Distinct roles of two SEC scaffold proteins,AFF1 and AFF4,in regulating RNA polymerase Ⅱ transcription elongation

The super elongation complex(SEC)containing positive transcription elongation factor b plays a critical role in regulating transcription elongation.AFF1 and AFF4,two members of the AF4/FMR2 family,act as central scaffold proteins of SEC and are associated with various human diseases.However,their precise roles in transcriptional control remain unclear.Here,we investigate differences in the genomic distribution patterns of AFF1 and AFF4 around transcription start sites(TSSs).AFF1 mainly binds upstream of the TSS,while AFF4 is enriched downstream of the TSS.Notably,disruption of AFF4 results in slow elongation and early termination in a subset of AFF4-bound active genes,whereas AFF1 deletion leads to fast elongation and transcriptional readthrough in the same subset of genes.Additionally,AFF1 knockdown increases AFF4 levels at chromatin,and vice versa.In summary,these findings demonstrate that AFF1 and AFF4 function antagonistically to regulate RNA polymerase Ⅱ transcription.

The tumor-selective over-expression of the human Hsp 70 gene is attributed to the aberrant controls at both initiation and elongation levels of transcription

The tumor selective over-expression of the human Hsp70 gene has been well documented in human tumors,linked to the poor prognosis,being refractory to chemo-and radio-therapies as well as the advanced stage of tumorous lesions in particular.However,both the nature and details of aberrations in the control of the Hsp70 expression in tumor remain enigmatic.By comparing various upstream segments of the Hsp70 gene for each''s ability to drive the luciferase reporter genes in the context of the tumor cell lines varying in their p53 status and an immortal normal liver cell line,we demonstrated in a great detail the defects in the control mechanisms at the both initiation and elongation levels of transcription being instrumental to the tumor selective profile of its expression.Our data should not only offer new insights into our understanding of the tumor specific over-expression of the human Hsp70 gene,but also paved the way for the rational utilization of the tumor selective mechanism with the Hsp70 at the central stage fortargeting the therapeutic gene expression to human tumors.

GLTSCR1 coordinates alternative splicing and transcription elongation of ZO1 to regulate colorectal cancer progression

Alternative splicing(AS)and transcription elongation are vital biological processes,and their dysregulation causes multiple diseases,including tumors.However,the coregulatory mechanism of AS and transcription elongation in tumors remains unclear.This study demonstrates a novel AS pattern of tight junction protein 1(ZO1)regulated by the RNA polymerase II elongation rate in colorectal cancer(CRC).Glioma tumor suppressor candidate region gene 1(GLTSCR1)decreases the transcription elongation rate of ZO1 to provide a time window for binding of the splicing factor HuR to the specific motif in intron 22 of ZO1 and spliceosome recognition of the weak 3 and 5 splice sites in exon 23 to promote exon 23 inclusion.Since exon 23 inclusion in ZO1 suppresses migration and invasion of CRC cells,our findings suggest a novel potential therapeutic target for CRC.

An intermediate state of T7 RNA polymerase provides another pathway of nucleotide selection

Phage T7 RNA polymerase is a single-subunit transcription enzyme, transcribing template DNA to RNA. Nucleoside triphosphate （NTP） selection and translocation are two critical steps of the transcription elongation. Here, using all-atom molecular dynamics simulations, we found that between pre- and post-translocation states of T7 RNA polymerase an intermediate state exists, where the O helix C-terminal residue tyrosine 639, which plays important roles in translocation, locates between its pre- and post-translocation positions and the side chain of the next template DNA nucleotide has moved into the active site. NTP selection in this intermediate state was studied, revealing that the selection in the intermediate state can be achieved relying on the effect of Watson-Crick interaction between NTP and template DNA nucleotide, effect of stability of the components near the active site such as the nascent DNA-RNA hybrid and role of tyrosine 639. This indicates that another NTP-selection pathway can also exist besides the main pathway where NTP selection begins at the post-translocation state upon the entry of NTE

Npac Is A Co-factor of Histone H3K36me3 and Regulates Transcriptional Elongation in Mouse Embryonic Stem Cells

Chromatin modification contributes to pluripotency maintenance in embryonic stem cells(ESCs).However,the related mechanisms remain obscure.Here,we show that Npac,a"reader"of histone H3 lysine 36 trimethylation(H3K36me3),is required to maintain mouse ESC(mESC)pluripotency since knockdown of Npac causes mESC differentiation.Depletion of Npac in mouse embryonic fibroblasts(MEFs)inhibits reprogramming efficiency.Furthermore,our chromatin immunoprecipitation followed by sequencing(ChIP-seq)results of Npac reveal that Npac co-localizes with histone H3K36me3 in gene bodies of actively transcribed genes in mESCs.Interestingly,we find that Npac interacts with positive transcription elongation factor b(p-TEFb),Ser2-phosphorylated RNA PolⅡ(RNA PolⅡSer2P),and Ser5-phosphorylated RNA PolⅡ(RNA PolⅡSer5 P).Furthermore,depletion of Npac disrupts transcriptional elongation of the pluripotency genes Nanog and Rif1.Taken together,we propose that Npac is essential for the transcriptional elongation of pluripotency genes by recruiting p-TEFb and interacting with RNA PolⅡSer2P and Ser5P.

The INO80 chromatin remodeling complex promotes thermo-morphogenesis by connecting H2A.Z eviction and active transcription in Arabidopsis.

Global warming imposes a major threat to plant growth and crop production. In some plants including Arabidopsis thaliana, elevated temperatures induce a series of morphological and developmental adjustments, termed thermomorphogenesis to facilitate plant cooling under high-temperature conditions. Plant thermal response is suppressed by histone variant H2A.Z. At warm temperatures, H2A.Z is evicted from nucleosomes at thermo-responsive genes, resulting in their expression changes. However, the mechanisms that regulate H2A.Z eviction and subsequent transcription changes are largely unknown. Here, we show that the INO80 chromatin remodeling complex (INO80-C) promotes thermomorphogenesis and activates the expression of thermo-responsive and auxin-related genes. INO80-C associates with PHYTOCHROME-INTERACTING FACTOR 4 (PIF4), a potent regulator in thermomorphogenesis, and mediates temperature-induced H2A.Z eviction at PIF4 targets. Moreover, INO80-C directly interacts with COMPASS-like and transcription elongation factors to promote active histone modification Histone H3 lysine 4 trimethylation (H3K4me3) and RNA Polymerase II (RNA Pol II) elongation, leading to the thermal induction of transcription. Notably, transcription elongation factors SPT4 and SPT5 are required for the H2A.Z eviction at PIF4 targets, suggesting the cooperation of INO80-C and transcription elongation in H2A.Z removal. Our results demonstrate that the (PIF4)-(INO80-C)-(COMPASS-like)-(transcription elongator) module controls plant thermal response, and establish a link between H2A.Z eviction and active transcription.

Linking circular intronic RNA degradation and function in transcription by RNase H1

Circular intronic RNAs(ci RNAs) escaping from DBR1 debranching of intron lariats are co-transcriptionally produced from prem RNA splicing, but their turnover and mechanism of action have remained elusive. We report that RNase H1 degrades a subgroup of ci RNAs in human cells. Many ci RNAs contain high GC% and tend to form DNA:RNA hybrids(R-loops) for RNase H1 cleavage, a process that appears to promote Pol II transcriptional elongation at ci RNA-producing loci. One ci RNA, ciankrd52, shows a stronger ability of R-loop formation than that of its cognate pre-m RNA by maintaining a locally open RNA structure in vitro. This allows the release of pre-m RNA from R-loops by ci-ankrd52 replacement and subsequent ci RNA removal via RNase H1 for efficient transcriptional elongation. We propose that such an R-loop dependent ci RNA degradation likely represents a mechanism that on one hand limits ci RNA accumulation by recruiting RNase H1 and on the other hand resolves Rloops for transcriptional elongation at some GC-rich ci RNA-producing loci.

Mechanism and factors that control HIV-1 transcription and latency activation

After reverse transcription, the HIV-1 proviral DNA is integrated into the host genome and thus subjected to transcription by the host RNA polymerase Ⅱ （Pol Ⅱ）. With the identification and characterization of human P-TEFb in the late 1990s as a specific host cofactor required for HIV-1 transcription, it is now believed that the elongation stage of Pol Ⅱ transcription plays a particularly important role in regulating HIV-1 gene expression. HIV-1 uses a sophisticated scheme to recruit human P-TEFb and other cofactors to the viral long terminal repeat （LTR） to produce full-length HIV-1 transcripts. In this process, P-TEFb is regulated by the reversible association with various transcription factors/ cofactors to form several multi-subunit complexes （e.g., 7SK snRNP, super elongation complexes （SECs）, and the Brd4-P-TEFb complex） that collectively constitute a P-TEFb network for controlling cellular and HIV-1 transcription. Recent progresses in HIV-1 transcription were reviewed in the paper, with the emphasis on the mechanism and factors that control HIV-1 transcription and latency activation.

Sequence data reveal a high diversity of Cantharellus associated with endemic vegetation in Madagascar

This revision of Cantharellus in Madagascar deals with species that are associated with strictly endemic host trees and shrubs.Based on morphological differences and molecular sequence data of the tef-1 gene,five new species are proposed(C.albidolutescens,C.ambohitantelyensis,C.ibityensis,C.paucifurcatus and C.sebosus),as well as one new subspecies,C.subincarnatus ssp.rubrosalmoneus,whereas C.decolorans and C.platyphyllus ssp.bojeriensis are epitypified.A key is provided to all Cantharellus that grow with native vegetation in Madagascar.

Developmental regulation of neuronal gene expression by Elongator complex protein 1 dosage

Familial dysautonomia(FD), a hereditary sensory and autonomic neuropathy, is caused by a mutation in the Elongator complex protein 1(ELP1) gene that leads to a tissue-specific reduction of ELP1 protein. Our work to generate a phenotypic mouse model for FD headed to the discovery that homozygous deletion of the mouse Elp1 gene leads to embryonic lethality prior to mid-gestation. Given that FD is caused by a reduction, not loss, of ELP1, we generated two new mouse models by introducing different copy numbers of the human FD ELP1 transgene into the Elp1 knockout mouse(Elp1) and observed that human ELP1 expression rescues embryonic development in a dose-dependent manner. We then conducted a comprehensive transcriptome analysis in mouse embryos to identify genes and pathways whose expression correlates with the amount of ELP1. We found that ELP1 is essential for the expression of genes responsible for nervous system development. Further, gene length analysis of the differentially expressed genes showed that the loss of Elp1 mainly impacts the expression of long genes and that by gradually restoring Elongator, their expression is progressively rescued. Finally, through evaluation of co-expression modules, we identified gene sets with unique expression patterns that depended on ELP1 expression.