped sequences lead to confusion between paralogous genes and genes from different haplotypes; and (iii) the lack of chromosome assignment and orientation of the sequencing contigs does not allow for reconstructing rearrangement phylogeny and studying chromosome evolution. Developing high-resolution physical maps for species with newly sequenced genomes is a timely and cost-effective investment that will facilitate genome annotation, evolutionary analysis, and re-sequencing of individual genomes from natural populations7,8.
Here, we present innovative approaches to chromosome preparation, fluorescent in situ hybridization (FISH), and imaging that facilitate rapid development of physical maps. Using An. gambiae as an example, we demonstrate that the development of physical chromosome maps can potentially improve genome assemblies and, thus, the quality of genomic analyses. First, we use a high-pressure method to prepare polytene chromosome spreads. This method, originally developed for Drosophila9, allows the user to visualize more details on chromosomes than the regular squashing technique10. Second, a fully automated, front-end system for FISH is used for high-throughput physical genome mapping. The automated slide staining system runs multiple assays simultaneously and dramatically reduces hands-on time11. Third, an automatic fluorescent imaging system, which includes a motorized slide stage, automatically scans and photographs labeled chromosomes after FISH12. This system is especially useful for identifying and visualizing multiple chromosomal plates on the same slide. In addition, the scanning process captures a more uniform FISH result. Overall, the automated high-throughput physical mapping protocol is more efficient than a standard manual protocol.

High-throughput Physical Mapping of Chromosomes using Automated in situ Hybridization

Genome assemblies based on massively parallel DNA sequencing technologies are usually highly fragmented. The development of physical chromosome maps can potentially improve genome assemblies. Here, we demonstrate innovative approaches to chromosome preparation, fluorescent in situ hybridization, and imaging that significantly increase throughput of the physical map development.

תפוקה גבוהה מיפוי פיזי של הכרומוזומים באמצעות אוטומטי<em&gt; באתרו</em&gt; הכלאה

Projects to obtain whole-genome sequences for 10,000 vertebrate species1 and for 5,000 insect and related arthropod species2 are expected to take place ...

Isolation of Ribosome Bound Nascent Polypeptides in vitro to Identify Translational Pause Sites Along mRNA

The rate of translational elongation is non-uniform. mRNA secondary structure, codon usage and mRNA associated proteins may alter ribosome movement on the messagefor review see 1. However, it's now widely accepted that synonymous codon usage is the primary cause of non-uniform translational elongation rates1. Synonymous codons are not used with identical frequency. A bias exists in the use of synonymous codons with some codons used more frequently than others2. Codon bias is organism as well as tissue specific2,3. Moreover, frequency of codon usage is directly proportional to the concentrations of cognate tRNAs4. Thus, a frequently used codon will have higher multitude of corresponding tRNAs, which further implies that a frequent codon will be translated faster than an infrequent one. Thus, regions on mRNA enriched in rare codons (potential pause sites) will as a rule slow down ribosome movement on the message and cause accumulation of nascent peptides of the respective sizes5-8. These pause sites can have functional impact on the protein expression, mRNA stability and protein foldingfor review see 9. Indeed, it was shown that alleviation of such pause sites can alter ribosome movement on mRNA and subsequently may affect the efficiency of co-translational (in vivo) protein folding1,7,10,11. To understand the process of protein folding in vivo, in the cell, that is ultimately coupled to the process of protein synthesis it is essential to gain comprehensive insights into the impact of codon usage/tRNA content on the movement of ribosomes along mRNA during translational elongation.
Here we describe a simple technique that can be used to locate major translation pause sites for a given mRNA translated in various cell-free systems6-8. This procedure is based on isolation of nascent polypeptides accumulating on ribosomes during in vitro translation of a target mRNA. The rationale is that at low-frequency codons, the increase in the residence time of the ribosomes results in increased amounts of nascent peptides of the corresponding sizes. In vitro transcribed mRNA is used for in vitro translational reactions in the presence of radioactively labeled amino acids to allow the detection of the nascent chains. In order to isolate ribosome bound nascent polypeptide complexes the translation reaction is layered on top of 30% glycerol solution followed by centrifugation. Nascent polypeptides in polysomal pellet are further treated with ribonuclease A and resolved by SDS PAGE. This technique can be potentially used for any protein and allows analysis of ribosome movement along mRNA and the detection of the major pause sites. Additionally, this protocol can be adapted to study factors and conditions that can alter ribosome movement and thus potentially can also alter the function/conformation of the protein.

Isolation of Ribosome Bound Nascent Polypeptides in vitro to Identify Translational Pause Sites Along mRNA

A technique to identify translational pause sites on mRNA is described. This procedure is based on isolation of nascent polypeptides accumulating on ribosomes during in vitro translation of a target mRNA, followed by the size analysis of the nascent chains using a denaturing gel electrophoresis.

הבידוד של הריבוזום פוליפפטידים המתהווה כרוכים<em&gt; במבחנה</em&gt; כדי לזהות אתרים השהה של תרגום לאורך ה-mRNA

The rate of translational elongation is non-uniform. mRNA secondary structure, codon usage and mRNA associated proteins may alter ribosome movement on the ...

Visualization and Analysis of mRNA Molecules Using Fluorescence In Situ Hybridization in Saccharomyces cerevisiae

The Fluorescence in situ Hybridization (FISH) method allows one to detect nucleic acids in the native cellular environment. Here we provide a protocol for using FISH to quantify the number of mRNAs in single yeast cells. Cells can be grown in any condition of interest and then fixed and made permeable. Subsequently, multiple single-stranded deoxyoligonucleotides conjugated to fluorescent dyes are used to label and visualize mRNAs. Diffraction-limited fluorescence from single mRNA molecules is quantified using a spot-detection algorithm to identify and count the number of mRNAs per cell. While the more standard quantification methods of northern blots, RT-PCR and gene expression microarrays provide information on average mRNAs in the bulk population, FISH facilitates both the counting and localization of these mRNAs in single cells at single-molecule resolution.

Visualization and Analysis of mRNA Molecules Using Fluorescence In Situ Hybridization in Saccharomyces cerevisiae

This protocol describes an experimental procedure for performing Fluorescence in situ Hybridization (FISH) for counting mRNAs in single cells at single-molecule resolution.

הדמיה וניתוח של מולקולות ה-mRNA באמצעות הקרינה<em&gt; באתרו</em&gt; הכלאה ב<em&gt; Cerevisiae Saccharomyces</em

The Fluorescence in situ Hybridization (FISH) method allows one to detect nucleic acids in the native cellular environment. Here we provide a protocol for ...