Dataset Information

Analysis of the interactome of B2-SINE RNA transcripts

ABSTRACT: B2-SINEs are noncoding RNAs which are transcribed by RNA polymerase III (Pol III) from short interspersed nuclear elements (SINEs), which are high copy number transposable elements in the mouse genome. Unexpectedly have observed significant induction of non-coding RNAs from the B2-SINE subclass of repeat element RNAs in DRG neurons following sciatic nerve injury. We next sought to identify intracellular targets of GI-SINEs, by protein pull-down from sciatic nerve axoplasm using biotinylated B2-SINE RNA as bait. We generated two constructs from the B2 consensus sequence, comprising 5’ (1-75nt) and 3’ (75-166nt) sequences, both predicted to retain their respective structures, and used the constructs to pull down axoplasm proteins for mass spectrometry analysis

INSTRUMENT(S):

ORGANISM(S): Mus Musculus (mouse)

TISSUE(S): Sciatic Nerve, Peripheral Nervous System Neuron Differentiation

SUBMITTER: Juan Oses-Prieto

LAB HEAD: Mike Fainzilber

PROVIDER: PXD041633 | Pride | 2025-09-29

REPOSITORIES: Pride

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Publications

Repeat-element RNAs integrate a neuronal growth circuit.

Zahavi Eitan Erez EE Koppel Indrek I Kawaguchi Riki R Oses-Prieto Juan A JA Briner Adam A Monavarfeshani Aboozar A Dalla Costa Irene I van Niekerk Erna E Lee Jinyoung J Matoo Samaneh S Hegarty Shane S Donahue Ryan J RJ Sahoo Pabitra K PK Ben-Dor Shifra S Feldmesser Ester E Ryvkin Julia J Leshkowitz Dena D Perry Rotem Ben-Tov RB Cheng Yuyan Y Farber Eli E Abraham Ofri O Samra Nitzan N Okladnikov Nataliya N Alber Stefanie S Albus Christin A CA Rishal Ida I Ulitsky Igor I Tuszynski Mark H MH Twiss Jeffery L JL He Zhigang Z Burlingame Alma L AL Fainzilber Mike M

Cell 20250516 16

Neuronal growth and regeneration are regulated by local translation of mRNAs in axons. We examined RNA polyadenylation changes upon sensory neuron injury and found upregulation of a subset of polyadenylated B2-SINE repeat elements, hereby termed GI-SINEs (growth-inducing B2-SINEs). GI-SINEs are induced from ATF3 and other AP-1 promoter-associated extragenic loci in injured sensory neurons but are not upregulated in lesioned retinal ganglion neurons. Exogenous GI-SINE expression elicited axonal g ...[more]

PMID: 40381624

Similar Datasets

Project description:The cellular accumulation of short non-coding RNAs (ncRNAs) transcribed by RNA Polymerase III (Pol III) is a hallmark of various cellular stressors and inflammatory-associated diseases. Yet, the mechanisms driving the accumulation of these RNAs are largely undefined. Infection with several DNA viruses is known to significantly alter the cellular Pol III transcriptome, leading to the induction of a class of non-coding retrotransposons known as short interspersed nuclear elements (SINE) and tRNA genes. Here, we sought to define the mechanisms driving Pol III transcribed ncRNA abundance during viral infection, using the murine herpesvirus MHV68 as a model. Our findings reveal that while the expression of Pol III transcripts, such as the murine-specific family of B2 SINE ncRNAs and pre-tRNAs, significantly increase during MHV68 infection, Pol III genomic occupancy is enhanced at a much fewer subset of B2 SINE and tRNA genes. Using DNA motif analyses and a convolutional neural network (CNN) based model, we identified non-promoter sequence elements within B2 SINE genes that distinguish infection-induced loci. We found that infection-induced B2 SINE genes are enriched for signal sequences that confer polyadenylation, and endogenous B2 SINE ncRNA polyadenylation depends on mRNA cleavage and polyadenylation (CPSF) machinery. We discovered that mRNA CPSF components are recruited to sites of Pol III transcription in response to MHV68 infection in a manner dependent on Pol III occupancy. Chromatin-associated B2 SINE ncRNAs are also bound by the CPSF complex, suggesting an RNA-dependent, co-transcriptional polyadenylation of B2 SINE ncRNAs. This uncovers an inducible, coupled relationship between Pol III transcription and mRNA-like polyadenylation of ncRNAs. Also, CPSF recruitment to Pol III genes is not restricted to murine genomes but also occurs at human SINE and tRNA genes, suggesting that this previously unknown coupled relationship may be a widespread feature of Pol III transcription.

Project description:More than 97% of the mammalian genome is non-protein coding, and repetitive elements account for more than 50% of noncoding space. However, the functional importance of many non-coding RNAs generated by these elements and their connection with pathologic processes remains elusive. We have previously shown that B2 RNAs, a class of non-coding RNAs that belong to the B2 family of SINE repeats, mediate the transcriptional activation of stress response genes (SRGs) upon application of a stimulus. Notably, B2 RNAs bind RNA Polymerase II (RNA Pol II) and suppress SRG transcription during pro-stimulation state. Upon application of a stimulus, B2 RNAs are processed into fragments and degraded, which in turn releases RNA Pol II from suppression and upregulates SRGs. Here, we demonstrate a novel role for B2 RNAs in transcriptome response to amyloid beta toxicity and pathology in mouse hippocampus. In healthy hippocampi, activation of SRGs is followed by a transient upregulation of pro-apoptotic factors, such as p53 and miRNA-34c, which target SRGs creating a negative feedback loop that facilitates return to the pro-stimulation state. Using an integrative RNA genomics approach, we show that in mouse hippocampi with amyloid pathology and in an in vitro cell culture model of amyloid beta toxicity, this regulatory loop is dysfunctional due to increased levels of B2 RNA processing, constitutively elevated SRG expression and high p53 levels. Evidence indicates that Hsf1, a master regulator of stress response, mediates B2 RNA processing in cells, and is upregulated during amyloid toxicity accelerating the processing of SINE RNAs and SRG hyper-activation. This data attributes a role to SINE RNA processing in a pathological process as well as a new function to Hsf1 that is independent of its transcription factor activity. Our study reveals that in mouse, SINE RNAs constitute a novel pathway deregulated in amyloid beta pathology, with potential implications for similar cases in the human brain, such as Alzheimer’s disease (AD).

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	SINE_TMT_1percentFDR.xlsx	Xlsx
	SINE_TMT_1percentFDR_quant.xlsx	Xlsx
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