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The USB1 de novo variant is catalytically active and correctly processes U6 snRNA. (A) Total RNA extracted from the indicated BEBV cell lines were treated with T4 PNK or with buffer only (PNKBuff) in mild acidic conditions. RNA was subsequently treated with poly(A) polymerase (PAP). Nontreated RNA was loaded as a control, ( n = 2). (B) 3′ RACE analysis of U6 oligo(U) tails in the indicated cell lines. At least 24 clones per sample in each experiment ( n = 2) were sequenced. Bars and error bars are averages of the number of U's within U6 oligo(U) tails and SEM from two independent experiments. (C and D) Indicated cell lines were treated with actinomycin D for 0, 4, and 8 h. RNA samples were processed by northern blotting for detection of U6 and 5S ( n = 2). L: marker of known length (67 nucleotides). U6 signals were normalized through the corresponding 5S signals and successively expressed as fold decrease over U6 signal at time 0. Error bars are averages of SEM from two independent experiments. (E and F) U6 relative abundance quantification by qPCR analysis on patients and control cell lines (ctr1 n = 2, ctr2 n = 3, ctr3 n = 1, USB1 −/− n = 3, P1 n = 3) (E), and USB1 −/− cells transduced with the indicated <t>lentiviral</t> constructs ( n = 2) (F). U6 signals were normalized through the corresponding 5S signals and successively expressed as fold decrease over U6 signal at time 0. Error bars are averages of SEM from two independent experiments. EV, empty vector. Source data are available for this figure: .
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The USB1 de novo variant is catalytically active and correctly processes U6 snRNA. (A) Total RNA extracted from the indicated BEBV cell lines were treated with T4 PNK or with buffer only (PNKBuff) in mild acidic conditions. RNA was subsequently treated with poly(A) polymerase (PAP). Nontreated RNA was loaded as a control, ( n = 2). (B) 3′ RACE analysis of U6 oligo(U) tails in the indicated cell lines. At least 24 clones per sample in each experiment ( n = 2) were sequenced. Bars and error bars are averages of the number of U's within U6 oligo(U) tails and SEM from two independent experiments. (C and D) Indicated cell lines were treated with actinomycin D for 0, 4, and 8 h. RNA samples were processed by northern blotting for detection of U6 and 5S ( n = 2). L: marker of known length (67 nucleotides). U6 signals were normalized through the corresponding 5S signals and successively expressed as fold decrease over U6 signal at time 0. Error bars are averages of SEM from two independent experiments. (E and F) U6 relative abundance quantification by qPCR analysis on patients and control cell lines (ctr1 n = 2, ctr2 n = 3, ctr3 n = 1, USB1 −/− n = 3, P1 n = 3) (E), and USB1 −/− cells transduced with the indicated <t>lentiviral</t> constructs ( n = 2) (F). U6 signals were normalized through the corresponding 5S signals and successively expressed as fold decrease over U6 signal at time 0. Error bars are averages of SEM from two independent experiments. EV, empty vector. Source data are available for this figure: .
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The USB1 de novo variant is catalytically active and correctly processes U6 snRNA. (A) Total RNA extracted from the indicated BEBV cell lines were treated with T4 PNK or with buffer only (PNKBuff) in mild acidic conditions. RNA was subsequently treated with poly(A) polymerase (PAP). Nontreated RNA was loaded as a control, ( n = 2). (B) 3′ RACE analysis of U6 oligo(U) tails in the indicated cell lines. At least 24 clones per sample in each experiment ( n = 2) were sequenced. Bars and error bars are averages of the number of U's within U6 oligo(U) tails and SEM from two independent experiments. (C and D) Indicated cell lines were treated with actinomycin D for 0, 4, and 8 h. RNA samples were processed by northern blotting for detection of U6 and 5S ( n = 2). L: marker of known length (67 nucleotides). U6 signals were normalized through the corresponding 5S signals and successively expressed as fold decrease over U6 signal at time 0. Error bars are averages of SEM from two independent experiments. (E and F) U6 relative abundance quantification by qPCR analysis on patients and control cell lines (ctr1 n = 2, ctr2 n = 3, ctr3 n = 1, USB1 −/− n = 3, P1 n = 3) (E), and USB1 −/− cells transduced with the indicated <t>lentiviral</t> constructs ( n = 2) (F). U6 signals were normalized through the corresponding 5S signals and successively expressed as fold decrease over U6 signal at time 0. Error bars are averages of SEM from two independent experiments. EV, empty vector. Source data are available for this figure: .
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The USB1 de novo variant is catalytically active and correctly processes U6 snRNA. (A) Total RNA extracted from the indicated BEBV cell lines were treated with T4 PNK or with buffer only (PNKBuff) in mild acidic conditions. RNA was subsequently treated with poly(A) polymerase (PAP). Nontreated RNA was loaded as a control, ( n = 2). (B) 3′ RACE analysis of U6 oligo(U) tails in the indicated cell lines. At least 24 clones per sample in each experiment ( n = 2) were sequenced. Bars and error bars are averages of the number of U's within U6 oligo(U) tails and SEM from two independent experiments. (C and D) Indicated cell lines were treated with actinomycin D for 0, 4, and 8 h. RNA samples were processed by northern blotting for detection of U6 and 5S ( n = 2). L: marker of known length (67 nucleotides). U6 signals were normalized through the corresponding 5S signals and successively expressed as fold decrease over U6 signal at time 0. Error bars are averages of SEM from two independent experiments. (E and F) U6 relative abundance quantification by qPCR analysis on patients and control cell lines (ctr1 n = 2, ctr2 n = 3, ctr3 n = 1, USB1 −/− n = 3, P1 n = 3) (E), and USB1 −/− cells transduced with the indicated <t>lentiviral</t> constructs ( n = 2) (F). U6 signals were normalized through the corresponding 5S signals and successively expressed as fold decrease over U6 signal at time 0. Error bars are averages of SEM from two independent experiments. EV, empty vector. Source data are available for this figure: .
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The USB1 de novo variant is catalytically active and correctly processes U6 snRNA. (A) Total RNA extracted from the indicated BEBV cell lines were treated with T4 PNK or with buffer only (PNKBuff) in mild acidic conditions. RNA was subsequently treated with poly(A) polymerase (PAP). Nontreated RNA was loaded as a control, ( n = 2). (B) 3′ RACE analysis of U6 oligo(U) tails in the indicated cell lines. At least 24 clones per sample in each experiment ( n = 2) were sequenced. Bars and error bars are averages of the number of U's within U6 oligo(U) tails and SEM from two independent experiments. (C and D) Indicated cell lines were treated with actinomycin D for 0, 4, and 8 h. RNA samples were processed by northern blotting for detection of U6 and 5S ( n = 2). L: marker of known length (67 nucleotides). U6 signals were normalized through the corresponding 5S signals and successively expressed as fold decrease over U6 signal at time 0. Error bars are averages of SEM from two independent experiments. (E and F) U6 relative abundance quantification by qPCR analysis on patients and control cell lines (ctr1 n = 2, ctr2 n = 3, ctr3 n = 1, USB1 −/− n = 3, P1 n = 3) (E), and USB1 −/− cells transduced with the indicated lentiviral constructs ( n = 2) (F). U6 signals were normalized through the corresponding 5S signals and successively expressed as fold decrease over U6 signal at time 0. Error bars are averages of SEM from two independent experiments. EV, empty vector. Source data are available for this figure: .

Journal: Journal of Human Immunity

Article Title: A heterozygous USB1 variant linked to immunodeficiency

doi: 10.70962/jhi.20250110

Figure Lengend Snippet: The USB1 de novo variant is catalytically active and correctly processes U6 snRNA. (A) Total RNA extracted from the indicated BEBV cell lines were treated with T4 PNK or with buffer only (PNKBuff) in mild acidic conditions. RNA was subsequently treated with poly(A) polymerase (PAP). Nontreated RNA was loaded as a control, ( n = 2). (B) 3′ RACE analysis of U6 oligo(U) tails in the indicated cell lines. At least 24 clones per sample in each experiment ( n = 2) were sequenced. Bars and error bars are averages of the number of U's within U6 oligo(U) tails and SEM from two independent experiments. (C and D) Indicated cell lines were treated with actinomycin D for 0, 4, and 8 h. RNA samples were processed by northern blotting for detection of U6 and 5S ( n = 2). L: marker of known length (67 nucleotides). U6 signals were normalized through the corresponding 5S signals and successively expressed as fold decrease over U6 signal at time 0. Error bars are averages of SEM from two independent experiments. (E and F) U6 relative abundance quantification by qPCR analysis on patients and control cell lines (ctr1 n = 2, ctr2 n = 3, ctr3 n = 1, USB1 −/− n = 3, P1 n = 3) (E), and USB1 −/− cells transduced with the indicated lentiviral constructs ( n = 2) (F). U6 signals were normalized through the corresponding 5S signals and successively expressed as fold decrease over U6 signal at time 0. Error bars are averages of SEM from two independent experiments. EV, empty vector. Source data are available for this figure: .

Article Snippet: Those inserts (with the addition of an HA tag at the C-terminal when indicated) were subcloned into the lentiviral pWPI backbone (RRID:Addgene_12254) by GenScript.

Techniques: Variant Assay, Control, Clone Assay, Northern Blot, Marker, Transduction, Construct, Plasmid Preparation