A transcriptome-wide antitermination mechanism sustaining identity of embryonic stem cells

Kainov, Yaroslav A.; Makeyev, Eugene V.

doi:10.1038/s41467-019-14204-z

Cited by 22 publications

(19 citation statements)

References 89 publications

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“…Another type of transcripts that we and other teams observed in hen2-2 and se-2 plants are truncated or misprocessed transcripts spanning the first intron ( 14 , 15 , 35 , 68 ). Similar 5′ transcript derived from protein coding genes have also been observed in human cells depleted from ARS2 and result from premature transcription termination rather than from compromised splicing of full-length pre-mRNAs ( 19 , 34 , 69 ). However, both SE and ARS2 do interact with splicing factors.…”

Section: Discussionmentioning

confidence: 53%

“…Among the proteins that co-purify with FLAG-SE, both HOS5 and CPL1 have been implicated in splicing ( 56 ), and a previous study detected several auxiliary factors of the U1 snRNP as SE interactants ( 11 ). A very recent study suggests that the ARS2-mediated recruitment of U1 snRNP to 5′ proximal pre-mRNA sequences favours splicing and full-length transcription, and disfavours premature transcription and degradation ( 69 ). Hence, the increased accumulation of truncated or mis-spliced transcripts in se-2 hen2-2 double mutants may also be explained by a dual role of SE in recruiting either splicing factors or NEXT.…”

Section: Discussionmentioning

confidence: 99%

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SERRATE interacts with the nuclear exosome targeting (NEXT) complex to degrade primary miRNA precursors in Arabidopsis

Bajczyk

Lange

Bielewicz

et al. 2020

Nucleic Acids Research

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Abstract SERRATE/ARS2 is a conserved RNA effector protein involved in transcription, processing and export of different types of RNAs. In Arabidopsis, the best-studied function of SERRATE (SE) is to promote miRNA processing. Here, we report that SE interacts with the nuclear exosome targeting (NEXT) complex, comprising the RNA helicase HEN2, the RNA binding protein RBM7 and one of the two zinc-knuckle proteins ZCCHC8A/ZCCHC8B. The identification of common targets of SE and HEN2 by RNA-seq supports the idea that SE cooperates with NEXT for RNA surveillance by the nuclear exosome. Among the RNA targets accumulating in absence of SE or NEXT are miRNA precursors. Loss of NEXT components results in the accumulation of pri-miRNAs without affecting levels of miRNAs, indicating that NEXT is, unlike SE, not required for miRNA processing. As compared to se-2, se-2 hen2-2 double mutants showed increased accumulation of pri-miRNAs, but partially restored levels of mature miRNAs and attenuated developmental defects. We propose that the slow degradation of pri-miRNAs caused by loss of HEN2 compensates for the poor miRNA processing efficiency in se-2 mutants, and that SE regulates miRNA biogenesis through its double contribution in promoting miRNA processing but also pri-miRNA degradation through the recruitment of the NEXT complex.

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Section: Discussionmentioning

confidence: 53%

Section: Discussionmentioning

confidence: 99%

SERRATE interacts with the nuclear exosome targeting (NEXT) complex to degrade primary miRNA precursors in Arabidopsis

Bajczyk

Lange

Bielewicz

et al. 2020

Nucleic Acids Research

View full text Add to dashboard Cite

show abstract

“…Another type of transcripts that we and other teams observed in hen2-2 and se-2 plants are truncated or misprocessed transcripts spanning the first intron (14,15,35,68). Similar 5′ transcript derived from protein coding genes have also been observed in human cells depleted from ARS2 and result from premature transcription termination rather than from compromised splicing of full-length pre-mRNAs (19,34,69). However, both SE and ARS2 do interact with splicing factors.…”

Section: Discussionmentioning

confidence: 53%

“…Among the proteins that co-purify with FLAG-SE, both HOS5 and CPL1 have been implicated in splicing (56), and a previous study detected several auxiliary factors of the U1 snRNP as SE interactants (70). A very recent study suggests that the ARS2-mediated recruitment of U1 snRNP to 5′ proximal pre-mRNA sequences favours splicing and full-length transcription, and disfavours premature transcription and degradation (69). Hence, the increased accumulation of truncated or mis-spliced transcripts in se-2 hen2-2 double mutants may also be explained by a dual role of SE in recruiting either splicing factors or NEXT.…”

Section: Discussionmentioning

confidence: 99%

SERRATE interacts with the nuclear exosome targeting (NEXT) complex to degrade primary miRNA precursors in Arabidopsis

Bajczyk

Lange

Bielewicz

et al. 2020

Preprint

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SERRATE/ARS2 is a conserved RNA effector protein involved in transcription, processing and export of different types of RNAs. In Arabidopsis, the best-studied function of SERRATE (SE) is to promote miRNA processing. Here, we report that SE interacts with the Nuclear Exosome Targeting (NEXT) complex, comprising the RNA helicase HEN2, the RNA binding protein RBM7 and one of the two zincknuckle proteins ZCCHC8A/ZCCHC8B. The identification of common targets of SE and HEN2 by RNAseq supports the idea that SE cooperates with NEXT for RNA surveillance by the nuclear exosome.Among the RNA targets accumulating in absence of SE or NEXT are miRNA precursors. Loss of NEXT components results in the accumulation of pri-miRNAs without affecting levels of miRNAs, indicating that NEXT is, unlike SE, not required for miRNA processing. As compared to se-2, se-2 hen2-2 double mutants showed increased accumulation of pri-miRNAs, but partially restored levels of mature miRNAs and attenuated developmental defects. We propose that the slow degradation of pri-miRNAs caused by loss of HEN2 compensates for the poor miRNA processing efficiency in se-2 mutants, and that SE regulates miRNA biogenesis through its double contribution in promoting miRNA processing but also pri-miRNA degradation through the recruitment of the NEXT complex. IntroductionIn plants, many miRNAs are encoded by independent RNA polymerase II transcription units. The primary transcripts contain a 5' cap structure as well as a poly(A) tail at the 3' end (1), and sometimes introns. The primary or spliced pri-miRNAs adopt stem loop structures which are processed by the nuclear endonuclease Dicer like 1 (DCL1) (2) in two sequential reactions. The first step creates shorter miRNA precursors called pre-miRNAs. The second step produces miRNA/miRNA* duplexes of mostly 21 nt with 2 nt overhangs at both 3' ends. DCL1 associates with the double stranded RNA binding 2 protein HYPONASTIC LEAVES 1 (HYL1) and the zinc finger domain-containing RNA effector protein SERRATE (3-5). Both HYL1 and SE interact with DCL1 as well as with each other (6-8). DCL1, SE and HYL1 form the core of the plant Microprocessor complex and co-localize within the nucleus in special structures known as dicing bodies (D-bodies) (7). In absence of HYL1 or upon reduced activity of SE, dicing by DCL1 is not completely abolished but less efficient and less accurate (3-5). The importance of SE for the biogenesis of miRNAs is illustrated by the phenotype of se mutants. Complete loss of SE expression as in the null mutant se-4 is embryonic lethal, while the se-1 mutation, which results in the expression of a truncated SE lacking 20 amino acids at its C-terminus, severely affects developmental timing, phylotaxy, meristem function and patterning of leaves and flowers (4,9). The se-2 mutation, in which the SE protein is truncated by 40 amino acids from the C-terminus, additionally displays the hyponastic leave shape that is characteristic for many miRNA biogenesis mutants including hyl1-2, hst-1 and ago1-25 (10-13).In ad...

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“…While the 5′ end of Xist does not harbor obvious U1 snRNA binding sites (66), we and others have found that Repeat A associates with protein components of the U1 and other snRNPs ( Supplementary Table S3; (7,16,21)). Moreover, several proteins that were identified as Xist cofactors in recent genetic and proteomic screens -namely NXF1, SRRT, and SCAF4 -have known roles in suppressing premature cleavage and polyadenylation (10,21,26,(67)(68)(69). Future work will determine whether these proteins or others mediate Xist's antiterminator activity.…”

Section: Discussionmentioning

confidence: 99%

Elements at the 5′ end ofXistharbor SPEN-independent transcriptional antiterminator activity

Trotman

Lee

Cherney

et al. 2020

Preprint

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The Xist lncRNA requires Repeat A, a conserved RNA element located in its 5′ end, to induce gene silencing during X-chromosome inactivation. Intriguingly, Repeat A is also required for the production of Xist. While silencing by Repeat A requires the protein SPEN, how Repeat A promotes Xist production remains unclear. We report that in mouse embryonic stem cells, expression of a transgene comprising the first two kilobases of Xist (Xist-2kb) causes transcriptional readthrough of multiple downstream polyadenylation sequences. Readthrough required Repeat A and the ~750 nucleotides downstream but did not require SPEN. Despite associating with SPEN and chromatin, Xist-2kb did not robustly silence transcription, whereas a transgene comprising Xist's first 5.5 kilobases robustly silenced transcription and read through its polyadenylation sequence. Longer, spliced Xist transgenes also induced robust silencing yet terminated efficiently. Thus, in contexts examined here, Xist requires sequence elements beyond its first two kilobases to robustly silence transcription, and the 5′ end of Xist harbors SPENindependent transcriptional antiterminator activity that can repress proximal cleavage and polyadenylation. In endogenous contexts, this antiterminator activity may help produce full-length Xist RNA while rendering the Xist locus resistant to silencing by the same repressive complexes that the lncRNA recruits to other genes.

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A transcriptome-wide antitermination mechanism sustaining identity of embryonic stem cells

Cited by 22 publications

References 89 publications

SERRATE interacts with the nuclear exosome targeting (NEXT) complex to degrade primary miRNA precursors in Arabidopsis

SERRATE interacts with the nuclear exosome targeting (NEXT) complex to degrade primary miRNA precursors in Arabidopsis

SERRATE interacts with the nuclear exosome targeting (NEXT) complex to degrade primary miRNA precursors in Arabidopsis

Elements at the 5′ end ofXistharbor SPEN-independent transcriptional antiterminator activity

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