Podcasts about ichip

In this episode of the Epigenetics Podcast, we caught up with Dr. Hodaka Fujii, Professor of Biochemistry and Genome Biology at Hirosaki University Graduate School of Medicine and School of Medicine, to talk about his work on the development of locus-specific ChIP technologies. The goal of conventional chromatin immunoprecipitation (ChIP) assays is to find genomic locations of transcription factor binding or genome-wide profiles of histone tail modifications.  In contrast to that, the guest of this episode, Dr. Fujii, has developed methods such as insertional chromatin immunoprecipitation (iChIP) and engineered DNA-binding molecule-mediated chromatin immunoprecipitation (enChIP) to identify the factors that are binding to specific sites on the genome. In iChIP, LexA binding sites are inserted into the genomic region of interest. In parallel, the DNA-binding domain of LexA, fused with FLAG epitope tags and a nuclear localization signal, is expressed in the same cells. After crosslinking and chromatin preparation, the resulting chromatin is immunoprecipitated with an antibody against the tag. This allows proteins or RNA interacting with the region of interest to be analyzed with the appropriate downstream application. The enChIP takes a similar approach, but does not require insertion of the LexA binding sites. Instead, a FLAG-tagged dCas9 protein together with the respective guide RNA are used to target the region of the genome of interest. After the IP and the purification DNA, RNA, or proteins can be analyzed accordingly. The lack of the requirement of to insert the LexA binding sites into the genome makes enChIP much more straightforward than iChIP. In this interview, we discuss the story behind how Dr. Fujii got into the field of epigenetics, how he developed iChIP, and how the method was improved over the years. Furthermore, we discuss the development of enChIP and how this can be used as an alternate method to Hi-C.   References   Akemi Hoshino, Satoko Matsumura, … Hodaka Fujii (2004) Inducible Translocation Trap (Molecular Cell) DOI: 10.1016/j.molcel.2004.06.017 Akemi Hoshino, Hodaka Fujii (2009) Insertional chromatin immunoprecipitation: a method for isolating specific genomic regions (Journal of Bioscience and Bioengineering) DOI: 10.1016/j.jbiosc.2009.05.005 Toshitsugu Fujita, Hodaka Fujii (2013) Efficient isolation of specific genomic regions and identification of associated proteins by engineered DNA-binding molecule-mediated chromatin immunoprecipitation (enChIP) using CRISPR (Biochemical and Biophysical Research Communications) DOI: 10.1016/j.bbrc.2013.08.013 Toshitsugu Fujita, Miyuki Yuno, … Hodaka Fujii (2015) Identification of Non-Coding RNAs Associated with Telomeres Using a Combination of enChIP and RNA Sequencing (PLOS ONE) DOI: 10.1371/journal.pone.0123387 Toshitsugu Fujita, Miyuki Yuno, Hodaka Fujii (2016) Efficient sequence-specific isolation of DNA fragments and chromatin by in vitro enChIP technology using recombinant CRISPR ribonucleoproteins (Genes to Cells) DOI: 10.1111/gtc.12341 Toshitsugu Fujita, Miyuki Yuno, … Hodaka Fujii (2017) Identification of physical interactions between genomic regions by enChIP-Seq (Genes to Cells) DOI: 10.1111/gtc.12492 Toshitsugu Fujita, Fusako Kitaura, … Hodaka Fujii (2017) Locus-specific ChIP combined with NGS analysis reveals genomic regulatory regions that physically interact with the Pax5 promoter in a chicken B cell line (DNA Research) DOI: 10.1093/dnares/dsx023   Contact   Active Motif on Twitter Epigenetics Podcast on Twitter Active Motif on Linked-In Active Motif on Facebook eMail: podcast@activemotif.com

Podgodz 256 Recorded 1 August 2017 There’s this weird blue stuff up in the sky Snowfall Next week movies: The Hitman’s Bodyguard or Logan Lucky   Adds/Drops/Updates   Add: Drop: Updates: Mr. Biggs coming back?   Shows that pissed me off/weren’t good     Top 10 shows of the Week   Up for contention but not making the list this week Do By Friday: Hand Taint Skip to the End #77: Valerian and the title that never ends Roadwork #76:On Your Knees, Admiral No Agenda #952 iChip, #953: His Name is Nimrod Defocused #159: I am No One’s Father, Papa, or Daddy (Kingsman) Roderick on the Line #255: The Fancy-Enough Window No Such Thing As A Fish: NSTAA Barking Spy   Top 10 10) Eureka Podcast #228: The Boys Read More →

Podgodz 256 Recorded 1 August 2017 There's this weird blue stuff up in the sky Snowfall Next week movies: The Hitman's Bodyguard or Logan Lucky   Adds/Drops/Updates   Add: Drop: Updates: Mr. Biggs coming back?   Shows that pissed me off/weren’t good     Top 10 shows of the Week   Up for contention but not making the list this week Do By Friday: Hand Taint Skip to the End #77: Valerian and the title that never ends Roadwork #76:On Your Knees, Admiral No Agenda #952 iChip, #953: His Name is Nimrod Defocused #159: I am No One's Father, Papa, or Daddy (Kingsman) Roderick on the Line #255: The Fancy-Enough Window No Such Thing As A Fish: NSTAA Barking Spy   Top 10 10) Eureka Podcast #228: The Boys Read More →

Despite being diminutive in size, iChips have the potential to make big impacts on drug development and medical treatment testing. Lawrence Livermore National Lab is replicating the human body on a miniature scale, specifically focusing on brain physiology. Capturing human physiology outside the body allows scientists to probe and understand the human body without using human subjects. Staff scientist Elizabeth Wheeler describes how her group is using biology, 3D bioprinting, microchips and other technology to recreate human physiology outside the body. Series: "Lawrence Livermore National Lab Science on Saturday" [Science] [Show ID: 31475]

Despite being diminutive in size, iChips have the potential to make big impacts on drug development and medical treatment testing. Lawrence Livermore National Lab is replicating the human body on a miniature scale, specifically focusing on brain physiology. Capturing human physiology outside the body allows scientists to probe and understand the human body without using human subjects. Staff scientist Elizabeth Wheeler describes how her group is using biology, 3D bioprinting, microchips and other technology to recreate human physiology outside the body. Series: "Lawrence Livermore National Lab Science on Saturday" [Science] [Show ID: 31475]

Despite being diminutive in size, iChips have the potential to make big impacts on drug development and medical treatment testing. Lawrence Livermore National Lab is replicating the human body on a miniature scale, specifically focusing on brain physiology. Capturing human physiology outside the body allows scientists to probe and understand the human body without using human subjects. Staff scientist Elizabeth Wheeler describes how her group is using biology, 3D bioprinting, microchips and other technology to recreate human physiology outside the body. Series: "Lawrence Livermore National Lab Science on Saturday" [Science] [Show ID: 31475]

Despite being diminutive in size, iChips have the potential to make big impacts on drug development and medical treatment testing. Lawrence Livermore National Lab is replicating the human body on a miniature scale, specifically focusing on brain physiology. Capturing human physiology outside the body allows scientists to probe and understand the human body without using human subjects. Staff scientist Elizabeth Wheeler describes how her group is using biology, 3D bioprinting, microchips and other technology to recreate human physiology outside the body. Series: "Lawrence Livermore National Lab Science on Saturday" [Science] [Show ID: 31475]