TY - JOUR
T1 - Set3 HDAC mediates effects of overlapping noncoding transcription on gene induction kinetics
AU - Kim, Taesoo
AU - Xu, Zhenyu
AU - Clauder-Münster, Sandra
AU - Steinmetz, Lars M.
AU - Buratowski, Stephen
N1 - Funding Information:
We are grateful to Angelika Amon (MIT) for sharing unpublished work, Sebastian Marquardt for the northern blot analysis protocol, and Ollie Rando (University of Massachusetts, Worcester) and all members of the Buratowski lab for helpful advice and discussions. T.K. is a Special Fellow of the Leukemia and Lymphoma Society. This research was supported by grants GM068717 to L.M.S. and GM46498 and GM56663 to S.B. from the US National Institutes of Health.
PY - 2012/9/14
Y1 - 2012/9/14
N2 - The Set3 histone deacetylase complex (Set3C) binds histone H3 dimethylated at lysine 4 (H3K4me2) to mediate deacetylation of histones in 5′-transcribed regions. To discern how Set3C affects gene expression, genome-wide transcription was analyzed in yeast undergoing a series of carbon source shifts. Deleting SET3 primarily caused changes during transition periods, as genes were induced or repressed. Surprisingly, a majority of Set3-affected genes are overlapped by noncoding RNA (ncRNA) transcription. Many Set3-repressed genes have H3K4me2 instead of me3 over promoter regions, due to either reduced H3K4me3 or ncRNA transcription from distal or antisense promoters. Set3C also represses internal cryptic promoters, but in different regions of genes than the Set2/Rpd3S pathway. Finally, Set3C stimulates some genes by repressing an overlapping antagonistic antisense transcript. These results show that overlapping noncoding transcription can fine-tune gene expression, not via the ncRNA but by depositing H3K4me2 to recruit the Set3C deacetylase.
AB - The Set3 histone deacetylase complex (Set3C) binds histone H3 dimethylated at lysine 4 (H3K4me2) to mediate deacetylation of histones in 5′-transcribed regions. To discern how Set3C affects gene expression, genome-wide transcription was analyzed in yeast undergoing a series of carbon source shifts. Deleting SET3 primarily caused changes during transition periods, as genes were induced or repressed. Surprisingly, a majority of Set3-affected genes are overlapped by noncoding RNA (ncRNA) transcription. Many Set3-repressed genes have H3K4me2 instead of me3 over promoter regions, due to either reduced H3K4me3 or ncRNA transcription from distal or antisense promoters. Set3C also represses internal cryptic promoters, but in different regions of genes than the Set2/Rpd3S pathway. Finally, Set3C stimulates some genes by repressing an overlapping antagonistic antisense transcript. These results show that overlapping noncoding transcription can fine-tune gene expression, not via the ncRNA but by depositing H3K4me2 to recruit the Set3C deacetylase.
UR - http://www.scopus.com/inward/record.url?scp=84866392310&partnerID=8YFLogxK
U2 - 10.1016/j.cell.2012.08.016
DO - 10.1016/j.cell.2012.08.016
M3 - Article
C2 - 22959268
AN - SCOPUS:84866392310
SN - 0092-8674
VL - 150
SP - 1158
EP - 1169
JO - Cell
JF - Cell
IS - 6
ER -