Chromosomes & Regulation, RNA Control of Gene Expression

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Biochemistry & Molecular Bio.
Course Code
David Gross

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Feb 24 Notes • chromosomes have large-scale structure o chromosome organization affects gene expression from some unusual chromosomes o Ex.  lampbrush chromosomes (from oocytes) have loops that always have same genes in them & are actively transcribed  this reflects interphase chromosomes (active, non-condensed chromosomes) • 3C technique (chromosome-conformation-capture) o reveals chromosome structure o process  formaldehyde nonspecifically crosslinks regions of DNA(crosslinking proteins)  restriction enzymes cleave & create compatible ends, can be religated w/ ligases  removal of crosslinks/proteins (heat treatment & proteolysis), using pairs of primers can tell if 2 regions linked o problem is that need to know which 2 regions to look @ o add on processes:  4C – 3C followed by microarray (CHIP) analysis, can see what other regions of DNAare close to region of interest  Hi-C – 3C followed by high-throughput sequencing o using restriction enzyme that cleaves away from recognition site allows sequencing the linked fragments to find if 2 sequences of DNAare close in a biological context • location within nucleus can affect chromatin structure o there are “neighborhoods” for gene silencing & gene expression o when the cell changes in response to a signal genes can be moved from a silencing part of the nucleus to an expressive part • why does location matter o histone code & chromatin structure can spread through code-reader/writer complexes o complexes not necessarily limited to changing sequential parts of DNA o by changing physical proximity, chromatin changes can be spread to other regions of chromosome o also true for other epigenetic changes (DNA methylation) o Ex. X-chromosome inactivation • RNAAntisense Purification (RAP) o Xist RNArecruits PRC2 (polycomb repressive complex 2) o PRC2 promotes histone methylation @ K27 (silencing mark) o where H3K27me is found Xist RNAis found o contact map of X-chromosome has been generated & Xist RNAlocalizes to other X chromosome regions based on the existing conformation o Xist, once contacted to chromosome, pulls new regions into it’s active location by the bundling of the previous region • Chromatin regulation by RNA o long noncoding RNA’s (lnRNAs) are non- protein coding regions of genome, often regulate gene expression  found on opposite strands, in intron regions, divergently transcribed& even within genes they regulate  recruit chromatin remodeling factors & modifying enzymes (DNA methylation enzymes) cause site-specific chromatin changes • Regulatory RNAin control of gene expression o Euk:
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