NOV 23, 2016 8:00 AM PST

Studying Kinetics of Chromatin Assembly with SWATH-MS

Sponsored by: SCIEX OMICS, SCIEX OMICS
Speakers

Abstract
DATE: November 23rd, 2016
TIME: 8:00AM PT, 11:00AM ET


The structure of chromatin is critical for many aspects of cellular physiology and is considered to be the primary medium to store epigenetic information. The nucleosomes together with the non-histone proteins define a stable chromatin structure. Despite its stability, this structure is disassembled and reassembled during DNA replication, repair, recombination or transcription. During all those processes, defined chromatin regions become accessible to be bound by the required factors, resulting in extensive nucleosome turnover at given genomic loci. The dual nature of chromatin requires a continuous interplay between stable and dynamic structures, which has to be coordinated at the molecular level to maintain the epigenetic information stored in the chromatin structure.
Despite the biological relevance of these processes, little is known about the order of chromatin assembly steps, the molecular mechanisms that coordinate the required cellular machinery in time and the quality control of this assembly. 
To address these questions, our lab uses an in-vitro system that resembles the formation of chromatin on double-stranded DNA. This in-vitro system not only enables us to dissect critical steps of assembly but also to verify predictions we make based on proteomics analysis of captured nascent chromatin (NCC) in living cells.
In order to study the dynamics of chromatin-bound proteins, we applied label free quantitative SWATH-MS (sequential window acquisition of all theoretical fragment-ion spectra) at different assembly times, allowing us to describe distinct aspects of chromatin assembly such as the appearance and disappearance of histone modifications, the levels of histone chaperones, the activity of histone writers/erasers or the concentration of distinct DNA-binding factors. Based on these results, we have accomplished a classification of chromatin factors into functional groups depending on their binding kinetics.

Learning Objective 1: Develop an experimental outline to study chromatin assembly in vitro and in vivo with quantitative proteomics

Learning Objective 2: Establish a SWATH proteomics pipeline combined with statistical data analysis to determine protein binding kinetics

Show Resources
You May Also Like
MAY 11, 2021 10:00 AM PDT
C.E. CREDITS
MAY 11, 2021 10:00 AM PDT
Date: May 11, 2021 Time: 10:00zm PDT Your samples are some of the most valuable assets in the laboratory. After spending countless hours on extraction and preparation, your conclusions could...
JUN 09, 2021 7:00 AM PDT
C.E. CREDITS
JUN 09, 2021 7:00 AM PDT
Date: June 9, 2021 Time: 09 June 2021, 7am PDT, 10am EDT, 4pm CEST cells with dramatic implications on the validity of past cell culture related research. The fact that at least 509 cell lin...
SEP 14, 2021 7:00 AM PDT
C.E. CREDITS
SEP 14, 2021 7:00 AM PDT
Date: September 14, 2021 Time: 7am PDT, 10am EDT, 4pm CEST A conventional thermal cycler has long been a commodity product in the lab and end-point PCR techniques can be completed almost wit...
JUL 15, 2021 9:00 AM PDT
JUL 15, 2021 9:00 AM PDT
Date: July 15, 2021 Time: 9:00am (PDT), 12:00pm (EDT) The Pisces workflow robust, easy-to-use, end-to-end multi-omics solution for highly multiplexed targeted Spatial RNA analysis. VeranomeB...
JUL 15, 2021 8:00 AM PDT
C.E. CREDITS
JUL 15, 2021 8:00 AM PDT
Date: July 15, 2021 Time: 8:00am (PDT), 11:00am (EDT) High dimensional full spectrum flow cytometry grants unprecedented access to previously unattainable parameters in cellular biology. Flu...
OCT 20, 2021 10:00 AM PDT
C.E. CREDITS
OCT 20, 2021 10:00 AM PDT
Date: October 20, 2021 Time:10:00am (PDT), 1:00pm (EDT) As the prevalence of Diabetes continues to rise in many areas across the globe, healthcare providers continue to look for methods that...
Loading Comments...
Show Resources