total rna extraction from drosophila larvae brain and s2 schneider cells

Drosophila Nervous System에서 유전자의 Poly(A) 길이를 정량화합니다.

Most eukaryotic mRNAs are posttranscriptionally polyadenylated at their 3&#8242; terminus in the nucleus by the addition of non-templated adenosines by canonical poly(A) polymerases. An intact poly(A) tail is pivotal throughout the lifecycle of mRNA, as it is essential for mRNA nuclear export1, facilitates interaction with poly(A)-binding proteins to enhance translational efficiency2, and imparts resistance against degradation3. In certain cases, the poly(A) tail can also undergo extension in the cytoplasm, facilitated by noncanonical poly(A) polymerases4. In the cytoplasm, poly (A) tail length dynamically changes and influences the life span of the mRNA molecule. Numerous polymerases and deadenylases are known for modulating tail length5,6,7. For example, the shortening of poly(A) tails correlates with translational repression, whereas the lengthening of poly(A) tails enhances translation8,9.
Accumulating genomic studies have demonstrated the fundamental significance of the poly(A) tail length across various facets of eukaryotic biology. This includes roles in germ-cell development, early embryonic development, neuronal synaptic plasticity for learning and memory, and the inflammatory response10. There have been numerous methods and assays developed for measuring poly(A) tail lengths. For example, the RNase H/oligo(dT) assay takes advantage of RNase H in the presence or absence of oligo(dT) to study poly(A) tail length11,12. Other methods to study poly(A) tail include the PCR amplification of 3&#39; ends such as rapid amplification of cDNA ends poly(A) test (RACE-PAT)12,13 and the ligase-mediated poly(A) test (LM-PAT)14. Further modifications of the PAT assay include ePAT15 and sPAT16. Enzymatic G-tailing17,18 or G/I-tailing&#160;of the 3&#39; end are other variations of the PAT assay. Further modification of these techniques includes the use of fluorescently labeled primers along with capillary gel electrophoresis for high-resolution analysis, referred to as the high-resolution poly(A) test (Hire-PAT)19. These PCR-driven assays allow fast and high-sensitivity poly(A) length quantitation.
With the development of next-generation sequencing, a high-throughput sequencing method, such as PAL-seq20 and TAIL-seq21, allows polyadenylation analyses at a transcriptome-wide scale. However, these methods provide only short sequencing reads of 36-51 nucleotides. Therefore, FLAM-Seq22 was developed for global tail length profiling of full-length mRNA and provides long reads. Nanopore technology23 provides PCR-independent, direct RNA, or direct cDNA sequencing for poly(A) tail length estimations. However, these high-throughput methods are not without limitations. They require large amounts of starting materials, are expensive, and time-consuming. Moreover, analyzing rare transcripts can be extremely challenging with high-throughput methods, and low-throughput PCR-based methods still provide an advantage when a small number of transcripts need to be analyzed, for pilot experiments, and validation of other methods.
We have recently demonstrated that Dscam1 mRNAs contain short poly(A) tails in Drosophila, which necessitates a non-canonical binding of the cytoplasmic poly(A)-binding protein on Dscam1 3&#39;UTR using the G/I tailing method24. Here we provide a streamlined procedure for tissue preparation and quantifying poly(A) length of mRNAs from the Drosophila nervous system and Drosophila S2 cells.

저자 스포트라이트: Poly A Tail Analysis Techniques를 통한 mRNA 연구의 지평 개척

Drosophila Larva Brain and Cell Line의 Poly A 꼬리 길이 측정

Polyadenylation is a post-transcription modification. This add poly-A tails to the three-prime end of mRNA molecules. Dysregulation of polyadenylation has been associated with abnormal gene expression and various diseases, including neurological disorders.Our method provides a cost-effective, high-resolution analysis for measuring poly-A lengths. High-throughput methods for poly-A tail analysis, like next generation sequencing, and a high-throughput sequencing provides high-content information. However, analyzing rare transcripts can be extremely challenging with these methods.PCR-based methods are usually low-throughput. However, they can be easily used to analyze a small number of transcripts. The GI-tailing method is one of them.With this method, we discovered that Dscam mRNAs contain short poly-A tails. Dscam is a neuronal cell adhesion molecule. It is involved in many important neurodevelopmental processes.Because Dscam mRNA contains short poly-A tails unlike most mRNAs, Dscam mRNA translation is under unique gene regulation, which is one of the questions we are trying to answer.

Drosophila 유충 뇌 및 S2 슈나이더 세포에서 총 RNA 추출

먼저, 짧은 원심분리를 통해 절개된 초파리 뇌에서 PBS를 제거합니다. 그런 다음 600마이크로리터의 RNA 용해 완충액을 샘플에 추가하고 플라스틱 유봉으로 10회 균질화합니다. 실체 현미경으로 튜브가 완전히 용해되었는지 검사합니다.섭씨 4도에서 1000G에서 5분 동안 원심분리하여 조직 파편을 제거합니다. 제거된 상층액을 새 미세 원심분리기 튜브로 옮깁니다. 제조업체의 지침에 따라 RNA 마이크로 준비 키트를 사용하여 RNA를 분리합니다.S2 세포의 경우 PBS를 제거하고 RNA를 분리합니다. 260 및 280 나노미터에서 광학 밀도 비율을 측정하여 RNA 순도와 양을 측정합니다. 전기영동을 위해 샘플을 준비하려면 RNA 샘플을 마이크로리터당 40나노그램으로 희석하고 RNA 로딩 염료를 추가합니다.가열 샘플amp섭씨 70도에서 5분 동안 가열합니다. 아가로스 겔에서 RNA ladder와 샘플을 로드합니다. MOPS 버퍼에서 100볼트에서 60분 동안 전기영동을 수행하고 UV 투광기에서 겔을 시각화합니다.아가로스 전기영동에 의한 초파리 유충 뇌에서 분리된 RNA의 시각화는 약 600개의 뉴클레오티드에서 단일 RNA 밴드를 보여주었으며, 이는 온전한 RNA 준비를 나타냅니다.

total-rna-extraction-from-drosophila-larvae-brain-s2-schneider

Research

JoVE Journal

Neuroscience

Total RNA Extraction from Drosophila Larvae Brain and S2 Schneider Cells

134 조회수.  University of Nevada, Reno. 먼저, 짧은 원심분리를 통해 절개된 초파리 뇌에서 PBS를 제거합니다. 그런 다음 600마이크로리터의 RNA 용해 완충액을 샘플에 추가하고 플라스틱 유봉으로 10회 균질화합니다. 실체 현미경으로 튜브가 완전히 용해되었는지 검사합니다.섭씨 4도에서 1000G에서 5분 동안 원심분리하여 조직 파편을 제거합니다. 제거된 상층액을 새 미세 원심분리기 튜브로 옮깁니다. 제조업체?...

비디오: Drosophila 유충 뇌 및 S2 슈나이더 세포에서 총 RNA 추출

Measurement of Poly A Tail Length from Drosophila Larva Brain and Cell Line

Polyadenylation is a crucial posttranscriptional modification that adds poly(A) tails to the 3' end of mRNA molecules. The length of the poly(A) tail is tightly regulated by cellular processes. Dysregulation of mRNA polyadenylation has been associated with abnormal gene expression and various diseases, including cancer, neurological disorders, and developmental abnormalities. Therefore, comprehending the dynamics of polyadenylation is vital for unraveling the complexities of mRNA processing and posttranscriptional gene regulation. 
This paper presents a method for measuring poly(A) tail lengths in RNA samples isolated from Drosophila larval brains and Drosophila Schneider S2 cells. We employed the guanosine/inosine (G/I) tailing approach, which involves the enzymatic addition of G/I residues at the 3' end of mRNA using yeast poly(A) polymerase. This modification protects the RNA's 3' end from enzymatic degradation. The protected full-length poly(A) tails are then reverse-transcribed using a universal antisense primer. Subsequently, PCR amplification is performed using a gene-specific oligo that targets the gene of interest, along with a universal sequence oligo used for reverse transcription. 
This generates PCR products encompassing the poly(A) tails of the gene of interest. Since polyadenylation is not a uniform modification and results in tails of varying lengths, the PCR products display a range of sizes, leading to a smear pattern on agarose gel. Finally, the PCR products are subjected to high-resolution capillary gel electrophoresis, followed by quantification using the sizes of the poly(A) PCR products and the gene-specific PCR product. This technique offers a straightforward and reliable tool for analyzing poly(A) tail lengths, enabling us to gain deeper insights into the intricate mechanisms governing mRNA regulation.

The protocol describes an efficient and reliable method for quantifying the poly(A) length of the gene of interest from the Drosophila nervous system, which can be easily adapted to tissues or cell types from other species.

Polyadenylation is a crucial posttranscriptional modification that adds poly(A) tails to the 3' end of mRNA molecules. The length of the poly(A) tail is ...