Endogenous retroviruses co-opted as divergently transcribed regulatory elements shape the regulatory landscape of embryonic stem cells
Publikation: Bidrag til tidsskrift › Tidsskriftartikel › Forskning › fagfællebedømt
Standard
Endogenous retroviruses co-opted as divergently transcribed regulatory elements shape the regulatory landscape of embryonic stem cells. / Bakoulis, Stylianos; Krautz, Robert; Alcaraz, Nicolas; Salvatore, Marco; Andersson, Robin.
I: Nucleic acids symposium series, Bind 50, Nr. 4, 088, 2022, s. 2111-2127.Publikation: Bidrag til tidsskrift › Tidsskriftartikel › Forskning › fagfællebedømt
Harvard
APA
Vancouver
Author
Bibtex
}
RIS
TY - JOUR
T1 - Endogenous retroviruses co-opted as divergently transcribed regulatory elements shape the regulatory landscape of embryonic stem cells
AU - Bakoulis, Stylianos
AU - Krautz, Robert
AU - Alcaraz, Nicolas
AU - Salvatore, Marco
AU - Andersson, Robin
PY - 2022
Y1 - 2022
N2 - Transposable elements are an abundant source of transcription factor binding sites, and favorable genomic integration may lead to their recruitment by the host genome for gene regulatory functions. However, it is unclear how frequent co-option of transposable elements as regulatory elements is, to which regulatory programs they contribute and how they compare to regulatory elements devoid of transposable elements. Here, we report a transcription initiation-centric, in-depth characterization of the transposon-derived regulatory landscape of mouse embryonic stem cells. We demonstrate that a substantial number of transposable element insertions, in particular endogenous retroviral elements, are associated with open chromatin regions that are divergently transcribed into unstable RNAs in a cell-type specific manner, and that these elements contribute to a sizable proportion of active enhancers and gene promoters. We further show that transposon subfamilies contribute differently and distinctly to the pluripotency regulatory program through their repertoires of transcription factor binding site sequences, shedding light on the formation of regulatory programs and the origins of regulatory elements.
AB - Transposable elements are an abundant source of transcription factor binding sites, and favorable genomic integration may lead to their recruitment by the host genome for gene regulatory functions. However, it is unclear how frequent co-option of transposable elements as regulatory elements is, to which regulatory programs they contribute and how they compare to regulatory elements devoid of transposable elements. Here, we report a transcription initiation-centric, in-depth characterization of the transposon-derived regulatory landscape of mouse embryonic stem cells. We demonstrate that a substantial number of transposable element insertions, in particular endogenous retroviral elements, are associated with open chromatin regions that are divergently transcribed into unstable RNAs in a cell-type specific manner, and that these elements contribute to a sizable proportion of active enhancers and gene promoters. We further show that transposon subfamilies contribute differently and distinctly to the pluripotency regulatory program through their repertoires of transcription factor binding site sequences, shedding light on the formation of regulatory programs and the origins of regulatory elements.
KW - CHROMATIN-STATE DISCOVERY
KW - GENOME BROWSER DATABASE
KW - TRANSPOSABLE ELEMENTS
KW - FACTOR-BINDING
KW - SYSTEMATIC DISSECTION
KW - UNIFIED ARCHITECTURE
KW - SHADOW ENHANCERS
KW - GENE-EXPRESSION
KW - READ ALIGNMENT
KW - PROMOTERS
U2 - 10.1093/nar/gkac088
DO - 10.1093/nar/gkac088
M3 - Journal article
C2 - 35166831
VL - 50
SP - 2111
EP - 2127
JO - Nucleic acids symposium series
JF - Nucleic acids symposium series
SN - 0261-3166
IS - 4
M1 - 088
ER -
ID: 298478999