C2H2-zinc-finger transcription factors bind RNA and function in diverse post-transcriptional regulatory processes

p53-induced RNA-binding protein ZMAT3 inhibits transcription of a hexokinase to suppress mitochondrial respiration

The tumor suppressor p53 is a transcription factor that controls the expression of hundreds of genes. Emerging evidence suggests that the p53-induced RNA-binding protein ZMAT3 is a key splicing regulator that functions in p53-dependent tumor suppression in vitro and in vivo . However, the mechanism by which ZMAT3 functions in the p53 pathway is largely unclear. Here, we discovered a function of ZMAT3 in inhibiting transcription of HKDC1 , a hexokinase that regulates glucose metabolism and mitochondrial respiration. Using quantitative proteomics, we identified HKDC1 as the most significantly upregulated protein in ZMAT3 -depleted colorectal cancer cells. ZMAT3 depletion results in increased mitochondrial respiration that was rescued upon depletion of HKDC1 , suggesting that HKDC1 is a critical downstream effector of ZMAT3 . Unexpectedly, ZMAT3 did not bind to the HKDC1 RNA or DNA but the identification of the ZMAT3-interactome uncovered its interaction with the oncogenic transcription factor JUN. ZMAT3 depletion resulted in increased JUN binding at the HKDC1 promoter and increased HKDC1 transcription that was rescued upon JUN depletion, suggesting that JUN activates HKDC1 transcription in ZMAT3-depleted cells. Collectively, these data reveal a mechanism by which ZMAT3 regulates transcription and demonstrates that HKDC1 is a key component of the ZMAT3-regulated transcriptome in the context of mitochondrial respiration regulation.

Integrated Genomic and Transcriptomic Analysis Reveals a Transcription Factor Gene Set Facilitating Gonadal Differentiation in the Pacific Oyster Crassostrea gigas

BACKGROUND/OBJECTIVES

The Pacific oyster Crassostrea gigas has emerged as a promising model system for sex determination studies due to its complex reproduction strategy and sex reversal. Transcription factors (TFs) play crucial roles in sex determination and gonadal differentiation. Despite previous research revealing functions of several conserved sex-determining pathway genes, such as Dmrt1, Foxl2, and SoxH, little is known about the other essential TF regulators driving C. gigas gonadal differentiation and development.

METHODS

In this study, a systematic identification of TFs revealed 1167 TF genes in the C. gigas genome. Comparative transcriptome analysis of C. gigas female and male gonads demonstrated 123 differentially expressed TF genes.

RESULTS

The majority of these sex-related TF genes were up-regulated in female or male gonads from the inactive stage to the mature stage. Moreover, this TF gene set was deeply conserved and showed similar regulation in the Kumamoto oyster Crassostrea sikamea gonads, suggesting their important regulatory roles in gonadal differentiation and development in Crassostrea oysters. Furthermore, two BTB TF gene clusters were identified in the C. gigas genome, both of which were specifically expressed in the male gonad. Gene numbers of each BTB gene cluster showed significant variations among six Crassostrea species.

CONCLUSIONS

To the best of our knowledge, this study provides the first report of the whole TF family in C. gigas. The sex-related TF gene set will be a valuable resource for further research aimed at uncovering TF gene regulatory networks in oyster sex determination and gonadal differentiation.

Environmental Exposure, Epitranscriptomic Perturbations, and Human Diseases

Epitranscriptomics is a rapidly evolving field, and it examines how chemical modifications on RNA regulate gene expression. Increasing lines of evidence support that exposure to various environmental agents can change substantially chemical modifications on RNA, thereby perturbing gene expression and contributing to disease development in humans. However, the molecular mechanisms through which environmental exposure impairs RNA modification-associated proteins ("reader", "writer", and "eraser" or RWE proteins) and alters the landscape of RNA modifications remain poorly understood. Here, we provide our perspectives on the current knowledge about how environmental exposure alters the epitranscriptome, where we focus on dynamic changes in RNA modifications and their regulatory proteins elicited by exposure to environmental agents. We discuss how these epitranscriptomic alterations may contribute to the development of human diseases, especially neurodegeneration and cancer. We also discuss the potential and technical challenges of harnessing RNA modifications as biomarkers for monitoring environmental exposure. Finally, we emphasize the need to integrate multiomics approaches to decipher the complex interplay between environmental exposure and the epitranscriptome and offer a forward-looking viewpoint on future research priorities that may inform public health interventions and environmental regulations.

Protein-interaction network analysis reveals a role of Prp19 splicing factor in transcription of both intron-containing and intron-lacking genes

We have previously demonstrated that the transcription-dependent interaction of the promoter and terminator ends of a gene, which results in the formation of a gene loop, is facilitated by the interaction of the general transcription factor TFIIB with the CF1, CPF and Rat1 termination complexes. To further elucidate the protein-protein interactions that stabilize gene loop, we performed mass spectrometry of affinity purified termination complexes from chromatin fraction. Quantitative proteomic analysis revealed additional interactions of termination factors with TFIID and SAGA complex. Since gene looping of intron-containing genes involves additional contacts of the promoter and terminator with the intron, we examined if termination factors interact with the splicing factors as well. All three termination complexes displayed statistically significant interactions with Prp19, Prp43, Sub2, Snu114, Brr2 and Smb1 splicing factors. Since Prp43 and Prp19 consistently emerged as the interactor of both initiation and termination factors, we affinity-purified both and performed mass spectrometry. Prp19 exhibited interactions with subunits of TFIID, CPF complex, and the RSC chromatin remodeling complex. These interactions were observed exclusively in the chromatin context, thereby implicating the factor in transcription of protein coding genes. Since fewer than 4% of yeast genes contain introns, we hypothesized that Prp19 might have a broader role in RNAPII transcription cycle. Auxin-mediated depletion of Prp19 resulted in about two-fold decrease in transcription of a subset of both intron-containing and intron-lacking genes. Specifically, the promoter recruitment of TBP registered a significant decline in the absence of Prp19. Chromatin immunoprecipitation (ChIP) analysis revealed crosslinking of Prp19 to the promoter proximal as well as downstream regions of both intronic and non-intronic genes. These findings demonstrate that Prp19 has a novel role in the initiation step of transcription in yeast.

Transcriptomic characterisation of acute myeloid leukemia cell lines bearing the same t(9;11) driver mutation reveals different molecular signatures

BACKGROUND

Acute myeloid leukemia (AML) is the most common type of acute leukemia, accounting for 20% of cases in children and adolescents. Genome-wide studies have identified genes that are commonly mutated in AML, including many epigenetic regulators involved in either DNA methylation (DNMT3A, TET2, IDH1/2) or histone post-translational modifications (ASXL1, EZH2, MLL1). Several cell lines derived from AML patients are widely used in cancer research. Whether important differences in these cell lines exist remains poorly characterised.

RESULTS

Here, we used RNA sequencing (RNA-Seq) to contrast the transcriptome of four commonly used AML-derived cell lines: THP-1, NOMO-1, MOLM-13 bearing the common initiating t(9;11) translocation, and MV4.11 bearing the t(4;11) translocation. Gene set enrichment analyses and comparison of key transcription and epigenetic regulator genes revealed important differences in the transcriptome, distinguishing these AML models. Among these, we found striking differences in the expression of clusters of genes located on chromosome 19 encoding Zinc Finger (ZNF) transcriptional repressors. Low expression of many ZNF genes within these clusters is associated with poor survival in AML patients.

CONCLUSION

The present study offers a valuable resource by providing a detailed comparative characterisation of the transcriptome of cell lines within the same AML subtype used as models for leukemia research.

A Distinct Mechanism of RNA Recognition by the Transcription Factor GATA1

Several human transcription factors (TFs) have been reported to directly bind RNA through noncanonical RNA-binding domains; however, most of these TFs remain to be further validated as bona fide RNA-binding proteins (RBPs). Our systematic analysis of RBP discovery data sets reveals a varied set of candidate TF-RBPs that encompass most TF families. These candidate RBPs include members of the GATA family that are essential factors in embryonic development. Investigation of the RNA-binding features of GATA1, a major hematopoietic TF, reveals robust sequence independent binding to RNAs in vitro. Moreover, RNA binding by GATA1 is competitive with DNA binding, which occurs through a shared binding surface spanning the DNA-binding domain and arginine-rich motif (ARM)-like domain. We show that the ARM-like domain contributes substantially to high-affinity DNA binding and electrostatically to plastic RNA recognition, suggesting that the separable RNA-binding domain assigned to the ARM-domain in GATA1 is an oversimplification of a more complex recognition network. These biochemical data demonstrate a unified integration of DNA- and RNA-binding surfaces within GATA1, whereby the ARM-like domain provides an electrostatic surface for RNA binding but does not fully dominate GATA1-RNA interactions, which may also apply to other TF-RBPs. This competitive DNA/RNA binding activity using overlapping nucleic acid binding regions points to the possibility of RNA-mediated regulation of the GATA1 function during hematopoiesis. Our study highlights the multifunctionality of DNA-binding domains in RNA recognition and supports the need for robust characterization of predicted noncanonical RNA-binding domains such as ARM-like domains.

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 and targets 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 poly-adenylated transcripts, tend to be m6A-modified at low levels. Thus, the m6A modification acts on a conserved quality control mechanism that targets misprocessed mRNAs for nuclear retention and decay.

The RNA Revolution in the Central Molecular Biology Dogma Evolution

Human genome projects in the 1990s identified about 20,000 protein-coding sequences. We are now in the RNA revolution, propelled by the realization that genes determine phenotype beyond the foundational central molecular biology dogma, stating that inherited linear pieces of DNA are transcribed to RNAs and translated into proteins. Crucially, over 95% of the genome, initially considered junk DNA between protein-coding genes, encodes essential, functionally diverse non-protein-coding RNAs, raising the gene count by at least one order of magnitude. Most inherited phenotype-determining changes in DNA are in regulatory areas that control RNA and regulatory sequences. RNAs can directly or indirectly determine phenotypes by regulating protein and RNA function, transferring information within and between organisms, and generating DNA. RNAs also exhibit high structural, functional, and biomolecular interaction plasticity and are modified via editing, methylation, glycosylation, and other mechanisms, which bestow them with diverse intra- and extracellular functions without altering the underlying DNA. RNA is, therefore, currently considered the primary determinant of cellular to populational functional diversity, disease-linked and biomolecular structural variations, and cell function regulation. As demonstrated by RNA-based coronavirus vaccines' success, RNA technology is transforming medicine, agriculture, and industry, as did the advent of recombinant DNA technology in the 1980s.