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Results for “chromatin-bound RNA sequencing”

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PubMed2026

Transposable element-driven expansion of enhancer RNA repertoires underlies regulatory innovation and polyploid adaptation in cereal crops.

Cereal genomes have undergone repeated polyploidization and transposable element (TE) proliferation, collectively generating complex regulatory landscapes. However, the evolutionary trajectories and functional implications of these landscapes remain largely unexplored. Using chromatin-bound RNA sequencing across seven cereal species, we systematically mapped 45,952 regulatory element transcripts (RETs), including 32,867 distal RETs corresponding to enhancer RNAs (eRNAs). Our analysis revealed that 56% of lineage-specific eRNAs originated from TE expansions, indicating that TEs serve as major reservoirs of species-specific regulatory innovation in cereals. Notably, we identified remarkable conservation in defense-related functions, root-specific expression, and TE-derived origins of eRNAs across both ancient and recent evolutionary layers of Triticeae, suggesting recurrent recruitment of TE-derived, root-associated regulatory elements throughout Triticeae evolution. Furthermore, we found that young eRNA pairs in hexaploid wheat with high sequence similarity, many originating from RLG_famc8.3 and DTC_famc4.3, exhibited pronounced root specificity and coordinated expression, suggesting targeted amplification and refinement of successful ancestral regulatory strategies established after Triticeae divergence. To facilitate community access, we developed Cereal-eRNAdb (http://bioinfo.cemps.ac.cn/Cereal-eRNAdb/), a comprehensive database integrating 69,426 eRNAs with functional annotations across 296 samples. Our findings suggest that TE-mediated innovation of root-specific eRNAs may contribute to Triticeae adaptation and provide a foundational resource for exploiting regulatory variation in cereal crop breeding.

Enhancer RNAs↗

PubMed1978

Studies on the regulation of RNA synthesis in neuronal and glial nuclei isolated from rat brain.

In searching for regulatory mechanisms involved in the cell-specific neuronal and glial transcription a cell-free transcriptional system has been developed using neuronal and glial rat brain chromatin and partially purified neuronal and glial nuclear rat brain RNA polymerases. Both free and chromatin-bound (engaged) neuronal and glial RNA polymerase fractions were separated from isolated neuronal and glial rat brain nuclei to determine their transcriptive efficiency. A double number of RNA initiation sites was measured on the neuronal when compared to the glial chromatin, independently of whether the neuronal or the glial RNA polymerase preparation was used for the determination. Structural modification of the neuronal and glial chromatin template by acetylation with acetyl-coenzyme A leads to an increase of the total number of RNA initiation sites available for exogenously added rat brain RNA polymerase. This indicates that acetylation of chromatin-bound proteins is capable to render primarily restricted gene sequences transcriptable. A positive correlation exists between the extent of acetate uptake by neuronal and glial chromatin-bound histone fractions and the extent of the increase of the number of RNA initiation sites is specifically related to histone acetylation rather than to acetylation of any other chromatin protein. Significant information in this respect could be achieved by dissociation of chromatin into its principal components and selectively reconstituting DNA with specifically acetylated histone and non-histone proteins.

Animals↗

PubMed1975

Cell-free transcription of mammalian chromatin. Quantitative measurement of newly synthesized globin messenger RNA sequences.

Transcription of globin mRNA sequences from rabbit marrow chromatin was detected by hybridization with globin complementary DNA (cDNA). The presence of newly synthesized RNA in cDNA-globin mRNA hybrids isolated by Cs2SO4 density equilibrium centrifugation required the addition of both rabbit marrow chromatin and DNA-dependent RNA polymerase (Escherichia coli) to the transcription reaction. No globin mRNA sequences were detected in RNA transcribed from rabbit liver chromatin or from rabbit marrow DNA. Selective transcription of globin mRNA sequences was therefore tissue-specific and dependent on the presence of chromosomal proteins. Globin mRNA sequences synthesized by E. coli RNA polymerase were distinguished from those synthesized by chromatin-bound (endogenous) RNA polymerases by the use of alpha-amanitin. A typical reaction with rabbit marrow chromatin yielded 100 mug of purified RNA which contained approximately 5 ng (0.005%) of globin mRNA sequences synthesized by E. coli RNA polymerase, 1 ng (0.001%) of globin mRNA seqeences synthesized by endogenous RNA polymerases, and 4 ng (0.004%) of globin mRNA sequences derived from chromatin-associated (endogenous) RNA. Forty per cent of the globin mRNA sequences derived from endogenous RNA could be removed by poly(U)-Sepharose chromatography. The accurate measurement of globin mRNA sequences required improved conditions for the purification and hybridization of RNA transcribed from chromatin.

Animals↗

PubMed1978

Developmental transitions between chromatin-bound and soluble RNA polymerase subspecies in the soybean hypocotyl.

RNA polymerase enzymes isolated from soybean hypocotyl tissue during successive developmental stages (2-8 days old) have been fractionated by Sephadex column isoelectric focusing. Both the enzymes bound to chromatin and those enzymes free in the soluble phase were investigated during development with respect to their distribution within these two pools. All observed activites were classified according to their alpha-amanitin sensitivity and isoelectric points. Two Class I subspecies (Ia, Ib) and two Class III subspecies (IIIa, IIIb) were continually present bound to chromatin throughout the developmental sequences except the IIb form which was absent at the latest stage. However, a great multiplicity (9 total) of Class II activities (totally inhibited by alpha-amanitin) were observed to be bound to chromatin at the 2nd day stage. These forms were first released from the chromatin complex and recovered in a soluble pool (4th day stage). Subsequent hypocotyl development was accompanied by the gradual disappearance of these Class II subspecies from this pool (6th day) until only two soluble species and one chromatin-bound Class II activity remained (8th day). These observations indicate that the early development of this tissue is accompanied by a dramatic alteration in the conplexity of chromatin-bound RNA polymerase subspecies. Such events may in part determine the domain of RNA secies synthesized at successive developmental stages.

Chromatin↗

PubMed1978

Developmental restrictions on hormone modulated gene transcription. II. Hormone induced interactions of RNA polymerase with chromatin.

Chromatin-bound and soluble RNA polymerase subspecies have been isolated and fractionated by isoelectric focusing at various times (0, 6, 12 and 18 h) following auxin treatment of 4 day (responsive) and 8 day (unresponsive) soybean hypocotyls. Young 4 day seedlings displayed two well defined phases of auxin induced gene transcription. Phase I (6 h) evidenced the selective dissociation of many RNA polymerase subspecies from the chromatin complex which was accompanied by the retention of three class II enzymes. Phase II occurred after 12 h of treatment when the dissociated enzymes including some species which were soluble in the 0 h controls became re-associated with chromatin. These induced RNA polymerases may be responsible for the synthesis of auxin induced RNAs. In contrast, the unresponsive 8 day hypocotyl did not display two phases of auxin induction. Phase one, the dissociation of the chromatin bound enzymes, occurred at 12 h (compared to 6 h for the 4 day seedling) and was not followed by the later translocation of any soluble enzymes towards the chromatin complex. The results support earlier findings suggesting that the developmental "phasing out" of RNA polymerase subspecies limits the hormone induced growth response of this tissue and thus is regarded as an off switch for the transcription of such hormone controlled gene sequences.

2,4-Dichlorophenoxyacetic Acid↗

PubMed1979

Developmental restrictions on transcription: determinants of the developmental program and their role in aging.

A developing plant system, the soybean hypocotyl has been used to investigate early transcription events which restrict auxin induced cellular proliferation to the appropriate developmental stage. Auxin treatment of 4-day old seedlings resulted in an early (6 hour) activation of chromatin-bound RNA polymerase activity wihich approached 200% of control values by 18 hours. This occurred without a detectable alteration in chromatin template capacity (assayed with exogenous RNA polymerase) and resulted in the synthesis of "induced RNA transcripts" as determined in vitro by nearest neighbor analysis. In contrast, auxin treatment of unresponsive 8-day old seedlings did not alter the chromatin-bound RNA polymerase activity. Hormonal activation did, however, result in the exposure of "induced template" regions in chromatin which could only be transcribed in vitro if exogenous RNA polymerase was included in the transcription reaction. Isoelectric focusing of the endogenous chromatin-bound and soluble RNA polymerase enzymes from successive developmental stages revealed that the chromatin-bound enzymes at the 2-day stage were first released from the chromatin complex and could be recovered in the soluble pool (4-day stage). This was followed by a gradual disappearance of these subspecies (6-day stage) until only a limited ensemble of RNA polymerase subspecies remained bound to chromatin and free in the soluble pool (8-day stage). Similar analyses of both the bound and free enzymes at the 4 and 8-day stages following auxin treatment revealed that the 4-day soluble enzymes could be induced to rebind to the chromatin complex in a defined sequence after hormone treatment while those of the 8-day hypocotyl were unable to do so. These developmental events indicate that the select loss of certain RNA polymerase subspecies serves to restrict the hormone responsivness of this tissue to the early developmental stages. Such restrictions could thus commit the constituent hypocotyl cells to their terminal post-mitotic phase of development.

2,4-Dichlorophenoxyacetic Acid↗

PubMed1977

Effect of proteolysis of transcriptional fidelity of reconstituted chromatin.

The effect of proteolysis on the transcriptional properties of reconstituted rat liver chromatin was studied. Within the sensitivity of currently available methods, proteolysis of chromosomal proteins by chromatin-bound protease during chromatin reconstitution has no apparent effect on: (1) number of initiation sites, (2) proportion of reiterating and unique sequences of DNA transcribed, (3) size of the RNA transcribed, and (4) transcription of DNA sequences complementary to poly(A) containing messenger RNA.

Animals↗