Transcription-driven chromatin repression of Intragenic transcription start sites
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Transcription-driven chromatin repression of Intragenic transcription start sites. / Nielsen, Mathias; Ard, Ryan; Leng, Xueyuan; Ivanov, Maxim; Kindgren, Peter Robert; Pelechano, Vicent; Marquardt, Sebastian.
I: PLOS Genetics, Bind 15, Nr. 2, e1007969, 01.02.2019, s. 1-33.Publikation: Bidrag til tidsskrift › Tidsskriftartikel › Forskning › fagfællebedømt
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T1 - Transcription-driven chromatin repression of Intragenic transcription start sites
AU - Nielsen, Mathias
AU - Ard, Ryan
AU - Leng, Xueyuan
AU - Ivanov, Maxim
AU - Kindgren, Peter Robert
AU - Pelechano, Vicent
AU - Marquardt, Sebastian
N1 - MN, RA, XL, and MI contributed equally to this paper.
PY - 2019/2/1
Y1 - 2019/2/1
N2 - Progression of RNA polymerase II (RNAPII) transcription relies on the appropriately positioned activities of elongation factors. The resulting profile of factors and chromatin signatures along transcription units provides a “positional information system” for transcribing RNAPII. Here, we investigate a chromatin-based mechanism that suppresses intragenic initiation of RNAPII transcription. We demonstrate that RNAPII transcription across gene promoters represses their function in plants. This repression is characterized by reduced promoter-specific molecular signatures and increased molecular signatures associated with RNAPII elongation. The conserved FACT histone chaperone complex is required for this repression mechanism. Genome-wide Transcription Start Site (TSS) mapping reveals thousands of discrete intragenic TSS positions in fact mutants, including downstream promoters that initiate alternative transcript isoforms. We find that histone H3 lysine 4 mono-methylation (H3K4me1), an Arabidopsis RNAPII elongation signature, is enriched at FACT-repressed intragenic TSSs. Our analyses suggest that FACT is required to repress intragenic TSSs at positions that are in part characterized by elevated H3K4me1 levels. In sum, conserved and plant-specific chromatin features correlate with the co-transcriptional repression of intragenic TSSs. Our insights into TSS repression by RNAPII transcription promise to inform the regulation of alternative transcript isoforms and the characterization of gene regulation through the act of pervasive transcription across eukaryotic genomes.
AB - Progression of RNA polymerase II (RNAPII) transcription relies on the appropriately positioned activities of elongation factors. The resulting profile of factors and chromatin signatures along transcription units provides a “positional information system” for transcribing RNAPII. Here, we investigate a chromatin-based mechanism that suppresses intragenic initiation of RNAPII transcription. We demonstrate that RNAPII transcription across gene promoters represses their function in plants. This repression is characterized by reduced promoter-specific molecular signatures and increased molecular signatures associated with RNAPII elongation. The conserved FACT histone chaperone complex is required for this repression mechanism. Genome-wide Transcription Start Site (TSS) mapping reveals thousands of discrete intragenic TSS positions in fact mutants, including downstream promoters that initiate alternative transcript isoforms. We find that histone H3 lysine 4 mono-methylation (H3K4me1), an Arabidopsis RNAPII elongation signature, is enriched at FACT-repressed intragenic TSSs. Our analyses suggest that FACT is required to repress intragenic TSSs at positions that are in part characterized by elevated H3K4me1 levels. In sum, conserved and plant-specific chromatin features correlate with the co-transcriptional repression of intragenic TSSs. Our insights into TSS repression by RNAPII transcription promise to inform the regulation of alternative transcript isoforms and the characterization of gene regulation through the act of pervasive transcription across eukaryotic genomes.
U2 - 10.1371/journal.pgen.1007969
DO - 10.1371/journal.pgen.1007969
M3 - Journal article
C2 - 30707695
VL - 15
SP - 1
EP - 33
JO - P L o S Genetics
JF - P L o S Genetics
SN - 1553-7390
IS - 2
M1 - e1007969
ER -
ID: 212871883