Café

diff --git a/biblio/25801028.mdwn b/biblio/25801028.mdwn
new file mode 100644 (file)
index 0000000..e0b046e
--- /dev/null
+++ b/biblio/25801028.mdwn
@@ -0,0 +1,12 @@
+[[!meta title="The 3D organization of chromatin explains evolutionary fragile genomic regions."]]
+[[!tag chromosome breakpoint synteny]]
+
+Berthelot C, Muffato M, Abecassis J, Roest Crollius H.
+
+Cell Rep. 2015 Mar 24;10(11):1913-24. doi: 10.1016/j.celrep.2015.02.046
+
+The 3D organization of chromatin explains evolutionary fragile genomic regions.
+
+[[!pmid 25801028 desc="Explains the power law distribution of breakpoints in mammals and yeast with chromosome contacts (Hi-C) and open chromatin (ENCODE)."]]
+
+“We [...] reconstruct the ancestral gene order in the 95-million-year-old ancestral genome of Boreoeutheria, the last common ancestor of primates, rodents, and laurasiatherians. [...] This reconstructed genome was further annotated with respect to its intergenic regions [...] their lengths, GC content and their proportion of conserved non-coding sequence as defined by GERP. [...] We then identified evolutionary rearrangement breakpoints that have occurred in the human, mouse, dog, cow, and horse lineages. [...] We identified a total of 751 breakpoints, 20 of which correspond to independent breakpoint reuse. [...] The identified breakpoints show the typical characteristics of rearrangement breakpoints; i.e., they occur in GC-rich, gene-dense regions possessing lower proportions of conserved non-coding sequence. [...] Breakpoint events per intergene increase as a power law of intergene length rather than a proportionality law. [...] Ancestral intergenes with high CNE content have been disrupted by significantly fewer breakpoints than intergenes of similar length with lower CNE content. [...] Rpeated elements and recombination frequencies are distributed radically differently from breakpoints, eliminating them as potential candidates to explain the breakpoint pattern. [...] The density of open chromatin is similar to the pattern of breakpoints with the proportion of DNA in an open state decreasing as intergene size increases. [...] Simulating inversions in the human genome according to contact probability [...] rearrangements were allowed to occur only between open chromatin regions, using chromatin state profiles for different cell types published by the ENCODE consortium.  Under this model, the simulated average number of breakpoints per intergene closely reproduces the relationship with intergene length observed in real data.”

diff --git a/tags/chromosome.mdwn b/tags/chromosome.mdwn
index 9c9cf0d3537d1c4188b20135b8e0727c6e721209..74f69441744f41ef82473cca89495908771c1607 100644 (file)
--- a/tags/chromosome.mdwn
+++ b/tags/chromosome.mdwn
@@ -1,7 +1,3 @@
 [[!meta title="pages tagged chromosome"]]
 
-... _in progress_ ...
-
- - The ancestral amniote has 49 chromosomes according to [[Sacerdot and coll., 2018|biblio/30333059]].
-
 [[!inline pages="tagged(chromosome)" limit=0]]

diff --git a/tags/synteny.mdwn b/tags/synteny.mdwn
index 4ece12565bdc1c3ef44a93c8e8937c71454db038..83c8fa61a9419714959d17ab2004f95f8800df8e 100644 (file)
--- a/tags/synteny.mdwn
+++ b/tags/synteny.mdwn
@@ -5,6 +5,12 @@ breakpoints (~30 per Gb), associated with segmental duplication or Alu element
 enrichment.  They often bore signatures of non-homology based mechanisms, and
 were enriched near CTCF-binding events.
 
+[[Berthelot and coll. (2015)|biblio/25801028]] show that breakpoint
+distribution follows a power law and explain it with a model that requires
+breakpoints to be in open regions (ENCODE) interacting with each other (Hi-C).
+
+The ancestral amniote has 49 chromosomes according to [[Sacerdot and coll., 2018|biblio/30333059]].
+
 [[Renschler and coll. (2019)|biblio/31601616]] found 20 synteny breakpoints
 (SB) per Mb on average. “Approximately 75% of SBs stay within the A or B
 compartment”  “Overlaps of TAD boundaries and SB breakpoints in all comparisons