Structural basis for transcriptional start site control of HIV-1 RNA fate

Brown, Joshua D.; Kharytonchyk, Siarhei; Chaudry, Issac; Iyer, Aishwarya S.; Carter, Hannah M.; Becker, Ghazal; Desai, Yash; Glang, Lindsay; Choi, Seung Hyuk; Singh, Karndeep; Lopresti, Michael; Orellana, Matthew R; Rodriguez, Tatiana; Oboh, Ubiomo; Hijji, Jana; Ghinger, Frances Grace; Stewart, Kailan; Francis, Dillion; Edwards, Bryce; Chen, Patrick; Case, David A.; Telesnitsky, Alice; Summers, Michael F.

doi:10.1126/science.aaz7959

Cited by 82 publications

(117 citation statements)

References 51 publications

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“…The equilibrium between the two alternative 5′ UTR structures mentioned above [ 24 , 46 , 47 ] and their differential tendencies to splice suggests a model for how loss of distant suppressor elements might cause oversplicing from D1. The 5′ UTR structures are in a dynamic equilibrium, each favoring a specific folding, but able to occasionally adopt the other conformation.…”

Section: Oversplicing—when Hiv-1 Splicing Gets Out Of Controlmentioning

confidence: 99%

HIV-1: To Splice or Not to Splice, That Is the Question

Emery

Swanstrom

2021

Viruses

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The transcription of the HIV-1 provirus results in only one type of transcript—full length genomic RNA. To make the mRNA transcripts for the accessory proteins Tat and Rev, the genomic RNA must completely splice. The mRNA transcripts for Vif, Vpr, and Env must undergo splicing but not completely. Genomic RNA (which also functions as mRNA for the Gag and Gag/Pro/Pol precursor polyproteins) must not splice at all. HIV-1 can tolerate a surprising range in the relative abundance of individual transcript types, and a surprising amount of aberrant and even odd splicing; however, it must not over-splice, which results in the loss of full-length genomic RNA and has a dramatic fitness cost. Cells typically do not tolerate unspliced/incompletely spliced transcripts, so HIV-1 must circumvent this cell policing mechanism to allow some splicing while suppressing most. Splicing is controlled by RNA secondary structure, cis-acting regulatory sequences which bind splicing factors, and the viral protein Rev. There is still much work to be done to clarify the combinatorial effects of these splicing regulators. These control mechanisms represent attractive targets to induce over-splicing as an antiviral strategy. Finally, splicing has been implicated in latency, but to date there is little supporting evidence for such a mechanism. In this review we apply what is known of cellular splicing to understand splicing in HIV-1, and present data from our newer and more sensitive deep sequencing assays quantifying the different HIV-1 transcript types.

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Section: Oversplicing—when Hiv-1 Splicing Gets Out Of Controlmentioning

confidence: 99%

HIV-1: To Splice or Not to Splice, That Is the Question

Emery

Swanstrom

2021

Viruses

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show abstract

“…Among retroviruses, although a cis -packaging mechanism had initially been suggested for human immunodeficiency virus type 2 (HIV-2), it is now generally accepted that packaging of retroviral gRNA takes place independently from Gag translation ( 26 ). It has been proposed that, in HIV-1, two pools of gRNA differing by the RNA structure ( 27 , 28 ) and/or its post-transcriptional modifications ( 29 ) co-exist, and that only one is packaged. Intracytoplasmic compartmentalization of the Gag and the gRNA and the Rev-dependent nuclear-export mechanism of the gRNA play a critical role in specific packaging of HIV-1 gRNA ( 30–32 ).…”

Section: Introductionmentioning

confidence: 99%

A purine loop and the primer binding site are critical for the selective encapsidation of mouse mammary tumor virus genomic RNA by Pr77Gag

Chameettachal

Vivet-Boudou

Pitchai

et al. 2021

Nucleic Acids Research

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Retroviral RNA genome (gRNA) harbors cis-acting sequences that facilitate its specific packaging from a pool of other viral and cellular RNAs by binding with high-affinity to the viral Gag protein during virus assembly. However, the molecular intricacies involved during selective gRNA packaging are poorly understood. Binding and footprinting assays on mouse mammary tumor virus (MMTV) gRNA with purified Pr77Gag along with in cell gRNA packaging study identified two Pr77Gag binding sites constituting critical, non-redundant packaging signals. These included: a purine loop in a bifurcated stem-loop containing the gRNA dimerization initiation site, and the primer binding site (PBS). Despite these sites being present on both unspliced and spliced RNAs, Pr77Gag specifically bound to unspliced RNA, since only that could adopt the native bifurcated stem–loop structure containing looped purines. These results map minimum structural elements required to initiate MMTV gRNA packaging, distinguishing features that are conserved amongst divergent retroviruses from those perhaps unique to MMTV. Unlike purine-rich motifs frequently associated with packaging signals, direct involvement of PBS in gRNA packaging has not been documented in retroviruses. These results enhance our understanding of retroviral gRNA packaging/assembly, making it not only a target for novel therapeutic interventions, but also development of safer gene therapy vectors.

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“…The equilibrium between two alternative 5' UTR structures mentioned above [22,41,42] and their differential tendencies to splice suggests a model for how loss of distant suppressor elements might cause oversplicing from D1. The 5' UTR structures are in a dynamic equilibrium, each favoring a specific folding, but able to occasionally adopt the other conformation.…”

Section: Oversplicing -When Hiv-1 Splicing Gets Out Of Controlmentioning

confidence: 99%

HIV- 1: To Splice Or Not To Splice, That Is THE Question

Swanstrom¹,

Emery²

2021

Preprint

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HIV-1 transcribes only one kind of transcript – the full length genomic RNA. To make the mRNA transcripts for the accessory proteins Tat and Rev, the genomic RNA must completely splice. The mRNA transcripts for Vif, Vpr, and Env must splice but not completely. Genomic RNA (which also functions as mRNA for the Gag and Gag/Pro/Pol precursor polyproteins) must not splice at all. HIV-1 can tolerate a surprising range in the relative abundance of individual transcript types, and a surprising amount of aberrant and even odd splicing; however, it must not over-splice, which results in the loss of full length genomic RNA and has a dramatic fitness cost. Cells typically do not tolerate unspliced/incompletely spliced transcripts, so HIV-1 has to circumvent this cell policing mechanism to allow some splicing while suppressing most. Splicing is controlled by RNA secondary structure, cis-acting regulatory sequences which bind splicing factors, and the viral protein Rev. There is still much work to be done to clarify the combinatorial effects of these splicing regulators. These control mechanisms represent attractive targets to induce over-splicing as an antiviral strategy. Finally, splicing has been implicated in latency, but to date there is little supporting evidence for such a mechanism. In this review we apply what is known of cellular splicing to understand splicing in HIV-1, and also present data from our newer and more sensitive deep sequencing assays quantifying the different HIV-1 transcript types.

show abstract

Structural basis for transcriptional start site control of HIV-1 RNA fate

Cited by 82 publications

References 51 publications

HIV-1: To Splice or Not to Splice, That Is the Question

HIV-1: To Splice or Not to Splice, That Is the Question

A purine loop and the primer binding site are critical for the selective encapsidation of mouse mammary tumor virus genomic RNA by Pr77Gag

HIV- 1: To Splice Or Not To Splice, That Is THE Question

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