Biology subjects

Smith, H. W.

Publications and source records attributed to Smith, H. W..

5 recordsLinked to original sources

bioRxiv2026

Pumilio and Brain tumor regulate the expression of Smaug during the Drosophila maternal-to-zygotic transition

During the Drosophila maternal-to-zygotic transition, maternally deposited RNAs are cleared in a temporally controlled manner. The RNA-binding protein Smaug is a major regulator of maternal mRNA decay and its expression at both the RNA and protein level is limited to a narrow temporal window during the MZT. Here we show that Pumilio RNA-binding protein promotes degradation of smaug mRNA at the end of the MZT through Pumilio-binding cis-elements in the smaug 3 untranslated region, and that disruption of this regulation leads to ectopic Smaug protein expression beyond its normal developmental window. We further find that another RNA-binding protein, Brain tumor, also contributes to repression of ectopic Smaug expression. Transcriptome-wide analyses of embryos lacking Pumilio reveal that it directly regulates hundreds of maternal mRNAs after zygotic genome activation, with many of these Pumilio targets also regulated by Brain tumor. The ectopic Smaug protein that results from loss of either Pumilio or Brain tumor causes widespread downregulation of mRNAs that contain Smaug binding sites. Together, these findings define a post-transcriptional regulatory pathway in which Pumilio and Brain tumor ensure orderly progression of the Drosophila maternal-to-zygotic by clearing smaug mRNA and preventing ectopic Smaug activity.

developmental biology↗

bioRxiv2026

Subnuclear cofactor partitioning underlies auxin-dependent transcriptional regulation

Cellular and organismal function relies on the precise activation and repression of gene expression by DNA-binding transcription factors (TFs). Many TFs occur in large gene families, and a key question in biology is how divergent functions emerge in TF families during evolution. Here we discover the biochemical mechanism for transcriptional activation by the Marchantia polymorpha AUXIN RESPONSE FACTOR1 (MpARF1) TF, which relies on direct recruitment of the Mediator complex into subnuclear MpARF1 clusters. We find that the Mediator recruitment region was the evolutionary innovation that converted ARF repressors into activators, switching binding specificity from co-repressor to co-activator. We demonstrate that this evolutionary innovation can be recreated, thereby revealing a deeply conserved mechanism based on competition between ARF clusters at the heart of the transcriptional auxin response.

plant biology↗

bioRxiv2023

N-6-methyladenosine (m6A) Promotes the Nuclear Retention of mRNAs with Intact 5' Splice Site Motifs

In humans, misprocessed mRNAs containing intact 5' Splice Site (5'SS) motifs are nuclear retained and targeted for decay by ZFC3H1, a component of the Poly(A) Exosome Targeting complex, and U1-70K, a component of the U1 snRNP. In S. pombe, the ZFC3H1 homolog, Red1, binds to the YTH-domain containing protein Mmi1 to target certain RNA transcripts to nuclear foci for nuclear retention and decay. Here we show that YTHDC1 and YTHDC2, two YTH domain-containing proteins that bind to N-6-methyladenosine (m6A) modified RNAs, interact with ZFC3H1 and U1-70K, and are required for the nuclear retention of mRNAs with intact 5'SS motifs. Disruption of m6A deposition inhibits both the nuclear retention of these transcripts and their accumulation in YTHDC1-enriched foci that are adjacent to nuclear speckles. Endogenous RNAs with intact 5'SS motifs, such as intronic polyadenylated transcripts, tend to be m6A-modified at low levels. Thus, m6A modification acts in a conserved quality control mechanism that targets misprocessed mRNAs for nuclear retention and decay.

molecular biology↗

bioRxiv2021

ZFC3H1 and U1-70K promote the nuclear retention of mRNAs with 5' splice site motif within nuclear speckles

Quality control of mRNA represents an important regulatory mechanism for gene expression in eukaryotes. One component of this quality control is the nuclear retention and decay of misprocessed RNAs. Previously, we demonstrated that mature mRNAs containing a 5 splice site (5SS) motif, which is typically found in misprocessed RNAs such as intronic polyadenylated (IPA) transcripts, are nuclear retained and degraded. Here we demonstrate that these transcripts require the zinc finger protein ZFC3H1 for their decay and nuclear retention into nuclear speckles. Furthermore, we find that U1-70K, a component of the U1 snRNP spliceosomal complex, is also required for their nuclear retention and likely functions in the same pathway as ZFC3H1. Finally, we show that the disassembly of nuclear speckles impairs the nuclear retention of mRNAs with 5SS motifs. Together, our results suggest a model where mRNAs with 5SS motifs are recognized by U1 snRNP, which then acts with ZFC3H1 to both promote their decay and prevent nuclear export of these mRNAs by sequestering them in nuclear speckles. Our results highlight a splicing independent role of U1 snRNP and indicate that it works in conjunction with ZFC3H1 in preventing the nuclear export of misprocessed mRNAs.

molecular biology↗

bioRxiv2019

TPR is required for the nuclear export of mRNAs and lncRNAs from intronless and intron-poor genes

While splicing has been shown to enhance nuclear export, it has remained unclear whether mRNAs generated from intronless genes use specific machinery to promote their export. Here we investigate the role of the major nuclear pore basket protein, TPR, in regulating mRNA and lncRNA nuclear export in human cells. By sequencing mRNA from the nucleus and cytosol of control and TPR-depleted cells, we provide evidence that TPR is required for the nuclear export of mRNAs and lncRNAs that are generated from intronless and intron-poor genes, and we validate this with reporter constructs. Moreover, in TPR-depleted cells reporter mRNAs generated from intronless genes accumulate in nuclear speckles and are bound to Nxf1. These observations suggest that TPR acts downstream of Nxf1 recruitment, and may allow mRNAs to leave nuclear speckles and properly dock with the nuclear pore. In summary, our study provides one of the first examples of a factor that is required for the nuclear export of intronless and intron-poor mRNAs and lncRNAs.

molecular biology↗