Sequence Preference Research Articles

The forkhead DNA-binding domain binds specific G2-rich RNA sequences

Abstract Transcription factors contain a DNA-binding domain ensuring specific recognition of DNA target sequences. The family of forkhead (FOX) transcription factors is composed of dozens of paralogs in mammals. The forkhead domain (FHD) is a segment of about 100 amino acids that binds an A-rich DNA sequence. Using DNA and RNA PCR-SELEX, we show that recombinant FOXL2 proteins, either wild-type or carrying the oncogenic variant C134W, recognize similar DNA-binding sites. This suggests that the oncogenic variant does not alter the intrinsic sequence-specificity of FOXL2. Most importantly, we show that FOXL2 binds G2-rich RNA sequences whereas it virtually fails to bind similar sequences in DNA chemistry. Interestingly, a statistically significant subset of genes responding to the knock-down of FOXL2/Foxl2 harbor such G2-rich sequences and are involved in crucial signaling pathways and cellular processes. In addition, we show that FOXA1, FOXO3a and chimeric FOXL2 proteins containing the FHD of the former are also able to interact with some of the preferred FOXL2-binding sequences. Our results point to an unexpected and novel characteristic of the forkhead domain, the biological relevance of which remains to be explored.

Single-Cell Revelation of Extensive Heterogeneity in the Human Lymphocyte and Neutrophil/Monocyte Lineage Restriction Process Despite Highly Co-Regulated Changes in Cell Cycle Control

The production of mature blood lineages in humans has been viewed as a hierarchical process in which the primitive cells with multi-lineage potential generate a series of progenitors with increasingly reduced self-renewal abilities and restricted lineage potentials. This concept has been largely supported by phenotypic characterization of starting CD34+ subsets of human CD45+ cells isolated from different hematopoietic tissues and assayed for their mature cell outputs in supportive systems in vitro or post-transplant and more recently by tracking changes in their molecular composition. Such experiments have suggested that cells that give rise to the lymphocyte lineages (L) share a common origin almost exclusively with the neutrophil and monocyte (macrophage) lineages (NM). However, the mechanisms that regulate the subsequent separation of these lineages starting from cells with presumed restricted L+NM potential have remained elusive. To address this question, we first developed a culture system that supports outputs of differentiated B (CD19+) and NM (CD15+/CD14+) from ≥50% of single CD34+ cells plated on a stromal layer of MS-5 feeders in a medium containing human IL-7, SCF and FLT3L. Use of this clonal assay revealed that cells with B+NM bi-potential constitute 20% of the CD45RA-CLEC12A- (RA-C-) cell subset of the CB “P-Mix” phenotype (CD34+CD38medCD71-CD10-, Blood 133:927, 2019); with the CD45RA+CLEC12A- (RA+C-) and CLEC12A+ (C+) cells displaying largely restricted outputs of only B- (30%) or only NM- (50%) progeny phenotypes, respectively. These same 3 “progenitor” phenotypes (RA-C-, RA+C-, C+) were also found to be regenerated in xenografted immunodeficient mice as well as in a further optimized in vitro system and their clonal output types and numbers consistent with the outputs of those isolated from fresh CB. To analyze T-cell lineage (T) restriction in parallel, we then further modified this culture system to include adherent DLL4, that we found allows B, T, N and M progeny to be produced from single input CB cells at a 40-60% efficiency, with numerous clones derived from single RA+C- cells containing B+T+M, or B+M, or B+T or T-only; a few with B- or M- only, and none with N. In contrast, under the same conditions, half of the documented C+ outputs were exclusively N with much lower lymphoid outputs of T-only or T+N/M. Together, these findings reveal the unanticipated importance of the external stimuli in revealing lineage potentials when these are undergoing restrictive changes. We then asked if and how these identified early phenotypes might change their cycling properties during the course of their progression. For this, the rate and progeny content of sequential cell divisions during the stimulated expansion of the CFSE labelled RA-C- input cells were measured under a supportive liquid culture condition. Throughout a 6-day period, almost all of the C+ progeny and a slightly lower proportion of the RA+C- outputs were generated from cells that transit through the cell cycle within 24 hours, whereas cells maintaining an undifferentiated RA-C- phenotype divided at significantly slower rates, suggesting a simultaneously initiated shortening of the cell cycle transit time during both L- and NM- restriction. In agreement with these functional results, a recent single-cell CITE-seq dataset generated in parallel showed higher expression of genes involved in cycling activities in the early L- and NM-restricted subsets as compared to the unrestricted RA-C- cells. Taken together, these results reveal important and disconnected features in the cell cycle control and previously unrecognized complex patterns in the biological outputs and molecular changes during the steps of L and NM restriction. In addition, they set the stage to enable preferred sequences and molecular changes responsible for normal and regenerative needs to be identified and their potential relevance to the formation of human lymphoblastic and myeloid leukemias to be characterized.

Engineering of cytosine base editors with DNA damage minimization and editing scope diversification.

Cytosine base editors (CBEs), which enable precise C-to-T substitutions, have been restricted by potential safety risks, including DNA off-target edits, RNA off-target edits and additional genotoxicity such as DNA damages induced by double-strand breaks (DSBs). Though DNA and RNA off-target edits have been ameliorated via various strategies, evaluation and minimization of DSB-associated DNA damage risks for most CBEs remain to be resolved. Here we demonstrate that YE1, an engineered CBE variant with minimized DNA and RNA off-target edits, could induce prominent DSB-associated DNA damage risks, manifested as γH2AX accumulation in human cells. We then perform deaminase engineering for two deaminases lamprey LjCDA1 and human APOBEC3A, and generate divergent CBE variants with eliminated DSB-associated DNA damage risks, in addition to minimized DNA/RNA off-target edits. Furthermore, the editing scopes and sequence preferences of APOBEC3A-derived CBEs could be further diversified by internal fusion strategy. Taken together, this study provides updated evaluation platform for DSB-associated DNA damage risks of CBEs and further generates a series of safer toolkits with diversified editing signatures to expand their applications.

High-Accuracy Prediction of Stabilizing Surface Mutations to the Three-Helix Bundle, UBA(1), with EmCAST.

The accurate modeling of energetic contributions to protein structure is a fundamental challenge in computational approaches to protein analysis and design. We describe a general computational method, EmCAST (empirical Cα stabilization), to score and optimize the sequence to the structure in proteins. The method relies on an empirical potential derived from the database of the Cα dihedral angle preferences for all possible four-residue sequences, using the data available in the Protein Data Bank. Our method produces stability predictions that naturally correlate one-to-one with the experimental results for solvent-exposed mutation sites. EmCAST predicted four mutations that increased the stability of a three-helix bundle, UBA(1), from 2.4 to 4.8 kcal/mol by optimizing residues in both helices and turns. For a set of eight variants, the predicted and experimental stabilizations correlate very well (R2 = 0.97) with a slope near 1 and with a 0.16 kcal/mol standard error for EmCAST predictions. Tests against literature data for the stability effects of surface-exposed mutations show that EmCAST outperforms the existing stability prediction methods. UBA(1) variants were crystallized to verify and analyze their structures at an atomic resolution. Thermodynamic and kinetic folding experiments were performed to determine the magnitude and mechanism of stabilization. Our method has the potential to enable the rapid, rational optimization of natural proteins, expand the analysis of the sequence/structure relationship, and supplement the existing protein design strategies.

Mycobacterial RNase E cleaves with a distinct sequence preference and controls the degradation rates of most Mycolicibacterium smegmatis mRNAs

The mechanisms and regulation of RNA degradation in mycobacteria have been subject to increased interest following the identification of interplay between RNA metabolism and drug resistance. Mycobacteria encode multiple ribonucleases predicted to participate in mRNA degradation and/or processing of stable RNAs. RNase E is hypothesized to play a major role in mRNA degradation because of its essentiality in mycobacteria and its role in mRNA degradation in gram-negative bacteria. Here, we defined the impact of RNase E on mRNA degradation rates transcriptome-wide in the nonpathogenic model Mycolicibacterium smegmatis. RNase E played a rate-limiting role in degradation of the transcripts encoded by at least 89% of protein-coding genes, with leadered transcripts often being more affected by RNase E repression than leaderless transcripts. There was an apparent global slowing of transcription in response to knockdown of RNase E, suggesting that M.smegmatis regulates transcription in responses to changes in mRNA degradation. This compensation was incomplete, as the abundance of most transcripts increased upon RNase E knockdown. We assessed the sequence preferences for cleavage by RNase E transcriptome-wide in M.smegmatis and Mycobacterium tuberculosis and found a consistent bias for cleavage in C-rich regions. Purified RNase E had a clear preference for cleavage immediately upstream of cytidines, distinct from the sequence preferences of RNase E in gram-negative bacteria. We furthermore report a high-resolution map of mRNA cleavage sites in M. tuberculosis, which occur primarily within the RNase E-preferred sequence context, confirming that RNase E has a broad impact on the M.tuberculosis transcriptome.

Inter-species association mapping links splice site evolution to METTL16 and SNRNP27K.

Eukaryotic genes are interrupted by introns that are removed from transcribed RNAs by splicing. Patterns of splicing complexity differ between species, but it is unclear how these differences arise. We used inter-species association mapping with Saccharomycotina species to correlate splicing signal phenotypes with the presence or absence of splicing factors. Here, we show that variation in 5' splice site sequence preferences correlate with the presence of the U6 snRNA N6-methyladenosine methyltransferase METTL16 and the splicing factor SNRNP27K. The greatest variation in 5' splice site sequence occurred at the +4 position and involved a preference switch between adenosine and uridine. Loss of METTL16 and SNRNP27K orthologs, or a single SNRNP27K methionine residue, was associated with a preference for +4 U. These findings are consistent with splicing analyses of mutants defective in either METTL16 or SNRNP27K orthologs and models derived from spliceosome structures, demonstrating that inter-species association mapping is a powerful orthogonal approach to molecular studies. We identified variation between species in the occurrence of two major classes of 5' splice sites, defined by distinct interaction potentials with U5 and U6 snRNAs, that correlates with intron number. We conclude that variation in concerted processes of 5' splice site selection by U6 snRNA is associated with evolutionary changes in splicing signal phenotypes.

Hip-spine syndrome in adult spinal deformity patients

With the increasing prevalence of hip-spine syndrome, it is crucial to appreciate the biomechanical interplay between hip and spine degeneration or deformity and the consequential compensatory changes. Adult spinal deformity (ASD) patients are uniquely affected as a concomitant hip osteoarthritis (HOA) may impact their baseline and postoperative sagittal alignment. Similarly, severe HOA patients undergoing total hip replacement with concomitant spinal deformity may require personalized surgical planning for the placement of their acetabular component. If surgical intervention is required in ASD patients, the authors’ preferred sequence is to perform spinal realignment first. If major realignment is not planned, we recommend treating the most symptomatic pathology. Further investigation is required to evaluate the impact of hip pathology on radiographic and patient-reported outcomes following ASD surgery and vice versa.

Elongation rate of RNA polymerase II affects pausing patterns across 3′ UTRs

Yeast mRNAs are polyadenylated at multiple sites in their 3' untranslated regions (3' UTRs), and poly(A) site usage is regulated by the rate of transcriptional elongation by RNA polymerase II (Pol II). Slow Pol II derivatives favor upstream poly(A) sites, and fast Pol II derivatives favor downstream poly(A) sites. Transcriptional elongation and polyadenylation are linked at the nucleotide level, presumably reflecting Pol II dwell time at each residue that influences the level of polyadenylation. Here, we investigate the effect of Pol II elongation rate on pausing patterns and the relationship between Pol II pause sites and poly(A) sites within 3' UTRs. Mutations that affect Pol II elongation rate alter sequence preferences at pause sites within 3' UTRs, and pausing preferences differ between 3' UTRs and coding regions. In addition, sequences immediately flanking the pause sites show preferences that are largely independent of Pol II speed. In wild-type cells, poly(A) sites are preferentially located< 50 nucleotides upstream from Pol II pause sites, but this spatial relationship is diminished in cells harboring Pol II speed mutants. Based on a random forest classifier, Pol II pause sites are modestly predicted by the distance to poly(A) sites but are better predicted by the chromatin landscape in Pol II speed derivatives. Transcriptional regulatory proteins can influence the relationship between Pol II pausing and polyadenylation but in a manner distinct from Pol II elongation rate derivatives. These results indicate a complex relationship between Pol II pausing and polyadenylation.

Variation in the CENP-A sequence association landscape across diverse inbred mouse strains

Centromeres are crucial for chromosome segregation, but their underlying sequences evolve rapidly, imposing strong selection for compensatory changes in centromere-associated kinetochore proteins to assure the stability of genome transmission. While this co-evolution is well documented between species, it remains unknown whether population-level centromere diversity leads to functional differences in kinetochore protein association. Mice (Mus musculus) exhibit remarkable variation in centromere size and sequence, but the amino acid sequence of the kinetochore protein CENP-A is conserved. Here, we apply k-mer-based analyses to CENP-A chromatin profiling data from diverse inbred mouse strains to investigate the interplay between centromere variation and kinetochore protein sequence association. We show that centromere sequence diversity is associated with strain-level differences in both CENP-A positioning and sequence preference along the mouse core centromere satellite. Our findings reveal intraspecies sequence-dependent differences in CENP-A/centromere association and open additional perspectives for understanding centromere-mediated variation in genome stability.

Nuclear receptor RXRα binds the precursor of miR-103 to inhibit its maturation

BackgroundThe maturation of microRNAs (miRNAs) successively undergoes Drosha, Dicer, and Argonaute ˗mediated processing, however, the intricate regulations of the individual miRNA maturation are largely unknown. Retinoid x receptor alpha (RXRα) belongs to nuclear receptors that regulate gene transcription by binding to DNA elements, however, whether RXRα binds to miRNAs to exert physiological functions is not known.ResultsIn this work, we found that RXRα directly binds to the precursor of miR-103 (pre-miR-103a-2) via its DNA-binding domain with a preferred binding sequence of AGGUCA. The binding of RXRα inhibits the processing of miR-103 maturation from pre-miR-103a-2. Mechanistically, RXRα prevents the nuclear export of pre-miR-103a-2 for further processing by inhibiting the association of exportin-5 with pre-miR-103a-2. Pathophysiologically, the negative effect of RXRα on miR-103 maturation correlates to the positive effects of RXRα on the expression of Dicer, a target of miR-103, and on the inhibition of breast cancer.ConclusionsOur findings unravel an unexpected role of transcription factor RXRα in specific miRNA maturation at post-transcriptional level through pre-miRNA binding, and present a mechanistic insight regarding RXRα role in breast cancer progression.

Engineering RsDddA as mitochondrial base editor with wide target compatibility and enhanced activity

Double-stranded DNA-specific cytidine deaminase (DddA) base editors hold great promise for applications in bio-medical research, medicine, and biotechnology. Strict sequence preference on spacing region presents a challenge for DddA editors to reach their full potential. To overcome this sequence-context constraint, we analyzed a protein dataset and identified a novel DddAtox homolog from Ruminococcus sp. AF17-6 (RsDddA). We engineered RsDddA for mitochondrial base editing in a mammalian cell line and demonstrated RsDddA-derived cytosine base editors (RsDdCBE) offered a broadened NC sequence compatibility and exhibited robust editing efficiency. Moreover, our results suggest the average frequencies of mitochondrial genome-wide off-target editing arising from RsDdCBE are comparable to canonical DdCBE and its variants.

The Influence of KE and EW Dipeptides in the Composition of the Thymalin Drug on Gene Expression and Protein Synthesis Involved in the Pathogenesis of COVID-19.

Thymalin is an immunomodulatory drug containing a polypeptide extract of thymus that has demonstrated efficacy in the therapy of acute respiratory distress syndrome and chronic obstructive pulmonary disease, as well as in complex therapy related to severe COVID-19 in middle-aged and elderly patients.. KE and EW dipeptides are active substances of Thymalin. There is evidence that KE stimulates cellular immunity and nonspecific resistance in organisms, exerting an activating effect on macrophages, blood lymphocytes, thymocytes, and neutrophils, while EW reduces angiotensin-induced vasoconstriction and preserves endothelium-dependent vascular relaxation by inhibiting ACE2, the target protein of SARS-CoV-2. However, the mechanism of the immunomodulatory action of Thymalin, KE, and EW during COVID-19 remains unclear. To identify the potential mechanism of action underlying the immunomodulatory activity of Thymalin and its active components, EW and KE dipeptides, we assessed inflammatory response in the context of COVID-19. Interactions between EW and KE dipeptides and double-stranded DNA (dsDNA) were investigated by molecular modeling and docking using ICM-Pro. Analysis of the possible effect of EW and KE dipeptides on gene expression and protein synthesis involved in the pathogenesis of COVID-19 was conducted through the use of bioinformatics methods, including a search for promoter sequences in the Eukaryotic Promoter Database, the determination of genes associated with the development of COVID-19 using the PathCards database of human biological pathways (pathway unification database), identification of the relationship between proteins through cluster analysis in the STRING database ('Search Tool for Retrieval of Interacting Genes/Proteins'), and assessment of the functional enrichment of protein-protein interaction (PPI) using the terms of gene ontology (GO) and the Markov cluster algorithm (MCL). After that, in vitro studying of a lipopolysaccharide (LPS)-induced model of inflammation using human peripheral blood mononuclear cells was performed. ELISA was applied to assess the level of cytokines (IL-1β, IL-6, TNFα) in the supernatant of cells with or without the impact of EW and KE peptides. Blood samples were obtained from four donors; for each cytokine, ELISA was performed 2-4 times, with two parallel experimental or control samples for each experiment (experiments to assess the effects of peptides on LPS-stimulated cells were repeated four times, while additional experiments with unstimulated cells were performed two times). Using molecular docking, GGAG was found to be the best dsDNA sequence in the classical B-form for binding the EW dipeptide, while GCGC is the preferred dsDNA sequence in the curved nucleosomal form for the KE dipeptide. Cluster analysis revealed that potential target genes for the EW and KE peptides encode the AKT1 and AKT2 proteins involved in the development of the cytokine storm. The specific targets for the EW peptide are the ACE2 and CYSLTR1 genes, and specific target for the KE peptide is the CHUK gene. Protein products of the ACE2, CYSLTR1, and CHUK genes are functionally associated with IL-1β, IL-6, TNF-α, IL-4, and IL-10 cytokines. An in vitro model of an inflammatory reaction demonstrated that Thymalin and EW and KE dipeptides reduced the synthesis of IL-1β, IL-6, and TNF-α cytokines in human peripheral blood mononuclear cells by 1.4-6.0 times. The immunomodulatory effect of Thymalin under the inflammatory response conditions in COVID-19 is based on the potential ability of its active components, EW and KE dipeptides, to regulate protein synthesis involved in the development of the cytokine storm.

Single-valued neutrosophic dynamic aggregation information with time sequence preference for IoT technology in supply chain management

The Internet of thing (IoT) is a global platform for connecting intelligent objects over the Internet. It facilitates the integration of the “supply chain (SC)” and “information and communication technology (ICT)” infrastructures inside a company and with its vendors and clients. The “supply chain management (SCM)” is presently required if a firm wishes to keep up with the rapid evolution of its consumers’ needs. Several research has demonstrated that manufacturing companies must expedite the transition of their attention to sustainable development and the application of innovative technologies, such as IoT, in order to achieve their organizational objectives most efficiently. This study intends to examine the IoT’s applicability in SCM and assess the most popular IoT systems. The difficulty of identifying the best suitable IoT system is dependent on a multitude of variables, which are sometimes stated as incomplete and unreliable estimations. In order to reach an outcome, this paper proposes a multi-criteria paradigm for IoT solution selection in a single-valued neutrosophic environment. Single-valued neutrosophic set (SiVNS) is a strong model to address uncertain information in terms of three membership functions, namely indeterminacy, truthfulness, and falsity. The goal of this study is to introduce some dynamic single-valued neutrosophic aggregation operators (AOs) for multi-period decision-making problems that involve uncertain single-valued neutrosophic information. We develop novel Einstein AOs named as “dynamic single-valued neutrosophic Einstein weighted averaging (DSiVNEWA) operator and dynamic single-valued neutrosophic Einstein weighted geometric (DSiVNEWG) operator”. Several characteristics of the suggested AOs are investigated. Additionally, we develop a multi-stage dynamic decision analysis utilizing ideal solutions. To illustrate the proposed technique, a numerical example is presented. Comparison and authenticity analyses are conducted to ascertain the efficacy and superiority of the suggested multi-stage dynamic decision analysis in the practical situation.

Sequence dependencies and mutation rates of localized mutational processes in cancer

BackgroundCancer mutations accumulate through replication errors and DNA damage coupled with incomplete repair. Individual mutational processes often show nucleotide sequence and functional region preferences. As a result, some sequence contexts mutate at much higher rates than others, with additional variation found between functional regions. Mutational hotspots, with recurrent mutations across cancer samples, represent genomic positions with elevated mutation rates, often caused by highly localized mutational processes.MethodsWe count the 11-mer genomic sequences across the genome, and using the PCAWG set of 2583 pan-cancer whole genomes, we associate 11-mers with mutational signatures, hotspots of single nucleotide variants, and specific genomic regions. We evaluate the mutation rates of individual and combined sets of 11-mers and derive mutational sequence motifs.ResultsWe show that hotspots generally identify highly mutable sequence contexts. Using these, we show that some mutational signatures are enriched in hotspot sequence contexts, corresponding to well-defined sequence preferences for the underlying localized mutational processes. This includes signature 17b (of unknown etiology) and signatures 62 (POLE deficiency), 7a (UV), and 72 (linked to lymphomas). In some cases, the mutation rate and sequence preference increase further when focusing on certain genomic regions, such as signature 62 in transcribed regions, where the mutation rate is increased up to 9-folds over cancer type and mutational signature average.ConclusionsWe summarize our findings in a catalog of localized mutational processes, their sequence preferences, and their estimated mutation rates.

Preferential nucleation of (O, Y/La/Ce/Hf)-core nano-clusters in multi-element micro-alloyed ferritic alloys: A first-principles study

The high creep strength and high radiation resistance of nanostructured ferritic alloys (NFAs) have been generally attributed to the high-density precipitation of (O, Y)-core nano-clusters and nano-oxides. In this work, the early-stage nucleation of (O, X)-core (X = La, Ce, and Hf) nano-clusters (NCs) with respect to (O, Y)-core NCs in multi-element micro-alloyed NFAs was investigated using first-principles calculations. Their competitive precipitation preference and possible growth sequence were predicted. The (O–O) pair was suggested as the most fundamental core of all types of NCs. Yttrium always has the strongest affinity with the (O–O) pairs to initiate the nucleation of NCs during the early-stage nucleation. Under the absence or depletion of yttrium, other types of (O, X)-core (X = La, Ce, Hf) structures could form, leading to different nucleation paths with the preference ordering of (O, La)-core &amp;gt; (O, Ce)-core &amp;gt; (O, Hf)-core. NC nucleation and composition in NFAs would, thus, strongly depend on the number availabilities of micro-alloying solute species in the neighborhood of the (O–O) pairs.

Using TLC-MALDI-TOF to Interrogate In Vitro Peptidyl Proximal Preferences of PARP14 and Glycohydrolase Specificity.

The transfer of ADP-ribose (ADPr) from nicotinamide adenine dinucleotide (NAD+) to target proteins is mediated by a class of human diphtheria toxin-like ADP-ribosyltransferases (ARTDs; previously referred to as poly-ADP-ribose polymerases or PARPs) and the removal of ADPr is catalyzed by a family of glycohydrolases. Although thousands of potential ADPr modification sites have been identified using high-throughput mass-spectrometry, relatively little is known about the sequence specificity encoded near the modification site. Herein, we present a matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF) method that facilitates the in vitro analysis of proximal factors that guide ARTD target selection. We identify a minimal 5-mer peptide sequence that is necessary and sufficient to drive glutamate/aspartate targeting using PARP14 while highlighting the importance of the adjacent residues in PARP14 targeting. We measure the stability of the resultant ester bond and show that non-enzymatic removal is pH and temperature dependent, sequence independent, and occurs within hours. Finally, we use the ADPr-peptides to highlight differential activities within the glycohydrolase family and their sequence preferences. Our results highlight (1) the utility of MALDI-TOF in analyzing proximal ARTD-substrate interactions and (2) the importance of peptide sequences in governing ADPr transfer and removal.

Optimized infrared photoactivatable ribonucleoside-enhanced crosslinking and immunoprecipitation (IR-PAR-CLIP) protocol identifies novel IGF2BP3-interacting RNAs in colon cancer cells.

The conserved family of RNA-binding proteins (RBPs), IGF2BPs, plays an essential role in posttranscriptional regulation controlling mRNA stability, localization, and translation. Mammalian cells express three isoforms of IGF2BPs: IGF2BP1-3. IGF2BP3 is highly overexpressed in cancer cells, and its expression correlates with a poor prognosis in various tumors. Therefore, revealing its target RNAs with high specificity in healthy tissues and in cancer cells is of crucial importance. Photoactivatable-ribonucleoside-enhanced crosslinking and immunoprecipitation (PAR-CLIP) identifies the binding sites of RBPs on their target RNAs at nucleotide resolution in a transcriptome-wide manner. Here, we optimized the PAR-CLIP protocol to study RNA targets of endogenous IGF2BP3 in a human colorectal carcinoma cell line. To this end, we first established an immunoprecipitation protocol to obtain highly pure endogenous IGF2BP3-RNA complexes. Second, we modified the protocol to use highly sensitive infrared (IR) fluorescent dyes instead of radioactive probes to visualize IGF2BP3-crosslinked RNAs. We named the modified method "IR-PAR-CLIP." Third, we compared RNase cleavage conditions and found that sequence preferences of the RNases impact the number of the identified IGF2BP3 targets and introduce a systematic bias in the identified RNA motifs. Fourth, we adapted the single adapter circular ligation approach to increase the efficiency in library preparation. The optimized IR-PAR-CLIP protocol revealed novel RNA targets of IGF2BP3 in a human colorectal carcinoma cell line. We anticipate that our IR-PAR-CLIP approach provides a framework for studies of other RBPs.

Probabilistic Parking Functions

We consider the notion of classical parking functions by introducing randomness and a new parking protocol, as inspired by the work presented in the paper ``Parking Functions: Choose your own adventure,'' (arXiv:2001.04817) by Carlson, Christensen, Harris, Jones, and Rodríguez. Among our results, we prove that the probability of obtaining a parking function, from a length $n$ preference vector, is independent of the probabilistic parameter $p$. We also explore the properties of a preference vector given that it is a parking function and discuss the effect of the probabilistic parameter $p$. Of special interest is when $p=1/2$, where we demonstrate a sharp transition in some parking statistics. We also present several interesting combinatorial consequences of the parking protocol. In particular, we provide a combinatorial interpretation for the array described in OEIS A220884 as the expected number of preference sequences with a particular property related to occupied parking spots. Lastly, we connect our results to other weighted phenomena in combinatorics and provide further directions for research.

Comparison Between EPI DWI and PROPELLER DWI in Brain MR Imaging

EPI DWI is a routinely used sequence in brain imaging but it has limitations when it comes to SNR and artifact reduction. PROPELLER DWI has the benefit of improving image quality compared to EPI DWI. The aim of this study is to compare the EPI DWI sequence in brain MR imaging with the PROPELLER DWI sequence. The objective is to identify which sequence is more beneficial in brain imaging by evaluating image quality and the depiction of pathologies. A total of 101 patients (55 females and 46 males, mean age 56 years) underwent brain MRI examination on a 1.5 T scanner. EPI DWI and PROPELLER DWI sequences were acquired in every exam and were reviewed by 2 radiologists. The images were evaluated by performing a quantitative analysis based on Relative Contrast and a qualitative analysis (overall image quality, conspicuousness of lesions, artifact reduction, etc.). In both the qualitative and quantitative analysis PROPELLER DWI achieved better results than EPI DWI. PROPELLER DWI showed statistical significance in the overall image quality (P < 0.001), the elimination of susceptibility (P < 0.001) and flow pulsation artifacts (P < 0.001), as well as in the contrast between CSF with white (P < 0.001) and grey matter (P < 0.001). Also, PROPELLER DWI presented better delineation of pathologies like ischemic strokes, metastasis, tumors and vasogenic edemas than conventional EPI DWI. PROPELLER DWI was the preferred sequence during the image evaluation. Compared to EPI DWI, PROPELLER DWI managed to reduce susceptibility and flow pulsation whilst achieving higher image quality and lesion delineation and earlier depiction of ischemic strokes than the conventional EPI DWI. PROPELLER DWI may be incorporated in brain MR imaging replacing EPI DWI.

The effects of length and sequence of gRNA on Cas13b and Cas13d activity in vitro and in vivo.

Cas13 are the only CRISPR/Cas systems found so far, which target RNA strand while preserving chromosomal integrity. Cas13b or Cas13d cleaves RNA by the crRNA guidance. However, the effect of the characteristics of the spacer sequences, such as the length and sequence preference, on the activity of Cas13b and Cas13d remains unclear. Our study shows that neither Cas13b nor Cas13d has a particular preference for the sequence composition of gRNA, including the sequence of crRNA and its flanking sites on target RNA. However, the crRNA, complementary to the middle part of the target RNA, seems to show higher cleavage efficiency for both Cas13b and Cas13d. As for the length of crRNAs, the most appropriate crRNA length for Cas13b is 22-25nt and crRNA as short as 15nt is still functional. Whereas, Cas13d requires longer crRNA, and 22-30nt crRNA can achieve good effect. Both Cas13b and Cas13d show the ability to process precursor crRNAs. Our study suggests that Cas13b may have a stronger precursor processing ability than Cas13d. There are few in vivo studies on the application of Cas13b or Cas13d in mammals. With the methods of transgenic mice and hydrodynamic injection via tail vein, our study showed that both of them had high knock-down efficiency against target RNA in vivo. These results indicate that Cas13b and Cas13d have great potential for in vivo RNA operation and disease treatment without damaging genomic DNA.