The authors would like to acknowledge the National Health and Medical Research Council of Australia Project Grant APP1103176 for the support of this work.

All experimental procedures involving animal tissue collection were approved by the University of Newcastle&#39;s Animal Care and Ethics Committee.
1. Immunofluorescence Staining of the Paraffin-embedded Epididymal Sections (Figures 1 and 2)
<ol>
	<li>Immediately after the euthanasia of adult mice via CO2 inhalation (Swiss mice, over 8 weeks old), carefully dissect the epididymis (using surgical scissors and tweezers) free of overlying connective tissue and fat and immerse in Bouin&#8217;s fixative solution (&#62; ten times volume/tissue weight) for overnight fixation.</li>
	<li>Wash the tissue with 70% ethanol with 2&#215; changes daily for 2 days and then dehydrate through graded ethanol (70%, 95% and 100%) in preparation for infiltration and embedding into a paraffin block.</li>
	<li>Section the paraffin blocks at a thickness of 4-6 &#181;m and mount on the slides in preparation for immunofluorescence staining.</li>
	<li>In a fume hood, dewax the epididymal paraffin sections by adding a sufficient amount of xylene to the slide jar to completely immerse the tissue section (3&#215; 5 min each time).</li>
	<li>Rehydrate the tissue sections by the immersion in graded ethanol solutions diluted in purified H2O (100% ethanol 5 min, 100% ethanol 5 min, 90% ethanol 1 min, 80% ethanol 1 min, 70% ethanol 1 min, and 50% ethanol 1 min).</li>
	<li>Wash the sections in a slide jar once for 5 min with sufficient phosphate buffered saline (PBS) to completely immerse the entire tissue section (follow these directions for all subsequent washes).</li>
	<li>Decant appropriate antigen retrieval solution (i.e., 10 mmol/L sodium citrate, 50 mmol/L Tris pH 10.5 or alternative antigen retrieval solution(s), depending on the antigen to be detected) into a slide rack and microwave until boiling. Immerse the slides into this solution and subject the tissue sections to heat-induced antigen retrieval conditions optimized for individual antibodies (see Table 1). 
	Caution: Ensure that the slides are fully immersed in antigen retrieval solution during the antigen retrieval process.</li>
	<li>Remove the slide container from the microwave and cool to room temperature.</li>
	<li>Rinse the slides with PBS and use a liquid-repellent slide marker pen to trace around the tissue section.</li>
	<li>Place the slides in a humidified container (created by a moistened tissue at the base of the container), and apply blocking solution (3% BSA/PBS, previously filtered through a 0.45 &#181;m filter) for 1 h at 37 &#176;C.</li>
	<li>Rinse the slides once with PBS.</li>
	<li>Incubate the sections with appropriate primary antibody diluted to an experimentally optimized concentration in filtered 1% BSA/PBS at 4 &#176;C overnight (1:60 for anti-DNM1, DNM2 and DNM3 antibodies; 1:100 for anti-ATP6V1B1 antibody, see Table of Materials for antibody details). 
	Note: To distinguish specific from non-specific antibody binding, it is necessary to include stringent negative (i.e., secondary antibody only, primary antibody preabsorbed against immunizing peptide) and positive controls24.</li>
	<li>Rewarm the slides by placing at room temperature for 30 min.</li>
	<li>Wash the slides 3&#215; with PBS on a shaking platform (60 rpm) for 10 min each.</li>
	<li>Incubate the sections with appropriate secondary antibody diluted in 1% BSA/PBS (filtered through a 0.45 &#181;m filter) at 37 &#176;C for 1 h (1:400 dilution for all secondary antibodies, see Table of Materials for antibody details). 
	CAUTION: Keep the slide container in the dark from this step onwards. For dual labeling, choose a compatible combination of secondary antibodies (i.e., secondary antibodies must have been raised in different species).</li>
	<li>Wash the slides 3&#215; with PBS on a shaking platform (60 rpm) for 10 min each.</li>
	<li>Counterstain the sections with propidium iodide (PI, 7.48 &#956;mol/L) or 4&#900;,6-diamidino-2-phenylindole (DAPI, 4.37 &#956;mol/L) for 2 min at room temperature to label the cell nucleus.</li>
	<li>Wash the slides twice with PBS on a shaking platform (60 rpm) for 5 min each.</li>
	<li>Mount the sections with 10% Mowiol 4-88 prepared in a solution of 30% glycerol in 0.2 mol/L Tris (pH 8.5) and 2.5% 1, 4-diazabicyclo-(2.2.2)-octane.</li>
	<li>Seal the coverslip with nail varnish and store the slides at 4 &#176;C for future observation. 
	CAUTION: It is recommended to perform the imaging of the slides as soon as practical after the preparation to avoid excessive loss of fluorescence.</li>
</ol>
2&#160; Isolation of Epididymosomes from the Mouse Caput Epididymis (Figure 3)
<ol>
	<li>Immediately after the euthanasia of adult mice via CO2 inhalation (Swiss mice over 8 weeks old), perfuse their vasculature with PBS (pre-warmed to 37 &#176;C) to minimize the blood contamination of epididymal tissue. 
	CAUTION: Blood plasma contains diverse populations of exosomes, which are of similar size to epididymosomes25. The efficacy of blood clearance from epididymal tissue can be accessed via the inspection of the initial segment, a highly vascularized epididymal segment located proximal to the caput segment (i.e., zone 1 in Figure 1A)</li>
	<li>Carefully dissect the epididymis free of overlying fat and connective tissue, and rinse with modified Biggers, Whitten, and Whittingham medium (BWW; pH 7.4, osmolality of 300 mmol/kg water26,27) to reduce any potential for surface blood contamination.</li>
	<li>Blot the epididymal tissue to remove excess media, dissect the caput epididymis (i.e., zones 2-5 in Figure 1A) and transfer to a fresh Petri dish (35 &#215; 10 mm) containing BWW medium. Ensure that the amount of medium is sufficient for the final recovery. 
	Note: For 6 caput epididymides, it is recommended to use 1.1 mL of the medium to allow for a recovery of ~900 &#181;L, which is then evenly split and applied atop of 2 pre-prepared gradients (see step 2.9).</li>
	<li>Make a number of small incisions into the caput tissue with a razor blade. Do not mince the tissue and thus avoid contaminating the sample with excessive cytosolic contents. Incubate the plate containing the tissue with mild agitation at 37 &#176;C&#160;for 30 min to release the luminal contents.</li>
	<li>Filter the resultant suspension through 70 &#181;m membranes to remove the cellular debris.</li>
	<li>Collect the filtrate and subject this to successive centrifugation steps at 4 &#176;C with increasing velocity in order to eliminate cellular debris (i.e., 500 &#215; g, 2,000 &#215; g, 4,000 &#215; g, 8,000 &#215; g, 5 min each; 17,000 &#215; g for 20 min, and finally 17,000 &#215; g for an additional 10 min or until no pellet is formed after centrifugation). 
	CAUTION: It is important to assess the color of the pellet after the initial 500 &#215; g centrifugation step to ensure minimal blood contamination is present. Discard any samples in which this pellet displays pink coloration.</li>
	<li>Prepare discontinuous iodixanol gradients (comprising 40%, 20%, 10%, 5% layers) by diluting a density gradient medium (comprising 60% (w/v) aqueous iodixanol) with a solution of 0.25 mol/L sucrose and 10 mmol/L Tris (pH 7.5).</li>
	<li>Prepare the gradient in an ultracentrifuge tube (11 &#215; 35 mm), with each fraction of 450 &#181;L (Figure 3). Visually inspect the gradient after the application of each fraction to ensure that the interfaces are successfully formed between each layer prior to loading the epididymal fluid sample. Prepare each gradient fresh on the day of use, however, the epididymal luminal fluid sample can be preserved at 4 &#176;C for up to 2 h prior to loading.</li>
	<li>Carefully add 450 &#181;L of epididymal luminal fluid suspension (corresponding to the material collected from the caput of 3 epididymides) atop of a single gradient.</li>
	<li>Ultracentrifuge the gradients at 160,000 &#215; g at 4 &#176;C for 18 h. 
	CAUTION: Since this centrifugation is conducted at very high speed, all ultracentrifuge tubes must be paired and balanced precisely. Check the tubes to ensure that they are free of any visible damage that could compromise their integrity.</li>
	<li>Gently remove 12 equal fractions (each consisting of 185 &#181;L) starting from the uppermost layer and progressing toward the bottom of the gradient. Pool the equivalent fractions recovered from each gradient if applicable (up to two gradients). 
	Note: Mouse epididymosomes are most highly enriched in fractions 9 - 1122, see Figure 4 and Discussion.</li>
	<li>After the recovery and pooling of fractions 9 &#8211; 11, dilute into 2 mL of PBS, and ultracentrifuge the samples at 100,000 &#215; g at 4 &#176;C for 3 h (13 &#215; 56 mm tube) to pellet the epididymosomes. 
	CAUTION: Since the epididymosome pellet can be difficult to see, ensure that the orientation of the tubes is noted as they are placed into the rotor and mark the tube to indicate the expectant position of the epididymosome pellet. Ensure that each tube contains a sufficient volume (i.e., exceeding 50% of its total capacity) to preclude the risk of tube collapse.</li>
	<li>Carefully aspirate and discard the supernatant without disturbing the epididymosome pellet.</li>
	<li>Assess the epididymosome purity (Figure 4).</li>
	<li>Resuspend the epididymosome pellet into desired medium according to the downstream application(s). For instance, BWW medium is generally used for the experiments involving co-incubation with spermatozoa or alternatively an appropriate lysis buffer in preparation for the resolution of the epididymal proteome via SDS-PAGE.</li>
</ol>
3. Immunofluorescence Staining of mECap18 Cells
<ol>
	<li>Preparation of sterile coverslips (to be conducted in a cell culture hood)
	<ol>
		<li>Soak the coverslips (12 &#215; 12 mm) in 70% ethanol for 10 min and disinfect by drying under high temperature above an ethanol lamp.</li>
		<li>Cool the coverslip for 10 s before transferring to a 12 well plate.</li>
		<li>Apply sterile poly-L-lysine solution to cover the coverslip and settle for 10 min at room temperature.</li>
		<li>Discard the poly-L-lysine solution and rinse the coverslip with sterile H2O or appropriate medium.</li>
	</ol>
	</li>
	<li>Preparation mECap18 cells
	<ol>
		<li>Passage the aliquots of 2 &#215; 105 mECap18 cells in each well of the 12 well plate containing the coverslips.</li>
		<li>Culture the cells with mECap18 cell medium (DMEM supplemented with 1% L-glutamine, 1% sodium pyruvate, 1% penicillin/streptomycin, and 50 &#956;mol/L 5&#945;-androstan-17&#946;-ol-3-oneC-IIIN) containing 10% fetal calf serum (FBS) in a 37 &#176;C incubator under an atmosphere 5% CO2 overnight.</li>
		<li>Once the cells adhere to the coverslip, discard the medium and rinse the cells twice with PBS.</li>
		<li>Add a sufficient amount of 4% paraformaldehyde (PFA) diluted in PBS to immerse the entire coverslip and fix the cells at room temperature for 15 min.</li>
		<li>Discard the PFA solution and rinse the coverslips twice in PBS.</li>
	</ol>
	</li>
	<li>Immunofluorescence staining
	<ol>
		<li>Permeabilize mECap18 cells by immersion in 0.1% Triton X-100 in PBS for 10 min.</li>
		<li>Rinse the coverslips with PBS.</li>
		<li>Block mECap18 cells with 3% BSA and proceed with immunolabeling of cells utilizing equivalent protocols to those described for epididymal tissue sections.</li>
	</ol>
	</li>
</ol>
4. Isolation of Proteins from Conditioned Cell Culture Medium
<ol>
	<li>Collection of conditioned cell culture medium
	<ol>
		<li>Passage aliquots of 4 &#215; 105 mECap18 cells in each well of 6 well plate with mECap18 cell medium supplemented with 10% FBS for 24&#160;h.</li>
		<li>Wash mECap18 cells three times with mECap18 cell medium (prepared without FBS) to remove residual FBS and any associated protein contaminants.</li>
		<li>Add 1.5 mL of mECap18 cell medium (prepared without FBS) to each well and incubate with mECap18 cells for 12 h in a 37&#176;C incubator under 5% CO2. 
		Note: mECap18 cells at this step can be assessed for different target antigens according to experimental design.</li>
		<li>After 12 h incubation, collect the cell medium and centrifuge at 2,000 &#215; g for 10 min to remove all cellular debris. 
		Note: The duration of incubation is able to be altered in accordance with experimental design/endpoint assessment and in consideration of the cell&#8217;s tolerance to applied treatment(s). It is recommended to tailor the timing of incubation based on specific experimental regimens to ensure that optimal results are achieved.</li>
		<li>Assess mECap18 cell viability via the application of a standard trypan blue exclusion assay28. Discard all material in which cell viability has declined below 90% to eliminate bias introduced by proteins released from dead or moribund cells.</li>
		<li>Isolate proteins from cell medium as follows or preserve medium at -80 &#176;C.</li>
	</ol>
	</li>
	<li>Protein isolation (to be conducted in a fume hood)
	<ol>
		<li>Add 20% volume of chilled 100% trichloroacetic acid to 80% volume of conditioned cell medium to precipitate the proteins released from the cultured mECap18 cells. Incubate at 4 &#176;C overnight with constant mixing.</li>
		<li>After the incubation, pellet precipitated protein by centrifugation (17, 000 &#215; g, 4 &#176;C for 10 min). 
		Note: Due to the limited quantity of protein expected to be secreted into the medium, it is possible that the pellet will not be easily visualized after centrifugation. It is therefore imperative to correctly orientate the tube prior to the centrifugation and take care not to disturb the expectant pellet location during removal of the supernatant.</li>
		<li>Discard the supernatant and wash the pellet twice with chilled acetone prior to the re-centrifugation (17, 000 &#215; g, 4 &#176;C for 10 min).</li>
		<li>Carefully remove and discard the supernatant before air-drying any residual acetone within a fume hood.</li>
		<li>Resuspend the protein pellet in an appropriate extraction buffer in preparation for endpoint analysis to detect complete secretory protein profiles and/or individual target proteins (e.g., SDS-PAGE, immunoblotting).</li>
	</ol>
	</li>
</ol>

The authors have nothing to disclose.

These studies incorporated the use of Bouin&#39;s fixed epididymal tissue that had been subjected to paraffin embedding and standard sectioning protocols. Bouin&#39;s fixative solution comprises a mixture of formaldehyde, picric acid and acetic acid, with each component having a specific and complementary function. Thus, formaldehyde reacts with primary amines to form protein cross-links, picric acid slowly penetrates the tissue forming salts and hence coagulation of basic proteins and conversely, acetic acid rapidly pen...

The spermatozoa of all mammalian species acquire the potential to display forward progressive motility and to fertilize an ovum during their prolonged descent through the epididymis, a highly specialized region of the male extra-testicular duct system, which may take 7 - 14 days to navigate (depending on the species)1. Due to the extreme condensation of the paternal chromatin and the shedding of the majority of cytoplasm that accompanies the cytodifferentiation of spermatozoa within the testes, their subsequent functional maturation is driven exclusively by their interaction with the epididymal microenvironment. This milieu is, in turn, created by the secretory and absorptive activity of the lining epididymal soma and displays an exceptional level of segment-segment variation1. Thus, the most active segments in terms of protein synthesis and secretion are those located in the proximal portion of the epididymis (namely, the caput and corpus)2. This activity mirrors the functional profile of spermatozoa, with the cells first beginning to display hallmarks of functional competence (i.e., progressive motility and the ability to bind to acid-solubilized zona glycoproteins) following their passage through the caput epididymis3. These functional attributes continue to develop before reaching optimal levels as the sperm reach the distal epididymal segment (cauda), wherein they are stored in a quiescent state in readiness for ejaculation. The formation and maintenance of this sperm storage reservoir is also intimately tied to the lining epithelium, which in the cauda is dominated by strong absorptive activity4,5. Although anatomical differences have been reported6,7,8, such regionalized division of labor appears to be a characteristic of the epididymis that is shared among the majority of mammalian species studied to date, including our own9,10. Indeed, from a clinical perspective, it is known that epididymal dysfunction makes an important contribution to the etiology of male factor infertility11, thus highlighting the importance of understanding the regulation of this specialized tissue.
It is therefore regrettable that our understanding of epididymal physiology, and the mechanisms that regulate the sequential phases of sperm maturation and storage within this tissue, remain to be fully resolved. Among the contributing factors, limiting advances in epididymal research are the overall complexity of this tissue and knowledge of the mechanisms that exert regulatory control over its luminal microenvironment. Anatomically, we know that beyond the distinction of caput, corpus and cauda segments, the epididymis can be further subdivided into several zones (Figure 1A), each separated by septa12 and characterized by discrete profiles of gene/protein expression13,14,15,16,17,18. Indeed, on the basis of detailed transcriptional profiling of segmental gene expression in the epididymis, as many as 6 and 9 distinct epididymal zones have been reported in the mouse and rat models, respectively19,20. Such complexity presumably reflects the composition of the epididymal soma, a pseudostratified epithelium comprising numerous different cell types; each differing with respect to their abundance, distribution and secretory/absorptive activities along the length of the tract. Thus, principal cells are by far the most abundant epididymal cell type constituting upwards of 80% of all epithelial cells. Accordingly, principal cells are responsible for the bulk of epididymal protein biosynthesis and secretion5. In contrast, the clear cell population, which rank as the second most abundant cell type within the epididymal soma, are primarily involved in selective absorption of luminal components and the acidification of this microenvironment5. Adding another tier of complexity, androgens and other lumicrine factors of testicular origin exert differential control over each of these epididymal cell types depending on their positioning along the tract.
Despite the limitations imposed by such complexity, significant inroads continue to be made into resolving the mechanistic basis of epididymal function. A key to these studies has been the application of advanced mass spectrometry strategies to establish broad scale inventories of the epididymal proteome, in tandem with detailed analyses of individual proteins selected from among these initial surveys. An illustration of this approach is our recent characterization of the DNM family of mechanoenzymes in the mouse model21. Our initial interest in DNM was fueled by its dual action in the coupling of exo- and endocytotic processes. Building on these observations, we were able to demonstrate that the three canonical isoforms of DNM (DNM1 - DNM3) are highly expressed in the mouse epididymis and appropriately positioned to fulfill regulatory roles in protein secretion and absorption21. Moreover, we were able to clearly differentiate each DNM isoform on the basis of their cellular and sub-cellular localization, thus suggesting that they possess complementary, as opposed to redundant, activity within the epididymal epithelium21.
Here, we describe the experimental methodology employed for the study of DNM expression in the mouse epididymis with the hope that this information will find wider application in the characterization of alternative epididymal proteins and thus contribute to our understanding of the function of this important element of the male reproductive tract. Specifically, we describe the development of robust methodology for immunofluorescence labeling of target proteins in paraffin-embedded epididymal sections and the subsequent detection of the spatial distribution of these proteins via immunofluorescence microscopy. We further document our recently optimized protocols22 for the isolation and characterization of epididymosomes; small exosome-like vesicles that constitute key elements of the epididymal secretory profile and appear to hold a prominent role in promoting sperm maturation23. As a complementary approach, we also describe the immunofluorescence detection of target proteins in an immortalized mouse caput epididymal epithelial (mECap18) cell line and the use of this resource as a model with which to explore the regulation of epididymal secretory activity in vitro.

<table><tbody><tr><td>Dynamin 1 antibody</td><td>Abcam</td><td>ab108458</td><td>&lt;strong&gt;Host species&lt;/strong&gt;: Rabbit, &lt;strong&gt;Isotype&lt;/strong&gt;: IgG, &lt;strong&gt;Class&lt;/strong&gt;: polyclonal</td></tr><tr><td>Dynamin 2 antibody</td><td>Santa Cruz</td><td>sc-6400</td><td>&lt;strong&gt;Host species&lt;/strong&gt;: Goat, &lt;strong&gt;Isotype&lt;/strong&gt;: IgG, &lt;strong&gt;Class&lt;/strong&gt;: polyclonal</td></tr><tr><td>Dynamin 3 antibody</td><td>Proteintech</td><td>14737-1-AP</td><td>&lt;strong&gt;Host species&lt;/strong&gt;: Rabbit, &lt;strong&gt;Isotype&lt;/strong&gt;: IgG, &lt;strong&gt;Class&lt;/strong&gt;: polyclonal</td></tr><tr><td>ATP6V1B1 antibody</td><td>Santa Cruz</td><td>sc-21206</td><td>&lt;strong&gt;Host species&lt;/strong&gt;: Goat, &lt;strong&gt;Isotype&lt;/strong&gt;: IgG, &lt;strong&gt;Class&lt;/strong&gt;: polyclonal</td></tr><tr><td>CD9 antibody</td><td>BD Pharmingen</td><td>553758</td><td>&lt;strong&gt;Host species&lt;/strong&gt;: Rat, &lt;strong&gt;Isotype&lt;/strong&gt;: IgG, &lt;strong&gt;Class&lt;/strong&gt;: monoclonal</td></tr><tr><td>Flotillin-1 antibody</td><td>Sigma</td><td>F1180</td><td>&lt;strong&gt;Host species&lt;/strong&gt;: Rabbit, &lt;strong&gt;Isotype&lt;/strong&gt;: IgG, &lt;strong&gt;Class&lt;/strong&gt;: polyclonal</td></tr><tr><td>ALOX15 antibody</td><td>Abcam</td><td>ab80221</td><td>&lt;strong&gt;Host species&lt;/strong&gt;: Rabbit, &lt;strong&gt;Isotype&lt;/strong&gt;: IgG, &lt;strong&gt;Class&lt;/strong&gt;: polyclonal</td></tr><tr><td>TUBB antibody</td><td>Santa Cruz</td><td>sc-5274</td><td>&lt;strong&gt;Host species&lt;/strong&gt;: Mouse, &lt;strong&gt;Isotype&lt;/strong&gt;: IgG, &lt;strong&gt;Class&lt;/strong&gt;: monoclonal</td></tr><tr><td>PSMD7 antibody</td><td>Abcam</td><td>ab11436</td><td>&lt;strong&gt;Host species&lt;/strong&gt;: Rabbit, &lt;strong&gt;Isotype&lt;/strong&gt;: IgG, &lt;strong&gt;Class&lt;/strong&gt;: polyclonal</td></tr><tr><td>Anti Rabbit Alexa Fluor 488</td><td>Thermo</td><td>A11008</td><td>&lt;strong&gt;Host species&lt;/strong&gt;: Goat, &lt;strong&gt;Isotype&lt;/strong&gt;: IgG, &lt;strong&gt;Class&lt;/strong&gt;: polyclonal</td></tr><tr><td>Anti Goat Alexa Fluor 488</td><td>Thermo</td><td>A11055</td><td>&lt;strong&gt;Host species&lt;/strong&gt;: Donkey, &lt;strong&gt;Isotype&lt;/strong&gt;: IgG, &lt;strong&gt;Class&lt;/strong&gt;: polyclonal</td></tr><tr><td>Anti Goat Alexa Fluor 594</td><td>Thermo</td><td>A11058</td><td>&lt;strong&gt;Host species&lt;/strong&gt;: Donkey, &lt;strong&gt;Isotype&lt;/strong&gt;: IgG, &lt;strong&gt;Class&lt;/strong&gt;: polyclonal</td></tr><tr><td>Anti Rat Alexa Fluor 594</td><td>Thermo</td><td>A11007</td><td>&lt;strong&gt;Host species&lt;/strong&gt;: Goat, &lt;strong&gt;Isotype&lt;/strong&gt;: IgG, &lt;strong&gt;Class&lt;/strong&gt;: polyclonal</td></tr><tr><td>Anti Rabbit HRP</td><td>Millipore</td><td>DC03L</td><td>&lt;strong&gt;Host species&lt;/strong&gt;: Goat, &lt;strong&gt;Isotype&lt;/strong&gt;: IgG, &lt;strong&gt;Class&lt;/strong&gt;: polyclonal</td></tr><tr><td>Anti Rat HRP</td><td>Millipore</td><td>DC01L</td><td>&lt;strong&gt;Host species&lt;/strong&gt;: Goat, &lt;strong&gt;Isotype&lt;/strong&gt;: IgG, &lt;strong&gt;Class&lt;/strong&gt;: polyclonal</td></tr><tr><td>Anti Mouse HRP</td><td>Santa Cruz</td><td>sc-2005</td><td>&lt;strong&gt;Host species&lt;/strong&gt;: Goat, &lt;strong&gt;Isotype&lt;/strong&gt;: IgG, &lt;strong&gt;Class&lt;/strong&gt;: polyclonal</td></tr><tr><td>4&#039;, 6-diamidino-2-phenylindole (DAPI)</td><td>Sigma</td><td>D9564</td><td></td></tr><tr><td>propidium iodide (PI)</td><td>Sigma</td><td>P4170</td><td></td></tr><tr><td>Mowiol 4-88</td><td>Calbiochem</td><td>475904</td><td></td></tr><tr><td>Bovine serum albumin (BSA)</td><td>Sigma</td><td>A7906</td><td></td></tr><tr><td>fetal bovine serum (FBS)</td><td>Bovogen</td><td>SFBS-F</td><td></td></tr><tr><td>DMEM</td><td>Thermo</td><td>11960-044</td><td></td></tr><tr><td>L-glutamine</td><td>Thermo</td><td>25030-081</td><td></td></tr><tr><td>penicillin/streptomycin</td><td>Thermo</td><td>15140-122</td><td></td></tr><tr><td>5&amp;alpha;-androstan-17&amp;beta;-ol-3-oneC-IIIN</td><td>Sigma</td><td>A8380</td><td></td></tr><tr><td>sodium pyruvate</td><td>Thermo</td><td>11360-070</td><td></td></tr><tr><td>Trypsin-ethylenediaminetetraacetic acid (EDTA)</td><td>Sigma</td><td>T4049</td><td></td></tr><tr><td>Paraformaldehyde (PFA)</td><td>EMS</td><td>15710</td><td></td></tr><tr><td>Xylene</td><td>VWR Chemicals</td><td>1330-20-7</td><td></td></tr><tr><td>Ethanol</td><td>VWR Chemicals</td><td>64-17-5</td><td></td></tr><tr><td>Phosphate buffered saline (PBS)</td><td>Sigma</td><td>P4417</td><td></td></tr><tr><td>Sodium citrate</td><td>Sigma</td><td>S1804</td><td></td></tr><tr><td>Tris</td><td>Astral</td><td>0497-5KG</td><td></td></tr><tr><td>Glycerol</td><td>Sigma</td><td>G5516</td><td></td></tr><tr><td>1, 4-diazabicyclo-(2.2.2)-octane</td><td>Sigma</td><td>D2522</td><td></td></tr><tr><td>Poly-L-gysine</td><td>Sigma</td><td>P4832</td><td></td></tr><tr><td>Triton X-100</td><td>Sigma</td><td>78787</td><td></td></tr><tr><td>Trypan blue</td><td>Sigma</td><td>T6146</td><td></td></tr><tr><td>Trichloroacetic acid</td><td>Sigma</td><td>T9159</td><td></td></tr><tr><td>Acetone</td><td>Ajax Finechem</td><td>A6-2.5 L GL</td><td></td></tr><tr><td>Sucrose</td><td>Sigma</td><td>S0389</td><td></td></tr><tr><td>Poly (vinyl alcohol)</td><td>Sigma</td><td>P8136</td><td></td></tr><tr><td>D-Glucose</td><td>Ajax Finechem</td><td>783-500G</td><td></td></tr><tr><td>OptiPrep Density Gradient Medium</td><td>Sigma</td><td>D1556</td><td></td></tr><tr><td>Fluorescence microscopy</td><td>Zeiss</td><td>Zeiss Axio Imager A1</td><td></td></tr><tr><td>Ultracentrifuge</td><td>BECKMAN COULTER</td><td>Optima Max-XP</td><td></td></tr><tr><td>Microcentrifuges</td><td>Eppendorf</td><td>5424R</td><td></td></tr><tr><td>Incubator</td><td>Heracell</td><td>150</td><td></td></tr><tr><td>Large Orbital Shaker</td><td>Ratek</td><td>OM7</td><td></td></tr><tr><td>Microwave</td><td>LG</td><td>MS3840SR /00</td><td></td></tr><tr><td>Lab pH Meter</td><td>MeterLab</td><td>PHM220</td><td></td></tr><tr><td>Liquid-repellent slide marker</td><td>Daido Sangyo</td><td>Mini</td><td></td></tr><tr><td>Coverslip</td><td>Thermo</td><td>586</td><td></td></tr><tr><td>6 well plate</td><td>CELLSTAR</td><td>657160</td><td></td></tr><tr><td>12 well plate</td><td>CELLSTAR</td><td>665180</td><td></td></tr><tr><td>Slide</td><td>Mikro-Glass</td><td>SF41296PLMK</td><td></td></tr><tr><td>0.45 &amp;micro;m filter</td><td>Millox-HV</td><td>SLHV033RS</td><td></td></tr><tr><td>Kimwipes Dustfree Paper</td><td>KIMTECH</td><td>34155</td><td></td></tr><tr><td>Ultracentrifuge tube (2.2 ml, 11 &amp;times; 35 mm)</td><td>BECKMAN COULTER</td><td>347356</td><td></td></tr><tr><td>Ultracentrifuge tube (3.2 ml, 13 &amp;times; 56 mm)</td><td>BECKMAN COULTER</td><td>362305</td><td></td></tr><tr><td>Cell strainer 70 &amp;micro;m Nylon</td><td>FALCON</td><td>352350</td><td></td></tr><tr><td>Petri dish 35 &amp;times; 10 mm with cams</td><td>SARSTED</td><td>82.1135.500</td><td></td></tr><tr><td>Slide jar</td><td>TRAJAN</td><td>#23 319 00</td><td></td></tr></tbody></table>

analysis of epididymal protein synthesis and secretion

The mammalian epididymis generates one of the most complex intraluminal fluids of any endocrine gland in order to support the post-testicular maturation and storage of spermatozoa. Such complexity arises due to the combined secretory and absorptive activity of the lining epithelial cells. Here, we describe the techniques for the analysis of epididymal protein synthesis and secretion by focusing on the model protein family of dynamin (DNM) mechanoenzymes; large GTPases that have the potential to regulate bi-directional membrane trafficking events. For the study of protein expression in epididymal tissue, we describe robust methodology for immunofluorescence labeling of target proteins in paraffin-embedded sections and the subsequent detection of the spatial distribution of these proteins via immunofluorescence microscopy. We also describe optimized methodology for the isolation and characterization of exosome like vesicles, known as epididymosomes, which are secreted into the epididymal lumen to participate in intercellular communication with maturing sperm cells. As a complementary approach, we also describe the immunofluorescence detection of target proteins in an SV40-immortalized mouse caput epididymal epithelial (mECap18) cell line. Moreover, we discuss the utility of the mECap18 cell line as a suitable in vitro model with which to explore the regulation of epididymal secretory activity. For this purpose, we describe the culturing requirements for the maintenance of the mECap18 cell line and the use of selective pharmacological inhibition regimens that are capable of influencing their secretory protein profile. The latter are readily assessed via harvesting of conditioned culture medium, concentration of secreted proteins via trichloroacetic acid/acetone precipitation and their subsequent analysis via SDS-PAGE and immunoblotting. We contend that these combined methods are suitable for the analysis of alternative epididymal protein targets as a prelude to determining their functional role in sperm maturation and/or storage.

Figure 1 and Figure 2 show representative results of immunofluorescence localization of DNM in the mouse caput epididymis. Each of the three DNM isoforms investigated display distinct localization profiles. Thus, DNM1 is characterized by relatively modest diffuse labeling of the epididymal cells throughout the initial segment and caput epididymis (Figure 2A). By contrast, the DNM2 is...

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Analysis of Epididymal Protein Synthesis and Secretion

Here, we report the immunofluorescence localization of dynamin to illustrate the protocols for the detection of proteins in paraffin-embedded mouse epididymal sections and those of an immortalized epididymal cell line (mECap18). We also describe the protocols for the isolation of secretory proteins from both epididymal fluid and conditioned cell media.

The mammalian epididymis generates one of the most complex intraluminal fluids of any endocrine gland in order to support the post-testicular maturation ...

analysis-of-epididymal-protein-synthesis-and-secretion

Research

JoVE Journal

Developmental Biology

9.3K Views.  University of Newcastle. Here, we report the immunofluorescence localization of dynamin to illustrate the protocols for the detection of proteins in paraffin-embedded mouse epididymal sections and those of an immortalized epididymal cell line (mECap18). We also describe the protocols for the isolation of secretory proteins from both epididymal fluid and conditioned cell media.

Video: Analysis of Epididymal Protein Synthesis and Secretion

Quantitative Immunofluorescence to Measure Global Localized Translation

The mechanisms regulating mRNA translation are involved in various biological processes, such as germ line development, cell differentiation, and organogenesis, as well as in multiple diseases. Numerous publications have convincingly shown that specific mechanisms tightly regulate mRNA translation. Increased interest in the translation-induced regulation of protein expression has led to the development of novel methods to study and follow de novo protein synthesis in cellulo. However, most of these methods are complex, making them costly and often limiting the number of mRNA targets that can be studied. This manuscript proposes a method that requires only basic reagents and a confocal fluorescence imaging system to measure and visualize the changes in mRNA translation that occur in any cell line under various conditions. This method was recently used to show localized translation in the subcellular structures of adherent cells over a short period of time, thus offering the possibility of visualizing de novo translation for a short period during a variety of biological processes or of validating changes in translational activity in response to specific stimuli.

This manuscript describes a method to visualize and quantify localized translation events in subcellular compartments. The approach proposed in this manuscript requires a basic confocal imaging system and reagents and is rapid and cost-effective.

The mechanisms regulating mRNA translation are involved in various biological processes, such as germ line development, cell differentiation, and ...

Biochemistry

Polysome Profiling in Leishmania, Human Cells and Mouse Testis

Proper protein expression at the right time and in the right amounts is the basis of normal cell function and survival in a fast-changing environment. For a long time, the gene expression studies were dominated by research on the transcriptional level. However, the steady-state levels of mRNAs do not correlate well with protein production, and the translatability of mRNAs varies greatly depending on the conditions. In some organisms, like the parasite Leishmania, the protein expression is regulated mostly at the translational level. Recent studies demonstrated that protein translation dysregulation is associated with cancer, metabolic, neurodegenerative and other human diseases. Polysome profiling is a powerful method to study protein translation regulation. It allows to measure the translational status of individual mRNAs or examine translation on a genome-wide scale. The basis of this technique is the separation of polysomes, ribosomes, their subunits and free mRNAs during centrifugation of a cytoplasmic lysate through a sucrose gradient. Here, we present a universal polysome profiling protocol used on three different models - parasite Leishmania major, cultured human cells and animal tissues. Leishmania cells freely grow in suspension and cultured human cells grow in adherent monolayer, while mouse testis represents an animal tissue sample. Thus, the technique is adapted to all of these sources. The protocol for the analysis of polysomal fractions includes detection of individual mRNA levels by RT-qPCR, proteins by Western blot and analysis of ribosomal RNAs by electrophoresis. The method can be further extended by examination of mRNAs association with the ribosome on a transcriptome level by deep RNA-seq and analysis of ribosome-associated proteins by mass spectroscopy of the fractions. The method can be easily adjusted to other biological models.

Polysome Profiling in Leishmania, Human Cells and Mouse Testis

The overall goal of polysome profiling technique is analysis of translational activity of individual mRNAs or transcriptome mRNAs during protein synthesis. The method is important for studies of protein synthesis regulation, translation activation and repression in health and multiple human diseases.

Proper protein expression at the right time and in the right amounts is the basis of normal cell function and survival in a fast-changing environment. For ...

RiboTag Immunoprecipitation in the Germ Cells of the Male Mouse

Quantifying differences in mRNA abundance is a classic approach to understand the impact of a given gene mutation on cell physiology. However, characterizing differences in the translatome (the whole of translated mRNAs) provides an additional layer of information particularly useful when trying to understand the function of RNA regulating or binding proteins. A number of methods for accomplishing this have been developed, including ribosome profiling and polysome analysis. However, both methods carry significant technical challenges and cannot be applied to specific cell populations within a tissue unless combined with additional sorting methods. In contrast, the RiboTag method is a genetic-based, efficient, and technically straightforward alternative that allows the identification of ribosome associated RNAs from specific cell populations without added sorting steps, provided an applicable cell-specific Cre driver is available. This method consists of breeding to generate the genetic models, sample collection, immunoprecipitation, and downstream RNA analyses. Here, we outline this process in adult male mouse germ cells mutant for an RNA binding protein required for male fertility. Special attention is paid to considerations for breeding with a focus on efficient colony management and the generation of correct genetic backgrounds and immunoprecipitation in order to reduce background and optimize output. Discussion of troubleshooting options, additional confirmatory experiments, and potential downstream applications is also included. The presented genetic tools and molecular protocols represent a powerful way to describe the ribosome-associated RNAs of specific cell populations in complex tissues or in systems with aberrant mRNA storage and translation with the goal of informing on the molecular drivers of mutant phenotypes.

Here, we describe the immunoprecipitation of ribosomes and associated RNA from select populations of adult male mouse germ cells using the RiboTag system. Strategic breeding and careful immunoprecipitation result in clean, reproducible results that inform on the germ cell translatome and provide insight into the mechanisms of mutant phenotypes.

Quantifying differences in mRNA abundance is a classic approach to understand the impact of a given gene mutation on cell physiology. However, ...

Eukaryotic Polyribosome Profile Analysis

Protein synthesis is a complex cellular process that is regulated at many levels. For example, global translation can be inhibited at the initiation phase or the elongation phase by a variety of cellular stresses such as amino acid starvation or growth factor withdrawal. Alternatively, translation of individual mRNAs can be regulated by mRNA localization or the presence of cognate microRNAs. Studies of protein synthesis frequently utilize polyribosome analysis to shed light on the mechanisms of translation regulation or defects in protein synthesis. In this assay, mRNA/ribosome complexes are isolated from eukaryotic cells.  A sucrose density gradient separates mRNAs bound to multiple ribosomes known as polyribosomes from mRNAs bound to a single ribosome or monosome. Fractionation of the gradients allows isolation and quantification of the different ribosomal populations and their associated mRNAs or proteins. Differences in the ratio of polyribosomes to monosomes under defined conditions can be indicative of defects in either translation initiation or elongation/termination. Examination of the mRNAs present in the polyribosome fractions can reveal whether the cohort of individual mRNAs being translated changes with experimental conditions. In addition, ribosome assembly can be monitored by analysis of the small and large ribosomal subunit peaks which are also separated by the gradient. In this video, we present a method for the preparation of crude ribosomal extracts from yeast cells, separation of the extract by sucrose gradient and interpretation of the results.  This procedure is readily adaptable to mammalian cells.

This article describes a protocol for the extraction of translating ribosomes from eukaryotic cells. Once extracted, ribosomes are separated into monosomes and polyribosomes by sucrose gradient fractionation to allow different ribosomal populations to be analyzed. As such, this method is the gold standard for examining the regulation of translation.

Protein synthesis is a complex cellular process that is regulated at many levels. For example, global translation can be inhibited at the initiation phase ...

Biology

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.

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

Isolation of Primary Mouse Hepatocytes for Nascent Protein Synthesis Analysis by Non-radioactive L-azidohomoalanine Labeling Method

Hepatocytes are parenchymal cells of the liver and engage multiple metabolic functions, including synthesis and secretion of proteins essential for systemic energy homeostasis. Primary hepatocytes isolated from the murine liver constitute a valuable biological tool to understand the functional properties or alterations occurring in the liver. Herein we describe a method for the isolation and culture of primary mouse hepatocytes by performing a two-step collagenase perfusion technique and discuss their utilization for investigating protein metabolism. The liver of an adult mouse is sequentially perfused with ethylene glycol-bis tetraacetic acid (EGTA) and collagenase, followed by the isolation of hepatocytes with the density gradient buffer. These isolated hepatocytes are viable on culture plates and maintain the majority of endowed characteristics of hepatocytes. These hepatocytes can be used for assessments of protein metabolism including nascent protein synthesis with non-radioactive reagents. We show that the isolated hepatocytes are readily controlled and comprise a higher quality and volume stability of protein synthesis linked to energy metabolism by utilizing the chemo-selective ligation reaction with a Tetramethylrhodamine (TAMRA) protein detection method and western blotting analyses. Therefore, this method is valuable for investigating hepatic nascent protein synthesis linked to energy homeostasis. The following protocol outlines the materials and methods for the isolation of high-quality primary mouse hepatocytes and detection of nascent protein synthesis.

Here, we present a protocol for the isolation of healthy and functional primary mouse hepatocytes. Instructions for detecting hepatic nascent protein synthesis by non-radioactive labeling substrate were provided to help understand the mechanisms underlying protein synthesis in the context of energy-metabolism homeostasis in the liver.

Hepatocytes are parenchymal cells of the liver and engage multiple metabolic functions, including synthesis and secretion of proteins essential for ...

Medicine

Polysome Fractionation and Analysis of Mammalian Translatomes on a Genome-wide Scale

mRNA translation plays a central role in the regulation of gene expression and represents the most energy consuming process in mammalian cells. Accordingly, dysregulation of mRNA translation is considered to play a major role in a variety of pathological states including cancer. Ribosomes also host chaperones, which facilitate folding of nascent polypeptides, thereby modulating function and stability of newly synthesized polypeptides. In addition, emerging data indicate that ribosomes serve as a platform for a repertoire of signaling molecules, which are implicated in a variety of post-translational modifications of newly synthesized polypeptides as they emerge from the ribosome, and/or components of translational machinery. Herein, a well-established method of ribosome fractionation using sucrose density gradient centrifugation is described. In conjunction with the in-house developed &#8220;anota&#8221; algorithm this method allows direct determination of differential translation of individual mRNAs on a genome-wide scale. Moreover, this versatile protocol can be used for a variety of biochemical studies aiming to dissect the function of ribosome-associated protein complexes, including those that play a central role in folding and degradation of newly synthesized polypeptides.

Ribosomes play a central role in protein synthesis. Polyribosome (polysome) fractionation by sucrose density gradient centrifugation allows direct determination of translation efficiencies of individual mRNAs on a genome-wide scale. In addition, this method can be used for biochemical analysis of ribosome- and polysome-associated factors such as chaperones and signaling molecules.

mRNA translation plays a central role in the regulation of gene expression and represents the most energy consuming process in mammalian cells. ...

Phosphopeptide Analysis of Rodent Epididymal Spermatozoa

Spermatozoa are quite unique amongst cell types. Although produced in the testis, both nuclear gene transcription and translation are switched off once the pre-cursor round cell begins to elongate and differentiate into what is morphologically recognized as a spermatozoon. However, the spermatozoon is very immature, having no ability for motility or egg recognition. Both of these events occur once the spermatozoa transit a secondary organ known as the epididymis. During the ~12 day passage that it takes for a sperm cell to pass through the epididymis, post-translational modifications of existing proteins play a pivotal role in the maturation of the cell. One major facet of such is protein phosphorylation. In order to characterize phosphorylation events taking place during sperm maturation, both pure sperm cell populations and pre-fractionation of phosphopeptides must be established. Using back flushing techniques, a method for the isolation of pure spermatozoa of high quality and yield from the distal or caudal epididymides is outlined. The steps for solubilization, digestion, and pre-fractionation of sperm phosphopeptides through TiO2 affinity chromatography are explained. Once isolated, phosphopeptides can be injected into MS to identify both protein phosphorylation events on specific amino acid residues and quantify the levels of phosphorylation taking place during the sperm maturation processes.

Proteomic analysis of any cell type is highly dependent on both purity and pre-fractionation of the starting material in order to de-complexify the sample prior to liquid chromatography mass spectrometry (MS). By using back-flushing techniques, pure spermatozoa can be obtained from rodents. Following digestion, phosphopeptides can be enriched using TiO2.

Spermatozoa are quite unique amongst cell types. Although produced in the testis, both nuclear gene transcription and translation are switched off once ...

Xenopus laevis as a Model to Identify Translation Impairment

Protein synthesis is a fundamental process to gene expression impacting diverse biological processes notably adaptation to environmental conditions. The initiation step, which involves the assembly of the ribosomal subunits at the mRNA initiation codon, involved initiation factor including eIF4G1. Defects in this rate limiting step of translation are linked to diverse disorders. To study the potential consequences of such deregulations, Xenopus laevis oocytes constitute an attractive model with high degrees of conservation of essential cellular and molecular mechanisms with human. In addition, during meiotic maturation, oocytes are transcriptionally repressed and all necessary proteins are translated from preexisting, maternally derived mRNAs. This inexpensive model enables exogenous mRNA to become perfectly integrated with an effective translation. Here is described a protocol for assessing translation with a factor of interest (here eIF4G1) using stored maternal mRNA that are the first to be polyadenylated and translated during oocyte maturation as a physiological readout. At first, mRNA synthetized by in vitro transcription of plasmids of interest (here eIF4G1) are injected in oocytes and kinetics of oocyte maturation by Germinal Vesicle Breakdown detection is determined. The studied maternal mRNA target is the serine/threonine-protein-kinase mos. Its polyadenylation and its subsequent translation are investigated together with the expression and phosphorylation of proteins of the mos signaling cascade involved in oocyte maturation. Variations of the current protocol to put forward translational defects are also proposed to emphasize its general applicability. In light of emerging evidence that aberrant protein synthesis may be involved in the pathogenesis of neurological disorders, such a model provides the opportunity to easily assess this impairment and identify new targets.

Xenopus laevis as a Model to Identify Translation Impairment

Protein synthesis control occurs mainly at the translation initiation step, deficiencies in which are linked to diverse disorders. To better understand their etiology, we described here a protocol using Xenopus laevis oocytes assessing the translation of mos transcript in the presence of a mutant of translation initiation factor eIF4G1.

Protein synthesis is a fundamental process to gene expression impacting diverse biological processes notably adaptation to environmental conditions. The ...

An Easy Method for Plant Polysome Profiling

Translation of mRNA to protein is a fundamental and highly regulated biological process. Polysome profiling is considered as a gold standard for the analysis of translational regulation. The method described here is an easy and economical way for fractionating polysomes from various plant tissues. A sucrose gradient is made without the need for a gradient maker by sequentially freezing each layer. Cytosolic extracts are then prepared in a buffer containing cycloheximide and chloramphenicol to immobilize the cytosolic and chloroplastic ribosomes to mRNA and are loaded onto the sucrose gradient. After centrifugation, six fractions are directly collected from the bottom to the top of the gradient, without piercing the ultracentrifugation tube. During collection, the absorbance at 260 nm is read continuously to generate a polysome profile that gives a snapshot of global translational activity. Fractions are then pooled to prepare three different mRNA populations: the polysomes, mRNAs bound to several ribosomes; the monosomes, mRNAs bound to one ribosome; and mRNAs that are not bound to ribosomes. mRNAs are then extracted. This protocol has been validated for different plants and tissues including Arabidopsis thaliana seedlings and adult plants, Nicotiana benthamiana, Solanum lycopersicum, and Oryza sativa leaves.

This protocol describes an easy method to extract and fractionate transcripts from plant tissues on the basis of the number of bound ribosomes. It allows a global estimate of translation activity and the determination of the translational status of specific mRNAs.

Translation of mRNA to protein is a fundamental and highly regulated biological process. Polysome profiling is considered as a gold standard for the ...

Analysis of Epididymal Protein Synthesis and Secretion

Summary

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Chapters in this video

Quantitative Immunofluorescence to Measure Global Localized Translation

Polysome Profiling in Leishmania, Human Cells and Mouse Testis

RiboTag Immunoprecipitation in the Germ Cells of the Male Mouse

Eukaryotic Polyribosome Profile Analysis

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

Isolation of Primary Mouse Hepatocytes for Nascent Protein Synthesis Analysis by Non-radioactive L-azidohomoalanine Labeling Method

Polysome Fractionation and Analysis of Mammalian Translatomes on a Genome-wide Scale

Phosphopeptide Analysis of Rodent Epididymal Spermatozoa

Xenopus laevis as a Model to Identify Translation Impairment

An Easy Method for Plant Polysome Profiling