From e46fb20c98ec0ce0bbeb0299f4a2b8aa1131dd72 Mon Sep 17 00:00:00 2001 From: Charles Plessy Date: Thu, 12 Apr 2018 19:10:15 +0900 Subject: [PATCH] =?utf8?q?caf=C3=A9s?= MIME-Version: 1.0 Content-Type: text/plain; charset=utf8 Content-Transfer-Encoding: 8bit --- biblio/29618487.mdwn | 10 ++++++++++ 1 file changed, 10 insertions(+) create mode 100644 biblio/29618487.mdwn diff --git a/biblio/29618487.mdwn b/biblio/29618487.mdwn new file mode 100644 index 00000000..58f7311f --- /dev/null +++ b/biblio/29618487.mdwn @@ -0,0 +1,10 @@ +[[!meta title="Integrated analysis sheds light on evolutionary trajectories of young transcription start sites in the human genome."]] +[[!tag repeat promoter evolution CAGE]] + +Li C, Lenhard B, Luscombe NM. + +Genome Res. 2018 Apr 4. pii: gr.231449.117. doi:10.1101/gr.231449.117 + +Integrated analysis sheds light on evolutionary trajectories of young transcription start sites in the human genome. + +[[!pmid 29618487 desc="Uses “sequence homology is a reasonable proxy for TSS age”. Found polyA artefacts in the FANTOM5 HeliScopeCAGE libraries. Concludes that “1) new TSSs tend to have weaker transcription than old ones; 2) they tend to appear in repeat elements and associate with transcripts of uncertain functional status; 3) they are less likely to have a clear regulatory role, as demonstrated by the weaker regulatory potential from functional genomic data; 4) they also tend to appear in already active chromatin regions (e.g. near existing TSSs); and 5) new TSSs evolve more rapidly during their early phase of existence, which may be explained by the inherent instability of neighboring sequences or lack of a vital function”. Suggests that new promoters first have a TATA box, and then may lose it: “We also found that ~50% of young LTR-associated TSSs contain a TATA-box motif 25~35 bp upstream (Supplemental Fig. S6) – a TATA-box motif upstream to the TSS is found in many, but not all LTR consensus sequences – whereas the proportion drops to ~30% for old LTR-associated TSSs. This suggests that a substantial fraction of TATA-less promoters may have originated as LTR- derived TATA-box containing promoters.” Strong association between young TSS and repeat elements: “~70% of young TSSs have at least one repeat element within ±100 bp, but that only 24% of old TSSs do.”"]] -- 2.47.3