[urls] Gene regulation

[shouldsee]

Pointers to useful references in gene regulation

1. nucleosome remodellers,AR 2009

   Therefore, chromatin structure not only provides a packaging solution, but also an opportunity for regulation

2. Slides by Cortijo for GI

3. Is spatial structure of DNA a fractal?

4. Topology by sequencing (HiSeq), Science 2016

5. Topological associating domains (TADs), Science Advances 2018

6. Non-coding RNA's

   ncRNA are promiscuous regulators who dip its hands in all aspects: 1. Chromatin remodeling. 2. Regulation of transcription 3. Regulation of transcript stability and translation. In other words, a unifying framework is absent.

7. Integrative analyses of 111 human epigenomes, nature2015, citing chromHMM

Videos:

1. Chromatin package remodelling

paradigm around RNAPII:

• Basal transcription is present around TATA-based promoters, which recruits the formation of per-initiation complex
• Transcription is further promoted in the present of mediator complex
• trans-cis interplay is complex and involves things like p300/PRC/mediator/SWI/SNF.
• most of these are qualitative arguments based on Western Blots/Southern Blots/Biochemistry/Molecular-Cloning/Structural Analyses and lacking a quantitative basis.

MISC

databases:

• ENCODE: Encyclopedia of DNA elements

• Roadmap epigenetics

• Blueprint

• PCSD: Plant Chromatin State Database

• Semi-Automated Genome Annotation (SAGA) softwares: chromHMM (762 cite for its 2012 original correspondence, see WoK citation report), Segway (DBN-based, 1 cite bioRxiv paper) . Neither outlines the inference framework and are mostly details of application.

Experiments

• First ChIP-Seq, 43 pages of supplements

(from lec slides) (http://www.activemotif.com/catalog/704/epigenetic-services-1)