NDLI: Critical Parameters for Efficient Sonication and Improved Chromatin Immunoprecipitation of High Molecular Weight Proteins

Content Provider	PubMed Central
Author	Pchelintsev, Nikolay A. Adams, Peter D. Nelson, David M.
Editor	Min, Wu
Copyright Year	2016
Abstract	Solubilization of cross-linked cells followed by chromatin shearing is essential for successful chromatin immunoprecipitation (ChIP). However, this task, typically accomplished by ultrasound treatment, may often become a pitfall of the process, due to inconsistent results obtained between different experiments under seemingly identical conditions. To address this issue we systematically studied ultrasound-mediated cell lysis and chromatin shearing, identified critical parameters of the process and formulated a generic strategy for rational optimization of ultrasound treatment. We also demonstrated that whereas ultrasound treatment required to shear chromatin to within a range of 100–400 bp typically degrades large proteins, a combination of brief sonication and benzonase digestion allows for the generation of similarly sized chromatin fragments while preserving the integrity of associated proteins. This approach should drastically improve ChIP efficiency for this class of proteins.
Related Links	http://dx.doi.org/10.1371/journal.pone.0148023
Starting Page	148023
File Format	PDF
ISSN	19326203
e-ISSN	19326203
Journal	PLoS ONE
Issue Number	1
Volume Number	11
Language	English
Publisher	Public Library of Science
Publisher Date	2016-01-01
Access Restriction	Open
Rights Holder	Public Library of Science
Subject Keyword	Biochemistry, Genetics and Molecular Biology(all) Agricultural and Biological Sciences(all) Medicine(all) Research in Higher Education
Content Type	Text
Resource Type	Article
Subject	Multidisciplinary

Sl.	Authority	Responsibilities	Communication Details
1	Ministry of Education (GoI), Department of Higher Education	Sanctioning Authority	https://www.education.gov.in/ict-initiatives
2	Indian Institute of Technology Kharagpur	Host Institute of the Project: The host institute of the project is responsible for providing infrastructure support and hosting the project	https://www.iitkgp.ac.in
3	National Digital Library of India Office, Indian Institute of Technology Kharagpur	The administrative and infrastructural headquarters of the project	Dr. B. Sutradhar bsutra@ndl.gov.in
4	Project PI / Joint PI	Principal Investigator and Joint Principal Investigators of the project	Dr. B. Sutradhar bsutra@ndl.gov.in Prof. Saswat Chakrabarti will be added soon
5	Website/Portal (Helpdesk)	Queries regarding NDLI and its services	support@ndl.gov.in
6	Contents and Copyright Issues	Queries related to content curation and copyright issues	content@ndl.gov.in
7	National Digital Library of India Club (NDLI Club)	Queries related to NDLI Club formation, support, user awareness program, seminar/symposium, collaboration, social media, promotion, and outreach	clubsupport@ndl.gov.in
8	Digital Preservation Centre (DPC)	Assistance with digitizing and archiving copyright-free printed books	dpc@ndl.gov.in
9	IDR Setup or Support	Queries related to establishment and support of Institutional Digital Repository (IDR) and IDR workshops	idr@ndl.gov.in

Chromatin Immunoprecipitation (ChIP): Revisiting the Efficacy of Sample Preparation, Sonication, Quantification of Sheared DNA, and Analysis via PCR

Improved Elution Conditions for Native Co-Immunoprecipitation

Chromatin Immunoprecipitation to Analyze DNA Binding Sites of HMGA2

Development of Gel-Filter Method for High Enrichment of Low-Molecular Weight Proteins from Serum

Molecular Design of Bisphosphonate-Modified Proteins for Efficient Bone Targeting In Vivo

Interaction of Gamma-Herpesvirus Genome Maintenance Proteins with Cellular Chromatin

Chromatin Computation

Interactions of Archaeal Chromatin Proteins Alba1 and Alba2 with Nucleic Acids

Bradykinin Release Avoids High Molecular Weight Kininogen Endocytosis

Critical Parameters for Efficient Sonication and Improved Chromatin Immunoprecipitation of High Molecular Weight Proteins

Similar Documents

Chromatin Immunoprecipitation (ChIP): Revisiting the Efficacy of Sample Preparation, Sonication, Quantification of Sheared DNA, and Analysis via PCR

Improved Elution Conditions for Native Co-Immunoprecipitation

Chromatin Immunoprecipitation to Analyze DNA Binding Sites of HMGA2

Development of Gel-Filter Method for High Enrichment of Low-Molecular Weight Proteins from Serum

Molecular Design of Bisphosphonate-Modified Proteins for Efficient Bone Targeting In Vivo

Interaction of Gamma-Herpesvirus Genome Maintenance Proteins with Cellular Chromatin

Chromatin Computation

Interactions of Archaeal Chromatin Proteins Alba1 and Alba2 with Nucleic Acids

Bradykinin Release Avoids High Molecular Weight Kininogen Endocytosis

Critical Parameters for Efficient Sonication and Improved Chromatin Immunoprecipitation of High Molecular Weight Proteins