TY - JOUR
T1 - IL-1 transcriptional responses to lipopolysaccharides are regulated by a complex of RNA binding proteins
AU - Shi, Lihua
AU - Song, Li
AU - Maurer, Kelly
AU - Dou, Ying
AU - Patel, Vishesh R.
AU - Su, Chun
AU - Leonard, Michelle E.
AU - Lu, Sumei
AU - Hodge, Kenyaita M.
AU - Torres, Annabel
AU - Chesi, Alessandra
AU - Grant, Struan F.A.
AU - Wells, Andrew D.
AU - Zhang, Zhe
AU - Petri, Michelle A.
AU - Sullivan, Kathleen E.
N1 - Funding Information:
This work was supported by National Institutes of Health (NIH) Grant R01 ES017627 and the Wallace Chair of Pediatrics (K.E.S.). S.F.A.G. is funded by the Daniel B. Burke Endowed Chair for Diabetes Research, Children’s Hospital of Philadelphia, and NIH Grant R01 HG010067. A.D.W. is supported by NIH Grants R01 AI130115 and R01 AI123539.
Publisher Copyright:
© 2020 by The American Association of Immunologists, Inc.
PY - 2020/3/1
Y1 - 2020/3/1
N2 - The IL1A and IL1B genes lie in close proximity on chromosome 2 near the gene for their natural inhibitor, IL1RN. Despite diverse functions, they are all three inducible through TLR4 signaling but with distinct kinetics. This study analyzed transcriptional induction kinetics, chromosome looping, and enhancer RNA production to understand the distinct regulation of these three genes in human cells. IL1A, IL1B, and IL1RN were rapidly induced after stimulation with LPS; however, IL1B mRNA production was less inhibitable by iBET151, suggesting it does not use pause-release regulation. Surprisingly, chromatin looping contacts between IL1A and IL1B were highly intermingled, although those of IL1RN were distinct, and we focused on comparing IL1A and IL1B transcriptional pathways. Our studies demonstrated that enhancer RNAs were produced from a subset of the regulatory regions, that they were critical for production of the mRNAs, and that they bound a diverse array of RNA binding proteins, including p300 but not CBP. We, furthermore, demonstrated that recruitment of p300 was dependent on MAPKs. Integrator is another RNA binding protein recruited to the promoters and enhancers, and its recruitment was more dependent on NF-κB than MAPKs. We found that integrator and NELF, an RNA polymerase II pausing protein, were associated with RNA in a manner that facilitated interaction. We conclude that IL1A and IL1B share many regulatory contacts, signaling pathways, and interactions with enhancer RNAs. A complex of protein interactions with enhancer RNAs emphasize the role of enhancer RNAs and the overall structural aspects of transcriptional regulation.
AB - The IL1A and IL1B genes lie in close proximity on chromosome 2 near the gene for their natural inhibitor, IL1RN. Despite diverse functions, they are all three inducible through TLR4 signaling but with distinct kinetics. This study analyzed transcriptional induction kinetics, chromosome looping, and enhancer RNA production to understand the distinct regulation of these three genes in human cells. IL1A, IL1B, and IL1RN were rapidly induced after stimulation with LPS; however, IL1B mRNA production was less inhibitable by iBET151, suggesting it does not use pause-release regulation. Surprisingly, chromatin looping contacts between IL1A and IL1B were highly intermingled, although those of IL1RN were distinct, and we focused on comparing IL1A and IL1B transcriptional pathways. Our studies demonstrated that enhancer RNAs were produced from a subset of the regulatory regions, that they were critical for production of the mRNAs, and that they bound a diverse array of RNA binding proteins, including p300 but not CBP. We, furthermore, demonstrated that recruitment of p300 was dependent on MAPKs. Integrator is another RNA binding protein recruited to the promoters and enhancers, and its recruitment was more dependent on NF-κB than MAPKs. We found that integrator and NELF, an RNA polymerase II pausing protein, were associated with RNA in a manner that facilitated interaction. We conclude that IL1A and IL1B share many regulatory contacts, signaling pathways, and interactions with enhancer RNAs. A complex of protein interactions with enhancer RNAs emphasize the role of enhancer RNAs and the overall structural aspects of transcriptional regulation.
UR - http://www.scopus.com/inward/record.url?scp=85079907554&partnerID=8YFLogxK
UR - http://www.scopus.com/inward/citedby.url?scp=85079907554&partnerID=8YFLogxK
U2 - 10.4049/jimmunol.1900650
DO - 10.4049/jimmunol.1900650
M3 - Article
C2 - 31953354
AN - SCOPUS:85079907554
SN - 0022-1767
VL - 204
SP - 1334
EP - 1344
JO - Journal of Immunology
JF - Journal of Immunology
IS - 5
ER -