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Genomic analysis of ADAR1 binding and its involvement in multiple RNA processing pathways.

Bahn JH, Ahn J, Lin X, Zhang Q, Lee JH, Civelek M, Xiao X - Nat Commun (2015)

Bottom Line: Similarly, ADAR1 interacts with DROSHA and DGCR8 in the nucleus and possibly out-competes DGCR8 in primary miRNA binding, which enhances mature miRNA expression.These functions are dependent on ADAR1's editing activity, at least for a subset of targets.Our study unfolds a broad landscape of the functional roles of ADAR1.

View Article: PubMed Central - PubMed

Affiliation: Department of Integrative Biology and Physiology and the Molecular Biology Institute, University of California Los Angeles, Los Angeles, California 90095, USA.

ABSTRACT
Adenosine deaminases acting on RNA (ADARs) are the primary factors underlying adenosine to inosine (A-to-I) editing in metazoans. Here we report the first global study of ADAR1-RNA interaction in human cells using CLIP-seq. A large number of CLIP sites are observed in Alu repeats, consistent with ADAR1's function in RNA editing. Surprisingly, thousands of other CLIP sites are located in non-Alu regions, revealing functional and biophysical targets of ADAR1 in the regulation of alternative 3' UTR usage and miRNA biogenesis. We observe that binding of ADAR1 to 3' UTRs precludes binding by other factors, causing 3' UTR lengthening. Similarly, ADAR1 interacts with DROSHA and DGCR8 in the nucleus and possibly out-competes DGCR8 in primary miRNA binding, which enhances mature miRNA expression. These functions are dependent on ADAR1's editing activity, at least for a subset of targets. Our study unfolds a broad landscape of the functional roles of ADAR1.

No MeSH data available.


Schematic models of ADAR1 function in the nucleus on 3' UTR processing and miRNA biogenesisThese regulatory mechanisms are mainly executed by ADAR1 binding to non-Alu regions. ADAR1 may compete with other cleavage and polyadenylation factors (CF Im68, CstF64 and CstF64τ) in binding to 3' UTRs. In the presence of ADAR1, the three proteins impose reduced regulatory influence on ADAR1-bound 3' UTRs than on other 3' UTRs. Upon ADAR1 KD, these proteins could gain more access to the 3' UTRs and exert regulation. The proximal cleavage site is often chosen in the presence of ADAR1, whereas the distal site is used upon ADAR1 KD. These outcomes reflect combinatorial regulation by the cleavage and polyadenylation factors that have opposing impacts on alternative 3' UTR usage. For pri-miRNA processing, ADAR1 may bind to (and edit) the nascent primary transcript prior to DROSHA/DGCR8 binding. The Microprocessor then cleaves the pri-miRNA with or without binding to the RNA. The binding of ADAR1 mainly promotes the processing of pri-miRNA, leading to enhanced miRNA expression level.
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Figure 5: Schematic models of ADAR1 function in the nucleus on 3' UTR processing and miRNA biogenesisThese regulatory mechanisms are mainly executed by ADAR1 binding to non-Alu regions. ADAR1 may compete with other cleavage and polyadenylation factors (CF Im68, CstF64 and CstF64τ) in binding to 3' UTRs. In the presence of ADAR1, the three proteins impose reduced regulatory influence on ADAR1-bound 3' UTRs than on other 3' UTRs. Upon ADAR1 KD, these proteins could gain more access to the 3' UTRs and exert regulation. The proximal cleavage site is often chosen in the presence of ADAR1, whereas the distal site is used upon ADAR1 KD. These outcomes reflect combinatorial regulation by the cleavage and polyadenylation factors that have opposing impacts on alternative 3' UTR usage. For pri-miRNA processing, ADAR1 may bind to (and edit) the nascent primary transcript prior to DROSHA/DGCR8 binding. The Microprocessor then cleaves the pri-miRNA with or without binding to the RNA. The binding of ADAR1 mainly promotes the processing of pri-miRNA, leading to enhanced miRNA expression level.

Mentions: A unifying model for the roles of ADAR1 in both 3' UTR formation and miRNA biogenesis is a binding competition model between ADAR1 and other related proteins (Fig. 5). Our analysis of canonical 3' UTR processing factors (CF Im68, CstF64 and CstF64τ) strongly suggests that ADAR1 binding could preclude binding of the other proteins. To provide further evidence, we carried out a cellular fractionation experiment and observed that ADAR1 proteins are predominantly localized in the chromatin fraction in U87MG cells (Supplementary Fig. 11). This data indicate that ADAR1 could occupy nascent RNAs shortly after they were produced, thus rendering an advantage in the competition model. The Microprocessor, DROSHA and DCGR8, are relatively enriched in the nucleoplasmic fraction of U87MG cells (Supplementary Fig. 11). Thus, for microRNA processing, the competition model also applies where ADAR1 first occupies (and possibly edits) the nascent pri-miRNA transcripts through recognition of the double stranded regions and, subsequently, the Microprocessor cleaves the substrates. The Microprocessor may or may not bind to the RNA in this case, but the pri-miRNA cleavage is enhanced by the presence of ADAR1 (Fig. 5).


Genomic analysis of ADAR1 binding and its involvement in multiple RNA processing pathways.

Bahn JH, Ahn J, Lin X, Zhang Q, Lee JH, Civelek M, Xiao X - Nat Commun (2015)

Schematic models of ADAR1 function in the nucleus on 3' UTR processing and miRNA biogenesisThese regulatory mechanisms are mainly executed by ADAR1 binding to non-Alu regions. ADAR1 may compete with other cleavage and polyadenylation factors (CF Im68, CstF64 and CstF64τ) in binding to 3' UTRs. In the presence of ADAR1, the three proteins impose reduced regulatory influence on ADAR1-bound 3' UTRs than on other 3' UTRs. Upon ADAR1 KD, these proteins could gain more access to the 3' UTRs and exert regulation. The proximal cleavage site is often chosen in the presence of ADAR1, whereas the distal site is used upon ADAR1 KD. These outcomes reflect combinatorial regulation by the cleavage and polyadenylation factors that have opposing impacts on alternative 3' UTR usage. For pri-miRNA processing, ADAR1 may bind to (and edit) the nascent primary transcript prior to DROSHA/DGCR8 binding. The Microprocessor then cleaves the pri-miRNA with or without binding to the RNA. The binding of ADAR1 mainly promotes the processing of pri-miRNA, leading to enhanced miRNA expression level.
© Copyright Policy
Related In: Results  -  Collection

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Figure 5: Schematic models of ADAR1 function in the nucleus on 3' UTR processing and miRNA biogenesisThese regulatory mechanisms are mainly executed by ADAR1 binding to non-Alu regions. ADAR1 may compete with other cleavage and polyadenylation factors (CF Im68, CstF64 and CstF64τ) in binding to 3' UTRs. In the presence of ADAR1, the three proteins impose reduced regulatory influence on ADAR1-bound 3' UTRs than on other 3' UTRs. Upon ADAR1 KD, these proteins could gain more access to the 3' UTRs and exert regulation. The proximal cleavage site is often chosen in the presence of ADAR1, whereas the distal site is used upon ADAR1 KD. These outcomes reflect combinatorial regulation by the cleavage and polyadenylation factors that have opposing impacts on alternative 3' UTR usage. For pri-miRNA processing, ADAR1 may bind to (and edit) the nascent primary transcript prior to DROSHA/DGCR8 binding. The Microprocessor then cleaves the pri-miRNA with or without binding to the RNA. The binding of ADAR1 mainly promotes the processing of pri-miRNA, leading to enhanced miRNA expression level.
Mentions: A unifying model for the roles of ADAR1 in both 3' UTR formation and miRNA biogenesis is a binding competition model between ADAR1 and other related proteins (Fig. 5). Our analysis of canonical 3' UTR processing factors (CF Im68, CstF64 and CstF64τ) strongly suggests that ADAR1 binding could preclude binding of the other proteins. To provide further evidence, we carried out a cellular fractionation experiment and observed that ADAR1 proteins are predominantly localized in the chromatin fraction in U87MG cells (Supplementary Fig. 11). This data indicate that ADAR1 could occupy nascent RNAs shortly after they were produced, thus rendering an advantage in the competition model. The Microprocessor, DROSHA and DCGR8, are relatively enriched in the nucleoplasmic fraction of U87MG cells (Supplementary Fig. 11). Thus, for microRNA processing, the competition model also applies where ADAR1 first occupies (and possibly edits) the nascent pri-miRNA transcripts through recognition of the double stranded regions and, subsequently, the Microprocessor cleaves the substrates. The Microprocessor may or may not bind to the RNA in this case, but the pri-miRNA cleavage is enhanced by the presence of ADAR1 (Fig. 5).

Bottom Line: Similarly, ADAR1 interacts with DROSHA and DGCR8 in the nucleus and possibly out-competes DGCR8 in primary miRNA binding, which enhances mature miRNA expression.These functions are dependent on ADAR1's editing activity, at least for a subset of targets.Our study unfolds a broad landscape of the functional roles of ADAR1.

View Article: PubMed Central - PubMed

Affiliation: Department of Integrative Biology and Physiology and the Molecular Biology Institute, University of California Los Angeles, Los Angeles, California 90095, USA.

ABSTRACT
Adenosine deaminases acting on RNA (ADARs) are the primary factors underlying adenosine to inosine (A-to-I) editing in metazoans. Here we report the first global study of ADAR1-RNA interaction in human cells using CLIP-seq. A large number of CLIP sites are observed in Alu repeats, consistent with ADAR1's function in RNA editing. Surprisingly, thousands of other CLIP sites are located in non-Alu regions, revealing functional and biophysical targets of ADAR1 in the regulation of alternative 3' UTR usage and miRNA biogenesis. We observe that binding of ADAR1 to 3' UTRs precludes binding by other factors, causing 3' UTR lengthening. Similarly, ADAR1 interacts with DROSHA and DGCR8 in the nucleus and possibly out-competes DGCR8 in primary miRNA binding, which enhances mature miRNA expression. These functions are dependent on ADAR1's editing activity, at least for a subset of targets. Our study unfolds a broad landscape of the functional roles of ADAR1.

No MeSH data available.