도움을 청하기 위해 Karyn Esser, Nobuya Koike, Noeon Park에게 감사드립니다. 이 작품은 부분적으로 NIH / NIGMS (R01GM114424)가 S.-HY에, Robert A. Welch Foundation (AU-1731)과 NIH / NIA (R01AG045828)가 ZC

동물 보호는 기관 동물 관리 및 사용위원회 (IACUC) 지침에 따라 수행되었으며, 절차는 휴스턴에있는 텍사스 보건 과학 센터의 승인을받은 동물 프로토콜에 따라 수행되었습니다. 1. 가교 골격근에서의 핵 분리 <ol><li> 이전에 자세하게 설명 된 바와 같이, 약 20 주령의 C57BL / 6 수컷 마우스에서 단리 된 뒷다리 골격 근육을 체중을 줄이고 빙냉 인산 완충 식염수 (PBS)에서 말린 것. 참고 : 우리는 일반적으로 하나의 마우스에서 1.0 - 1.5 g의 골격근을 얻습니다. <ol><li> 얼음에 10 ML PBS를 포함 50 ML 원추형 튜브에 다진 골격 근육 조직을 놓으십시오. </li></ol></li><li> 4 X에서 300 XG에서 5 분 동안 원심 분리하십시오. </li><li> 조심스럽게 흡인으로 PBS 상등액을 제거합니다. </li><li> 1, 2, 3 및 4 mL의 물을 가진 참조 튜브를 사용하여 각 50 mL 튜브의 펠릿 체적을 측정합니다. </li><li> 7 권 추가빙냉 된 1 % 포름 알데히드를 PBS에 넣고 프로브 조직 균질기를 사용하여 얼음 위에서 시료를 균질화합니다 ( 표 2 참조). 참고 : 선택 사항 : 균질화 절차는 차가운 방에서 수행 할 수 있습니다. </li><li> 실온에서 10 분간 배양하여 샘플을 교차 결합시킨다. </li><li> 1 M 글리신을 0.125 M의 최종 농도로 첨가하여 가교 결합 반응을 켄 칭하고 실온에서 5 분 동안 배양한다. </li><li> 4 ° C에서 5 분 동안 3,000 xg에서 샘플을 원심 분리하십시오. 포부를 통해 상징액을 제거하십시오. </li><li> 새로 첨가 된 프로 테아 제 억제제 (0.2 mM 페닐 메틸 술 포닐 플루오 라이드 (PMSF))를 함유하는 얼음 - 차가운 염기 완충액 (pH 7.3의 10 mM HEPES-KOH, 10 mM EDTA, 10 mM KCl, 5 mM MgCl2, 0.5 mM DTT) , 및 10 μg / mL leupeptin). 4 ℃에서 5 분간 3,000 g으로 원심 분리하고주의 깊게 흡인에 의해 상등액을 제거한다. </li><li> 6 ML의 용해 버퍼 (10 MM HEPES-KOH에서 p에서 펠렛을 Resuspend새로 첨가 된 프로테아제 억제제 (0.2 mM PMSF, 10 μg / mL leupeptin)가 포함 된 2 차 항체 (H 7.3, 10 mM EDTA, 10 mM KCl, 5 mM MgCl 2 , 0.5 mM DTT, 1 % Triton X- </li><li> prechilled 15 ML Dounce 호모 제 나이저에 샘플을 전송하고 얼음에 10 분 동안 품어. 핵을 해제하기 위해 꽉 유봉과 15 스트로크 다음 느슨한 유봉을 사용하여 15 슬로우 스트로크와 얼음에 각 샘플을 균질. </li><li> 셀 스트레이너 (기공 크기 : 100 μm)를 통해 균질 액 (6 mL)을 여과하고 4 mL의 용해 완충액으로 헹구십시오. 4 ° C에서 10 분 동안 1,000 xg에서 샘플을 원심 분리하십시오. 얼음처럼 차가운 염기 완충액 5 mL에 Resuspend하고 단단한 유봉으로 핵을 방출하기 위해 10 회 dounce합니다. <ol><li> 분광 광도계 (OD260 / OD280)로 DNA 농도 측정을 위해 20 μL의 분취 량을 제거하고 필요한 경우 트리 판 블루로 현미경으로 관찰합니다 (아래 참조) ( 그림 1A ). </li></ol></li><li> 서스펜션을 통해 필터링셀 스트레이너 (기공 크기 : 70 μm), 튜브를 헹구고 상기와 같이 2 mL베이스 완충액으로 다시 여과한다. </li><li> 점차적으로 감소 된 구멍 크기 (40 μm, 30 μm, 20 μm 및 10 μm)의 세포 여과기로 단계 1.13 에서처럼 여과를 반복하십시오. 참고 : 총 6 개의 구멍 크기의 여과기가 1.12-1.14 단계에서 사용되었습니다. </li><li> 4 ℃에서 1,000g에서 10 분간 원심 분리한다. 뜨는을 제거하고 500 μL 기본 버퍼에서 펠렛을 resuspend. </li><li> 위와 같이 DNA 농도를 측정하십시오. 참고 : 한 동물의 두 가지 뒷다리를 결합하여 약 200 μg의 핵 DNA를 얻었습니다. 선택적으로 트리 판 블루 얼룩 (재고 농도 0.4 %, 1시 5 분 희석)과 현미경 관찰 20 μL 저장; 핵은 파란색으로 얼룩지게됩니다 ( 그림 1B ). </li><li> 4 ℃에서 1,000g에서 10 분간 원심 분리하고 상등액을 버린다. -80 ° C에 저장 펠렛. </li></ol> 2. 초음파 처리 &lt;ol&gt; <li> SDS 용해 버퍼 500 μL에서 샘플을 해동하고 부드러운 pipetting와 resuspend. </li><li> 얼음에 유리 바이알에 핵 DNA 현탁액을 전송합니다. </li><li> 접시 모양의 변환기에서 초음파 음향 에너지의 초점을 맞춘 버스트로 초음파 처리를 실행하십시오. 장비 세부 사항은 표 자료 를 참조하십시오. 다음 설정을 사용하십시오 : 버스트 당 사이클 : 200; 강도 : 5; 듀티 사이클 : 20; 온도 4 - 6 ° C; 30 초 온 / 오프. 참고 : sonication 효능을 평가하는 예제가 그림 2에 나와 있습니다. </li><li> sonicated 염색질을 1.5 ML 튜브로 전송하십시오. 15 분 12,000 XG에서 원심 분리기 및 새로운 튜브로 뜨는을 전송하십시오. 65 ° C에서 하룻밤 역방향 crosslinking위한 새로운 1.5 ML 튜브에 sonicated 샘플 (~ 7-10 μg / 근육 샘플) 50 μL를 전송합니다. -80 ° C에서 나머지 샘플을 고정 시키십시오. </li></ol> 3. 초음파 및 정량 평가 <ol><li> 1.0 추가보존 50 μL sonicated 샘플에 RNase A (500 U / ML RNase A : 20,000 U / ML RNase T1) μL과 37에서 30 분 품어 ° C. </li><li> 프로 테아 제 K (10 MG / ML) 8 μL를 추가하고 55에서 30 분 품어 ° C. </li><li> DNA 추출 키트를 사용하여 DNA를 수확하십시오. <ol><li> 결합 버퍼 5 부피를 추가하고이를 회전 컬럼에 가하고 4,000 xg, 10 분간 원심 분리한다. </li><li> 패스 스루를 같은 컬럼에 넣고 다시 원심 분리하십시오. </li><li> 13,000 xg, 1 분에 2 회 세척 완충액으로 씻으십시오. </li><li> 13,000 xg, 1 분에 다시 원심 분리하여 컬럼을 건조시킨다. </li><li> H 2 O 50 μL를 넣고 13,000 xg에서 1 분간 원심 분리하여 DNA를 용리한다. </li><li> 패스 스루를 같은 컬럼에 넣고 다시 원심 분리하십시오. </li></ol></li><li> 분광 광도계 (OD260 / OD280)로 DNA 양을 정량하십시오. 초음파 처리 된 제품 ( 그림 2 )의 크기와 양 (1 μg)을 평가하기 위해 0.8 % 젤에서 샘플을 실행하십시오. 참고 : 평균 염색질 수율은 약 ~ 20 %입니다. </li></ol> 4. 칩 <ol><li> 이전에 저장된 염색질을 -80 ° C에서 녹이고 튜브 당 ~ 100 - 120 μg로 염색질을 분액합니다. 방사 면역 침전 분석 (RIPA) 버퍼 (20mM 트리스 -HCl (pH 7.4), 150mM NaCl, 1mM EDTA, 1mM NaF, 1mM Na3VO4, 1mM PMSF, 1x 프로테아제 억제제 칵테일 (PIC), 0.1 % Na- 데 옥시 콜레이트 w / v), 1 % 트리톤 X-100). <ol><li> 각 그룹에 여러 개의 샘플이있는 경우, 같은 양의 염색질 DNA를 ~ 100 - 120 μg / sample의 최종 양으로 합치십시오. 10 %를 입력으로 저장하십시오. </li></ol></li><li> BSA 사전 차단 (~ 2 시간, 4 ° C) 단백질 A / G 아가로 오스 (비 치킨 항체) 또는 IgY 비드 (치킨 항체) 40 μL (RIPA 완충액에 50 % v / v 슬러리)를 첨가하고 4 ° C에서 3 시간 동안 회전기. </li><li> 1,000 xg, 10 분에서 원심 분리기로 신중하게 상청액을 새 튜브로 옮긴다. </li><li> ~ 1 μg 항체 당 항체를 ~25 - 100 μg 염색질 DNA. </li><li> 4 ° C에서 약 15 rpm으로 하룻밤 부드럽게 회전시킨다. </li><li> BSA - 사전 차단 (~ 2 H, 4 ° C) 단백질 A / G 아가로 오스 (비 치킨 항체) 또는 IgY 구슬 (치킨 항체) 믹스 10 μL를 추가하고 차가운 방에서 2 시간 동안 회전합니다. </li><li> 구슬을 다음과 같이 씻으십시오. RIPA 완충액 1 mL 씩으로 2 회 3 분간 씻고 고염 완충액 (20 mM Tris-HCl (pH 7.4), 500 mM NaCl, 2 mM EDTA, 1 mM PMSF, 1 % Triton X-100) 1 분간 LiCl 완충액 (20mM Tris-HCl (pH 7.4), 250mM LiCl, 2mM EDTA, 1mM PMSF, 1 % Na- 데 옥시 콜레이트, 0.5 % NP40)로 3 분간 두 번 씻는다. <ol><li> 1 분간 Tris-EDTA (TE) 완충액 (10mM Tris-HCl (pH 7.4), 1mM EDTA)으로 3 분간 씻는다. 그런 다음 용리 완충액 (20 mM Tris-HCl, 5 mM EDTA 및 0.5 % SDS)으로 DNA를 용리한다. </li></ol></li><li> 1,000 g에서 1 분간 원심 분리하고 조심스럽게 상층 액을 제거한다. </li><li> 용리 버퍼 50 μL로 비드를 Resuspend. </li><li> 10 시간 동안 품어 라.65 ℃에서 분. </li><li> 5 분 동안 12,000 g에서 원심 분리하십시오. </li><li> 새 튜브에 뜨는을 전송, 또 다른 50 μL를 추가하고 5 분 12,000 g에 다시 한번 원심 분리기. 최종 용리 부피는 100 μL입니다. </li><li> 역 가교 결합 및 DNA 용리. <ol><li> 65 ° C에서 밤새 용리 된 염색질을 배양한다. </li><li> 37 ℃에서 30 분 동안 배양하고 RNase A 1.0 μL를 첨가한다. </li><li> 프로 테아 제 K (10 MG / ML) 8 μL를 추가하고 55에서 30 분 품어 ° C. </li><li> 제조 업체의 프로토콜에 따라 50 μL에서 용출 볼륨과 PCR 청소 키트를 사용하여 DNA를 수확. </li></ol></li><li> 이전에 설명한대로 실시간 qPCR로 프로파일을 분석하십시오 25 , 26 . 참고 : 프라이머 서열은 그림 3 범례에 나와 있습니다. 데이터는 평균 ± SEM으로 표시됩니다 ( 그림 3 ). </li></ol>

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E., Ahima, R. S., Greenbaum, L. E., Kaestner, K. H. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Foxa2+integrates+the+transcriptional+response+of+the+hepatocyte+to+fasting.">Foxa2 integrates the transcriptional response of the hepatocyte to fasting.</a> Cell Metab. 2 (2), 141-148 (2005).</li><li>Gade, P., Kalvakolanu, D. V. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Chromatin+immunoprecipitation+assay+as+a+tool+for+analyzing+transcription+factor+activity.">Chromatin immunoprecipitation assay as a tool for analyzing transcription factor activity.</a> Methods Mol Biol. 809, 85-104 (2012).</li><li>Kondratov, R. V., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=BMAL1-dependent+circadian+oscillation+of+nuclear+CLOCK:+posttranslational+events+induced+by+dimerization+of+transcriptional+activators+of+the+mammalian+clock+system.">BMAL1-dependent circadian oscillation of nuclear CLOCK: posttranslational events induced by dimerization of transcriptional activators of the mammalian clock system.</a> Genes Dev. 17 (15), 1921-1932 (2003).</li><li>Ripperger, J. A., Schibler, U. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Rhythmic+CLOCK-BMAL1+binding+to+multiple+E-box+motifs+drives+circadian+Dbp+transcription+and+chromatin+transitions.">Rhythmic CLOCK-BMAL1 binding to multiple E-box motifs drives circadian Dbp transcription and chromatin transitions.</a> Nat Genet. 38 (3), 369-374 (2006).</li><li>Laplante, M., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=DEPTOR+cell-autonomously+promotes+adipogenesis,+and+its+expression+is+associated+with+obesity.">DEPTOR cell-autonomously promotes adipogenesis, and its expression is associated with obesity.</a> Cell Metab. 16 (2), 202-212 (2012).</li><li>Blechman, J., Amir-Zilberstein, L., Gutnick, A., Ben-Dor, S., Levkowitz, G. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=The+metabolic+regulator+PGC-1alpha+directly+controls+the+expression+of+the+hypothalamic+neuropeptide+oxytocin.">The metabolic regulator PGC-1alpha directly controls the expression of the hypothalamic neuropeptide oxytocin.</a> J Neurosci. 31 (42), 14835-14840 (2011).</li></ol>

저자는 공개 할 것이 없습니다.

여기서 우리는 가교 결합 된 골격 근육 조직이 고품질의 핵을 분리하는 데 사용되는 견고한 방법을 설명합니다. 순차적 인 여과가 파편으로부터 핵을 효과적으로 분리하기 위해 수행되었고, 접시 형 변환기의 초음파 음향 에너지가 ChIP 분석을 위해 염색질을 전단했다. 그 결과는 표적 프로모터에 BMAL1의 24 시간 특정 결합을 보여 주었다. ChIP는 가교 결합이 일어날 때 게놈 DNA?...

골격근은 생리학 및 행동에 중요한 역할을합니다. 다핵 근섬유는 액틴과 미오신이 수축력을 생성하는 근육 절개 (sarcomeres)라고 불리는 기능 단위를 형성하는 근원 섬유 (myofibrils)로 구성됩니다. 골격근은 체내에서 가장 큰 대사 기관이기도하며, 식후 80 %를 초과하는 포도당 섭취량과 인슐린 반응과 대사 항상성을 조절합니다 1 , 2 . 근육 생리와 신진 대사는 24 시간 내내 시계에 의해 밀접하게 조절되며, 본질적인 생물학적 타이머 인 3 , 4 , 5 , 6 . 예를 들어, 생체 시계 핵심 구성 요소 중 하나 인 Bmal1 의 골격 근육 특이 적 결실은 인슐린 저항성을 초래하고 골격근에서의 포도당 섭취를 감소 시켰으며 동물은 제 2 형 당뇨병을 발생시키는 것으로 밝혀졌습니다. 나는또한 골격근은 전신 대사 및 생리를 조절하기 위해 myokines를 분비하는 내분비 기관으로 점차 인식되고 있습니다. 골격근에서의 이러한 조절 기능을 완전히 이해하려면 역학 연구가 필요합니다. ChIP는 DNA 결합 단백질의 프로모터 모집을 묘사하는 강력한 접근법입니다. ChIP는 처음에 염색질 DNA 9 , 10 에서 뉴 클레오 솜 조직을 확인하기 위해 개발되었습니다. 포름 알데히드, 디메틸 설페이트 또는 자외선 조사 (UV) 11,12를 사용하여 다양한 방법으로 단백질과 염색질 DNA를 가교 결합시키는 것으로보고되었습니다. 포름 알데히드 교차 결합은 가장 일반적으로 사용되는 것으로, 염색질 구조와 DNA- 단백질 상호 작용을 보존합니다 9 , 13 , 14 . 교차 결합 크로마토 그래피in은 sonication에 의해 파쇄되고 관심의 특정 DNA 결합 단백질 15 , 16 에 대한 항체와 immunoprecipitated입니다. 최근 몇 년 동안 ChIP와 NGS가 결합 된 ChIP-sequencing (ChIP-seq)이 게놈 차원의 전사 인자 바인딩 17 을 조사하고 경우에 따라 시간 경과에 따른 동적 변화를 모니터링하기 위해 개발되었습니다 18 , 19 , 20 . 예를 들어 circadian ChIP-seq 연구는 circadian clock 구성 요소와 히스톤 마커의 게놈 결합의 고도로 조율 ​​된 서열을 밝혀 냈습니다.이 마커는 ~ 24 시간 circadian cycle 18 동안 일시적으로 정확한 유전자 발현을 유도합니다. 가장 많이 사용되는 ChIP 프로토콜은 연조직 ( 예 : 간, 뇌 등 ) 용으로 설계되었으며, 골격활 근육. 섬유가 풍부한 골격근을 균질화하고 고품질 핵 21을 분리하는 것은 기술적으로 어렵습니다. 특히 교차 결합이 필요한 ChIP 실험의 경우 더욱 그렇습니다. 최근 근육 ChIP 연구 22에서 , 위성 세포는 근섬유로부터 분리되었고, 핵은 조직 소화를 포함하는 장기간의 절차를 통해 양 세포 유형으로부터 준비되었다. 격리 된 핵에서 포름 알데히드 가교 결합을 수행하기까지 전체 공정을 완료하는 데 약 3 시간이 걸렸습니다. 이 절차로 인해 근육 조직이 근육 조직을 효율적으로 균질화되지 못하도록 만들었으며 고품질의 핵을 생성 할 수 있었지만 조직 수집에서 핵 가교로의 상당한 시간 지연으로 인해 DNA가 변경 될 위험이 있습니다 - 단백질 상호 작용. 대조적으로, 대부분의 연구는 실시간 DNA-protei를 보존하기 위해 실험적 치료 또는 조직 수집 직후 가교 결합을 수행했다바인딩 12 . 가교 결합 이전의 핵 분리의 두 번째 단점은 전형적으로 3 ~ 4 시간 간격으로 발생하는 24 시간 샘플 수집과 같이 시간에 민감한 애플리케이션을 배제한다는 점입니다. 핵을 가교 결합시키지 않으면 절개 직후에 분리가 진행되어야하며, 시간이 경과 된 후에 가교 샘플을 함께 처리 할 수 ​​있으므로 실험 일관성이 향상됩니다. 미가공 골격근으로부터의 핵 분리에 대한 다른 프로토콜도보고되었다. 두 개의 연구는 잔류 근원 섬유 및 세포 잔해로부터 핵을 분리하기위한 구배 초 원심 분리의 사용을 기술하고있다 23 , 24 . 수크로오스 또는 콜로이드 성 구배 초 원심 분리가 미가 교 근육 조직에 효과적이지만, 본 발명자들의 실험에 의하면 가교 결합 후 구배 초 원심 분리가 세포를 세포로부터 분리 시키는데 실패했다그라디언트에 ebris. 따라서 우리는 가교 된 마우스 골격 근육 조직을 이용하여 고품질의 핵을 분리하는 절차를 개발했습니다. 그라디언트 초 원심 분리보다는 핵을 파편과 효과적으로 분리하기 위해 연속 여과 방식을 고안했습니다. 초음파 처리 후, 염색질 샘플은 표적 프로모터에 결합하는 BMAL1 단백질의 일주기 패턴을 나타내는 ChIP 연구에 성공적으로 적용되었다. 우리의 방법은 근육 조직에 대한 다양한 기계 연구에 광범위하게 적용될 수 있습니다.

<table border="0" cellpadding="0" cellspacing="0" width="765">
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		<tr height="20">
			<td height="20" style="height:20px;width:216px;">Materials</td>
			<td style="width:143px;"></td>
			<td style="width:119px;"></td>
			<td style="width:288px;"></td>
		</tr>
		<tr height="20">
			<td height="20" style="height:20px;width:216px;">Formaldehyde solution</td>
			<td style="width:143px;">Sigma Aldrich</td>
			<td style="width:119px;">F8775&#160;</td>
			<td></td>
		</tr>
		<tr height="20">
			<td height="20" style="height:20px;width:216px;">Glycine</td>
			<td style="width:143px;">Fisher Scientific</td>
			<td style="width:119px;">BP381-5</td>
			<td></td>
		</tr>
		<tr height="20">
			<td height="20" style="height:20px;width:216px;">Trypan Blue solution (0.4%)</td>
			<td style="width:143px;">Fisher Scientific</td>
			<td style="width:119px;">15250061</td>
			<td></td>
		</tr>
		<tr height="20">
			<td height="20" style="height:20px;width:216px;">RNase A</td>
			<td style="width:143px;">Sigma Aldrich</td>
			<td style="width:119px;">10109142001</td>
			<td></td>
		</tr>
		<tr height="20">
			<td height="20" style="height:20px;width:216px;">Protease K</td>
			<td style="width:143px;">Sigma Aldrich</td>
			<td style="width:119px;">3115887001</td>
			<td></td>
		</tr>
		<tr height="57">
			<td height="57" style="height:57px;width:216px;">Chicken Anti-BMAL1 antibody</td>
			<td style="width:143px;"></td>
			<td style="width:119px;"></td>
			<td style="width:288px;">Generated in chicken (Cocalico Biologicals) against antigen aa 318-579, and IgY was affinity purified using the same antigen.&#160;</td>
		</tr>
		<tr height="20">
			<td height="20" style="height:20px;width:216px;">Chicken IgY Precipitating Resin</td>
			<td style="width:143px;">GenScript</td>
			<td style="width:119px;">L00405</td>
			<td></td>
		</tr>
		<tr height="20">
			<td height="20" style="height:20px;width:216px;"></td>
			<td style="width:143px;"></td>
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			<td height="20" style="height:20px;width:216px;">Equipment</td>
			<td style="width:143px;"></td>
			<td style="width:119px;"></td>
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		</tr>
		<tr height="38">
			<td height="38" style="height:38px;width:216px;">KINEMATICA&#160;Polytron PT2100 Benchtop Homogenizer</td>
			<td style="width:143px;">Fisher Scientific</td>
			<td style="width:119px;">08-451-178</td>
			<td></td>
		</tr>
		<tr height="20">
			<td height="20" style="height:20px;width:216px;">15mL Dounce tissue grinder</td>
			<td style="width:143px;">Whearton</td>
			<td style="width:119px;">357544</td>
			<td></td>
		</tr>
		<tr height="20">
			<td height="20" style="height:20px;width:216px;">Falcon Cell Strainers 100&#181;m</td>
			<td style="width:143px;">Fisher Scientific</td>
			<td style="width:119px;">08-771-19</td>
			<td></td>
		</tr>
		<tr height="20">
			<td height="20" style="height:20px;width:216px;">Falcon Cell Strainers 70&#181;m</td>
			<td style="width:143px;">Fisher Scientific</td>
			<td style="width:119px;">08-771-1</td>
			<td></td>
		</tr>
		<tr height="20">
			<td height="20" style="height:20px;width:216px;">Falcon Cell Strainers 40&#181;m</td>
			<td style="width:143px;">Fisher Scientific</td>
			<td style="width:119px;">08-771-2</td>
			<td></td>
		</tr>
		<tr height="20">
			<td height="20" style="height:20px;width:216px;">pluriStrainer 30 &#181;m</td>
			<td style="width:143px;">PluriSelect</td>
			<td style="width:119px;">43-50030-03</td>
			<td></td>
		</tr>
		<tr height="20">
			<td height="20" style="height:20px;width:216px;">pluriStrainer 20 &#181;m</td>
			<td style="width:143px;">PluriSelect</td>
			<td style="width:119px;">43-50020-03</td>
			<td></td>
		</tr>
		<tr height="20">
			<td height="20" style="height:20px;width:216px;">pluriStrainer 10 &#181;m</td>
			<td style="width:143px;">PluriSelect</td>
			<td style="width:119px;">43-50010-03</td>
			<td></td>
		</tr>
		<tr height="38">
			<td height="38" style="height:38px;width:216px;">Covaris S2 Focused-ultrasonicator</td>
			<td style="width:143px;">Covaris</td>
			<td style="width:119px;">Model S2</td>
			<td></td>
		</tr>
		<tr height="20">
			<td height="20" style="height:20px;">Labquake&#160;</td>
			<td>Thermo Scientific</td>
			<td>C415110</td>
			<td></td>
		</tr>
		<tr height="20">
			<td height="20" style="height:20px;">CCD Microscope Camera</td>
			<td>&#160;Leica Microsystems</td>
			<td>DFC3000 G</td>
			<td></td>
		</tr>
		<tr height="20">
			<td height="20" style="height:20px;width:216px;"></td>
			<td style="width:143px;"></td>
			<td style="width:119px;"></td>
			<td></td>
		</tr>
		<tr height="20">
			<td height="20" style="height:20px;width:216px;">Reagent Kit</td>
			<td style="width:143px;"></td>
			<td style="width:119px;"></td>
			<td></td>
		</tr>
		<tr height="20">
			<td height="20" style="height:20px;width:216px;">DNA extraction kit</td>
			<td style="width:143px;">Thermo Scientific</td>
			<td style="width:119px;">K0691</td>
			<td></td>
		</tr>
		<tr height="20">
			<td height="20" style="height:20px;width:216px;"></td>
			<td style="width:143px;"></td>
			<td style="width:119px;"></td>
			<td></td>
		</tr>
		<tr height="20">
			<td height="20" style="height:20px;width:216px;">Buffers</td>
			<td style="width:143px;"></td>
			<td style="width:119px;"></td>
			<td></td>
		</tr>
		<tr height="76">
			<td height="76" style="height:76px;width:216px;">All buffer components are discribed in the protocol. Each component was purchased from Sigma Aldrich</td>
			<td style="width:143px;"></td>
			<td style="width:119px;"></td>
			<td></td>
		</tr>
	</tbody>
</table>

a filtration-based method of preparing high-quality nuclei from cross-linked skeletal muscle for chromatin immunoprecipitation

Chromatin immunoprecipitation (ChIP)은 염색질 DNA에 결합하는 단백질을 결정하는 강력한 방법입니다. 그러나, 섬유가 풍부한 골격근은 근원 섬유의 오염을 최소화하면서 고품질의 핵을 분리하는 기술적 어려움으로 인해 ChIP에 대한 도전 과제였습니다. 이전의 프로토콜은 가교 결합 전에 핵을 정제하려고 시도했는데, 이는 연장 된 핵 준비 과정 동안 DNA- 단백질 상호 작용의 변화를 초래할 위험이있다. 현재의 프로토콜에서, 우리는 먼저 쥐에서 수집 한 골격 근육 조직을 교차 결합시키고, 조직을 다듬고 초음파 처리 하였다. 우리는 초 원심 분리가 교차 결합 된 근육 조직을 사용하여 근원 섬유에서 핵을 분리 할 수 ​​없다는 것을 발견했기 때문에 중요한 근섬유 오염이없는 고품질의 핵을 얻기 위해 순차 여과 절차를 고안했습니다. 우리는 초음파 장비를 사용하여 염색질을 준비하고, 항 -BALAL1 항체로 ChIP 분석을 실시하여 강력한 일사 항 결합유전자 발기인을 표적으로하는 BMAL1의 패턴. 이 여과 프로토콜은 cross-linked 골격근 조직으로부터 고품질의 핵을 분리하는 데 쉽게 적용 할 수있는 방법으로, 일주기 및 기타 시간에 민감한 연구에 일관된 시료 처리가 가능합니다. 차세대 시퀀싱 (NGS)과 함께, 우리의 방법은 골격 근육 기능에 초점을 맞춘 다양한 기계 및 게놈 연구를 위해 배치 될 수 있습니다.

여기에서는 실시간 DNA- 단백질 상호 작용을 보존하기 위해 조직 수집 직후에 포름 알데히드 가교 결합을 수행했습니다. 그러나, 우리는 핵 분리 23 , 24에 일반적으로 사용되는 자당이나 콜로이드 그라디언트가 근원 섬유에서 핵을 분리하는 데 효과적이지 않음을 발견했습니다 (데이터는 표시되지 않음). 그 이유는 교차 결합이 ?...

Watch this Scientific Journal Video about A Filtration-based Method of Preparing High-quality Nuclei from Cross-linked Skeletal Muscle for Chromatin Immunoprecipitation at JoVE.com

A Filtration-based Method of Preparing High-quality Nuclei from Cross-linked Skeletal Muscle for Chromatin Immunoprecipitation

우리는 cross-linked 마우스 골격근으로부터 고품질의 핵을 분리하기위한 여과 기반의 프로토콜을 제시했습니다. 우리는 초 원심 분리의 필요성을 제거하여 쉽게 적용 할 수있게했습니다. 우리는 핵에서 준비한 염색질이 염색질 면역 침전 및 염색질 면역 침전 시퀀싱 연구에 적합 함을 보여줍니다.

Chromatin Immunoprecipitation을위한 Cross-linked Skeletal Musculus로부터 고품질 핵을 준비하기위한 Filtration 기반 방법

Chromatin immunoprecipitation (ChIP) is a powerful method to determine protein binding to chromatin DNA. Fiber-rich skeletal muscle, however, has been a ...

a-filtration-based-method-preparing-high-quality-nuclei-from-cross

Universidad de Cartagena UDEC

Research

JoVE Journal

Biochemistry

8.8K 조회수.  University of Texas Health Science Center at Houston.  우리는 cross-linked 마우스 골격근으로부터 고품질의 핵을 분리하기위한 여과 기반의 프로토콜을 제시했습니다. 우리는 초 원심 분리의 필요성을 제거하여 쉽게 적용 할 수있게했습니다. 우리는 핵에서 준비한 염색질이 염색질 면역 침전 및 염색질 면역 침전 시퀀싱 연구에 적합 함을 보여줍니다. 

비디오: A Filtration-based Method of Preparing High-quality Nuclei from Cross-linked Skeletal Muscle for Chromatin Immunoprecipitation

A Facile and Efficient Approach for the Production of Reversible Disulfide Cross-linked Micelles

Nanomedicine is an emerging form of therapy that harnesses the unique properties of particles that are nanometers in scale for biomedical application. Improving drug delivery to maximize therapeutic outcomes and to reduce drug-associated side effects are some of the cornerstones of present-day nanomedicine. Nanoparticles in particular have found a wide application in cancer treatment. Nanoparticles that offer a high degree of flexibility in design, application, and production based on the tumor microenvironment are projected to be more effective with rapid translation into clinical practice. The polymeric micellar nano-carrier is a popular choice for drug delivery applications.
In this article, we describe a simple and effective protocol for synthesizing drug-loaded, disulfide cross-linked micelles based on the self-assembly of a well-defined amphiphilic linear-dendritic copolymer (telodendrimer, TD). TD is composed of polyethylene glycol (PEG) as the hydrophilic segment and a thiolated cholic acid cluster as the core-forming hydrophobic moiety attached stepwise to an amine-terminated PEG using solution-based peptide chemistry. Chemotherapy drugs, such as paclitaxel (PTX), can be loaded using a standard solvent evaporation method. The O2-mediated oxidation was previously utilized to form intra-micellar disulfide cross-links from free thiol groups on the TDs. However, the reaction was slow and not feasible for large-scale production. Recently, an H2O2-mediated oxidation method was explored as a more feasible and efficient approach, and it was 96 times faster than the previously reported method. Using this approach, 50 g of PTX-loaded, disulfide cross-linked nanoparticles have been successfully produced with narrow particle size distribution and high drug loading efficiency. The stability of the resulting micelle solution is analyzed using disrupting conditions such as co-incubation with a detergent, sodium dodecyl sulfate, with or without a reducing agent. The drug-loaded, disulfide cross-linked micelles demonstrated less hemolytic activity when compared to their non-cross-linked counterparts.

To deliver cancer drugs to tumor sites with high specificity and reduced side effects, new methods based on nanoparticles are required. Here, we describe disulfide cross-linked micelles that can be easily prepared by hydrogen peroxide-mediated oxidation and are able to dissociate efficiently under a reducing tumor environment to release payloads.

가역 디설파이드 가교 미셀 제조를위한 손쉬운 효율적인 접근법

Nanomedicine is an emerging form of therapy that harnesses the unique properties of particles that are nanometers in scale for biomedical application. ...

연구

생화학

An Efficient Method for the Isolation of Highly Purified RNA from Seeds for Use in Quantitative Transcriptome Analysis

Plant seeds accumulate large amounts of storage reserves comprising biodegradable organic matter. Humans rely on seed storage reserves for food and as industrial materials. Gene expression profiles are powerful tools for investigating metabolic regulation in plant cells. Therefore, detailed, accurate gene expression profiles during seed development are required for crop breeding. Acquiring highly purified RNA is essential for producing these profiles. Efficient methods are needed to isolate highly purified RNA from seeds. Here, we describe a method for isolating RNA from seeds containing large amounts of oils, proteins, and polyphenols, which have inhibitory effects on high-purity RNA isolation. Our method enables highly purified RNA to be obtained from seeds without the use of phenol, chloroform, or additional processes for RNA purification. This method is applicable to Arabidopsis, rapeseed, and soybean seeds. Our method will be useful for monitoring the expression patterns of low level transcripts in developing and mature seeds.

We have succeeded in establishing a method for RNA isolation from plant seeds containing large amounts of oils, proteins, and polyphenols, which have inhibitory effects on high-purity RNA isolation. Our method is suitable for monitoring the expression of genes with low level transcripts in seeds.

양 사체 (Transcriptome) 분석에있는 사용을위한 씨앗에서 매우 정제 된 RNA의 분리를위한 효율적인 방법

Plant seeds accumulate large amounts of storage reserves comprising biodegradable organic matter. Humans rely on seed storage reserves for food and as ...

A Simple Fractionated Extraction Method for the Comprehensive Analysis of Metabolites, Lipids, and Proteins from a Single Sample

Understanding of complex biological systems requires the measurement, analysis and integration of multiple compound classes of the living cell, usually determined by transcriptomic, proteomic, metabolomics and lipidomic measurements. In this protocol, we introduce a simple method for the reproducible extraction of metabolites, lipids and proteins from biological tissues using a single aliquot per sample. The extraction method is based on a methyl tert-butyl ether: methanol: water system for liquid: liquid partitioning of hydrophobic and polar metabolites into two immiscible phases along with the precipitation of proteins and other macromolecules as a solid pellet. This method, therefore, provides three different fractions of specific molecular composition, which are fully compatible with common high throughput 'omics' technologies such as liquid chromatography (LC) or gas chromatography (GC) coupled to mass spectrometers. Even though the method was initially developed for the analysis of different plant tissue samples, it has proved to be fully compatible for the extraction and analysis of biological samples from systems as diverse as algae, insects, and mammalian tissues and cell cultures.

A protocol for comprehensive extraction of lipids, metabolites and proteins from biological tissues using one sample is presented.

단일 시료의 대사 산물, 지질 및 단백질의 종합 분석을위한 간단한 분취 추출 방법

Understanding of complex biological systems requires the measurement, analysis and integration of multiple compound classes of the living cell, usually ...

Improved Protocol for Chromatin Immunoprecipitation from Mouse Skeletal Muscle

We describe an efficient and reproducible protocol for the preparation of chromatin from adult mouse skeletal muscle, a physically resistant tissue with a high content of structural proteins. Dissected limb muscles from adult mice are physically disrupted by mechanical homogenisation, or a combination of mincing and douncing, in a hypotonic buffer before formaldehyde fixation of the cell lysate. The fixed nuclei are purified by further cycles of mechanical homogenisation or douncing and sequential filtrations to remove cell debris. The purified nuclei can be sonicated immediately or at a later stage after freezing. The chromatin can be efficiently sonicated and is suitable for chromatin immunoprecipitation experiments, as illustrated by the profiles obtained for transcription factors, RNA polymerase II, and covalent histone modifications. The binding events detected using chromatin prepared by this protocol are predominantly those taking place in the muscle fiber nuclei despite the presence of chromatin from other fiber-associated satellite and endothelial cells. This protocol is therefore adapted to study gene regulation in the adult mouse skeletal muscle.

A novel protocol for the preparation of chromatin from adult mouse skeletal muscle adapted to the study of gene regulation in muscle fibers by chromatin immunoprecipitation is presented.

마우스 골격 근육에서 Chromatin Immunoprecipitation에 대 한 향상 된 프로토콜

We describe an efficient and reproducible protocol for the preparation of chromatin from adult mouse skeletal muscle, a physically resistant tissue with a ...

Utilizing a Comprehensive Immunoprecipitation Enrichment System to Identify an Endogenous Post-translational Modification Profile for Target Proteins

It is now well-appreciated that post-translational modifications (PTMs) play an integral role in regulating a protein&#39;s structure and function, which may be essential for a given protein&#39;s role both physiologically and pathologically. Enrichment of PTMs is often necessary when investigating the PTM status of a target protein, because PTMs are often transient and relatively low in abundance. Many pitfalls are encountered when enriching for a PTM of a target protein, such as buffer incompatibility, the target protein antibody is not IP-compatible, loss of PTM signal, and others. The degree of difficulty is magnified when investigating multiple PTMs like acetylation, ubiquitination, SUMOylation 2/3, and tyrosine phosphorylation for a given target protein. Studying a combination of these PTMs may be necessary, as crosstalk between PTMs is prevalent and critical for protein regulation. Often, these PTMs are studied in different lysis buffers and with unique inhibitor compositions. To simplify the process, a unique denaturing lysis system was developed that effectively isolates and preserves these four PTMs; thus, enabling investigation of potential crosstalk in a single lysis system. A unique filter system was engineered to remove contaminating genomic DNA from the lysate, which is a problematic by-product of denaturing buffers. Robust affinity matrices targeting each of the four PTMs were developed in concert with the buffer system to maximize the enrichment and detection of the endogenous states of these four PTMs. This comprehensive PTM detection toolset streamlines the process of obtaining critical information about whether a protein is modified by one or more of these PTMs.

Investigating multiple, endogenous post-translational modifications for a target protein can be extremely challenging. Techniques described here utilize an optimized lysis buffer and filter system developed with specific PTM-targeting, affinity matrices to detect the acetylation, ubiquitination, SUMOylation 2/3, and tyrosine phosphorylation modifications for a target protein using a single, streamlined system.

대상 단백질에 대 한 내 생 포스트 번역 상 수정 프로필을 식별 하는 포괄적인 Immunoprecipitation 농축 시스템을 활용 하 여

It is now well-appreciated that post-translational modifications (PTMs) play an integral role in regulating a protein&#39;s structure and function, which ...

Method for Efficient Refolding and Purification of Chemoreceptor Ligand Binding Domain

Identification of natural ligands of chemoreceptors and structural studies aimed at elucidation of the molecular basis of the ligand specificity can be greatly facilitated by the production of milligram amounts of pure, folded ligand binding domains. Attempts to heterologously express periplasmic ligand binding domains of bacterial chemoreceptors in Escherichia coli (E. coli) often result in their targeting into inclusion bodies. Here, a method is presented for protein recovery from inclusion bodies, its refolding and purification, using the periplasmic dCACHE ligand binding domain of Campylobacter jejuni (C. jejuni) chemoreceptor Tlp3 as an example. The approach involves expression of the protein of interest with a cleavable His6-tag, isolation and urea-mediated solubilisation of inclusion bodies, protein refolding by urea depletion, and purification by means of affinity chromatography, followed by tag removal and size-exclusion chromatography. The circular dichroism spectroscopy is used to confirm the folded state of the pure protein. It has been demonstrated that this protocol is generally useful for production of milligram amounts of dCACHE periplasmic ligand binding domains of other bacterial chemoreceptors in a soluble and crystallisable form.

A procedure is presented for the refolding of the dCACHE periplasmic ligand binding domain of Campylobacter jejuni chemoreceptor Tlp3 from inclusion bodies and the purification to yield milligram quantities of protein.

효율적인 Refolding 및 Chemoreceptor Ligand 바인딩 도메인의 정화 방법

Identification of natural ligands of chemoreceptors and structural studies aimed at elucidation of the molecular basis of the ligand specificity can be ...

Activated Cross-linked Agarose for the Rapid Development of Affinity Chromatography Resins - Antibody Capture as a Case Study

The purification of monoclonal antibodies (mAbs) is commonly achieved by Protein A affinity chromatography, which can account for up to 25% of the overall process costs. Alternative, cost-effective capture steps are therefore valuable for industrial-scale manufacturing, where large quantities of a single mAb are produced. Here we present a method for the immobilization of a DsRed-based epitope ligand to a cross-linked agarose resin allowing the selective capture of the HIV-neutralizing antibody 2F5 from crude plant extracts without using Protein A. The linear epitope ELDKWA was first genetically fused to the fluorescent protein DsRed and the fusion protein was expressed in transgenic tobacco (Nicotiana tabacum) plants before purification by immobilized metal-ion affinity chromatography. Furthermore, a method based on activated cross-linked agarose was optimized for high ligand density, efficient coupling and low costs. The pH and buffer composition and the soluble ligand concentration were the most important parameters during the coupling procedure, which was improved using a design-of-experiments approach. The resulting affinity resin was tested for its ability to selectively bind the target mAb in a crude plant extract and the elution buffer was optimized for high mAb recovery, product activity and affinity resin stability. The method can easily be adapted to other antibodies with linear epitopes. The new resins allow gentler elution conditions than Protein A and could also reduce the costs of an initial capture step for mAb production.

In this procedure, a DsRed-based epitope ligand is immobilized to produce a highly selective affinity resin for the capture of monoclonal antibodies from crude plant extracts or cell culture supernatants, as an alternative to Protein A.

선호도 크로마토그래피 수지의 신속한 개발을 위한 활성화된 상호 연결 아가로스 - 사례 연구로서의 항체 포획

The purification of monoclonal antibodies (mAbs) is commonly achieved by Protein A affinity chromatography, which can account for up to 25% of the overall ...

Quantification of Protein Interaction Network Dynamics using Multiplexed Co-Immunoprecipitation

Dynamic protein-protein interactions control cellular behavior, from motility to DNA replication to signal transduction. However, monitoring dynamic interactions among multiple proteins in a protein interaction network is technically difficult. Here, we present a protocol for Quantitative Multiplex Immunoprecipitation (QMI), which allows quantitative assessment of fold changes in protein interactions based on relative fluorescence measurements of Proteins in Shared Complexes detected by Exposed Surface epitopes (PiSCES). In QMI, protein complexes from cell lysates are immunoprecipitated onto microspheres, and then probed with a labeled antibody for a different protein in order to quantify the abundance of PiSCES. Immunoprecipitation antibodies are conjugated to different MagBead spectral regions, which allows a flow cytometer to differentiate multiple parallel immunoprecipitations and simultaneously quantify the amount of probe antibody associated with each. QMI does not require genetic tagging and can be performed using minimal biomaterial compared to other immunoprecipitation methods. QMI can be adapted for any defined group of interacting proteins, and has thus far been used to characterize signaling networks in T cells and neuronal glutamate synapses. Results have led to new hypothesis generation with potential diagnostic and therapeutic applications. This protocol includes instructions to perform QMI, from the initial antibody panel selection through to running assays and analyzing data. The initial assembly of a QMI assay involves screening antibodies to generate a panel, and empirically determining an appropriate lysis buffer. The subsequent reagent preparation includes covalently coupling immunoprecipitation antibodies to MagBeads, and biotinylating probe antibodies so they can be labeled by a streptavidin-conjugated fluorophore. To run the assay, lysate is mixed with MagBeads overnight, and then beads are divided and incubated with different probe antibodies, and then a fluorophore label, and read by flow cytometry. Two statistical tests are performed to identify PiSCES that differ significantly between experimental conditions, and results are visualized using heatmaps or node-edge diagrams.

Quantitative Multiplex Immunoprecipitation (QMI) uses flow cytometry for sensitive detection of differences in the abundance of targeted protein-protein interactions between two samples. QMI can be performed using a small amount of biomaterial, does not require genetically engineered tags, and can be adapted for any previously defined protein interaction network.

멀티플렉스 동시 면역 침전을 이용한 단백질 상호 작용 네트워크 역학의 정량화

Dynamic protein-protein interactions control cellular behavior, from motility to DNA replication to signal transduction. However, monitoring dynamic ...

Preparation of High-Quality Fermented Fish Product

This protocol provides a method for preparation of industrialized fermented fish product with sturgeon (Aquilaria sinensis) meat product. The procedures were: (1) pretreatment of farmed sturgeon including decapitation, evisceration, skinning-off, cleaning and cutting; (2) marinating fish cubes in 6-12% (w/v) salt solution (1:1, fish cube mass to solution volume); (3) drying fish cubes to a water content of 50-60% by hot air (40-60 &#176;C) or by vacuum; (4) fermentation involving inoculating fish cubes with 0.4-1.6% (w/w) S. cerevisiae in flavor solution to fish cubes and fermenting at 25-35 &#176;C for 6-10 h; (5) sealing fish cubes in vacuum packages with marinating and fermenting solutions; (6) sterilizing at 115-121 &#176;C for 10-20 min. The sturgeon meat product prepared by this method has delicious taste which is mellow and thick, has various types and large amounts of volatile flavor compounds such as alcohols and esters which could mask musty and unpleasant odor from fish, has moderate salt content but good texture properties such as high springiness, gumminess and chewiness, and has bright russet color and attractive appearance. This new technique could also be applied in the processing of other fish to provide convenient fish snack foods which could be stored at room temperature. It is appropriate for both marine and freshwater fish.

The goal of the protocol is to provide an industrialized fish fermentation technique based on inoculation of Saccharomyces cerevisiae.

고품질 발효 생선 제품 준비

This protocol provides a method for preparation of industrialized fermented fish product with sturgeon (Aquilaria sinensis) meat product. The procedures ...

Label-Free Immunoprecipitation Mass Spectrometry Workflow for Large-scale Nuclear Interactome Profiling

Immunoaffinity purification mass spectrometry (IP-MS) has emerged as a robust quantitative method of identifying protein-protein interactions. This publication presents a complete interaction proteomics workflow designed for identifying low abundance protein-protein interactions from the nucleus that could also be applied to other subcellular compartments. This workflow includes subcellular fractionation, immunoprecipitation, sample preparation, offline cleanup, single-shot label-free mass spectrometry, and downstream computational analysis and data visualization. Our protocol is optimized for detecting compartmentalized, low abundance interactions that are difficult to identify from whole cell lysates (e.g., transcription factor interactions in the nucleus) by immunoprecipitation of endogenous proteins from fractionated subcellular compartments. The sample preparation pipeline outlined here provides detailed instructions for the preparation of HeLa cell nuclear extract, immunoaffinity purification of endogenous bait protein, and quantitative mass spectrometry analysis. We also discuss methodological considerations for performing large-scale immunoprecipitation in mass spectrometry-based interaction profiling experiments and provide guidelines for evaluating data quality to distinguish true positive protein interactions from nonspecific interactions. This approach is demonstrated here by investigating the nuclear interactome of the CMGC kinase, DYRK1A, a low abundance protein kinase with poorly defined interactions within the nucleus.

Described is a proteomics workflow for identifying protein interaction partners from a nuclear subcellular fraction using immunoaffinity enrichment of a given protein of interest and label-free mass spectrometry. The workflow includes subcellular fractionation, immunoprecipitation, filter aided sample preparation, offline cleanup, mass spectrometry, and a downstream bioinformatics pipeline.

대규모 핵 상호 작용 프로파일링을 위한 라벨 없는 면역 침전 질량 분광 워크플로우

Immunoaffinity purification mass spectrometry (IP-MS) has emerged as a robust quantitative method of identifying protein-protein interactions. This ...